Solvation of lithium ion in dimethoxyethane and propylene carbonate

Science.gov (United States)

Chaban, Vitaly

2015-07-01

Solvation of the lithium ion (Li+) in dimethoxyethane (DME) and propylene carbonate (PC) is of scientific significance and urgency in the context of lithium-ion batteries. I report PM7-MD simulations on the composition of Li+ solvation shells (SH) in a few DME/PC mixtures. The equimolar mixture features preferential solvation by PC, in agreement with classical MD studies. However, one DME molecule is always present in the first SH, supplementing the cage formed by five PC molecules. As PC molecules get removed, DME gradually substitutes vacant places. In the PC-poor mixtures, an entire SH is populated by five DME molecules.

Solvation structures of lithium halides in methanol–water mixtures

International Nuclear Information System (INIS)

Sarkar, Atanu; Dixit, Mayank Kumar; Tembe, B.L.

2015-01-01

Highlights: • Potentials of mean force for Li + -halides are calculated in methanol–water mixtures. • Stable CIP for x methanol = 1.0 becomes unstable at and below x methanol = 0.75. • The Li + ion is preferentially solvated by methanol molecules. • The halide ions are preferentially solvated by water molecules. - Abstract: The potentials of mean force (PMFs) for the ion pairs, Li + −Cl − , Li + −Br − and Li + −I − have been calculated in five methanol–water compositions. The results obtained are verified by trailing the trajectories and calculating the ion pair distance residence times. Local structures around the ions are studied using the radial distribution functions, density profiles, orientational correlation functions, running coordination numbers and excess coordination numbers. The major change in PMF is observed as the methanol mole fraction (x methanol ) is changed from 1.0 to 0.75. The stable contact ion pair occurring for x methanol = 1.0 becomes unstable at and below x methanol = 0.75. The preferential solvation data show that the halide ions are always preferentially solvated by water molecules. Although the lithium ion is preferentially solvated by methanol molecules, there is significant affinity towards water molecules as well

Standard electrode potential, Tafel equation, and the solvation thermodynamics.

Science.gov (United States)

Matyushov, Dmitry V

2009-06-21

Equilibrium in the electronic subsystem across the solution-metal interface is considered to connect the standard electrode potential to the statistics of localized electronic states in solution. We argue that a correct derivation of the Nernst equation for the electrode potential requires a careful separation of the relevant time scales. An equation for the standard metal potential is derived linking it to the thermodynamics of solvation. The Anderson-Newns model for electronic delocalization between the solution and the electrode is combined with a bilinear model of solute-solvent coupling introducing nonlinear solvation into the theory of heterogeneous electron transfer. We therefore are capable of addressing the question of how nonlinear solvation affects electrochemical observables. The transfer coefficient of electrode kinetics is shown to be equal to the derivative of the free energy, or generalized force, required to shift the unoccupied electronic level in the bulk. The transfer coefficient thus directly quantifies the extent of nonlinear solvation of the redox couple. The current model allows the transfer coefficient to deviate from the value of 0.5 of the linear solvation models at zero electrode overpotential. The electrode current curves become asymmetric in respect to the change in the sign of the electrode overpotential.

Advanced dielectric continuum model of preferential solvation

Science.gov (United States)

Basilevsky, Mikhail; Odinokov, Alexey; Nikitina, Ekaterina; Grigoriev, Fedor; Petrov, Nikolai; Alfimov, Mikhail

2009-01-01

A continuum model for solvation effects in binary solvent mixtures is formulated in terms of the density functional theory. The presence of two variables, namely, the dimensionless solvent composition y and the dimensionless total solvent density z, is an essential feature of binary systems. Their coupling, hidden in the structure of the local dielectric permittivity function, is postulated at the phenomenological level. Local equilibrium conditions are derived by a variation in the free energy functional expressed in terms of the composition and density variables. They appear as a pair of coupled equations defining y and z as spatial distributions. We consider the simplest spherically symmetric case of the Born-type ion immersed in the benzene/dimethylsulfoxide (DMSO) solvent mixture. The profiles of y(R ) and z(R ) along the radius R, which measures the distance from the ion center, are found in molecular dynamics (MD) simulations. It is shown that for a given solute ion z(R ) does not depend significantly on the composition variable y. A simplified solution is then obtained by inserting z(R ), found in the MD simulation for the pure DMSO, in the single equation which defines y(R ). In this way composition dependences of the main solvation effects are investigated. The local density augmentation appears as a peak of z(R ) at the ion boundary. It is responsible for the fine solvation effects missing when the ordinary solvation theories, in which z =1, are applied. These phenomena, studied for negative ions, reproduce consistently the simulation results. For positive ions the simulation shows that z ≫1 (z =5-6 at the maximum of the z peak), which means that an extremely dense solvation shell is formed. In such a situation the continuum description fails to be valid within a consistent parametrization.

Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

International Nuclear Information System (INIS)

Wishart, J.F.

2011-01-01

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

Thermodynamic functions of ion solvation in normal alcohols of aliphatic series

International Nuclear Information System (INIS)

Sergeeva, I.A.

1978-01-01

Thermodynamic functions of ion solvation of alkali, alkaline earth metals and halogenides in 9 alcohols are calculated using the earlier suggested method. It is shown that summary values are in good accord with experimental ones, the deviations do not surpass 0-5%, solvation energies of one and the same electrolyte in the series of n-alcohols do not change, enthalpy and entropy of solvation increase from lower alcohols to higher ones

Nonpolar solvation dynamics for a nonpolar solute in room ...

Indian Academy of Sciences (India)

Sandipa Indra

2018-01-30

Jan 30, 2018 ... Keywords. Solvation dynamics; nonpolar solvation; ionic liquid; molecular dynamics; linear response theory. 1. ... J. Chem. Sci. (2018) 130:3 spectrum of the excited probe molecule for imida- .... Therefore, the solute and the RTIL ions interact only ... interval of 30 ps from a long equilibrium trajectory of dura-.

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

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.

Proton solvation and proton transfer in chemical and electrochemical processes

International Nuclear Information System (INIS)

Lengyel, S.; Conway, B.E.

1983-01-01

This chapter examines the proton solvation and characterization of the H 3 O + ion, proton transfer in chemical ionization processes in solution, continuous proton transfer in conductance processes, and proton transfer in electrode processes. Topics considered include the condition of the proton in solution, the molecular structure of the H 3 O + ion, thermodynamics of proton solvation, overall hydration energy of the proton, hydration of H 3 O + , deuteron solvation, partial molal entropy and volume and the entropy of proton hydration, proton solvation in alcoholic solutions, analogies to electrons in semiconductors, continuous proton transfer in conductance, definition and phenomenology of the unusual mobility of the proton in solution, solvent structure changes in relation to anomalous proton mobility, the kinetics of the proton-transfer event, theories of abnormal proton conductance, and the general theory of the contribution of transfer reactions to overall transport processes

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)

Recent results on solvation dynamics of electron and spur reactions of solvated electron in polar solvents studied by femtosecond laser spectroscopy and picosecond pulse radiolysis

International Nuclear Information System (INIS)

Mostafavi, M.

2006-01-01

Here, we report several studies done recently at ELYSE laboratory on the solvation dynamics of electron and on the kinetics of solvated electron in the spur reactions, performed by femtosecond laser spectroscopy and picosecond pulse radiolysis, respectively. Solvated electrons have been produced in polyol (1,2-Etanediol, 1,2-Propanediol and 1,3-Propanediol) by two-photon ionization of the solvent with 263 nm femtosecond laser pulses at room temperature. The two-photon absorption coefficient of these solvents at 263 nm has been determined. The dynamics of electron solvation in polyols has been studied by pump-probe transient absorption spectroscopy. So, time resolved absorption spectra ranging from 430 to 720 nm have been measured (Figure 1). A blue shift of the spectra is observed for the first tens of picoseconds. Using Bayesian data analysis method, the observed solvation dynamics are reconstructed with different models: stepwise mechanisms, continuous relaxation models or combinations of stepwise and continuous relaxation. That analysis clearly indicates that it is not obvious to select a unique model to describe the solvation dynamics of electron in diols. We showed that several models are able to reproduce correctly the data: a two-step model, a heterogeneous or bi-exponential continuous relaxation model and even a hybrid model with a stepwise transition and homogeneous continuous relaxation. Nevertheless, the best fits are given by the continuous spectral relaxation models. The fact that the time-evolution of the absorption spectrum of the solvated electron in diols can be accurately described by the temperature dependent absorption spectrum of the ground state solvated electron suggests that the spectral blue shift is mostly caused by the continuous relaxation of the electron trapped in a large distribution of solvent cages. Similar trends on electron solvation dynamics are observed in the cases of 1,2-ethanediol, 1,3-propanediol and 1,2 propanediol

Solvation of the electron in alcohols studied using the Argonne picosecond pulse radiolysis system

International Nuclear Information System (INIS)

Jonah, C.D.; Kenney-Wallace, G.A.

1979-01-01

With a stroboscopic pulse radiolysis system, it is possible to measure the reactions of solvated electrons and dry electrons and the solvation time of electrons in alcohols from 20 psec to 350 psec. The solvation in alcohol and alcohol-alkane solutions is a complex process which depends on the microscopic structure of the fluid, so that the studies of solvation in alcohols as a function of temperature or as a function of the concentration of the alcohols must take into account the structure of the fluid being studied. The relaxation processes may not be dominant at low temperature. However, in room temperature alcohols, pre-existing traps are the dominant means of electron trapping. The extrapolation to water may be reasonable since water and alcohols both give similar final species. To obtain such idea of the solvation process in alcohols, the change of the absorption of electrons at 500 nm was measured. At very low concentration of alcohols in alkanes, electrons form a complex with a cluster of alcohol molecules, and the most probable size of this cluster is two alcohols (C 4 , C 10 ). The species formed is not solvated electrons, since the characteristic spectrum of solvated electrons is absent, and the conductivity of the species is far above that of solvated electrons. (Yamashita, S.)

Preferential solvation: dividing surface vs excess numbers.

Science.gov (United States)

Shimizu, Seishi; Matubayasi, Nobuyuki

2014-04-10

How do osmolytes affect the conformation and configuration of supramolecular assembly, such as ion channel opening and actin polymerization? The key to the answer lies in the excess solvation numbers of water and osmolyte molecules; these numbers are determinable solely from experimental data, as guaranteed by the phase rule, as we show through the exact solution theory of Kirkwood and Buff (KB). The osmotic stress technique (OST), in contrast, purposes to yield alternative hydration numbers through the use of the dividing surface borrowed from the adsorption theory. However, we show (i) OST is equivalent, when it becomes exact, to the crowding effect in which the osmolyte exclusion dominates over hydration; (ii) crowding is not the universal driving force of the osmolyte effect (e.g., actin polymerization); (iii) the dividing surface for solvation is useful only for crowding, unlike in the adsorption theory which necessitates its use due to the phase rule. KB thus clarifies the true meaning and limitations of the older perspectives on preferential solvation (such as solvent binding models, crowding, and OST), and enables excess number determination without any further assumptions.

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...

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

Science.gov (United States)

Sedlmeier, Felix; Netz, Roland R.

2013-03-01

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 ΔCp 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.

Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water.

Science.gov (United States)

Esser, Alexander; Forbert, Harald; Sebastiani, Federico; Schwaab, Gerhard; Havenith, Martina; Marx, Dominik

2018-02-01

Spectroscopy in the terahertz frequency regime is a sensitive tool to probe solvation-induced effects in aqueous solutions. Yet, a systematic understanding of spectral lineshapes as a result of distinct solvation contributions remains terra incognita. We demonstrate that modularization of amino acids in terms of functional groups allows us to compute their distinct contributions to the total terahertz response. Introducing the molecular cross-correlation analysis method provides unique access to these site-specific contributions. Equivalent groups in different amino acids lead to look-alike spectral contributions, whereas side chains cause characteristic but additive complexities. Specifically, hydrophilic solvation of the zwitterionic groups in valine and glycine leads to similar terahertz responses which are fully decoupled from the side chain. The terahertz response due to H-bonding within the large hydrophobic solvation shell of valine turns out to be nearly indistinguishable from that in bulk water in direct comparison to the changes imposed by the charged functional groups that form strong H-bonds with their hydration shells. Thus, the hydrophilic groups and their solvation shells dominate the terahertz absorption difference, while on the same intensity scale, the influence of hydrophobic water can be neglected.

Solvation of ions in the gas-phase: a molecular dynamics simulation

Science.gov (United States)

Cabarcos, Orlando M.; Lisy, James M.

1996-07-01

Molecular dynamics simulations have been performed on the collision between a cesium ion and a cluster of twenty methanol molecules. This process, generating a solvated ion, was studied over a range (1 to 25 eV) of eight collision energies. Preliminary analysis of this gas phase solvation has included the distribution of final ion cluster sizes, fragmentation patterns, solvation timescales and energetics. Two distinct patterns have emerged: a ballistic penetration of the neutral cluster at the higher collision energies and an evaporative evolution of the cluster ion at lower collision energies.

Ultrafast transient-absorption of the solvated electron in water

International Nuclear Information System (INIS)

Kimura, Y.; Alfano, J.C.; Walhout, P.K.; Barbara, P.F.

1994-01-01

Ultrafast near infrared (NIR)-pump/variable wavelength probe transient-absorption spectroscopy has been performed on the aqueous solvated electron. The photodynamics of the solvated electron excited to its p-state are qualitatively similar to previous measurements of the dynamics of photoinjected electrons at high energy. This result confirms the previous interpretation of photoinjected electron dynamics as having a rate-limiting bottleneck at low energies presumably involving the p-state

The charge-asymmetric nonlocally determined local-electric (CANDLE) solvation model

Energy Technology Data Exchange (ETDEWEB)

Sundararaman, Ravishankar; Goddard, William A. [Joint Center for Artificial Photosynthesis, Pasadena, California 91125 (United States)

2015-02-14

Many important applications of electronic structure methods involve molecules or solid surfaces in a solvent medium. Since explicit treatment of the solvent in such methods is usually not practical, calculations often employ continuum solvation models to approximate the effect of the solvent. Previous solvation models either involve a parametrization based on atomic radii, which limits the class of applicable solutes, or based on solute electron density, which is more general but less accurate, especially for charged systems. We develop an accurate and general solvation model that includes a cavity that is a nonlocal functional of both solute electron density and potential, local dielectric response on this nonlocally determined cavity, and nonlocal approximations to the cavity-formation and dispersion energies. The dependence of the cavity on the solute potential enables an explicit treatment of the solvent charge asymmetry. With four parameters per solvent, this “CANDLE” model simultaneously reproduces solvation energies of large datasets of neutral molecules, cations, and anions with a mean absolute error of 1.8 kcal/mol in water and 3.0 kcal/mol in acetonitrile.

Theory of optical spectra of solvated electrons

International Nuclear Information System (INIS)

Kestner, N.R.

1975-01-01

During the last few years better theoretical models of solvated electron have been developed. These models allow one to calculate a priori the observable properties of the trapped electron. One of the most important and most widely determined properties is the optical spectrum. In this paper we consider the predictions of the theories not only as to the band maximum but line shape and width. In addition we will review how the theories predict these will depend on the solvent, pressure, temperature, and solvent density. In all cases extensive comparisons will be made with experimental work. In addition four new areas will be explored and recent results will be presented. These concern electrons in dense polar gases, the time development of the solvated electron spectrum, solvated electrons in mixed solvents, and photoelectron emission spectra (PEE) as it relates to higher excited states. This paper will review all recent theoretical calculations and present a critical review of the present status and future developments which are anticipated. The best theories are quite successful in predicting trends, and qualitative agreement concerning band maximum. The theory is still weak in predicting line shape and line width

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NARCIS (Netherlands)

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

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

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...

Thermodynamics of solvation and solvophobic effect in formamide

International Nuclear Information System (INIS)

Sedov, I.A.; Stolov, M.A.; Solomonov, B.N.

2013-01-01

Highlights: • Enthalpies of solution of apolar organic compounds in formamide were measured. • Gibbs free energies of solution were experimentally determined. • Influence of the solvophobic effect on solvation thermodynamics was studied. • Thermodynamic features of solutions in formamide resemble those of aqueous solutions. -- Abstract: Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes

Difference rule-a new thermodynamic principle: prediction of standard thermodynamic data for inorganic solvates.

Science.gov (United States)

Jenkins, H Donald Brooke; Glasser, Leslie

2004-12-08

We present a quite general thermodynamic "difference" rule, derived from thermochemical first principles, quantifying the difference between the standard thermodynamic properties, P, of a solid n-solvate (or n-hydrate), n-S, containing n molecules of solvate, S (water or other) and the corresponding solid parent (unsolvated) salt: [P[n-solvate] - P[parent

Dipole moments of molecules solvated in helium nanodroplets

International Nuclear Information System (INIS)

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

2003-01-01

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

Ionic liquids: radiation chemistry, solvation dynamics and reactivity patterns

International Nuclear Information System (INIS)

Wishart, J.F.; Funston, A.M.; Szreder, T.

2006-01-01

Ionic liquids (ILs) are a rapidly expanding family of condensed-phase media with important applications in energy production, nuclear fuel and waste processing, improving the efficiency and safety of industrial chemical processes, and pollution prevention. ILs are nonvolatile, noncombustible, highly conductive, recyclable and capable of dissolving a wide variety of materials. They are finding new uses in chemical synthesis, catalysis, separations chemistry, electrochemistry and other areas. Ionic liquids have dramatically different properties compared to conventional molecular solvents, and they provide a new and unusual environment to test our theoretical understanding of charge transfer and other reactions. We are interested in how IL properties influence physical and dynamical processes that determine the stability and lifetimes of reactive intermediates and thereby affect the courses of chemical reactions and product distributions. Successful use of ionic liquids in radiation-filled environments, where their safety advantages could be significant, requires an understanding of ionic liquid radiation chemistry. For example, characterizing the primary steps of IL radiolysis will reveal radiolytic degradation pathways and suggest ways to prevent them or mitigate their effects on the properties of the material. An understanding of ionic liquid radiation chemistry will also facilitate pulse radiolysis studies of general chemical reactivity in ILs, which will aid in the development of energy production, chemical industry and environmental applications. Pulse radiolysis of [R 4 N][NTf 2 ] [R 4 N][N(CN) 2 ], and [R 4 P][N(CN) 2 ] ionic liquids produces solvated electrons that absorb over a broad range in the near infrared and persisting for hundreds of nanoseconds. Systematic cation variation shows that solvated electron's spectroscopic properties depend strongly on the lattice structure of the ionic liquid. Very early in our radiolysis studies it became evident that

Unusual solvation through both p-orbital lobes of a carbene carbon

Energy Technology Data Exchange (ETDEWEB)

Hadad, C. Z., E-mail: cacier.hadad@udea.edu.co [Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, A. A. 1226 Medellín (Colombia); Jenkins, Samantha [College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081 (China); Flórez, Elizabeth [Departamento de Ciencias Básicas, Universidad de Medellín, Carrera 87 N° 30-65, Medellín (Colombia)

2015-03-07

As a result of a configurational space search done to explain the experimental evidence of transient specific solvation of singlet fluorocarbene amide with tetrahydrofuran, we found that the most stable structures consist in a group in which each oxygen of two tetrahydrofuran molecules act as electron donor to its respective empty p-orbital lobe of the carbene carbon atom, located at each side of the carbene molecular plane. This kind of species, which to our knowledge has not been reported before, explains very well the particular experimental characteristics observed for the transient solvation of this system. We postulate that the simultaneous interaction to both p-orbital lobes seems to confer a special stability to the solvation complexes, because this situation moves away the systems from the proximity of the corresponding transition states for the ylide products. Additionally, we present an analysis of other solvation complexes and a study of the nature of the involved interactions.

Ionic Liquids: Radiation Chemistry, Solvation Dynamics and Reactivity Patterns

International Nuclear Information System (INIS)

Wishart, J.F.

2008-01-01

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

IONIC LIQUIDS: RADIATION CHEMISTRY, SOLVATION DYNAMICS AND REACTIVITY PATTERNS

International Nuclear Information System (INIS)

WISHART, J.F.

2007-01-01

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

1 SUPPLEMENTARY INFORMATION Nonpolar Solvation Dynamics ...

Indian Academy of Sciences (India)

IITP

. S. NP. ( t. ) ( )t. SNeqm. NP. (a). (b). Figure S2. (a) Nonequilibrium solvation response functions calculated after averaging over different number of nonequilibrium trajectories. The response function converges after averaging over more than ...

Analysis of biomolecular solvation sites by 3D-RISM theory.

Science.gov (United States)

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Improvements to the APBS biomolecular solvation software suite.

Science.gov (United States)

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Improving accuracy of electrochemical capacitance and solvation energetics in first-principles calculations

Science.gov (United States)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

2018-04-01

Reliable first-principles calculations of electrochemical processes require accurate prediction of the interfacial capacitance, a challenge for current computationally efficient continuum solvation methodologies. We develop a model for the double layer of a metallic electrode that reproduces the features of the experimental capacitance of Ag(100) in a non-adsorbing, aqueous electrolyte, including a broad hump in the capacitance near the potential of zero charge and a dip in the capacitance under conditions of low ionic strength. Using this model, we identify the necessary characteristics of a solvation model suitable for first-principles electrochemistry of metal surfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectric-only region at the interface. The dielectric nonlinearity, caused by the saturation of dipole rotational response in water, creates the capacitance hump, while ionic nonlinearity, caused by the compactness of the diffuse layer, generates the capacitance dip seen at low ionic strength. We show that none of the previously developed solvation models simultaneously meet all these criteria. We design the nonlinear electrochemical soft-sphere solvation model which both captures the capacitance features observed experimentally and serves as a general-purpose continuum solvation model.

Electrical resistivities and solvation enthalpies for solutions of salts in liquid alkali metals

International Nuclear Information System (INIS)

Hubberstey, P.; Dadd, A.T.

1982-01-01

An empirical correlation is shown to exist between the resistivity coefficients drho/dc for solutes in liquid alkali metals and the corresponding solvation enthalpies Usub(solvn) of the neutral gaseous solute species. Qualitative arguments based on an electrostatic solvation model in which the negative solute atom is surrounded by a solvation sphere of positive solvent ion cores are used to show that both parameters are dependent on the charge density of the solute atom and hence on the extent of charge transfer from solvent to solute. Thus as the charge density of the solute increases, the solvation enthalpy increases regularly and the resistivity coefficients pass through a maximum to give the observed approximately parabolic drho/dc versus Usub(solvn) relationship. (Auth.)

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.

Febuxostat-Minoxidil Salt Solvates: Crystal Structures, Characterization, Interconversion and Solubility Performance

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Li-Yang Li

2018-02-01

Full Text Available Three febuxostat-minoxidil salt solvates with acetone (ACE, tetrahydrofuran (THF and isopropanol (IPA are synthesized by solvent-assisted grinding and characterized by infrared (IR, nuclear magnetic resonance (1H-NMR, single crystal and powder X-ray diffraction (PXRD, thermogravimetry (TG and differential scanning calorimetry (DSC. These febuxostat-minoxidil salt solvates feature isostructural with the same stoichiometries (1:1:1 molecule ratio. The proton transfers from the carboxylic group of febuxostat (FEB to imino N atom of minoxidil (MIN, which forms the motif with combined R 2 2 (9 R 4 2 (8 R 2 2 (9 graph set in the three solvates. The solvents occupy the different positions related to the motif, which results in the apparent differences in PXRD patterns before/after desolvation although they are isostructures. The FEB-MIN·THF was more thermostable than FEB-MIN·ACE and FEB-MIN·IPA relative to solvent removal from DSC patterns, which is different from the results from the solvent-exchange experiments in chemical kinetics. All three salt solvates exhibit increased equilibrium solubility compared to FEB in aqueous medium.

Competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion by acetonitrile and water

Science.gov (United States)

Chaban, Vitaly

2014-10-01

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 field derivation is repeated for every new system. Development cost increases drastically as new chemical species are supplied. This work represents an alternative simulation approach, PM7-MD, by coupling the latest semiempirical parametrization, PM7, with equation-of-motion propagation scheme and temperature coupling. Using a competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion in acetonitrile and water, the work demonstrates efficiency and robustness of PM7-MD.

Studies of base pair sequence effects on DNA solvation based on all

Indian Academy of Sciences (India)

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 ...

Benzonitrile: Electron affinity, excited states, and anion solvation

Science.gov (United States)

Dixon, Andrew R.; Khuseynov, Dmitry; Sanov, Andrei

2015-10-01

We report a negative-ion photoelectron imaging study of benzonitrile and several of its hydrated, oxygenated, and homo-molecularly solvated cluster anions. The photodetachment from the unsolvated benzonitrile anion to the X ˜ 1 A 1 state of the neutral peaks at 58 ± 5 meV. This value is assigned as the vertical detachment energy (VDE) of the valence anion and the upper bound of adiabatic electron affinity (EA) of benzonitrile. The EA of the lowest excited electronic state of benzonitrile, a ˜ 3 A 1 , is determined as 3.41 ± 0.01 eV, corresponding to a 3.35 eV lower bound for the singlet-triplet splitting. The next excited state, the open-shell singlet A ˜ 1 A 1 , is found about an electron-volt above the triplet, with a VDE of 4.45 ± 0.01 eV. These results are in good agreement with ab initio calculations for neutral benzonitrile and its valence anion but do not preclude the existence of a dipole-bound state of similar energy and geometry. The step-wise and cumulative solvation energies of benzonitrile anions by several types of species were determined, including homo-molecular solvation by benzonitrile, hydration by 1-3 waters, oxygenation by 1-3 oxygen molecules, and mixed solvation by various combinations of O2, H2O, and benzonitrile. The plausible structures of the dimer anion of benzonitrile were examined using density functional theory and compared to the experimental observations. It is predicted that the dimer anion favors a stacked geometry capitalizing on the π-π interactions between the two partially charged benzonitrile moieties.

Absolute single-ion solvation free energy scale in methanol determined by the lithium cluster-continuum approach.

Science.gov (United States)

Pliego, Josefredo R; Miguel, Elizabeth L M

2013-05-02

Absolute solvation free energy of the lithium cation in methanol was calculated by the cluster-continuum quasichemical theory of solvation. Clusters with up to five methanol molecules were investigated using X3LYP, MP2, and MP4 methods with DZVP, 6-311+G(2df,2p), TZVPP+diff, and QZVPP+diff basis sets and including the cluster solvation through the PCM and SMD continuum models. Our calculations have determined a value of -118.1 kcal mol(-1) for the solvation free energy of the lithium, in close agreement with a value of -116.6 kcal mol(-1) consistent with the TATB assumption. Using data of solvation and transfer free energy of a pair of ions, electrode potentials and pKa, we have obtained the solvation free energy of 25 ions in methanol. Our analysis leads to a value of -253.6 kcal mol(-1) for the solvation free energy of the proton, which can be compared with the value of -263.5 kcal mol(-1) obtained by Kelly et al. using the cluster pair approximation. Considering that this difference is due to the methanol surface potential, we have estimated that it corresponds to -0.429 V.

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.

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.

Solvated protein-DNA docking using HADDOCK

NARCIS (Netherlands)

van Dijk, Marc; Visscher, Koen M; Bonvin, Alexandre M.J.J; Kastritis, Panagiotis L.

2013-01-01

Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the

Influence of temperature and molecular structure on ionic liquid solvation layers.

Science.gov (United States)

Wakeham, Deborah; Hayes, Robert; Warr, Gregory G; Atkin, Rob

2009-04-30

Atomic force microscopy (AFM) force profiling is used to investigate the structure of adsorbed and solvation layers formed on a mica surface by various room temperature ionic liquids (ILs) ethylammonium nitrate (EAN), ethanolammonium nitrate (EtAN), ethylammonium formate (EAF), propylammonium formate (PAF), ethylmethylammonium formate (EMAF), and dimethylethylammonium formate (DMEAF). At least seven layers are observed for EAN at 14 degrees C (melting point 13 degrees C), decreasing as the temperature is increased to 30 degrees C due to thermal energy disrupting solvophobic forces that lead to segregation of cation alkyl tails from the charged ammonium and nitrate moieties. The number and properties of the solvation layers can also be controlled by introducing an alcohol moiety to the cation's alkyl tail (EtAN), or by replacing the nitrate anion with formate (EAF and PAF), even leading to the detection of distinct cation and anion sublayers. Substitution of primary by secondary or tertiary ammonium cations reduces the number of solvation layers formed, and also weakens the cation layer adsorbed onto mica. The observed solvation and adsorbed layer structures are discussed in terms of the intermolecular cohesive forces within the ILs.

Relaxation dynamics following transition of solvated electrons

International Nuclear Information System (INIS)

Barnett, R.B.; Landman, U.; Nitzan, A.

1989-01-01

Relaxation dynamics following an electronic transition of an excess solvated electron in clusters and in bulk water is studied using an adiabatic simulation method. In this method the solvent evolves classically and the electron is constrained to a specified state. The coupling between the solvent and the excess electron is evaluated via the quantum expectation value of the electron--water molecule interaction potential. The relaxation following excitation (or deexcitation) is characterized by two time scales: (i) a very fast (/similar to/20--30 fs) one associated with molecular rotations in the first solvation shell about the electron, and (ii) a slower stage (/similar to/200 fs), which is of the order of the longitudinal dielectric relaxation time. The fast relaxation stage exhibits an isotope effect. The spectroscopical consequences of the relaxation dynamics are discussed

Strong Stretching of Poly(ethylene glycol) Brushes Mediated by Ionic Liquid Solvation.

Science.gov (United States)

Han, Mengwei; Espinosa-Marzal, Rosa M

2017-09-07

We have measured forces between mica surfaces coated with a poly(ethylene glycol) (PEG) brush solvated by a vacuum-dry ionic liquid, 1-ethyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, with a surface forces apparatus. At high grafting density, the solvation mediated by the ionic liquid causes the brush to stretch twice as much as in water. Modeling of the steric repulsion indicates that PEG behaves as a polyelectrolyte; the hydrogen bonding between ethylene glycol and the imidazolium cation seems to effectively charge the polymer brush, which justifies the strong stretching. Importantly, under strong polymer compression, solvation layers are squeezed out at a higher rate than for the neat ionic liquid. We propose that the thermal fluctuations of the PEG chains, larger in the brush than in the mushroom configuration, maintain the fluidity of the ionic liquid under strong compression, in contrast to the solid-like squeezing-out behavior of the neat ionic liquid. This is the first experimental study of the behavior of a polymer brush solvated by an ionic liquid under nanoconfinement.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

Science.gov (United States)

Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

2017-08-17

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

Study of the effect hydrogen binding in the solvation of alkaline earth cations with MeOH in nitromethane using 1 H NMR technique and determination of ionic solvation number

CERN Document Server

Alizadeh, N

2001-01-01

A proton NMR method for the study of the effect hydrogen binding and determination of solvation numbers of alkaline earth cations with methanol (MeOH) in in tromethane (NM) as diluent is described. The method is based on monitoring the resonance frequency of MeOH protons as a function of MeOH to metal ion mole ratio at constant metal ion concentration. the average solvation number of cation, n, at any MeOH/ metal ion mole ration was calculated from the NMR chemical shift-mole ration data and was plotted against the mole ration values. The solvation numbers of alkaline earth cations were obtained from the limiting values of the corresponding n, vs. mole ratio plots.

Study of the effect hydrogen binding in the solvation of alkaline earth cations with MeOH in nitromethane using 1 H NMR technique and determination of ionic solvation number

International Nuclear Information System (INIS)

Alizadeh, N.

2001-01-01

A proton NMR method for the study of the effect hydrogen binding and determination of solvation numbers of alkaline earth cations with methanol (MeOH) in in tromethane (NM) as diluent is described. The method is based on monitoring the resonance frequency of MeOH protons as a function of MeOH to metal ion mole ratio at constant metal ion concentration. the average solvation number of cation, n, at any MeOH/ metal ion mole ration was calculated from the NMR chemical shift-mole ration data and was plotted against the mole ration values. The solvation numbers of alkaline earth cations were obtained from the limiting values of the corresponding n, vs. mole ratio plots

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

Science.gov (United States)

Pliego, Josefredo R.

2017-07-01

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

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.

Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules.

Science.gov (United States)

Martins, Silvia A; Sousa, Sergio F

2013-06-05

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.

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

Selective solvation extraction of gold from alkaline cyanide solution by alkyl phosphorus esters

Energy Technology Data Exchange (ETDEWEB)

Miller, J.D.; Wan, R.Y.; Mooiman, M.B.; Sibrell, P.L.

1987-01-01

Research efforts have shown that solvation extraction of gold from alkaline cyanide solution is possible by alkyl phosphorus esters. Both tributyl phosphate (TBP) and dibutyl butyl phosphonate (DBBP) appear to be effective extractants for gold and exhibit high loading capacities exceeding 30 gpl. Selective solvation extraction of gold from alkaline cyanide solution can be achieved with selectivity factors relative to other cyanoanions as high as 1000 under certain circumstances. Variables influencing the selectivity such as ionic strength, temperature, and extractant structure, are discussed in terms of the extraction chemistry, which seems to involve the solvation of a M dot, dot, dot Au(CN)2 ion pair.

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.

Interfacial solvation thermodynamics

International Nuclear Information System (INIS)

Ben-Amotz, Dor

2016-01-01

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. (paper)

Generalized Born Models of Macromolecular Solvation Effects

Science.gov (United States)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Enthalpy-entropy compensation: the role of solvation.

Science.gov (United States)

Dragan, Anatoliy I; Read, Christopher M; Crane-Robinson, Colyn

2017-05-01

Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation-an intrinsically compensatory process-can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.

Applications of the solvation parameter model in reversed-phase liquid chromatography.

Science.gov (United States)

Poole, Colin F; Lenca, Nicole

2017-02-24

The solvation parameter model is widely used to provide insight into the retention mechanism in reversed-phase liquid chromatography, for column characterization, and in the development of surrogate chromatographic models for biopartitioning processes. The properties of the separation system are described by five system constants representing all possible intermolecular interactions for neutral molecules. The general model can be extended to include ions and enantiomers by adding new descriptors to encode the specific properties of these compounds. System maps provide a comprehensive overview of the separation system as a function of mobile phase composition and/or temperature for method development. The solvation parameter model has been applied to gradient elution separations but here theory and practice suggest a cautious approach since the interpretation of system and compound properties derived from its use are approximate. A growing application of the solvation parameter model in reversed-phase liquid chromatography is the screening of surrogate chromatographic systems for estimating biopartitioning properties. Throughout the discussion of the above topics success as well as known and likely deficiencies of the solvation parameter model are described with an emphasis on the role of the heterogeneous properties of the interphase region on the interpretation and understanding of the general retention mechanism in reversed-phase liquid chromatography for porous chemically bonded sorbents. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

Science.gov (United States)

Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

2005-03-01

The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

Spectral luminescence studies of eosin solvation in water-alcohol mixtures

Energy Technology Data Exchange (ETDEWEB)

Ketsle, G.A.; Levshin, L.V.; Mel' nikov, G.V.; Saletskii, A.M.

1987-11-01

The authors investigate the effects of solvation of eosin molecules in binary water-propanol mixtures with the goal of assessing eosin as a candidate dye laser material. The fluorescence was measured with a Hitachi spectrofluorimeter and the absorption spectra were taken on a Specord spectrophotometer. Absorption and fluorescence were measured for different amounts of propanol in the solvent. Data are also given on excitation and de-excitation kinetics between ground and excited states. Values for quantum yields of fluorescence and phosphorescence, average excited state lifetime, and molecular volume of the dye with the solvated shell are tabulated.

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

Pulse radiolysis study in ethanol and N-propanol of the solvated electron formation and reactivity at low temperatures

International Nuclear Information System (INIS)

Bono Merino, M.R.

1978-01-01

The electron solvation process in polar media has been studied in liquid ethanol and n-propanol at temperatures near their melting points. The results show that using the change of absorption at a given wavelength to determine the solvation time leads to a value which varies with the wavelength considered. Furthermore, for n-propanol it appears that the process occurs without a definite order. Studies of the spectral shifts show that the passage from the initial to the final spectrum (solvated electron spectrum) involves intermediate transient spectra which probably correspond to partly solvated states of the electron. The interpretation of these various results points out the ambiguity of the kinetic measurements: the simultaneous existence of several partly solvated states of the electron is not consistent with the hypothesis previously admitted that the molar extinction coefficient at a given wavelength is unique and does not vary with time. The reaction of the solvated electron with acetone has been studied in ethanol in the temperature range from +25 to -105 0 C: this reaction is diffusion controlled [fr

Solvation in atomic liquids: connection between Gaussian field theory and density functional theory

Directory of Open Access Journals (Sweden)

V. Sergiievskyi

2017-12-01

Full Text Available For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core — indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional.

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.

Preferential Solvation of Silver (I) Bromate in Methanol-Dimethylsulfoxide Mixtures

Science.gov (United States)

Janardhanan, S.; Kalidas, C.

1984-06-01

The solubiltiy of silver bromate, the Gibbs transfer energy of Ag+ and BrO3- and the solvent transport number in methanol-dimethyl sulfoxide mixtures are reported. The solubility of silver bromate increases with addition of DMSO. The Gibbs energy of transfer of the silver ion (based on the ferrocene reference method) decreases, while that of the bromate ion becomes slightly negative with the addition of DMSO. The solvent transport number A passes through a maximum (⊿ = 1.0 at XDMSO = 0.65. From these results, it is concluded that the silver ion is preferentially solvated by DMSO whereas the bromate ion shows no preferential solvation.

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

International Nuclear Information System (INIS)

Boees, Elvis S.; Bernardi, Edson; Stassen, Hubert; Goncalves, Paulo F.B.

2008-01-01

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

Comparison of solvation dynamics of electrons in four polyols

Energy Technology Data Exchange (ETDEWEB)

Lampre, I.; Pernot, P.; Bonin, J. [Laboratoire de Chimie Physique/ELYSE, Universite Paris-Sud 11, UMR 8000, Bat. 349, Orsay F-91405 (France); CNRS, Orsay F-91405 (France); Mostafavi, M. [Laboratoire de Chimie Physique/ELYSE, Universite Paris-Sud 11, UMR 8000, Bat. 349, Orsay F-91405 (France); CNRS, Orsay F-91405 (France)], E-mail: mehran.mostafavi@lcp.u-psud.fr

2008-10-15

Using pump-probe transient absorption spectroscopy, we studied the solvation dynamics of the electron in liquid polyalcohols: ethane-1,2-diol, propane-1,2-diol, propane-1,3-diol and propane-1,2,3-triol. Time-resolved absorption spectra ranging from 440 to 720 nm were measured. Our study shows that the excess electron in the diols presents an intense and wide absorption band in the visible and near-IR spectral domain at early time after two-photon ionization of the neat solvent. Then, for the first tens of picoseconds, the electron spectrum shifts toward the blue domain and its bandwidth decreases as the red part of the initial spectrum rapidly drops, while the blue part hardly evolves. In contrast, in the triol, the absorption spectrum of the electron is early situated in the visible range after the pump pulse and then solely evolves in the red part. The Bayesian data analysis of the observed picosecond solvation dynamics with different models is in favor of a heterogeneous continuous relaxation. That is corroborated by the analogy between the change in the absorption band with increasing time or decreasing temperature. That tends to indicate a similar organization disorder of the solvent. Moreover, the electron solvation dynamics is very fast in propane-1,2,3-triol despite its high viscosity and highlight the role of the OH-group in that process.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

Science.gov (United States)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

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.

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 PF 6 - 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.

Polarizability and Aqueous Solvation of the Sulfate Dianion

Czech Academy of Sciences Publication Activity Database

Jungwirth, Pavel; Curtis, J. E.; Tobias, D. J.

2003-01-01

Roč. 367, - (2003), s. 704-710 ISSN 0009-2614 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : polarizability * aqueous solvation * dianion Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.438, year: 2003

Silver atom solvation and desolvation in ice matrices: study of solvation shell geometry by electron spin resonance and electron spin echo methods

Energy Technology Data Exchange (ETDEWEB)

Kevan, L; Narayana, P A

1978-01-01

Results of studies of the solvation shell structure of silver atoms in ice matrix at 4/sup 0/K by electron spin resonance (ESR) and electron spin echo spectrometry are reported. Drastic change in the hyperfine coupling constant of the silver atom was noted when the silver atom initially produced at 4/sup 0/K was warmed to 77/sup 0/K and reexamined by ESR at 4/sup 0/K. This suggested a very drastic rearrangement of the water molecules surrounding the silver atom. The geometric arrangement of water molecules around the silver atom produced at 4/sup 0/K was what would be expected for a solvated silver ion, indicating that no rearrangement had occurred after the silver atom formed. The addition of a little thermal excitation (heating to 77/sup 0/K) results in the geometry changes than can be explained by assuming either that a water molecule rotates around one of its OH bands or by the development of a hydrogen bond between the silver atom and one of the first solvation shell water molecules. Optical excitation in the absorption band of the silver atom in the ice matrix at 400nm resulted in desolvation of the silver ion or a reversion to the structure originally obtained by reaction of solver salts in ic matrix with radiation produced electrons. This was best explained by a charge transfer mechanism. (BLM)

Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation

Science.gov (United States)

Cota, Roberto; Ottosson, Niklas; Bakker, Huib J.; Woutersen, Sander

2018-05-01

We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H2O and D2O . This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ˜1.6 for NaCl and ˜1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.

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

Science.gov (United States)

Bakhshiev, N G; Kiselev, M B

1991-09-01

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

Phase Equilibria and Ionic Solvation in the Lithium Tetrafluoroborate-Dimethylsulfoxide System

Science.gov (United States)

Gafurov, M. M.; Kirillov, S. A.; Gorobets, M. I.; Rabadanov, K. Sh.; Ataev, M. B.; Tretyakov, D. O.; Aydemirov, K. M.

2015-01-01

The phase diagram and electrical conductivity isotherms for the lithium tetrafluoroborate (LiBF4)-dimethylsulfoxide (DMSO) system and Raman spectra of DMSO and the LiBF4-DMSO solution were studied. Spectroscopic signatures of a H-bond between DMSO and BF4 - ions were found. The bonds of Li+ ions to the solvent were stronger than the bonds in DMSO dimers because formation of the solvate destroyed dimeric DMSO molecules. The τω values for DMSO molecules in the Li+-ion solvate shell of the LiBF4-DMSO system were similar to those for associated solvent molecules.

Fluorescent probe studies of polarity and solvation within room temperature ionic liquids: a review.

Science.gov (United States)

Pandey, Shubha; Baker, Sheila N; Pandey, Siddharth; Baker, Gary A

2012-09-01

Ionic liquids display an array of useful and sometimes unconventional, solvent features and have attracted considerable interest in the field of green chemistry for the potential they hold to significantly reduce environmental emissions. Some of these points have a bearing on the chemical reactivity of these systems and have also generated interest in the physical and theoretical aspects of solvation in ionic liquids. This review presents an introduction to the field of ionic liquids, followed by discussion of investigations into the solvation properties of neat ionic liquids or mixed systems including ionic liquids as a major or minor component. The ionic liquid based multicomponent systems discussed are composed of other solvents, other ionic liquids, carbon dioxide, surfactants or surfactant solutions. Although we clearly focus on fluorescence spectroscopy as a tool to illuminate ionic liquid systems, the issues discussed herein are of general relevance to discussions of polarity and solvent effects in ionic liquids. Transient solvation measurements carried out by means of time-resolved fluorescence measurements are particularly powerful for their ability to parameterize the kinetics of the solvation process in ionic liquids and are discussed as well.

Mutagenicity of Tween 80-solvated mild gasification products in the Ames salmonella microsomal assay system

Energy Technology Data Exchange (ETDEWEB)

1992-01-13

The results of the Tween 80-solvated Ames testing of six mild gasification samples indicate significant mutagenic activity only in the composite materials (MG-119 and MG-120), previously suspected from the DMSO-solvated assays, which had shown some variable but ultimately insignificant mutagenic responses. The activity of these samples from the Tween 80-solvated assays was quite low when compared to either the positive controls or the SRC-II HD coal-liquefaction reference material. The class of mutagenic activity expressed by these samples solvated in Tween 80 was that of an indirect-acting, frameshift mutagen(s) since significant activity was found only on tester strain TA98 in the presence of the metabolic activation fraction (S9). Because DMSO and other solvents have been shown to affect the mutagenic activity of certain pure chemicals, the possibility of solvent/mutagen interactions in complex mixtures such as coal-derived liquids exists. Thus, the testing of the genotoxic activity of undefined, chemically complex compounds may require the use of at least two solvent systems to reduce the possibility of artifactual findings. 10 refs., 4 tabs.

A sensitive fluorescent probe for the polar solvation dynamics at protein-surfactant interfaces.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Singha, Subhankar; Jun, Yongwoong; Chakraborty, Sandipan; Sengupta, Jhimli; Das, Ranjan; Ahn, Kyo-Han; Pal, Samir Kumar

2017-05-17

Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition. Over the years it has been shown that the solvation dynamics of a fluorescent probe at biomolecular surfaces and interfaces account for the relaxation dynamics of polar residues and associated water molecules. However, the sensitivity of the dynamics depends largely on the localization and exposure of the probe. For noncovalent fluorescent probes, localization at the region of interest in addition to surface exposure is an added challenge compared to the covalently attached probes at the biological interfaces. Here we have used a synthesized donor-acceptor type dipolar fluorophore, 6-acetyl-(2-((4-hydroxycyclohexyl)(methyl)amino)naphthalene) (ACYMAN), for the investigation of the solvation dynamics of a model protein-surfactant interface. A significant structural rearrangement of a model histone protein (H1) upon interaction with anionic surfactant sodium dodecyl sulphate (SDS) as revealed from the circular dichroism (CD) studies is nicely corroborated in the solvation dynamics of the probe at the interface. The polarization gated fluorescence anisotropy of the probe compared to that at the SDS micellar surface clearly reveals the localization of the probe at the protein-surfactant interface. We have also compared the sensitivity of ACYMAN with other solvation probes including coumarin 500 (C500) and 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM). In comparison to ACYMAN, both C500 and DCM fail to probe the interfacial solvation dynamics of a model protein-surfactant interface. While C500 is found to be delocalized from the protein-surfactant interface, DCM becomes destabilized upon the formation of the interface (protein-surfactant complex). The timescales obtained from this novel probe have also been compared with other femtosecond resolved studies and molecular dynamics simulations.

Comparison between implicit and hybrid solvation methods for the ...

Indian Academy of Sciences (India)

Administrator

Both implicit solvation method (dielectric polarizable continuum model, DPCM) and hybrid ... the free energy change (ΔGsol) as per the PCM ... Here the gas phase change is written as ΔGg = ΔEelec + ..... bution to the field of electrochemistry.

Photoinduced electron transfer and solvation in iodide-doped acetonitrile clusters.

Science.gov (United States)

Ehrler, Oli T; Griffin, Graham B; Young, Ryan M; Neumark, Daniel M

2009-04-02

We have used ultrafast time-resolved photoelectron imaging to measure charge transfer dynamics in iodide-doped acetonitrile clusters I(-)(CH(3)CN)(n) with n = 5-10. Strong modulations of vertical detachment energies were observed following charge transfer from the halide, allowing interpretation of the ongoing dynamics. We observe a sharp drop in the vertical detachment energy (VDE) within 300-400 fs, followed by a biexponential increase that is complete by approximately 10 ps. Comparison to theory suggests that the iodide is internally solvated and that photodetachment results in formation of a diffuse electron cloud in a confined cavity. We interpret the initial drop in VDE as a combination of expansion of the cavity and localization of the excess electron on one or two solvent molecules. The subsequent increase in VDE is attributed to a combination of the I atom leaving the cavity and rearrangement of the acetonitrile molecules to solvate the electron. The n = 5-8 clusters then show a drop in VDE of around 50 meV on a much longer time scale. The long-time VDEs are consistent with those of (CH(3)CN)(n)(-) clusters with internally solvated electrons. Although the excited-state created by the pump pulse decays by emission of a slow electron, no such decay is seen by 200 ps.

Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane.

Science.gov (United States)

Chaban, Vitaly

2015-07-01

Electrolyte solutions based on the propylene carbonate (PC)-dimethoxyethane (DME) mixtures are of significant importance and urgency due to emergence of lithium-ion batteries. Solvation and coordination of the lithium cation in these systems have been recently attended in detail. However, analogous information concerning anions (tetrafluoroborate, hexafluorophosphate) is still missed. This work reports PM7-MD simulations (electronic-structure level of description) to include finite-temperature effects on the anion solvation regularities in the PC-DME mixture. The reported result evidences that the anions appear weakly solvated. This observation is linked to the absence of suitable coordination sites in the solvent molecules. In the concentrated electrolyte solutions, both BF4(-) and PF6(-) prefer to exist as neutral ion pairs (LiBF4, LiPF6).

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

Science.gov (United States)

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

2016-09-01

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

Solution thermodynamics and preferential solvation of sulfamethazine in (methanol + water) mixtures

International Nuclear Information System (INIS)

Delgado, Daniel R.; Almanza, Ovidio A.; Martínez, Fleming; Peña, María A.; Jouyban, Abolghasem; Acree, William E.

2016-01-01

Highlights: • Solubility of sulfamethazine (SMT) was measured in (methanol + water) mixtures. • SMT solubility was correlated with Jouyban–Acree model. • Gibbs energy, enthalpy, and entropy of dissolution of SMT were calculated. • Non-linear enthalpy–entropy relationship was observed for SMT. • Preferential solvation of SMT by methanol was analyzed by using the IKBI method. - Abstract: The solubility of sulfamethazine (SMT) in {methanol (1) + water (2)} co-solvent mixtures was determined at five different temperatures from (293.15 to 313.15) K. The sulfonamide exhibited its highest mole fraction solubility in pure methanol (δ 1 = 29.6 MPa 1/2 ) and its lowest mole fraction solubility in water (δ 2 = 47.8 MPa 1/2 ) at each of the five temperatures studied. The Jouyban–Acree model was used to correlate/predict the solubility values. The respective apparent thermodynamic functions Gibbs energy, enthalpy, and entropy of solution were obtained from the solubility data through the van’t Hoff and Gibbs equations. Apparent thermodynamic quantities of mixing were also calculated for this drug using values of the ideal solubility reported in the literature. A non-linear enthalpy–entropy relationship was noted for SMT in plots of both the enthalpy vs. Gibbs energy of mixing and the enthalpy vs. entropy of mixing. These plots suggest two different trends according to the slopes obtained when the composition of the mixtures changes. Accordingly, the mechanism for SMT transfer processes in water-rich mixtures from water to the mixture with 0.70 in mass fraction of methanol is entropy driven. Conversely, the mechanism is enthalpy driven in mixtures whenever the methanol composition exceeds 0.70 mol fraction. An inverse Kirkwood–Buff integral analysis of the preferential solvation of SMT indicated that the drug is preferentially solvated by water in water-rich mixtures but is preferentially solvated by methanol in methanol-rich mixtures.

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......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...

Electron spin resonance of the solvation of radiation-produced silver atoms in alcohol-water mixtures

International Nuclear Information System (INIS)

Li, A.S.W.; Kevan, L.

1982-01-01

Frozen solutions of silver salts exposed to 60 Co γ-irradiation form silver atoms by reaction of radiation-produced electrons with the silver ion. At 4 K the silver atoms are initially produced in a nonequilibrium or presolvated state and upon brief thermal excitation to 77 K the first solvation shell geometry changes towards an equilibrium or solvated silver atom. This is most pronounced in water but also occurs in methanol, ethanol and n-propanol matrices. The changes in the electron spin resonance magnetic parameters upon silver atom solvation have been determined. In alcohol-water mixtures Ag 0 is preferentially solvated by polycrystalline water at low alcohol concentration. Above a particular alcohol mole percent Ag 0 suddenly changes its environment to a glassy alcohol one. This sudden change occurs at 17, 13 and 6 mol % methanol, ethanol and n-propanol, respectively. These mole percents correlate with the minimum of the excess enthalpy of mixing and with the hydrogen atom trapping ability of these alcohol-water mixtures. The results also suggest that the local environmental disorder around Ag 0 increases with alcohol chain length in alcohol-water frozen solutions. (author)

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

Science.gov (United States)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

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].

Continuous registration of optical absorption spectra of periodically produced solvated electrons

International Nuclear Information System (INIS)

Krebs, P.

1975-01-01

Absorption spectra of unstable intermediates, such as solvated electrons, were usually taken point by point, recording the time-dependent light absorption after their production by a flash. The experimental arrangement for continuous recording of the spectra consists of a conventional one beam spectral photometer with a stabilized white light source, a monochromator, and a light detector. By periodic production of light absorbing intermediates such as solvated electrons, e.g., by ac uv light, a small ac signal is modulated on the light detector output which after amplification can be continuously recorded as a function of wavelength. This method allows the detection of absorption spectra when disturbances from the outside provide a signal-to-noise ratio smaller than 1

Microscopic picture of the aqueous solvation of glutamic acid

NARCIS (Netherlands)

Leenders, E.J.M.; Bolhuis, P.G.; Meijer, E.J.

2008-01-01

We present molecular dynamics simulations of glutamic acid and glutamate solvated in water, using both density functional theory (DFT) and the Gromos96 force field. We focus on the microscopic aspects of the solvation−particularly on the hydrogen bond structures and dynamics−and investigate the

Highly Stable Lithium Metal Batteries Enabled by Regulating the Solvation of Lithium Ions in Nonaqueous Electrolytes.

Science.gov (United States)

Zhang, Xue-Qiang; Chen, Xiang; Cheng, Xin-Bing; Li, Bo-Quan; Shen, Xin; Yan, Chong; Huang, Jia-Qi; Zhang, Qiang

2018-05-04

Safe and rechargeable lithium metal batteries have been difficult to achieve because of the formation of lithium dendrites. Herein an emerging electrolyte based on a simple solvation strategy is proposed for highly stable lithium metal anodes in both coin and pouch cells. Fluoroethylene carbonate (FEC) and lithium nitrate (LiNO 3 ) were concurrently introduced into an electrolyte, thus altering the solvation sheath of lithium ions, and forming a uniform solid electrolyte interphase (SEI), with an abundance of LiF and LiN x O y on a working lithium metal anode with dendrite-free lithium deposition. Ultrahigh Coulombic efficiency (99.96 %) and long lifespans (1000 cycles) were achieved when the FEC/LiNO 3 electrolyte was applied in working batteries. The solvation chemistry of electrolyte was further explored by molecular dynamics simulations and first-principles calculations. This work provides insight into understanding the critical role of the solvation of lithium ions in forming the SEI and delivering an effective route to optimize electrolytes for safe lithium metal batteries. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Internal energy effects on the solvation and reactivity of multiply charged biomolecules for electrospray ionization mass spectroscopy. [Bovine ubiquitin

Energy Technology Data Exchange (ETDEWEB)

Light-Wahl, K.J.; Winger, B.E.; Rockwood, A.L.; Smith, R.D.

1992-06-01

Mild (capillary) interface conditions which do not completely desolvate the ions of proteins in electrospray ionization mass spectrometry (ESI-MS) may be required to probe the higher order structures and weak associations. For the small protein bovine ubiquitin, two ion distributions (unsolvated ions and unresolved solvated ions) were observed. The resolvable solvation for leucine-enkephalin with methanol and water shows that the use of countercurrent N{sub 2} flow at the capillary affects the solvation observed. 2 figs. (DLC)

Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model.

Science.gov (United States)

Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai

2018-04-23

To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described

Solvation dynamics of lithium salts in wet nitrobenzene

Czech Academy of Sciences Publication Activity Database

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

2006-01-01

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

Solvated electrons at elevated temperatures in different alcohols: Temperature and molecular structure effects

Energy Technology Data Exchange (ETDEWEB)

Yan, Yu [Department of Nuclear Engineering and Management, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Lin, Mingzhang [Nuclear Science and Engineering Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1195 (Japan); Katsumura, Yosuke, E-mail: katsu@n.t.u-tokyo.ac.j [Department of Nuclear Engineering and Management, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Nuclear Professional School, Graduate School of Engineering, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Fu, Haiying; Muroya, Yusa [Nuclear Professional School, Graduate School of Engineering, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan)

2010-12-15

The absorption spectra of solvated electrons in pentanol, hexanol and octanol are measured from 22 to 200, 22 to 175 and 50 to150 {sup o}C, respectively, at a fixed pressure of 15 MPa, using nanosecond pulse radiolysis technique. The results show that the peak positions of the absorption spectra have a red-shift (shift to longer wavelengths) as temperature increases, similar to water and other alcohols. Including the above mentioned data, a compilation of currently available experimental data on the energy of absorption maximum (E{sub max}) of solvated electrons changed with temperature in monohydric alcohols, diols and triol is presented. E{sub max} of solvated electron is larger in those alcohols that have more OH groups at all the temperatures. The molecular structure effect, including OH numbers, OH position and carbon chain length, is investigated. For the primary alcohols with same OH group number and position, the temperature coefficient increases with increase in chain length. For the alcohols with same chain length and OH numbers, temperature coefficient is larger for the symmetric alcohols than the asymmetric ones.

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

Science.gov (United States)

Husowitz, B; Talanquer, V

2007-02-07

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

Solvation quantities from a COSMO-RS equation of state

International Nuclear Information System (INIS)

Panayiotou, C.; Tsivintzelis, I.; Aslanidou, D.; Hatzimanikatis, V.

2015-01-01

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

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

Science.gov (United States)

Limmer, Krista; Williams, Kristen; Andzelm, Jan

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

The solvation of carbohydrates in dimethylsulfoxide and water

International Nuclear Information System (INIS)

Berger, S.; Diaz, M.D.; Horwat, Ch.

1999-01-01

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

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...

Thermodynamics of sublimation and solvation for bicyclo-derivatives of 1,3-thiazine

International Nuclear Information System (INIS)

Ol’khovich, Marina V.; Blokhina, Svetlana V.; Sharapova, Angelica V.; Perlovich, German L.; Proshin, Alexey N.

2013-01-01

Highlights: • Temperature dependencies of saturated vapor pressure of new bicyclo-derivatives were obtained. • Thermodynamic functions of sublimation and solvation were calculated. • The correlations between thermodynamic functions and molecular descriptors are discussed. - Abstract: Temperature dependencies of saturated vapor pressure of novel bicyclo-derivatives of 1,3-thiazine with methoxy- and carbonyl-substituents have been obtained by method of transference by means of an inert gas carrier. Thermodynamic functions of sublimation have been calculated. Correlations between thermodynamic functions of sublimation and thermophysical properties of the substances and molecular descriptors have been established. The enthalpies of solvation of compounds were calculated using the measured values of enthalpies of sublimation and of standard enthalpies of solution in hexane and buffer

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.

Solvation of excess electrons trapped in charge pockets on molecular surfaces

Science.gov (United States)

Jalbout, Abraham F.

This work considers the ability of hydrogen fluoride (HF) to solvate excess electrons located on cyclic hydrocarbon surfaces. The principle applied involves the formation of systems in which excess electrons can be stabilized not only on concentrated molecular surface charge pockets but also by HF. Recent studies have shown that OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), at the same time, the hydrogen atoms on the opposite side of this surface form a pocket of positive charge can attract the excess electron. This density can be further stabilized by the addition of an HF molecule that can form an 'anion with an internally solvated electron' (AISE) state. These systems are shown to be stable with respect to vertical electron detachment (VDE).

Infrared spectroscopy of model electrochemical interfaces in ultrahigh vacuum: some implications for ionic and chemisorbate solvation at electrode surfaces

Science.gov (United States)

Villegas, Ignacio; Kizhakevariam, Naushad; Weaver, Michael J.

1995-07-01

The utility of infrared reflection-absorption spectroscopy (IRAS) for examining structure and bonding for model electrochemical interfaces in ultrahigh vacuum (UHV) is illustrated, focusing specifically on the solvation of cations and chemisorbed carbon monoxide on Pt(111). These systems were chosen partly in view of the availability of IRAS data (albeit limited to chemisorbate vibrations) for the corresponding in-situ metal-solution interfaces, enabling direct spectral comparisons to be made with the "UHV electrochemical model" systems. Kelvin probe measurements of the metal-UHV surface potential changes (ΔΦ) attending alterations in the interfacial composition are also described: these provide the required link to the in-situ electrode potentials as well as yielding additional insight into surface solvation. Variations in the negative electronic charge density and, correspondingly, in the cation surface concentration (thereby mimicking charge-induced alterations in the electrode potential below the potential of zero charge) are achieved by potassium atom dosage onto Pt(111). Of the solvents selected for discussion here — deuterated water, methanol, and acetonitrile — the first two exhibit readily detectable vibrational bands which provide information on the ionic solvation structure. Progressively dosing these solvents onto Pt(111) in the presence of low potassium coverages yields marked alterations in the solvent vibrational bands which can be understood in terms of sequential cation solvation. Comparison between these spectra for methanol with analogous data for sequential methanol solvation of gas-phase alkali cations enables the influence of the interfacial environment to be assessed. The effects of solvating chemisorbed CO are illustrated for acetonitrile; the markedly larger shifts in CO frequencies and binding sites for dilute CO adlayers can be accounted for in terms of short-range coadsorbate interactions in addition to longer-range Stark effects

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

Energy Technology Data Exchange (ETDEWEB)

Yang, Pei-Kun, E-mail: peikun@isu.edu.tw

2016-06-15

Highlights: • We modify the Poisson equation. • The dielectric polarization was calculated from the modified Poisson equation. • The solvation free energies of the solutes were calculated from the dielectric polarization. • The calculated solvation free energies were similar to those obtained from MD simulations. - Abstract: The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein–protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density N{sub bulk}; and relative solvent molecular density g. For a molecular solute, 4πr{sup 2}p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss’s law of Maxwell’s equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solvation thermodynamics of L-cystine, L-tyrosine, and L-leucine in aqueous-electrolyte media

Science.gov (United States)

Roy, Sanjay; Guin, Partha Sarathi; Mahali, Kalachand; Dolui, Bijoy Krishna

2017-12-01

Solubilities of L-cystine, L-tyrosine, and L-leucine in aqueous NaCl media at 298.15 K have been studied. Indispensable and related solvent parameters such as molar mass, molar volume, etc., were also determined. The results are used to evaluate the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy and dipole-dipole interaction effects during the course of solvation. Various weak interactions involving solute-solvent or solvent-solvent molecules were characterized in order to find their role on the solvation of these amino acids.

Additive scheme for calculation of solvation enthalpies of heterocyclic aromatic compounds. Sublimation/vaporization enthalpy at 298.15 K

International Nuclear Information System (INIS)

Solomonov, Boris N.; Nagrimanov, Ruslan N.; Mukhametzyanov, Timur A.

2016-01-01

Highlights: • Additivity scheme for solvation enthalpies estimation of heteroaromatic compounds was proposed. • Method for determination of vaporization/sublimation enthalpies directly at 298.15 K was developed. • Solution enthalpies of 25 heteroaromatic compounds were measured. • Vaporization/sublimation enthalpies of 44 heteroaromatic compounds were determined. • Obtained values are in good agreement with the results of conventional methods. - Abstract: Hereby we propose a method for determination of vaporization and sublimation enthalpies of heterocyclic and carbonyl-containing aromatic compounds at 298.15 K. According to this method vaporization and sublimation enthalpies at 298.15 K are determined based on enthalpies of solvation and solution. Solvation enthalpies of heteroatomatic and carbonyl-containing compounds are calculated using an additive scheme from the solvation enthalpy of closest aromatic hydrocarbon and contributions related to the exchange of CH-groups of hydrocarbon with corresponding substituent atoms or groups. Measured solution enthalpies together with calculated solvation enthalpies allowed to calculate corresponding vaporization and sublimation enthalpies at 298.15 K for a large number of heterocyclic and carbonyl-containing compounds. We have also found that in a number of cases instead of solution enthalpy in benzene at 298.15 K fusion enthalpy at the melting temperature can be used. Comparison between literature data and calculated vaporization and sublimation enthalpies demonstrates satisfactory performance of the proposed method.

Additive scheme for calculation of solvation enthalpies of heterocyclic aromatic compounds. Sublimation/vaporization enthalpy at 298.15 K

Energy Technology Data Exchange (ETDEWEB)

Solomonov, Boris N., E-mail: boris.solomonov@kpfu.ru; Nagrimanov, Ruslan N.; Mukhametzyanov, Timur A.

2016-06-10

Highlights: • Additivity scheme for solvation enthalpies estimation of heteroaromatic compounds was proposed. • Method for determination of vaporization/sublimation enthalpies directly at 298.15 K was developed. • Solution enthalpies of 25 heteroaromatic compounds were measured. • Vaporization/sublimation enthalpies of 44 heteroaromatic compounds were determined. • Obtained values are in good agreement with the results of conventional methods. - Abstract: Hereby we propose a method for determination of vaporization and sublimation enthalpies of heterocyclic and carbonyl-containing aromatic compounds at 298.15 K. According to this method vaporization and sublimation enthalpies at 298.15 K are determined based on enthalpies of solvation and solution. Solvation enthalpies of heteroatomatic and carbonyl-containing compounds are calculated using an additive scheme from the solvation enthalpy of closest aromatic hydrocarbon and contributions related to the exchange of CH-groups of hydrocarbon with corresponding substituent atoms or groups. Measured solution enthalpies together with calculated solvation enthalpies allowed to calculate corresponding vaporization and sublimation enthalpies at 298.15 K for a large number of heterocyclic and carbonyl-containing compounds. We have also found that in a number of cases instead of solution enthalpy in benzene at 298.15 K fusion enthalpy at the melting temperature can be used. Comparison between literature data and calculated vaporization and sublimation enthalpies demonstrates satisfactory performance of the proposed method.

Negative ion photoelectron spectroscopy of solvated electron cluster anions, (H2O)n- and (NH3)n-

International Nuclear Information System (INIS)

Lee, G.H.; Arnold, S.T.; Eaton, J.G; Sarkas, H.W.; Bowen, K.H.; Ludewigt, C.; Haberland, H.

1991-01-01

The photodetachment spectra of (H 2 O) - n=2-69 and (NH 3 ) - n=41-1100 have been recorded, and vertical detachment energies (VDEs) were obtained from the spectra. For both systems, the cluster anion VDEs increase smoothly with increasing sizes and most species plot linearly with n -1/3 , extrapolating to a VDE (n = ∞) value which is very close to the photoelectric threshold energy for the corresponding condensed phase solvated electron system. The linear extrapolation of this data to the analogous condensed phase property suggests that these cluster anions are gas phase counterparts to solvated electrons, i.e. they are embryonic forms of hydrated and ammoniated electrons which mature with increasing cluster size toward condensed phase solvated electrons. (orig.)

Negative ion photoelectron spectroscopy of solvated electron cluster anions, (H2O){/n -} and (NH3){/n -}

Science.gov (United States)

Lee, G. H.; Arnold, S. T.; Eaton, J. G.; Sarkas, H. W.; Bowen, K. H.; Ludewigt, C.; Haberland, H.

1991-03-01

The photodetachment spectra of (H2O){/n =2-69/-} and (NH3){/n =41-1100/-} have been recorded, and vertical detachment energies (VDEs) were obtained from the spectra. For both systems, the cluster anion VDEs increase smoothly with increasing sizes and most species plot linearly with n -1/3, extrapolating to a VDE ( n=∞) value which is very close to the photoelectric threshold energy for the corresponding condensed phase solvated electron system. The linear extrapolation of this data to the analogous condensed phase property suggests that these cluster anions are gas phase counterparts to solvated electrons, i.e. they are embryonic forms of hydrated and ammoniated electrons which mature with increasing cluster size toward condensed phase solvated electrons.

Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

Energy Technology Data Exchange (ETDEWEB)

Daily, Michael D. [Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Chun, Jaehun [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Heredia-Langner, Alejandro [National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Wei, Guowei [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Baker, Nathan A. [Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

2013-11-28

Implicit solvent models are important tools for calculating solvation free energies for chemical and biophysical studies since they require fewer computational resources but can achieve accuracy comparable to that of explicit-solvent models. In past papers, geometric flow-based solvation models have been established for solvation analysis of small and large compounds. In the present work, the use of realistic experiment-based parameter choices for the geometric flow models is studied. We find that the experimental parameters of solvent internal pressure p = 172 MPa and surface tension γ = 72 mN/m produce solvation free energies within 1 RT of the global minimum root-mean-squared deviation from experimental data over the expanded set. Our results demonstrate that experimental values can be used for geometric flow solvent model parameters, thus eliminating the need for additional parameterization. We also examine the correlations between optimal values of p and γ which are strongly anti-correlated. Geometric analysis of the small molecule test set shows that these results are inter-connected with an approximately linear relationship between area and volume in the range of molecular sizes spanned by the data set. In spite of this considerable degeneracy between the surface tension and pressure terms in the model, both terms are important for the broader applicability of the model.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

Energy Technology Data Exchange (ETDEWEB)

Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

2017-10-24

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

NARCIS (Netherlands)

Kastritis, P.; Visscher, K.M.; van Dijk, A.D.J.; Bonvin, A.M.J.J.

2013-01-01

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

NARCIS (Netherlands)

Kastritis, Panagiotis L.; Visscher, Koen M.; van Dijk, Aalt D.J.; Bonvin, Alexandre M.J.J.

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on

Effect of solvation on reactions of aluminium, gallium, indium, zinc and cadmium with azo compounds

International Nuclear Information System (INIS)

Savvin, S.B.

1985-01-01

Colour reactions have been examined between Al, Ga, In, Zn, Cd and reagents of a group of chromotropic acid 2.7-bisazo derivatives (Picramin B, Picramin M, Methanyl B, sulphonitrophenol M, sulphonitrophenol B) in organo-aqueous solutions containing acetone, propanol, DMFA, DMSO and acetic acid. Sensitive colour reactions occur in all the cases in aceton- or propanol-containing solutions: more sensitive than in water for Al, Ga, In; new reactions for Zn and Cd which are specific for organo-aqueous media and not observed in aqueous solutions. Sensitive reactions are observed only for Al and Ga in DMSO or DMFA solutions. Zn, Cd and In do not give colour reactions in such solutions. Differences in colour reactions for the elements in DMFA- and DMSO-containing media are connected with different solvation effects of the solvents on certain cations. Preferable solvation of some cations has been confirmed by infrared studies and is in agreement with the data reported on selective solvation

Modelling the Preferential Solvation of Ferulic Acid in {2-Propanol (1 + Water (2} Mixtures at 298.15 K

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Abolghasem Jouyban 1,2, Fleming Martínez 3 *

2017-12-01

Full Text Available Background: Recently Haq et al. reported the equilibrium solubility in {2-propanol (1 + water (2} mixtures at several temperatures with some numerical correlation analysis. Nevertheless, no attempt was made to evaluate the preferential solvation of this compound by the solvents. Methods: Preferential solvation of ferulic acid in the saturated mixtures at 298.15 K was analyzed based on the inverse Kirkwood-Buff integrals as described in the literature. Results: Ferulic acid is preferentially solvated by water in water-rich mixtures (0.00 < x1 < 0.19 but preferentially solvated by 2-propanol in mixtures with composition 0.19 < x1 < 1.00. Conclusion: These results could be interpreted as a consequence of hydrophobic hydration around the non-polar groups of the solute in the former case (0.00 < x1 < 0.19. Moreover, in the last case (0.19 < x1 < 1.00, the observed trend could be a consequence of the acid behavior of ferulic acid in front to 2-propanol molecules because this cosolvent is more basic than water as described by the respective solvatochromic parameters.

6,6'-Dimethoxygossypol: molecular structure, crystal polymorphism, and solvate formation

Science.gov (United States)

6,6´-Dimethoxygossypol (DMG) is a naturally produced derivative of gossypol that is found in relatively high concentration in some Gossypium barbadense cotton varieties. Like gossypol, DMG forms an equimolar solvate with acetic acid, but it was not clear if, like gossypol, the compound would form c...

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.

A molecular dynamics study for the isomerization of Ar solvated (benzene){sub 2}-K{sup +} heteroclusters

Energy Technology Data Exchange (ETDEWEB)

Alberti, M. [CERQT, Departament de Quimica Fisica Parc Cientific, Universitat de Barcelona, Marti i Franques, 1, 08028 Barcelona (Spain); Pacifici, L. [Department of Mathematics and Computer Science, University of Perugia, via Vanvitelli, 1 06123 Perugia (Italy); Lagana, A. [Department of Chemistry, University of Perugia, via Elce di Sotto, 8 06123 Perugia (Italy)], E-mail: lag@dyn.unipg.it; Aguilar, A. [CERQT, Departament de Quimica Fisica Parc Cientific, Universitat de Barcelona, Marti i Franques, 1, 08028 Barcelona (Spain)

2006-08-21

A dynamical study of the (benzene){sub 2}-K{sup +} heteroclusters solvated by Ar atoms has been performed using an analytical force field of the atom (ion)-bond type. An analysis of the relevant calculated structural and energetic properties of these systems is made to understand involved molecular processes. The key effect found in the calculations is the tieing up of the two rings to sandwich K{sup +} and the weaking of this effect by solvation.

Photo-illuminated diamond as a solid-state source of solvated electrons in water for nitrogen reduction.

Science.gov (United States)

Zhu, Di; Zhang, Linghong; Ruther, Rose E; Hamers, Robert J

2013-09-01

The photocatalytic reduction of N₂ to NH₃ is typically hampered by poor binding of N₂ to catalytic materials and by the very high energy of the intermediates involved in this reaction. Solvated electrons directly introduced into the reactant solution can provide an alternative pathway to overcome such limitations. Here we demonstrate that illuminated hydrogen-terminated diamond yields facile electron emission into water, thus inducing reduction of N₂ to NH₃ at ambient temperature and pressure. Transient absorption measurements at 632 nm reveal the presence of solvated electrons adjacent to the diamond after photoexcitation. Experiments using inexpensive synthetic diamond samples and diamond powder show that photocatalytic activity is strongly dependent on the surface termination and correlates with the production of solvated electrons. The use of diamond to eject electrons into a reactant liquid represents a new paradigm for photocatalytic reduction, bringing electrons directly to reactants without requiring molecular adsorption to the surface.

A solvated electron lithium electrode for secondary batteries

Science.gov (United States)

Sammells, A. F.; Semkow, K. W.

1986-09-01

Attention is given to a novel method for the achievement of high electro-chemical reversibility in Li-based nonaqueous cells, using a liquid negative electrode that consists of Li dissolved in liquid ammonia as a solvated electron Li electrode. The containment of this liquid negative active material from direct contact to a liquid nonaqueous electrolyte in the positive electrode compartment was realized through the use of a Li-intercalated, electronically conducting ceramic membrane.

Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile

Science.gov (United States)

Zanith, Caroline C.; Pliego, Josefredo R.

2015-03-01

The continuum solvation models SMD and SM8 were developed using 2,346 solvation free energy values for 318 neutral molecules in 91 solvents as reference. However, no solvation data of neutral solutes in methanol was used in the parametrization, while only few solvation free energy values of solutes in dimethyl sulfoxide and acetonitrile were used. In this report, we have tested the performance of the models for these important solvents. Taking data from literature, we have generated solvation free energy, enthalpy and entropy values for 37 solutes in methanol, 21 solutes in dimethyl sulfoxide and 19 solutes in acetonitrile. Both SMD and SM8 models have presented a good performance in methanol and acetonitrile, with mean unsigned error equal or less than 0.66 and 0.55 kcal mol-1 in methanol and acetonitrile, respectively. However, the correlation is worse in dimethyl sulfoxide, where the SMD and SM8 methods present mean unsigned error of 1.02 and 0.95 kcal mol-1, respectively. Our results point out the SMx family of models need be improved for dimethyl sulfoxide solvent.

Quantitative prediction of solvation free energy in octanol of organic compounds.

Science.gov (United States)

Delgado, Eduardo J; Jaña, Gonzalo A

2009-03-01

The free energy of solvation, DeltaGS0, in octanol of organic compounds 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 DeltaGS0 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.

Examination of hydrogen-bonding interactions between dissolved solutes and alkylbenzene solvents based on Abraham model correlations derived from measured enthalpies of solvation

Energy Technology Data Exchange (ETDEWEB)

Varfolomeev, Mikhail A.; Rakipov, Ilnaz T. [Chemical Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008 (Russian Federation); Acree, William E., E-mail: acree@unt.edu [Department of Chemistry, 1155 Union Circle # 305070, University of North Texas, Denton, TX 76203-5017 (United States); Brumfield, Michela [Department of Chemistry, 1155 Union Circle # 305070, University of North Texas, Denton, TX 76203-5017 (United States); Abraham, Michael H. [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)

2014-10-20

Highlights: • Enthalpies of solution measured for 48 solutes dissolved in mesitylene. • Enthalpies of solution measured for 81 solutes dissolved in p-xylene. • Abraham model correlations derived for enthalpies of solvation of solutes in mesitylene. • Abraham model correlations derived for enthalpies of solvation of solutes in p-xylene. • Hydrogen-bonding enthalpies reported for interactions of aromatic hydrocarbons with hydrogen-bond acidic solutes. - Abstract: Enthalpies of solution at infinite dilution of 48 organic solutes in mesitylene and 81 organic solutes in p-xylene were measured using isothermal solution calorimeter. Enthalpies of solvation for 92 organic vapors and gaseous solutes in mesitylene and for 130 gaseous compounds in p-xylene were determined from the experimental and literature data. Abraham model correlations are determined from the experimental enthalpy of solvation data. The derived correlations describe the experimental gas-to-mesitylene and gas-to-p-xylene solvation enthalpies to within average standard deviations of 1.87 kJ mol{sup −1} and 2.08 kJ mol{sup −1}, respectively. Enthalpies of X-H⋯π (X-O, N, and C) hydrogen bond formation of proton donor solutes (alcohols, amines, chlorinated hydrocarbons etc.) with mesitylene and p-xylene were calculated based on the Abraham solvation equation. Obtained values are in good agreement with the results determined using conventional methods.

Rotation and solvation of ammonium ion

International Nuclear Information System (INIS)

Perrin, C.L.; Gipe, R.K.

1987-01-01

From nitrogen-15 spin-lattice relaxation times and nuclear Overhauser enhancements, the rotational correlations time tau/sub c/ for 15 NH 4 + was determined in s series of solvents. Values of tau/sub c/ range from 0.46 to 20 picoseconds. The solvent dependent of tau/sub c/ cannot be explained in terms of solvent polarity, molecular dipole moment, solvent basicity, solvent dielectric relaxation, or solvent viscosity. The rapid rotation and the variation with solvent can be accounted for by a model that involves hydrogen bonding of an NH proton to more than one solvent molecule in a disordered solvation environment. 25 references, 1 table

The role of solvation in the binding selectivity of the L-type calcium channel.

Science.gov (United States)

Boda, Dezső; Henderson, Douglas; Gillespie, Dirk

2013-08-07

We present grand canonical Monte Carlo simulation results for a reduced model of the L-type calcium channel. While charged residues of the protein amino acids in the selectivity filter are treated explicitly, most of the degrees of freedom (including the rest of the protein and the solvent) are represented by their dielectric response, i.e., dielectric continua. The new aspect of this paper is that the dielectric coefficient in the channel is different from that in the baths. The ions entering the channel, thus, cross a dielectric boundary at the entrance of the channel. Simulating this case has been made possible by our recent methodological development [D. Boda, D. Henderson, B. Eisenberg, and D. Gillespie, J. Chem. Phys. 135, 064105 (2011)]. Our main focus is on the effect of solvation energy (represented by the Born energy) on monovalent vs. divalent ion selectivity in the channel. We find no significant change in selectivity by changing the dielectric coefficient in the channel because the larger solvation penalty is counterbalanced by the enhanced Coulomb attraction inside the channel as soon as we use the Born radii (fitted to experimental hydration energies) to compute the solvation penalty from the Born equation.

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.

Isotope effect in enthalpy of solvation of the lithium ion

International Nuclear Information System (INIS)

Krestov, G.A.; Egorov, G.I.; Korolev, V.P.

1989-01-01

At 298.15 K, the authors determined the standard enthalpies of solution for 6 LiCl and 7 LiCl in water, heavy water, dimethylsulfoxide (DMSO) and aqueous solutions of DMSO. The authors have established that solvation of 6 Li + is differentiated in water and DMSO to a greater degree than for 7 Li +

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

DEFF Research Database (Denmark)

Svendsen, Casper Steinmann; Blædel, Kristoffer L.; Christensen, Anders Steen

2013-01-01

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiq......An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules...

Water-enhanced solvation of organics

Energy Technology Data Exchange (ETDEWEB)

Lee, Jane H. [Univ. of California, Berkeley, CA (United States)

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 γ_s vs x_w/x_s curve. From graph shape Δ(log γ_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 Δ(log γ_acid)/Δ(x_w/x_acid) = -0.25. In methylcyclohexanone, the decrease of the activity coefficient of propionic acid was -0.19. Activity coefficient of propionic acid in methylcyclohexanone stopped decreasing once the water reached a 2:1 water to acid mole ratio, implying a stoichiometric relation between water, ketone, and acid. Except for 2,3-butanediol, activity coefficients of the solutes studied decreased monotonically with water content. Activity coefficient curves of ethanol, 1,2-propanediol and 2,3-butanediol did not level off at large water/solute mole ratio. Solutes investigated by solid-liquid equilibrium were citric acid, gallic acid, phenol, xylenols, 2-naphthol. Saturation concentration of citric acid in anhydrous butyl acetate increased from 0.0009 to 0.087 mol/L after 1.3 % (g/g) water co-dissolved into organic phase. Effect of water-enhanced solvation for citric acid is very large but very small for phenol and its derivatives.

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

DEFF Research Database (Denmark)

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

1979-01-01

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

Solvation dynamics in triton-X-100 and triton-X-165 micelles: Effect of micellar size and hydration

Science.gov (United States)

Kumbhakar, Manoj; Nath, Sukhendu; Mukherjee, Tulsi; Pal, Haridas

2004-09-01

Dynamic Stokes' shift measurements using coumarin 153 as the fluorescence probe have been carried out to study solvation dynamics in two nonionic micelles, viz., triton-X-100 (TX-100) and triton-X-165 (TX-165). In both the micelles, the solvent relaxation dynamics is biexponential in nature. While the fast solvation time τs1 is seen to be almost similar for both the micelles, the slow solvation time τs2 is found to be appreciably smaller in TX-165 than in TX-100 micelle. Dynamic light scattering measurements indicate that the TX-165 micelles are substantially smaller in size than that of TX-100. Assuming similar core size for both the micelles, as expected from the similar chemical structures of the nonpolar ends for both the surfactants, the Palisade layer is also indicated to be substantially thinner for TX-165 micelles than that of TX-100. The aggregation number of TX-165 micelles is also found to be substantially smaller than that of TX-100 micelles. Fluorescence spectral studies of C153 dye in the two micelles indicate that the Palisade layer of TX-165 micelles is more polar than that of TX-100 micelles. Fluorescence anisotropy measurements indicate that the microviscosity in the Palisade layer of TX-165 micelles is also lower than that of TX-100 micelles. Based on these results it is inferred that the structure of the Palisade layer of TX-165 micelles is quite loose and have higher degree hydration in comparison to that of TX-100 micelles. Due to these structural differences in the Palisade layers of TX-165 and TX-100 micelles the solvation dynamics is faster in the former micelles than in the latter. It has been further inferred that in the present systems the collective response of the water molecules at somewhat away from the probes is responsible for the faster component of the solvation time, which does not reflect much of the structural changes of the micellar Palisade layer. On the contrary, the slower solvation time component, which is mainly due to

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

International Nuclear Information System (INIS)

Jozefowicz, Marek; Heldt, Janina R.

2003-01-01

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

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.

Solvation of o-hydroxybenzoic acid in pure and modified supercritical carbon dioxide, according to numerical modeling data

Science.gov (United States)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2015-08-01

The dissolution of an elementary fragment of crystal structure (an o-hydroxybenzoic acid ( o-HBA) dimer) in both pure and modified supercritical (SC) carbon dioxide by adding methanol (molar fraction, 0.035) at T = 318 K, ρ = 0.7 g/cm3 is simulated. Features of the solvation mechanism in each solvent are revealed. The solvation of o-HBA in pure SC CO2 is shown to occur via electron donor-acceptor interactions. o-HBA forms a solvate complex in modified SC CO2 through hydrogen bonds between the carboxyl group and methanol. The hydroxyl group of o-HBA participates in the formation of an intramolecular hydrogen bond, and not in interactions with the solvent. It is concluded that the o-HBA-methanol complex is a stable molecular structure, and its lifetime is one order of magnitude higher than those of other hydrogen bonds in fluids.

Enthalpies of solution, enthalpies of fusion and enthalpies of solvation of polyaromatic hydrocarbons: Instruments for determination of sublimation enthalpy at 298.15 K

Energy Technology Data Exchange (ETDEWEB)

Solomonov, Boris N., E-mail: boris.solomonov@ksu.ru; Varfolomeev, Mikhail A.; Nagrimanov, Ruslan N.; Mukhametzyanov, Timur A.; Novikov, Vladimir B.

2015-12-20

Graphical abstract: - Highlights: • Solution enthalpies of aromatic hydrocarbons were measured at 298.15 K. • Solution enthalpy of aromatic hydrocarbons in benzene is equal to their fusion enthalpy. • Method for calculation of solvation enthalpy of aromatic hydrocarbons was proposed. • Approach for estimation of aromatic hydrocarbons sublimation enthalpy was developed. • Obtained sublimation enthalpies coincide well with the recommended literature data. - Abstract: In this work a simple method for calculation of solvation enthalpies of polyaromatic hydrocarbons (PAHs) in various solvents at 298.15 K was proposed. According to this method the enthalpy of solvation of any polyaromatic hydrocarbon in a particular solvent can be calculated on the basis of the general formula of the compound, the solvation enthalpy of benzene in the same solvent and parameter related to the contribution of hydrogen atom into solvation enthalpy. The validity of the proposed method was confirmed by the comparison of calculated and experimentally measured values of solvation enthalpies of PAHs in benzene, tetrahydrofuran and acetonitrile. This method was used for determination of the sublimation enthalpy of PAHs at 298.15 K based on the general relationship between the enthalpy of sublimation/vaporization of the compound of interest and its enthalpies of solution and solvation in the same solvent at 298.15 K. Enthalpies of solution at infinite dilution of several PAHs were measured in acetonitrile, benzene and tetrahydrofuran at 298.15 K. It was shown that solution enthalpies of PAHs in benzene at 298.15 K are approximately equal to their fusion enthalpies at the melting temperature. Solvation enthalpies of 15 PAHs at 298.15 K calculated according to the proposed method together with corresponding fusion enthalpy values (at the melting temperature) were used to calculate the sublimation enthalpy values at 298.15 K. Comparison of the obtained results with recommended values of

Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

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Mohammad Firoz Khan

2016-12-01

Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.

Mutagenicity of Tween 80-solvated mild gasification products in the Ames salmonella microsomal assay system. [Quarterly report, October--December 1991

Energy Technology Data Exchange (ETDEWEB)

1992-01-13

The results of the Tween 80-solvated Ames testing of six mild gasification samples indicate significant mutagenic activity only in the composite materials (MG-119 and MG-120), previously suspected from the DMSO-solvated assays, which had shown some variable but ultimately insignificant mutagenic responses. The activity of these samples from the Tween 80-solvated assays was quite low when compared to either the positive controls or the SRC-II HD coal-liquefaction reference material. The class of mutagenic activity expressed by these samples solvated in Tween 80 was that of an indirect-acting, frameshift mutagen(s) since significant activity was found only on tester strain TA98 in the presence of the metabolic activation fraction (S9). Because DMSO and other solvents have been shown to affect the mutagenic activity of certain pure chemicals, the possibility of solvent/mutagen interactions in complex mixtures such as coal-derived liquids exists. Thus, the testing of the genotoxic activity of undefined, chemically complex compounds may require the use of at least two solvent systems to reduce the possibility of artifactual findings. 10 refs., 4 tabs.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

Science.gov (United States)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

Science.gov (United States)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Lieb-Liniger-like model of quantum solvation in CO-4HeN clusters

Science.gov (United States)

Farrelly, D.; Iñarrea, M.; Lanchares, V.; Salas, J. P.

2016-05-01

Small 4He clusters doped with various molecules allow for the study of "quantum solvation" as a function of cluster size. A peculiarity of quantum solvation is that, as the number of 4He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of "microscopic superfluidity." Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the 4He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of 4He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 4He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of 4He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially—for very small N—provides a central, if relatively weak, attraction to organize the cluster; as more 4He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the quantum mechanism of the transition from a molecular

Ejection of solvated ions from electrosprayed methanol/water nanodroplets studied by molecular dynamics simulations.

Science.gov (United States)

Ahadi, Elias; Konermann, Lars

2011-06-22

The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model.

Pulse radiolysis study on solvated electrons in ionic liquid with controlling water content

International Nuclear Information System (INIS)

Yang Jinfeng; Kondoh, T.; Yoshida, Y.; Nagaishi, R.

2006-01-01

Room-temperature ionic liquids, which are nonvolatile and nonflammable, have been proposed as 'green solvents' for new applications in chemical synthesis, separation chemistry, electrochemistry and other areas. In the separation chemistry, the hydrophobic ionic liquids have been practically expected to be alternative to traditional organic solvents for solvent extraction of 4f and 5f elements from the viewpoints of the immiscibility in water, especially in the spent nuclear fuel reprocessing. However, the chemical reaction or kinetics studies are important to apply the ionic liquids for various processes. To understand the effects of ionic liquids on chemical reactions, pulse radiolysis studies of ionic liquid have been carried out on nanosecond scale by using a 27 MeV electron beam and an analyzing light source of xenon lamp. In the experiment, a hydrophobic ionic liquid of diethylmethyl(2-methoxy)ammonium-bis(trifluoromethanesulfonyl)imide (DEMMA-TFSI) salt was used. The ionic liquid of DEMMA-TFSI was prepared by reacting equimolar amounts of diethylmethyl(2-methoxy)ammonium chloride (C 10 H 20 F 6 N 2 O 5 S 2 Cl, >98%, Nisshinbo) with lithium bis(trifluoromethanesulfonyl)imide (LiN(SO 2 CF 3 ) 2 , SynQuest Labs., Inc.) in aqueous solutions at room temperature. The ionic liquid was separated from the aqueous phase, purified by repeated extractions with water to LiCl and excess reagent, and finally dried at 110 degree C under vacuum. The transient absorptions of the ionic liquid were measured at wavelengths from 350 to 1400 nm, in which two photodiodes of silicon ( 1000 nm) were used. The spectrum of solvated electrons in the ionic liquid of DEMMA-TFSI was obtained with an absorption peak of 1060 nm and a wide bandwidth of about 600 nm (FWHM). The decay constant of the solvated electrons in the ionic liquid was 1.54 x 10 7 s -1 , which is independent on the wavelength. The absorption peak of the spectrum was blue-shifted from 1060 to 780 nm with increasing water

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered

Science.gov (United States)

Guthrie, J. Peter

2014-03-01

For the fifth time I have provided a set of solvation energies (1 M gas to 1 M aqueous) for a SAMPL challenge. In this set there are 23 blind compounds and 30 supplementary compounds of related structure to one of the blind sets, but for which the solvation energy is readily available. The best current values of each compound are presented along with complete documentation of the experimental origins of the solvation energies. The calculations needed to go from reported data to solvation energies are presented, with particular attention to aspects which are new to this set. For some compounds the vapor pressures (VP) were reported for the liquid compound, which is solid at room temperature. To correct from VPsubcooled liquid to VPsublimation requires ΔSfusion, which is only known for mannitol. Estimated values were used for the others, all but one of which were benzene derivatives and expected to have very similar values. The final compound for which ΔSfusion was estimated was menthol, which melts at 42 °C so that modest errors in ΔSfusion will have little effect. It was also necessary to look into the effects of including estimated values of ΔCp on this correction. The approximate sizes of the effects of inclusion of ΔCp in the correction from VPsubcooled liquid to VPsublimation were estimated and it was noted that inclusion of ΔCp invariably makes ΔGS more positive. To extend the set of compounds for which the solvation energy could be calculated we explored the use of boiling point (b.p.) data from Reaxys/Beilstein as a substitute for studies of the VP as a function of temperature. B.p. data are not always reliable so it was necessary to develop a criterion for rejecting outliers. For two compounds (chlorinated guaiacols) it became clear that inclusion represented overreach; for each there were only two independent pressure, temperature points, which is too little for a trustworthy extrapolation. For a number of compounds the extrapolation from lowest

Solvation-based vapour pressure model for (solvent + salt) systems in conjunction with the Antoine equation

International Nuclear Information System (INIS)

Senol, Aynur

2013-01-01

Highlights: • Vapour pressures of (solvent + salt) systems have been estimated through a solvation-based model. • Two structural forms of the generalized solvation model using the Antoine equation have been performed. • A simplified concentration-dependent vapour pressure model has been also processed. • The model reliability analysis has been performed in terms of a log-ratio objective function. • The reliability of the models has been interpreted in terms of the statistical design factors. -- Abstract: This study deals with modelling the vapour pressure of a (solvent + salt) system on the basis of the principles of LSER. The solvation model framework clarifies the simultaneous impact of several physical variables such as the vapour pressure of a pure solvent estimated by the Antoine equation, the solubility and solvatochromic parameters of the solvent and the physical properties of the ionic salt. It has been analyzed independently the performance of two structural forms of the generalized model, i.e., a relation depending on an integration of the properties of the solvent and the ionic salt and a relation on a reduced property-basis. A simplified concentration-dependent vapour pressure model has been also explored and implemented on the relevant systems. The vapour pressure data of sixteen (solvent + salt) systems have been processed to analyze statistically the reliability of existing models in terms of a log–ratio objective function. The proposed vapour pressure models match relatively well the observed performance, yielding the overall design factors of 1.066 and 1.073 for the solvation-based models with the integrated and reduced properties, and 1.008 for the concentration-based model, respectively

Characterization of solvated electrons in hydrogen cyanide clusters: (HCN)n- (n=3, 4)

Science.gov (United States)

Wu, Di; Li, Ying; Li, Zhuo; Chen, Wei; Li, Zhi-Ru; Sun, Chia-Chung

2006-02-01

Theoretical studies of the solvated electrons (HCN)n- (n =3, 4) reveal a variety of electron trapping possibilities in the (HCN)n (n =3, 4) clusters. Two isomers for (HCN)3- and four isomers for (HCN)4- are obtained at the MP2/aug -cc-pVDZ+dBF (diffusive bond functions) level of theory. In view of vertical electron detachment energies (VDEs) at the CCSD(T) level, the excess electron always "prefers" locating in the center of the system, i.e., the isomer with higher coordination number shows larger VDE value. However, the most stable isomers of the solvated electron state (HCN)3- and (HCN)4- are found to be the linear C∞ν and D∞h structures, respectively, but not the fullyl symmetric structures which have the largest VDE values.

Intensity of f-f bands of neodymium chloride alcohol solvates

International Nuclear Information System (INIS)

Bukietynska, K.; Jezowski-Trzebiatowska, B.; Keller, B.

1981-01-01

Recent results revealed that in alcohol solutions of lanthanide chlorides, at least in the case of Eu 3+ and Yb 3+ ions, there exist mixed solvates, i.e. both chloride ions and solvent molecules are present in the Ln 3+ ion first coordination sphere. This conclusion was drawn from an analysis of the charge transfer transitions in the spectra of Eu 3+ and Yb 3+ chlorides in alcohols (methyl, ethyl, n-propyl), where two separate C.T.bands were observed and identified as C.T. transitions from the alcohol molecule and chloride ion to the Ln 3+ ion. In our previous paper we have reported that the energy of the first f-d transition in the Pr 3+ chloride alcohol solvates varied for different alcohols. These data also confirmed our suggestion that alcohol molecules are present in the first coordination sphere of the lanthanide ion. In the work reported here, we have tried to apply the intensity analysis method to the solution spectra of neodymium chloride dissolved in simple aliphatic alcohols like methanol, ethanol and n-propanol. Experimental details are given. Results are presented and discussed. (author)

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)

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

Science.gov (United States)

Nakamura, Issei

2014-05-29

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Wave–particle interactions in a resonant system of photons and ion-solvated water

Energy Technology Data Exchange (ETDEWEB)

Konishi, Eiji, E-mail: konishi.eiji.27c@st.kyoto-u.ac.jp

2017-02-26

Highlights: • We consider a QED model of rotating water molecules with ion solvation effects. • The equations of motion are cast in terms of a conventional free electron laser. • We offer a new quantum coherence mechanism induced by collective instability. - Abstract: We investigate a laser model for a resonant system of photons and ion cluster-solvated rotating water molecules in which ions in the cluster are identical and have very low, non-relativistic velocities and direction of motion parallel to a static electric field induced in a single direction. This model combines Dicke superradiation with wave–particle interaction. As the result, we find that the equations of motion of the system are expressed in terms of a conventional free electron laser system. This result leads to a mechanism for dynamical coherence, induced by collective instability in the wave–particle interaction.

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

Science.gov (United States)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Preferential solvation of ions in mixed solvents. 6: Univalent anions in aqueous organic solvents according to the inverse Kirkwood-Buff integral (IKBI) approach

International Nuclear Information System (INIS)

Marcus, Yizhak

2007-01-01

The inverse Kirkwood-Buff integral (IKBI) approach is applied to the preferential solvation of F - , Cl - , Br - , I - , and ClO 4 - in aqueous mixtures of the co-solvents (S) methanol (MeOH), ethanol (EtOH), t-butanol (t-BuOH), 1,2-ethanediol (EG), glycerol (Gly), acetone (Me 2 CO), acetonitrile (MeCN), formamide (FA), N,N-dimethylformamide (DMF), N,N,N',N',N'',N''-hexamethyl phosphoric triamide (HMPT), and dimethylsulfoxide (DMSO), as far as the relevant data exist in the literature. Fluoride anions are selectively solvated by the water up to large mole fractions (x S ≥ 0.4) of S = EtOH, t-BuOH, Me 2 CO, MeCN, and DMF, and up to lower contents (x S ∼ 0.1) of MeOH, EG, FA, and DMSO. The other anions are preferentially solvated by water to diminishing extent as their sizes become larger, and the largest ones show some preference for S in water-rich mixtures of MeOH and FA, whereas in aqueous Gly even chloride is preferentially solvated by the Gly. The competition between the co-solvent and the anion for the hydrogen bonds that water molecules donate is the main cause for the observed preferential solvation behaviour

Solvatochromism and preferential solvation of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone by UV-vis absorption and laser-induced fluorescence measurements

Science.gov (United States)

Sasirekha, V.; Vanelle, P.; Terme, T.; Ramakrishnan, V.

2008-12-01

Solvation characteristics of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone ( 1) in pure and binary solvent mixtures have been studied by UV-vis absorption spectroscopy and laser-induced fluorescence techniques. The binary solvent mixtures used as CCl 4 (tetrachloromethane)-DMF ( N, N-dimethylformamide), AN (acetonitrile)-DMSO (dimethylsulfoxide), CHCl 3 (chloroform)-DMSO, CHCl 3-MeOH (methanol), and MeOH-DMSO. The longest wavelength band of 1 has been studied in pure solvents as well as in binary solvent mixtures as a function of the bulk mole fraction. The Vis absorption band maxima show an unusual blue shift with increasing solvent polarity. The emission maxima of 1 show changes with varying the pure solvents and the composition in the case of binary solvent mixtures. Non-ideal solvation characteristics are observed in all binary solvent mixtures. It has been observed that the quantity [ ν-(Xν+Xν)] serves as a measure of the extent of preferential solvation, where ν˜ and X are the position of band maximum in wavenumbers (cm -1) and the bulk mole fraction values, respectively. The preferential solvation parameters local mole fraction ( X2L), solvation index ( δs2), and exchange constant ( k12) are evaluated.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Science.gov (United States)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-01-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Science.gov (United States)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

2015-12-28

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

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

Energy Technology Data Exchange (ETDEWEB)

Yadav, Hari O. S., E-mail: cyz108802@chemistry.iitd.ac.in, E-mail: hariyadav.iitd@gmail.com; Shrivastav, Gourav; Agarwal, Manish; Chakravarty, Charusita [Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016 (India)

2016-06-28

The extent to which solvent-mediated effective interactions between nanoparticles can be predicted based on structure and associated thermodynamic estimators for bulk solvents and for solvation of single and pairs of nanoparticles is studied here. As a test of the approach, we analyse the strategy for creating temperature-independent solvent environments using a series of homologous chain fluids as solvents, as suggested by an experimental paper [M. I. Bodnarchuk et al., J. Am. Chem. Soc. 132, 11967 (2010)]. Our conclusions are based on molecular dynamics simulations of Au{sub 140}(SC{sub 10}H{sub 21}){sub 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

Solubility and preferential solvation of some n-alkyl-parabens in methanol + water mixtures at 298.15 K

International Nuclear Information System (INIS)

Cárdenas, Zaira J.; Jiménez, Daniel M.; Delgado, Daniel R.; Almanza, Ovidio A.; Jouyban, Abolghasem; Martínez, Fleming; Acree, William E.

2017-01-01

Highlights: • Parabens equilibrium solubility was determined in methanol + water binary mixtures at 298.15 K. • Solubility values were correlated with the Jouyban-Acree model. • Preferential solvation parameters were derived by using the IKBI method. • δx 1,3 values are negative in water-rich mixtures but positive in the other mixtures. - Abstract: Methyl, ethyl and propyl parabens equilibrium solubility was determined in (methanol + water) binary mixtures at 298.15 K. The mole fraction solubility of these compounds increased in 503 (from 2.40 × 10 −4 to 0.121), 1377 (from 9.86 × 10 −5 to 0.136) and 4597 (from 3.73 × 10 −5 to 0.171) times when passing from neat water to neat methanol, for methyl, ethyl and propyl parabens, respectively. All these solubility values were correlated with the Jouyban-Acree model. Preferential solvation parameters by methanol (δx 1,3 ) of these parabens were derived from their thermodynamic solution properties using the inverse Kirkwood-Buff integrals (IKBI) method. For all compounds δx 1,3 values are negative in water-rich mixtures but positive in mixtures with methanol mole fraction greater than 0.32. It is conjecturable that in the former case the hydrophobic hydration around non-polar groups of parabens plays a relevant role in the solvation. Besides, the preferential solvation of these solutes by methanol in mixtures of similar co-solvent compositions and in methanol-rich mixtures could be explained in terms of the higher basic behaviour of methanol.

Time-dependent friction and solvation time correlation function

International Nuclear Information System (INIS)

Samanta, Alok; Ali, Sk Musharaf; Ghosh, Swapan K

2005-01-01

We have derived a new relation between the time-dependent friction and solvation time correlation function (STCF) for non-polar fluids. The friction values calculated using this relation and simulation results on STCF for a Lennard-Jones fluid are shown to have excellent agreement with the same obtained through mode-coupling theory. Also derived is a relation between the time-dependent dielectric friction and STCF for polar fluids. Routes are thus provided to obtain the time-dependent friction (non-polar as well as dielectric) from an experimentally measured quantity like STCF, even if the interparticle interaction potential is not known

Preferential solvation of ions in mixed solvents. 6: Univalent anions in aqueous organic solvents according to the inverse Kirkwood-Buff integral (IKBI) approach

Energy Technology Data Exchange (ETDEWEB)

Marcus, Yizhak [Department of Inorganic and Analytical Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: ymarcus@vms.huji.ac.il

2007-10-15

The inverse Kirkwood-Buff integral (IKBI) approach is applied to the preferential solvation of F{sup -}, Cl{sup -}, Br{sup -}, I{sup -}, and ClO{sub 4}{sup -} in aqueous mixtures of the co-solvents (S) methanol (MeOH), ethanol (EtOH), t-butanol (t-BuOH), 1,2-ethanediol (EG), glycerol (Gly), acetone (Me{sub 2}CO), acetonitrile (MeCN), formamide (FA), N,N-dimethylformamide (DMF), N,N,N',N',N'',N''-hexamethyl phosphoric triamide (HMPT), and dimethylsulfoxide (DMSO), as far as the relevant data exist in the literature. Fluoride anions are selectively solvated by the water up to large mole fractions (x{sub S} {>=} 0.4) of S = EtOH, t-BuOH, Me{sub 2}CO, MeCN, and DMF, and up to lower contents (x{sub S} {approx} 0.1) of MeOH, EG, FA, and DMSO. The other anions are preferentially solvated by water to diminishing extent as their sizes become larger, and the largest ones show some preference for S in water-rich mixtures of MeOH and FA, whereas in aqueous Gly even chloride is preferentially solvated by the Gly. The competition between the co-solvent and the anion for the hydrogen bonds that water molecules donate is the main cause for the observed preferential solvation behaviour.

Preferential solvation of single ions in mixed solvents: Part 1. New experimental approach and solvation of monovalent ions in methanol-water and acetonitrile-water mixture. Part 2. Theoretical computation and comparison with experimental data

International Nuclear Information System (INIS)

Rege, Aarti C.; Venkataramani, B.; Gupta, A.R.

1999-06-01

Preferential solvation of single ion solutions has been studied with Li + , Na + , K + and Ag +- forms of Dowex 50W resins of different cross-linkings in methanol-water and acetonitrile (AN)- water mixtures. The solvent uptake by this alkali metal ionic forms of Dowex 50W resins was studied in an isopiestic set-up using 2,4,6 and 8 m LiCl solutions in 11.0, 20.8, 44.3 and 70.2 % (w/w) methanol-water mixtures and that of Na +- and Ag +- forms using 14.6 to 94.3 % (w/w) AN - water mixtures. The solvent sorbed in the resin phase was extracted by Rayleigh-type distillation and analysed gas chromatographically. The data were analysed by the N s (mole fraction of the organic solvent in the resin phase) vs n t au (total solvent content in the resin phase) plots and separation factor, alpha(ratio of mole fraction of the solvents in the resin and solution phases) or N s vs m (molality in the resin phase) plots. The limiting values of these plots gave the composition of the solvent in the primary solvation shell around the single ion. The compositions of the primary solvation shell around Li + , Na + , and K + in methanol-water mixtures and Na + and Ag + in acetonitrile (AN) - water mixtures have been computed using Franks equation and the approach of Marcus and compared with the experimental results obtained with the above mentioned ionic forms of Dowex 50W resins in different mixed solvents. The experimental results for Li + showed good agreement with the values computed using Franks equation for all methanol-water composition. However, in the case of Na + and K + in methanol-water mixtures and Na + in AN-water mixtures, there was agreement only at lower organic solvent content and the Franks equation predicted higher values for the organic solvent in the primary solvation shell around the cation at higher organic solvent content as compared to experimental results

Electrochemical redox reactions in solvated silica sol-gel glass

International Nuclear Information System (INIS)

Opallo, M.

2002-01-01

The studies of electrochemical redox reactions in solvated silica sol-gel glass were reviewed. The methodology of the experiments with emphasis on the direct preparation of the solid electrolyte and the application ultra microelectrodes was described. Generally, the level of the electrochemical signal is not much below that observed in liquid electrolyte. The current depends on time elapsed after gelation, namely the longer time, the smaller current. The differences between electrochemical behaviour of the redox couples in monoliths and thin layers were described. (author)

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program

DEFF Research Database (Denmark)

Svendsen, Casper Steinmann; Blædel, Kristoffer; Christensen, Anders S

2013-01-01

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiq......An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules...... such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase....

The initial stages of NaCl dissolution: Ion or ion pair solvation?

Science.gov (United States)

Klimes, Jiri; Michaelides, Angelos

2009-03-01

The interaction of water with rock salt (NaCl) is important in a wide variety of natural processes and human activities. A lot is known about NaCl dissolution at the macroscopic level but we do not yet have a detailed atomic scale picture of how salt crystals dissolve. Here we report an extensive series of density functional theory, forcefield and molecular dynamics studies of water clusters at flat and defective NaCl surfaces and NaCl clusters. The focus is on answering seemingly elementary questions such as how many water molecules are needed before it becomes favorable to extract an ion or a pair of ions from the crystal or the cluster. It turns out, however, that the answers to these questions are not so straightforward: below a certain number of water molecules (˜ 12) solvation of individual ions is less costly and above this number solvation of ion pairs is favored. These results reveal a hitherto unknown complexity in the NaCl dissolution process born out of a subtle interplay between water-water and water-ion interactions.

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

Energy Technology Data Exchange (ETDEWEB)

Delgado, Alain [Istituto Nanoscienze - CNR, Centro S3, via Campi 213/A, 41125 Modena (Italy); Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, Calle 30 # 502, 11300 La Habana (Cuba); Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea [Istituto Nanoscienze - CNR, Centro S3, via Campi 213/A, 41125 Modena (Italy)

2015-10-14

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

Time-dependent radiolytic yields at room temperature and temperature-dependent absorption spectra of the solvated electrons in polyols

International Nuclear Information System (INIS)

Lin Mingzhang; Mostafavi, M.; Lampre, I.; Muroya, Y.; Katsumura, Y.

2007-01-01

The molar extinction coefficients at the absorption maximum of the solvated electron spectrum have been evaluated to be 900, 970, and 1000 mol -1 ·m 2 for 1,2-ethanediol (12ED), 1,2-propanediol (12PD), and 1,3-propanediol (13PD), respectively. These values are two-third or three-fourth of the value usually reported in the published report. Picosecond pulse radiolysis studies have aided in depicting the radiolytic yield of the solvated electron in these solvents as a function of time from picosecond to microsecond. The radiolytic yield in these viscous solvents is found to be strongly different from that of the water solution. The temperature dependent absorption spectra of the solvated electron in 12ED, 12PD, and 13PD have been also investigated. In all the three solvents, the optical spectra shift to the red with increasing temperature. While the shape of the spectra does not change in 13PD, a widening on the blue side of the absorption band is observed in 12ED and 12PD at elevated temperatures. (authors)

Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics.

Science.gov (United States)

Roy, Susmita; Yashonath, Subramanian; Bagchi, Biman

2015-03-28

A self-consistent mode coupling theory (MCT) with microscopic inputs of equilibrium pair correlation functions is developed to analyze electrolyte dynamics. We apply the theory to calculate concentration dependence of (i) time dependent ion diffusion, (ii) intermediate scattering function of the constituent ions, and (iii) ion solvation dynamics in electrolyte solution. Brownian dynamics with implicit water molecules and molecular dynamics method with explicit water are used to check the theoretical predictions. The time dependence of ionic self-diffusion coefficient and the corresponding intermediate scattering function evaluated from our MCT approach show quantitative agreement with early experimental and present Brownian dynamic simulation results. With increasing concentration, the dispersion of electrolyte friction is found to occur at increasingly higher frequency, due to the faster relaxation of the ion atmosphere. The wave number dependence of intermediate scattering function, F(k, t), exhibits markedly different relaxation dynamics at different length scales. At small wave numbers, we find the emergence of a step-like relaxation, indicating the presence of both fast and slow time scales in the system. Such behavior allows an intriguing analogy with temperature dependent relaxation dynamics of supercooled liquids. We find that solvation dynamics of a tagged ion exhibits a power law decay at long times-the decay can also be fitted to a stretched exponential form. The emergence of the power law in solvation dynamics has been tested by carrying out long Brownian dynamics simulations with varying ionic concentrations. The solvation time correlation and ion-ion intermediate scattering function indeed exhibit highly interesting, non-trivial dynamical behavior at intermediate to longer times that require further experimental and theoretical studies.

Electrochemical behaviours of Eu(III/E(II and Ce(IV/Ce(III in H3PO4-H2O media : solvation and complexation reactions

Directory of Open Access Journals (Sweden)

Belqat B.

2018-01-01

Full Text Available Many kinds of rare earth elements (REE such as europium and cerium have been make them essential elements in many high-tech components. The electrochemical studies can be presented as an interesting indication for europium and cerium extraction from phosphoric solutions, including solvation and complexation reactions. The normal redox potentials of Eu3+/Eu2+ and Ce4+/Ce3+ systems have been determined in H3PO4-H2O media with various phosphoric acid concentration. The solvation of these elements in phosphoric media is characterized by their transfer activity coefficients "f" calculated from the corresponding normal redox potentials. The corresponding solvation increases with increasing the H3PO4 concentration. For each REE, the electrochemical properties depend on its number of charges and on its basic properties. Results suggest that solvation and complexation of REE phosphates are important in controlling REE concentration.

Optically Controlled Electron-Transfer Reaction Kinetics and Solvation Dynamics : Effect of Franck-Condon States

NARCIS (Netherlands)

Gupta, Kriti; Patra, Aniket; Dhole, Kajal; Samanta, Alok Kumar; Ghosh, Swapan K.

2017-01-01

Experimental results for optically controlled electron-transfer reaction kinetics (ETRK) and nonequilibrium solvation dynamics (NESD) of Coumarin 480 in DMPC vesicle show their dependence on excitation wavelength λex. However, the celebrated Marcus theory and linear-response-theory-based approaches

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

Czech Academy of Sciences Publication Activity Database

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

2015-01-01

Roč. 17, č. 25 (2015), s. 4712-4721 ISSN 1466-8033 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : trospium chloride * solvate screening * x-ray crystallography * Jana2006 Subject RIV: FR - Pharmacology ; Medidal Chemistry Impact factor: 3.849, year: 2015

Equilibrium and nonequilibrium solvation and solute electronic structure

International Nuclear Information System (INIS)

Kim, H.J.; Hynes, J.T.

1990-01-01

When a molecular solute is immersed in a polar and polarizable solvent, the electronic wave function of the solute system is altered compared to its vacuum value; the solute electronic structure is thus solvent-dependent. Further, the wave function will be altered depending upon whether the polarization of the solvent is or is not in equilibrium with the solute charge distribution. More precisely, while the solvent electronic polarization should be in equilibrium with the solute electronic wave function, the much more sluggish solvent orientational polarization need not be. We call this last situation non-equilibrium solvation. We outline a nonlinear Schroedinger equation approach to these issues

Effect of the composition of a solution on the enthalpies of solvation of piperidine in methanol-acetonitrile and dimethylsulfoxide-acetonitrile mixed solvents

Science.gov (United States)

Kuz'mina, I. A.; Volkova, M. A.; Sitnikova, K. A.; Sharnin, V. A.

2014-01-01

Heat effects of dissolution of piperidine (ppd) are measured by calorimetry at 298.15 K over the range of composition of acetonitrile-methanol (AN-MeOH) mixed solvents. Based on the Δsol H ○(ppd)AN-MeOH values obtained using the literature data on Δsol H ○ (ppd) in acetonitrile-dimethylsulfoxide (AN-DMSO) mixed solvents and the vaporization enthalpy of ppd, the enthalpies of solvation of amine in AN-MeOH and AN-DMSO binary mixtures are calculated. A rise in the exothermicity of solvation of piperidine is observed upon the transition from AN to DMSO and MeOH, due mainly to the enhanced solvation of the amino group of ppd as a result of changes in the acid-base properties of the mixed solvent.

High-dimensional neural network potentials for solvation: The case of protonated water clusters in helium

Science.gov (United States)

Schran, Christoph; Uhl, Felix; Behler, Jörg; Marx, Dominik

2018-03-01

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner. This approach yields an excellent agreement with a mean absolute deviation as small as 0.04 kJ mol-1 for the interaction energy between helium and both hydronium and Zundel cations compared with coupled cluster reference calculations with an energetically converged basis set. The construction and improvement of the potential can be performed in a highly automated way, which opens the door for applications to a variety of reactive molecules to study the effect of solvation on the solute as well as the solute-induced structuring of the solvent. Furthermore, we show that this NNP approach yields very convincing agreement with the coupled cluster reference for properties like many-body spatial and radial distribution functions. This holds for the microsolvation of the protonated water monomer and dimer by a few helium atoms up to their solvation in bulk helium as obtained from path integral simulations at about 1 K.

Elucidating the Solvation Structure and Dynamics of Lithium Polysulfides Resulting from Competitive Salt and Solvent Interactions

Energy Technology Data Exchange (ETDEWEB)

Rajput, Nav Nidhi; Murugesan, Vijayakumar; Shin, Yongwoo; Han, Kee Sung; Lau, Kah Chun; Chen, Junzheng; Liu, Jun; Curtiss, Larry A.; Mueller, Karl T.; Persson, Kristin A.

2017-04-10

Fundamental molecular level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applica-tions. In particular, exhaustive knowledge of solvation structure, stability and transport properties is critical for developing stable electrolytes for fast charging and high energy density next-generation energy storage systems. Here we report the correlation between solubility, solvation structure and translational dynamics of a lithium salt (Li-TFSI) and polysulfides species using well-benchmarked classical molecular dynamics simulations combined with nuclear magnetic resonance (NMR). It is observed that the polysulfide chain length has a significant effect on the ion-ion and ion-solvent interaction as well as on the diffusion coefficient of the ionic species in solution. In particular, extensive cluster formation is observed in lower order poly-sulfides (Sx2-; x≤4), whereas the longer polysulfides (Sx2-; x>4) show high solubility and slow dynamics in the solu-tion. It is observed that optimal solvent/salt ratio is essen-tial to control the solubility and conductivity as the addi-tion of Li salt increases the solubility but decreases the mo-bility of the ionic species. This work provides a coupled theoretical and experimental study of bulk solvation struc-ture and transport properties of multi-component electro-lyte systems, yielding design metrics for developing optimal electrolytes with improved stability and solubility.

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. Copyright © 2014 John Wiley & Sons, Inc.

Enthalpies of fusion and enthalpies of solvation of aromatic hydrocarbons derivatives: Estimation of sublimation enthalpies at 298.15 K

Energy Technology Data Exchange (ETDEWEB)

Solomonov, Boris N., E-mail: boris.solomonov@kpfu.ru; Nagrimanov, Ruslan N.; Varfolomeev, Mikhail A.; Buzyurov, Aleksey V.; Mukhametzyanov, Timur A.

2016-03-20

Graphical abstract: - Highlights: • Solution enthalpies of aromatic hydrocarbons derivatives (ArHD) were measured at 298.15 K. • Solution enthalpies of ArHD in benzene at 298.15 K are equal to their fusion enthalpy at melting point. • Sublimation enthalpies of 80 ArHD were calculated as a sum of fusion and solvation enthalpies. • Obtained sublimation enthalpies are in good agreement with the recommended literature data. - Abstract: Enthalpy of sublimation of solid compound can be found using the values of solution enthalpy and solvation enthalpy in any solvent. In this work enthalpies of solution at infinite dilution of a number of aromatic hydrocarbons derivatives in benzene were measured at 298.15 K. Comparison between experimental and literature solution enthalpies in benzene at 298.15 K and fusion enthalpies at melting temperature of aromatic hydrocarbon derivatives showed, that these values are approximately equal. Thereby, fusion enthalpies at melting temperature can be used instead of their solution enthalpies in benzene at 298.15 K for calculation of sublimation enthalpies at 298.15 K. Solvation enthalpies in benzene at 298.15 K required for this procedure were calculated using group additivity scheme. The sublimation enthalpies of 80 aromatic hydrocarbons derivatives at 298.15 K were evaluated as a difference between fusion enthalpies at melting temperature and solvation enthalpies in benzene at 298.15 K. Obtained in this work values of sublimation enthalpy at 298.15 K for studied compounds were in a good agreement with available literature data.

Thermodynamics of coproportionation reactions of homogeneous samarium (3) and yttrium (3) nitrates solvates with neutral organic phosphorus compounds

International Nuclear Information System (INIS)

Pyartman, A.K.

1995-01-01

Reaction heats of homogeneous samarium (3) and yttrium (3) nitrate solvates coproportionation with neutral organophosphoric compounds (tri-n.-butylphosphate, diisooctylmethylphosphonate, diisoamylmethylphosphonate) at T=298.15 K in hexane have been measured by thermochemical method. It has been ascertained that enthalpies of coproportionation reactions practically do not depend on the nature, concentration of rare earth metal (3) nitrate solvates in hexane, nature of neutral organophosphoric compound and constitute 1.1±-.2 kJ/mol. The Gibbs free energy of coproportionation reactions is -5.43 kJ/mol, while entropy of the reactions in 14.5±0.7 J/mol·K. 8 refs., 1 tab

Impact of structural modification of 1,2,4-thiadiazole derivatives on thermodynamics of solubility and solvation processes in 1-octanol and n-hexane

International Nuclear Information System (INIS)

Surov, Artem O.; Bui, Cong Trinh; Volkova, Tatyana V.; Proshin, Alexey N.; Perlovich, German L.

2016-01-01

Highlights: • Solubility processes of some 1,2,4-thiadiazoles in n-hexane and 1-octanol were investigated. • Solvation processes of some 1,2,4-thiadiazoles in n-hexane and 1-octanol were studied. • Transfer processes from n-hexane to 1-octanol were evaluated. • Impact of various substituents in 1,2,4-thiadiazoles on the mentioned processes was studied. - Abstract: Influence of a structural modification on thermodynamic aspects of solubility and solvation processes of the 1,2,4-thiadiazole drug-like compounds in pharmaceutically relevant solvents n-hexane and 1-octanol was investigated. The solubility of the compounds in 1-octanol does not substantially depend on the nature and position of the substituent in the phenyl moiety. In n-hexane, however, the introduction of any substituent in the phenyl ring of the 1,2,4-thiadiazole molecule reduces the solubility in the solvent. In order to rationalize the relationships between the structure of 1,2,4-thiadiazoles and their solubility, the latter was considered in terms of two fundamental processes: sublimation and solvation. It was found that for the most of the compounds the solubility change in both solvents is a consequence of competition between the sublimation and solvation contributions, i.e. the introduction of substituents leads to growth of the sublimation Gibbs energy and increase in the solvation Gibbs energy. Thermodynamic parameters of the transfer process of the compounds from n-hexane to 1-octanol, which is a model of the blood–brain barrier (BBB), were also analyzed.

A conductivity study of preferential solvation of lithium ion in acetonitrile-dimethyl sulfoxide mixtures

International Nuclear Information System (INIS)

Mozhzhukhina, Nataliia; Longinotti, M. Paula; Corti, Horacio R.; Calvo, Ernesto J.

2015-01-01

The electrical mobility of LiPF 6 in acetonitrile–dimethyl sulfoxide (ACN–DMSO) mixtures, a potential electrolyte in oxygen cathodes of lithium-air batteries, has been studied using a very precise conductance technique, which allowed the determination of the infinite dilution molar conductivity and association constant of the salt in the whole composition range. In the search for preferential Li + ion solvation, we also measured the electrical conductivity of tetrabutylammonium hexafluorophosphate (TBAPF 6 ), a salt formed by a bulky cation, over the same composition range. The results show a qualitative change in the curvature of the LiPF 6 molar conductivity composition dependence for ACN molar fraction (x ACN ) ∼ 0.95, which was not observed for TBAPF 6 . The dependence of the measured Li/Li + couple potential with solvent composition also showed a pronounced change around the same composition. We suggest that these observations can be explained by Li + ion preferential solvation by DMSO in ACN–DMSO mixtures with very low molar fractions of DMSO

A shell-resolved analysis of preferential solvation of coffee ingredients in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate

Science.gov (United States)

Zeindlhofer, Veronika; Berger, Magdalena; Steinhauser, Othmar; Schröder, Christian

2018-05-01

Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hydrogen bonding of the anions to hydroxy groups of the solutes can be detected, their concentration at the surface is less enhanced compared to the cations. The decomposition into solvation shells by Voronoi tessellation reveals that structural features are only observed in the first solvation shell. Nevertheless, the depletion of water and the excess concentration of the ions and, in particular, of the cations are visible in the next solvation shells as well. Therefore, classical arguments of hydrotropic theory fail to explain this behavior.

Ionic association and solvation in solutions of magnesium and nickel perchlorates in acetonitrile

Science.gov (United States)

Kalugin, O. N.; Agieienko, V. N.; Otroshko, N. A.; Moroz, V. V.

2009-02-01

The paper presents the conductometric data on solutions of Mg(ClO4)2 and Ni(ClO4)2 in acetonitrile over the temperature ranges 5-55°C for Mg(ClO4)2 and 25-75°C for Ni(ClO4)2. The extended Lee-Wheaton equation for unsymmetrical electrolytes was used to determine the limiting equivalent conductivities of the Mg2+, Ni2+, and ClO{4/-} ions and first-step ionic association constants with the formation of [KtClO4]+ ion pairs. Lower ionic association constants for Ni(ClO4)2 compared with Mg(ClO4)2 were a consequence of stronger non-Coulomb repulsion in the formation of [KtClO4]+ ion pairs because of the formation of a firmer solvation shell by the nickel compared with magnesium cation. The structure-dynamic parameter of ionic solvation was estimated. It was found that spatial-time correlations in the nearest environment of ions increased in the series ClO{4/-} > Mg2+ > Ni2+.

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

A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide

Science.gov (United States)

Cordeiro, João M. M.; Soper, Alan K.

2013-01-01

The solvation of N-methylformamide (NMF) by dimethylsulfoxide (DMSO) in a 20% NMF/DMSO liquid mixture is investigated using a combination of neutron diffraction augmented with isotopic substitution and Monte Carlo simulations. The aim is to investigate the solute-solvent interactions and the structure of the solution. The results point to the formation of a hydrogen bond (H-bond) between the H bonded to the N of the amine group of NMF and the O of DMSO particularly strong when compared with other H-bonded liquids. Moreover, a second cooperative H-bond is identified with the S atom of DMSO. As a consequence of these H-bonds, molecules of NMF and DMSO are rather rigidly connected, establishing very stable dimmers in the mixture and very well organized first and second solvation shells.

Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

International Nuclear Information System (INIS)

Elkins, Madeline H.; Williams, Holly L.; Neumark, Daniel M.

2015-01-01

The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism

Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

Science.gov (United States)

Elkins, Madeline H.; Williams, Holly L.; Neumark, Daniel M.

2015-06-01

The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism.

Dynamics of electron solvation in methanol: Excited state relaxation and generation by charge-transfer-to-solvent

Energy Technology Data Exchange (ETDEWEB)

Elkins, Madeline H.; Williams, Holly L. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Neumark, Daniel M. [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

2015-06-21

The charge-transfer-to-solvent dynamics (CTTS) and excited state relaxation mechanism of the solvated electron in methanol are studied by time-resolved photoelectron spectroscopy on a liquid methanol microjet by means of two-pulse and three-pulse experiments. In the two-pulse experiment, CTTS excitation is followed by a probe photoejection pulse. The resulting time-evolving photoelectron spectrum reveals multiple time scales characteristic of relaxation and geminate recombination of the initially generated electron which are consistent with prior results from transient absorption. In the three-pulse experiment, the relaxation dynamics of the solvated electron following electronic excitation are measured. The internal conversion lifetime of the excited electron is found to be 130 ± 40 fs, in agreement with extrapolated results from clusters and the non-adiabatic relaxation mechanism.

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Science.gov (United States)

Nguyen, Crystal N; Young, Tom Kurtzman; Gilson, Michael K

2012-07-28

The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and

Effect of Preferential Solvation of Polymer Chains on Vapor-Pressure Osmometry Results. Computer Simulation Study.

Czech Academy of Sciences Publication Activity Database

Svoboda, Martin; Lísal, Martin; Limpouchová, Z.; Procházka, Karel

2018-01-01

Roč. 23, č. 3 (2018), s. 244-251 ISSN 1023-666X R&D Projects: GA ČR GA15-19542S Institutional support: RVO:67985858 Keywords : vapor-pressure osmometry * simulation * solvatation Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry

Solvation of carbonaceous molecules by para-H{sub 2} and ortho-D{sub 2} clusters. I. Polycyclic aromatic hydrocarbons

Energy Technology Data Exchange (ETDEWEB)

Calvo, F., E-mail: florent.calvo@univ-grenoble-alpes.fr [Univ. Grenoble Alpes, LIPHY, F-38000 Grenoble, France and CNRS, LIPHY, F-38000 Grenoble (France); Yurtsever, E. [Koç University, Rumelifeneriyolu, Sariyer, Istanbul 34450 (Turkey)

2016-06-14

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C{sub 54}H{sub 18}) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H{sub 2}. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.

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...... 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....

Solvation of actinide salts in water using a polarizable continuum model.

Science.gov (United States)

Kumar, Narendra; Seminario, Jorge M

2015-01-29

In order to determine how actinide atoms are dressed when solvated in water, density functional theory calculations have been carried out to study the equilibrium structure of uranium plutonium and thorium salts (UO2(2+), PuO2(2+), Pu(4+), and Th(4+)) both in vacuum as well as in solution represented by a conductor-like polarizable continuum model. This information is of paramount importance for the development of sensitive nanosensors. Both UO2(2+) and PuO2(2+) ions show coordination number of 4-5 with counterions replacing one or two water molecules from the first coordination shell. On the other hand, Pu(4+), has a coordination number of 8 both when completely solvated and also in the presence of chloride and nitrate ions with counterions replacing water molecules in the first shell. Nitrates were found to bind more strongly to Pu(IV) than chloride anions. In the case of the Th(IV) ion, the coordination number was found to be 9 or 10 in the presence of chlorides. Moreover, the Pu(IV) ion shows greater affinity for chlorides than the Th(IV) ion. Adding dispersion and ZPE corrections to the binding energy does not alter the trends in relative stability of several conformers because of error cancelations. All structures and energetics of these complexes are reported.

17O NMR Studies of the Solvation State of cissolidustrans Isomers of Amides and Model Protected Peptides

Science.gov (United States)

Gerothanassis; Vakka; Troganis

1996-06-01

17O shielding constants have been utilized to investigate solvation differences of the cissolidustrans isomers of N-methylformamide (NMF), N-ethylformamide (NEF), and tert-butylformamide (TBF) in a variety of solvents with particular emphasis on aqueous solution. Comparisons are also made with protected peptides of the formulas CH3CO-YOH, CH3CO-Y-NHR (Y = Pro, Sar), and CH3CO-Y-Z-NHR (Y = Pro; Z = D-Ala) selectively enriched in 17O at the acetyl oxygen atom. Hydration at the amide oxygen induces large and specific modifications of the 17O shielding constants, which are practically the same for the cis and trans isomers of NMF, NEF, and the protected peptides. For tert-butylformamide, the strong deshielding of the trans isomer compared to that of the cis isomer may be attributed to an out-of-plane (torsion-angle) deformation of the amide bond andsolidusor a significant reduction of solvation of the trans isomer due to steric inhibition of the bulky tert-butyl group. Good linear correlation between delta(17O) of amides and delta(17O) of acetone was found for different solvents which have varying dielectric constants and solvation abilities. Sum-over-states calculations, within the solvaton model, underestimate effects of the dielectric constant of the medium on 17O shielding, while finite-perturbation-theory calculations give good agreement with the experiment.

Establishing linear solvation energy relationships between VOCs and monolayer-protected gold nanoclusters using quartz crystal microbalance.

Science.gov (United States)

Li, Chi-Lin; Lu, Chia-Jung

2009-08-15

Linear solvation energy relationships (LSERs) have been recognized as a useful model for investigating the chemical forces behind the partition coefficients between vapor molecules and absorbents. This study is the first to determine the solvation properties of monolayer-protected gold nanoclusters (MPCs) with different surface ligands. The ratio of partition coefficients/MPC density (K/rho) of 18 volatile organic compounds (VOCs) for four different MPCs obtained through quartz crystal microbalance (QCM) experiments were used for the LSER model calculations. LSER modeling results indicate that all MPC surfaces showed a statistically significant (pattraction, 4-methoxythiophenol-capped MPCs can also interact with polar organics (s=1.04). Showing a unique preference for the hydrogen bond basicity of vapors (b=1.11), 2-benzothiazolethiol-capped MPCs provide evidence of an intra-molecular, proton-shift mechanism on surface of nano-gold.

First crystal structures of pharmaceutical ibrutinib: systematic solvate screening and characterization

Czech Academy of Sciences Publication Activity Database

Zvoníček, V.; Skořepová, E.; Dušek, Michal; Babor, M.; Zvatora, P.; Šoós, M.

2017-01-01

Roč. 17, č. 6 (2017), s. 3116-3127 ISSN 1528-7483 R&D Projects: GA MŠk LO1603; GA ČR GA17-23196S EU Projects: European Commission(XE) CZ.2.16/3.1.00/24510 Institutional support: RVO:68378271 Keywords : Ibrutinib solvates * anticancer drug * Raman spectroscopy * powder X-ray diffraction * crystal structure Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 4.055, year: 2016

Variation of the solvation number of Eu(III) in mixed system of methanol and water

International Nuclear Information System (INIS)

Suganuma, H.; Arisaka, M.; Omori, T.; Satoh, I.; Choppin, G.R.

1999-01-01

The stability constants (β 1 ) of the monofluoride complex of Eu(III) have been determined in mixed solvents of methanol and water at a 0.10 M ionic strength using a solvent extraction technique. The values of ln β 1 increase as the mole fraction of methanol in the mixed solvent system increases. The variation in the stability constants can be correlated with both the large effect due to the solvation of F and the small effect due to both (1) the solvation of cations in connection with complexation and (2) the electrostatic attraction between Eu 3+ and F - . Based on the variation in the sum of (1) and (2) in water and the mixed solvent solutions, it was determined that the coordination number (CN) of Eu(III) varied from a mixture of CN = 9 and 8 to CN = 8 at about a 0.03 mole fraction of methanol in the mixed solvent. (orig.)

Solvation in supercritical water

International Nuclear Information System (INIS)

Cochran, H.D.; Cummings, P.T.; Karaborni, S.

1991-01-01

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

Phospholipid bilayer affinities and solvation characteristics by electrokinetic chromatography with a nanodisc pseudostationary phase.

Science.gov (United States)

Penny, William M; Steele, Harmen B; Ross, J B Alexander; Palmer, Christopher P

2017-03-01

Phospholipid bilayer nanodiscs composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and synthetic maleic acid-styrene copolymer belts have been introduced as a pseudostationary phase (PSP) in electrokinetic chromatography and demonstrated good performance. The nanodiscs provide a suitable migration range and high theoretical plate counts. Using this nanodisc pseudostationary phase, the affinity of the bilayer structure for probe solutes was determined and characterized. Good correlation is observed between retention factors and octanol water partition coefficients for particular categories of solutes, but the general correlation is weak primarily because the nanodiscs show stronger affinity than octanol for hydrogen bond donors. This suggests that a more appropriate application of this technology is to measure and characterize interactions between solutes and lipid bilayers directly. Linear solvation energy relationship analysis of the nanodisc-solute interactions in this study demonstrates that the nanodiscs provide a solvation environment with low cohesivity and weak hydrogen bond donating ability, and provide relatively strong hydrogen bond acceptor strength. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A linear solvation energy relationship model of organic chemical partitioning to dissolved organic carbon.

Science.gov (United States)

Kipka, Undine; Di Toro, Dominic M

2011-09-01

Predicting the association of contaminants with both particulate and dissolved organic matter is critical in determining the fate and bioavailability of chemicals in environmental risk assessment. To date, the association of a contaminant to particulate organic matter is considered in many multimedia transport models, but the effect of dissolved organic matter is typically ignored due to a lack of either reliable models or experimental data. The partition coefficient to dissolved organic carbon (K(DOC)) may be used to estimate the fraction of a contaminant that is associated with dissolved organic matter. Models relating K(DOC) to the octanol-water partition coefficient (K(OW)) have not been successful for many types of dissolved organic carbon in the environment. Instead, linear solvation energy relationships are proposed to model the association of chemicals with dissolved organic matter. However, more chemically diverse K(DOC) data are needed to produce a more robust model. For humic acid dissolved organic carbon, the linear solvation energy relationship predicts log K(DOC) with a root mean square error of 0.43. Copyright © 2011 SETAC.

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

Czech Academy of Sciences Publication Activity Database

Bardhan, J. P.; Jungwirth, Pavel; Makowski, L.

Roč. 137, č. 12 ( 2012 ), 124101/1-124101/6 ISSN 0021-9606 R&D Projects: GA MŠk LH12001 Institutional research plan: CEZ:AV0Z40550506 Keywords : ion solvation * continuum models * linear response Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.164, year: 2012

Contribution to the study of solvated electrons in water and alcohols and of radiolytic processes in organic carbonates by picosecond pulse radiolysis

International Nuclear Information System (INIS)

Torche, Faycal

2012-01-01

This work is part of the study area of the interaction of radiation with polar liquids. Using the picosecond electron accelerator ELYSE, studies were conducted using the techniques of pulse radiolysis combined with absorption spectrophotometry Time-resolved in the field of a picosecond. This work is divided into two separate chapters. The first study addresses the temporal variation of the radiolytic yield of solvated electron in water and simple alcohols. Due to original detection system mounted on the accelerator ELYSE, composed of a flash lamp specifically designed for the detection and a streak-camera used for the first time in absorption spectroscopy, it was possible to record the time-dependent radiolytic yields of the solvated electron from ten picoseconds to a few hundred nanoseconds. The scavenging of the electron solvated by methyl viologen, was utilized to reevaluate the molar extinction coefficient of the absorption spectrum of solvated electron in water and ethanol from isobestic points which corresponds to the intersection of the absorption spectra of solvated electron which disappears and methyl viologen which is formed during the reaction. The second chapter is devoted to the study of liquid organic carbonates such as dimethyl carbonate (DMC), diethyl carbonate (DEC) and propylene carbonate (PC). This family of carbonate which compose the electrolytes lithium batteries, has never been investigated by pulse radiolysis. The studies were focused on the PC in the light of these physicochemical characteristics, including its very high dielectric constant and its strong dipole moment of 4.9 D. The first results were obtained on aqueous solutions containing propylene carbonate to observe the reactions of reduction and oxidation of PC by radiolytic species of water (solvated electron and OH radicals). Then, after the identification (spectral and kinetic) of the species formed by interaction with the OH radical as the PC* radical resulting from the

Development and application of QM/MM methods to study the solvation effects and surfaces

Energy Technology Data Exchange (ETDEWEB)

Dibya, Pooja Arora [Iowa State Univ., Ames, IA (United States)

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize the computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this work

Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

International Nuclear Information System (INIS)

You, Zhi-Qiang; Herbert, John M.; Mewes, Jan-Michael; Dreuw, Andreas

2015-01-01

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents

Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

Energy Technology Data Exchange (ETDEWEB)

You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States); Mewes, Jan-Michael; Dreuw, Andreas [Interdisciplinary Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany)

2015-11-28

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.

17O NMR Studies of the Solvation State of cis/trans Isomers of Amides and Model Protected Peptides

Science.gov (United States)

Gerothanassis, Ioannis P.; Vakka, Constantina; Troganis, Anastasios

1996-06-01

17O shielding constants have been utilized to investigate solvation differences of the cis/trans isomers ofN-methylformamide (NMF),N-ethylformamide (NEF), andtert-butylformamide (TBF) in a variety of solvents with particular emphasis on aqueous solution. Comparisons are also made with protected peptides of the formulas CH3CO-YOH, CH3CO-Y-NHR (Y = Pro, Sar), and CH3CO-Y-Z-NHR (Y = Pro; Z =D-Ala) selectively enriched in17O at the acetyl oxygen atom. Hydration at the amide oxygen induces large and specific modifications of the17O shielding constants, which are practically the same for the cis and trans isomers of NMF, NEF, and the protected peptides. Fortert-butylformamide, the strong deshielding of the trans isomer compared to that of the cis isomer may be attributed to an out-of-plane (torsion-angle) deformation of the amide bond and/or a significant reduction of solvation of the trans isomer due to steric inhibition of the bulkytert-butyl group. Good linear correlation between δ(17O) of amides and δ(17O) of acetone was found for different solvents which have varying dielectric constants and solvation abilities. Sum-over-states calculations, within the solvaton model, underestimate effects of the dielectric constant of the medium on17O shielding, while finite-perturbation-theory calculations give good agreement with the experiment.

Electron detachment energies in high-symmetry alkali halide solvated-electron anions

Science.gov (United States)

Anusiewicz, Iwona; Berdys, Joanna; Simons, Jack; Skurski, Piotr

2003-07-01

We decompose the vertical electron detachment energies (VDEs) in solvated-electron clusters of alkali halides in terms of (i) an electrostatic contribution that correlates with the dipole moment (μ) of the individual alkali halide molecule and (ii) a relaxation component that is related to the polarizability (α) of the alkali halide molecule. Detailed numerical ab initio results for twelve species (MX)n- (M=Li,Na; X=F,Cl,Br; n=2,3) are used to construct an interpolation model that relates the clusters' VDEs to their μ and α values as well as a cluster size parameter r that we show is closely related to the alkali cation's ionic radius. The interpolation formula is then tested by applying it to predict the VDEs of four systems [i.e., (KF)2-, (KF)3-, (KCl)2-, and (KCl)3-] that were not used in determining the parameters of the model. The average difference between the model's predicted VDEs and the ab initio calculated electron binding energies is less than 4% (for the twelve species studied). It is concluded that one can easily estimate the VDE of a given high-symmetry solvated electron system by employing the model put forth here if the α, μ and cation ionic radii are known. Alternatively, if VDEs are measured for an alkali halide cluster and the α and μ values are known, one can estimate the r parameter, which, in turn, determines the "size" of the cluster anion.

Role of trapped and solvated electrons in Ps formation

International Nuclear Information System (INIS)

Stepanov, S.V.; Byakov, V.M.; Mikhin, K.V.; He, C.; Hirade, T.

2005-01-01

Role of trapped and solvated electrons in Ps formation is discussed. Combination of thermalized positron with such electrons is possible from the view point of the energy balance and may results in Ps formation. This process proceeds during all e = lifetime matter. Fitting of raw experimental e + -e - annihilation spectra has to be based on an adequate physical input, which often leads to necessity of nonexponential deconvolution of the spectra. We have interpreted the Ps formation data in polyethylene, ethylene-methylmethacrylate and polymethylmethacrylate in dark and in light vs. tome of the measurement and temperature. parameters characterized accumulation of trapped electrons and their recombination with counter ions and positrons are obtained. (author)

Effect of halogen substitution on the enthalpies of solvation and hydrogen bonding of organic solutes in chlorobenzene and 1,2-dichlorobenzene derived using multi-parameter correlations

Energy Technology Data Exchange (ETDEWEB)

Varfolomeev, Mikhail A.; Rakipov, Ilnaz T.; Khachatrian, Artashes A. [Department of Physical Chemistry, Kazan Federal University, Kremlevskaya 18, Kazan 420008 (Russian Federation); Acree, William E., E-mail: acree@unt.edu [Department of Chemistry, 1155 Union Circle # 305070, University of North Texas, Denton, TX 76203-5017 (United States); Brumfield, Michela [Department of Chemistry, 1155 Union Circle # 305070, University of North Texas, Denton, TX 76203-5017 (United States); Abraham, Michael H. [Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ (United Kingdom)

2015-10-10

Graphical abstract: - Highlights: • Enthalpies of solution measured for 43 solutes dissolved in chlorobenzene. • Enthalpies of solution measured for 72 solutes dissolved in 1,2-dichlorobenzene. • Mathematical expressions derived for predicting enthalpies of solvation of solutes in chlorobenzene. • Mathematical expressions derived for predicting enthalpies of solvation of solutes in 1,2-chlorobenzene. - Abstract: Enthalpies of solution at infinite dilution at 298 K, Δ{sub soln}H{sup A/Solvent}, have been measured by isothermal solution calorimetry for 43 and 72 organic solutes dissolved in chlorobenzene and 1,2-dichlorobenzene, respectively. The measured Δ{sub soln}H{sup A/Solvent} data, along with published Δ{sub soln}H{sup A/Solvent} values taken from the published literature for solutes dissolved in both chlorobenzene solvents, were converted to enthalpies of solvation, Δ{sub solv}H{sup A/Solvent}, using standard thermodynamic equations. Abraham model correlations were developed from the experimental Δ{sub solv}H{sup A/Solvent} data. The best derived correlations describe the experimental gas-to-chlorobenzene and gas-to-1,2-dichlorobenzene enthalpies of solvation to within standard deviations of 1.5 kJ mol{sup −1} and 1.9 kJ mol{sup −1}, respectively. Enthalpies of X−H…π (X – O, N, and C) hydrogen bond formation of proton donor solutes (alcohols, amines, chlorinated hydrocarbons, etc.) with chlorobenzene and 1,2-dichlorobenzene were calculated based on the Abraham solvation equation. Obtained values are in good agreement with the results determined using conventional methods.

Computational solvation analysis of biomolecules in aqueous ionic liquid mixtures : From large flexible proteins to small rigid drugs.

Science.gov (United States)

Zeindlhofer, Veronika; Schröder, Christian

2018-06-01

Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Since not all possible combinations of cations and anions can be tested experimentally, fundamental knowledge on the interaction of the ionic liquid ions with water and with biomolecules is mandatory to optimize the solvation behavior, the biodegradability, and the costs of the ionic liquid. Here, we report on current computational approaches to characterize the impact of the ionic liquid ions on the structure and dynamics of the biomolecule and its solvation layer to explore the full potential of ionic liquids.

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

Science.gov (United States)

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

2017-06-13

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

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

Directory of Open Access Journals (Sweden)

Weiwei Mou

2011-12-01

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

Towards a stable ion-solvating polymer electrolyte for advanced alkaline water electrolysis

DEFF Research Database (Denmark)

Aili, David; Wright, Andrew G.; Kraglund, Mikkel Rykær

2017-01-01

Advanced alkaline water electrolysis using ion-solvating polymer membranes as electrolytes represents a new direction in the field of electrochemical hydrogen production. Polybenzimidazole membranes equilibrated in aqueous KOH combine the mechanical robustness and gas-tightness of a polymer...... stability in alkaline environments. The novel electrolytes are extensively characterized with respect to physicochemical and electrochemical properties and the chemical stability is assessed in 0-50 wt% aqueous KOH for more than 6 months at 88 degrees C. In water electrolysis tests using porous 3...

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

Czech Academy of Sciences Publication Activity Database

Kolář, Michal; Fanfrlík, Jindřich; Hobza, Pavel

2011-01-01

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

Conformational Behavior of Polymer Chains of Different Architectures in Strongly Endothermic Solvent Mixtures: Specific Solvation Effects.

Czech Academy of Sciences Publication Activity Database

Suchá, L.; Limpouchová, Z.; Procházka, Karel

2017-01-01

Roč. 295, č. 8 (2017), s. 1391-1403 ISSN 0303-402X R&D Projects: GA ČR GA15-19542S Institutional support: RVO:67985858 Keywords : cononsolvency * preferential solvation * star polymer Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 1.723, year: 2016

Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

Science.gov (United States)

Harmon, Tyler S.; Holehouse, Alex S.; Pappu, Rohit V.

2018-04-01

Intracellular biomolecular condensates are membraneless organelles that encompass large numbers of multivalent protein and nucleic acid molecules. The bodies assemble via a combination of liquid–liquid phase separation and gelation. A majority of condensates included multiple components and show multilayered organization as opposed to being well-mixed unitary liquids. Here, we put forward a simple thermodynamic framework to describe the emergence of spatially organized droplets in multicomponent systems comprising of linear multivalent polymers also known as associative polymers. These polymers, which mimic proteins and/or RNA have the architecture of domains or motifs known as stickers that are interspersed by flexible spacers known as linkers. Using a minimalist numerical model for a four-component system, we have identified features of linear multivalent molecules that are necessary and sufficient for generating spatially organized droplets. We show that differences in sequence-specific effective solvation volumes of disordered linkers between interaction domains enable the formation of spatially organized droplets. Molecules with linkers that are preferentially solvated are driven to the interface with the bulk solvent, whereas molecules that have linkers with negligible effective solvation volumes form cores in the core–shell architectures that emerge in the minimalist four-component systems. Our modeling has relevance for understanding the physical determinants of spatially organized membraneless organelles.

Solvation analysis of some Solvatochromic probes in binary mixtures of reline, ethaline, and glyceline with DMSO

Czech Academy of Sciences Publication Activity Database

Harifi-Mood, A.R.; Ghobadi, R.; Matić, S.; Minofar, Babak; Řeha, David

2016-01-01

Roč. 22, OCT 2016 (2016), s. 845-853 ISSN 0167-7322 R&D Projects: GA ČR GA13-21053S; GA MŠk(CZ) LM2015055 Institutional support: RVO:61388971 Keywords : Deep eutectic solvents * Solvatochromic parameters * Preferential solvation Subject RIV: EE - Microbiology, Virology Impact factor: 3.648, year: 2016

Compound forming extractants, solvating solvents and inert solvents IUPAC chemical data series

CERN Document Server

Marcus, Y; Kertes, A S

2013-01-01

Equilibrium Constants of Liquid-Liquid Distribution Reactions, Part III: Compound Forming Extractants, Solvating Solvents, and Inert Solvents focuses on the compilation of equilibrium constants of various compounds, such as acids, ions, salts, and aqueous solutions. The manuscript presents tables that show the distribution reactions of carboxylic and sulfonic acid extractants and their dimerization and other reactions in the organic phase and extraction reactions of metal ions from aqueous solutions. The book also states that the inorganic anions in these solutions are irrelevant, since they d

Expanding the structural landscape of niclosamide: a high Z ' polymorph, two new solvates and monohydrate H_A

DEFF Research Database (Denmark)

Sovago, Ioana; Bond, Andrew D.

2015-01-01

to be twinned by twofold rotation around that axis. The acetonitrile molecules occupy channels in the structure. A complete structure is provided for niclosamide monohydrate, C13H8Cl2N2O4·H2O, polymorph HA, obtained by Rietveld refinement against laboratory powder X-ray diffraction data. It has been suggested...... that this compound is related to the methanol solvate of niclosamide [Harriss, Wilson & Radosevljevic Evans (2014). Acta Cryst. C70, 758-763], but it is found that the two are not fully isostructural: they contain isostructural two-dimensional layers, but the layers are arranged differently in the two structures....... This suggests that HA may have the potential for polytypism, and features in the Rietveld difference curve indicate that a polytype fully isostructural with the methanol solvate might be present....

Thermodynamic aspects of solubility, solvation and partitioning processes of some sulfonamides

Energy Technology Data Exchange (ETDEWEB)

Perlovich, German L., E-mail: glp@isc-ras.r [Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432 Chernogolovka (Russian Federation); Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo (Russian Federation); Ryzhakov, Alex M. [Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo (Russian Federation); Strakhova, Nadezda N.; Kazachenko, Vladimir P. [Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432 Chernogolovka (Russian Federation); Schaper, Klaus-Juergen [Research Center Borstel, Leibniz Center for Medicine and Biosciences, D-23845 Borstel (Germany); Raevsky, Oleg A. [Department of Computer-Aided Molecular Design, Institute of Physiologically Active Compounds, Russian Academy of Sciences, 142432 Chernogolovka (Russian Federation)

2011-05-15

Research highlights: {yields} The thermodynamic aspects of sublimation processes of some sulfonamides were studied by investigating the temperature dependence of vapor pressure using the transpiration method. {yields} Solubility processes of the compounds in water, phosphate buffer with pH 7.4 and n-octanol were investigated and corresponding thermodynamic functions were calculated as well. {yields} Thermodynamic characteristics of the sulfonamides solvation were evaluated. - Abstract: The thermodynamic aspects of sublimation processes of three sulfonamides with the general structures C{sub 6}H{sub 5}-SO{sub 2}NH-C{sub 6}H{sub 4}-R (R = 4-NO{sub 2}) and 4-NH{sub 2}-C{sub 6}H{sub 4}-SO{sub 2}NH-C{sub 6}H{sub 4}-R (R = 4-NO{sub 2}; 4-CN) were studied by investigating the temperature dependence of vapor pressure using the transpiration method. These data together with those obtained earlier for C{sub 6}H{sub 5}-SO{sub 2}NH-C{sub 6}H{sub 4}-R (R = 4-Cl) and 4-NH{sub 2}-C{sub 6}H{sub 4}-SO{sub 2}NH-C{sub 6}H{sub 4}-R (R = 4-Cl; 4-OMe; 4-C{sub 2}H{sub 5}) were analyzed and compared. A correlation was derived between sublimation Gibbs free energies and the sum of H-bond acceptor factors of the molecules. Solubility processes of the compounds in water, phosphate buffer with pH 7.4 and n-octanol (as phases modeling various drug delivery pathways) were investigated and corresponding thermodynamic functions were calculated as well. Thermodynamic characteristics of the sulfonamides solvation were evaluated. Also in this case a correlation between solubility/solvation Gibbs free energy values and the sum of H-bond acceptor factors was observed. For the sulfonamides with various substituents at para-position the processes of transfer from one solvent (water or buffer) to n-octanol were studied by a diagram method combined with analysis of enthalpic and entropic terms. Distinguishing between enthalpy and entropy, as is possible through the present approach, leads to the insight

Solvation numbers and hydration constant for thorium(IV) in ethanol-water medium

International Nuclear Information System (INIS)

Sedaira, H.; Idriss, K.A.; Hashem, E.Y.

1996-01-01

The solvation number and hydration constant of Th 4+ in ethanol-water medium were determined at 25 degrees C using UV-spectral and electrochemical measurements. A solvate formation equilibrium is demonstrated and characterized. Three molecules of ethanol (S) can bond to the metal cation with strengths comparable to that for H 2 O to form ThS 3 (H 2 O) 3 4+ . Formation of thorium monochelate with lawsone (2-hydroxy-1.4-naphthoquinone) eliminates bonding with alcohol molecules. The dissociation constant of the chelating agent s K a and the formation contant of the monochelated metal ion s K f * that are essentially independent of the solution composition are evaluated. Hydration titrations involving thorium-lawsone monochlate are performed and the data obtained from the changes of pH with solvent composition are analyzed. The solution independent constant, s K f * for thorium-lawsone complex formation in mixed aqueous ethanol is given by log x K f * =vpK a + log s K h - log [LH] - vpH + 3 log v where vpK a is the dissociation constant of the chelating agent LH in the solvent system of v volume fraction of water and s K h is the solution-independent hydration constant of thorium (IV) in the solvent system. Log-values for the constants s K h , s K f * and s K z * are found to be 7.8 ±0.02, 11.38±0.04 and -0.753, respectively

Trimesic acid dimethyl sulfoxide solvate: space group revision

Directory of Open Access Journals (Sweden)

Sylvain Bernès

2008-07-01

Full Text Available The structure of the title solvate, C9H6O6·C2H6OS, was determined 30 years ago [Herbstein, Kapon & Wasserman (1978. Acta Cryst. B34, 1613–1617], with data collected at room temperature, and refined in the space group P21. The present redetermination, based on high-resolution diffraction data, shows that the actual space group is more likely to be P21/m. The crystal structure contains layers of trimesic acid molecules lying on mirror planes. A mirror plane also passes through the S and O atoms of the solvent molecule. The molecules in each layer are interconnected through strong O—H...O hydrogen bonds, forming a two-dimensional supramolecular network within each layer. The donor groups are the hydroxyls of the trimesic acid molecules, while the acceptors are the carbonyl or the sulfoxide O atoms.

Luminescence study on solvation of americium(III), curium(III) and several lanthanide(III) ions in nonaqueous and binary mixed solvents

International Nuclear Information System (INIS)

Kimura, T.; Nagaishi, R.; Kato, Y.; Yoshida, Z.

2001-01-01

The luminescence lifetimes of An(III) and Ln(III) ions [An=Am and Cm; Ln=Nd, Sm, Eu, Tb and Dy] were measured in dimethyl sulfoxide(DMSO), N,N-dimethylformamide(DMF), methanol(MeOH), water and their perdeuterated solvents. Nonradiative decay rates of the ions were in the order of H 2 O > MeOH > DMF > DMSO, indicating that O-H vibration is more effective quencher than C-H, C=O, and S=O vibrations in the solvent molecules. Maximal lifetime ratios τ D /τ H were observed for Eu(III) in H 2 O, for Sm(III) in MeOH and DMF, and for Sm(III) and Dy(III) in DMSO. The solvent composition in the first coordination sphere of Cm(III) and Ln(III) in binary mixed solvents was also studied by measuring the luminescence lifetime. Cm(III) and Ln(III) were preferentially solvated by DMSO in DMSO-H 2 O, by DMF in DMF-H 2 O, and by H 2 O in MeOH-H 2 O over the whole range of the solvent composition. The order of the preferential solvation, i.e., DMSO > DMF > H 2 O > MeOH, correlates with the relative basicity of these solvents. The Gibbs free energy of transfer of ions from water to nonaqueous solvents was further estimated from the degree of the preferential solvation. (orig.)

Synthesis and IR spectroscopic investigation of solvated complexes of dioxomolybdenum (6) with salicylal-S-methyl isothiosemicarbazone

International Nuclear Information System (INIS)

Abramenko, V.L.; Sergienko, V.S.

1996-01-01

The complex of MoO 2 L (H 2 L-S-methylizothiosemicarbazone of salicyl aldehyde) and its seven solvated derivatives MoO 2 LxSolv, have been synthesized, their IR spectroscopic study being conducted. The conclusions on the structure of the complexes studied are confirmed by ata of x-ray diffraction analysis. Refs. 4, tabs. 1

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

International Nuclear Information System (INIS)

Carnevale, V.; Raugei, S.

2009-01-01

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

Estimate of electrostatic solvation free energy of electron in various polar solvents by using modified born equation

International Nuclear Information System (INIS)

Yamashita, Kazuo; Kitamura, Mitsutaka; Imai, Hideo

1976-01-01

The modified Born equation was tentatively applied to estimate the electrostatic free energies of solvation of the electron in various polar solvents. The related data of halide ions and a datum of the hydration free energy of the electron obtained by radiation chemical studies were used for the numerical calculations. (auth.)

Hydroxamic acid interactions with solvated cerium hydroxides in the flotation of monazite and bastnäsite—Experiments and DFT study

Energy Technology Data Exchange (ETDEWEB)

Sarvaramini, A., E-mail: amin.sarvaramini.1@ulaval.ca; Azizi, D., E-mail: dariush.azizi.1@ulaval.ca; Larachi, F., E-mail: faical.larachi@gch.ulaval.ca

2016-11-30

Highlights: • Experimental and DFT studies of hydroxamic acid adsorption on monazite and bastnäsite. • Highest bastnäsite and monazite floatability observed at pH 7–9. • First solvation layer of cerium hydroxides consisted of up to 10 water molecules. • Solvated Ce(OH){sub 2}{sup +} and Ce(OH){sup 2+} cations interact with up to 3 collector anions. • Interaction of zero-charge solvated Ce(OH){sub 3} involves up to 2 collector anions. - Abstract: Density functional theory (DFT) simulations and experiments were performed to clarify the interaction mechanisms between hydroxamic acid collectors and cerium hydroxides during the flotation of bastnäsite and monazite minerals. These minerals showed considerable floatability at moderately alkaline pH which was related to the adsorption of hydroxamic acids on their surfaces as confirmed by vibrational spectroscopic and zeta potential measurements. DFT simulations showed that at moderately alkaline pH, the interactions between solvated Ce(OH){sup 2+} and Ce(OH){sub 2}{sup +} and heptyl-hydroxamic acid (HHA) anions resulted in the formation of, respectively, [Ce(OH)(HHA){sub x}(H{sub 2}O){sub y}]{sup 2−x} (x[y = ] = 1[6],2[3],3[1]) and [Ce(OH){sub 2}(HHA){sub x}(H{sub 2}O){sub y}]{sup 1−x} (x[y = ] = 1[5],2[1],3[0]) complexes. The collector anions were found to interact directly through formation of two covalent bonds between their two polar-head oxygen atoms and cerium in the hydroxide complexes. However, formation of such new bonds resulted in breakage of a few covalent/electrostatic bonds between cerium and water molecules initially present in the first hydration shell of the rare-earth metal cation. Building up in the electric double layer of the semi-soluble minerals, these complexes, and by extension, those from other rare-earth elements belonging to monazite and bastnäsite, are speculated to play a role in the interactions between rare-earth minerals and hydroxamic acid collectors.

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.

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

KAUST Repository

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

2016-01-01

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.

Crystal structure and packing analysis of nitrofurantoin N,N-dimethylformamide solvate

Energy Technology Data Exchange (ETDEWEB)

Cvetkovski, A., E-mail: aleksandar.cvetkovski@ugd.edu.mk [University Goce Delcev, Faculty of Medical Sciences, Krste Misirkov bb (Macedonia, The Former Yugoslav Republic of); Ferretti, V. [University of Ferrara, Department of Chemical and Pharmaceutical Sciences (Italy)

2016-07-15

The N, N′-dimethylformamide solvated crystal of the drug nitrofurantoin has been prepared and analysed by single-crystal X-ray diffraction. The two co-crystallized molecules, in the 1 : 1 stoichiometric ratio, are linked by a medium/strong N–H···O hydrogen bond (N···O is 2.759 (3) Å) and a weaker C–H···O interaction to form isolated supramolecular adducts, that in turn are packed into the lattice framework mainly through C–H···O hydrogen bonds. Two-dimensional fingerprint plots of Hirshfeld surfaces are used to visualize, analyze and compare intermolecular interactions found in the title compound and in similar structures.

Spectroscopic and computational studies of ionic clusters as models of solvation and atmospheric reactions

Science.gov (United States)

Kuwata, Keith T.

Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems. A crucial component of the process of stratospheric ozone depletion is the action of polar stratospheric clouds (PSCs) to convert the reservoir species HCl and chlorine nitrate (ClONO2) to photochemically labile compounds. Quantum chemistry was used to explore one possible mechanism by which this activation is effected: Cl- + ClONO2 /to Cl2 + NO3- eqno(1)Correlated ab initio calculations predicted that the direct reaction of chloride ion with ClONO2 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl2-NO3- is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl2-NO3- cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs. Quantum chemistry was also applied to the hydration of nitrosonium ion (NO+), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO+(H2O)n. The large degree of covalent interaction between NO+ and the lone pairs of the H2O ligands is contrasted with the weak electrostatic bonding between iodide ion and H2O. Finally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters Cl/-(H2O)n and Cl-(NH3)n. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H2O ligands than predicted by ab initio calculations. Nevertheless, for n /ge 5, cluster structure is dominated by water-water interactions, with Cl- only partially solvated by the

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

in calculations of Gibbs free energies and reaction rates for the reaction between the OH radical and the DNA nucleobase adenine using Density Functional Theory at the ωB97X-D/6-311++G(2df,2pd) level with the Eckart tunneling correction. The solvent, water, has been included through either the implicit...... polarizable continuum model (PCM) or through explicit modelling of micro-solvation by a single water molecule at the site of reaction as well as the combination of both. Scrutiny of the thermodynamics and kinetics of the individual sub-reactions suggests that the qualitative differences introduced...

SO2 Solvation in the 1-Ethyl-3-Methylimidazolium Thiocyanate Ionic Liquid by Incorporation into the Extended Cation-Anion Network.

Science.gov (United States)

Firaha, Dzmitry S; Kavalchuk, Mikhail; Kirchner, Barbara

We have carried out an ab initio molecular dynamics study on the sulfur dioxide (SO 2 ) solvation in 1-ethyl-3-methylimidazolium thiocyanate for which we have observed that both cations and anions play an essential role in the solvation of SO 2 . Whereas, the anions tend to form a thiocyanate- and much less often an isothiocyanate-SO 2 adduct, the cations create a "cage" around SO 2 with those groups of atoms that donate weak interactions like the alkyl hydrogen atoms as well as the heavy atoms of the [Formula: see text]-system. Despite these similarities between the solvation of SO 2 and CO 2 in ionic liquids, an essential difference was observed with respect to the acidic protons. Whereas CO 2 avoids accepting hydrogen bonds form the acidic hydrogen atoms of the cations, SO 2 can from O(SO 2 )-H(cation) hydrogen bonds and thus together with the strong anion-adduct it actively integrates in the hydrogen bond network of this particular ionic liquid. The fact that SO 2 acts in this way was termed a linker effect by us, because the SO 2 can be situated between cation and anion operating as a linker between them. The particular contacts are the H(cation)[Formula: see text]O(SO 2 ) hydrogen bond and a S(anion)-S(SO 2 ) sulfur bridge. Clearly, this observation provides a possible explanation for the question of why the SO 2 solubility in these ionic liquids is so high.

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

International Nuclear Information System (INIS)

Baggioli, Alberto; Castiglione, Franca; Raos, Guido; Crescenzi, Orlando; Field, Martin J.

2013-01-01

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

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

Science.gov (United States)

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

2015-09-03

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

Organic solvation of intercalated cations in V/sub 2/O/sub 5/ xerogels

International Nuclear Information System (INIS)

Lemordant, D.; Bouhaouss, A.; Aldbert, P.; Baffier, N.

1986-01-01

V/sub 2/O/sub 5/ xerogels (V/sub 2/O/sub 5/, 1.6H/sub 2/O) undergo a topotactic reversible exchange reaction at room temperature in organic solvents containing monovalent alkali or divalent (Mn/sup 2+/) cations. Basal spacing are dependent on solvent type and charge-to-radius ratio of guest cations. From the interlayer distances, two solvation stages have been inferred, depending on the nature of the solvent and of the cation, except with Cs/sup +/ for which no intracrystalline swelling by organic solvents is observed

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

Science.gov (United States)

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

2010-06-01

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

Revealing the Solvation Structure and Dynamics of Carbonate Electrolytes in Lithium-Ion Batteries by Two-Dimensional Infrared Spectrum Modeling.

Science.gov (United States)

Liang, Chungwen; Kwak, Kyungwon; Cho, Minhaeng

2017-12-07

Carbonate electrolytes in lithium-ion batteries play a crucial role in conducting lithium ions between two electrodes. Mixed solvent electrolytes consisting of linear and cyclic carbonates are commonly used in commercial lithium-ion batteries. To understand how the linear and cyclic carbonates introduce different solvation structures and dynamics, we performed molecular dynamics simulations of two representative electrolyte systems containing either linear or cyclic carbonate solvents. We then modeled their two-dimensional infrared (2DIR) spectra of the carbonyl stretching mode of these carbonate molecules. We found that the chemical exchange process involving formation and dissociation of lithium-ion/carbonate complexes is responsible for the growth of 2DIR cross peaks with increasing waiting time. In addition, we also found that cyclic carbonates introduce faster dynamics of dissociation and formation of lithium-ion/carbonate complexes than linear carbonates. These findings provide new insights into understanding the lithium-ion mobility and its interplay with solvation structure and ultrafast dynamics in carbonate electrolytes used in lithium-ion batteries.

Solvation thermodynamics of phenylalcohols in lamellar phase surfactant dispersions

International Nuclear Information System (INIS)

Martyniak, A.; Scheuermann, R.; Dilger, H.; Tucker, I.M.; Burkert, T.; Hashmi, A.S.K.; Vujosevic', D.; Roduner, E.

2006-01-01

The distribution and the stability of five phenylalcohols in a lamellar phase composed of simple bilayers separated by water at 298 and 348K is explored using avoided-level-crossing muon-spin resonance (ALC-μSR). The dependence of the alignment of the bilayer chains on temperature appears to be a crucial factor determining the phenylalcohol partitioning: increasing order of the surfactant tails leads to expulsion of the solute. Moreover, we observed a systematic trend, the longer the chain the deeper the phenyl group dips into the lipid bilayer. Recent studies have shown that the hydrophobic effect is adequate to describe membrane partitioning of small amphiphilic molecules. The solvation thermodynamic properties ΔG sol , ΔH sol , and ΔS sol which determine the solute transfer from the double layer into water prove that the distribution also strongly depends on shape, chemical nature and different structure of phenylalcohols

Solvation thermodynamics of phenylalcohols in lamellar phase surfactant dispersions

Energy Technology Data Exchange (ETDEWEB)

Martyniak, A. [Institut fuer Physikalische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Scheuermann, R. [Laboratory for muon Spin Spectroscopy, Paul Scherrer Institute, CH-5232 Villigen (Switzerland); Dilger, H. [Institut fuer Physikalische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Tucker, I.M. [Unilever Research and Development, Port Sunlight, Wirral CH63 3JW (United Kingdom); Burkert, T. [Institut fuer Organische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Hashmi, A.S.K. [Institut fuer Organische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Vujosevic' , D. [Institut fuer Physikalische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany); Roduner, E. [Institut fuer Physikalische Chemie, University of Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart (Germany)]. E-mail: e.roduner@ipc.uni-stuttgart.de

2006-03-31

The distribution and the stability of five phenylalcohols in a lamellar phase composed of simple bilayers separated by water at 298 and 348K is explored using avoided-level-crossing muon-spin resonance (ALC-{mu}SR). The dependence of the alignment of the bilayer chains on temperature appears to be a crucial factor determining the phenylalcohol partitioning: increasing order of the surfactant tails leads to expulsion of the solute. Moreover, we observed a systematic trend, the longer the chain the deeper the phenyl group dips into the lipid bilayer. Recent studies have shown that the hydrophobic effect is adequate to describe membrane partitioning of small amphiphilic molecules. The solvation thermodynamic properties {delta}G{sub sol}, {delta}H{sub sol}, and {delta}S{sub sol} which determine the solute transfer from the double layer into water prove that the distribution also strongly depends on shape, chemical nature and different structure of phenylalcohols.

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-11-15

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

Lieb-Liniger-like model of quantum solvation in CO-{sup 4}He{sub N} clusters

Energy Technology Data Exchange (ETDEWEB)

Farrelly, D. [Departamento de Matemáticas y Computación, Universidad de La Rioja, 26006 Logroño (Spain); Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300 (United States); Iñarrea, M.; Salas, J. P. [Área de Física Aplicada, Universidad de La Rioja, 26006 Logroño (Spain); Lanchares, V. [Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300 (United States)

2016-05-28

Small {sup 4}He clusters doped with various molecules allow for the study of “quantum solvation” as a function of cluster size. A peculiarity of quantum solvation is that, as the number of {sup 4}He atoms is increased from N = 1, the solvent appears to decouple from the molecule which, in turn, appears to undergo free rotation. This is generally taken to signify the onset of “microscopic superfluidity.” Currently, little is known about the quantum mechanics of the decoupling mechanism, mainly because the system is a quantum (N + 1)-body problem in three dimensions which makes computations difficult. Here, a one-dimensional model is studied in which the {sup 4}He atoms are confined to revolve on a ring and encircle a rotating CO molecule. The Lanczos algorithm is used to investigate the eigenvalue spectrum as the number of {sup 4}He atoms is varied. Substantial solvent decoupling is observed for as few as N = 5 {sup 4}He atoms. Examination of the Hamiltonian matrix, which has an almost block diagonal structure, reveals increasingly weak inter-block (solvent-molecule) coupling as the number of {sup 4}He atoms is increased. In the absence of a dopant molecule the system is similar to a Lieb-Liniger (LL) gas and we find a relatively rapid transition to the LL limit as N is increased. In essence, the molecule initially—for very small N—provides a central, if relatively weak, attraction to organize the cluster; as more {sup 4}He atoms are added, the repulsive interactions between the identical bosons start to dominate as the solvation ring (shell) becomes more crowded which causes the molecule to start to decouple. For low N, the molecule pins the atoms in place relative to itself; as N increases the atom-atom repulsion starts to dominate the Hamiltonian and the molecule decouples. We conclude that, while the notion of superfluidity is a useful and correct description of the decoupling process, a molecular viewpoint provides complementary insights into the

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.

Pulse radiolysis study on temperature and pressure dependence of the yield of solvated electron in methanol from room temperature to supercritical condition

International Nuclear Information System (INIS)

Han, Zhenhui; He, Hui; Lin, Mingzhang; Muroya, Yusa; Katsumura, Yosuke

2012-09-01

A new concept of nuclear reactor, supercritical water-cooled reactor (SCWR), has been proposed, which is based on the success of the use of supercritical water (SCW) in fossil fuel power plants for more than three decades. This new concept reactor has advantages of higher thermal conversion efficiency, simplicity in structure, safety, etc, and it has been selected as one of the reactor concepts for the next generation nuclear reactor systems. In these reactors, the same as in boiling water reactors (BWR) and pressurized water reactors (PWR), water is used not only as a coolant but also as a moderator. It is very important to understand the behavior of the radiolysis products of water under the supercritical condition, since the water is exposed to a strong radiation field under very high temperature condition. Usually, in order to predict the concentrations of water decomposition products with carrying out some kinds of computer simulations, knowledge of the temperature and/or pressure dependent G-values (denoting the experimentally measured radiolytic yields) as well as of the rate constants of a set of reactions becomes very important. Therefore, in recent years, two groups from Argonne National Laboratory and The University of Tokyo, simultaneously conducted two projects aimed at obtaining basic data on radiolysis of SCW. However, it is still lack of reliable radiolytic yields of water decomposition products in very high temperature region. As we known, the properties of solvated electrons in polar liquid are very helpful for our understanding how they play a central role in many processes, such as solvation and reducing reactions. The solvated electron can also be used as a probe to determine the dynamic nature of the polar liquid systems. Comparing to water, the primary alcohols have much milder critical points, for example, for water and methanol, the critical temperature and pressure are 374 deg. C and 22.1 MPa and 239.5 deg. C and 8.1 MPa, respectively

The mechanism for enhanced oxidation degradation of dioxin-like PCBs (PCB-77) in the atmosphere by the solvation effect.

Science.gov (United States)

Xin, Mei-Ling; Yang, Jia-Wen; Li, Yu

2017-07-11

The reaction pathways of PCB-77 in the atmosphere with ·OH, O 2 , NO x , and 1 O 2 were inferred based on density functional theory calculations with the 6-31G* basis set. The structures the reactants, transition states, intermediates, and products were optimized. The energy barriers and reaction heats were obtained to determine the energetically favorable reaction pathways. To study the solvation effect, the energy barriers and reaction rates for PCB-77 with different polar and nonpolar solvents (cyclohexane, benzene, carbon tetrachloride, chloroform, acetone, dichloromethane, ethanol, methanol, acetonitrile, dimethylsulfoxide, and water) were calculated. The results showed that ·OH preferentially added to the C5 atom of PCB-77, which has no Cl atom substituent, to generate the intermediate IM5. This intermediate subsequently reacted with O 2 via pathway A to generate IM5a, with an energy barrier of 7.27 kcal/mol and total reaction rate of 8.45 × 10 -8  cm 3 /molecule s. Pathway B involved direct dehydrogenation of IM5 to produce the OH-PCBs intermediate IM5b, with an energy barrier of 28.49 kcal/mol and total reaction rate of 1.15 × 10 -5  cm 3 /molecule s. The most likely degradation pathway of PCB-77 in the atmosphere is pathway A to produce IM5a. The solvation effect results showed that cyclohexane, carbon tetrachloride, and benzene could reduce the reaction energy barrier of pathway A. Among these solvents, the solvation effect of benzene was the largest, and could reduce the total reaction energy barrier by 25%. Cyclohexane, carbon tetrachloride, benzene, dichloromethane, acetone, and ethanol could increase the total reaction rate of pathway A. The increase in the reaction rate of pathway A with benzene was 8%. The effect of solvents on oxidative degradation of PCB-77 in the atmosphere is important. Graphical abstract The reaction pathways of PCB-77 in the atmosphere with •OH, O2, NOx, and 1O2 were inferred based on density functional theory

Effect of temperature on solvation behaviour of diclofenac sodium salt in aqueous glycine and L-proline solutions

International Nuclear Information System (INIS)

Ryshetti, Suresh; Gardas, Ramesh L; Tangeda, Savitha Jyostna

2015-01-01

Highlights: • Solvation behaviour of diclofenac drug studied in aqueous solutions. • Density and speed of sound of drug in aq. glycine and L-proline are measured. • Hydrophobic nature of diclofenac sodium salt is studied. • Effect of temperature on solvation of diclofenac sodium salt is analysed. - Abstract: Apparent molar volume (V 2,ϕ ) and apparent molar isentropic compressibility (K s,2,ϕ ) of diclofenac sodium salt (DSS) drug within the concentration range of (0.001 to 0.008) mol · kg −1 in (0.01, 0.03 and 0.05) mol · kg −1 aqueous glycine and L-proline solutions are computed from the experimental density (ρ) and speed of sound (u) values at T = (293.15 to 313.15) K and atmospheric pressure. Derived parameters such as partial molar properties, transfer partial molar properties, hydration numbers and Hepler’s constant are computed from the data of V 2,ϕ and K s,2,ϕ . These parameters have been used to understand the effect of temperature on interactions between DSS drug and aqueous glycine/L-proline solution. Furthermore, the structure making and breaking ability of DSS drug in probed solutions are analysed at experimental conditions

Energetic aspects of diclofenac acid in crystal modifications and in solutions--mechanism of solvation, partitioning and distribution.

Science.gov (United States)

Perlovich, German L; Surov, Artem O; Hansen, Lars Kr; Bauer-Brandl, Annette

2007-05-01

Temperature dependency of saturated vapor pressure and heat capacity for the diclofenac acid (Form II) were measured and thermodynamic functions of sublimation calculated (DeltaG(sub)(298) = 49.3 kJ x mol(-1); DeltaH(sub)(298) = 115.6 +/- 1.3 kJ x mol(-1); DeltaS(sub)(298) = 222 +/- 4 J x mol(-1) x K(-1)). Crystal polymorphic Forms I (P2(1)/c) and II (C2/c) of diclofenac acid have been prepared and characterized by X-ray diffraction experiments. The difference between crystal lattice energies of the two forms were obtained by solution calorimetry: DeltaDeltaH(sol)(I --> II) = 1.6 +/- 0.4 kJ x mol(-1). Temperature dependencies of the solubility in buffers with pH 2.0 and 7.4, n-octanol and n-hexane were measured. The thermodynamic functions of solubility, solvation, and transfer processes were deduced. Specific and non-specific solvation terms were distinguished using the transfer from the "inert" n-hexane to the other solvents. The transfer of diclofenac acid molecules from the buffers to n-octanol (partitioning and distribution) is an entropy driven process. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Dynamics of solvation and desolvation of rubidium attached to He nanodroplets

International Nuclear Information System (INIS)

Vangerow, J. von; John, O.; Stienkemeier, F.; Mudrich, M.

2015-01-01

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

Dynamics of solvation and desolvation of rubidium attached to He nanodroplets

Science.gov (United States)

von Vangerow, J.; John, O.; Stienkemeier, F.; Mudrich, M.

2015-07-01

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

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.

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

DEFF Research Database (Denmark)

Biasin, Elisa; van Driel, Tim B.; Levi, Gianluca

2018-01-01

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray free-electron lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV-Vis pump laser pulse with the sample......, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work, a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules is described, and it is demonstrated how its use can enhance the structural...... sensitivity of the time-resolved X-ray scattering experiment. This method is applied on time-resolved X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL, and the key parameters involved are explored. It is shown that a combined analysis of the anisotropic...

Generalized linear solvation energy model applied to solute partition coefficients in ionic liquid-supercritical carbon dioxide systems

Czech Academy of Sciences Publication Activity Database

Planeta, Josef; Karásek, Pavel; Hohnová, Barbora; Šťavíková, Lenka; Roth, Michal

2012-01-01

Roč. 1250, SI (2012), s. 54-62 ISSN 0021-9673 R&D Projects: GA ČR(CZ) GAP206/11/0138; GA ČR(CZ) GAP106/12/0522; GA ČR(CZ) GPP503/11/P523 Institutional research plan: CEZ:AV0Z40310501 Keywords : ionic liquid * supercritical carbon dioxide * solvation energy model Subject RIV: BJ - Thermodynamics Impact factor: 4.612, year: 2012

Film Thickness Formation in Nanoscale due to Effects of Elastohydrodynamic, Electrostatic and Surface force of Solvation and Van der Waals

Directory of Open Access Journals (Sweden)

M.F. Abd Al-Samieh

2017-03-01

Full Text Available The mechanism of oil film with a thickness in the nanoscale is discussed in this paper. A polar lubricant of propylene carbonate is used as the intervening liquid between contiguous bodies in concentrated contacts. A pressure caused by the hydrodynamic viscous action in addition to double layer electrostatic force, Van der Waals inter-molecular forces, and solvation pressure due to inter-surface forces is considered in calculating the ultrathin lubricating films. The numerical solution has been carried out, using the Newton-Raphson iteration technique, applied for the convergence of the hydrodynamic pressure. The results show that, at separations beyond about five molecular diameters of the intervening liquid, the formation of a lubricant film thickness is governed by combined effects of viscous action and surface force of an attractive Van der Waals force and a repulsive double layer force. At smaller separations below about five molecular diameters of the intervening liquid, the effect of solvation force is dominant in determining the oil film thickness

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

Science.gov (United States)

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH

Energy Technology Data Exchange (ETDEWEB)

Tian, Ye [Sanford-Burnham-Prebys Medical Discovery Institute (United States); Schwieters, Charles D. [National Institutes of Health, Center for Information Technology (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford-Burnham-Prebys Medical Discovery Institute (United States)

2017-01-15

Structure determination of proteins by NMR is unique in its ability to measure restraints, very accurately, in environments and under conditions that closely mimic those encountered in vivo. For example, advances in solid-state NMR methods enable structure determination of membrane proteins in detergent-free lipid bilayers, and of large soluble proteins prepared by sedimentation, while parallel advances in solution NMR methods and optimization of detergent-free lipid nanodiscs are rapidly pushing the envelope of the size limit for both soluble and membrane proteins. These experimental advantages, however, are partially squandered during structure calculation, because the commonly used force fields are purely repulsive and neglect solvation, Van der Waals forces and electrostatic energy. Here we describe a new force field, and updated energy functions, for protein structure calculations with EEFx implicit solvation, electrostatics, and Van der Waals Lennard-Jones forces, in the widely used program Xplor-NIH. The new force field is based primarily on CHARMM22, facilitating calculations with a wider range of biomolecules. The new EEFx energy function has been rewritten to enable OpenMP parallelism, and optimized to enhance computation efficiency. It implements solvation, electrostatics, and Van der Waals energy terms together, thus ensuring more consistent and efficient computation of the complete nonbonded energy lists. Updates in the related python module allow detailed analysis of the interaction energies and associated parameters. The new force field and energy function work with both soluble proteins and membrane proteins, including those with cofactors or engineered tags, and are very effective in situations where there are sparse experimental restraints. Results obtained for NMR-restrained calculations with a set of five soluble proteins and five membrane proteins show that structures calculated with EEFx have significant improvements in accuracy, precision

Theoretical Investigation of the Effect of the Rare Gas Matrices on the Vibrational Spectra of Solvated Molecular Ions: Cu+CO

Czech Academy of Sciences Publication Activity Database

Bludský, Ota; Šilhan, Martin; Nachtigall, Petr

2002-01-01

Roč. 117, č. 20 (2002), s. 9298-9305 ISSN 0021-9606 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : vibrational spectra * solvated molecular ions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.998, year: 2002

Linear solvation energy relationships: "rule of thumb" for estimation of variable values

Science.gov (United States)

Hickey, James P.; Passino-Reader, Dora R.

1991-01-01

For the linear solvation energy relationship (LSER), values are listed for each of the variables (Vi/100, π*, &betam, αm) for fundamental organic structures and functional groups. We give the guidelines to estimate LSER variable values quickly for a vast array of possible organic compounds such as those found in the environment. The difficulty in generating these variables has greatly discouraged the application of this quantitative structure-activity relationship (QSAR) method. This paper present the first compilation of molecular functional group values together with a utilitarian set of the LSER variable estimation rules. The availability of these variable values and rules should facilitate widespread application of LSER for hazard evaluation of environmental contaminants.

On the relation between Marcus theory and ultrafast spectroscopy of solvation kinetics

Science.gov (United States)

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.; Mundy, Christopher J.

2018-01-01

The phenomena of solvent exchange control the process of solvating ions, protons, and charged molecules. Building upon our extension of Marcus' philosophy of electron transfer, we provide a new perspective of ultrafast solvent exchange mechanism around ions measurable by two-dimensional infrared (2DIR) spectroscopy. In this theory, solvent rearrangement drives an ion-bound water to an activated state of higher coordination number, triggering ion-water separation that leads to the solvent-bound state of the water molecule. This ion-bound to solvent-bound transition rate for a BF4--water system is computed using ab initio molecular dynamics and Marcus theory, and is found to be in excellent agreement with the 2DIR measurement.

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

International Nuclear Information System (INIS)

Chaumont, A.; Wipff, G.

2006-01-01

We report a molecular dynamics study of halide anions X - and their inclusion complexes X - - L 4+ with a macro-tri-cyclic tetrahedral host L 4+ built from four quaternary ammonium sites, in an ionic liquid (IL) based on the 1-butyl-3-methyl-imidazolium (BMI + ) cation and the PF 6 - anion. The 'dry' and 'humid' forms of the [BMI][PF 6 ] IL are compared, showing the importance of IL ions in the 'dry' IL and, in some cases, of water molecules in the 'humid' IL. In the 'dry' IL the F - , Cl - , Br - and I - un-complexed halides are surrounded by 4-5 BMI + cations whose binding mode evolves from hydrogen bonding to facial coordination along this series. Solvent humidity has the largest impact on the solvation of F - whose first shell BMI + cations are all displaced by H 2 O molecules, while the first solvation shell of Cl - , Br - and I - comprises 3-4 BMI + cations plus ca. 4 H 2 O molecules. The solvation of the L 4+ host and of its X - - L 4+ complex mainly involves PF 6 - anions in the 'dry' IL, and additional H 2 O molecules in the 'humid' IL. The question of anion binding selectivity is addressed by free energy perturbation calculations which predict that, in the 'dry' liquid, F - is preferred over Cl - , Br - and I - , which contrasts with the aqueous solution where L 4+ is selective for Cl - . In the 'humid' liquid however, there is no F - /Cl - discrimination, showing the importance of small amounts of water on the complexation selectivity. (authors)

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

Science.gov (United States)

Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

2012-07-01

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

Dynamics of solvation and desolvation of rubidium attached to He nanodroplets

Energy Technology Data Exchange (ETDEWEB)

Vangerow, J. von; John, O.; Stienkemeier, F.; Mudrich, M., E-mail: mudrich@physik.uni-freiburg.de [Physikalisches Institut, Universität Freiburg, 79104 Freiburg (Germany)

2015-07-21

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

Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program.

Directory of Open Access Journals (Sweden)

Casper Steinmann

Full Text Available An interface between semi-empirical methods and the polarized continuum model (PCM of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41. The interface includes energy gradients and is parallelized. For large molecules such as ubiquitin a reasonable speedup (up to a factor of six is observed for up to 16 cores. The SCF convergence is greatly improved by PCM for proteins compared to the gas phase.

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

Science.gov (United States)

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

2017-07-21

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

Pressure effect on the amide I frequency of the solvated α-helical structure in water

International Nuclear Information System (INIS)

Takekiyo, T; Yoshimura, Y; Shimizu, A; Koizumi, T; Kato, M; Taniguchi, Y

2007-01-01

As a model system of the pressure dependence of the amide I mode of the solvated α-helical structure in a helical peptide, we have calculated the frequency shifts of the amide I modes as a function of the distance between trans-N-methylacetamide (t-NMA) dimer and a water molecule (d C=O···H-O ) by the density-functional theory (DFT) method at the B3LYP/6-31G++(d,p) level. Two amide I frequencies at 1652 and 1700 cm -1 were observed under this calculation. The former is ascribed to the amide I mode forming the intermolecular hydrogen bond (H-bond) between t-NMA and H 2 O in addition to the intermolecular H-bond in the t-NMA dimer. The latter is due to the amide I mode forming only the intermolecular H-bond in the t-NMA dimer. We have found that the amide I frequency at 1652 cm -1 shifts to a lower frequency with decreasing d C=O···H-O ) (i.e., increasing pressure), whereas that at 1700 cm -1 shifts to a higher frequency. The amide I frequency shift of 1652 cm -1 is larger than that of 1700 cm -1 by the intermolecular H-bond. Thus, our results clearly indicate that the pressure-induced amide I frequency shift of the solvated α-helical structure correlates with the change in d C=O···H-O )

New chiral zwitterionic phosphorus heterocycles: synthesis, structure, properties and application as chiral solvating agents.

Science.gov (United States)

Sheshenev, Andrey E; Boltukhina, Ekaterina V; Grishina, Anastasiya A; Cisařova, Ivana; Lyapkalo, Ilya M; Hii, King Kuok Mimi

2013-06-17

A family of new chiral zwitterionic phosphorus-containing heterocycles (zPHC) have been derived from methylene-bridged bis(imidazolines). These structures were unambiguously determined, including single-crystal XRD analysis for two compounds. The stability, acid/base and electronic properties of these dipolar phosphorus heterocycles were subsequently investigated. zPHCs can be successfully employed as a new class of chiral solvating agents for the enantiodifferentiation of chiral carboxylic and sulfonic acids by NMR spectroscopy. The stoichiometry and binding constants for the donor-acceptor complexes formed were established by NMR titration methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Continuum model of non-equilibrium solvation and solvent effect on ultra-fast processes

International Nuclear Information System (INIS)

Li Xiangyuan; Fu Kexiang; Zhu Quan

2006-01-01

In the past 50 years, non-equilibrium solvation theory for ultra-fast processes such as electron transfer and light absorption/emission has attracted particular interest. A great deal of research efforts was made in this area and various models which give reasonable qualitative descriptions for such as solvent reorganization energy in electron transfer and spectral shift in solution, were developed within the framework of continuous medium theory. In a series of publications by the authors, we clarified that the expression of the non-equilibrium electrostatic free energy that is at the dominant position of non-equilibrium solvation and serves as the basis of various models, however, was incorrectly formulated. In this work, the authors argue that reversible charging work integration was inappropriately applied in the past to an irreversible path linking the equilibrium or the non-equilibrium state. Because the step from the equilibrium state to the nonequilibrium state is factually thermodynamically irreversible, the conventional expression for non-equilibrium free energy that was deduced in different ways is unreasonable. Here the authors derive the non-equilibrium free energy to a quite different form according to Jackson integral formula. Such a difference throws doubts to the models including the famous Marcus two-sphere model for solvent reorganization energy of electron transfer and the Lippert-Mataga equation for spectral shift. By introducing the concept of 'spring energy' arising from medium polarizations, the energy constitution of the non-equilibrium state is highlighted. For a solute-solvent system, the authors separate the total electrostatic energy into different components: the self-energies of solute charge and polarized charge, the interaction energy between them and the 'spring energy' of the solvent polarization. With detailed reasoning and derivation, our formula for non-equilibrium free energy can be reached through different ways. Based on the

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

Science.gov (United States)

Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

2011-10-01

Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

LINEAR SOLVATION ENERGY RELATIONSHIPS FOR CHARACTERIZATION OF MLC SYSTEMS WITH SODIUM DODECYL SULPHATE MOBILE PHASES MODIFIED BY ALIPHATIC ALCOHOLS OR CARBOXYLIC ACIDS

NARCIS (Netherlands)

Markov, Vadym V.; Boichenko, Alexander P.; Loginova, Lidia P.

2012-01-01

The Linear Solvation Energy Relationships (LSER) have been successfully used for the modeling of partition and retention of the set of test compounds in different systems. The properties of micellar chromatographic systems with the mobile phases on the basis of sodium dodecylsulphate modified (ODS)

Pharmaceutical solvates, hydrates and amorphous forms: A special emphasis on cocrystals.

Science.gov (United States)

Healy, Anne Marie; Worku, Zelalem Ayenew; Kumar, Dinesh; Madi, Atif M

2017-08-01

Active pharmaceutical ingredients (APIs) may exist in various solid forms, which can lead to differences in the intermolecular interactions, affecting the internal energy and enthalpy, and the degree of disorder, affecting the entropy. Differences in solid forms often lead to differences in thermodynamic parameters and physicochemical properties for example solubility, dissolution rate, stability and mechanical properties of APIs and excipients. Hence, solid forms of APIs play a vital role in drug discovery and development in the context of optimization of bioavailability, filing intellectual property rights and developing suitable manufacturing methods. In this review, the fundamental characteristics and trends observed for pharmaceutical hydrates, solvates and amorphous forms are presented, with special emphasis, due to their relative abundance, on pharmaceutical hydrates with single and two-component (i.e. cocrystal) host molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

A Density Functional Theory Evaluation of Hydrophobic Solvation: Ne, Ar and Kr in a 50-Water Cluster. Implications for the Hydrophobic Effect.

Science.gov (United States)

Kobko, Nadya; Marianski, Mateusz; Asensio, Amparo; Wieczorek, Robert; Dannenberg, J J

2012-06-15

The physical explanation for the hydrophobic effect has been the subject of disagreement. Physical organic chemists tend to use a explanation related to pressure, while many biochemists prefer an explanation that involves decreased entropy of the aqueous solvent. We present DFT calculations at the B3LYP/6-31G(d,p) and X3LYP/6-31G(d,p) levels on the solvation of three noble gases (Ne, Ar, and Kr) in clusters of 50 waters. Vibrational analyses show no substantial decreases in the vibrational entropies of the waters in any of the three clusters. The observed positive free energies of transfer from the gas phase or from nonpolar solvents to water appear to be due to the work needed to make a suitable hole in the aqueous solvent. We distinguish between hydrophobic solvations (explicitly studied here) and the hydrophobic effect that occurs when a solute (or transition state) can decrease its volume through conformational change (which is not possible for the noble gases).

NMR Study of Solvation Effect on Geometry of Proton-Bound Homodimers of Increasing Size

KAUST Repository

Gurinov, Andrei A.

2017-10-24

Hydrogen bond geometries in the proton-bound homodimers of quinoline and acridine derivatives in an aprotic polar solution have been experimentally studied using 1H NMR at 120 K. The reported results show that increase of the dielec-tric permittivity of the medium results in contraction of the N…N distance. The degree of contraction depends on the homodimer\\'s size and its substituent-specific solvation features. Neither of these effects can be reproduced using conven-tional implicit solvent models employed in computational studies. In general, the N…N distance in the homodimers of pyridine, quinoline, and acridine derivatives decreases in the sequence gas phase > solid state > polar solvent.

NMR Study of Solvation Effect on Geometry of Proton-Bound Homodimers of Increasing Size

KAUST Repository

Gurinov, Andrei A.; Denisov, Gleb S.; Borissova, Alexandra O.; Goloveshkin, Alexander S.; Greindl, Julian; Limbach, Hans-Heinrich; Shenderovich, Ilya G.

2017-01-01

Hydrogen bond geometries in the proton-bound homodimers of quinoline and acridine derivatives in an aprotic polar solution have been experimentally studied using 1H NMR at 120 K. The reported results show that increase of the dielec-tric permittivity of the medium results in contraction of the N…N distance. The degree of contraction depends on the homodimer's size and its substituent-specific solvation features. Neither of these effects can be reproduced using conven-tional implicit solvent models employed in computational studies. In general, the N…N distance in the homodimers of pyridine, quinoline, and acridine derivatives decreases in the sequence gas phase > solid state > polar solvent.

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

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

1995-06-01

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

Protonic charge defect structures in floating water bridges observed as Zundel and Eigen solvation arrangements

Science.gov (United States)

Teschke, Omar; de Castro, Jose Roberto; Valente Filho, Juracyr Ferraz; Soares, David Mendez

2017-10-01

Protonic arrangements were detected in water bridge structures using confocal Raman microscopy, and the spectra show two formed structures. The measured Raman spectra were modified using the voltage applied to the bridge structure, which changed the proportion of these two species. Initially, for a 6.3 kV applied voltage, there was a measurable increase in the bridge current above the Ohmic contribution and the observed Raman spectrum of this new injected specie corresponded to the computed spectrum for the Zundel protonic arrangement. As the voltage further increases a contribution from the Eigen proton solvation specie is added to the measured spectrum.

Effect of ionic liquid on the solvation behavior of nonaqueous N,N′-salicylidenephenylediamine Schiff base (Salophen) solutions at 298.15 K

International Nuclear Information System (INIS)

Shekaari, Hemayat; Elhami-Kalvanagh, Rasoul; Bezaatpour, Abolfazl

2013-01-01

Highlights: • Salophen schiff base and ionic liquid, [BMIm]Br were synthesized. • Thermodynamic properties of Salophen + [BMIm]Br + organic solvents were measured. • The calculated parameters were used to interpretation of the solute–solvent interactions. • The results show that the predominant interactions are nonpolar–nonpolar interactions. • Solubility of Salophen increase with increasing of [BMIm]Br concentrations. -- Abstract: Thermodynamic properties of N,N′-salicylidenephenylediamine Schiff base (Salophen) in the solutions of ionic liquid, 1-butyl-3-methylimidazolium bromide ([BMIm]Br) + organic solvents (N,N-dimethylacetamide DMA, and dimethylsulfoxide DMSO) have been measured at 298.15 K. The measured density and viscosity values have been used to calculate apparent molar volumes, V ϕ , standard partial molar volumes, V ϕ 0 , standard partial molar volumes of transfer, Δ tr V ϕ 0 , viscosity B-coefficients, and solvation numbers, B/V ϕ 0 , for the solutions being studied. All of these parameters were used to interpret the solute–solvent interactions and solvation process occurring between ionic liquid and Salophen

A chiral aluminum solvating agent (CASA) for 1H NMR chiral analysis of alcohols at low temperature.

Science.gov (United States)

Seo, Min-Seob; Jang, Sumin; Kim, Hyunwoo

2018-03-16

A chiral aluminum solvating agent (CASA) was demonstrated to be a general and efficient reagent for 1H NMR chiral analysis of alcohols. The sodium salt of the CASA (CASA-Na) showed a complete baseline peak separation of the hydroxyl group for various chiral alcohols including primary, secondary, and tertiary alcohols with alkyl and aryl substituents in CD3CN. Due to the weak intermolecular interaction, 1H NMR measurement at low temperature (-40 to 10 °C) was required.

Quantum chemical approach for condensed-phase thermochemistry (V): Development of rigid-body type harmonic solvation model

Science.gov (United States)

Tarumi, Moto; Nakai, Hiromi

2018-05-01

This letter proposes an approximate treatment of the harmonic solvation model (HSM) assuming the solute to be a rigid body (RB-HSM). The HSM method can appropriately estimate the Gibbs free energy for condensed phases even where an ideal gas model used by standard quantum chemical programs fails. The RB-HSM method eliminates calculations for intra-molecular vibrations in order to reduce the computational costs. Numerical assessments indicated that the RB-HSM method can evaluate entropies and internal energies with the same accuracy as the HSM method but with lower calculation costs.

An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.

Science.gov (United States)

Hirano, Kenji; Yokogawa, Daisuke; Sato, Hirofumi; Sakaki, Shigeyoshi

2010-06-17

Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.

Theoretical-experimental study of the solvation enthalpy of acetone in dilute aqueous solution

International Nuclear Information System (INIS)

Arroyo, S. Tolosa; Martin, J.A. Sanson; Garcia, A. Hidalgo

2005-01-01

The present paper describes molecular dynamics simulations of aqueous solutions at infinite dilution with acetone as solute. Lennard-Jones with electrostatic term (12-6-1 potentials) were employed to describe the solute-solvent interactions. The Morokuma decomposition scheme of ab initio interaction energies at the SCF level and the ESIE charges on the solute atoms were used to reproduce the exchange and Coulomb electrostatic contributions of the solute-water interaction potential. Some extensions, such as including the dispersion component evaluated at MP2 level, were added to the traditional calculation procedures in order to improve the results of the solvation enthalpy. The results obtained with the EX-DIS-ES model were compared with the experimental calorimetry values, the observed agreement being acceptable

Nonequilibrium quantum solvation with a time-dependent Onsager cavity

Science.gov (United States)

Kirchberg, H.; Nalbach, P.; Thorwart, M.

2018-04-01

We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere and (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general enhanced. This is reflected in a temporally increasing linewidth of the absorptive part of the response. Furthermore, the effective frequency-dependent response function shows two peaks in the absorptive part which are symmetrically shifted around the eigenfrequency. By contrast, a breathing sphere reduces damping as compared to the static sphere. Interestingly, we find a non-monotonous dependence of the relaxation rate on the breathing rate and a resonant suppression of damping when both rates are comparable. Moreover, the linewidth of the absorptive part of the response function is strongly reduced for times when the breathing sphere reaches its maximal extension.

The reactivity of allyl and propargyl alcohols with solvated electrons: temperature and solvent effects

International Nuclear Information System (INIS)

Afanassiev, A.M.; Okazaki, K.; Freeman, G.R.

1979-01-01

The rate constants K 1 for the reaction of solvated electrons with allyl alcohol in a number of hydroxylic solvents differ by up to two orders of magnitude and decrease in the order tert-butyl alcohol > 2-propanol > l-propanol approximately ethanol > methanol approximately ethylene glycol > water. In methanol and ethylene glycol the rate constants (7 x 10 7 M -1 s -1 at 298 K) and activation energies (16 kJ/mol) are equal, in spite of a 32-fold difference in solvent viscosity (0.54 and 17.3 cP, respectively) and 3-fold difference in its activation energy (11 and 32 kJ/mol, respectively). The reaction in tert-butyl alcohol is nearly diffusion controlled and has a high activation energy that is characteristic of transport in that liquid (E 1 = 31 kJ/mol, E sub(eta) = 39 kJ/mol). The activation energies in the other alcohols are all 16 kJ/mol, and it is 14 kJ/mol in water. They do not correlate with transport properties. The solvent effect is connected primarily with the entropy of activation. The rate constants correlate with the solvated electron trap depth. When the electron affinity of the scavenger is small, a favorable configuration of solvent molecules about the electron/scavenger encounter pair is required for the electron jump to take place. The behavior of the rate parameters for propargyl alcohol is similar to that for allyl alcohol, but k 1 , A 1 , and E 1 are larger for the former. The ratio k(propargyl)/k(allyl) at 298 K equals 10.5 in water and decreases through the series, reaching 1.3 in tert-butyl alcohol. Rate parameters for several other scavengers are also reported. (author)

Effects of functional group substitution on electron spectra and solvation dynamics in a family of ionic liquids

International Nuclear Information System (INIS)

Wishart, James F.; Lall-Ramnarine, Sharon I.; Raju, Ravinder; Scumpia, Alexander; Bellevue, Sherly; Ragbir, Revans; Engel, Robert

2005-01-01

Ionic liquids containing ether-, alcohol- and alkyl-functionalized quaternary ammonium dications were studied by pulse radiolysis. Spectra on nanosecond timescales revealed that solvation of the excess electron is particularly slow in the case of the alcohol-derivatized ionic liquids. The blue shift of the electron spectrum to the customary 650 nm peak takes 25-40 ns at 21 deg. C. Comparison with the relaxation dynamics observed in viscous 1,2,6-trihydroxyhexane reveals the hindering effect of the ionic liquid lattice on hydroxypropyl side chain reorientation

Enthalpies of solvation of ethylene oxide oligomers CH{sub 3}O(CH{sub 2}CH{sub 2}O){sub n}CH{sub 3} (n = 1 to 4) in different H-bonding solvents: Methanol, chloroform, and water. Group contribution method as applied to the polar oligomers

Energy Technology Data Exchange (ETDEWEB)

Barannikov, Vladimir P., E-mail: vpb@isc-ras.ru [Institute of Solution Chemistry, Russian Academy of Sciences, Academicheskaya Str. 1, Ivanovo 153045 (Russian Federation); Guseynov, Sabir S.; Vyugin, Anatoliy I. [Institute of Solution Chemistry, Russian Academy of Sciences, Academicheskaya Str. 1, Ivanovo 153045 (Russian Federation)

2011-12-15

Highlights: > Solvation enthalpy is found for ethylene oxide oligomers in chloroform and methanol. > Coefficients of solute-solute interaction are determined for oligomers in methanol. > Enthalpies of hydrogen bonding of oligomers with chloroform and water are estimated. > Additivity scheme is developed for describing enthalpies of solvation of oligomers. - Abstract: The enthalpies of solution and solvation of ethylene oxide oligomers CH{sub 3}O(CH{sub 2}CH{sub 2}O){sub n}CH{sub 3} (n = 1 to 4) in methanol and chloroform have been determined from calorimetric measurements at T = 298.15 K. The enthalpic coefficients of pairwise solute-solute interaction for methanol solutions have been calculated. The enthalpic characteristics of the oligomers in methanol, chloroform, water and tetrachloromethane have been compared. The hydrogen bonding of the oligomers with chloroform and water molecules is exhibited in the values of solvation enthalpy and coefficient of solute-solute interaction. This effect is not observed for methanol solvent. The thermochemical data evidence an existence of multi-centred hydrogen bonds in associates of polyethers with the solvent molecules. Enthalpies of hydrogen bonding of the oligomers with chloroform and water have been estimated. The additivity scheme has been developed to describe the enthalpies of solvation of ethylene oxide oligomers, unbranched monoethers and n-alkanes in chloroform, methanol, water, and tetrachloromethane. The correction parameters for contribution of repeated polar groups and correction term for methoxy-compounds have been introduced. The obtained group contributions permit to describe the enthalpies of solvation of unbranched monoethers and ethylene oxide oligomers in the solvents with standard deviation up to 0.6 kJ . mol{sup -1}. The values of group contributions and corrections are strongly influenced by solvent properties.

Cluster Formation of Polyphilic Molecules Solvated in a DPPC Bilayer

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Xiang-Yang Guo

2017-10-01

Full Text Available We analyse the initial stages of cluster formation of polyphilic additive molecules which are solvated in a dipalmitoylphosphatidylcholine (DPPC lipid bilayer. Our polyphilic molecules comprise an aromatic (trans-bilayer core domain with (out-of-bilayer glycerol terminations, complemented with a fluorophilic and an alkyl side chain, both of which are confined within the aliphatic segment of the bilayer. Large-scale molecular dynamics simulations (1 μ s total duration of a set of six of such polyphilic additives reveal the initial steps towards supramolecular aggregation induced by the specific philicity properties of the molecules. For our intermediate system size of six polyphiles, the transient but recurrent formation of a trimer is observed on a characteristic timescale of about 100 ns. The alkane/perfluoroalkane side chains show a very distinct conformational distribution inside the bilayer thanks to their different philicity, despite their identical anchoring in the trans-bilayer segment of the polyphile. The diffusive mobility of the polyphilic additives is about the same as that of the surrounding lipids, although it crosses both bilayer leaflets and tends to self-associate.

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous p$K_a$, and cyclohexane–water log D

CERN Document Server

Tielker, Nicolas; Heil, Jochen; Kloss, Thomas; Ehrhart, Sebastian; Güssregen, Stefan; Schmidt, K. Friedemann; Kast, Stefan M.

2016-01-01

We predict cyclohexane–water distribution coefficients (log D7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pKa) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the “Minnesota Solvation Database” (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol−1 for water and 0.8–0.9 kcal mol−1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pKa model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE...

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

Science.gov (United States)

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations

Formation of clusters (ions solvated with products of radiolysis) during irradiation of certain chloralkanes in the condensed phase

International Nuclear Information System (INIS)

Sukhov, F.F.; Karatun, A.A.; Slovokhotova, N.A.

1983-01-01

Using the infrared spectroscopy method, the radiolysis of the 2-chloropropane and 2-chloro-2-methylpropane was investigated in various phase states and in argon matrix at 15 and 77 K. A conclusion is drawn that the reaction of the radiation dehydrochlorination in the chloralkanes investigated occurs under certain conditions in the vicinity of ions, mostly; as this takes place, unique clusters composed of radiolysis products, i.e. ions solvated with complexes of alkane and hydrogen chloride are being formed. (author)

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).

The solvation reaction field for a hydrogen atom in a dielectric continuum

International Nuclear Information System (INIS)

Chipman, D.M.

1996-01-01

A reaction field exists even for a nonpolar solute embedded in a spherical cavity within a surrounding homogeneous dielectric continuum. This arises from the tail of the electronic wave function that penetrates beyond the cavity boundary into the dielectric region. This effect, which is neglected or treated only in cursory fashion in most reaction field implementations, is examined in detail for the simple case of a ground state hydrogen atom, where very accurate solutions of the relevant equations can be obtained. Properties considered include the penetration of the electron outside the cavity, the electronic density at the nucleus, the electron binding energy, the electrostatic free energy of solvation, the polarizability, and the vertical 1s→2p excitation energy. Also, the effect of the common approximation of neglecting the volume polarization and treating only the surface polarization contribution to the reaction field is critically evaluated. copyright 1996 American Institute of Physics

Solvated electron: criticism of a suggested correlation of chemical potential with optical absorption energy

International Nuclear Information System (INIS)

Farhataziz, M.

1984-01-01

A recent theoretical treatment of the absorption spectrum of the solvated electron, e - sub(s), maintains that rigorously μ 0 >= -0.75 Esub(av), which gives empirical relationship, μ 0 >= -(0.93 +- 0.02)Esub(max). For e - sub(s) in a particular solvent at a temperature and pressure, μ 0 , Esub(av) and Esub(max) are standard chemical potential, average energy of the absorption spectrum and the energy at the absorption maximum respectively. The temperature and pressure effects on the absorption spectrum of e - sub(s) in water and liquid ammonia do not support the equality sign in the above cited relationships. The implications of inequality expressed above are discussed for e - sub(s) in water and liquid ammonia. (author)

A non-solvated form of [(Z-O-methyl-N-(2-methylphenylthiocarbamato-κS](triphenylphosphane-κPgold(I: crystal structure and Hirshfeld surface analysis

Directory of Open Access Journals (Sweden)

Chien Ing Yeo

2016-10-01

Full Text Available The title compound, [Au(C9H10NOS(C18H15P], features a near linear P—Au—S arrangement defined by phosphane P and thiolate S atoms with the minor distortion from the ideal [P—Au—S is 177.61 (2°] being traced in part to the close intramolecular approach of an O atom [Au...O = 3.040 (2 Å]. The packing features supramolecular layers lying parallel to (011 sustained by a combination of C—H...π and π–π [inter-centroid distance = 3.8033 (17 Å] interactions. The molecular structure and packing are compared with those determined for a previously reported hemi-methanol solvate [Kuan et al. (2008. CrystEngComm, 10, 548–564]. Relatively minor differences are noted in the conformations of the rings in the Au-containing molecules. A Hirshfeld surface analysis confirms the similarity in the packing with the most notable differences relating to the formation of C—H...S contacts between the constituents of the solvate.

Structural and dynamical properties of solvated electrons; a study of kinetic spectroscopy using pulse radiolysis

International Nuclear Information System (INIS)

Huis, C. van

1977-01-01

In this thesis the pulse radiolysis experiments of hexamethyl-phosphortriamide (HMPA), propanol-1, 3-methylpentane and mixtures of propanol-1 and 3-methylpentane are reported. In the pulse radiolysis of HMPA, carried out at room temperature, the high yield of esub(s) - (G=2) and the very high wavelength of the maximum absorption (max= 2200 nm) in the esub(s) - absorption spectrum are explained by considering the aprotic nature and the molecular structure of this compound. In the experiment with propanol-1 (temperature range 93deg-123degK) a temporal shift to lower wavelengths in the time range of 10 s-10 ms is observed. In further experiments biphenyl was used as electron scavenger. It was concluded that after the electron pulse the following sequence of events takes place: 1) electron redistribution in times shorter than 1 s; 2) dipole reorientation during 10 s-10 ms; 3) recombination of a part of the solvated electrons; 4) a reaction of the solvated electrons with the neighbouring propanol-1 molecules. In the experiments with 3-methylpentane at 103deg-113degK an esub(s) - absorption band with third order decay kinetics was observed. This is attributed to geminate recombination. The activation energy of the recombination process was 0.4 eV. The experiments with mixtures of propanol-1 and 3-methylpentane were carried out at 103degK. At low propanol-1 concentrations the build-up at 500 nm obeys first order kinetics, whereas at high concentrations this build-up can be split up into three first order components, as was measured in pure propanol-1. The half-lives of the three components were in the ratio of 1:10:100. In the last chapter theoretical models for the electron redistribution and the matric relaxation are discussed and compared with the experiments

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

Science.gov (United States)

Li, Shen; Bradley, Philip

2013-01-01

When proteins bind to their DNA target sites, ordered water molecules are often present at the protein-DNA interface bridging protein and DNA through hydrogen bonds. What is the role of these ordered interfacial waters? Are they important determinants of the specificity of DNA sequence recognition, or do they act in binding in a primarily non-specific manner, by improving packing of the interface, shielding unfavorable electrostatic interactions, and solvating unsatisfied polar groups that are inaccessible to bulk solvent? When modeling details of structure and binding preferences, can fully implicit solvent models be fruitfully applied to protein-DNA interfaces, or must the individualistic properties of these interfacial waters be accounted for? To address these questions, we have developed a hybrid implicit/explicit solvation model that specifically accounts for the locations and orientations of small numbers of DNA-bound water molecules while treating the majority of the solvent implicitly. Comparing the performance of this model to its fully implicit counterpart, we find that explicit treatment of interfacial waters results in a modest but significant improvement in protein sidechain placement and DNA sequence recovery. Base-by-base comparison of the performance of the two models highlights DNA sequence positions whose recognition may be dependent on interfacial water. Our study offers large-scale statistical evidence for the role of ordered water for protein DNA recognition, together with detailed examination of several well-characterized systems. In addition, our approach provides a template for modeling explicit water molecules at interfaces that should be extensible to other systems. PMID:23444044

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.

Ionic strength independence of charge distributions in solvation of biomolecules

International Nuclear Information System (INIS)

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

2014-01-01

Electrostatic forces enormously impact the structure, interactions, and function of biomolecules. We perform all-atom molecular dynamics simulations for 5 proteins and 5 RNAs to determine the dependence on ionic strength of the ion and water charge distributions surrounding the biomolecules, as well as the contributions of ions to the electrostatic free energy of interaction between the biomolecule and the surrounding salt solution (for a total of 40 different biomolecule/solvent combinations). 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

Resonant Pump-dump Quantum Control of Solvated Dye Molecules with Phase Jumps

Science.gov (United States)

Konar, Arkaprabha; Lozovoy, Vadim; Dantus, Marcos

2014-03-01

Quantum coherent control of two photon and multiphoton excitation processes in atomic and condensed phase systems employing phase jumps has been well studied and understood. Here we demonstrate coherent quantum control of a two photon resonant pump-dump process in a complex solvated dye molecule. Phase jump in the frequency domain via a pulse shaper is employed to coherently enhance the stimulated emission by an order of magnitude when compared to transform limited pulses. Red shifted stimulated emission from successive low energy Stokes shifted excited states leading to narrowband emission are observed upon scanning the pi step across the excitation spectrum. A binary search space routine was also employed to investigate the effects of other types of phase jumps on stimulated emission and to determine the optimum phase that maximizes the emission. Understanding the underlying mechanism of this kind of enhancement will guide us in designing pulse shapes for enhancing stimulated emission, which can be further applied in the field of imaging.

One barbiturate and two solvated thiobarbiturates containing the triply hydrogen-bonded ADA/DAD synthon, plus one ansolvate and three solvates of their coformer 2,4-diaminopyrimidine.

Science.gov (United States)

Hützler, Wilhelm Maximilian; Egert, Ernst; Bolte, Michael

2016-09-01

A path to new synthons for application in crystal engineering is the replacement of a strong hydrogen-bond acceptor, like a C=O group, with a weaker acceptor, like a C=S group, in doubly or triply hydrogen-bonded synthons. For instance, if the C=O group at the 2-position of barbituric acid is changed into a C=S group, 2-thiobarbituric acid is obtained. Each of the compounds comprises two ADA hydrogen-bonding sites (D = donor and A = acceptor). We report the results of cocrystallization experiments of barbituric acid and 2-thiobarbituric acid, respectively, with 2,4-diaminopyrimidine, which contains a complementary DAD hydrogen-bonding site and is therefore capable of forming an ADA/DAD synthon with barbituric acid and 2-thiobarbituric acid. In addition, pure 2,4-diaminopyrimidine was crystallized in order to study its preferred hydrogen-bonding motifs. The experiments yielded one ansolvate of 2,4-diaminopyrimidine (pyrimidine-2,4-diamine, DAPY), C4H6N4, (I), three solvates of DAPY, namely 2,4-diaminopyrimidine-1,4-dioxane (2/1), 2C4H6N4·C4H8O2, (II), 2,4-diaminopyrimidine-N,N-dimethylacetamide (1/1), C4H6N4·C4H9NO, (III), and 2,4-diaminopyrimidine-1-methylpyrrolidin-2-one (1/1), C4H6N4·C5H9NO, (IV), one salt of barbituric acid, viz. 2,4-diaminopyrimidinium barbiturate (barbiturate is 2,4,6-trioxopyrimidin-5-ide), C4H7N4(+)·C4H3N2O3(-), (V), and two solvated salts of 2-thiobarbituric acid, viz. 2,4-diaminopyrimidinium 2-thiobarbiturate-N,N-dimethylformamide (1/2) (2-thiobarbiturate is 4,6-dioxo-2-sulfanylidenepyrimidin-5-ide), C4H7N4(+)·C4H3N2O2S(-)·2C3H7NO, (VI), and 2,4-diaminopyrimidinium 2-thiobarbiturate-N,N-dimethylacetamide (1/2), C4H7N4(+)·C4H3N2O2S(-)·2C4H9NO, (VII). The ADA/DAD synthon was succesfully formed in the salt of barbituric acid, i.e. (V), as well as in the salts of 2-thiobarbituric acid, i.e. (VI) and (VII). In the crystal structures of 2,4-diaminopyrimidine, i.e. (I)-(IV), R2(2)(8) N-H...N hydrogen-bond motifs are preferred and, in two

Crystal structures of two solvates of (18-crown-6potassium acetate

Directory of Open Access Journals (Sweden)

Phil Liebing

2016-12-01

Full Text Available The crystal and molecular strutures of two solvated forms of [K(18c6]OAc (18c6 = 18-crown-6 = 1,4,7,10,13,16-hexaoxacyclooctadecane and OAc = acetate were determined by single-crystal X-ray diffraction, namely (acetato-κ2O,O′(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium dihydrate, [K(CH3COO(C12H24O6]·2H2O (1 and (acetato-κ2O,O′aqua(1,4,7,10,13,16-hexaoxacyclooctadecane-κ6Opotassium acetic acid monosolvate [K(CH3COO(C12H24O6(H2O]·CH3COOH (2. In both compounds, the acetate anion is bonded to the potassium ion in a chelating fashion and the metal atom is consequently slightly displaced from the O6 plane of the crown ether. In the crystals, O—H...O hydrogen bonds lead to a polymeric ladder structure in the dihydrate 1, while the acetic acid hydrate 2 features inversion dimers.

Solubility and solvation of alkali metal perchlorates, tetramethyl and tetraethylammonium in aqua-ketone solvents

International Nuclear Information System (INIS)

Kireev, A.A.; Pak, T.G.; Bezuglyj, V.D.

1998-01-01

The KClO 4 , RbClO 4 , CsClO 4 , (CH 3 ) 4 NClO 4 , (C 2 H 5 ) 4 NClO 4 solubility in water and water-acetone, water-methylethylketone mixtures is determined through the method of isothermal saturation at 298.15 K. Dissociation constants of alkali metals perchlorates in acetone and its 90% mixtures (by volume) are determined conductometrically. Solubility products and standard energies of the Gibbs transfer of the studied electrolytes from water into water-acetone and water-methylethylketone solvents. It is established that the Gibbs standard energies of Na + , K + , Rb + and Cs + cations transfer from water to water-ketone solvents are close to each other. It is shown that the effect of acetone and methylethylketone on solvation of the studied electrolytes is practically similar

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; English, Niall J.; Schwingenschlö gl, Udo; Coker, David F.

2015-01-01

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

Molecular hydrogen solvated in water – A computational study

International Nuclear Information System (INIS)

Śmiechowski, Maciej

2015-01-01

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

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

International Nuclear Information System (INIS)

Schurhammer, R.

2001-12-01

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 Asφ 4 + (TA + ) and Bφ 4 - (TB - ) ions have the same free energy of solvation in any solvent. The two ions are found to be solvated differently in pure liquids (water, chloroform, acetonitrile) as at a chloroform / water interface. These results are confirmed by free energy calculations and by simulations on iso-volume spherical S + and S - ions, which perfectly meet the TATB criteria. The many methodological tests performed show the importance of (i) the corrected treatment of 'long range interactions' (ii) the precise repartition of atomic charges (iii) the solvent models, especially for water, on the + / - charge discrimination by solvent. In the second part, in relation to the liquid / liquid extraction of cations from water to supercritical CO 2 , we report the behaviour of ions (Cs + , UO 2 2+ , Eu 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 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 2 . (author)

Solvation effect on decomposition rate of 10-methyl-10-phenylphenoxarsonium iodide in some alcohols and ketones

International Nuclear Information System (INIS)

Gavrilov, V.I.; Gumerov, N.S.; Rakhmatullin, R.R.

1989-01-01

By the method of conductometry decomposition kinetics of 10-methyl-10phenylphenoxarsonium iodide in methanol, ethanol, 2-propanol, 1-butanol, 1-pentanol and methyl ethyl ketone at initial concentration of the salt 0.00024-0.003 mol/l, is studied. It is shown that at the temperatures up to 80-95 deg C practically no decomposition of arsonium salt in methanol and ethanol is observed. With an increase in the length of alcohol alkyl radical the decomposition rate increases. The values of activation enrgy both for alcohols and ketone are approximately the same. At the same time, decomposition rate in alcohol proved much slower than in ketone, which is related to iodide-ion solvation in protic solvents

Solvation effect on decomposition rate of 10-methyl-10-phenylphenoxarsonium iodide in some alcohols and ketones

Energy Technology Data Exchange (ETDEWEB)

Gavrilov, V I; Gumerov, N S; Rakhmatullin, R R [Kazanskij Khimiko-Tekhnologicheskij Inst., Kazan (USSR)

1989-03-01

By the method of conductometry decomposition kinetics of 10-methyl-10phenylphenoxarsonium iodide in methanol, ethanol, 2-propanol, 1-butanol, 1-pentanol and methyl ethyl ketone at initial concentration of the salt 0.00024-0.003 mol/l, is studied. It is shown that at the temperatures up to 80-95 deg C practically no decomposition of arsonium salt in methanol and ethanol is observed. With an increase in the length of alcohol alkyl radical the decomposition rate increases. The values of activation enrgy both for alcohols and ketone are approximately the same. At the same time, decomposition rate in alcohol proved much slower than in ketone, which is related to iodide-ion solvation in protic solvents.

Microscopic solvation of a lithium atom in water-ammonia mixed clusters: solvent coordination and electron localization in presence of a counterion.

Science.gov (United States)

Pratihar, Subha; Chandra, Amalendu

2008-07-14

The microsolvation structures and energetics of water-ammonia mixed clusters containing a lithium atom, i.e., Li(H(2)O)(n)(NH(3)), n = 1-5, are investigated by means of ab initio theoretical calculations. Several structural aspects such as the solvent coordination to the metal ion and binding motifs of the free valence electron of the metal are investigated. We also study the energetics aspects such as the dependence of vertical ionization energies on the cluster size, and all these structural and energetics aspects are compared to the corresponding results of previously studied anionic water-ammonia clusters without a metal ion. It is found that the Li-O and Li-N interactions play a very important role in stabilizing the lithium-water-ammonia clusters, and the presence of these metal ion-solvent interactions also affect the characteristics of electron solvation in these clusters. This is seen from the spatial distribution of the singly occupied molecular orbital (SOMO) which holds the ejected valence electron of the Li atom. For very small clusters, SOMO electron density is found to exist mainly at the vicinity of the Li atom, whereas for larger clusters, it is distributed outside the first solvation shell. The free dangling hydrogens of water and ammonia molecules are involved in capturing the SOMO electron density. In some of the conformers, OH{e}HO and OH{e}HN types of interactions are found to be present. The presence of the metal ion at the center of the cluster ensures that the ejected electron is solvated at a surface state only, whereas both surface and interiorlike states were found for the free electron in the corresponding anionic clusters without a metal ion. The vertical ionization energies of the present clusters are found to be higher than the vertical detachment energies of the corresponding anionic clusters which signify a relatively stronger binding of the free electron in the presence of the positive metal counterion. The shifts in different

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. © 2011 American Chemical Society

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

Energy Technology Data Exchange (ETDEWEB)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

2016-03-21

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

Band resolution of optical spectra of solvated electrons in water, alcohols, and tetrahydrofuran

International Nuclear Information System (INIS)

Jou, F.-Y.; Freeman, G.R.

1979-01-01

The optical absorption spectra of solvated electrons in water, alcohols, and tetrahydrofuran are empirically resolved into two Gaussian bands and a continuum tail. The first Gaussian band covers most of the low energy side of the spectrum. The second Gaussian band lies at an energy slightly above that of the absorption maximum of the total spectrum. With the exception of tert-butyl alcohol, in water and alcohols the following were observed: (a) the first Gaussian bands have the same half-width, but the oscillator strength in water is about double that in an alcohol; (b) the second Gaussian bands have similar half-widths and oscillator strengths; (c) the continuum tails have similar half-widths, yet that in water possesses only about one third as much oscillator strength as the one in alcohol. In tert-butyl alcohol and tetrahydrofuran the first Gaussian band and the continuum tail each carry nearly half of the total oscillator strength. (author)

Exploration of spectroscopic properties of solvated tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III)red hybrid organic complex for solution processed OLEDs and displays

International Nuclear Information System (INIS)

Chitnis, Dipti; Thejokalyani, N.; Dhoble, S.J.

2017-01-01

In order to explore the spectroscopic properties of a novel europium activated hybrid organic tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III), Eu(TTA) 3 bipy phosphor in various solvents at different pH and molar concentrations, UV–vis optical absorption and photoluminescence spectra were carried out. With a variation in the solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid, formic acid) media, staggering differences in optical absorptions and optical densities were noticed with hypsochromic shift in the absorption peaks. The optical density was found to be maximum for the complex with pH= 7.0 and the intensity as well as optical density gradually decreased when pH is lowered to 6.0 or raised to 8.0 (at an interval of 0.5), proving that the complex is pH sensitive. It's optical energy gap and stokes shift values in various organic solvents were also calculated on the basis of Lippert-Mataga plot. The exploration of spectroscopic properties of solvated Eu(TTA) 3 bipy complex demonstrates its prospective for solution processed OLEDs and display devices. - Graphical abstract: Pictorial depiction of photoluminescence in solvated Eu(TTA) 3 bipy complex under UV light.

Solvation molar enthalpies and heat capacities of n-alkanes and n-alkylbenzenes on stationary phases of wide-ranging polarity.

Science.gov (United States)

Lebrón-Aguilar, Rosa; Quintanilla-López, Jesús Eduardo; Santiuste, José María

2010-12-03

A comparison of the most usual gas chromatographic methods for the calculation of partial molar enthalpies of solvation (Δ(sol)H(o)) has been carried out. Those methods based on the fitting of lnV(g) or ln(k/T) vs. 1/T and ln(k/T) vs. (1/T and the temperature arrangement, T(a)) are the most adequate ones for obtaining Δ(sol)H(o) values. However, the latter is the only reliable option for Δ(sol)H(o) estimation when commercial WCOT capillary columns are used, since in this case the estimation of some variables involved in the V(g) determination is less accurate or even impossible. Consequently, in this paper, Δ(sol)H(o) obtained from ln(k/T) vs. (1/T+T(a)) fitting at 373.15 and 298.15K for n-alkanes and n-alkylbenzenes on 12 commercial capillary columns coated with stationary phases covering the 203-3608 McReynolds polarity range are reported. Moreover, molar heat capacities of solvation at constant pressure (Δ(sol)C(p)(o)) have also been calculated using this method. A clear influence on Δ(sol)H(o) of the type and content of the substitution group in the stationary phase was observed. In addition, a linear relationship of Δ(sol)C(p)(o) with the van der Waals volume of the n-alkanes and the temperature gradient of density of the stationary phase was found. The effect of the size of the hydrocarbon on both thermodynamic variables was also investigated. Copyright © 2010 Elsevier B.V. All rights reserved.

Surface Solvation of Halogen Anions in Water Clusters: An ab initio Molecular Dynamics Study of the Cl-(H.sub.2./sub.O).sub.6./sub. Complex

Czech Academy of Sciences Publication Activity Database

Tobias, D. J.; Jungwirth, Pavel; Parrinello, M.

2001-01-01

Roč. 114, č. 16 (2001), s. 7036-7044 ISSN 0021-9606 R&D Projects: GA MŠk LN00A032 Grant - others:NATO Science Program(XE) CLG-974459 Institutional research plan: CEZ:AV0Z4040901 Keywords : cluster * ab initio molecular dynamics * anionic solvation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.147, year: 2001

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)

Exploration of spectroscopic properties of solvated tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III)red hybrid organic complex for solution processed OLEDs and displays

Energy Technology Data Exchange (ETDEWEB)

Chitnis, Dipti [Department of Physics, RTM Nagpur University, Nagpur 440033 (India); Thejokalyani, N., E-mail: thejokalyani@rediffmail.com [Department of Applied Physics, Laxminarayan Institute of Technology, Nagpur 440033 (India); Dhoble, S.J. [Department of Physics, RTM Nagpur University, Nagpur 440033 (India)

2017-05-15

In order to explore the spectroscopic properties of a novel europium activated hybrid organic tris(thenoyltrifluoroacetonate)(2,2′-bipyridine)europium(III), Eu(TTA){sub 3}bipy phosphor in various solvents at different pH and molar concentrations, UV–vis optical absorption and photoluminescence spectra were carried out. With a variation in the solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid, formic acid) media, staggering differences in optical absorptions and optical densities were noticed with hypsochromic shift in the absorption peaks. The optical density was found to be maximum for the complex with pH= 7.0 and the intensity as well as optical density gradually decreased when pH is lowered to 6.0 or raised to 8.0 (at an interval of 0.5), proving that the complex is pH sensitive. It's optical energy gap and stokes shift values in various organic solvents were also calculated on the basis of Lippert-Mataga plot. The exploration of spectroscopic properties of solvated Eu(TTA){sub 3}bipy complex demonstrates its prospective for solution processed OLEDs and display devices. - Graphical abstract: Pictorial depiction of photoluminescence in solvated Eu(TTA){sub 3}bipy complex under UV light.

The cavity electromagnetic field within the polarizable continuum model of solvation

Energy Technology Data Exchange (ETDEWEB)

Pipolo, Silvio, E-mail: silvio.pipolo@nano.cnr.it [Center S3, CNR Institute of Nanoscience, Modena (Italy); Department of Physics, University of Modena and Reggio Emilia, Modena (Italy); Corni, Stefano, E-mail: stefano.corni@nano.cnr.it [Center S3, CNR Institute of Nanoscience, Modena (Italy); Cammi, Roberto, E-mail: roberto.cammi@unipr.it [Department of Chemistry, Università degli studi di Parma, Parma (Italy)

2014-04-28

Cavity field effects can be defined as the consequences of the solvent polarization induced by the probing electromagnetic field upon spectroscopies of molecules in solution, and enter in the definitions of solute response properties. The polarizable continuum model of solvation (PCM) has been extended in the past years to address the cavity-field issue through the definition of an effective dipole moment that couples to the external electromagnetic field. We present here a rigorous derivation of such cavity-field treatment within the PCM starting from the general radiation-matter Hamiltonian within inhomogeneous dielectrics and recasting the interaction term to a dipolar form within the long wavelength approximation. To this aim we generalize the Göppert-Mayer and Power-Zienau-Woolley gauge transformations, usually applied in vacuo, to the case of a cavity vector potential. Our derivation also allows extending the cavity-field correction in the long-wavelength limit to the velocity gauge through the definition of an effective linear momentum operator. Furthermore, this work sets the basis for the general PCM treatment of the electromagnetic cavity field, capable to describe the radiation-matter interaction in dielectric media beyond the long-wavelength limit, providing also a tool to investigate spectroscopic properties of more complex systems such as molecules close to large nanoparticles.

An experimental point of view on hydration/solvation in halophilic proteins.

Science.gov (United States)

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.

Network topology for the formation of solvated electrons in binary CaO–Al2O3 composition glasses

Science.gov (United States)

Akola, Jaakko; Kohara, Shinji; Ohara, Koji; Fujiwara, Akihiko; Watanabe, Yasuhiro; Masuno, Atsunobu; Usuki, Takeshi; Kubo, Takashi; Nakahira, Atsushi; Nitta, Kiyofumi; Uruga, Tomoya; Weber, J. K. Richard; Benmore, Chris J.

2013-01-01

Glass formation in the CaO–Al2O3 system represents an important phenomenon because it does not contain typical network-forming cations. We have produced structural models of CaO–Al2O3 glasses using combined density functional theory–reverse Monte Carlo simulations and obtained structures that reproduce experiments (X-ray and neutron diffraction, extended X-ray absorption fine structure) and result in cohesive energies close to the crystalline ground states. The O–Ca and O–Al coordination numbers are similar in the eutectic 64 mol % CaO (64CaO) glass [comparable to 12CaO·7Al2O3 (C12A7)], and the glass structure comprises a topologically disordered cage network with large-sized rings. This topologically disordered network is the signature of the high glass-forming ability of 64CaO glass and high viscosity in the melt. Analysis of the electronic structure reveals that the atomic charges for Al are comparable to those for Ca, and the bond strength of Al–O is stronger than that of Ca–O, indicating that oxygen is more weakly bound by cations in CaO-rich glass. The analysis shows that the lowest unoccupied molecular orbitals occurs in cavity sites, suggesting that the C12A7 electride glass [Kim SW, Shimoyama T, Hosono H (2011) Science 333(6038):71–74] synthesized from a strongly reduced high-temperature melt can host solvated electrons and bipolarons. Calculations of 64CaO glass structures with few subtracted oxygen atoms (additional electrons) confirm this observation. The comparable atomic charges and coordination of the cations promote more efficient elemental mixing, and this is the origin of the extended cage structure and hosted solvated (trapped) electrons in the C12A7 glass. PMID:23723350

Solvation of positive ions in water: the dominant role of water-water interaction

International Nuclear Information System (INIS)

Krekeler, Christian; Site, Luigi Delle

2007-01-01

Local polarization effects, induced by monovalent and divalent positive ions in water, influence (and in turn are influenced by) the large-scale structural properties of the solvent. Experiments can only distinguish this process of interplay in a generic qualitative way. Instead, first-principles calculations can address the question at both the electronic and atomistic scale, accounting for electronic polarization as well as geometrical conformations. For this reason we study the extension of the scales' interconnection by means of first-principle Car-Parrinello molecular dynamics applied to systems of different size. In this way we identify the general aspects dominating the physics of the first solvation shell and their connection to the effects related to the formation of the outer shells and eventually the bulk. We show that while the influence of the ions is extended to the first shell only, the water-water interaction is instead playing a dominant role even within the first shell independently of the size or the charge of the ion. (fast track communication)

Chemisorption of a hydrogen adatom on metal doped α-Zr (0 0 0 1 surfaces in a vacuum and an implicit solvation environment

Directory of Open Access Journals (Sweden)

Cheng Zeng

2017-12-01

Full Text Available First-principles calculations have been carried out to investigate the adsorption of a hydrogen adatom on 24 metal doped α-Zr (0 0 0 1 surfaces in both a vacuum and an implicit solvation environment. The dopant are the elements in the 4th and 5th periods in the periodic table. Doping elements at the tail of the 4th and 5th periods can significantly reduce the hydrogen pickup in a vacuum environment. A weighted d-band center theory is used to analyze the doping effect. On the other hand, the hydrogen adsorption energies in water are relatively lower for all doped slabs and the surface adsorption of hydrogen adatom is stronger than that in a vacuum environment, especially, for the slabs with doping elements at the tail of the 4th and 5th periods. In the solvation environment, electronegativity difference affects the adsorption. Doping elements Ag, Ga, Ge, Sn, and Sb can reduce the hydrogen pickup in vacuum, while Ag and Cu can reduce the hydrogen pickup of the zirconium alloys in solvent environment.

Mutual solubility between hexane and three-n-butyl phosphate solvates of lanthanide(III) and thorium(IV) nitrates at various temperatures

International Nuclear Information System (INIS)

Keskinov, V.A.; Lishuk, V.V.; Pyartman, A.K.

2007-01-01

Phase diagrams of binary liquid systems of hexane-rare earth(III) nitrates solvates (rare earth - neodymium, gadolinium, yttrium, ytterbium, lutetium) and thorium(IV) with tri-n-butylphosphate are studied at different temperatures. Phase diagrams of binary systems consist of fields of homogeneous solutions and field of stratification into two liquid phases (I, II): phase I is enriched by hexane, and phase II - [Ln(NO 3 ) 3 (TBP) 3 ] (Ln=Nd, Gd, Y, Yb and Lu) or [Th(NO 3 ) 4 (TBP) 2 ]. Field of stratification into two liquid phases are decreased with growing temperature in binary systems [ru

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer

Science.gov (United States)

Chen, Mohan; Zheng, Lixin; Santra, Biswajit; Ko, Hsin-Yu; DiStasio, Robert A., Jr.; Klein, Michael L.; Car, Roberto; Wu, Xifan

2018-03-01

Proton transfer via hydronium and hydroxide ions in water is ubiquitous. It underlies acid-base chemistry, certain enzyme reactions, and even infection by the flu. Despite two centuries of investigation, the mechanism underlying why hydroxide diffuses slower than hydronium in water is still not well understood. Herein, we employ state-of-the-art density-functional-theory-based molecular dynamics—with corrections for non-local van der Waals interactions, and self-interaction in the electronic ground state—to model water and hydrated water ions. At this level of theory, we show that structural diffusion of hydronium preserves the previously recognized concerted behaviour. However, by contrast, proton transfer via hydroxide is less temporally correlated, due to a stabilized hypercoordination solvation structure that discourages proton transfer. Specifically, the latter exhibits non-planar geometry, which agrees with neutron-scattering results. Asymmetry in the temporal correlation of proton transfer leads to hydroxide diffusing slower than hydronium.

Ligand solvation effect on Dy3+ complexing with benzoic, p-, o-, m-aminobenzoic, 4-pyridinecarboxylic acids., and with pyridine and 4-aminopyridine in aqua and aqua-organic media

International Nuclear Information System (INIS)

Elistratova, Yu.G.; Mustafina, A.R.; Devyatov, F.V.; Sarvarova, N.N.

1996-01-01

Substituent effect on stability of Dy 3+ complexes with aminobenzoic acids (o , p-, m-isomers), pyridinecarboxylic acids and p-aminopyridine was estimated on the base of pH-metric and magnetooptic data. It was concluded that the more the efficiency of ligand's solvation the less the substituent effects the complex stability. 15 refs., 3 figs., 2 tabs

The role of concavo-convex walls of a nanopore on the density profile, adsorption, solvation force, and capillary condensation of confined fluids: A DFT study

International Nuclear Information System (INIS)

Helmi, Abbas; Keshavarzi, Ezat

2014-01-01

Highlights: • The effect of concavo-convex walls of nanopores on the density profile was studied. • For HS fluids the contact density at concave wall is greater than for convex wall. • For Yukawa fluid the contact density at concave wall can be less than convex wall. • Capillary condensation was observed for Yukawa fluids in the homocentric pores. - Abstract: We investigate the effects of concavo-convex walls of a nanopore on the structure and certain thermodynamic properties of confined fluids. Adsorption, solvation force, and capillary condensation in a nanopore formed between two homocentric spheres will be determined using the MFMT. For hard sphere fluids, contact density is greater at the concave wall than it is at the convex wall. In Yukawa fluids, for the thermodynamic state in which the energy effect is the dominant factor, contact density at a concave wall is less than that at a convex wall; this will be reversed for the thermodynamic state in which the entropy effect is the dominant factor. It is possible to find thermodynamic states in which contact densities at concave and convex walls become identical. The adsorption and solvation force of hard sphere fluid show an oscillatory behavior versus H. Capillary condensation is in certain cases observed for Yukawa fluids

Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

Science.gov (United States)

Khavrutskii, Ilja V; Wallqvist, Anders

2010-11-09

This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

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. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

International Nuclear Information System (INIS)

Marassi, Francesca M.; Ding, Yi; Schwieters, Charles D.; Tian, Ye; Yao, Yong

2015-01-01

The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential

Solvation and Ion Pair Association in Aqueous Metal Sulfates: Interpretation of NDIS raw data by isobaric-isothermal molecular dynamics simulation

International Nuclear Information System (INIS)

Chialvo, Ariel A.; Simonson, J. Michael

2010-01-01

We analyzed the solvation behavior of aqueous lithium, nickel, and ytterbium sulfates at ambient conditions in terms of the relevant radial distributions functions and the corresponding first-order difference of the sulfur-site neutron weighted distribution functions generated by isothermal-isobaric molecular dynamics simulation. We determined of the partial contributions to the neutron weighted distribution functions, to identify the main peaks, and the effect of the contact ion-pair configuration on the resulting H-S coordination number. Finally, we assessed the extent of the ion-pair formation according to Poirier-DeLap formalism and highlighted the significant increase of the ion-pair association exhibited by these salts with cation charge.

Synthesis of Tertiary and Quaternary Amine Derivatives from Wood Resin as Chiral NMR Solvating Agents

Directory of Open Access Journals (Sweden)

Tiina Laaksonen

2015-11-01

Full Text Available Chiral tertiary and quaternary amine solvating agents for NMR spectroscopy were synthesized from the wood resin derivative (+-dehydroabietylamine (2. The resolution of enantiomers of model compounds [Mosher’s acid (3 and its n-Bu4N salt (4] (guests by (+-dehydroabietyl-N,N-dimethylmethanamine (5 and its ten different ammonium salts (hosts was studied. The best results with 3 were obtained using 5 while with 4 the best enantiomeric resolution was obtained using (+-dehydroabietyl-N,N-dimethylmethanaminium bis(trifluoromethane-sulfonimide (6. The compounds 5 and 6 showed a 1:1 complexation behaviour between the host and guest. The capability of 5 and 6 to recognize the enantiomers of various α-substituted carboxylic acids and their n-Bu4N salts in enantiomeric excess (ee determinations was demonstrated. A modification of the RES-TOCSY NMR pulse sequence is described, allowing the enhancement of enantiomeric discrimination when the resolution of multiplets is insufficient.

A dual cryogenic ion trap spectrometer for the formation and characterization of solvated ionic clusters

Energy Technology Data Exchange (ETDEWEB)

Marsh, Brett M.; Voss, Jonathan M.; Garand, Etienne, E-mail: egarand@chem.wisc.edu [Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706 (United States)

2015-11-28

A new experimental approach is presented in which two separate cryogenic ion traps are used to reproducibly form weakly bound solvent clusters around electrosprayed ions and messenger-tag them for single-photon infrared photodissociation spectroscopy. This approach thus enables the vibrational characterization of ionic clusters comprised of a solvent network around large and non-volatile ions. We demonstrate the capabilities of the instrument by clustering water, methanol, and acetone around a protonated glycylglycine peptide. For water, cluster sizes with greater than twenty solvent molecules around a single ion are readily formed. We further demonstrate that similar water clusters can be formed around ions having a shielded charge center or those that do not readily form hydrogen bonds. Finally, infrared photodissociation spectra of D{sub 2}-tagged GlyGlyH{sup +} ⋅ (H{sub 2}O){sub 1−4} are presented. They display well-resolved spectral features and comparisons with calculations reveal detailed information on the solvation structures of this prototypical peptide.

Polymorphism and solvates of 3,3'-dihydroxy-ss,ss-carotene-4,4'-dione: Screening and their thermodynamics

Energy Technology Data Exchange (ETDEWEB)

Guo, J.; Ulrich, J. [Martin Luther University Halle-Wittenberg, Center for Engineering Sciences/ TVT, 06099, Halle Saale (Germany)

2010-03-15

3,3'-dihydroxy-ss,ss-carotene-4,4'-dione (DCD) is a carotenoid used for the pink coloration in animal and fish foods. Two nonsolvated and two solvated forms of this compound have been discovered and characterized using different analytical techniques. The thermodynamic stability of the relevant polymorphs is revealed. The transformation rate depends strongly on the selection of solvent medium. Moreover, different chemical stability refers to the shelf life is studied correlating to the different polymorphs. The results show the possibilities to improve the pigmentation efficiency and chemical stability by a changing in the crystal polymorphs. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Predictions of flavonoid solubility in ionic liquids by COSMO-RS: experimental verification, structural elucidation, and solvation characterization

DEFF Research Database (Denmark)

Guo, Zheng; Lue, Bena-Marie; Thomsen, Kaj

2007-01-01

Predictions of the solubility of flavonoids in a large variety of ionic liquids (ILs) with over 1800 available structures were examined based on COSMO-RS computation. The results show that the solubilities of flavonoids are strongly anion-dependent. Experimental measurement of the solubilities...... of esculin and rutin in 12 ILs with varying anions and cations show that predicted and experimental results generally have a good agreement. Based on the sound physical basis of COSMO-RS, the solubility changes of flavonoids were quantitatively associated with solvation interactions and structural...... characteristics of ILs. COSMO-RS derived parameters, i.e. misfit, H-bonding and van der Waals interaction energy, are shown to be capable of characterizing the complicated multiple interactions in the IL system effectively. H-bonding interaction is the most dominant interaction for ILs (followed by misfit and van...

Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

Science.gov (United States)

Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2014-06-05

Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

Novel dimer based descriptors with solvational computation for QSAR study of oxadiazoylbenzoyl-ureas as novel insect-growth regulators.

Science.gov (United States)

Fan, Feng; Cheng, Jiagao; Li, Zhong; Xu, Xiaoyong; Qian, Xuhong

2010-02-01

Molecular aggregation state of bioactive compounds plays a key role in its bio-interactive procedure. In this article, based on the structure information of dimers, the simplest model of molecular aggregation state, and combined with solvational computation, total four descriptors (DeltaV, MR2, DeltaE(1), and DeltaE(2)) were calculated for QSAR study of a novel insect-growth regulator, N-(5-phenyl-1,3,4-oxadiazol-2-yl)-N'-benzoyl urea. Two QSAR models were constructed with r(2) = 0.671, q(2) = 0.516 and r(2) = 0.816, q(2) = 0.695, respectively. It implicates that the bioactivity may strongly depend on the characters of molecular aggregation state, especially on the dimeric transport ability from oil phase to water phase. Copyright 2009 Wiley Periodicals, Inc.

Ionic association and solvation of the ionic liquid 1-hexyl-3-methylimidazolium chloride in molecular solvents revealed by vapor pressure osmometry, conductometry, volumetry, and acoustic measurements.

Science.gov (United States)

Sadeghi, Rahmat; Ebrahimi, Nosaibah

2011-11-17

A systematic study of osmotic coefficient, conductivity, volumetric and acoustic properties of solutions of ionic liquid 1-hexyl-3-methylimidazolium chloride ([C(6)mim][Cl]) in various molecular solvents has been made at different temperatures in order to study of ionic association and solvation behavior of [C(6)mim][Cl] in different solutions. Precise measurements on electrical conductances of solutions of [C(6)mim][Cl] in water, methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and acetonitrile at 293.15, 298.15, and 303.15 K are reported and analyzed with Barthel's low-concentration chemical model (lcCM) to obtain the limiting molar conductivities and association constants of this ionic liquid in the investigated solvents. Strong ion pairing was found for the ionic liquid in 2-propanol, 1-butanol, and 1-propanol, whereas ion association in acetonitrile, methanol and ethanol is rather weak and in water the ionic liquid is fully dissociated. In the second part of this work, the apparent molar volumes and isentropic compressibilities of [C(6)mim][Cl] in water, methanol, ethanol, acetonitrile, 1-propanol, 2-propanol, and 1-butanol are obtained at the 288.15-313.15 K temperature range at 5 K intervals at atmospheric pressure from the precise measurements of density and sound velocity. The infinite dilution apparent molar volume and isentropic compressibility values of the free ions and ion pairs of [C(6)mim][Cl] in the investigated solvents as well as the excess molar volume of the investigated solutions are determined and their variations with temperature and type of solvents are also studied. Finally, the experimental measurements of osmotic coefficient at 318.15 K for binary solutions of [C(6)mim][Cl] in water, methanol, ethanol, 2-propanol, and acetonitrile are taken using the vapor pressure osmometry (VPO) method and from which the values of the solvent activity, vapor pressure, activity coefficients, and Gibbs free energies are calculated. The results are

Barium isotope fractionation during the experimental transformation of aragonite to witherite and of gypsum to barite, and the effect of ion (de)solvation.

Science.gov (United States)

Böttcher, Michael E; Neubert, Nadja; von Allmen, Katja; Samankassou, Elias; Nägler, Thomas F

2018-06-01

In this study, we present the experimental results for stable barium (Ba) isotope fractionation ( 137 Ba/ 134 Ba) during the transformation of aragonite (CaCO 3 ) and gypsum (CaSO 4 ·2H 2 O) in Ba-bearing aqueous solution to witherite (BaCO 3 ) and barite (BaSO 4 ), respectively. The process was studied at three temperatures between 4 and 60 °C. In all cases, the transformation leads to a relative enrichment of the lighter 134 Ba isotope in the solid compared to the aqueous solution, with 137/134 Ba enrichment factors between -0.11 and -0.17 ‰ for BaCO 3 , and -0.21 and -0.26 ‰ for BaSO 4 . The corresponding mass-dependent 138/134 Ba enrichment factors are -0.15 to -0.23 ‰ for BaCO 3 , and -0.28 to -0.35 ‰ for BaSO 4 . The magnitude of isotope fractionation is within the range of recent reports for witherite and barite formation, as well as trace Ba incorporation into orthorhombic aragonite, and no substantial impact of temperature can be found between 4 and 80 °C. In previous studies, ion (de)solvation has been suggested to impact both the crystallization process of Ba-bearing solids and associated Ba isotope fractionation. Precipitation experiments of BaSO 4 and BaCO 3 using an methanol-containing aqueous solution indicate only a minor effect of ion and crystal surface (de)solvation on the overall Ba isotope fractionation process.

The solvation of L-serine in mixtures of water with some aprotic solvents at 298.15 K

Science.gov (United States)

Mezhevoi, I. N.; Badelin, V. G.

2009-03-01

The integral enthalpies of solution Δsol H m of L-serine in mixtures of water with acetonitrile, 1,4-dioxane, dimethylsulfoxide (DMSO), and acetone were measured by solution calorimetry at organic component concentrations up to 0.31 mole fractions. The standard enthalpies of solution (Δsol H°), transfer (Δtr H°), and solvation (Δsolv H°) of L-serine from water into mixed solvents were calculated. The dependences of Δsol H°, Δsolv H°, and Δtr H° on the composition of aqueous-organic solvents contained extrema. The calculated enthalpy coefficients of pair interactions of the amino acid with cosolvent molecules were positive and increased in the series acetonitrile, 1,4-dioxane, DMSO, acetone. The results obtained were interpreted from the point of view of various types of interactions in solutions and the influence of the nature of organic solvents on the thermochemical characteristics of solutions.

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.

Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K+ channels

Science.gov (United States)

Liu, Xuejiao; Lu, Benzhuo

2017-12-01

Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential. However, the traditional PNP model is a continuum mean-field model and has no or underestimates the discrete ion effects, in particular the ion solvation or self-energy (which can be described by Born model). It is known that the dehydration effect (closely related to ion size) is crucial to selective permeation in potassium channels. Therefore, we incorporated Born solvation energy into the PNP model to account for ion hydration and dehydration effects when passing through inhomogeneous dielectric channel environments. A variational approach was adopted to derive a Born-energy-modified PNP (BPNP) model. The model was applied to study a cylindrical nanopore and a realistic KcsA channel, and three-dimensional finite element simulations were performed. The BPNP model can distinguish different ion species by ion radius and predict selectivity for K+ over Na+ in KcsA channels. Furthermore, ion current rectification in the KcsA channel was observed by both the PNP and BPNP models. The I -V curve of the BPNP model for the KcsA channel indicated an inward rectifier effect for K+ (rectification ratio of ˜3 /2 ) but indicated an outward rectifier effect for Na+ (rectification ratio of ˜1 /6 ) .

Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models using Density Functional Theory

OpenAIRE

Marianski, Mateusz; Dannenberg, J. J.

2012-01-01

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum...

Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling.

Science.gov (United States)

Wang, Changhao; Ren, Pengyu; Luo, Ray

2017-12-14

Solvent-mediated electrostatic interactions were well recognized to be important in the structure and function of molecular systems. Ionic interaction is an important component in electrostatic interactions, especially in highly charged molecules, such as nucleic acids. Here, we focus on the quality of the widely used Poisson-Boltzmann surface area (PBSA) continuum models in modeling ionic interactions by comparing with both explicit solvent simulations and the experiment. In this work, the molality-dependent chemical potentials for sodium chloride (NaCl) electrolyte were first simulated in the SPC/E explicit solvent. Our high-quality simulation agrees well with both the previous study and the experiment. Given the free-energy simulations in SPC/E as the benchmark, we used the same sets of snapshots collected in the SPC/E solvent model for PBSA free-energy calculations in the hope to achieve the maximum consistency between the two solvent models. Our comparative analysis shows that the molality-dependent chemical potentials of NaCl were reproduced well with both linear PB and nonlinear PB methods, although nonlinear PB agrees better with SPC/E and the experiment. Our free-energy simulations also show that the presence of salt increases the hydrophobic effect in a nonlinear fashion, in qualitative agreement with previous theoretical studies of Onsager and Samaras. However, the lack of molality-dependency in the nonelectrostatics continuum models dramatically reduces the overall quality of PBSA methods in modeling salt-dependent energetics. These analyses point to further improvements needed for more robust modeling of solvent-mediated interactions by the continuum solvation frameworks.

CL 14: Solvation structure and dynamics of room temperature ionic liquids

International Nuclear Information System (INIS)

Musat, Raluca M.; Polyansky, Dmitriy; Crowell, Robert A.; Thomas, Marie; Wishart, James F.; Takahashi, Kenji; Katsumura, Yosuke

2010-01-01

Room temperature ionic liquids (RTILs) have emerged as a new class of solvents that, due to their unique properties (e.g., low volatility, large electrochemical window, high conductivity, etc.), have several potential applications. Among these are their possible use in nuclear fuel reprocessing, dye sensitized solar cells, and CO 2 sequestration. The properties of a given class of RTILs depend strongly on the choice of the counter anion. In this contribution we present new results using both static and time-resolved EXAFS (ca. 1 ns resolution) and time resolved optical absorption spectroscopy on a series of bromide containing imidazolium salts. The static results provide detailed information of the solvation shell of the bromide ion while the time-resolved data shed light on the nature and chemical behavior of the lowest lying charge transfer band, the physical motion of the bromine atom and its conversion to di-bromide. The photochemistry of the charge transfer (CT) band of the room temperature ionic liquid 1-hexyl-3-methylimidazolium bromide is investigated using ultrafast transient absorption spectroscopy (TA) in the near-IR and steady state UV absorption. Irradiation of the CT band at 266 nm results in the steady state production of di-bromide which absorbs strongly at 266 nm. It is shown that this photoproduct, which is apparently very stable, adversely affects ultrafast transient absorption measurements. Flowing and simultaneously translating the sample mitigates this effect and reveals new transient species and dynamics within the detection window of 850 nm to 1250 nm. (authors)

Solvation of fluoroform and fluoroform-dimethylether dimer in liquid krypton: a theoretical cryospectroscopic study.

Science.gov (United States)

Kohls, Emilija; Mishev, Anastas; Pejov, Ljupčo

2013-08-07

A hybrid, sequential statistical physics-quantum mechanical electronic-quantum mechanical nuclei approach has been applied to study the C-H stretching frequencies of bare fluoroform dissolved in liquid krypton under cryogenic conditions (at ~130 K), as well as upon blue shifting hydrogen bonding interactions with dimethylether in the same solvent. The structure of the liquid at 130 K was generated by Monte Carlo simulations of cryogenic Kr solutions containing either fluoroform or fluoroform and dimethylether molecules. Statistically uncorrelated configurations were appropriately chosen from the equilibrated MC runs and supermolecular clusters containing solute and solvent molecules (either standalone or embedded in the "bulk" part of the solvent treated as a polarizable continuum) were subjected to quantum mechanical electronic (QMel) and subsequent quantum mechanical nuclei (QMnuc) calculations. QMel calculations were implemented to generate the in-liquid 1D intramolecular C-H stretching vibrational potential of the fluoroform moiety and subsequently in the QMnuc phase the corresponding anharmonic C-H stretching frequency was computed by diagonalization techniques. Finally, the constructed vibrational density of states histograms were compared to the experimental Raman bands. The calculated anharmonic vibrational frequency shifts of the fluoroform C-H stretching mode upon interaction with dimethylether in liquid Kr are in very good agreement with the experimental data (20.3 at MP2 level vs. 16.6 cm(-1) experimentally). Most of this relatively large frequency blue shift is governed by configurations characterized by a direct C-H···O contact between monomers. The second population detected during MC simulations, characterized by reversed orientation of the monomers, has a minor contribution to the spectral appearance. The experimentally observed trend in the corresponding bandwidths is also correctly reproduced by our theoretical approach. Solvation of the

A molecular Debye-Hückel theory of solvation in polar fluids: An extension of the Born model

Science.gov (United States)

Xiao, Tiejun; Song, Xueyu

2017-12-01

A dielectric response theory of solvation beyond the conventional Born model for polar fluids is presented. The dielectric response of a polar fluid is described by a Born response mode and a linear combination of Debye-Hückel-like response modes that capture the nonlocal response of polar fluids. The Born mode is characterized by a bulk dielectric constant, while a Debye-Hückel mode is characterized by its corresponding Debye screening length. Both the bulk dielectric constant and the Debye screening lengths are determined from the bulk dielectric function of the polar fluid. The linear combination coefficients of the response modes are evaluated in a self-consistent way and can be used to evaluate the electrostatic contribution to the thermodynamic properties of a polar fluid. Our theory is applied to a dipolar hard sphere fluid as well as interaction site models of polar fluids such as water, where the electrostatic contribution to their thermodynamic properties can be obtained accurately.

The energy of hydration and solvation of indium salts in the acetylacetone-InCl3-water system

International Nuclear Information System (INIS)

Kulawik, I.; Baumgartner, T.

1978-01-01

On the base of the previous papers concerning the investigations in the extraction systems the experiments were performed for the determination of thermodynamical distribution coefficient of indium salts between two phases in the system: acetylacetone-InCl 3 -water and the energy of hydration and solvation of that system. The results of the surface and interfacial potentials measurements of the system were presented as a function of the InCl 3 concentration in the system before the extraction. The extraction coefficients of indium as a function of concentration of InCl 3 in this system were determined. The method of the visible absorption spectra was used to the determination of concentration of indium in both phases after the extraction. The relation between the percentage of the extraction and the extraction coefficient was determined. The investigations were performed in the system containing 0.1 M HCl and 0.001 M HCl in the aqueous phase. The results of experiments are tabulated and graphically presented in figures. (author)

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

Science.gov (United States)

Wang, Meiting; Li, Pengfei; Jia, Xiangyu; Liu, Wei; Shao, Yihan; Hu, Wenxin; Zheng, Jun; Brooks, Bernard R; Mei, Ye

2017-10-23

The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed. The QM solvation free energies were calculated indirectly via a series of MM states using the multistate Bennett acceptance ratio (MBAR) and the MM-to-QM corrections were applied at the two endpoints using thermodynamic perturbation (TP). Previously, it has been shown (Jia et al. J. Chem. Theory Comput. 2016, 12, 499-511) that this method provides the minimal variance in the results without running QM simulations. However, if there is insufficient overlap in phase space between the MM and QM Hamiltonians, this method fails. In this work, we propose, for the first time, a quantity termed the reweighting entropy that serves as a metric for the reliability of the TP calculations. If the reweighting entropy is below a certain threshold (0.65 for the solvation free energy calculations in this work), this MM-to-QM correction should be avoided and two alternative methods can be employed by either introducing a semiempirical state or conducting nonequilibrium simulations. However, the results show that the QM methods are not guaranteed to yield better results than the MM methods. Further improvement of the QM methods are imperative, especially the treatment of the van der Waals and the electrostatic interactions between the QM region and the MM region in the first shell. We also propose a scheme for the calculation of the van der Waals parameters for the solute molecules in nonaqueous solvent, which improves the quality of the

Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics.

Science.gov (United States)

Kovalenko, Andriy; Gusarov, Sergey

2018-01-31

In this work, we will address different aspects of self-consistent field coupling of computational chemistry methods at different time and length scales in modern materials and biomolecular science. Multiscale methods framework yields dramatically improved accuracy, efficiency, and applicability by coupling models and methods on different scales. This field benefits many areas of research and applications by providing fundamental understanding and predictions. It could also play a particular role in commercialization by guiding new developments and by allowing quick evaluation of prospective research projects. We employ molecular theory of solvation which allows us to accurately introduce the effect of the environment on complex nano-, macro-, and biomolecular systems. The uniqueness of this method is that it can be naturally coupled with the whole range of computational chemistry approaches, including QM, MM, and coarse graining.

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

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

2015-04-01

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

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

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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.

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

International Nuclear Information System (INIS)

2011-01-01

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

Interaction of silicene with amino acid analogues—from physical to chemical adsorption in gas and solvated phases

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Jagvaral, Yesukhei; He, Haiying; Pandey, Ravindra

2018-01-01

Silicene is an emerging 2D material, and an understanding of its interaction with amino acids, the basic building blocks of protein, is of fundamental importance. In this paper, we investigate the nature of adsorption of amino-acid analogues on silicene employing density functional theory and an implicit solvation model. Amino acid analogues are defined as CH3-R molecules, where R is the functional group of the amino acid side chain. The calculated results find three distinct groups within the amino-acid analogues considered: (i) group I, which includes MeCH3 and MeSH, interacts with silicene via the van der Waals dispersive terms leading to physisorbed configurations; (ii) group II strongly interacts with silicene forming Si-O/N chemical bonds in the chemisorbed configurations; and (iii) group III, which consists of the phenyl group, interacts with silicene via π-π interactions leading to physisorbed configurations. The results show that the lateral chains of the amino acids intrinsically determine the interactions between protein and silicene at the interface under the given physiological conditions.

Solvating additives drive solution-mediated electrochemistry and enhance toroid growth in non-aqueous Li-O2 batteries

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Aetukuri, Nagaphani B.; McCloskey, Bryan D.; García, Jeannette M.; Krupp, Leslie E.; Viswanathan, Venkatasubramanian; Luntz, Alan C.

2015-01-01

Given their high theoretical specific energy, lithium-oxygen batteries have received enormous attention as possible alternatives to current state-of-the-art rechargeable Li-ion batteries. However, the maximum discharge capacity in non-aqueous lithium-oxygen batteries is limited to a small fraction of its theoretical value due to the build-up of insulating lithium peroxide (Li2O2), the battery’s primary discharge product. The discharge capacity can be increased if Li2O2 forms as large toroidal particles rather than as a thin conformal layer. Here, we show that trace amounts of electrolyte additives, such as H2O, enhance the formation of Li2O2 toroids and result in significant improvements in capacity. Our experimental observations and a growth model show that the solvating properties of the additives prompt a solution-based mechanism that is responsible for the growth of Li2O2 toroids. We present a general formalism describing an additive’s tendency to trigger the solution process, providing a rational design route for electrolytes that afford larger lithium-oxygen battery capacities.

Characterizing the selectivity of stationary phases and organic modifiers in reversed-phase high-performance liquid chromatographic systems by a general solvation equation using gradient elution.

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Du, C M; Valko, K; Bevan, C; Reynolds, D; Abraham, M H

2000-11-01

Retention data for a set of 69 compounds using rapid gradient elution are obtained on a wide range of reversed-phase stationary phases and organic modifiers. The chromatographic stationary phases studied are Inertsil (IN)-ODS, pentafluorophenyl, fluoro-octyl, n-propylcyano, Polymer (PLRP-S 100), and hexylphenyl. The organic solvent modifiers are 2,2,2-trifluoroethanol (TFE); 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP); isopropanol; methanol (MeOH); acetonitrile (AcN); tetrahydrofuran; 1,4-dioxane; N,N-dimethylformamide; and mixed solvents of dimethylsulfoxide (DMSO) with AcN and DMSO with MeOH (1:1). A total of 25 chromatographic systems are analyzed using a solvation equation. In general, most of the systems give reasonable statistics. The selectivity of the reversed phase-high-performance liquid chromatographic (HPLC) systems with respect to the solute's dipolarity-polarity, hydrogen-bond acidity, and basicity are reflected in correspondingly large coefficients in the solvation equation. We wanted to find the most orthogonal HPLC systems, showing the highest possible selectivity difference in order to derive molecular descriptors using the gradient retention times of a compound. We selected eight chromatographic systems that have a large range of coefficients of interest (s, a, and b) similar to those found in water-solvent partitions used previously to derive molecular descriptors. The systems selected are IN-ODS phases with AcN, MeOH, TFE, and HFIP as mobile phase, PLRP-S 100 phase with AcN, propylcyano phase with AcN and MeOH, and fluorooctyl phase with TFE. Using the retention data obtained for a compound in the selected chromatographic systems, we can estimate the molecular descriptors with the faster and simpler gradient elution method.

Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant.

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Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree

2016-05-19

Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

International Nuclear Information System (INIS)

Sanyal, Tanmoy; Shell, M. Scott

2016-01-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

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Bardhan, Jaydeep P; Jungwirth, Pavel; Makowski, Lee

2012-09-28

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular "linear response" model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

Science.gov (United States)

Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

2012-01-01

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

Solvation consequences of polymer PVP with biological buffers MES, MOPS, and MOPSO in aqueous solutions

International Nuclear Information System (INIS)

Gupta, Bhupender S.; Chen, Bo-Ren; Lee, Ming-Jer

2015-01-01

Highlights: • Densities and viscosities data for aqueous solutions with PVP and/or buffer. • The studied buffers include MES, MOPS, and MOPSO. • DFT was used to estimate the binding energies of the (PVP + buffer) complexes. • The viscosity data were correlated with the Jones–Dole equation. • The investigated buffers behave as Kosmotropies. - Abstract: Densities and viscosities were measured for the aqueous buffer (MES, MOPS, or MOPSO) solutions containing different concentrations of polyvinylpyrrolidone (PVP) (5, 10, 15, 20 and 30) mass% at temperatures from (298.15 to 318.15) K under atmospheric pressure. The DFT calculations were also performed and the binding energies of the possible (PVP + buffer) complexes were obtained. The experimental and computational results reveal the interactions of the PVP with the constituent compounds in the aqueous buffer solutions. Additionally we have explored the solvation behavior of the buffers by measuring the densities and the viscosities data of the aqueous buffer solutions from (0.0 to 1.0) mol · kg"−"1 at temperatures from (298.15 to 318.15) K. The viscosity results were correlated with the Jones–Dole equation. The correlated results confirmed that all the investigated buffers behave as Kosmotropes (structure makers).

Solvation Effect on Complexation of Alkali Metal Cations by a Calix[4]arene Ketone Derivative.

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Požar, Josip; Nikšić-Franjić, Ivana; Cvetnić, Marija; Leko, Katarina; Cindro, Nikola; Pičuljan, Katarina; Borilović, Ivana; Frkanec, Leo; Tomišić, Vladislav

2017-09-14

The medium effect on the complexation of alkali metal cations with a calix[4]arene ketone derivative (L) was systematically examined in methanol, ethanol, N-methylformamide, N,N-dimethylformamide, dimethyl sulfoxide, and acetonitrile. In all solvents the binding of Na + cation by L was rather efficient, whereas the complexation of other alkali metal cations was observed only in methanol and acetonitrile. Complexation reactions were enthalpically controlled, while ligand dissolution was endothermic in all cases. A notable influence of the solvent on NaL + complex stability could be mainly attributed to the differences in complexation entropies. The higher NaL + stability in comparison to complexes with other alkali metal cations in acetonitrile was predominantly due to a more favorable complexation enthalpy. The 1 H NMR investigations revealed a relatively low affinity of the calixarene sodium complex for inclusion of the solvent molecule in the calixarene hydrophobic cavity, with the exception of acetonitrile. Differences in complex stabilities in the explored solvents, apart from N,N-dimethylformamide and acetonitrile, could be mostly explained by taking into account solely the cation and complex solvation. A considerable solvent effect on the complexation equilibria was proven to be due to an interesting interplay between the transfer enthalpies and entropies of the reactants and the complexes formed.

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

International Nuclear Information System (INIS)

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

2015-01-01

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

Characterizing the Solvated Structure of Photoexcited [Os(terpy2]2+ with X-ray Transient Absorption Spectroscopy and DFT Calculations

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Xiaoyi Zhang

2016-02-01

Full Text Available Characterizing the geometric and electronic structures of individual photoexcited dye molecules in solution is an important step towards understanding the interfacial properties of photo-active electrodes. The broad family of “red sensitizers” based on osmium(II polypyridyl compounds often undergoes small photo-induced structural changes which are challenging to characterize. In this work, X-ray transient absorption spectroscopy with picosecond temporal resolution is employed to determine the geometric and electronic structures of the photoexcited triplet state of [Os(terpy2]2+ (terpy: 2,2′:6′,2″-terpyridine solvated in methanol. From the EXAFS analysis, the structural changes can be characterized by a slight overall expansion of the first coordination shell [OsN6]. DFT calculations supports the XTA results. They also provide additional information about the nature of the molecular orbitals that contribute to the optical spectrum (with TD-DFT and the near-edge region of the X-ray spectra.

Looking for the best experimental conditions to detail the protein solvation shell in a binary aqueous solvent via small angle scattering

International Nuclear Information System (INIS)

Ortore, Maria Grazia; Sinibaldi, Raffaele; Spinozzi, Francesco; Carbini, Andrea; Carsughi, Flavio; Mariani, Paolo

2009-01-01

Protein hydration features attract particular interest in different fields, from biology up to physics, crossing chemistry and medicine. Particular attention is devoted to proteins dissolved in binary aqueous mixtures, since the presence of cosolvent can induce modifications in structural and functional properties. We have recently developed a methodology to obtain a quantitative description on protein solvation shell by a set of in-solution small angle scattering experiments, simultaneously analysed by a global-fit approach. In this paper, numerical simulations of small angle scattering curves are presented to figure out the sensitivity of the technique to different experimental conditions. Simulations concern two model proteins of different molecular weights and an unique cosolvent. A reliability test is introduced in order to find the best experimental conditions to be investigated, together with the most suitable scattering probe (neutrons or X-rays).

Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

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Bardhan, Jaydeep P; Knepley, Matthew G

2011-09-28

We analyze the mathematically rigorous BIBEE (boundary-integral based electrostatics estimation) approximation of the mixed-dielectric continuum model of molecular electrostatics, using the analytically solvable case of a spherical solute containing an arbitrary charge distribution. Our analysis, which builds on Kirkwood's solution using spherical harmonics, clarifies important aspects of the approximation and its relationship to generalized Born models. First, our results suggest a new perspective for analyzing fast electrostatic models: the separation of variables between material properties (the dielectric constants) and geometry (the solute dielectric boundary and charge distribution). Second, we find that the eigenfunctions of the reaction-potential operator are exactly preserved in the BIBEE model for the sphere, which supports the use of this approximation for analyzing charge-charge interactions in molecular binding. Third, a comparison of BIBEE to the recent GBε theory suggests a modified BIBEE model capable of predicting electrostatic solvation free energies to within 4% of a full numerical Poisson calculation. This modified model leads to a projection-framework understanding of BIBEE and suggests opportunities for future improvements. © 2011 American Institute of Physics

Solvation structure determination of nickel(II) ion in six nitriles using extended X-ray absorption fine structure spectroscopy

International Nuclear Information System (INIS)

Inada, Yasuhiro; Funahashi, Shigenobu

1997-01-01

The solvation structures of the nickel(II) ion in six nitriles have been determined using X-ray absorption fine structure spectroscopy. The coordination number and the Ni-N bond length are 6 and 206.9 ± 0.6 pm in acetonitrile, 5.9 ± 0.2 and 206.9 ± 0.6 pm in propionitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in butyronitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in isobutyronitrile, 6.0 ± 0.2 and 206.8 ± 0.6 pm in valeronitrile, and 6.0 ± 0.2 and 206.5 ± 0.7 pm in benzonitrile, respectively. The structure parameters around the nickel(II) ion in all the nitriles are not affected by the bulkiness of the nitrile molecules. On the basis of the obtained structure parameters, we have discussed the structural characteristics around the nickel(II) ion with nitrogen and oxygen donor solvents and the reaction mechanisms for nitrile exchange on the nickel(II) ion. (author)

Binuclear Copper(I Borohydride Complex Containing Bridging Bis(diphenylphosphino Methane Ligands: Polymorphic Structures of [(µ2-dppm2Cu2(η2-BH42] Dichloromethane Solvate

Directory of Open Access Journals (Sweden)

Natalia V. Belkova

2017-10-01

Full Text Available Bis(diphenylphosphinomethane copper(I tetrahydroborate was synthesized by ligands exchange in bis(triphenylphosphine copper(I tetrahydroborate, and characterized by XRD, FTIR, NMR spectroscopy. According to XRD the title compound has dimeric structure, [(μ2-dppm2Cu2(η2-BH42], and crystallizes as CH2Cl2 solvate in two polymorphic forms (orthorhombic, 1, and monoclinic, 2 The details of molecular geometry and the crystal-packing pattern in polymorphs were studied. The rare Twisted Boat-Boat conformation of the core Cu2P4C2 cycle in 1 is found being more stable than Boat-Boat conformation in 2.

Synthesis and Utilization of Trialkylammonium-Substituted Cyclodextrins as Water-Soluble Chiral NMR Solvating Agents for Anionic Compounds.

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Dowey, Alison E; Puentes, Cira Mollings; Carey-Hatch, Mira; Sandridge, Keyana L; Krishna, Nikhil B; Wenzel, Thomas J

2016-04-01

Cationic trialkylammonium-substituted α-, β-, and γ-cyclodextrins containing trimethyl-, triethyl-, and tri-n-propylammonium substituent groups were synthesized and analyzed for utility as water-soluble chiral nuclear magnetic resonance (NMR) solvating agents. Racemic and enantiomerically pure (3-chloro-2-hydroxypropyl)trimethyl-, triethyl-, and tri-n-propyl ammonium chloride were synthesized from the corresponding trialkyl amine hydrochloride and either racemic or enantiomerically pure epichlorohydrin. The ammonium salts were then reacted with α-, β-, and γ-cyclodextrins at basic pH to provide the corresponding randomly substituted cationic cyclodextrins. The (1) H NMR spectra of a range of anionic, aromatic compounds was recorded with the cationic cyclodextrins. Cyclodextrins with a single stereochemistry at the hydroxy group on the (2-hydroxypropyl)trialkylammonium chloride substituent were often but not always more effective than the corresponding cyclodextrin in which the C-2 position was racemic. In several cases, the larger triethyl or tri-n-propyl derivatives were more effective than the corresponding trimethyl derivative at causing enantiomeric differentiation. None of the cyclodextrin derivatives were consistently the most effective for all of the anionic compounds studied. © 2016 Wiley Periodicals, Inc.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model

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Diaz-Rodriguez, Sebastian; Bozada, Samantha M.; Phifer, Jeremy R.; Paluch, Andrew S.

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of 2.2± 0.2 log units (ranking 15 out of 62 entries), the correlation coefficient ( R) was 0.6± 0.1 (ranking 35), and 72± 6 % of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Boundary layer friction of solvate ionic liquids as a function of potential.

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Li, Hua; Rutland, Mark W; Watanabe, Masayoshi; Atkin, Rob

2017-07-01

Atomic force microscopy (AFM) has been used to investigate the potential dependent boundary layer friction at solvate ionic liquid (SIL)-highly ordered pyrolytic graphite (HOPG) and SIL-Au(111) interfaces. Friction trace and retrace loops of lithium tetraglyme bis(trifluoromethylsulfonyl)amide (Li(G4) TFSI) at HOPG present clearer stick-slip events at negative potentials than at positive potentials, indicating that a Li + cation layer adsorbed to the HOPG lattice at negative potentials which enhances stick-slip events. The boundary layer friction data for Li(G4) TFSI shows that at HOPG, friction forces at all potentials are low. The TFSI - anion rich boundary layer at positive potentials is more lubricating than the Li + cation rich boundary layer at negative potentials. These results suggest that boundary layers at all potentials are smooth and energy is predominantly dissipated via stick-slip events. In contrast, friction at Au(111) for Li(G4) TFSI is significantly higher at positive potentials than at negative potentials, which is comparable to that at HOPG at the same potential. The similarity of boundary layer friction at negatively charged HOPG and Au(111) surfaces indicates that the boundary layer compositions are similar and rich in Li + cations for both surfaces at negative potentials. However, at Au(111), the TFSI - rich boundary layer is less lubricating than the Li + rich boundary layer, which implies that anion reorientations rather than stick-slip events are the predominant energy dissipation pathways. This is confirmed by the boundary friction of Li(G4) NO 3 at Au(111), which shows similar friction to Li(G4) TFSI at negative potentials due to the same cation rich boundary layer composition, but even higher friction at positive potentials, due to higher energy dissipation in the NO 3 - rich boundary layer.

Reduction of uranium(IV) and its mixtures with an olefin or an alkyne in tetrahydrofuran solutions by solvated electrons

International Nuclear Information System (INIS)

Koulkes-Pujo, A.M.; Le Marechal, J.F.; Le Motais, B.; Folcher, G.

1985-01-01

The reduction of UCl 4 and its mixtures with different olefins (stilbene, St, diphenylethylene, DPE, acenaphtylene, Ac or with diphenylacetylene (DPA) was studied by pulse radiolysis of tetrahydrofuran (THF) solutions. U(III) was formed by U(IV) reaction either with the solvated electrons created by THF radiolysis or with the transitory anions St - and DPA - . In the latter case, the reaction proceeds via a first step leading to [St-U(IV)] - or [DPA-U(IV)] - . In the case of DPE - the first species, [DPE-U(IV)] - , does not lead to U(III) but is destroyed by THF(H) + giving DPE(H). and U(IV). Ac - does not react with U(IV). A mechanistic scheme of this electron attachment is discussed as well as its implication in catalytic hydrogenation of olefins in LiAlH 4 -UCl 4 solutions. It is concluded that the catalytic effect observed is rather the result of a hydride transfer from a uranium transient compound to the alkenes. 22 references, 8 figures, 1 table

Linear solvation energy relationships (LSER): 'rules of thumb' for Vi/100, π*, Βm, and αm estimation and use in aquatic toxicology

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Hickey, James P.

1996-01-01

This chapter provides a listing of the increasing variety of organic moieties and heteroatom group for which Linear Solvation Energy Relationship (LSER) values are available, and the LSER variable estimation rules. The listings include values for typical nitrogen-, sulfur- and phosphorus-containing moieties, and general organosilicon and organotin groups. The contributions by an ion pair situation to the LSER values are also offered in Table 1, allowing estimation of parameters for salts and zwitterions. The guidelines permit quick estimation of values for the four primary LSER variables Vi/100, π*, Βm, and αm by summing the contribtuions from its components. The use of guidelines and Table 1 significantly simplifies computation of values for the LSER variables for most possible organic comppounds in the environment, including the larger compounds of environmental and biological interest.

Application of a room temperature ionic liquid for nuclear spent fuel reprocessing: speciation of trivalent europium and solvatation effects; Application d'un liquide ionique basse temperature pour les procedes de separation: speciation de l'europium trivalent et effets solvatation

Energy Technology Data Exchange (ETDEWEB)

Moutiers, G.; Mekki, S. [CEA Saclay, Dept. de Physico-Chimie, Service de Chimie Physique, 91 - Gif sur Yvette (France); Billard, I. [IN2P3/CNRS, 69 - Villeurbanne (France)

2007-07-01

the electrochemical study. In the second chapter, we present the study of europium solvation in the ionic liquid media. In the third part, we expose the results concerning TTA solvation and its complexation with europium in bumimTf{sub 2}N under different conditions. Finally in the last chapter, we present the results obtained for the europium extraction in a three-stage extraction system: water/bumimTf{sub 2}N/supercritical CO{sub 2}. This work highlights the potential use of ionic liquids and particularly bumimTf{sub 2}N in the spent nuclear fuel reprocessing. The ability to extract quantitatively a trivalent lanthanide has been demonstrated. This fundamental study can be regarded as a feasibility demonstration to build an ionic liquid-containing extraction system, in the aim of possible large-scale application. (authors)

Application of a room temperature ionic liquid for nuclear spent fuel reprocessing: speciation of trivalent europium and solvatation effects

International Nuclear Information System (INIS)

Moutiers, G.; Mekki, S.; Billard, I.

2007-01-01

study. In the second chapter, we present the study of europium solvation in the ionic liquid media. In the third part, we expose the results concerning TTA solvation and its complexation with europium in bumimTf 2 N under different conditions. Finally in the last chapter, we present the results obtained for the europium extraction in a three-stage extraction system: water/bumimTf 2 N/supercritical CO 2 . This work highlights the potential use of ionic liquids and particularly bumimTf 2 N in the spent nuclear fuel reprocessing. The ability to extract quantitatively a trivalent lanthanide has been demonstrated. This fundamental study can be regarded as a feasibility demonstration to build an ionic liquid-containing extraction system, in the aim of possible large-scale application. (authors)

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.

Dynamics of electron solvation in I-(CH3OH)n clusters (4 ≤n≤ 11)

International Nuclear Information System (INIS)

Young, Ryan M.; Yandell, Margaret A.; Neumark, Daniel M.

2011-01-01

The dynamics of electron solvation following excitation of the charge-transfer-to-solvent precursor state in iodide-doped methanol clusters, I - (CH 3 OH) n=4-11 , are studied with time-resolved photoelectron imaging. This excitation produces a I ... (CH 3 OH) n - cluster that is unstable with respect to electron autodetachment and whose autodetachment lifetime increases monotonically from ∼800 fs to 85 ps as n increases from 4 to 11. The vertical detachment energy (VDE) and width of the excited state feature in the photoelectron spectrum show complex time dependence during the lifetime of this state. The VDE decreases over the first 100-400 fs, then rises exponentially to a maximum with a ∼1 ps time constant, and finally decreases by as much as 180 meV with timescales of 3-20 ps. The early dynamics are associated with electron transfer from the iodide to the methanol cluster, while the longer-time changes in VDE are attributed to solvent reordering, possibly in conjunction with ejection of neutral iodine from the cluster. Changes in the observed width of the spectrum largely follow those of the VDEs; the dynamics of both are attributed to the major rearrangement of the solvent cluster during relaxation. The relaxation dynamics are interpreted as a reorientation of at least one methanol molecule and the disruption and formation of the solvent network in order to accommodate the excess charge.

Building solids inside nano-space: from confined amorphous through confined solvate to confined 'metastable' polymorph.

Science.gov (United States)

Nartowski, K P; Tedder, J; Braun, D E; Fábián, L; Khimyak, Y Z

2015-10-14

The nanocrystallisation of complex molecules inside mesoporous hosts and control over the resulting structure is a significant challenge. To date the largest organic molecule crystallised inside the nano-pores is a known pharmaceutical intermediate - ROY (259.3 g mol(-1)). In this work we demonstrate smart manipulation of the phase of a larger confined pharmaceutical - indomethacin (IMC, 357.8 g mol(-1)), a substance with known conformational flexibility and complex polymorphic behaviour. We show the detailed structural analysis and the control of solid state transformations of encapsulated molecules inside the pores of mesoscopic cellular foam (MCF, pore size ca. 29 nm) and controlled pore glass (CPG, pore size ca. 55 nm). Starting from confined amorphous IMC we drive crystallisation into a confined methanol solvate, which upon vacuum drying leads to the stabilised rare form V of IMC inside the MCF host. In contrast to the pure form, encapsulated form V does not transform into a more stable polymorph upon heating. The size of the constraining pores and the drug concentration within the pores determine whether the amorphous state of the drug is stabilised or it recrystallises into confined nanocrystals. The work presents, in a critical manner, an application of complementary techniques (DSC, PXRD, solid-state NMR, N2 adsorption) to confirm unambiguously the phase transitions under confinement and offers a comprehensive strategy towards the formation and control of nano-crystalline encapsulated organic solids.

Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

Energy Technology Data Exchange (ETDEWEB)

Machesky, Michael L. [Illinois State Water Survey, Champaign, IL; Predota, M. [University of South Bohemia, Czech Republic; Wesolowski, David J [ORNL

2008-01-01

The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic

Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

International Nuclear Information System (INIS)

Machesky, Michael L.; Predota, M.; Wesolowski, David J.

2008-01-01

The detailed solvation structure at the (110) surface of rutile (α-TiO 2 ) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 (angstrom) of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 ± 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH znpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH znpc value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 ± 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H

1,1,3,3-Tetramethylguanidine solvated lanthanide aryloxides: pre-catalysts for intramolecular hydroalkoxylation.

Science.gov (United States)

Janini, Thomas E; Rakosi, Robert; Durr, Christopher B; Bertke, Jeffrey A; Bunge, Scott D

2009-12-21

The synthesis and structural characterization of six 1,1,3,3-tetramethylguanidine (H-TMG) solvated lanthanide aryloxide complexes are reported. Ln[N{Si(CH3)3}2]3 (Ln = Nd, La) was reacted with two equivalents of both H-TMG and HOAr {HOAr = HOC6H2(CMe3)2-2,6 (H-DBP) or HOC6H2(CMe3)2-2,6-CH3-4 (H-4MeDBP)} and one equivelent of ethanol (HOEt) to yield the corresponding [Nd(H-TMG)2(4MeDBP)2(OEt)] (1) and [La(H-TMG)2(DBP)2(OEt)] (2). Compounds 1 and 2 were further reacted with 4-pentyn-1-ol {HO(CH2)3C[triple bond]CH} to isolate [Nd(H-TMG)2(4MeDBP)2{O(CH2)3C[triple bond]CH}] (3) and [La(H-TMG)2(DBP)2{O(CH2)3C[triple bond]CH}] (4), respectively. Three equivalents of HOAr and one equivalent of H-TMG were additionally reacted with Ln[N{Si(CH3)3}2]3 to generate [Nd(4MeDBP)3(H-TMG)] (5) and [La(DBP)3(H-TMG)] (6). In order to examine the formation of 1-6, the interaction of H-TMG and HOAr was further examined in solution and the hydrogen bonded complexes (H-TMG:HOAr), 7 and 8, were isolated. Upon successful isolation of 1-6, the utility of 1, 2, 4 and 5 as pre-catalysts for the intramolecular hydroalkoxylation of 4-pentyn-1-ol was investigated. The bulk powders for all complexes were found to be in agreement with the crystal structures based on elemental analyses, FT-IR spectroscopy, and 1H and 13C NMR investigations.

Li+ solvation and kinetics of Li+-BF4-/PF6- ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

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Chang, Tsun-Mei; Dang, Liem X.

2017-10-01

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux, Impey, Madden, and McDonald approaches, and Grote-Hynes theory. We found that the residence times of EC around Li+ ions varied from 60 to 450 ps, depending on the correction method used. We found that the relaxation times changed significantly from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influences the dissociation kinetics of ion pairing.

Bis(1,3-dimethyl-1H-imidazolium hexafluorosilicate methanol 0.33-solvate

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Maxim V. Borzov

2013-08-01

Full Text Available The title compound, 6C5H9N2+·3SiF62−·CH3OH, (I, was prepared by recrystallization of the crude salt from methanol along with solvent-free 2C5H9N2+·SiF62− (II. Crystals of these solvatomorphs can be separated manually. The solvate (I crystallizes in a rare hexagonal space group P6/mcc. Its asymmetric unit comprises one half of an imidazolium cation bisected by the crystallographic m-plane, one-sixth and one-twelfth of two crystallographically independent SiF62– dianions (Si atoms are located on the 3.2 and 6/m inversion centres, and one-twelfth of a methanol molecule (C atoms are situated on the 622 inversion centres, other atoms are disordered between general positions. In (I, all F atoms of 3.2-located SiF62– dianions participate in the formation of symmetry-equivalent contacts to the H atoms of imidazolium fragments, thus forming rod-type ensembles positioned on the -6 axes. These `pillar' rods are, in turn, F...H interlinked through SiF62– dianions disordered around the 6/m centres. The twelvefold disordered methanol molecules are appended to this array by O—H...F hydrogen bonds to the 6/m located SiF62– dianions. In terms of graph-set notation, the first and second level networks in (I are N1 = C22(7[3R44(14]D22(4 and N2 = D22(5 (C—H...O hydrogen bonds are not considered. After locating all symmetrically independent atoms in the cation and anions, there remained a strong (> 3 e Å−3 residual electron density peak located at the 622 inversion centre. Treatment of this pre-refined model with the SQUEEZE procedure in PLATON [Spek (2009. Acta Cryst. D65, 148–155] revealed two voids per unit cell, indicative of the presence of the solvent methanol molecule disordered about the 622 inversion centre.

Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

Science.gov (United States)

Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

2015-12-28

Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

Detection of Intramolecular Charge Transfer and Dynamic Solvation in Eosin B by Femtosecond Two-Dimensional Electronic Spectroscopy

Science.gov (United States)

Ghosh, Soumen; Roscioli, Jerome D.; Beck, Warren F.

2014-06-01

We have employed 2D electronic photon echo spectroscopy to study intramolecular charge-transfer dynamics in eosin B. After preparation of the first excited singlet state (S_1) with 40-fs excitation pulses at 520 nm, the nitro group (--NO_2) in eosin B undergoes excited state torsional motion towards a twisted intramolecular charge transfer (TICT) state. As the viscosity of the surrounding solvent increases, the charge-transfer rate decreases because the twisting of the --NO_2 group is hindered. These conclusions are supported by the time evolution of the 2D spectrum, which provides a direct measure of the the ground-to-excited-state energy gap time-correlation function, M(t). In comparison to the inertial and diffusive solvation time scales exhibited by eosin Y, which lacks the nitro group, the M(t) function for eosin B exhibits under the same conditions an additional component on the 150-fs timescale that arises from quenching of the S_1 state by crossing to the TICT state. These results indicate that 2D electronic spectroscopy can be used as a sensitive probe of the rate of charge transfer in a molecular system and of the coupling to the motions of the surrounding solvent. (Supported by grant DE-SC0010847 from the Department of Energy, Office of Basic Energy Sciences, Photosynthetic Systems program.)

Dynamics of electron solvation in I(-)(CH3OH)n clusters (4 ≤ n ≤ 11).

Science.gov (United States)

Young, Ryan M; Yandell, Margaret A; Neumark, Daniel M

2011-03-28

The dynamics of electron solvation following excitation of the charge-transfer-to-solvent precursor state in iodide-doped methanol clusters, I(-)(CH(3)OH)(n = 4-11), are studied with time-resolved photoelectron imaging. This excitation produces a I···(CH(3)OH)(n)(-) cluster that is unstable with respect to electron autodetachment and whose autodetachment lifetime increases monotonically from ~800 fs to 85 ps as n increases from 4 to 11. The vertical detachment energy (VDE) and width of the excited state feature in the photoelectron spectrum show complex time dependence during the lifetime of this state. The VDE decreases over the first 100-400 fs, then rises exponentially to a maximum with a ~1 ps time constant, and finally decreases by as much as 180 meV with timescales of 3-20 ps. The early dynamics are associated with electron transfer from the iodide to the methanol cluster, while the longer-time changes in VDE are attributed to solvent reordering, possibly in conjunction with ejection of neutral iodine from the cluster. Changes in the observed width of the spectrum largely follow those of the VDEs; the dynamics of both are attributed to the major rearrangement of the solvent cluster during relaxation. The relaxation dynamics are interpreted as a reorientation of at least one methanol molecule and the disruption and formation of the solvent network in order to accommodate the excess charge.

Structural and computational study of 1,2,4-triazolin-5-thione derivative and its DMSO solvate

Science.gov (United States)

Dybała, Izabela; Wawrzycka-Gorczyca, Irena; Struga, Marta

2017-11-01

The solid state structure of 3-(4-phenyl-5-oxo-1,2,4-triazolin-1-ylmethyl)-4-cyclohexyl-1,2,4-triazolin-5-thione (1) was characterized by FT-IR and X-ray diffraction experiment. Additionally, molecular and crystal structure of its DMSO solvate (1DMSO) has been determined by X-ray diffraction method. The influence of DMSO molecules incorporation to the crystal lattice on geometry of triazolin-5-thione derivative molecule and crystal packing was analyzed. Non-covalent bonds within the crystals are additionally visualized by determination of Hirshfeld surfaces. According to results of conformational analysis in gas, molecule of triazolin-5-thione derivative adopts the lowest energy conformation in 1DMSO crystal. The crystal structure of 1 and 1DMSO were compared with previously described structurally similar compounds, in which the cyclohexyl substituent was replaced by aromatic one (phenyl/methoxyphenyl). Very interesting differences in molecules association were found by comparing the crystal structures of 1 and 1DMSO with their, mentioned above, aromatic derivatives. Interesting properties of triazolin-5-thione derivatives are connected with their π-electron delocalization effects, thus aromaticity of heterocyclic fragments has been investigated by means of the HOMA index. Comparison of aromaticity calculations results with association tendency of molecules shows that triazolin-5-one fragments reach higher aromaticity when nitrogen atom from this moiety acts as a donor in strong Nsbnd H⋯N hydrogen bonds.

Structure of Pigment Yellow 181 dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate from XRPD + DFT-D

International Nuclear Information System (INIS)

Streek, Jacco van de

2015-01-01

The relatively complex structure of a triclinic disolvate was solved from low-resolution laboratory powder diffraction data through the intermediate use of dummy atoms and the combination with quantum-mechanical calculations. With only a 2.6 Å resolution laboratory powder diffraction pattern of the θ phase of Pigment Yellow 181 (P.Y. 181) available, crystal-structure solution and Rietveld refinement proved challenging; especially when the crystal structure was shown to be a triclinic dimethylsulfoxide N-methyl-2-pyrrolidone (1:1:1) solvate. The crystal structure, which in principle has 28 possible degrees of freedom, was determined in three stages by a combination of simulated annealing, partial Rietveld refinement with dummy atoms replacing the solvent molecules and further simulated annealing. The θ phase not being of commercial interest, additional experiments were not economically feasible and additional dispersion-corrected density functional theory (DFT-D) calculations were employed to confirm the correctness of the crystal structure. After the correctness of the structure had been ascertained, the bond lengths and valence angles from the DFT-D minimized crystal structure were fed back into the Rietveld refinement as geometrical restraints (‘polymorph-dependent restraints’) to further improve the details of the crystal structure; the positions of the H atoms were also taken from the DFT-D calculations. The final crystal structure is a layered structure with an elaborate network of hydrogen bonds

Relation between the interfacial tension in an organic solvent-water system and the parameters of the solvating capacity of the solvent

International Nuclear Information System (INIS)

Nikitin, S.D.; Shmidt, V.S.

1987-01-01

It was shown that there is a linear relation between the empirical DE (diluent effect) and E/sub T/ parameters, which characterize the solvating capacity of the solvent, and the interfacial tension in an organic solvent-water two-phase system. Analysis of the sample correlation coefficients shows that the relation between the interfacial tension and the DE parameters of the solvents is closer to linear than the corresponding relation for the E/sub T/ parameters. During analysis of the data for 31 solvents it was established that the largest inverse correlation coefficient r = -0.98 is obtained with an equation of the DE = a + bσ/rho 1/3, type, were a and b are constants, and rho is the density of the solvent. The regression equation has the following form: DE = 7.586 - 0.147 σ/rho 1/3. Since the interfacial activity of hydrophobic surfactants decreases linearly with increase in the DE values, it follows from the obtained equation that decrease of the interfacial tension at the water-organic solvent interface must lead to a decrease in the interfacial activity of hydrophobic surfactants present in the system

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

Science.gov (United States)

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

2015-01-01

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

IR + VUV double resonance spectroscopy and extended density functional theory studies of ketone solvation by alcohol: 2-butanone·(methanol)n, n = 1-4 clusters.

Science.gov (United States)

Shin, Joong-Won; Bernstein, Elliot R

2017-09-28

Infrared plus vacuum ultraviolet (IR + VUV) photoionization vibrational spectroscopy of 2-butanone/methanol clusters [MEK·(MeOH) n , n = 1-4] is performed to explore structures associated with hydrogen bonding of MeOH molecules to the carbonyl functional group of the ketone. IR spectra and X3LYP/6-31++G(d,p) calculations show that multiple isomers of MEK·(MeOH) n are generated in the molecular beam as a result of several hydrogen bonding sites available to the clusters throughout the size range investigated. Isomer interconversion involving solvating MeOH rearrangement should probably occur for n = 1 and 2. The mode energy for a hydrogen bonded OH stretching transition gradually redshifts as the cluster size increases. Calculations suggest that the n = 3 cluster isomers adopt structures in which the MEK molecule is inserted into the cyclic MeOH hydrogen bond network. In larger structures, the cyclic network may be preserved.

The dynamics of Ca2+ ions within the solvation shell of calbindin D9k.

Directory of Open Access Journals (Sweden)

Elad Project

Full Text Available The encounter of a Ca(2+ ion with a protein and its subsequent binding to specific binding sites is an intricate process that cannot be fully elucidated from experimental observations. We have applied Molecular Dynamics to study this process with atomistic details, using Calbindin D9k (CaB as a model protein. The simulations show that in most of the time the Ca(2+ ion spends within the Debye radius of CaB, it is being detained at the 1st and 2nd solvation shells. While being detained near the protein, the diffusion coefficient of the ion is significantly reduced. However, due to the relatively long period of detainment, the ion can scan an appreciable surface of the protein. The enhanced propagation of the ion on the surface has a functional role: significantly increasing the ability of the ion to scan the protein's surface before being dispersed to the bulk. The contribution of this mechanism to Ca(2+ binding becomes significant at low ion concentrations, where the intervals between successive encounters with the protein are getting longer. The efficiency of the surface diffusion is affected by the distribution of charges on the protein's surface. Comparison of the Ca(2+ binding dynamics in CaB and its E60D mutant reveals that in the wild type (WT protein the carboxylate of E60 function as a preferred landing-site for the Ca(2+ arriving from the bulk, followed by delivering it to the final binding site. Replacement of the glutamate by aspartate significantly reduced the ability to transfer Ca(2+ ions from D60 to the final binding site, explaining the observed decrement in the affinity of the mutated protein to Ca(2+.

Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation.

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Michael M H Graf

2014-12-01

Full Text Available The flavoenzyme pyranose dehydrogenase (PDH from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation. This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications. A generalized approach to simulate all 32 possible aldohexopyranoses in the course of one or a few molecular dynamics (MD simulations is reported. Free energy calculations according to the one-step perturbation (OSP method revealed the solvation free energies (ΔGsolv of all 32 aldohexopyranoses in water, which have not yet been reported in the literature. The free energy difference between β- and α-anomers (ΔGβ-α of all d-stereoisomers in water were compared to experimental values with a good agreement. Moreover, the free-energy differences (ΔG of the 32 stereoisomers bound to PDH in two different poses were calculated from MD simulations. The relative binding free energies (ΔΔGbind were calculated and, where available, compared to experimental values, approximated from Km values. The agreement was very good for one of the poses, in which the sugars are positioned in the active site for oxidation at C1 or C2. Distance analysis between hydrogens of the monosaccharide and the reactive N5-atom of the flavin adenine dinucleotide (FAD revealed that oxidation is possible at HC1 or HC2 for pose A, and at HC3 or HC4 for pose B. Experimentally detected oxidation products could be rationalized for the majority of monosaccharides by combining ΔΔGbind and a reweighted distance analysis. Furthermore, several oxidation products were predicted for sugars that have not yet been tested experimentally, directing further analyses. This study rationalizes the relationship between binding free energies and substrate promiscuity in PDH, providing novel insights for its applicability in bioelectrochemistry. The results suggest that a similar approach could be applied to study

α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration.

Science.gov (United States)

Sirotkin, Vladimir A; Kuchierskaya, Alexandra A

2017-10-01

We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems. © 2017 Wiley Periodicals, Inc.

Fragmentation study of isolated and nano-solvated biomolecules induced by collision with multiply charged ions and neutral particles

International Nuclear Information System (INIS)

Bernigaud, V.

2009-01-01

This thesis concerns a gas phase study of the fragmentation of bio-molecular systems induced by slow collisions with multiply charged ions (in the keV-region), alkali atoms and rare gases. The main objective was to study the physical processes involved in the dissociation of highly electronically excited systems. In order to elucidate the intrinsic properties of certain biomolecules (porphyrins and amino acids) we have performed experiments in the gas phase with isolated systems. The obtained results demonstrate the high stability of porphyrins after electron removal and attachment. Furthermore, a dependence of the fragmentation pattern produced by multiply charged ions on the isomeric structure of the alanine molecule has been shown. In a second part of the thesis, a strong influence of the environment of the biomolecule on the fragmentation channels, their modification and their new opening, has been clearly proven. This phenomenon occurs in the presence of other surrounding biomolecules (clusters of nucleobases) as well as for molecules of a solvent (molecules of water, methanol and acetonitrile) in which the biomolecule is embedded. In order to extend these studies to larger systems, a new experimental set-up, based on an electro-spray ion source combined with a quadrupole mass filter has been developed. Due to the successful tests and proposed improvements of the device future experiments will become available concerning the fragmentation of large charged and solvated bio-molecular systems induced by collision processes. (author) [fr

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.

Temperature and isotope effects on the shape of the optical absorption spectrum of solvated electrons in water

International Nuclear Information System (INIS)

Jou, F.Y.; Freeman, G.R.

1979-01-01

The optical absorption spectra of solvated electrons in H 2 O and D 2 O have been measured at 274, 298, 340, and 380 K. All the spectra were fitted very well with the Gaussian and Lorentzian shape functions at the low- and high-energy sides of the absorption maximum, respectively, excluding the high-energy tail. The spectrum does not shift uniformly with temperature. The temperature coefficient of absorption decreases rapidly with increasing energy on the low-energy side of the absorption maximum, while it changes only slightly on the high-energy side. When the temperature increases the Lorentzian width remains constant, the Gaussian width varies proportionally to T/sup 1/2/, and the spectrum becomes more symmetrical. On going from H 2 O to D 2 O we found that the spectrum at a given A/A/sub max/ shows a shift of +0.05 eV in the low-energy wing. The shift decreases with increasing energy, reaching 0.03 eV at the absorption maximum. On the high-energy side of the band the shift becomes negative at hν > 2.2 eV. The shift on the low-energy side seems to be related to the difference of the zero-point energies of the inter- and intramolecular vibrations. The wavelength dependence of the temperature and isotope effects is consistent with the model that different types of excitation occur on the low- and high-energy sides of the absorption band. The temperature and isotopic dependence of the low-energy side are consistent with its width being due to phonon interactions

Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length.

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Reddy, M Rami; Erion, Mark D

2009-12-01

Molecular dynamics (MD) simulations in conjunction with thermodynamic perturbation approach was used to calculate relative solvation free energies of five pairs of small molecules, namely; (1) methanol to ethane, (2) acetone to acetamide, (3) phenol to benzene, (4) 1,1,1 trichloroethane to ethane, and (5) phenylalanine to isoleucine. Two studies were performed to evaluate the dependence of the convergence of these calculations on MD simulation length and starting configuration. In the first study, each transformation started from the same well-equilibrated configuration and the simulation length was varied from 230 to 2,540 ps. The results indicated that for transformations involving small structural changes, a simulation length of 860 ps is sufficient to obtain satisfactory convergence. In contrast, transformations involving relatively large structural changes, such as phenylalanine to isoleucine, require a significantly longer simulation length (>2,540 ps) to obtain satisfactory convergence. In the second study, the transformation was completed starting from three different configurations and using in each case 860 ps of MD simulation. The results from this study suggest that performing one long simulation may be better than averaging results from three different simulations using a shorter simulation length and three different starting configurations.

Radiolysis studies on reactive intermediates

International Nuclear Information System (INIS)

Kevan, L.

1977-11-01

A more quantitative characterization of the structure and reaction mechanism of solvated electrons produced by high energy chemistry was developed. Neutral atoms may undergo solvation in polar media to cause significant geometrical rearrangement. The geometrical arrangement of six OH bond oriented water molecules around a localized electron is the preferred geometry in frozen aqueous systems even at low solute ion concentration. The energy level structure of electrons in polar aqueous and alcoholic glasses was systematized from a comparison of photoconductivity and optical spectra. Experimental and theoretical evidence on electron solvation was evaluated to suggest the dominance of first solvation shell orientation in the solvation process. A laser photolysis study as a function of temperature suggests that electron solvation in ethanol glass occurs by a hindered molecular reorientation mechanism. In mixed polar and nonpolar glassy matrices it was shown that the electron is first solvated in the nonpolar matrix and is later transformed to a more stable species surrounded by the polar molecules. It was found that the spin lattice relaxation of solvated electrons is dominated by a new mechanism characteristic of disordered matrices which involves relaxation by tunneling modes in the matrix. The noninteracting spin packet model of electron spin resonance lines was shown to apply to solvated electrons in deuterated matrices but not in protiated matrices. A new type of recombination fluorescence experiment was devised which allows easy distinction between tunnelling and diffusive recombination mechanisms between solvate electrons and cations. Several theoretical studies have helped to delimit the applicability of an electron tunneling mechanism to solvated electron reactions. Electron spin echospectrometry was used to demonstrate that silver atoms undergo dramatic solvation and desolvation changes in frozen aqueous systems

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

International Nuclear Information System (INIS)

Genova, Alessandro; Pavanello, Michele; Ceresoli, Davide

2016-01-01

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH • radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH • radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

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Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Enhanced free energy of extraction of Eu3+ and Am3+ ions towards diglycolamide appended calix[4]arene: insights from DFT-D3 and COSMO-RS solvation models.

Science.gov (United States)

Ali, Sk Musharaf

2017-08-22

Density functional theory in conjunction with COSMO and COSMO-RS solvation models employing dispersion correction (DFT-D3) has been applied to gain an insight into the complexation of Eu 3+ /Am 3+ with diglycolamide (DGA) and calix[4]arene appended diglycolamide (CAL4DGA) in ionic liquids by studying structures, energetics, thermodynamics and population analysis. The calculated Gibbs free energy for both Eu 3+ and Am 3+ ions with DGA was found to be smaller than that with CAL4DGA. The entropy of complexation was also found to be reduced to a large extent with DGA compared to complexation with CAL4DGA. The solution phase free energy was found to be negative and was higher for Eu 3+ ion. The entropy of complexation was not only found to be further reduced but also became negative in the case of DGA alone. Though the entropy was found to be negative it could not outweigh the high negative enthalpic contribution. The same trend was observed in the solution where the free energy of extraction, ΔG, for Eu 3+ ions was shown to be higher than that for Am 3+ ions towards free DGA. But the values of ΔG and ΔΔG(= ΔG Eu -ΔG Am ) were found to be much higher with CAL4DGA (-12.58 kcal mol -1 ) in the presence of nitrate ions compared to DGA (-1.69 kcal mol -1 ) due to enhanced electronic interaction and positive entropic contribution. Furthermore, both the COSMO and COSMO-RS models predict very close values of ΔΔΔG (= ΔΔG CAL4DGA - ΔΔG nDGA ), indicating that both solvation models could be applied for evaluating the metal ion selectivity. The value of the reaction free energy was found to be higher after dispersion correction. The charge on the Eu and Am atoms for the complexes with DGA and CAL4DGA indicates the charge-dipole type interaction leading to strong binding energy. The present theoretical results support the experimental findings and thus might be of importance in the design of functionalized ligands.

Effects of compatibility of polymer binders with solvate ionic liquid electrolytes on discharge and charge reactions of lithium-sulfur batteries

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Nakazawa, Toshitada; Ikoma, Ai; Kido, Ryosuke; Ueno, Kazuhide; Dokko, Kaoru; Watanabe, Masayoshi

2016-03-01

Electrochemical reactions in Li-S cells with a solvate ionic liquid (SIL) electrolyte composed of tetraglyme (G4) and Li[TFSA] (TFSA: bis(trifluoromethanesulfonyl)amide) are studied. The sulfur cathode (S cathode) comprises sulfur, carbon powder, and a polymer binder. Poly(ethylene oxide) (PEO) and poly(vinyl alcohol) (PVA-x) with different degrees of saponification (x%) are used as binders to prepare the composite cathodes. For the Li-S cell containing PEO binder, lithium polysulfides (Li2Sm, 2 ≤ m ≤ 8), reaction intermediates of the S cathode, dissolve into the electrolyte, and Li2Sm acts as a redox shuttle in the Li-S cell. In contrast, in the Li-S cell with PVA-x binder, the dissolution of Li2Sm is suppressed, leading to high columbic efficiencies during charge-discharge cycles. The compatibility of the PVA-x binder with the SIL electrolyte changes depending on the degree of saponification. Decreasing the degree of saponification leads to increased electrolyte uptake by the PVA-x binder, increasing the charge and discharge capacities of Li-S cell. The rate capability of Li-S cell is also enhanced by the partial swelling of the PVA-x binder. The enhanced performance of Li-S cell containing PVA-x is attributed to the lowering of resistance of Li+ ion transport in the composite cathode.

The scavenging of the precursors of the solvated electrons fom the positron lifetime spectroscopy and the Doppler broadening of annihilation line shape technique

International Nuclear Information System (INIS)

Abbe, J.C.; Duplatre, G.; Maddock, A.G.; Haessler, A.

1979-01-01

The electron scavenging properties in water of two series of solutes are investigated, using the positron as a probe. For a better interpretation of the data, both the lifetime specroscopy and the Doppler broadening of annihilation line shape technique are used. All solutes inhibit the positronium (Ps) formation, by the scavenging of electron. The first series consists of the halate ions, that should follow the Hunt linear relation between the rate constant for reaction with the solvated electrons, ksub(e - sub(aq)+S) and that for its precursors(s), 1/C 37 . The Ps inhibition constants, k, are 0.14, 1.44 and 3.45M -1 for ClO 3 - , BrO 3 - and IO 3 - respectively. This sequence is quantitatively consistent with that of the respective ksub(e - sub(aq)+S). The second series includes the SeO 4 -- , Te(OH) 6 and BrO 4 - species, and the Ps inhibition constants are 5.62, 10.5 and 14.3 respectively. Theses values are much higher than expected from the ksub(e - sub(aq)+S) constants, on basis of the Hunt relation, in agreement with previous results from pulse radiolysis experiments

Crystal structure of 4′-allyl-4,5,6,7,2′,7′-hexachlorofluorescein allyl ester unknown solvate

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Lili Wang

2018-01-01

Full Text Available In the title compound, 4′-allyl-4,5,6,7,2′,7′-hexachlorofluorescein allyl ester {systematic name: prop-2-en-1-yl 2,3,4,5-tetrachloro-6-[2,7-dichloro-6-hydroxy-3-oxo-4-(prop-2-en-1-yl-3H-xanthen-9-yl]benzoate}, C26H14Cl6O5, accompanied by unknown solvate molecules, the dihedral angle between the xanthene ring system (r.m.s. deviation = 0.046 Å and the pentasubstituted benzene ring is 71.67 (9°. Both allyl groups are disordered over two sets of sites in statistical ratios. The scattering contributions of the disordered solvent molecules (both Ph2O and CHCl3, as identified by NMR were removed with the PLATON SQUEEZE algorithm [Spek (2015. Acta Cryst. C71, 9–18]. In the crystal, tetrameric supramolecular aggregates linked by O—H...O hydrogen bonds occur; these further interact with neighboring aggregates through C—Cl...π interactions arising from the benzene rings, forming infinite two-dimensional sheets. Each C6Cl4 ring shifts in the direction perpendicular to the two-dimensional sheet, exhibiting a helical chain in which every C6Cl4 ring is utilized as both a donor and an acceptor of Cl...π contacts. Thus, these two-dimensional sheets pack in a helical fashion, constructing a three-dimensional network.

Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory.

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Marianski, Mateusz; Dannenberg, J J

2012-02-02

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.

Directly relating gas-phase cluster measurements to solution-phase hydrolysis, the absolute standard hydrogen electrode potential, and the absolute proton solvation energy.

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Donald, William A; Leib, Ryan D; O'Brien, Jeremy T; Williams, Evan R

2009-06-08

Solution-phase, half-cell potentials are measured relative to other half-cell potentials, resulting in a thermochemical ladder that is anchored to the standard hydrogen electrode (SHE), which is assigned an arbitrary value of 0 V. A new method for measuring the absolute SHE potential is demonstrated in which gaseous nanodrops containing divalent alkaline-earth or transition-metal ions are reduced by thermally generated electrons. Energies for the reactions 1) M(H(2)O)(24)(2+)(g) + e(-)(g)-->M(H(2)O)(24)(+)(g) and 2) M(H(2)O)(24)(2+)(g) + e(-)(g)-->MOH(H(2)O)(23)(+)(g) + H(g) and the hydrogen atom affinities of MOH(H(2)O)(23)(+)(g) are obtained from the number of water molecules lost through each pathway. From these measurements on clusters containing nine different metal ions and known thermochemical values that include solution hydrolysis energies, an average absolute SHE potential of +4.29 V vs. e(-)(g) (standard deviation of 0.02 V) and a real proton solvation free energy of -265 kcal mol(-1) are obtained. With this method, the absolute SHE potential can be obtained from a one-electron reduction of nanodrops containing divalent ions that are not observed to undergo one-electron reduction in aqueous solution.

Characterization of volatile organic compound adsorption on multiwall carbon nanotubes under different levels of relative humidity using linear solvation energy relationship

International Nuclear Information System (INIS)

Li, Mei-syue; Wu, Siang Chen; Shih, Yang-hsin

2016-01-01

Highlights: • LSER equations successfully predicted VOC sorption on MCNT at different humidity. • The five parameters in LSER could be narrowed down to three ones. • Main interaction is dispersion and partly dipolarity as well as hydrogen-bonds. • With increasing RH, it changes to cavity formation and hydrogen-bond basicity. • This approach can facilitate the VOC control design and the fate prediction. - Abstract: Multiwall carbon nanotubes (MWCNTs) have been used as an adsorbent for evaluating the gas/solid partitioning of selected volatile organic compounds (VOCs). In this study, 15 VOCs were probed to determine their gas/solid partitioning coefficient (Log K d ) using inverse gas chromatography at different relative humidity (RH) levels. Interactions between MWCNTs and VOCs were analyzed by regressing the observed Log K d with the linear solvation energy relationship (LSER). The results demonstrate that the MWCNT carbonyl and carboxyl groups provide high adsorption capacity for the VOCs (Log K d 3.72–5.24 g/kg/g/L) because of the π-/n-electron pair interactions and hydrogen-bond acidity. The increasing RH gradually decreased the Log K d and shifted the interactions to dipolarity/polarizability, hydrogen-bond basicity, and cavity formation. The derived LSER equations provided adequate fits of Log K d , which is useful for VOC-removal processes and fate prediction of VOC contaminants by MWCNT adsorption in the environment.

Tunable solvation effects on the size-selective fractionation of metal nanoparticles in CO2 gas-expanded solvents.

Science.gov (United States)

Anand, Madhu; McLeod, M Chandler; Bell, Philip W; Roberts, Christopher B

2005-12-08

This paper presents an environmentally friendly, inexpensive, rapid, and efficient process for size-selective fractionation of polydisperse metal nanoparticle dispersions into multiple narrow size populations. The dispersibility of ligand-stabilized silver and gold nanoparticles is controlled by altering the ligand tails-solvent interaction (solvation) by the addition of carbon dioxide (CO2) gas as an antisolvent, thereby tailoring the bulk solvent strength. This is accomplished by adjusting the CO2 pressure over the liquid, resulting in a simple means to tune the nanoparticle precipitation by size. This study also details the influence of various factors on the size-separation process, such as the types of metal, ligand, and solvent, as well as the use of recursive fractionation and the time allowed for settling during each fractionation step. The pressure range required for the precipitation process is the same for both the silver and gold particles capped with dodecanethiol ligands. A change in ligand or solvent length has an effect on the interaction between the solvent and the ligand tails and therefore the pressure range required for precipitation. Stronger interactions between solvent and ligand tails require greater CO2 pressure to precipitate the particles. Temperature is another variable that impacts the dispersibility of the nanoparticles through changes in the density and the mole fraction of CO2 in the gas-expanded liquids. Recursive fractionation for a given system within a particular pressure range (solvent strength) further reduces the polydispersity of the fraction obtained within that pressure range. Specifically, this work utilizes the highly tunable solvent properties of organic/CO2 solvent mixtures to selectively size-separate dispersions of polydisperse nanoparticles (2 to 12 nm) into more monodisperse fractions (+/-2 nm). In addition to providing efficient separation of the particles, this process also allows all of the solvent and

Relating pressure tuned coupled column ensembles with the solvation parameter model for tunable selectivity in gas chromatography.

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Sharif, Khan M; Kulsing, Chadin; Chin, Sung-Tong; Marriott, Philip J

2016-07-15

The differential pressure drop of carrier gas by tuning the junction point pressure of a coupled column gas chromatographic system leads to a unique selectivity of the overall separation, which can be tested using a mixture of compounds with a wide range of polarity. This study demonstrates a pressure tuning (PT) GC system employing a microfluidic Deans switch located at the mid-point of the two capillary columns. This PT system allowed variations of inlet-outlet pressure differences of the two columns in a range of 52-17psi for the upstream column and 31-11psi for the downstream column. Peak shifting (differential migration) of compounds due to PT difference are related to a first order regression equation in a Plackett-Burman factorial study. Increased first (upstream) column pressure drop makes the second column characteristics more significant in the coupled column retention behavior, and conversely increased second (downstream) column pressure drop makes the first column characteristics more apparent; such variation can result in component swapping between polar and non-polar compounds. The coupled column system selectivity was evaluated in terms of linear solvation energy relationship (LSER) parameters, and their relation with different pressure drop effects has been constructed by applying multivariate principle component analysis (PCA). It has been found that the coupled column PT system descriptors provide a result that shows a clear clustering of different pressure settings, somewhat intermediate between those of the two commercial columns. This is equivalent to that obtained from a conventional single-column GC analysis where the interaction energy contributed from the stationary phases can be significantly adjusted by choice of midpoint PT. This result provides a foundation for pressure differentiation for selectivity enhancement. Copyright © 2016 Elsevier B.V. All rights reserved.

Solvation Mechanism of Task-Specific Ionic Liquids in Water: A Combined Investigation Using Classical Molecular Dynamics and Density Functional Theory.

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Yuvaraj, Surya V J; Zhdanov, Ravil K; Belosludov, Rodion V; Belosludov, Vladimir R; Subbotin, Oleg S; Kanie, Kiyoshi; Funaki, Kenji; Muramatsu, Atsushi; Nakamura, Takashi; Kawazoe, Yoshiyuki

2015-10-08

The solvation behavior of task-specific ionic liquids (TSILs) containing a common, L-histidine derived imidazolium cation [C20H28N3O3](+) and different anions, bromide-[Br](-) and bis(trifluoromethylsulfonyl)amide-[NTF2](-), in water is examined, computationally. These amino acid functionalized ionic liquids (ILs) are taken into account because of their ability to react with rare earth metal salts. It has been noted that the TSIL with [Br](-) is more soluble than its counterpart TSIL with [NTF2](-), experimentally. In this theoretical work, the combined classical molecular dynamics (CMD) and density functional theory (DFT) calculations are performed to study the behavior of the bulk phase of these two TSILs in the vicinity of water (H2O) molecules with different concentrations. Initially, all the constructed systems are equilibrated using the CMD method. The final structures of the equilibrated systems are extracted for DFT calculations. Under CMD operation, the radial distribution function (RDF) plots and viscosity of TSILs are analyzed to understand the effect of water on TSILs. In the DFT regime, binding energy per H2O, charge transfer, charge density mapping, and electronic density of states (EDOS) analyses are done. The CMD results along with the DFT results are consolidated to support the hydrophilic and hydrophobic nature of the TSILs. Interestingly, we have found a strong correlation between the viscosity and the EDOS results that leads to an understanding of the hydration properties of the TSILs.

Synthesis, Spatial Structure and Analgesic Activity of Sodium 3-Benzylaminocarbonyl-1-methyl-2,2-dioxo-1H-2λ6,1-benzothiazin-4-olate Solvates

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Igor V. Ukrainets

2016-10-01

Full Text Available In order to obtain and then test pharmocologically any possible conformers of the new feasible analgesic N-benzyl-4-hydroxy-1-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxamide, its 4-O-sodium salt was synthesized using two methods. X-ray diffraction study made possible to determine that, depending on the chosen synthesis conditions, the above-mentioned compound forms either monosolvate with methanol or monohydrate, where organic anion exists in the form of three different conformers. Pharmacological testing of the two known pseudo-enantiomeric forms of the original N-benzylamide and of the two solvates of its sodium salt was performed simultaneously under the same conditions and in equimolar doses. Comparison of the results obtained while studying the peculiarities of the synthesized compounds spatial structure and biological properties revealed an important structure-action relationship. In particular, it was shown that the intensity of analgesic effect of different conformational isomers of N-benzyl-4-hydroxy-1-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxamide may change considerably: while low active conformers are comparable with piroxicam, highly active conformers are more than twice as effective as meloxicam.

Solvatochromism of naringenin in aqueous alcoholic mixtures

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Faraji Mohammad

2016-01-01

Full Text Available The spectral change of naringenin was studied by Uv-vis spectrophotometric method in binary mixtures of water with methanol, ethanol and 1-propanol at 25°C. The effect of solvent was investigated by analysis of electron transition energy at the maximum absorption wavelength as a function of Kamlet and Taft parameters of mixtures by means of linear solvation energy relationships. The nonlinear response of solvatochromism was explained based on solute-solvent and solvent-solvent interactions. The possible preferential solvation of naringenin by each of solvents was studied through a modified preferential solvation model which considers the hydrogen bonding interactions between the prior solvents due to solvent-solvent interactions. The preferential solvation parameters and local mole fraction distribution around the solute were calculated. Results indicate that naringenin prefers to be more solvated by the complex solvating species and organic solvents than water.

An advanced study on non-homogeneous radiation physical chemistry

International Nuclear Information System (INIS)

Katsumura, Yosuke; Kudo, Hisaaki; Muroya, Yusa; Lin, Mingzhang; Han, Zhenhui; Yamada, Reiji; Nagaishi, Ryuji

2008-01-01

In order to characterize the radiolysis of supercritical fluids, the yields of solvated electron in methanol have been measured from room temperature to supercritical state, 280degC, at 9 MPa by pulse radiolysis with 4,4'-bipyridyl(BPY) taken as a scavenger. The change of the solvated electron yield is similar to that of hydrated electron observed in water. Further more, the yield of solvated electron dependent on BPY concentration has been measured and rate constant of the reaction of solvated electron toward the BPY has also determined from room temperature to supercritical state. On the basis of above data, mechanism of the temperature dependent yield of solvated electrons in methanol has been discussed. (author)

Characterization of volatile organic compound adsorption on multiwall carbon nanotubes under different levels of relative humidity using linear solvation energy relationship

Energy Technology Data Exchange (ETDEWEB)

Li, Mei-syue; Wu, Siang Chen; Shih, Yang-hsin, E-mail: yhs@ntu.edu.tw

2016-09-05

Highlights: • LSER equations successfully predicted VOC sorption on MCNT at different humidity. • The five parameters in LSER could be narrowed down to three ones. • Main interaction is dispersion and partly dipolarity as well as hydrogen-bonds. • With increasing RH, it changes to cavity formation and hydrogen-bond basicity. • This approach can facilitate the VOC control design and the fate prediction. - Abstract: Multiwall carbon nanotubes (MWCNTs) have been used as an adsorbent for evaluating the gas/solid partitioning of selected volatile organic compounds (VOCs). In this study, 15 VOCs were probed to determine their gas/solid partitioning coefficient (Log K{sub d}) using inverse gas chromatography at different relative humidity (RH) levels. Interactions between MWCNTs and VOCs were analyzed by regressing the observed Log K{sub d} with the linear solvation energy relationship (LSER). The results demonstrate that the MWCNT carbonyl and carboxyl groups provide high adsorption capacity for the VOCs (Log K{sub d} 3.72–5.24 g/kg/g/L) because of the π-/n-electron pair interactions and hydrogen-bond acidity. The increasing RH gradually decreased the Log K{sub d} and shifted the interactions to dipolarity/polarizability, hydrogen-bond basicity, and cavity formation. The derived LSER equations provided adequate fits of Log K{sub d}, which is useful for VOC-removal processes and fate prediction of VOC contaminants by MWCNT adsorption in the environment.

Solid state solvation effect and reduced amplified spontaneous emission threshold value of glass forming DCM derivative in PMMA films

Energy Technology Data Exchange (ETDEWEB)

Vembris, Aivars, E-mail: aivars.vembris@cfi.lu.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Street, Riga LV 1063 (Latvia); Zarins, Elmars; Kokars, Valdis [Institute of Applied Chemistry, Riga Technical University, 14/24 Azenes Street, Riga LV 1048 (Latvia)

2015-02-15

Molecule crystallization is one of the limitations for obtaining high-gain organic laser systems. One of the examples is well known red laser dye 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran (DCM). The lowest threshold value of amplified spontaneous emission was achieved by doping 2 wt% of DCM molecule in tris-(8-hydroxy quinoline) aluminum (Alq{sub 3}) matrix. Further increase of the DCM dye concentration makes the system less efficient as its threshold value increases. It is due to large intermolecular interaction, which induces photoluminescence quenching. Compounds with reduced intermolecular interaction could be prospective in organic laser systems due to higher possible doping. In this work photoluminescence and amplified spontaneous emission properties of modified DCM molecule in poly(methyl methacrylate) (PMMA) matrix were investigated. Bulky trityloxyethyl groups were attached to the donor part of DCM. These groups increase intermolecular distance wherewith reduce photoluminescence quenching. More than one order of magnitude lower excitation threshold energy of the amplified spontaneous emission was achieved in doped polymer films with investigated compound in comparison to doped polymer with DCM. It means that the investigated compound is more perspective as a laser material compared to the previously studied. In addition, amplified spontaneous emission maximum could be tuned within 15 nm by changing concentration from 0.1 wt% to 10 wt% DWK-1 in PMMA matrix due to solid state solvation effect. - Highlights: • Bulky groups attached to DCM dye reduce photoluminescence quenching. • Amplified spontaneous emission is in red spectral region. • Amplified spontaneous emission spectra were tuned by 15 nm. • Amplified spontaneous emission threshold value was reduced by one order of magnitude.

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

Science.gov (United States)

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

2015-06-09

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

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

International Nuclear Information System (INIS)

Yang Songqiu; Liu Jianyong; Zhou Panwang; Chen Junsheng; Han Keli; He Guozhong

2012-01-01

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: ► Mechanisms of subpicosecond fluorescence depletion spectroscopy. ► Quasi-continuous model was used to describe the solvational relaxation. ► The solvation dynamics of coumarin 153 in methanol has been measured.

Radiolysis studies on reactive intermediates. Technical progress report, November 1, 1978-November 1, 1979

International Nuclear Information System (INIS)

Kevan, L.

1979-11-01

Analysis methods for electron spin echo modulation patterns were improved and were used to determine the silver atom solvation structure in water and methanol and the geometry of solvated electrons in organic matrices. New evidence for presolvated electrons in polar matrices was obtained, and the mechanism of electron solvation in pure and in mixed matrices was clarified

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

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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.

Linear solvation energy relationships for toxicity of selected organic chemicals to Daphnia pulex and Daphnia magna

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Passino, Dora R.M.; Hickey, James P.; Frank, Anthony M.

1988-01-01

In the Laurentian Great Lakes, more than 300 contaminants have been identified in fish, other biota, water, and sediment. Current hazard assessment of these chemicals by the National Fisheries Research Center-Great Lakes is based on their toxicity, occurrence in the environment, and source. Although scientists at the Center have tested over 70 chemicals with the crustacean Daphnia pulex, the number of experimental data needed to screen the huge array of chemicals in the Great Lakes exceeds the practical capabilities of conducting bioassays. This limitation can be partly circumvented, however, by using mathematical models based on quantitative structure-activity relationships (QSAR) to provide rapid, inexpensive estimates of toxicity. Many properties of chemicals, including toxicity, bioaccumulation and water solubility are well correlated and can be predicted by equations of the generalized linear solvation energy relationships (LSER). The equation we used to model solute toxicity is Toxicity = constant + mVI/100 + s (π* + dδ) + bβm + aαm where VI = intrinsic (Van der Waals) molar volume; π* = molecular dipolarity/polarizability; δ = polarizability 'correction term'; βm = solute hydrogen bond acceptor basicity; and αm = solute hydrogen bond donor acidity. The subscript m designates solute monomer values for α and β. We applied the LSER model to 48-h acute toxicity data (measured as immobilization) for six classes of chemicals detected in Great Lakes fish. The following regression was obtained for Daphnia pulex (concentration = μM): log EC50 = 4.86 - 4.35 VI/100; N = 38, r2 = 0.867, sd = 0.403 We also used the LSER modeling approach to analyze to a large published data set of 24-h acute toxicity for Daphnia magna; the following regression resulted, for eight classes of compounds (concentration = mM): log EC50 = 3.88 - 4.52 VI/100 - 1.62 π* + 1.66 βm - 0.916 αm; N = 62, r2 = 0.859, sd = 0.375 In addition we developed computer software that identifies

Effect of unsaturation on the absorption of ethane and ethylene in imidazolium-based ionic liquids.

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Moura, Leila; Mishra, Manas; Bernales, Varinia; Fuentealba, Patricio; Padua, Agilio A H; Santini, Catherine C; Costa Gomes, Margarida F

2013-06-20

The influence of the presence of imidazolium side chain unsaturation on the solubility of ethane and ethylene was studied in three ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide-saturated alkyl side-chain in the cation; 1-methyl-3-(buten-3-yl)imidazolium bis(trifluorosulfonyl)imide-double bond in the side-chain of the cation; and 1-methyl-3-benzylimidazolium bis(trifluorosulfonyl)imide-benzyl group in the side-chain of the cation. The solubility of both gases decreases when the side-chain of the cations is functionalized with an unsaturated group. This can be explained by a less favorable enthalpy of solvation. The difference of solubility between ethane and ethylene can be explained from a balance of enthalpic and entropic factors: for the ionic liquid with the saturated alkyl side-chain and the benzyl-substituted side-chain, it is the favorable entropy of solvation that explains the larger ethylene solubility, whereas in the case of the saturated side-chain, it is the more favorable enthalpy of solvation. Molecular simulation allowed the identification of the mechanisms of solvation and the preferential solvation sites for each gas in the different ionic liquids. Simulations have shown that the entropy of solvation is more favorable when the presence of the gas weakens the cation-anion interactions or when the gas can be solvated near different sites of the ionic liquid.

Quantitative structure-retention relationship studies using immobilized artificial membrane chromatography I: amended linear solvation energy relationships with the introduction of a molecular electronic factor.

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Li, Jie; Sun, Jin; Cui, Shengmiao; He, Zhonggui

2006-11-03

Linear solvation energy relationships (LSERs) amended by the introduction of a molecular electronic factor were employed to establish quantitative structure-retention relationships using immobilized artificial membrane (IAM) chromatography, in particular ionizable solutes. The chromatographic indices, log k(IAM), were determined by HPLC on an IAM.PC.DD2 column for 53 structurally diverse compounds, including neutral, acidic and basic compounds. Unlike neutral compounds, the IAM chromatographic retention of ionizable compounds was affected by their molecular charge state. When the mean net charge per molecule (delta) was introduced into the amended LSER as the sixth variable, the LSER regression coefficient was significantly improved for the test set including ionizable solutes. The delta coefficients of acidic and basic compounds were quite different indicating that the molecular electronic factor had a markedly different impact on the retention of acidic and basic compounds on IAM column. Ionization of acidic compounds containing a carboxylic group tended to impair their retention on IAM, while the ionization of basic compounds did not have such a marked effect. In addition, the extra-interaction with the polar head of phospholipids might cause a certain change in the retention of basic compounds. A comparison of calculated and experimental retention indices suggested that the semi-empirical LSER amended by the addition of a molecular electronic factor was able to reproduce adequately the experimental retention factors of the structurally diverse solutes investigated.

Nucleofugalities of Neutral Leaving Groups in 80 % Aqueous Acetonitrile

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Sandra Jurić

2016-06-01

Full Text Available Nucleofugalites of tetrahydrothiophene, dimethyl sulfide and differently substituted pyridines in 80 % aqueous acetonitrile have been derived from the SN1 solvolysis rate constants of the corresponding X,Y-substituted benzhydryl derivatives (1–10. In sol-volysis of sulfonium ions in 80 % aqueous acetonitrile, where acetonitrile is a good cation solvator, the solvation of the reactant ground state is an important rate determining variable since the positive charge is almost entirely located on the leaving group. As a consequence, reaction rates of sulfonium ions are more sensitive to the substrate structure in 80 % aqueous acetonitrile than in pure and aqueous alcohols, which are less efficient as cation solvators. In solvolysis of pyridinium ions the solvation of the reactant ground state is less important, since the positive charge is considerably distributed between the carbon at the reaction center and the leaving group. In such cases the important rate determining variable is solvation of the transition state. Slower reactions of pyridinium sub-strates progress over later, carbocation-like transition states in which the solvation is more important, so those substrates solvolyze slightly faster in aqueous acetonitrile than in methanol (k80AN > kM. Faster reactions proceed over earlier TS in which the solvation is diminished, so those substrates solvolyze somewhat faster in methanol than in aqueous acetonitrile (k80AN kM. This work is licensed under a Creative Commons Attribution 4.0 International License.

Modeling vapor pressures of solvent systems with and without a salt effect: An extension of the LSER approach

International Nuclear Information System (INIS)

Senol, Aynur

2015-01-01

Highlights: • A new polynomial vapor pressure approach for pure solvents is presented. • Solvation models reproduce the vapor pressure data within a 4% mean error. • A concentration-basis vapor pressure model is also implemented on relevant systems. • The reliability of existing models was analyzed using log-ratio objective function. - Abstract: A new polynomial vapor pressure approach for pure solvents is presented. The model is incorporated into the LSER (linear solvation energy relation) based solvation model framework and checked for consistency in reproducing experimental vapor pressures of salt-containing solvent systems. The developed two structural forms of the generalized solvation model (Senol, 2013) provide a relatively accurate description of the salting effect on vapor pressure of (solvent + salt) systems. The equilibrium data spanning vapor pressures of eighteen (solvent + salt) and three (solvent (1) + solvent (2) + salt) systems have been subjected to establish the basis for the model reliability analysis using a log-ratio objective function. The examined vapor pressure relations reproduce the observed performance relatively accurately, yielding the overall design factors of 1.084, 1.091 and 1.052 for the integrated property-basis solvation model (USMIP), reduced property-basis solvation model and concentration-dependent model, respectively. Both the integrated property-basis and reduced property-basis solvation models were able to simulate satisfactorily the vapor pressure data of a binary solvent mixture involving a salt, yielding an overall mean error of 5.2%

Enthalpies of potassium iodide dissolution in dimethyl acetamide mixtures with water

International Nuclear Information System (INIS)

Privalova, N.M.; Gritsenko, S.I.; Vorob'ev, A.F.

1986-01-01

Enthalpies of potassium iodide dissolution in mixed dimethyl acetamide - water solvent at 298.15 K in the whole range of dimethyl acetamide compositions are measured by the calorimetric method. From the plots of KI dissolution enthalpy dependence and dependence of experimental ΔH p∞ 0 value deviations from calculational ones on solvent composition, as well as from the results of calculation of solvate shell composition of potassium iodide ions in the mixed solvent, it is obvious that in the region of 0-15 mol% concentrations of dimethyl acetamide insufficient enrichment of solvate ion shells by dimethyl acetamide (DMAA) occurs, in the region of 15-40 mol% DMAA compositions enrichment of solvate shells of ions by water occurs, in the region of 40-100 mol% DMAA enrichment of solvate ion shells by the organic component in comparison with mixture compostion occurs. Maximum enrichment of solvate ion shells by mixture components in three above mentioned regions of the mixed solvent occurs at 10, 30 and 80 mol% DMAA concentrations

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

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Wang, Yuan; Liang, Zuozhong

2017-12-01

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

Self-assembly in solvates of 2,4-diamino-6-(4-methyl- phenyl)-1,3,5-triazine and in its molecular adducts with some aliphatic dicarboxylic acids

Science.gov (United States)

Nandy, Purnendu; Nayak, Amrita; Biswas, Sharmita Nandy; Pedireddi, V. R.

2016-03-01

Solid state structures of 2,4-diamino-6-(4-methylphenyl)-1,3,5-triazine, 1, in the form of methanol and dimethylsulfoxide (DMSO) solvates, as well as supramolecular assemblies of 1 with various aliphatic dicarboxylic acids, oxalic (a), malonic (b), succinic (c), glutaric (d) and adipic (e) have been reported. Analysis of the assemblies has been carried out by single crystal X-ray diffraction and thermal methods. Triazine 1 yields anhydrous molecular adducts with acids a-d, upon co-crystallization either from CH3OH and DMSO solvents. However acid e gives anhydrous adduct from DMSO solvent, while it gives a methanol adduct from CH3OH. Structure determination reveals that molecular adducts 1a, 1d and 1e are in a 2:1 ratio of 1 and the corresponding acid. However the ratio is 1:1, in 1b, perhaps due to the involvement of one of the acid groups in the intramolecular hydrogen bonding and in adduct 1c the ratio observed is 3:2. Structural features in all these assemblies have been rationalised in terms of various recognition patterns formed between the acceptor and donor groups. A noteworthy feature is that -COOH groups in acid a establish interaction with 1 through amino groups, while such interactions are observed to be through hetero -N atoms in case of the acids b-e.

“Bligh and Dyer” and Folch Methods for Solid–Liquid–Liquid Extraction of Lipids from Microorganisms. Comprehension of Solvatation Mechanisms and towards Substitution with Alternative Solvents

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Cassandra Breil

2017-03-01

Full Text Available Bligh and Dyer (B & D or Folch procedures for the extraction and separation of lipids from microorganisms and biological tissues using chloroform/methanol/water have been used tens of thousands of times and are “gold standards” for the analysis of extracted lipids. Based on the Conductor-like Screening MOdel for realistic Solvatation (COSMO-RS, we select ethanol and ethyl acetate as being potentially suitable for the substitution of methanol and chloroform. We confirm this by performing solid–liquid extraction of yeast (Yarrowia lipolytica IFP29 and subsequent liquid–liquid partition—the two steps of routine extraction. For this purpose, we consider similar points in the ternary phase diagrams of water/methanol/chloroform and water/ethanol/ethyl acetate, both in the monophasic mixtures and in the liquid–liquid miscibility gap. Based on high performance thin-layer chromatography (HPTLC to obtain the distribution of lipids classes, and gas chromatography coupled with a flame ionisation detector (GC/FID to obtain fatty acid profiles, this greener solvents pair is found to be almost as effective as the classic methanol–chloroform couple in terms of efficiency and selectivity of lipids and non-lipid material. Moreover, using these bio-sourced solvents as an alternative system is shown to be as effective as the classical system in terms of the yield of lipids extracted from microorganism tissues, independently of their apparent hydrophilicity.

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

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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

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

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Clarisse Gravina Ricci

2018-02-01

Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

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Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

The isobutylene-isobutane alkylation process in liquid HF revisited.

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Esteves, P M; Araújo, C L; Horta, B A C; Alvarez, L J; Zicovich-Wilson, C M; Ramírez-Solís, A

2005-07-07

Details on the mechanism of HF catalyzed isobutylene-isobutane alkylation were investigated. On the basis of available experimental data and high-level quantum chemical calculations, a detailed reaction mechanism is proposed taking into account solvation effects of the medium. On the basis of our computational results, we explain why the density of the liquid media and stirring rates are the most important parameters to achieve maximum yield of alkylate, in agreement with experimental findings. The ab initio Car-Parrinello molecular dynamics calculations show that isobutylene is irreversibly protonated in the liquid HF medium at higher densities, leading to the ion pair formation, which is shown to be a minimum on the potential energy surface after optimization using periodic boundary conditions. The HF medium solvates preferentially the fluoride anion, which is found as solvated [FHF](-) or solvated F(-.)(HF)(3). On the other hand, the tert-butyl cation is weakly solvated, where the closest HF molecules appear at a distance of about 2.9 Angstrom with the fluorine termination of an HF chain.

Calculation of Five Thermodynamic Molecular Descriptors by Means of a General Computer Algorithm Based on the Group-Additivity Method: Standard Enthalpies of Vaporization, Sublimation and Solvation, and Entropy of Fusion of Ordinary Organic Molecules and Total Phase-Change Entropy of Liquid Crystals

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Rudolf Naef

2017-06-01

Full Text Available The calculation of the standard enthalpies of vaporization, sublimation and solvation of organic molecules is presented using a common computer algorithm on the basis of a group-additivity method. The same algorithm is also shown to enable the calculation of their entropy of fusion as well as the total phase-change entropy of liquid crystals. The present method is based on the complete breakdown of the molecules into their constituting atoms and their immediate neighbourhood; the respective calculations of the contribution of the atomic groups by means of the Gauss-Seidel fitting method is based on experimental data collected from literature. The feasibility of the calculations for each of the mentioned descriptors was verified by means of a 10-fold cross-validation procedure proving the good to high quality of the predicted values for the three mentioned enthalpies and for the entropy of fusion, whereas the predictive quality for the total phase-change entropy of liquid crystals was poor. The goodness of fit (Q2 and the standard deviation (σ of the cross-validation calculations for the five descriptors was as follows: 0.9641 and 4.56 kJ/mol (N = 3386 test molecules for the enthalpy of vaporization, 0.8657 and 11.39 kJ/mol (N = 1791 for the enthalpy of sublimation, 0.9546 and 4.34 kJ/mol (N = 373 for the enthalpy of solvation, 0.8727 and 17.93 J/mol/K (N = 2637 for the entropy of fusion and 0.5804 and 32.79 J/mol/K (N = 2643 for the total phase-change entropy of liquid crystals. The large discrepancy between the results of the two closely related entropies is discussed in detail. Molecules for which both the standard enthalpies of vaporization and sublimation were calculable, enabled the estimation of their standard enthalpy of fusion by simple subtraction of the former from the latter enthalpy. For 990 of them the experimental enthalpy-of-fusion values are also known, allowing their comparison with predictions, yielding a correlation

Calculation of Five Thermodynamic Molecular Descriptors by Means of a General Computer Algorithm Based on the Group-Additivity Method: Standard Enthalpies of Vaporization, Sublimation and Solvation, and Entropy of Fusion of Ordinary Organic Molecules and Total Phase-Change Entropy of Liquid Crystals.

Science.gov (United States)

Naef, Rudolf; Acree, William E

2017-06-25

The calculation of the standard enthalpies of vaporization, sublimation and solvation of organic molecules is presented using a common computer algorithm on the basis of a group-additivity method. The same algorithm is also shown to enable the calculation of their entropy of fusion as well as the total phase-change entropy of liquid crystals. The present method is based on the complete breakdown of the molecules into their constituting atoms and their immediate neighbourhood; the respective calculations of the contribution of the atomic groups by means of the Gauss-Seidel fitting method is based on experimental data collected from literature. The feasibility of the calculations for each of the mentioned descriptors was verified by means of a 10-fold cross-validation procedure proving the good to high quality of the predicted values for the three mentioned enthalpies and for the entropy of fusion, whereas the predictive quality for the total phase-change entropy of liquid crystals was poor. The goodness of fit ( Q ²) and the standard deviation (σ) of the cross-validation calculations for the five descriptors was as follows: 0.9641 and 4.56 kJ/mol ( N = 3386 test molecules) for the enthalpy of vaporization, 0.8657 and 11.39 kJ/mol ( N = 1791) for the enthalpy of sublimation, 0.9546 and 4.34 kJ/mol ( N = 373) for the enthalpy of solvation, 0.8727 and 17.93 J/mol/K ( N = 2637) for the entropy of fusion and 0.5804 and 32.79 J/mol/K ( N = 2643) for the total phase-change entropy of liquid crystals. The large discrepancy between the results of the two closely related entropies is discussed in detail. Molecules for which both the standard enthalpies of vaporization and sublimation were calculable, enabled the estimation of their standard enthalpy of fusion by simple subtraction of the former from the latter enthalpy. For 990 of them the experimental enthalpy-of-fusion values are also known, allowing their comparison with predictions, yielding a correlation coefficient R

Hydration thermodynamics beyond the linear response approximation.

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Raineri, Fernando O

2016-10-19

The solvation energetics associated with the transformation of a solute molecule at infinite dilution in water from an initial state A to a final state B is reconsidered. The two solute states have different potentials energies of interaction, [Formula: see text] and [Formula: see text], with the solvent environment. Throughout the A [Formula: see text] B transformation of the solute, the solvation system is described by a Hamiltonian [Formula: see text] that changes linearly with the coupling parameter ξ. By focusing on the characterization of the probability density [Formula: see text] that the dimensionless perturbational solute-solvent interaction energy [Formula: see text] has numerical value y when the coupling parameter is ξ, we derive a hierarchy of differential equation relations between the ξ-dependent cumulant functions of various orders in the expansion of the appropriate cumulant generating function. On the basis of this theoretical framework we then introduce an inherently nonlinear solvation model for which we are able to find analytical results for both [Formula: see text] and for the solvation thermodynamic functions. The solvation model is based on the premise that there is an upper or a lower bound (depending on the nature of the interactions considered) to the amplitude of the fluctuations of Y in the solution system at equilibrium. The results reveal essential differences in behavior for the model when compared with the linear response approximation to solvation, particularly with regards to the probability density [Formula: see text]. The analytical expressions for the solvation properties show, however, that the linear response behavior is recovered from the new model when the room for the thermal fluctuations in Y is not restricted by the existence of a nearby bound. We compare the predictions of the model with the results from molecular dynamics computer simulations for aqueous solvation, in which either (1) the solute

Relation between chemical properties in molten acetamide and water at 98 deg. C

International Nuclear Information System (INIS)

Petit, Nicole

1972-01-01

An attempt was made to establish the relation between the chemical properties of various cations in water and in molten acetamide at 98 deg. C. A solvent always possesses properties which have some effect on the reactivity of the solute. Various types of interactions (polar, electrostatic, Van der Waals forces, and hydrogen bonds) bind the solvent molecules to the dissolved molecules and ions. Interactions between the solute species and the solvent species are designated: solvation phenomena. In addition to solvation phenomena, another but less direct type of interaction occurs: the solvated ions find themselves in a sensibly continuous medium having a dielectric constant ε which can vary considerably. As the value of the dielectric constant decreases, the electrostatic interactions between the ions increase. The variation is such that these ions can only be considered free for values of ε > 40. This is the case for acetamide and water at 98 deg. C. The solvation of a chemical species belonging to an oxido-reducing system can only be effected by comparing the behavior of such a system with a reference system relatively insensitive to changes in the solvent. The reference system used was a ferrocene-ion/ferricinium couple. The solvation of a chemical species is characterized by a variable designated: the solvation activity coefficient. The chemical and electrochemical properties of various elements (alkali elements, alkaline earths, Cu, Zn, Cd, Hg, Pb, U, Al, Ce, and Eu) in neutral or acid media in acetamide were studied using various electrochemical techniques (principally polarography). These studies led to the establishment of a table of oxido-reducing potentials for molten acetamide. Comparisons with water at 98 deg. C indicate that the metallic cations are more solvated in acetamide than in water. The evaluation of solvation activity coefficients from polarographic measurements (E 1/2 , D M ) led to an approximate estimation of the differences in behavior

Solvation and complexation study by fluorescence spectroscopy of Eu(III) and Cm(III) ions in octanol solution and at the interface with water

International Nuclear Information System (INIS)

Vu, T.H.

2008-01-01

Polydentate N-donors ligands like bis-triazine-pyridine (BTP) and bis-triazine-bis-pyridine (BTBP) can selectively extract minor actinides (III) from lanthanides (III) ions and therefore have been studied in the field of nuclear waste reprocessing. The aim of the researches carried out during this thesis is a better description of this family in biphasic systems: speciation in the organic phase and around the interfacial area. After an exhaustive description of the solvation of europium(III) cation in mixed solutions n-octanol water with TRLIF spectrometry, the complexation with nitrogen ligands iPr-BTP, C5-BTBP and CyMe4-BTBP has been studied by TRLIF and ESI-MS techniques. For each compound, the inner sphere of europium has been described and the conditional stability constants determined. The composition of the organic medium, and particularly the hydration degree of n-octanol, has an impact on the nature and the ratio of species 'cation - counter ion - ligand - water'. With high water content (representative of extraction systems), the complexes observed with Cm(III) and Eu(III) have the same stoichiometry but the affinity towards the curium cation is higher and consistent to separation factors measured with biphasic systems. The method TIRF (total internal reflection fluorescence) was retained to study the behaviour of europium(III) inside the interfacial area. Fluorescence spectra of europium have been obtained but side signals and the high depth resolution of detection lead to difficulty in obtaining the signal of interfacial europium alone. The selected technique remains promising but some improvements need to be implemented for forthcoming measurement at liquid/liquid interface. (author) [fr

The inhibition of positronium by the chloride ion in water and the positron: Chloride reaction

International Nuclear Information System (INIS)

Beling, C.D.; Smith, F.A.

1983-01-01

A discussion is made of existing theories of Ps inhibition in the presence of Cl - ions. Our favoured interpretation of the data uses the thermalised pre-solvated positron as a common precursor of Ps and e + Cl - . Consideration is given to the prevention of solvation by the strong electric fields in the vicinity of Cl - ions, assuming best estimates for the solvation time, positron mobility and intermolecular spacing. An expression for the Ps inhibition constant K is derived on the basis of diffusive capture. The observed enhancement of Ps yield at higher Cl - concentrations is attributed to the scavenging by the Cl - ion of highly mobile species such as H 2 + O within times approx.=10 -14 s. Dissociation between e + Cl - and the solvated state esub(s) + is suggested as the cause of the ''missing fraction''. (orig.)

Alkaline cation complexing with calixarenes in electro-spray / mass spectrometry. Specificity for cesium, influence of solvation on ion species and radiolytic stability of the complexing media

International Nuclear Information System (INIS)

Allain, Francoise

2000-01-01

Radioactive waste management is a rather difficult issue. In order to reduce the volume of waste storage, particularly the Cs 135 (radioactive half-life 2.3 10 6 years), liquid-liquid extraction experiments have shown that crown calixarenes were able to selectively extract cesium cation in wastes. However, the stability under radiolysis of this type of macrocycle is unknown and is the theme of this thesis. Through the coupling of electro-spray and mass spectrometry, the selectivity of crown calixarenes for cesium has been confirmed. The necessity to optimize operating conditions during the utilization of this ionization mode was acknowledged for a correct interpretation of mass spectrum. The solvent nature, source temperature, applied voltage on the cone, gaseous phase stability and species ionization desorption rate are indeed parameters that should be taken into account. Experiments show that the solution species stability is inverse to the one in gaseous phase. In a solution, species stability is linked to the nature of the solvent (solvating power) whereas in gaseous phase, it is linked to the cationic affinity. In the current radiolysis conditions it has been demonstrated that calixarenes have a stable structure. Degradation products are very largely substitution products and do not hinder the caesium cation complexing. Concerning the quantitative aspect, an estimation was produced, however results are not satisfying: reference product synthesis is in fact necessary in order to establish calibration curves that will allow to precisely dose the various components derived from radiolysis [fr

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Both implicit solvation method (dielectric polarizable continuum model, DPCM) and hybrid solvation method (cluster-continuum model) were adopted to calculate the of mono-protonated form of 132-(demethoxycarbonyl) pheophytin (Pheo) in methanol. In the cluster-continuum model calculations, we considered ...

The spectroscopy and structure of some lanthanide chlorides in amide solutions

International Nuclear Information System (INIS)

Legendziewicz, J.; Bukietynska, K; Jezowsky-Trzebiatowska, B.

1974-01-01

The absorption spectra of Pr, Nd, Ho, and Er anhydrous and hydrated chlorides in formamide, methyl-, dimethyl-, and diethylformamide solutions have been investigated in the range of 8000 - 4200 cm -1 . By the Judd-Oefelt method of intensity analysis and by calculating the nepheloauxetic effect, the first coordination sphere of lanthanide ions and the approximate symmetry of amide solvates of anhydrous and hydrated lanthanide chlorides were determined. A difference between symmetry and coordination numbers for light and heavy lanthanide solvates has been found. Some considerations regarding the structure of lanthanide solvates and structure of amide molecules have been made. (B.T.)

Quantum chemical approach for condensed-phase thermochemistry (IV): Solubility of gaseous molecules

Science.gov (United States)

Ishikawa, Atsushi; Kamata, Masahiro; Nakai, Hiromi

2016-07-01

The harmonic solvation model (HSM) was applied to the solvation of gaseous molecules and compared to a procedure based on the ideal gas model (IGM). Examination of 25 molecules showed that (i) the accuracy of ΔGsolv was similar for both methods, but the HSM shows advantages for calculating ΔHsolv and TΔSsolv; (ii) TΔSsolv contributes more than ΔHsolv to ΔGsolv in the HSM, i.e. the solvation of gaseous molecules is entropy-driven, which agrees well with experimental understanding (the IGM does not show this); (iii) the temperature dependence of Henry's law coefficient was correctly reproduced with the HSM.

Valence-delocalization of the mixed-valence oxo-centered trinuclear iron propionates [FeIII2FeIIO(C2H5CO2)6(py)3[npy; n = 0, 1.5

International Nuclear Information System (INIS)

Nakamoto, Tadahiro; Katada, Motomi; Kawata, Satoshi; Kitagawa, Susumu; Sano, Hirotoshi; Konno, Michiko

1994-01-01

Mixed-valence trinuclear iron propionates [Fe III 2 Fe II O(C 2 H 5 CO 2 ) 6 (py) 3 [npy, where n = 0, 1.5, were synthesized and the structure of the pyridine-solvated complex was determined by single-crystal X-ray diffraction. Moessbauer spectra of the solvated propionate complex showed a temperature-dependent mixed-valence state related to phase transitions, reaching an almost delocalized valence state at room temperature. On the other hand, the non-solvated propionate showed a remarkable change of the spectral shape related to a phase transition, remaining in a localized valence state at higher temperatures up to room temperature. (orig.)

Computing pKa Values in Different Solvents by Electrostatic Transformation.

Science.gov (United States)

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

2016-07-12

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

A Structural Investigation of the D O Solvated, Acetone Solvated and ...

African Journals Online (AJOL)

NICO

dicarbonyl moiety,[(h5-C5H5)(CO)2Fe (1, 2 and 3 in Scheme 1). 2. Experimental. 2.1. General ... single crystal X-ray diffractometer at 173(2) K using Mo Ka radia- .... Absorption coefficient (mm–1). 1.304 ... 98.0. 100.0. Absorption correction.

Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.

Science.gov (United States)

Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu

2013-09-10

Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying

Dissolution behavior of silk fibroin in a low concentration CaCl2-methanol solvent: From morphology to nanostructure.

Science.gov (United States)

Shen, Tingting; Wang, Tao; Cheng, Guotao; Huang, Lan; Chen, Lei; Wu, Dayang

2018-02-05

Regenerated Silk biomaterials are usually pre-formed from silk fibroin solutions. However, the dissolution of silk fibroin in proper solvents by a simple and low cost way is still a challenge. Here, we employed a CaCl 2 -methanol solvent system with a very low CaCl 2 concentration of 6wt% to dissolve silk fibroin. During the dissolution process, the evaporation of methanol cause the changing of solvation sheath of ions in the solvent. The remaining solvent with the incomplete solvation sheath is absorbed by the silk fiber and interacts with fibroin chains to complete the solvation sheath, which accounts for the dissolution of silk fibroin. Silk fibroin dissolution stops as all the solvation sheaths are complete. The final CaCl 2 concentration is ca. 26% and silk fibroin is completely dissolved with a yield of about 90%. Silk fibroin is dissolved into multi-scale nanofibrils solution which is potential for producing regenerated silk fibroin materials for functional applications. Copyright © 2018. Published by Elsevier B.V.

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

Science.gov (United States)

Caricato, Marco

2018-04-01

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

Development of mathematical model of H{sub 2}O-HNO{sub 3}-UO{sub 2}(NO{sub 3}){sub 2}-TBP-Diluent System

Energy Technology Data Exchange (ETDEWEB)

Ochkin, A.; Gladilov, D.; Nekhaevskiy, S.; Merkushkin, A. [D. Mendeleev University of Chemical Technology of Russia, 9 Miusskay Sqr., Moscow, 125047 (Russian Federation)

2016-07-01

The nuclear fuel reprocessing is based on the PUREX process. Usually 30% TBP in hydrocarbon diluents is applied, then the composition of the organic phase can be expressed as H{sub 2}O-HNO{sub 3}-UO{sub 2}(NO{sub 3}){sub 2}-Pu(NO{sub 3}){sub 4}-TBP-diluent. The mathematical model of H{sub 2}O-HNO{sub 3}-UO{sub 2}(NO{sub 3}){sub 2}-TBP-dodecane system has been elaborated. Mole fractions and volume ones and rational activity coefficients have been used in order to create the system of equations on the base of mass action law. The method for calculating activity coefficients was provided. The formation constants of uranyl nitrate di-solvate and mono-solvate and di-solvate of acid have been determined. Interaction between uranyl nitrate di-solvate and dodecane and between TBP and dodecane was taken into account. Activity coefficients of nitric acid and uranyl nitrate in mixed solutions were considered. Errors of adequacy have been determined for the systems containing 30% and 12% TBP concentrations.

Unequal effect of ethanol-water on the stability of ct-DNA, poly[(dA-dT)]₂ and poly(rA)·poly(rU). Thermophysical properties.

Science.gov (United States)

Ruiz, Rebeca; Hoyuelos, Francisco J; Navarro, Ana M; Leal, José M; García, Begoña

2015-01-21

Ethanol affects unequally the thermal stability of DNA and RNA. It stabilizes RNA, while destabilizing DNA. The variation of the relative viscosity (η/η0) of [poly(dA-dT)]2 with temperature unveils transitions close to the respective denaturation temperature, calculated spectrophotometrically and calorimetrically. From the raw data densities and speeds of sound, the volumetric observables were calculated. In all cases studied, a change in sign from low to high ethanol content occurred for both partial molar volume (ϕV) and partial molar adiabatic compressibility (ϕK(S)). The minima, close to 10%, should correspond to the highest solvation and the maxima, close to 30%, to the lowest solvation. For 40-50% ethanol, the solvation increases again. The complex structure of ethanol-water, for which changes are observed in regions close to such critical concentrations, justifies the observed behaviour. The variation of ϕV and ϕK(S) was sharper for RNA compared with respect to DNA, indicating that the solvation sequence is poly(rA)·poly(rU) < ct-DNA < [poly(dA-dT)]2.

Thermodynamics of ionic processes in solutions

International Nuclear Information System (INIS)

Krestov, G.A.

1984-01-01

The present nitions about the mechanism of solvation of atomic-molecular particles and the structure of electrolyte and non electrolyte solutions are given. From common positions a wide range of interrelated problems (general and thermodynamic characteristic of ions, thermodynamic characteristic of ion solvation and various ionic reactions in solutions, structural changes of the solvent in the above processes etc...) is considered. The latest scientific data including those on the effect on the thermodynamio properties of low temperatures, various impurities (air, water), large ions, peculiarities of the structure of solvent molecules reflected. Considerable attention is given to new conceptions definitions, structural notions as well as theoretical and experimental methods of obtaining quantitative characteristics of ion solvation

Li ⁺ solvation and kinetics of Li⁺–BF₄^-/PF ₆ ^- ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

Energy Technology Data Exchange (ETDEWEB)

Chang, Tsun-Mei [Department of Chemistry, University of Wisconsin–Parkside, Kenosha, Wisconsin 53141, USA; Dang, Liem X. [Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 93352, USA

2017-10-28

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux; Impey, Madden, and McDonald approaches; and Grote-Hynes theory. We found the residence times of EC around Li+ ions varied from 70 to 450 ps, depending on the correction method used. We found the relaxation times changed significantly from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influence the dissociation kinetics of ion pairing. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

Radiolysis studies on reactive intermediates. Final report, February 1, 1970-August 31, 1980

International Nuclear Information System (INIS)

Kevan, L.

1980-08-01

Research highlights are briefly reviewed concerning studies of excess and solvated electrons, development of new electron spin resonance methods for maximizing the geometrical information about the surroundings of paramagnetic species in disordered systems, atom and ion solvation, and studies on other reactive intermediates. Titles of 155 research publications and 182 scientific talks presented on these areas are given

Solid polymer electrolyte lithium batteries

Science.gov (United States)

Alamgir, Mohamed; Abraham, Kuzhikalail M.

1993-01-01

This invention pertains to Lithium batteries using Li ion (Li.sup.+) conductive solid polymer electrolytes composed of solvates of Li salts immobilized in a solid organic polymer matrix. In particular, this invention relates to Li batteries using solid polymer electrolytes derived by immobilizing solvates formed between a Li salt and an aprotic organic solvent (or mixture of such solvents) in poly(vinyl chloride).

Hydrophilicity and Microsolvation of an Organic Molecule Resolved on the Sub-molecular Level by Scanning Tunneling Microscopy.

Science.gov (United States)

Lucht, Karsten; Loose, Dirk; Ruschmeier, Maximilian; Strotkötter, Valerie; Dyker, Gerald; Morgenstern, Karina

2018-01-26

Low-temperature scanning tunneling microscopy was used to follow the formation of a solvation shell around an adsorbed functionalized azo dye from the attachment of the first water molecule to a fully solvated molecule. Specific functional groups bind initially one water molecule each, which act as anchor points for additional water molecules. Further water attachment occurs in areas close to these functional groups even when the functional groups themselves are already saturated. In contrast, water molecules surround the hydrophobic parts of the molecule only when the two-dimensional solvation shell closes around them. This study thus traces hydrophilic and hydrophobic properties of an organic molecule down to a sub-molecular length scale. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of interaction in systems of MoCl/sub 5/-MeCl/sub 2/ (Me - Sn, Zn, Cd, Hg) - a solvent

Energy Technology Data Exchange (ETDEWEB)

Golub, A M; Trachevskii, V V; Ul' ko, N V [Kievskij Gosudarstvennyj Univ. (Ukrainian SSR)

1978-04-01

Interaction of Mo(5) with dichlorides of tin, zinc, cadmium and mercury in organic solvents was studied by preparative methods, by electron, epr, infrared spectrometry and by conductometry. A polynuclear diamagnetic compound with Mo(5):Sn(2) ratio of 2:1 formed in acetone. A coordination polynuclear compound of (MoOCl/sub 3/)/sub 2/xSnCl/sub 2/x2CH/sub 3/CN was isolated from acetonitrile. It is shown that formation of solvate-chloride and solvate complexes of Mo(5) in solvents depends both on the solvating capacity of the solvent and on stability of the MeCl/sup -3/ (Me is Sn, Zn, Cd, Hg) chloride complex, which grows in the Zn < Sn < Cd < Hg series.

The electron as a chemical entity 201 Farday lecture

International Nuclear Information System (INIS)

Dainton, F.S.

1975-01-01

After an introductory section, the subject is covered in sections, as follows: on 'dropping' an electron into a liquid or an amorphous solid; the preparation of solvated and trapped electrons in condensed media; the physical properties of solvated or trapped electrons (the E.S.R. spectrum and cavity structure; the equivalent conductance, mobility, diffusion constant, and Stokes radius of esub(s)sup(-); the ionic atmosphere relaxation time; the thermodynamic properties of esub(s)sup(-)); spectroscopic and other evidence concerning the cavities (the effects of pressure and temperature on the spectrum; direct evidence for a range of trap sizes for esub(t)sup(-)); the trapping and solvation mechanism; the chemical reactions of esub(s)sup(-); some applications of our knowledge of esub(s)sup(-). (U.K.)

Interfacial tension in systems involving TBP in dodecane, nitric acid, uranyl nitrate and water

International Nuclear Information System (INIS)

Kolarik, Z.; Pipkin, N.

1982-08-01

The interfacial tension was measured at 25 0 C in the systems TBP - n-dodecane/nitric acid - water and TBP - n-dodecane/nitric acid - uranyl nitrate - water. Empirical equations describing the interfacial tension as a function of the concentration of TBP in the starting organic phase and of uranium-(VI) and nitric acid in the equilibrium aqueous phase were suggested. In the absence of uranium (VI), the interfacial tension can also be correlated with the concentration of water in the equilibrium organic phase. Free TBP, hydrated or nonhydrated, and hydrated TBP solvates of nitric acid are interfacially active. Anhydrous TBP solvates of nitric acid and the TBP solvate of uranyl nitrate, which neither is hydrated, do not exhibit any visible interfacial activity. (orig.) [de

Hybrid perovskite solar cells: In situ investigation of solution-processed PbI2 reveals metastable precursors and a pathway to producing porous thin films

KAUST Repository

Barrit, Dounya

2017-04-17

The successful and widely used two-step process of producing the hybrid organic-inorganic perovskite CH3NH3PbI3, consists of converting a solution deposited PbI2 film by reacting it with CH3NH3I. Here, we investigate the solidification of PbI2 films from a DMF solution by performing in situ grazing incidence wide angle X-ray scattering (GIWAXS) measurements. The measurements reveal an elaborate sol–gel process involving three PbI2⋅DMF solvate complexes—including disordered and ordered ones—prior to PbI2 formation. The ordered solvates appear to be metastable as they transform into the PbI2 phase in air within minutes without annealing. Morphological analysis of air-dried and annealed films reveals that the air-dried PbI2 is substantially more porous when the coating process produces one of the intermediate solvates, making this more suitable for subsequent conversion into the perovskite phase. The observation of metastable solvates on the pathway to PbI2 formation open up new opportunities for influencing the two-step conversion of metal halides into efficient light harvesting or emitting perovskite semiconductors.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi; Mueller, Karl T.

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directly involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface.

Science.gov (United States)

Sarkar, Rupa; Ghosh, Manoranjan; Pal, Samir Kumar

2005-02-01

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.

Electrolyte Suitable for Use in a Lithium Ion Cell or Battery

Science.gov (United States)

McDonald, Robert C. (Inventor)

2014-01-01

Electrolyte suitable for use in a lithium ion cell or battery. According to one embodiment, the electrolyte includes a fluorinated lithium ion salt and a solvent system that solvates lithium ions and that yields a high dielectric constant, a low viscosity and a high flashpoint. In one embodiment, the solvent system includes a mixture of an aprotic lithium ion solvating solvent and an aprotic fluorinated solvent.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

Science.gov (United States)

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be

Characterisation of different polymorphs of tris(8-hydroxyquinolinatoaluminium(III using solid-state NMR and DFT calculations

Directory of Open Access Journals (Sweden)

Periasamy N

2009-11-01

Full Text Available Abstract Background Organic light emitting devices (OLED are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato-aluminium(III, known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D and two-dimensional (2D multiple-quantum magic-angle spinning (MQMAS NMR studies of the meridional (α-phase and the facial (δ-phase isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer from the solid-state NMR studies

Conformational analysis of cellobiose by electronic structure theories.

Science.gov (United States)

French, Alfred D; Johnson, Glenn P; Cramer, Christopher J; Csonka, Gábor I

2012-03-01

Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory. Published by Elsevier Ltd.

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture.

Science.gov (United States)

Mennucci, Benedetta; da Silva, Clarissa O

2008-06-05

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.

Radiolysis studies on reactive intermediates. Technical progress report, November 1, 1977--November 1, 1978

International Nuclear Information System (INIS)

Kevan, L.

1978-11-01

During the past year a more quantitative characterization was developed of the localization and solvation processes of excess electrons and in particular the presolvated state of excess electrons produced by high energy chemistry. In addition, it was demonstrated how radical environments may be studied by the tunnelling mode mechanism of electron spin-lattice relaxation and atom solvation and radical orientation on surfaces were studied by electron spin-echo modulation techniques

Some notes on diffusion of radionuclides through compacted clays

International Nuclear Information System (INIS)

Eriksen, T.E.

1989-05-01

The apparent diffusivities of some simple cations i.e. Sr 2+ , Cs + in water saturated bentonite indicates that diffusion takes place both in the pore solution and within the solvation sheath of the exchangeable cations. Data from some earlier diffusion experiments have been re-evaluated and the results suggest that diffusion within the solvation sheath of the exchangeable cations is the dominating mechanism for Sr 2+ and Cs + . (author)

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 calculated positron wavefunctions penetrate far outside the X− ions in the [X−, e+] sta propose that a bubble is formed around the [X−, e+] state, similar to the Ps bubble found in nearly all liquids. F−ions did not react w Preliminary results showed that CN− ions react with eaq+ while OH−ions are non...... in the Cl− case) at higher concentrations. This saturation and the high-concentration effects-in the angular correlation results were interpreted as caused by rather complicated spur effects, wh It is proposed that spur electrons may pick off the positron from the [X−, e+ states with an efficiency which...

Combined techniques for studying actinide complexes in room temperature ionic liquids

International Nuclear Information System (INIS)

Gaillard, C.; Billard, I.; Mekki, S.; Ouadi, A.; Hennig, Ch.; Denecke, M.A.

2007-01-01

Room temperature ionic liquids (RTILs) are a new class of solvents. Their main interest is related to their 'green' properties (non-volatile, non-flammable, etc.), but also from the variability of their physico-chemical properties (stability, hydrophobicity, viscosity) as a function of the RTIL cationic and anionic components. In the frame of the nuclear fuel reprocessing, RTILs are particularly attractive in order to improve existing processes or to develop new ones for actinide and lanthanide partitioning, in replacement of toxic solvents used nowadays, for metal electrodeposition or for liquid/liquid extraction by the use of task specific ionic liquids. However, despite the increasing number of publications devoted to ionic liquids, the solvation effects, the solute-solvent and solvent-solvent interactions are still hardly known. These fundamental aspects are of tremendous importance to the understanding of the solvating properties of these new solvents. In this frame, we have undertaken studies on the solvation and complexation of lanthanides (III) and actinides in RTILs, by the use of spectroscopic techniques. Experiments were led in various ionic liquids in order to highlight the role of the anionic part of the RTILs on the reactivity of the studied cations. Results have clearly shown that solvation phenomena in RTILs are not as 'simple' as in classical solvents. The dissolution of a Ln/An salt, even if complete, does not imply dissociation and solvation of the metal cation by the RTILs anions only. The nature of first co-ordination sphere of Ln/An depends on the competition between its counter-anions and the RTIL anions, which, in turn, influence the complexation reaction with other added anions such as chlorides. (authors)

Modified solution calorimetry approach for determination of vaporization and sublimation enthalpies of branched-chain aliphatic and alkyl aromatic compounds at T = 298.15 K

International Nuclear Information System (INIS)

Varfolomeev, Mikhail A.; Novikov, Vladimir B.; Nagrimanov, Ruslan N.; Solomonov, Boris N.

2015-01-01

Highlights: • Solution enthalpies of 18 branching-chain alkyl aromatic and aliphatic compounds in cyclohexane were measured. • Group contributions to the enthalpy of solvation due to branching and substitution in carbon chain were evaluated. • Modified solution calorimetry based approach for determination of vaporization/sublimation enthalpies was proposed. • This approach provides vaporization/sublimation enthalpies directly at T = 298.15 K. • Vaporization/sublimation enthalpies of 35 branched-chain alkyl aromatic and aliphatic compounds were determined. - Abstract: The enthalpies of solution, solvation and vaporization/sublimation are interrelated values combined in the simplest thermodynamic circle. Hence, experimental determination of vaporization/sublimation enthalpy can be substituted by experimentally simpler determination of solution enthalpy when solvation enthalpy is known. Previously it was found that solvation enthalpies of a wide range of unbranched aliphatic and aromatic solutes in saturated hydrocarbons are in good linear correlation with their molar refraction values. This allows to estimate the vaporization/sublimation enthalpy of any unbranched organic compound from its solution enthalpy in saturated hydrocarbon and molar refraction. In the present work this approach was modified for determination of vaporization/sublimation enthalpy of branched-chain alkyl aromatic and aliphatic compounds. Group contributions to the enthalpy of solvation due to the branching of carbon chain were evaluated. Enthalpies of solution at infinite dilution of 18 branched-chain aliphatic and alkyl aromatic compounds were measured at T = 298.15 K. Vaporization/sublimation enthalpies for 35 branched aliphatic and alkyl aromatic compounds were determined by using modified solution calorimetry approach. These values are in good agreement with available literature data on vaporization/sublimation enthalpies obtained by conventional methods.

Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

Science.gov (United States)

Park, Jin-Young; Woon, David E.

2004-01-01

Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

Quantum Chemical Benchmarking, Validation, and Prediction of Acidity Constants for Substituted Pyridinium Ions and Pyridinyl Radicals.

Science.gov (United States)

Keith, John A; Carter, Emily A

2012-09-11

Sensibly modeling (photo)electrocatalytic reactions involving proton and electron transfer with computational quantum chemistry requires accurate descriptions of protonated, deprotonated, and radical species in solution. Procedures to do this are generally nontrivial, especially in cases that involve radical anions that are unstable in the gas phase. Recently, pyridinium and the corresponding reduced neutral radical have been postulated as key catalysts in the reduction of CO2 to methanol. To assess practical methodologies to describe the acid/base chemistry of these species, we employed density functional theory (DFT) in tandem with implicit solvation models to calculate acidity constants for 22 substituted pyridinium cations and their corresponding pyridinyl radicals in water solvent. We first benchmarked our calculations against experimental pyridinium deprotonation energies in both gas and aqueous phases. DFT with hybrid exchange-correlation functionals provide chemical accuracy for gas-phase data and allow absolute prediction of experimental pKas with unsigned errors under 1 pKa unit. The accuracy of this economical pKa calculation approach was further verified by benchmarking against highly accurate (but very expensive) CCSD(T)-F12 calculations. We compare the relative importance and sensitivity of these energies to selection of solvation model, solvation energy definitions, implicit solvation cavity definition, basis sets, electron densities, model geometries, and mixed implicit/explicit models. After determining the most accurate model to reproduce experimentally-known pKas from first principles, we apply the same approach to predict pKas for radical pyridinyl species that have been proposed relevant under electrochemical conditions. This work provides considerable insight into the pitfalls using continuum solvation models, particularly when used for radical species.

Two-component self-assembly with solvent leading to "wet" and microcrystalline organogel fibers.

Science.gov (United States)

Löfman, Miika; Lahtinen, Manu; Rissanen, Kari; Sievänen, Elina

2015-01-15

The microcrystalline fibers of N-(2-aminoethyl)-3α-hydroxy-5β-cholan-24-amide 1 provided a useful model system for studying the complex relationship between morphology, experimental parameters, solvent, and the phenomenon of organogelation. The presence of solvents in the solid forms of 1 along with crystallization behavior suggested solvate formation and polymorphic behavior. Forty solid state- and xerogel samples of 1 formed in organic solvents and in three categories of experimental conditions were analyzed with single crystal X-ray diffraction (XRD), powder X-ray diffraction (PXRD), Raman microscopy, and attenuated total reflection Fourier-transform infrared spectroscopy (ATR FTIR). Two polymorphs and four isostructural aromatic solvates of 1 were found among some unknown forms in the samples. Single crystal X-ray structures of one polymorph and bromobenzene solvate were obtained, the latter from a xerogel. Multiple crystal forms could be present in a sample, and their contributions to gelation were estimated taking the experimental conditions into account. Gelator 1 could act as a variable component gelator, either alone or in combination with an aromatic solvent. The research brings new insight into the structures of microcrystalline organogel fibers, linking solvate/inclusion crystal formation with microcrystalline fibers of an organogelator for the first time. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular Design of Sulfonated Triblock Copolymer Permselective Membranes

Science.gov (United States)

2008-07-03

on DNA solvation in water [39] and simulations of polyacrylic acid with calcium counterion.[40] Mesoscale approaches to polyelectrolyte modeling...interacts strongly with both proton and potassium cation. Addition of three extra DMMP molecules does not change the nature of proton solvation. The ion...the potassium ion with K-O distance of 0.22nm. This does not mean a coordination of DMMP molecules by the ion. However, this result suggests a very

Influence of nitric acid on the kinetic of complexation of uranyl nitrate extracted by TBP

International Nuclear Information System (INIS)

Pushlenkov, M.F.; Zimenkov, V.V.

1982-02-01

The effect of nitric acid on the solvatation rate of uranyl nitrate with tributyl phosphate is studied. In the process of mass transfer, it is shown that nitric acid enables the extraction of uranyl nitrate, therefore its concentration in the organic phase exceeds that in equilibrium solution. Subsequently uranyl nitrate ''displaces'' nitric acid. The presence of the acid in aqueous and organic phases affects in a complicated manner the rate of solvatation of uranyl nitrate with tributyl phosphate [fr

Time-dependent stokes shifts of fluorescent dyes in the hydrophobic backbone region of a phospholipid bilayer: Combination of fluorescence spectroscopy and ab initio calculations

Czech Academy of Sciences Publication Activity Database

Sýkora, Jan; Slavíček, Petr; Jungwirth, Pavel; Barucha-Kraszewska, Justyna; Hof, Martin

2007-01-01

Roč. 111, č. 21 (2007), s. 5869-5877 ISSN 1520-6106 R&D Projects: GA AV ČR IAA400400503; GA MŠk LC512; GA MŠk(CZ) LC06063 Grant - others:GA ČR GP203/07/P449 Institutional research plan: CEZ:AV0Z40400503; CEZ:AV0Z40550506 Keywords : solvation dynamics * solvent relaxation * 9-anthroid acid * preferential solvation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.086, year: 2007

Structural and energetic properties of La3+ in water/DMSO mixtures

Science.gov (United States)

Montagna, Maria; Spezia, Riccardo; Bodo, Enrico

2017-11-01

By using molecular dynamics based on a custom polarizable force field, we have studied the solvation of La3+ in an equimolar mixture of dimethylsulfoxide (DMSO) with water. An extended structural analysis has been performed to provide a complete picture of the physical properties at the basis of the interaction of La3+ with both solvents. Through our simulations we found that, very likely, the first solvation shell in the mixture is not unlike the one found in pure water or pure DMSO and contains 9 solvent molecules. We have also found that the solvation is preferentially due to DMSO molecules with the water initially present in first shell quickly leaving to the bulk. The dehydration process of the first shell has been analyzed by both plain MD simulations and a constrained dynamics approach; the free energy profiles for the extraction of water from first shell have also been computed.

A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins

Science.gov (United States)

Xu, Jingjie; Lu, Benzhuo

2018-01-01

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations. PMID:29495644

Thermodynamics and kinetics of thermal decomposition of dibutylalkyl and dipentylalkyl phosphonate-nitric acid systems

International Nuclear Information System (INIS)

Chandran, K.; Brahmananda, C.V.S.; Anthonysamy, S.; Srinivasan, T.G.; Ganesan, V.

2013-01-01

Tributyl phosphate (TBP) is used in the reprocessing industry for the separation of uranium and plutonium from the spent nuclear fuels by PUREX process. A variety of dialkylalky/phosphonates were synthesised and their extraction behaviour on actinides was studied in this laboratory. The superior extraction characteristics of phosphonates make them useful for several metal recovery applications in the nuclear fuel cycle. However, higher solubility of phosphonates in aqueous phase as compared to TBP, introduces higher chances of the formation of thermally active 'red oil' like substances during the evaporation of aqueous streams. Thermal stability of neat and nitric acid solvated homologues of four dibutylalkyl phosphonates namely, dibutylpropyl phosphonate (DBPrP), dibutylbutyl phosphonate (DBBP), dibutylpentyl phosphonate (DBPP), dibutylhexyl phosphonate (DBHeP), and two dipentylalkyl phosphonates viz. dipentylbutyl phosphonate (DPBP), dipentylhexyl phosphonate (DPHeP) were studied. Experiments were conducted using an adiabatic calorimeter in heat-wait-search mode. Various stoichiometry of nitric acid-solvated DBalP and DPalP were prepared by equilibrating the respective organic with 4-15.6 M nitric acid followed by separation. Neat DBalP and DPalP are stable up to the temperature of ∼ 555 K while their acid-solvates decomposed in the temperature range 380-403 K. The results also indicated that the presence of nitric acid accelerated the decomposition of phosphonates. Decomposition of these acid solvated phosphonates is found to be exothermic and follows first order kinetics. The onset temperature, adiabatic temperature rise, pressure rise, decomposition enthalpy and activation energy were found to strongly depend on the nitric acid content of the acid-solvates. The studies also indicate that dibutylalkyl and dipentylalkyl phosphonates are also prone to form 'red oil' like substances under extreme conditions and can lead to run-away reactions

EFFECT OF AN ADDITIONAL HYDROPHILIC VERSUS HYDROPHOBIC COAT ON THE QUALITY OF DENTINAL SEALING PROVIDED BY TWO-STEP ETCH-AND-RINSE ADHESIVES

Science.gov (United States)

Silva, Safira Marques de Andrade; Carrilho, Marcela Rocha de Oliveira; Marquezini, Luiz; Garcia, Fernanda Cristina Pimentel; Manso, Adriana Pigozzo; Alves, Marcelo Corrêa; de Carvalho, Ricardo Marins

2009-01-01

Objective: To test the hypothesis that the quality of the dentinal sealing provided by two-step etch-and-rinse adhesives cannot be altered by the addition of an extra layer of the respective adhesive or the application of a more hydrophobic, non-solvated resin. Material and Methods: full-crown preparations were acid-etched with phosphoric acid for 15 s and bonded with Adper Single Bond (3M ESPE), Excite DSC (Ivoclar/Vivadent) or Prime & Bond NT (Dentsply). The adhesives were used according to the manufacturers' instructions (control groups) or after application to dentin they were a) covered with an extra coat of each respective system or b) coated with a non-solvated bonding agent (Adper Scotchbond Multi-Purpose Adhesive, 3M ESPE). Fluid flow rate was measured before and after dentin surfaces were acid-etched and bonded with adhesives. Results: None of the adhesives or experimental treatments was capable to block completely the fluid transudation across the treated dentin. Application of an extra coat of the adhesive did not reduce the fluid flow rate of adhesive-bonded dentin (p>0.05). Conversely, the application of a more hydrophobic non-solvated resin resulted in significant reductions in the fluid flow rate (padhesives. Conclusions: The quality of the dentinal sealing provided by etch-and-rinse adhesives can be significantly improved by the application of a more hydrophobic, non-solvated bonding agent. PMID:19466248

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

International Nuclear Information System (INIS)

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

2007-01-01

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

Nonlinear Poisson equation for heterogeneous media.

Science.gov (United States)

Hu, Langhua; Wei, Guo-Wei

2012-08-22

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Infrared rovibrational spectroscopy of OH–C2H2 in 4He nanodroplets: Parity splitting due to partially quenched electronic angular momentum

International Nuclear Information System (INIS)

Douberly, Gary E.; Liang, Tao; Raston, Paul L.; Marshall, Mark D.

2015-01-01

The T-shaped OH–C 2 H 2 complex is formed in helium droplets via the sequential pick-up and solvation of the monomer fragments. Rovibrational spectra of the a-type OH stretch and b-type antisymmetric CH stretch vibrations contain resolved parity splitting that reveals the extent to which electronic angular momentum of the OH moiety is quenched upon complex formation. The energy difference between the spin-orbit coupled 2 B 1 (A″) and 2 B 2 (A′) electronic states is determined spectroscopically to be 216 cm −1 in helium droplets, which is 13 cm −1 larger than in the gas phase [Marshall et al., J. Chem. Phys. 121, 5845 (2004)]. The effect of the helium is rationalized as a difference in the solvation free energies of the two electronic states. This interpretation is motivated by the separation between the Q(3/2) and R(3/2) transitions in the infrared spectrum of the helium-solvated 2 Π 3/2 OH radical. Despite the expectation of a reduced rotational constant, the observed Q(3/2) to R(3/2) splitting is larger than in the gas phase by ≈0.3 cm −1 . This observation can be accounted for quantitatively by assuming the energetic separation between 2 Π 3/2 and 2 Π 1/2 manifolds is increased by ≈40 cm −1 upon helium solvation

Ion Correlation Effects in Salt-Doped Block Copolymers

Science.gov (United States)

Brown, Jonathan R.; Seo, Youngmi; Hall, Lisa M.

2018-03-01

We apply classical density functional theory to study how salt changes the microphase morphology of diblock copolymers. Polymers are freely jointed and one monomer type favorably interacts with ions, to account for the selective solvation that arises from different dielectric constants of the microphases. By including correlations from liquid state theory of an unbound reference fluid, the theory can treat chain behavior, microphase separation, ion correlations, and preferential solvation, at the same coarse-grained level. We show good agreement with molecular dynamics simulations.