Restrained Proton Indicator in Combined Quantum-Mechanics/Molecular-Mechanics Dynamics Simulations of Proton Transfer through a Carbon Nanotube.

PubMed

Duster, Adam W; Lin, Hai

2017-09-14

Recently, a collective variable "proton indicator" was purposed for tracking an excess proton solvated in bulk water in molecular dynamics simulations. In this work, we demonstrate the feasibility of utilizing the position of this proton indicator as a reaction coordinate to model an excess proton migrating through a hydrophobic carbon nanotube in combined quantum-mechanics/molecular-mechanics simulations. Our results indicate that applying a harmonic restraint to the proton indicator in the bulk solvent near the nanotube pore entrance leads to the recruitment of water molecules into the pore. This is consistent with an earlier study that employed a multistate empirical valence bond potential and a different representation (center of excess charge) of the proton. We attribute this water recruitment to the delocalized nature of the solvated proton, which prefers to be in high-dielectric bulk solvent. While water recruitment into the pore is considered an artifact in the present simulations (because of the artificially imposed restraint on the proton), if the proton were naturally restrained, it could assist in building water wires prior to proton transfer through the pore. The potential of mean force for a proton translocation through the water-filled pore was computed by umbrella sampling, where the bias potentials were applied to the proton indicator. The free energy curve and barrier heights agree reasonably with those in the literature. The results suggest that the proton indicator can be used as a reaction coordinate in simulations of proton transport in confined environments.

A compact proton spectrometer for measurement of the absolute DD proton spectrum from which yield and ρR are determined in thin-shell inertial-confinement-fusion implosions.

PubMed

Rosenberg, M J; Zylstra, A B; Frenje, J A; Rinderknecht, H G; Johnson, M Gatu; Waugh, C J; Séguin, F H; Sio, H; Sinenian, N; Li, C K; Petrasso, R D; Glebov, V Yu; Hohenberger, M; Stoeckl, C; Sangster, T C; Yeamans, C B; LePape, S; Mackinnon, A J; Bionta, R M; Talison, B; Casey, D T; Landen, O L; Moran, M J; Zacharias, R A; Kilkenny, J D; Nikroo, A

2014-10-01

A compact, step range filter proton spectrometer has been developed for the measurement of the absolute DD proton spectrum, from which yield and areal density (ρR) are inferred for deuterium-filled thin-shell inertial confinement fusion implosions. This spectrometer, which is based on tantalum step-range filters, is sensitive to protons in the energy range 1-9 MeV and can be used to measure proton spectra at mean energies of ∼1-3 MeV. It has been developed and implemented using a linear accelerator and applied to experiments at the OMEGA laser facility and the National Ignition Facility (NIF). Modeling of the proton slowing in the filters is necessary to construct the spectrum, and the yield and energy uncertainties are ±<10% in yield and ±120 keV, respectively. This spectrometer can be used for in situ calibration of DD-neutron yield diagnostics at the NIF.

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.

Excited state intramolecular proton transfer reaction of 4'-N,N-diethylamino-3-hydroxyflavone and solvation dynamics in room temperature ionic liquids studied by optical Kerr gate fluorescence measurement.

PubMed

Kimura, Yoshifumi; Fukuda, Masanori; Suda, Kayo; Terazima, Masahide

2010-09-16

Fluorescence dynamics of 4'-N,N-diethylamino-3-hydroxyflavone (DEAHF) and its methoxy derivative (DEAMF) in various room temperature ionic liquids (RTILs) have been studied mainly by an optical Kerr gate method. DEAMF showed a single band fluorescence whose peak shifted with time by the solvation dynamics. The averaged solvation time determined by the fluorescence peak shift was proportional to the viscosity of the solvent except for tetradecyltrihexylphosphonium bis(trifluoromethanesulfonyl)amide. The solvation times were consistent with reported values determined with different probe molecules. DEAHF showed dual fluorescence due to the normal and tautomer forms produced by the excited state intramolecular proton transfer (ESIPT), and the relative intensities were dependent on the time and the solvent cation or anion species. By using the information of the fluorescence spectrum of DEAMF, the fluorescence spectrum of DEAHF at each delay time after the photoexcitation was decomposed into the normal and the tautomer fluorescence components, respectively. The normal component showed a very fast decay simulated by a biexponential function (2-3 and 20-30 ps) with an additional slower decay component. The tautomer component showed a rise with the time constants corresponding to the faster decay of the normal form with an additional instantaneous rise. The faster dynamics of the normal and tautomer population changes were assigned to the ESIPT process, while the slower decay of the fluorescence was attributed to the population decay from the excited state through the radiative and nonradiative processes. The average ESIPT time was much faster than the averaged solvation time of RTILs. Basically, the ESIPT kinetics in RTILs is similar to those in conventional liquid solvents like acetonitrile (Chou et al. J. Phys. Chem. A 2005, 109, 3777). The faster ESIPT is interpreted in terms of the activation barrierless process from the Franck-Condon state before the solvation of

GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects.

PubMed

Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

2018-02-09

15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach. Copyright © 2018 John Wiley & Sons, Ltd.

Protonic and Electronic Charge Carriers in Solvated Biomacromolecules

DTIC Science & Technology

1989-01-01

samples with sufficient mechanical strength. The pellets were approximately one millimeter thick and were placed between two platinium foil...attached to the vacuum line, Figure 2, by simply tilting them. The platinium electrodes were blocking for protons so all protonic carriers were released

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

PubMed

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

NASA Astrophysics Data System (ADS)

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.

A compact proton spectrometer for measurement of the absolute DD proton spectrum from which yield and pR are determined in thin-shell inertial-confinement-fusion implosions

DOE PAGES

Rosenberg, M. J.; Zylstra, A. B.; Frenje, J. A.; ...

2014-10-10

A compact, step range filter proton spectrometer has been developed for the measurement of the absolute DD proton spectrum, from which yield and areal density (ρR) are inferred for deuterium-filled thin-shell inertial confinement fusion implosions. This spectrometer, which is based on tantalum step-range filters, is sensitive to protons in the energy range 1-9 MeV and can be used to measure proton spectra at mean energies of ~1-3 MeV. It has been developed and implemented using a linear accelerator and applied to experiments at the OMEGA laser facility and the National Ignition Facility (NIF). Modeling of the proton slowing in themore » filters is necessary to construct the spectrum, and the yield and energy uncertainties are ±<10% in yield and ±120 keV, respectively. This spectrometer can be used for in situ calibration of DD-neutron yield diagnostics at the NIF« less

A compact proton spectrometer for measurement of the absolute DD proton spectrum from which yield and ρR are determined in thin-shell inertial-confinement-fusion implosions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenberg, M. J., E-mail: mrosenbe@mit.edu; Zylstra, A. B.; Frenje, J. A.

2014-10-01

A compact, step range filter proton spectrometer has been developed for the measurement of the absolute DD proton spectrum, from which yield and areal density (ρR) are inferred for deuterium-filled thin-shell inertial confinement fusion implosions. This spectrometer, which is based on tantalum step-range filters, is sensitive to protons in the energy range 1-9 MeV and can be used to measure proton spectra at mean energies of ~1-3 MeV. It has been developed and implemented using a linear accelerator and applied to experiments at the OMEGA laser facility and the National Ignition Facility (NIF). Modeling of the proton slowing in themore » filters is necessary to construct the spectrum, and the yield and energy uncertainties are ±<10% in yield and ±120 keV, respectively. This spectrometer can be used for in situ calibration of DD-neutron yield diagnostics at the NIF.« less

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

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

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.

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

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary 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. PMID:24205452

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side

Absolute total and partial dissociative cross sections of pyrimidine at electron and proton intermediate impact velocities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolff, Wania, E-mail: wania@if.ufrj.br; Luna, Hugo; Sigaud, Lucas

Absolute total non-dissociative and partial dissociative cross sections of pyrimidine were measured for electron impact energies ranging from 70 to 400 eV and for proton impact energies from 125 up to 2500 keV. MOs ionization induced by coulomb interaction were studied by measuring both ionization and partial dissociative cross sections through time of flight mass spectrometry and by obtaining the branching ratios for fragment formation via a model calculation based on the Born approximation. The partial yields and the absolute cross sections measured as a function of the energy combined with the model calculation proved to be a useful toolmore » to determine the vacancy population of the valence MOs from which several sets of fragment ions are produced. It was also a key point to distinguish the dissociation regimes induced by both particles. A comparison with previous experimental results is also presented.« less

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller

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

PubMed

van Noort, Paul C M

2012-04-01

Abraham solvation equations find widespread use in environmental chemistry. Until now, the intercept in these equations was determined by fitting experimental data. To simplify the determination of the coefficients in Abraham solvation equations, this study derives theoretical expressions for the value of the intercept for various partition processes. To that end, a modification of the description of the Ben-Naim standard state into the van der Waals volume is proposed. Differences between predicted and fitted values of the Abraham solvation equation intercept for the enthalpy of solvation, the entropy of solvation, solvent-water partitioning, air-solvent partitioning, partitioning into micelles, partitioning into lipid membranes and lipids, and chromatographic retention indices are comparable to experimental uncertainties in these values. Copyright © 2011 Elsevier Ltd. All rights reserved.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar

A unified perspective on preferential solvation and adsorption based on inhomogeneous solvation theory

NASA Astrophysics Data System (ADS)

Shimizu, Seishi; Matubayasi, Nobuyuki

2018-02-01

How cosolvents affects solvation has been revealed through the independent determination of solute-solvent and solute-cosolvent interactions guaranteed by the phase rule. Based on the first principles of inhomogeneous solvation theory, we present here a general matrix theory encompassing both preferential solvation and surface adsorption. The central role of the stability conditions, that govern how many excess numbers (surface excesses) are independently determinable, have been clarified from the first principles. The advantage of the inhomogeneous approach has been demonstrated to be in its ease in treating solvation and adsorption in a unified manner, while its disadvantage, for example in membrane dialysis experiments, can be overcome by the inhomogeneous-homogeneous conversion.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins

PubMed Central

Vorobjev, Yury N.; Vila, Jorge A.

2009-01-01

A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford–Schellman integral if the proteins contain more than ∼20–25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pKa's of the ionizable groups of these proteins within an average absolute value of 0.4 pK units and a maximum error of 1.2 pK units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford–Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics

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

DOE PAGES

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

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Proton transfer to charged platinum electrodes. A molecular dynamics trajectory study.

PubMed

Wilhelm, Florian; Schmickler, Wolfgang; Spohr, Eckhard

2010-05-05

A recently developed empirical valence bond (EVB) model for proton transfer on Pt(111) electrodes (Wilhelm et al 2008 J. Phys. Chem. C 112 10814) has been applied in molecular dynamics (MD) simulations of a water film in contact with a charged Pt surface. A total of seven negative surface charge densities σ between -7.5 and -18.9 µC cm(-2) were investigated. For each value of σ, between 30 and 84 initial conditions of a solvated proton within a water slab were sampled, and the trajectories were integrated until discharge of a proton occurred on the charged surfaces. We have calculated the mean rates for discharge and for adsorption of solvated protons within the adsorbed water layer in contact with the metal electrode as a function of surface charge density. For the less negative values of σ we observe a Tafel-like exponential increase of discharge rate with decreasing σ. At the more negative values this exponential increase levels off and the discharge process is apparently transport limited. Mechanistically, the Tafel regime corresponds to a stepwise proton transfer: first, a proton is transferred from the bulk into the contact water layer, which is followed by transfer of a proton to the charged surface and concomitant discharge. At the more negative surface charge densities the proton transfer into the contact water layer and the transfer of another proton to the surface and its discharge occur almost simultaneously.

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832

Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soniat, Marielle; Rick, Steven W., E-mail: srick@uno.edu; Kumar, Revati

2015-07-28

The role of the solvated excess proton and hydroxide ions in interfacial properties is an interesting scientific question with applications in a variety of aqueous behaviors. The role that charge transfer (CT) plays in interfacial behavior is also an unsettled question. Quantum calculations are carried out on clusters of water with an excess proton or a missing proton (hydroxide) to determine their CT. The quantum results are applied to analysis of multi-state empirical valence bond trajectories. The polyatomic nature of the solvated excess proton and hydroxide ion results in directionally dependent CT, depending on whether a water molecule is amore » hydrogen bond donor or acceptor in relation to the ion. With polyatomic molecules, CT also depends on the intramolecular bond distances in addition to intermolecular distances. The hydrated proton and hydroxide affect water’s liquid/vapor interface in a manner similar to monatomic ions, in that they induce a hydrogen-bonding imbalance at the surface, which results in charged surface waters. This hydrogen bond imbalance, and thus the charged waters at the surface, persists until the ion is at least 10 Å away from the interface.« less

Readily Made Solvated Electrons

ERIC Educational Resources Information Center

Ibanez, Jorge G.; Guerra-Millan, Francisco J.; Hugerat, Muhamad; Vazquez-Olavarrieta, Jorge L.; Basheer, Ahmad; Abu-Much, Riam

2011-01-01

The existence of solvated electrons has been known for a long time. Key methods for their production (i.e., photoionization of reducing ions, water radiolysis, and the reaction between H[middle dot] and OH[superscript -]) are unsuitable for most school laboratories. We describe a simple experiment to produce liquid ammonia and solvated electrons…

Preparation of cerium halide solvate complexes

DOEpatents

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

2013-08-06

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

The effect of co-solvent addition on Li-solvation in solvate electrolytes in Li-S batteries

NASA Astrophysics Data System (ADS)

Lau, Kah Chun; See, Kimberly A.; Wu, Heng-Liang; Shin, Minjeong; Curtiss, Larry A.; Gewirth, Andrew A.

Li?S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed `solvates' that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability, however, cosolvents that thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. In this work, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations are used to study the unique solvation structure of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether as co-solvent in solvate (MeCN)2?LiTFSI electrolyte that used in Li-S battery. The underlying design rules and implications to Li-S battery performance will be discussed. This work was supported as part of the Joint Center for Energy Storage Research, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

Thermodynamic-ensemble independence of solvation free energy.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-02-10

Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds. Theoretical estimates of the solvation free energy based on the canonical or grand-canonical ensemble are pertinent to experiments carried out under constant pressure without any conversion.

IR spectral assignments for the hydrated excess proton in liquid water.

PubMed

Biswas, Rajib; Carpenter, William; Fournier, Joseph A; Voth, Gregory A; Tokmakoff, Andrei

2017-04-21

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm -1 for every local proton configuration, with the region 2000-2600 cm -1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H + ⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H 5 O2+moiety.

IR spectral assignments for the hydrated excess proton in liquid water

NASA Astrophysics Data System (ADS)

Biswas, Rajib; Carpenter, William; Fournier, Joseph A.; Voth, Gregory A.; Tokmakoff, Andrei

2017-04-01

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5+O2 moiety.

Equilibrium constants and protonation site for N-methylbenzenesulfonamides

PubMed Central

Rosa da Costa, Ana M; García-Río, Luis; Pessêgo, Márcia

2011-01-01

Summary The protonation equilibria of four substituted N-methylbenzenesulfonamides, X-MBS: X = 4-MeO (3a), 4-Me (3b), 4-Cl (3c) and 4-NO2 (3d), in aqueous sulfuric acid were studied at 25 °C by UV–vis spectroscopy. As expected, the values for the acidity constants are highly dependent on the electron-donor character of the substituent (the pK BH+ values are −3.5 ± 0.2, −4.2 ± 0.2, −5.2 ± 0.3 and −6.0 ± 0.3 for 3a, 3b, 3c and 3d, respectively). The solvation parameter m* is always higher than 0.5 and points to a decrease in the importance of solvation on the cation stabilization as the electron-donor character of the substituent increases. Hammett plots of the equilibrium constants showed a better correlation with the σ+ substituent parameter than with σ, which indicates that the initial protonation site is the oxygen atom of the sulfonyl group. PMID:22238552

Proton transfer in liquid water confined inside graphene slabs

NASA Astrophysics Data System (ADS)

Tahat, Amani; Martí, Jordi

2015-09-01

The microscopic structure and dynamics of an excess proton in water constrained in narrow graphene slabs between 0.7 and 3.1 nm wide has been studied by means of a series of molecular dynamics simulations. Interaction of water and carbon with the proton species was modeled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of confinement on proton solvation structure and on its dynamical properties has been considered for varying densities. The system is organized in one interfacial and a bulk-like region, both of variable size. In the widest interplate separations, the lone proton shows a marked tendency to place itself in the bulk phase of the system, due to the repulsive interaction with the carbon atoms. However, as the system is compressed and the proton is forced to move to the vicinity of graphene walls it moves closer to the interface, producing a neat enhancement of the local structure. We found a marked slowdown of proton transfer when the separation of the two graphene plates is reduced. In the case of lowest distances between graphene plates (0.7 and 0.9 nm), only one or two water layers persist and the two-dimensional character of water structure becomes evident. By means of spectroscopical analysis, we observed the persistence of Zundel and Eigen structures in all cases, although at low interplate separations a signature frequency band around 2500 cm-1 suffers a blue shift and moves to characteristic values of asymmetric hydronium ion vibrations, indicating some unstability of the typical Zundel-Eigen moieties and their eventual conversion to a single hydronium species solvated by water.

Hydrophobic Solvation: Aqueous Methane Solutions

ERIC Educational Resources Information Center

Konrod, Oliver; Lankau, Timm

2007-01-01

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

Learning about Biomolecular Solvation from Water in Protein Crystals.

PubMed

Altan, Irem; Fusco, Diana; Afonine, Pavel V; Charbonneau, Patrick

2018-03-08

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

NASA Astrophysics Data System (ADS)

Eustis, Soren Newman

Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties

SN1 reactions in supercritical carbon dioxide in the presence of alcohols: the role of preferential solvation.

PubMed

Delgado-Abad, Thais; Martínez-Ferrer, Jaime; Acerete, Rafael; Asensio, Gregorio; Mello, Rossella; González-Núñez, María Elena

2016-07-06

Ethanol () inhibits SN1 reactions of alkyl halides in supercritical carbon dioxide (scCO2) and gives no ethers as products. The unexpected behaviour of alcohols in the reaction of alkyl halides with 1,3-dimethoxybenzene () in scCO2 under different conditions is rationalised in terms of Brønsted and Lewis acid-base equilibria of reagents, intermediates, additives and products in a singular solvent characterised by: (i) the strong quadrupole and Lewis acid character of carbon dioxide, which hinders SN2 paths by strongly solvating basic solutes; (ii) the weak Lewis base character of carbon dioxide, which prevents it from behaving as a proton sink; (iii) the compressible nature of scCO2, which enhances the impact of preferential solvation on carbon dioxide availability for the solvent-demanding rate determining step.

Preparation and physicochemical characterization of 5 niclosamide solvates and 1 hemisolvate.

PubMed

van Tonder, Elsa C; Mahlatji, Mabatane D; Malan, Sarel F; Liebenberg, Wilna; Caira, Mino R; Song, Mingna; de Villiers, Melgardt M

2004-02-23

The purpose of the study was to characterize the physicochemical, structural, and spectral properties of the 1:1 niclosamide and methanol, diethyl ether, dimethyl sulfoxide, N,N' dimethylformamide, and tetrahydrofuran solvates and the 2:1 niclosamide and tetraethylene glycol hemisolvate prepared by recrystallization from these organic solvents. Structural, spectral, and thermal analysis results confirmed the presence of the solvents and differences in the structural properties of these solvates. In addition, differences in the activation energy of desolvation, batch solution calorimetry, and the aqueous solubility at 25 degrees C, 24 hours, showed the stability of the solvates to be in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > methanol solvate > dimethyl sulfoxide solvate > N,N' dimethylformamide solvate. The intrinsic and powder dissolution rates of the solvates were in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > N,N' dimethylformamide solvate > methanol solvate > dimethyl sulfoxide solvate. Although these nonaqueous solvates had higher solubility and dissolution rates than the monohydrous forms, they were unstable in aqueous media and rapidly transformed to one of the monohydrous forms.

Anion Solvation in Carbonate-Based Electrolytes

DOE PAGES

von Wald Cresce, Arthur; Gobet, Mallory; Borodin, Oleg; ...

2015-11-16

The correlation between Li + solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li +, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li + solvation studies, this work focuses on the interactions between carbonate-based solvents andmore » two anions (hexafluorophosphate, PF 6–, and tetrafluoroborate, BF 4–) that are most frequently used in Li-ion batteries. The possible correlation between such interaction and the interphasial chemistry on cathode surface is also explored.« less

Biomolecular electrostatics and solvation: a computational perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

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

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

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

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

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

2012-11-01

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

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

PubMed Central

Svendsen, Hallvard F.; Merz, Kenneth M.

2009-01-01

A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster and the solvation free energy of the cluster calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a RMSD of 2.6 kcal/mol for anions, for cations the unsigned average error was 2.8 kcal/mol and the RMSD 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model. PMID:19425558

C-PCM based calculation of energy profiles for proton transfer in phosphorus-containing acid- N, N-dimethylformamide complexes

NASA Astrophysics Data System (ADS)

Fedorova, I. V.; Khatuntseva, E. A.; Krest'yaninov, M. A.; Safonova, L. P.

2016-02-01

Proton transfer along the hydrogen bond in complexes of DMF with H3PO4, H3PO3, CH3H2PO3, and their dimers has been investigated by the B3LYP/6-31++G** method in combination with the C-PCM model. When the Oacid···ODMF distance ( R) in the scanning procedure is not fixed, the energy profile in all cases has a single well. When this distance is fixed, there can be a proton transfer in all of the complexes in the gas phase at R > 2.6 Å; if solvation is taken into account, proton transfer can take place at R > 2.4 Å ( R > 2.5 Å for DMF complexes with CH3H2PO3 and its dimer). The height of the energy barrier to proton transfer increases with increasing R. Proton transfer is energetically most favorable in the DMF-phosphoric acid complexes. The structural and energetic characteristics of the hydrogen-bonded complexes calculated on the basis of the solvation model are compared with the same parameters for the complexes in the gas phase.

Rotational spectroscopic study of carbonyl sulfide solvated with hydrogen molecules.

PubMed

Michaud, Julie M; Jäger, Wolfgang

2008-10-14

Rotational spectra of small-sized (H(2))(N)-OCS clusters with N = 2-7 were measured using a pulsed-jet Fourier transform microwave spectrometer. These include spectra of pure (para-H(2))(N)-OCS clusters, pure (ortho-H(2))(N)-OCS clusters, and mixed ortho-H(2) and para-H(2) containing clusters. The rotational lines of ortho-H(2) molecules containing clusters show proton spin-proton spin hyperfine structure, and the pattern evolves as the number of ortho-H(2) molecules in the cluster increases. Various isotopologues of the clusters were investigated, including those with O(13)CS, OC(33)S, OC(34)S, and O(13)C(34)S. Nuclear quadrupole hyperfine structures of rotational transitions were observed for (33)S (nuclear spin quantum number I = 3/2) containing isotopologues. The (33)S nuclear quadrupole coupling constants are compared to the corresponding constant of the OCS monomer and those of the He(N)-OCS clusters. The assignment of the number of solvating hydrogen molecules N is supported by the analyses of the proton spin-proton spin hyperfine structures of the mixed clusters, the dependence of line intensities on sample conditions (pressure and concentrations), and the agreement of the (para-H(2))(N)-OCS and (ortho-H(2))(N)-OCS rotational constants with those from a previous infrared study [J. Tang and A. R. W. McKellar, J. Chem. Phys. 121, 3087 (2004)].

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

PubMed

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 (p<0.05) preference to hydrogen-bond acidic molecules. Through dipole-dipole attraction, 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.

A method for in situ absolute DD yield calibration of neutron time-of-flight detectors on OMEGA using CR-39-based proton detectors.

PubMed

Waugh, C J; Rosenberg, M J; Zylstra, A B; Frenje, J A; Séguin, F H; Petrasso, R D; Glebov, V Yu; Sangster, T C; Stoeckl, C

2015-05-01

Neutron time of flight (nTOF) detectors are used routinely to measure the absolute DD neutron yield at OMEGA. To check the DD yield calibration of these detectors, originally calibrated using indium activation systems, which in turn were cross-calibrated to NOVA nTOF detectors in the early 1990s, a direct in situ calibration method using CR-39 range filter proton detectors has been successfully developed. By measuring DD neutron and proton yields from a series of exploding pusher implosions at OMEGA, a yield calibration coefficient of 1.09 ± 0.02 (relative to the previous coefficient) was determined for the 3m nTOF detector. In addition, comparison of these and other shots indicates that significant reduction in charged particle flux anisotropies is achieved when bang time occurs significantly (on the order of 500 ps) after the trailing edge of the laser pulse. This is an important observation as the main source of the yield calibration error is due to particle anisotropies caused by field effects. The results indicate that the CR-39-nTOF in situ calibration method can serve as a valuable technique for calibrating and reducing the uncertainty in the DD absolute yield calibration of nTOF detector systems on OMEGA, the National Ignition Facility, and laser megajoule.

Differential geometry based solvation model. III. Quantum formulation

PubMed Central

Chen, Zhan; Wei, Guo-Wei

2011-01-01

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

Solvation structure of the halides from x-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antalek, Matthew; Hedman, Britt; Sarangi, Ritimukta, E-mail: ritis@slac.stanford.edu

2016-07-28

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

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.

PubMed

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD

Solvation effect on isomer stability and electronic structures of protonated serotonin

NASA Astrophysics Data System (ADS)

Omidyan, Reza; Amanollahi, Zohreh; Azimi, Gholamhassan

2017-07-01

Microsolvation effect on geometry and transition energies of protonated serotonin has been investigated by MP2 and CC2 quantum chemical methods. Also, conductor-like screening model, implemented recently in the MP2 and ADC(2) methods, was examined to address the bulk water environment's effect on the isomer stability and electronic transition energies of protonated serotonin. It has been predicted that the dipole moment of gas phase isomers plays the main role on the isomer stabilization in water solution and electronic transition shifts. Also, both red- and blue-shift effects have been predicted to take place on electronic transition energies, upon hydration.

Solvated Electrons in Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Ilich, Predrag-Peter; McCormick, Kathleen R.; Atkins, Adam D.; Mell, Geoffrey J.; Flaherty, Timothy J.; Bruck, Martin J.; Goodrich, Heather A.; Hefel, Aaron L.; Juranic, Nenad; Seleem, Suzanne

2010-01-01

A novel experiment is described in which solvated electrons in liquid ammonia reduce a benzyl alcohol carbon without affecting the aromatic ring. The reductive activity of solvated electrons can be partially or completely quenched through the addition of electron scavengers to the reaction mixture. The effectiveness of these scavengers was found…

Electron solvation and localization at interfaces

NASA Astrophysics Data System (ADS)

Harris, Charles B.; Szymanski, Paul; Garrett-Roe, Sean; Miller, Andre D.; Gaffney, Kelly J.; Liu, Simon H.; Bezel, Ilya

2003-12-01

Two-photon photoemission of thiolate/Ag(111), nitrile/Ag(111), and alcohol/Ag(111) interfaces elucidates electron solvation and localization in two dimensions. For low coverages of thiolates on Ag(111), the occupied (HOMO) and unoccupied (LUMO) electronic states of the sulfer-silver bond are localized due to the lattice gas structure of the adsorbate. As the coverage saturates and the adsorbate-adsorbate nearest neighbor distance decreases, the HOMO and LUMO delocalize across many adsorbate molecules. Alcohol- and nitrile-covered Ag(111) surfaces solvate excess image potential state (IPS) electrons. In the case of alcohol-covered surfaces, this solvation is due to a shift in the local workfunction of the surface. For two-monolayer coverages of nitriles/Ag(111), localization accompanies solvation of the IPS. The size of the localized electron can be estimated by Fourier transformation of the wavefunction from momentum- to position-space. The IPS electron localizes to 15 +/- 4 angstroms full-width at half maximum in the plane of the surface, i.e., to a single lattice site.

A method for in situ absolute DD yield calibration of neutron time-of-flight detectors on OMEGA using CR-39-based proton detectors

DOE PAGES

Waugh, C. J.; Rosenberg, M. J.; Zylstra, A. B.; ...

2015-05-27

Neutron time of flight (nTOF) detectors are used routinely to measure the absolute DD neutron yield at OMEGA. To check the DD yield calibration of these detectors, originally calibrated using indium activation systems, which in turn were cross-calibrated to NOVA nTOF detectors in the early 1990s, a direct in situ calibration method using CR-39 range filter proton detectors has been successfully developed. By measuring DD neutron and proton yields from a series of exploding pusher implosions at OMEGA, a yield calibration coefficient of 1.09 ± 0.02 (relative to the previous coefficient) was determined for the 3m nTOF detector. In addition,more » comparison of these and other shots indicates that significant reduction in charged particle flux anisotropies is achieved when bang time occurs significantly (on the order of 500 ps) after the trailing edge of the laser pulse. This is an important observation as the main source of the yield calibration error is due to particle anisotropies caused by field effects. The results indicate that the CR-39-nTOF in situ calibration method can serve as a valuable technique for calibrating and reducing the uncertainty in the DD absolute yield calibration of nTOF detector systems on OMEGA, the National Ignition Facility, and laser megajoule.« less

A method for in situ absolute DD yield calibration of neutron time-of-flight detectors on OMEGA using CR-39-based proton detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waugh, C. J.; Rosenberg, M. J.; Zylstra, A. B.

Neutron time of flight (nTOF) detectors are used routinely to measure the absolute DD neutron yield at OMEGA. To check the DD yield calibration of these detectors, originally calibrated using indium activation systems, which in turn were cross-calibrated to NOVA nTOF detectors in the early 1990s, a direct in situ calibration method using CR-39 range filter proton detectors has been successfully developed. By measuring DD neutron and proton yields from a series of exploding pusher implosions at OMEGA, a yield calibration coefficient of 1.09 ± 0.02 (relative to the previous coefficient) was determined for the 3m nTOF detector. In addition,more » comparison of these and other shots indicates that significant reduction in charged particle flux anisotropies is achieved when bang time occurs significantly (on the order of 500 ps) after the trailing edge of the laser pulse. This is an important observation as the main source of the yield calibration error is due to particle anisotropies caused by field effects. The results indicate that the CR-39-nTOF in situ calibration method can serve as a valuable technique for calibrating and reducing the uncertainty in the DD absolute yield calibration of nTOF detector systems on OMEGA, the National Ignition Facility, and laser megajoule.« less

A method for in situ absolute DD yield calibration of neutron time-of-flight detectors on OMEGA using CR-39-based proton detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waugh, C. J., E-mail: cjwaugh@mit.edu; Zylstra, A. B.; Frenje, J. A.

2015-05-15

Neutron time of flight (nTOF) detectors are used routinely to measure the absolute DD neutron yield at OMEGA. To check the DD yield calibration of these detectors, originally calibrated using indium activation systems, which in turn were cross-calibrated to NOVA nTOF detectors in the early 1990s, a direct in situ calibration method using CR-39 range filter proton detectors has been successfully developed. By measuring DD neutron and proton yields from a series of exploding pusher implosions at OMEGA, a yield calibration coefficient of 1.09 ± 0.02 (relative to the previous coefficient) was determined for the 3m nTOF detector. In addition,more » comparison of these and other shots indicates that significant reduction in charged particle flux anisotropies is achieved when bang time occurs significantly (on the order of 500 ps) after the trailing edge of the laser pulse. This is an important observation as the main source of the yield calibration error is due to particle anisotropies caused by field effects. The results indicate that the CR-39-nTOF in situ calibration method can serve as a valuable technique for calibrating and reducing the uncertainty in the DD absolute yield calibration of nTOF detector systems on OMEGA, the National Ignition Facility, and laser megajoule.« less

Protonation enthalpies of metal oxides from high temperature electrophoresis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez-Santiago, V; Fedkin, Mark V.; Lvov, Serguei N.

2012-01-01

Surface protonation reactions play an important role in the behavior of mineral and colloidal systems, specifically in hydrothermal aqueous environments. However, studies addressing the reactions at the solid/liquid interface at temperatures above 100 C are scarce. In this study, newly and previously obtained high temperature electrophoresis data (up to 260 C) zeta potentials and isoelectric points for metal oxides, including SiO2, SnO2, ZrO2, TiO2, and Fe3O4, were used in thermodynamic analysis to derive the standard enthalpies of their surface protonation. Two different approaches were used for calculating the protonation enthalpy: one is based on thermodynamic description of the 1-pKa modelmore » for surface protonation, and another one on a combination of crystal chemistry and solvation theories which link the relative permittivity of the solid phase and the ratio of the Pauling bond strength and bond length to standard protonation enthalpy. From this analysis, two expressions relating the protonation enthalpy to the relative permittivity of the solid phase were obtained.« less

Protonation enthalpies of metal oxides from high temperature electrophoresis.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez-Santiago, V; Fedkin, Mark V; Lvov, Serguei N.

2012-01-01

Surface protonation reactions play an important role in the behavior of mineral and colloidal systems, specifically in hydrothermal aqueous environments. However, studies addressing the reactions at the solid/liquid interface at temperatures above 100 C are scarce. In this study, newly and previously obtained high temperature electrophoresis data (up to 260 C) - zeta potentials and isoelectric points - for metal oxides, including SiO{sub 2}, SnO{sub 2}, ZrO{sub 2}, TiO{sub 2}, and Fe{sub 3}O{sub 4}, were used in thermodynamic analysis to derive the standard enthalpies of their surface protonation. Two different approaches were used for calculating the protonation enthalpy: one ismore » based on thermodynamic description of the 1-pKa model for surface protonation, and another one - on a combination of crystal chemistry and solvation theories which link the relative permittivity of the solid phase and the ratio of the Pauling bond strength and bond length to standard protonation enthalpy. From this analysis, two expressions relating the protonation enthalpy to the relative permittivity of the solid phase were obtained.« less

Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation

PubMed Central

Peng, Yuxing; Voth, Gregory A.

2011-01-01

In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are transported by the Grotthuss shuttling via hydrogen-bonded water molecules and protonatable residues. Proton transport through the D-pathway is a complicated process that is highly sensitive to alterations in the amino acids or the solvation structure in the channel, both of which can inhibit proton pumping and enzymatic activity. Simulations of proton transport in the hydrophobic cavity showed a clear redox state dependence. To study the mechanism of proton pumping in CcO, multi-state empirical valence bond (MS-EVB) simulations have been conducted, focusing on the proton transport through the D-pathway and the hydrophobic cavity next to the binuclear center. The hydration structures, transport pathways, effects of residues, and free energy surfaces of proton transport were revealed in these MS-EVB simulations. The mechanistic insight gained from them is herein reviewed and placed in context for future studies. PMID:22178790

Differential geometry based solvation model II: Lagrangian formulation.

PubMed

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

2011-12-01

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

Differential geometry based solvation model II: Lagrangian formulation

PubMed Central

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

2010-01-01

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

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

NASA Astrophysics Data System (ADS)

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.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

PubMed

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri; See, Kimberly A; Assary, Rajeev S; Zhu, Lingyang; Haasch, Richard T; Zhang, Shuo; Zhang, Zhengcheng; Curtiss, Larry A; Gewirth, Andrew A

2017-11-15

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN) 2 -LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li + at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN)(2)-LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Ramanmore » and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li+ at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.« less

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

PubMed

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

2016-08-23

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Anomalous Surface Diffusion of Protons on Lipid Membranes

PubMed Central

Wolf, Maarten G.; Grubmüller, Helmut; Groenhof, Gerrit

2014-01-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. PMID:24988343

Electron Solvation in Two Dimensions

NASA Astrophysics Data System (ADS)

Miller, A. D.; Bezel, I.; Gaffney, K. J.; Garrett-Roe, S.; Liu, S. H.; Szymanski, P.; Harris, C. B.

2002-08-01

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.

Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations.

PubMed

Qiao, Yu; Tu, Bin; Lu, Benzhuo

2014-05-07

Ionic finite size can impose considerable effects to both the equilibrium and non-equilibrium properties of a solvated molecular system, such as the solvation energy, ionic concentration, and transport in a channel. As discussed in our former work [B. Lu and Y. C. Zhou, Biophys. J. 100, 2475 (2011)], a class of size-modified Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) models can be uniformly studied through the general nonuniform size-modified PNP (SMPNP) equations deduced from the extended free energy functional of Borukhov et al. [I. Borukhov, D. Andelman, and H. Orland, Phys. Rev. Lett. 79, 435 (1997)] This work focuses on the nonuniform size effects to molecular solvation energy and to ion current across a channel for real biomolecular systems. The main contributions are: (1) we prove that for solvation energy calculation with nonuniform size effects (through equilibrium SMPNP simulation), there exists a simplified approximation formulation which is the same as the widely used one in PB community. This approximate form avoids integration over the whole domain and makes energy calculations convenient. (2) Numerical calculations show that ionic size effects tend to negate the solvation effects, which indicates that a higher molecular solvation energy (lower absolute value) is to be predicted when ionic size effects are considered. For both calculations on a protein and a DNA fragment systems in a 0.5M 1:1 ionic solution, a difference about 10 kcal/mol in solvation energies is found between the PB and the SMPNP predictions. Moreover, it is observed that the solvation energy decreases as ionic strength increases, which behavior is similar as those predicted by the traditional PB equation (without size effect) and by the uniform size-modified Poisson-Boltzmann equation. (3) Nonequilibrium SMPNP simulations of ion permeation through a gramicidin A channel show that the ionic size effects lead to reduced ion current inside the channel compared with the results

The solvated electron battery

NASA Astrophysics Data System (ADS)

Bennett, J.; Harney, D.; Mitchell, T.

A novel ambient temperture secondary battery using sodium and sulfur dissolved in liquid ammonia is being developed at ELTECH Systems corpooration. The key element of the system is the solvated electron electrode, a metallic liquid which is formed by ammonia and a number of alkali and alkaline earth metals. These solutions are excellent ionic and electronic conductors and have been shown to contain 'free' solvated electrons as the anionic species in solution. Sulfur was chosen as the cathodic reactant because of its high solubility in ammonia, and also because of the high solubiity and good conductivity of the polysulfide reaction products. Development efforts have thus far concentrated on basic electrochemical measurements and establishment of system feasibility.

Hydroxamic acids as weak base indicators: protonation in strong acid media.

PubMed

García, B; Ibeas, S; Hoyuelos, F J; Leal, J M; Secco, F; Venturini, M

2001-11-30

The protonation equilibria of N-phenylbenzohydroxamic, benzohydroxamic, salicylhydroxamic, and N-p-tolylcinnamohydroxamic acids have been studied at 25 degrees C in concentrated sulfuric, hydrochloric, and perchloric acid media; the UV-vis spectral measurements were analyzed using the Hammett equation and the Bunnett-Olsen and excess acidity methods. The medium effects observed in the UV spectral curves were corrected with the Cox-Yates and vector analysis methods. The H(A) acidity function based on benzamides provided the best results. The range of variation of the solvation coefficient m is similar to that of amides, this indicating similar solvation requirements for amides and hydroxamic acids. For the same substrate, the observed variations of pK(BH)(+) with the mineral acid used was justified by formation of solvent-separated ion pairs; for the same mineral acid, the observed changes in pK(BH)(+) can be explained by the solvation of BH(+). The change of the pK(BH)(+) values was in reasonably good agreement with the sequence of the catalytic efficiency of the mineral acids used, HCl > H(2)SO(4) > HClO(4).

Bond-valence methods for pKa prediction. II. Bond-valence, electrostatic, molecular geometry, and solvation effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bickmore, Barry R.; Rosso, Kevin M.; Tadanier, Christopher J.

2006-08-15

In a previous contribution, we outlined a method for predicting (hydr)oxy-acid and oxide surface acidity constants based on three main factors: bond valence, Me?O bond ionicity, and molecular shape. Here electrostatics calculations and ab initio molecular dynamics simulations are used to qualitatively show that Me?O bond ionicity controls the extent to which the electrostatic work of proton removal departs from ideality, bond valence controls the extent of solvation of individual functional groups, and bond valence and molecular shape controls local dielectric response. These results are consistent with our model of acidity, but completely at odds with other methods of predictingmore » acidity constants for use in multisite complexation models. In particular, our ab initio molecular dynamics simulations of solvated monomers clearly indicate that hydrogen bonding between (hydr)oxo-groups and water molecules adjusts to obey the valence sum rule, rather than maintaining a fixed valence based on the coordination of the oxygen atom as predicted by the standard MUSIC model.« less

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

DOE PAGES

Sadybekov, Arman; Krylov, Anna I.

2017-07-07

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadybekov, Arman; Krylov, Anna I.

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li-S Battery.

PubMed

See, Kimberly A; Wu, Heng-Liang; Lau, Kah Chun; Shin, Minjeong; Cheng, Lei; Balasubramanian, Mahalingam; Gallagher, Kevin G; Curtiss, Larry A; Gewirth, Andrew A

2016-12-21

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2 -LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2 -LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. The electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE PAGES

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun; ...

2016-11-16

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.

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, here 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 BF 4 --water system is then computed using ab initio molecular dynamics and Marcus theory, and is foundmore » to be in excellent agreement with the 2DIR measurement.« less

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

DOE PAGES

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.; ...

2017-12-24

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, here 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 BF 4 --water system is then computed using ab initio molecular dynamics and Marcus theory, and is foundmore » to be in excellent agreement with the 2DIR measurement.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.

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 inmore » excellent agreement with the 2DIR measurement.« less

Preferential solvation of lithium cations and impacts on oxygen reduction in lithium–air batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Dong; Qu, Deyu; Yang, Xiao -Qing

2015-09-16

The solvation of Li⁺ with eleven non-aqueous solvents commonly used as the electrolytes for Li batteries were studied. The solvation preferences of different solvents were compared by means of electrospray mass spectrometry and collision-induced dissociation. The relative strength of the solvent for the solvation of Li⁺ was determined. The Lewis acidity of the solvated Li⁺ cations was determined by the preferential solvation of the solvent in the solvation shell. The kinetics of the catalytic disproportionation of the O₂⁻ depends on the relative Lewis acidity of the solvated Li⁺ ion. The impact of the solvated Li⁺ cation on the O₂ redoxmore » reaction was also investigated.« less

Zero-point energy effects in anion solvation shells.

PubMed

Habershon, Scott

2014-05-21

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

Anomalous surface diffusion of protons on lipid membranes.

PubMed

Wolf, Maarten G; Grubmüller, Helmut; Groenhof, Gerrit

2014-07-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent.

PubMed

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

2015-06-07

We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation 〈Nsolv〉, and second osmotic virial coefficient B2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

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

PubMed

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

2016-09-01

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

Breaking the polar-nonpolar division in solvation free energy prediction.

PubMed

Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

2018-02-05

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94

Absolute quantification of carnosine in human calf muscle by proton magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Özdemir, Mahir S.; Reyngoudt, Harmen; DeDeene, Yves; Sazak, Hakan S.; Fieremans, Els; Delputte, Steven; D'Asseler, Yves; Derave, Wim; Lemahieu, Ignace; Achten, Eric

2007-12-01

Carnosine has been shown to be present in the skeletal muscle and in the brain of a variety of animals and humans. Despite the various physiological functions assigned to this metabolite, its exact role remains unclear. It has been suggested that carnosine plays a role in buffering in the intracellular physiological pHi range in skeletal muscle as a result of accepting hydrogen ions released in the development of fatigue during intensive exercise. It is thus postulated that the concentration of carnosine is an indicator for the extent of the buffering capacity. However, the determination of the concentration of this metabolite has only been performed by means of muscle biopsy, which is an invasive procedure. In this paper, we utilized proton magnetic resonance spectroscopy (1H MRS) in order to perform absolute quantification of carnosine in vivo non-invasively. The method was verified by phantom experiments and in vivo measurements in the calf muscles of athletes and untrained volunteers. The measured mean concentrations in the soleus and the gastrocnemius muscles were found to be 2.81 ± 0.57/4.8 ± 1.59 mM (mean ± SD) for athletes and 2.58 ± 0.65/3.3 ± 0.32 mM for untrained volunteers, respectively. These values are in agreement with previously reported biopsy-based results. Our results suggest that 1H MRS can provide an alternative method for non-invasively determining carnosine concentration in human calf muscle in vivo.

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

Bocian, Szymon; Škrinjar, Tea; Bolanca, Tomislav; Buszewski, Bogusław

2017-11-01

A series of core-shell-based stationary phases of varying surface chemistry were subjected to solvent adsorption investigation under ultra-HPLC conditions. Acetonitrile and water excess isotherms were measured using a minor disturbance method. It was observed that adsorption of organic solvent is unified under high pressure. Preferential solvation due to specific interactions between the stationary phases and solvent molecules was limited. The obtained results showed that the solvation process is almost independent of surface chemistry, in contrast to HPLC conditions in which specific interactions differentiate solvation processes.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

NASA Astrophysics Data System (ADS)

Serrano, Agostinho; Santos, Flávia M. T.; Greca, Ileana M.

2004-09-01

It is shown how basic aspects of ionic solvation structure, a fundamental topic for understanding different concepts and levels of representations of chemical structure and transformation, can be taught with the help of a Monte Carlo simulation package for molecular liquids. By performing a pair distribution function analysis of the solvation of Na + , Cl , and Ar in water, it is shown that it is feasible to explain the differences in solvation for these differently charged solutes. Visual representations of the solvated ions can also be employed to help the teaching activity. This may serve as an introduction to the study of solvation structure in chemistry undergraduate courses. The advantages of using tested, up-to-date scientific simulation programs as the fundamental bricks in the construction of virtual laboratories is also discussed.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration.

PubMed

Hofer, Thomas S; Hünenberger, Philippe H

2018-06-14

The absolute intrinsic hydration free energy G H + ,wat ◦ of the proton, the surface electric potential jump χ wat ◦ upon entering bulk water, and the absolute redox potential V H + ,wat ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na + ) and potassium (K + ) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for G H + ,wat ◦ , χ wat ◦ , and V H + ,wat ◦ , reported with statistical errors based on a confidence interval of 99%. The

Hydrated Excess Protons Can Create Their Own Water Wires.

PubMed

Peng, Yuxing; Swanson, Jessica M J; Kang, Seung-gu; Zhou, Ruhong; Voth, Gregory A

2015-07-23

Grotthuss shuttling of an excess proton charge defect through hydrogen bonded water networks has long been the focus of theoretical and experimental studies. In this work we show that there is a related process in which water molecules move ("shuttle") through a hydrated excess proton charge defect in order to wet the path ahead for subsequent proton charge migration. This process is illustrated through reactive molecular dynamics simulations of proton transport through a hydrophobic nanotube, which penetrates through a hydrophobic region. Surprisingly, before the proton enters the nanotube, it starts "shooting" water molecules into the otherwise dry space via Grotthuss shuttling, effectively creating its own water wire where none existed before. As the proton enters the nanotube (by 2-3 Å), it completes the solvation process, transitioning the nanotube to the fully wet state. By contrast, other monatomic cations (e.g., K(+)) have just the opposite effect, by blocking the wetting process and making the nanotube even drier. As the dry nanotube gradually becomes wet when the proton charge defect enters it, the free energy barrier of proton permeation through the tube via Grotthuss shuttling drops significantly. This finding suggests that an important wetting mechanism may influence proton translocation in biological systems, i.e., one in which protons "create" their own water structures (water "wires") in hydrophobic spaces (e.g., protein pores) before migrating through them. An existing water wire, e.g., one seen in an X-ray crystal structure or MD simulations without an explicit excess proton, is therefore not a requirement for protons to transport through hydrophobic spaces.

Iron Hydroperoxide Intermediate in Superoxide Reductase: Protonation or Dissociation First? MM Dynamics and QM/MM Metadynamics Study.

PubMed

David, Rolf; Jamet, Hélène; Nivière, Vincent; Moreau, Yohann; Milet, Anne

2017-06-13

Superoxide reductase is a mononuclear iron enzyme involved in superoxide radical detoxification in some bacteria. Its catalytic mechanism is associated with the remarkable formation of a ferric hydroperoxide Fe 3+ -OOH intermediate, which is specifically protonated on its proximal oxygen to generate the reaction product H 2 O 2 . Here, we present a computational study of the protonation mechanism of the Fe 3+ -OOH intermediate, at different levels of theory. This was performed on the whole system (solvated protein) using well-tempered metadynamics at the QM/MM (B3LYP/AmberFF99SB) level. Enabled by the development of a new set of force field parameters for the active site, a conformational MM study of the Fe 3+ -OOH species gave insights into its solvation pattern, in addition to generating the two starting conformations for the ab initio metadynamics setup. Two different protonation mechanisms for the Fe 3+ -OOH intermediate have been found depending on the starting structure. Whereas a possible mechanism involves at first the protonation of the hydroperoxide ligand and then dissociation of H 2 O 2 , the most probable one starts with an unexpected dissociation of the HOO - ligand from the iron, followed by its protonation. This favored reactivity was specifically linked to the influence of both the nearby conserved lysine 48 residue and the microsolvatation on the charge distribution of the oxygens of the HOO - ligand. These data highlight the crucial role of the whole environment, solvent, and protein, to describe accurately this second protonation step in superoxide reductase. This is clearly not possible with smaller models unable to reproduce correctly the mechanistically determinant charge distribution.

Thin Metallic Films From Solvated Metal Atoms

NASA Astrophysics Data System (ADS)

Trivino, Galo C.; Klabunde, Kenneth J.; Dale, Brock

1988-02-01

Metals were evaporated under vacuum and the metal atoms solvated by excess organic solvents at low temperature. Upon warming stable colloidal metal particles were formed by controlled metal atom clustering. The particles were stabilized toward flocculation by solvation and electrostatic effects. Upon solvent removal the colloidal particles grew to form thin films that were metallic in appearance, but showed higher resistivities than pure metallic films. Gold, palladium, platinium, and especially indium are discussed.

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

PubMed

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.

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel

2013-03-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the a the active site.

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2012-10-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the active site of the protein.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

PubMed

Hidayat, Yuniawan; Armunanto, Ria; Pranowo, Harno Dwi

2018-04-27

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH 3 interaction is weak electrostatically.

Advanced dielectric continuum model of preferential solvation

NASA Astrophysics Data System (ADS)

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.

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

Implicit solvation models provide, for many applications, an effective way of describing the electrostatic effects of aqueous solvation. Here we outline the main approximations behind the popular Generalized Born solvation model. We show how its accuracy, relative to the Poisson-Boltzmann treatment, can be significantly improved in a computationally inexpensive manner to make the model useful in the studies of large-scale conformational transitions at the atomic level. The improved model is tested in a molecular dynamics simulation of folding of a 46-residue (three helix bundle) protein. Starting from an extended structure at 450K, the protein folds to the lowest energy conformation within 6 ns of simulation time, and the predicted structure differs from the native one by 2.4 A (backbone RMSD).

Distinctive Solvation Patterns Make Renal Osmolytes Diverse

PubMed Central

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

2013-01-01

The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules. PMID:24209862

Dosimetric uncertainty in prostate cancer proton radiotherapy.

PubMed

Lin, Liyong; Vargas, Carlos; Hsi, Wen; Indelicato, Daniel; Slopsema, Roelf; Li, Zuofeng; Yeung, Daniel; Horne, Dave; Palta, Jatinder

2008-11-01

The authors we evaluate the uncertainty in proton therapy dose distribution for prostate cancer due to organ displacement, varying penumbra width of proton beams, and the amount of rectal gas inside the rectum. Proton beam treatment plans were generated for ten prostate patients with a minimum dose of 74.1 cobalt gray equivalent (CGE) to the planning target volume (PTV) while 95% of the PTV received 78 CGE. Two lateral or lateral oblique proton beams were used for each plan. The authors we investigated the uncertainty in dose to the rectal wall (RW) and the bladder wall (BW) due to organ displacement by comparing the dose-volume histograms (DVH) calculated with the original or shifted contours. The variation between DVHs was also evaluated for patients with and without rectal gas in the rectum for five patients who had 16 to 47 cc of visible rectal gas in their planning computed tomography (CT) imaging set. The uncertainty due to the varying penumbra width of the delivered protons for different beam setting options on the proton delivery system was also evaluated. For a 5 mm anterior shift, the relative change in the RW volume receiving 70 CGE dose (V70) was 37.9% (5.0% absolute change in 13.2% of a mean V70). The relative change in the BW volume receiving 70 CGE dose (V70) was 20.9% (4.3% absolute change in 20.6% of a mean V70) with a 5 mm inferior shift. A 2 mm penumbra difference in beam setting options on the proton delivery system resulted in the relative variations of 6.1% (0.8% absolute change) and 4.4% (0.9% absolute change) in V70 of RW and BW, respectively. The data show that the organ displacements produce absolute DVH changes that generally shift the entire isodose line while maintaining the same shape. The overall shape of the DVH curve for each organ is determined by the penumbra and the distance of the target in beam's eye view (BEV) from the block edge. The beam setting option producing a 2 mm sharper penumbra at the isocenter can reduce the

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Transient species involved in catalytic dioxygen/peroxide activation by hemoproteins: possible involvement of protonated Compound I species.

PubMed

Silaghi-Dumitrescu, Radu; Cooper, Chris E

2005-11-07

Interaction of hemoproteins with peroxide leads in several cases to transient formation of ferric peroxo, ferric hydroperoxo, and "high-valent", formally Fev, oxo or hydroxo Compound species. Here, density functional calculations on ferric peroxo, ferric hydroperoxo, Compound and protonated Compound heme active site models are reported. The theoretical results, including calculated isotropic Fermi contact couplings and anisotropic spin dipole couplings, are found to generally correlate well with experimental EPR/ENDOR data. Hydrogen bonding and solvation affect the ferric-peroxo/ferrous-superoxo electromerism. The transition between the two electromers appears smooth, but neither hydrogen bonding to up to two water molecules, nor solvation appear able to dramatically alter the redox state of the superoxo ligand or of the iron. The presence of almost one full unpaired electron on the iron and of one full unpaired electron on the dioxygenic ligand in the "ferric-peroxo" state suggests a possible description of non-protonated "ferric-peroxo" as {ferric-superoxo+porphyrin radical}. Emerging from the DFT data is the possibility that a protonated Compound has already been detected in ENDOR experiments on cytochrome P450. The general feasibility of a protonated Compound in P450 monooxygenases is probed in light of these findings. To encompass the multiple mechanisms available in P450 for substrate oxidation, we define "mechanistic promiscuity" as the feature allowing an enzyme to perform the same reaction, with the same product, using more than one mechanism.

Excess Electron Localization in Solvated DNA Bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Excess electron localization in solvated DNA bases.

PubMed

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Absolute rigidity spectrum of protons and helium nuclei above 10 GV/c

NASA Technical Reports Server (NTRS)

Golden, R. L.; Horan, S.; Kimbell, B.; Badhwar, G. D.; Lacy, J. L.; Zipse, J. E.; Daniel, R. R.; Stephens, S. A.

1985-01-01

Proton and helium nuclei differential spectra were gathered with a balloon borne magnet spectrometer. The data were fitted to the assumption that the differential flux can be represented by a power law in rigidity. In the rigidity range 10 to 25 GV/c the spectral indices were found to be -(2.74 plus or minus 0.04) for protons and -(2.71 plus or minus 0.05) for helium nuclei. A brief discussion is given by systematic errors.

Hydrated Excess Protons Can Create Their Own Water Wires

PubMed Central

2014-01-01

Grotthuss shuttling of an excess proton charge defect through hydrogen bonded water networks has long been the focus of theoretical and experimental studies. In this work we show that there is a related process in which water molecules move (“shuttle”) through a hydrated excess proton charge defect in order to wet the path ahead for subsequent proton charge migration. This process is illustrated through reactive molecular dynamics simulations of proton transport through a hydrophobic nanotube, which penetrates through a hydrophobic region. Surprisingly, before the proton enters the nanotube, it starts “shooting” water molecules into the otherwise dry space via Grotthuss shuttling, effectively creating its own water wire where none existed before. As the proton enters the nanotube (by 2–3 Å), it completes the solvation process, transitioning the nanotube to the fully wet state. By contrast, other monatomic cations (e.g., K+) have just the opposite effect, by blocking the wetting process and making the nanotube even drier. As the dry nanotube gradually becomes wet when the proton charge defect enters it, the free energy barrier of proton permeation through the tube via Grotthuss shuttling drops significantly. This finding suggests that an important wetting mechanism may influence proton translocation in biological systems, i.e., one in which protons “create” their own water structures (water “wires”) in hydrophobic spaces (e.g., protein pores) before migrating through them. An existing water wire, e.g., one seen in an X-ray crystal structure or MD simulations without an explicit excess proton, is therefore not a requirement for protons to transport through hydrophobic spaces. PMID:25369445

Preferential Solvation of an Asymmetric Redox Molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Kee Sung; Rajput, Nav Nidhi; Vijayakumar, M.

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-ionmore » 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.« less

SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trulove, Paul C.; Foley, Matthew P.

2012-09-30

The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF 3SO 3) in commonly used organic solvents; ethylene carbonate (EC), gamma-butyrolactone (GBL), and propylene carbonate (PC) was explored. Data from differential scanning calorimetry (DSC), Raman spectroscopy, and X-ray diffraction were correlated to provide insight into the solvation states present within a sample mixture. Data from DSC analyses allowed the construction of phase diagrams for each solvent system. Raman spectroscopy enabled the determination of specific solvation states present within a solvent-salt mixture, and X-ray diffraction data provided exact information concerning the structure of a solvates that couldmore » be isolated Thermal analysis of the various solvent-salt mixtures revealed the phase behavior of the model electrolytes was strongly dependent on solvent symmetry. The point groups of the solvents were (in order from high to low symmetry): C2V for EC, CS for GBL, and C1 for PC(R). The low symmetry solvents exhibited a crystallinity gap that increased as solvent symmetry decreased; no gap was observed for EC-LiTf, while a crystallinity gap was observed spanning 0.15 to 0.3 mole fraction for GBL-LiTf, and 0.1 to 0.33 mole fraction for PC(R)-LiTf mixtures. Raman analysis demonstrated the dominance of aggregated species in almost all solvent compositions. The AGG and CIP solvates represent the majority of the species in solutions for the more concentrated mixtures, and only in very dilute compositions does the SSIP solvate exist in significant amounts. Thus, the poor charge transport characteristics of CIP and AGG account for the low conductivity and transport properties of LiTf and explain why is a poor choice as a source of Li + ions in a Li-ion battery.« less

Decoding the spectroscopic features and time scales of aqueous proton defects

NASA Astrophysics Data System (ADS)

Napoli, Joseph A.; Marsalek, Ondrej; Markland, Thomas E.

2018-06-01

Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton defects in the water hydrogen bond network and the mechanisms for their interconversion remains a formidable challenge. Here, we use simulations treating the quantum nature of both the electrons and nuclei to show how the experimentally observed spectroscopic features and relaxation time scales can be elucidated using a physically transparent coordinate that encodes the overall asymmetry of the solvation environment of the proton defect. We demonstrate that this coordinate can be used both to discriminate the extremities of the features observed in the linear vibrational spectrum and to explain the molecular motions that give rise to the interconversion time scales observed in recent nonlinear experiments. This analysis provides a unified condensed-phase picture of the proton structure and dynamics that, at its extrema, encompasses proton sharing and spectroscopic features resembling the limiting Eigen [H3O(H2O)3]+ and Zundel [H(H2O)2]+ gas-phase structures, while also describing the rich variety of interconverting environments in the liquid phase.

How the shape of an H-bonded network controls proton-coupled water activation in HONO formation.

PubMed

Relph, Rachael A; Guasco, Timothy L; Elliott, Ben M; Kamrath, Michael Z; McCoy, Anne B; Steele, Ryan P; Schofield, Daniel P; Jordan, Kenneth D; Viggiano, Albert A; Ferguson, Eldon E; Johnson, Mark A

2010-01-15

Many chemical reactions in atmospheric aerosols and bulk aqueous environments are influenced by the surrounding solvation shell, but the precise molecular interactions underlying such effects have rarely been elucidated. We exploited recent advances in isomer-specific cluster vibrational spectroscopy to explore the fundamental relation between the hydrogen (H)-bonding arrangement of a set of ion-solvating water molecules and the chemical activity of this ensemble. We find that the extent to which the nitrosonium ion (NO+)and water form nitrous acid (HONO) and a hydrated proton cluster in the critical trihydrate depends sensitively on the geometrical arrangement of the water molecules in the network. Theoretical analysis of these data details the role of the water network in promoting charge delocalization.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

NASA Astrophysics Data System (ADS)

Hofer, Thomas S.; Hünenberger, Philippe H.

2018-06-01

The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained

A fast method for the determination of fractional contributions to solvation in proteins

PubMed Central

Talavera, David; Morreale, Antonio; Meyer, Tim; Hospital, Adam; Ferrer-Costa, Carles; Gelpi, Josep Lluis; de la Cruz, Xavier; Soliva, Robert; Luque, F. Javier; Orozco, Modesto

2006-01-01

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile. PMID:17001031

HCl, KCl and KOH solvation resolved solute-solvent interactions and solution surface stress

NASA Astrophysics Data System (ADS)

Zhang, Xi; Xu, Yan; Zhou, Yong; Gong, Yinyan; Huang, Yongli; Sun, Chang Q.

2017-11-01

An incorporation of the hydrogen bond (O:Hsbnd O or HB) cooperativity notion, contact angle detection, and the differential phonon spectrometrics (DPS) has enabled us to gain refined information on the HCl, KCl and KOH solvation resolved solute-solvent molecular interactions and the solution surface stresses. Results show that ionic polarization stiffens the solvent Hsbnd O bond phonon from 3200 to 3480 cm-1 in the hydration shells. The HO- in alkaline solution, however, shares not only the same Hsbnd O phonon redshift of compressed water from 3200 to < 3100 cm-1 but also the dangling bonds of H2O surface featured at 3610 cm-1. Salt and alkaline solvation enhances the solution surface stress by K+ and Cl- ionic polarization. The excessive H+ proton in acid solution forms a H↔H anti-HB that depresses the solution surface stress, instead. The solute capability of transforming the fraction of the O:Hsbnd O bonds of the solvent matrix is featured by: fH = 0 and fx ∝ 1-exp(-C/C0) (x = HO-, K+ and Cl-) towards saturation. Exercises not only confirm the presence of the H↔H anti-HB point fragilization, the O:⇔:O super-HB point compression, and ionic polarization dominating the performance of the respective HCl, KOH, and KCl solutions, but also demonstrate the power of the DPS that enables high resolution of solute-solute-solvent interactions and correlation between HB relaxation and solution surface stress.

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

PubMed

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.

Nonlinear functional for solvation in Density Functional Theory

NASA Astrophysics Data System (ADS)

Gunceler, Deniz; Sundararaman, Ravishankar; Schwarz, Kathleen; Letchworth-Weaver, Kendra; Arias, T. A.

2013-03-01

Density functional calculations of molecules and surfaces in a liquid can accelerate the development of many technologies ranging from solar energy harvesting to lithium batteries. Such studies require the development of robust functionals describing the liquid. Polarizable continuum models (PCM's) have been applied to some solvated systems; but they do not sufficiently capture solvation effects to describe highly polar systems like surfaces of ionic solids. In this work, we present a nonlinear fluid functional within the framework of Joint Density Functional Theory. The fluid is treated not as a linear dielectric, but as a distribution of dipoles that responds to the solute, which we describe starting from the exact free energy functional for point dipoles. We also show PCM's can be recovered as the linear limit of our functional. Our description is of similar computational cost to PCM's, and captures complex solvation effects like dielectric saturation without requiring new fit parameters. For polar and nonpolar molecules, it achieves millihartree level agreement with experimental solvation energies. Furthermore, our functional now makes it possible to investigate chemistry on the surface of lithium battery materials, which PCM's predict to be unstable. Supported as part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001086

On the calculation of the absolute grand potential of confined smectic-A phases

NASA Astrophysics Data System (ADS)

Huang, Chien-Cheng; Baus, Marc; Ryckaert, Jean-Paul

2015-09-01

We determine the absolute grand potential Λ along a confined smectic-A branch of a calamitic liquid crystal system enclosed in a slit pore of transverse area A and width L, using the rod-rod Gay-Berne potential and a rod-wall potential favouring perpendicular orientation at the walls. For a confined phase with an integer number of smectic layers sandwiched between the opposite walls, we obtain the excess properties (excess grand potential Λexc, solvation force fs and adsorption Γ) with respect to the bulk phase at the same μ (chemical potential) and T (temperature) state point. While usual thermodynamic integration methods are used along the confined smectic branch to estimate the grand potential difference as μ is varied at fixed L, T, the absolute grand potential at one reference state point is obtained via the evaluation of the absolute Helmholtz free energy in the (N, L, A, T) canonical ensemble. It proceeds via a sequence of free energy difference estimations involving successively the cost of localising rods on layers and the switching on of a one-dimensional harmonic field to keep layers integrity coupled to the elimination of inter-layers and wall interactions. The absolute free energy of the resulting set of fully independent layers of interacting rods is finally estimated via the existing procedures. This work opens the way to the computer simulation study of phase transitions implying confined layered phases.

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

PubMed

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.

How to study picosecond solvation dynamics using fluorescent probes with small Stokes shifts

NASA Astrophysics Data System (ADS)

Silori, Yogita; Dey, Shivalee; De, Arijit K.

2018-02-01

Xanthene dyes have wide ranging applications as fluorescent probes in analytical, biochemical and medical contexts. Being cationic/anionic in nature, the solvation dynamics of xanthene dyes confined within a negatively/positively charged interface are very interesting. Unfortunately, the floppy structure and small Stokes shift render any xanthene dye unsuitable for use as a solvation probe. Using di-sodium fluorescein, we present our work on the picosecond solvation dynamics of bulk and confined water (at pH = 9.2). We also propose a new methodology for studying picosecond solvation dynamics using any fluorescent dye with a small Stokes shift. We discuss how scattering contributions can be effectively removed, and propose an alternative way of defining zero time of solvation. Finally, we demonstrate the tuning location of the probe within confinement.

Aqueous solvation from the water perspective.

PubMed

Ahmed, Saima; Pasti, Andrea; Fernández-Terán, Ricardo J; Ciardi, Gustavo; Shalit, Andrey; Hamm, Peter

2018-06-21

The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S 1 back into the S 0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation.

Outer-sphere interaction of aluminum and gallium solvates with competitive anions in 1,2-propanediol solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrosyants, S.P.; Buslaeva, E.R.

1986-04-01

The interaction of aluminum and gallium solvates with ..pi..-acid ligand in 1,2-propanediol solutions has been investigated. The formation of associates of hexacoordinate aluminum solvates depends on the solvation of the anions in the bulk of the solution or on the faces of the solvento complexes. In the case of gallium the association of the solvates with the anions is determined by two factors: the existence of a configurational equilibrium for the solvento complexes and the preferential solvation of the competitive ..pi..-acid ligands.

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

PubMed

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

Feasibility study of proton-based quality assurance of proton range compensator

NASA Astrophysics Data System (ADS)

Park, S.; Jeong, C.; Min, B. J.; Kwak, J.; Lee, J.; Cho, S.; Shin, D.; Lim, Y. K.; Park, S. Y.; Lee, S. B.

2013-06-01

All patient specific range compensators (RCs) are customized for achieving distal dose conformity of target volume in passively scattered proton therapy. Compensators are milled precisely using a computerized machine. In proton therapy, precision of the compensator is critical and quality assurance (QA) is required to protect normal tissues and organs from radiation damage. This study aims to evaluate the precision of proton-based quality assurance of range compensator. First, the geometry information of two compensators was extracted from the DICOM Radiotherapy (RT) plan. Next, RCs were irradiated on the EBT film individually by proton beam which is modulated to have a photon-like percent depth dose (PDD). Step phantoms were also irradiated on the EBT film to generate calibration curve which indicates relationship between optical density of irradiated film and perpendicular depth of compensator. Comparisons were made using the mean absolute difference (MAD) between coordinate information from DICOM RT and converted depth information from the EBT film. MAD over the whole region was 1.7, and 2.0 mm. However, MAD over the relatively flat regions on each compensator selected for comparison was within 1 mm. These results shows that proton-based quality assurance of range compensator is feasible and it is expected to achieve MAD over the whole region less than 1 mm with further correction about scattering effect of proton imaging.

Photodynamics of intramolecular proton transfer in polar and nonpolar biflavonoid solutions

NASA Astrophysics Data System (ADS)

Bondarev, S. L.; Knyukshto, V. N.; Tikhomirov, S. A.; Buganov, O. V.; Pyrko, A. N.

2012-10-01

Using methods of steady state luminescence and femtosecond spectroscopy, we have studied the mechanism of intramolecular proton transfer in synthesized 3,7-dihydroxy-2,8-di(4-methoxyphenyl)-4H,6H-pyrano[3,2- g]chromen-4,6-dion in polar and nonpolar solutions, films, and polycrystals at 293 and 77 K. In an excited singlet state, intramolecular proton transfer occurs in two stages. At the first stage, a tautomer with one transferred proton (OTP tautomer) is formed from the Franck-Condon state within τ1 = 0.6 ps. At the second stage, the second proton is transferred within τ2 = 3.1 ps and a tautomer with two transferred protons (TTP tautomer) is formed, which fluoresces in toluene at 293 K with a high quantum yield, Φ f = 0.66, and the fluorescence spectrum of which is characterized by a large Stokes shift, 9900 cm-1. At 293 K, polar solvents (dimethylformamide, dimethyl sulfoxide, ethanol, etc.) solvate the BFV molecule in the ground state, while, in the excited state, an OTP tautomer is mainly formed. In polar ethanol at 77 K, a dual fluorescence spectrum is observed, which is caused by the fluorescence emission of polysolvates with λ{max/ f } = 460 nm and TTP phototautomers at λ{max/ f }= 610 nm.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

PubMed Central

Goossens, Spencer; Mehdizadeh Rahimi, Ali

2017-01-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water–co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute–solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water–co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

NASA Astrophysics Data System (ADS)

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Knepley, Matthew; Bardhan, Jaydeep P.

2017-03-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water-co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute-solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water-co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Elucidating Solvation Structures for Rational Design of Multivalent Electrolytes-A Review.

PubMed

Rajput, Nav Nidhi; Seguin, Trevor J; Wood, Brandon M; Qu, Xiaohui; Persson, Kristin A

2018-04-26

Fundamental molecular-level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applications. 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. Accordingly, there is growing interest in the rational design of electrolytes for beyond lithium-ion systems by tuning the molecular-level interactions of solvate species present in the electrolytes. Here we present a review of the solvation structure of multivalent electrolytes and its impact on the electrochemical performance of these batteries. A direct correlation between solvate species present in the solution and macroscopic properties of electrolytes is sparse for multivalent electrolytes and contradictory results have been reported in the literature. This review aims to illustrate the current understanding, compare results, and highlight future needs and directions to enable the deep understanding needed for the rational design of improved multivalent electrolytes.

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

PubMed

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n c), and a single solvent-dependent parameter: the dispersion scale factor (s 6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s 6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations.

PubMed

Kato, Mitsunori; Pisliakov, Andrei V; Warshel, Arieh

2006-09-01

The origin of the barrier for proton transport through the aquaporin channel is a problem of general interest. It is becoming increasingly clear that this barrier is not attributable to the orientation of the water molecules across the channel but rather to the electrostatic penalty for moving the proton charge to the center of the channel. However, the reason for the high electrostatic barrier is still rather controversial. It has been argued by some workers that the barrier is due to the so-called NPA motif and/or to the helix macrodipole or to other specific elements. However, our works indicated that the main reason for the high barrier is the loss of the generalized solvation upon moving the proton charge from the bulk to the center of the channel and that this does not reflect a specific repulsive electrostatic interaction but the absence of sufficient electrostatic stabilization. At this stage it seems that the elucidation and clarification of the origin of the electrostatic barrier can serve as an instructive test case for electrostatic models. Thus, we reexamine the free-energy surface for proton transport in aquaporins using the microscopic free-energy perturbation/umbrella sampling (FEP/US) and the empirical valence bond/umbrella sampling (EVB/US) methods as well as the semimacroscopic protein dipole Langevin dipole model in its linear response approximation version (the PDLD/S-LRA). These extensive studies help to clarify the nature of the barrier and to establish the "reduced solvation effect" as the primary source of this barrier. That is, it is found that the barrier is associated with the loss of the generalized solvation energy (which includes of course all electrostatic effects) upon moving the proton charge from the bulk solvent to the center of the channel. It is also demonstrated that the residues in the NPA region and the helix dipole cannot be considered as the main reasons for the electrostatic barrier. Furthermore, our microscopic and

Improvements to the APBS biomolecular solvation software suite.

PubMed

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

NASA Astrophysics Data System (ADS)

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.

Measurement of the Neutron Lifetime Using a Proton Trap

NASA Astrophysics Data System (ADS)

Dewey, M. S.; Gilliam, D. M.; Nico, J. S.; Wietfeldt, F. E.; Fei, X.; Snow, W. M.; Greene, G. L.; Pauwels, J.; Eykens, R.; Lamberty, A.; van Gestel, J.

2003-10-01

We report a new measurement of the neutron decay lifetime by the absolute counting of in-beam neutrons and their decay protons. Protons were confined in a quasi-Penning trap and counted with a silicon detector. The neutron beam fluence was measured by capture in a thin 6LiF foil detector with known absolute efficiency. The combination of these simultaneous measurements gives the neu­tron lifetime: τn=(886.8±1.2[stat]±3.2[syst]) s. The systematic uncertainty is dominated by uncertainties in the mass of the 6LiF deposit and the 6Li(n,t) cross section. This is the most precise measurement of the neutron lifetime to date using an in-beam method.

Prediction of solvation enthalpy of gaseous organic compounds in propanol

NASA Astrophysics Data System (ADS)

Golmohammadi, Hassan; Dashtbozorgi, Zahra

2016-09-01

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

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

PubMed Central

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

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Bucholz, Eric W.; Haskins, Justin B.; Monk, Joshua D.; Bauschlicher, Charles W.; Lawson, John W.

2017-01-01

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final post-cured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of phenolic chain structure and solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered, ethylene glycol (EGL) and H2O. In addition, three phenolic chain structures were considered including two novolac-type chains with either an ortho-ortho (OON) or ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through structural analysis of the solvation shell and hydrogen bonding environment as well as through quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of the simulations and analyses indicate that EGL provides a larger solvation free energy than H2O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, phenolic chain structure significantly impacts solvation performance with OON having limited intermolecular hydrogen bond formations while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H2O, and other similar solvents.

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations.

PubMed

Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Bauschlicher, Charles W; Lawson, John W

2017-04-06

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final postcured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of the phenolic chain structure and the solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered: ethylene glycol (EGL) and H 2 O. In addition, three phenolic chain structures are considered, including two novolac-type chains with either an ortho-ortho (OON) or an ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through a structural analysis of the solvation shell and the hydrogen-bonding environment as well as through a quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of simulations and the analyses indicate that EGL provides a higher solvation free energy than H 2 O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, the phenolic chain structure significantly affects the solvation performance, with OON having limited intermolecular hydrogen-bond formations, while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H 2 O, and other similar solvents.

Absolute Standard Hydrogen Electrode Potential Measured by Reduction of Aqueous Nanodrops in the Gas Phase

PubMed Central

Donald, William A.; Leib, Ryan D.; O'Brien, Jeremy T.; Bush, Matthew F.; Williams, Evan R.

2008-01-01

In solution, half-cell potentials are measured relative to those of other half cells, thereby establishing a ladder of thermochemical values that are referenced to the standard hydrogen electrode (SHE), which is arbitrarily assigned a value of exactly 0 V. Although there has been considerable interest in, and efforts toward, establishing an absolute electrochemical half-cell potential in solution, there is no general consensus regarding the best approach to obtain this value. Here, ion-electron recombination energies resulting from electron capture by gas-phase nanodrops containing individual [M(NH3)6]3+, M = Ru, Co, Os, Cr, and Ir, and Cu2+ ions are obtained from the number of water molecules that are lost from the reduced precursors. These experimental data combined with nanodrop solvation energies estimated from Born theory and solution-phase entropies estimated from limited experimental data provide absolute reduction energies for these redox couples in bulk aqueous solution. A key advantage of this approach is that solvent effects well past two solvent shells, that are difficult to model accurately, are included in these experimental measurements. By evaluating these data relative to known solution-phase reduction potentials, an absolute value for the SHE of 4.2 ± 0.4 V versus a free electron is obtained. Although not achieved here, the uncertainty of this method could potentially be reduced to below 0.1 V, making this an attractive method for establishing an absolute electrochemical scale that bridges solution and gas-phase redox chemistry. PMID:18288835

Heat Effect of the Protonation of Glycine and the Enthalpies of Resolvation of Participating Chemical Species in Water-Dimethylsulfoxide Solvent Mixtures

NASA Astrophysics Data System (ADS)

Isaeva, V. A.; Sharnin, V. A.

2018-02-01

Enthalpies of the protonation of glycine in water‒dimethylsulfoxide (DMSO) mixed solvents are determined calorimetrically in the range of DMSO mole fractions of 0.0 to 0.9, at T = 298.15 K and an ionic strength μ = 0.3 (NaClO4). It is established that the protonation of glycine becomes more exothermic with an increasing mole fraction of DMSO, and the enthalpies of resolvation of glycine and glycinium ions in water‒DMSO solvent mixtures are calculated. It is shown that the small changes in the enthalpy of protonation observed at low mole fractions of DMSO are caused by the contributions from the solvation of proton and protonated glycine cancelling each other out. The enthalpy term of the Gibbs energy of the reaction leading to the formation of glycinium ion is estimated along with the enthalpy of resolvation of the reacting species in the water‒DMSO mixed solvent.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

Benzonitrile: Electron affinity, excited states, and anion solvation

NASA Astrophysics Data System (ADS)

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.

Solvation of Cr 3+ cation in water-acetonitrile mixture studied by IR spectroscopy: molecular penetration into the solvation shells

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Wójcik, Marek; Lindgren, Jan

2000-09-01

Infrared spectra of mixtures of water and deuteroacetonitrile containing the Cr 3+ cation have been studied as a function of concentration, time and temperature. The CN stretching vibration of CD 3CN molecules has been used as a probe of the structural environments. The CN band in the spectra of the solutions is a superposition of four subbands, which may be attributed to CD 3CN bound in the first, second, and third solvation shells of the cation and to non-bound CD 3CN. The character of changes of the integral intensities of the subbands with time for various H 2O:Cr 3+ molar ratios are explained by suggesting mechanisms of molecular replacement within the solvation shells of Cr 3+.

Lifespan metabolic potential of the unicellular organisms expressed by Boltzmann constant, absolute temperature and proton mass

NASA Astrophysics Data System (ADS)

Atanasov, Atanas Todorov

2016-12-01

The unicellular organisms and phages are the first appeared fundamental living organisms on the Earth. The total metabolic energy (Els, J) of these organisms can be expressed by their lifespan metabolic potential (Als, J/kg) and body mass (M, kg): Els =Als M. In this study we found a different expression - by Boltzmann's constant (k, J/K), nucleon mass (mp+, kg) of protons (and neutrons), body mass (M, kg) of organism or mass (Ms) of biomolecules (proteins, nucleotides, polysaccharides and lipids) building organism, and the absolute temperature (T, K). The found equations are: Els= (M/mp+)kT for phages and Els=(Ms/mp+)kT for the unicellular organisms. From these equations the lifespan metabolic potential can be expressed as: Als=Els/M= (k/mp+)T for phages and Als=Els/M= (k/3.3mp+)T for unicellular organisms. The temperature-normated lifespan metabolic potential (Als/T, J/K.kg) is equals to the ratio between Boltzmann's constant and nucleon mass: Als/T=k/mp+ for phages and Als/T=k/3.3mp+ for unicellular organisms. The numerical value of the k/mp+ ratio is equals to 8.254×103 J/K.kg, and the numerical value of k/3.3mp+ ratio is equal to 2.497×103 J/K.kg. These values of temperature-normated lifespan metabolic potential could be considered fundamental for the unicellular organisms.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

PubMed

Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E

2015-01-29

Lithium-ion battery performance 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 used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.

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

PubMed

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.

Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

DOE PAGES

Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; ...

2015-11-17

The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–LiPF 6 as a model system. A coordination preference for EC over DMC to a Li+ was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC) n(DMC) m–Li+ and (EC) n(DMC) m–LiPF 6 solvates in the gas-phase and for an implicit solvent (asmore » a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC 4)–Li+ and (EC) 3–LiPF 6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li+ coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li+ solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li+ diffusion in the dilute (EC:DMC)LiPF 6 mixed solvent electrolyte was studied using the BOMD simulations.« less

Golden beam data for proton pencil-beam scanning.

PubMed

Clasie, Benjamin; Depauw, Nicolas; Fransen, Maurice; Gomà, Carles; Panahandeh, Hamid Reza; Seco, Joao; Flanz, Jacob B; Kooy, Hanne M

2012-03-07

Proton, as well as other ion, beams applied by electro-magnetic deflection in pencil-beam scanning (PBS) are minimally perturbed and thus can be quantified a priori by their fundamental interactions in a medium. This a priori quantification permits an optimal reduction of characterizing measurements on a particular PBS delivery system. The combination of a priori quantification and measurements will then suffice to fully describe the physical interactions necessary for treatment planning purposes. We consider, for proton beams, these interactions and derive a 'Golden' beam data set. The Golden beam data set quantifies the pristine Bragg peak depth-dose distribution in terms of primary, multiple Coulomb scatter, and secondary, nuclear scatter, components. The set reduces the required measurements on a PBS delivery system to the measurement of energy spread and initial phase space as a function of energy. The depth doses are described in absolute units of Gy(RBE) mm² Gp⁻¹, where Gp equals 10⁹ (giga) protons, thus providing a direct mapping from treatment planning parameters to integrated beam current. We used these Golden beam data on our PBS delivery systems and demonstrated that they yield absolute dosimetry well within clinical tolerance.

Differential geometry based solvation model I: Eulerian formulation

NASA Astrophysics Data System (ADS)

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

2010-11-01

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

An evaluation of the accuracy of geomagnetic data obtained from an unattended, automated, quasi-absolute station

USGS Publications Warehouse

Herzog, D.C.

1990-01-01

A comparison is made of geomagnetic calibration data obtained from a high-sensitivity proton magnetometer enclosed within an orthogonal bias coil system, with data obtained from standard procedures at a mid-latitude U.S. Geological Survey magnetic observatory using a quartz horizontal magnetometer, a Ruska magnetometer, and a total field magnetometer. The orthogonal coil arrangement is used with the proton magnetometer to provide Deflected-Inclination-Deflected-Declination (DIDD) data from which quasi-absolute values of declination, horizontal intensity, and vertical intensity can be derived. Vector magnetometers provide the ordinate values to yield baseline calibrations for both the DIDD and standard observatory processes. Results obtained from a prototype system over a period of several months indicate that the DIDD unit can furnish adequate absolute field values for maintaining observatory calibration data, thus providing baseline control for unattended, remote stations. ?? 1990.

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

PubMed

Nguyen, Duc D; Wei, Guo-Wei

2017-01-05

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

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

Interfacial solvation thermodynamics

NASA Astrophysics Data System (ADS)

Ben-Amotz, Dor

2016-10-01

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rane, Kaustubh, E-mail: rane@csi.tu-darmstadt.de; Vegt, Nico F. A. van der

2016-03-21

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

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

PubMed

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.

Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First-Principles and Classical Reactive Molecular Dynamics

DOE PAGES

Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...

2014-12-19

We report that lithium-ion battery performance 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 used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF more » $$\\bar{6}$$ anion. Li + prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li + solvation. Corresponding analysis for the PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less

Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

Ou, Shu-Ching; Drake, Justin A.; Pettitt, B. Montgomery

2017-01-01

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute–solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute–solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute–solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. PMID:27992228

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

PubMed

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.

The influence of patient positioning uncertainties in proton radiotherapy on proton range and dose distributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebl, Jakob, E-mail: jakob.liebl@medaustron.at; Francis H. Burr Proton Therapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114; Department of Therapeutic Radiology and Oncology, Medical University of Graz, 8036 Graz

2014-09-15

Purpose: Proton radiotherapy allows radiation treatment delivery with high dose gradients. The nature of such dose distributions increases the influence of patient positioning uncertainties on their fidelity when compared to photon radiotherapy. The present work quantitatively analyzes the influence of setup uncertainties on proton range and dose distributions. Methods: Thirty-eight clinical passive scattering treatment fields for small lesions in the head were studied. Dose distributions for shifted and rotated patient positions were Monte Carlo-simulated. Proton range uncertainties at the 50%- and 90%-dose falloff position were calculated considering 18 arbitrary combinations of maximal patient position shifts and rotations for two patientmore » positioning methods. Normal tissue complication probabilities (NTCPs), equivalent uniform doses (EUDs), and tumor control probabilities (TCPs) were studied for organs at risk (OARs) and target volumes of eight patients. Results: The authors identified a median 1σ proton range uncertainty at the 50%-dose falloff of 2.8 mm for anatomy-based patient positioning and 1.6 mm for fiducial-based patient positioning as well as 7.2 and 5.8 mm for the 90%-dose falloff position, respectively. These range uncertainties were correlated to heterogeneity indices (HIs) calculated for each treatment field (38% < R{sup 2} < 50%). A NTCP increase of more than 10% (absolute) was observed for less than 2.9% (anatomy-based positioning) and 1.2% (fiducial-based positioning) of the studied OARs and patient shifts. For target volumes TCP decreases by more than 10% (absolute) occurred in less than 2.2% of the considered treatment scenarios for anatomy-based patient positioning and were nonexistent for fiducial-based patient positioning. EUD changes for target volumes were up to 35% (anatomy-based positioning) and 16% (fiducial-based positioning). Conclusions: The influence of patient positioning uncertainties on proton range in therapy of small

The influence of patient positioning uncertainties in proton radiotherapy on proton range and dose distributions

PubMed Central

Liebl, Jakob; Paganetti, Harald; Zhu, Mingyao; Winey, Brian A.

2014-01-01

Purpose: Proton radiotherapy allows radiation treatment delivery with high dose gradients. The nature of such dose distributions increases the influence of patient positioning uncertainties on their fidelity when compared to photon radiotherapy. The present work quantitatively analyzes the influence of setup uncertainties on proton range and dose distributions. Methods: Thirty-eight clinical passive scattering treatment fields for small lesions in the head were studied. Dose distributions for shifted and rotated patient positions were Monte Carlo-simulated. Proton range uncertainties at the 50%- and 90%-dose falloff position were calculated considering 18 arbitrary combinations of maximal patient position shifts and rotations for two patient positioning methods. Normal tissue complication probabilities (NTCPs), equivalent uniform doses (EUDs), and tumor control probabilities (TCPs) were studied for organs at risk (OARs) and target volumes of eight patients. Results: The authors identified a median 1σ proton range uncertainty at the 50%-dose falloff of 2.8 mm for anatomy-based patient positioning and 1.6 mm for fiducial-based patient positioning as well as 7.2 and 5.8 mm for the 90%-dose falloff position, respectively. These range uncertainties were correlated to heterogeneity indices (HIs) calculated for each treatment field (38% < R2 < 50%). A NTCP increase of more than 10% (absolute) was observed for less than 2.9% (anatomy-based positioning) and 1.2% (fiducial-based positioning) of the studied OARs and patient shifts. For target volumes TCP decreases by more than 10% (absolute) occurred in less than 2.2% of the considered treatment scenarios for anatomy-based patient positioning and were nonexistent for fiducial-based patient positioning. EUD changes for target volumes were up to 35% (anatomy-based positioning) and 16% (fiducial-based positioning). Conclusions: The influence of patient positioning uncertainties on proton range in therapy of small lesions in the

SU-E-T-491: Importance of Energy Dependent Protons Per MU Calibration Factors in IMPT Dose Calculations Using Monte Carlo Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Randeniya, S; Mirkovic, D; Titt, U

2014-06-01

Purpose: In intensity modulated proton therapy (IMPT), energy dependent, protons per monitor unit (MU) calibration factors are important parameters that determine absolute dose values from energy deposition data obtained from Monte Carlo (MC) simulations. Purpose of this study was to assess the sensitivity of MC-computed absolute dose distributions to the protons/MU calibration factors in IMPT. Methods: A “verification plan” (i.e., treatment beams applied individually to water phantom) of a head and neck patient plan was calculated using MC technique. The patient plan had three beams; one posterior-anterior (PA); two anterior oblique. Dose prescription was 66 Gy in 30 fractions. Ofmore » the total MUs, 58% was delivered in PA beam, 25% and 17% in other two. Energy deposition data obtained from the MC simulation were converted to Gy using energy dependent protons/MU calibrations factors obtained from two methods. First method is based on experimental measurements and MC simulations. Second is based on hand calculations, based on how many ion pairs were produced per proton in the dose monitor and how many ion pairs is equal to 1 MU (vendor recommended method). Dose distributions obtained from method one was compared with those from method two. Results: Average difference of 8% in protons/MU calibration factors between method one and two converted into 27 % difference in absolute dose values for PA beam; although dose distributions preserved the shape of 3D dose distribution qualitatively, they were different quantitatively. For two oblique beams, significant difference in absolute dose was not observed. Conclusion: Results demonstrate that protons/MU calibration factors can have a significant impact on absolute dose values in IMPT depending on the fraction of MUs delivered. When number of MUs increases the effect due to the calibration factors amplify. In determining protons/MU calibration factors, experimental method should be preferred in MC dose calculations

Relative complexation energies for Li(+) ion in solution: molecular level solvation versus polarizable continuum model study.

PubMed

Eilmes, Andrzej; Kubisiak, Piotr

2010-01-21

Relative complexation energies for the lithium cation in acetonitrile and diethyl ether have been studied. Quantum-chemical calculations explicitly describing the solvation of Li(+) have been performed based on structures obtained from molecular dynamics simulations. The effect of an increasing number of solvent molecules beyond the first solvation shell has been found to consist in reduction of the differences in complexation energies for different coordination numbers. Explicit-solvation data have served as a benchmark to the results of polarizable continuum model (PCM) calculations. It has been demonstrated that the PCM approach can yield relative complexation energies comparable to the predictions based on molecular-level solvation, but at significantly lower computational cost. The best agreement between the explicit-solvation and the PCM results has been obtained when the van der Waals surface was adopted to build the molecular cavity.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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, bothmore » 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.« less

Infrared and Visible Absolute and Difference Spectra of Bacteriorhodopsin Photocycle Intermediates

PubMed Central

Hendler, Richard W.; Meuse, Curtis W.; Braiman, Mark S.; Smith, Paul D.; Kakareka, John W.

2014-01-01

We have used new kinetic fitting procedures to obtain IR absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear algebra-based procedures of Hendler et al. (2001) J. Phys. Chem. B, 105, 3319–3228, for obtaining clean absolute visible spectra of bR photocycle intermediates, were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm−1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle. PMID:21929858

Computational analysis of the solvation of coffee ingredients in aqueous ionic liquid mixtures.

PubMed

Zeindlhofer, Veronika; Khlan, Diana; Bica, Katharina; Schröder, Christian

2017-01-13

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C 2 mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show that classical Kirkwood-Buff theory is not appropriate to study solvation effects with increasing ionic liquid content. However, excess coordination numbers as well as the mean residence time of solvent molecules at the surface of the solutes can be determined by Voronoi tessellation. Since the volume of the hydration shells is also available by this method, solvation free energies will be discussed as a function of the ionic liquid concentration to yield a physical meaningful picture of solvation for the anisotropic solutes. Hydrogen bonding capabilities of the solutes and their relevance for experimental extraction yields from spent coffee grounds are also discussed.

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

PubMed

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.

Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.

PubMed

Oliveira, Ivan P; Martínez, Leandro

2016-08-21

Increasing the stability of proteins is important for their application in industrial processes. In the intracellular environment many small molecules, called osmolytes, contribute to protein stabilization under physical or chemical stress. Understanding the nature of the interactions of these osmolytes with proteins can help the design of solvents and mutations to increase protein stability in extracellular media. One of the most common stabilizing osmolyes is sorbitol and one of the most common chemical denaturants is urea. In this work, we use molecular dynamics simulations to obtain a detailed picture of the solvation of the Burkholderia cepacia lipase (BCL) in the presence of the protecting osmolyte sorbitol and of the urea denaturant. We show that both sorbitol and urea compete with water for interactions with the protein surface. Overall, sorbitol promotes the organization of water in the first solvation shell and displaces water from the second solvation shell, while urea causes opposite effects. These effects are, however, highly heterogeneous among residue types. For instance, the depletion of water from the first protein solvation shell by urea can be traced down essentially to the side chain of negatively charged residues. The organization of water in the first solvation shell promoted by sorbitol occurs at polar (but not charged) residues, where the urea effect is minor. By contrast, sorbitol depletes water from the second solvation shell of polar residues, while urea promotes water organization at the same distances. The interactions of urea with negatively charged residues are insensitive to the presence of sorbitol. This osmolyte removes water and urea particularly from the second solvation shell of polar and non-polar residues. In summary, we provide a comprehensive description of the diversity of protein-solvent interactions, which can guide further investigations on the stability of proteins in non-conventional media, and assist solvent and

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

PubMed

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

2014-08-01

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

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

PubMed

Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J Andrew

2017-07-13

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM ( M VISM) compares with atomistic VISM ( A VISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate M VISM's suitability to study the solvation properties of an interesting encounter complex, barnase-barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM's and MARTINI's applications in the near future.

The protoelectric potential map (PPM): an absolute two-dimensional chemical potential scale for a global understanding of chemistry.

PubMed

Radtke, Valentin; Himmel, Daniel; Pütz, Katharina; Goll, Sascha K; Krossing, Ingo

2014-04-07

We introduce the protoelectric potential map (PPM) as a novel, two-dimensional plot of the absolute reduction potential (peabs scale) combined with the absolute protochemical potential (Brønsted acidity: pHabs scale). The validity of this thermodynamically derived PPM is solvent-independent due to the scale zero points, which were chosen as the ideal electron gas and the ideal proton gas at standard conditions. To tie a chemical environment to these reference states, the standard Gibbs energies for the transfer of the gaseous electrons/protons to the medium are needed as anchor points. Thereby, the thermodynamics of any redox, acid-base or combined system in any medium can be related to any other, resulting in a predictability of reactions even over different media or phase boundaries. Instruction is given on how to construct the PPM from the anchor points derived and tabulated with this work. Since efforts to establish "absolute" reduction potential scales and also "absolute" pH scales already exist, a short review in this field is given and brought into relation to the PPM. Some comments on the electrochemical validation and realization conclude this concept article. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

NASA Astrophysics Data System (ADS)

Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

2017-09-01

The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Residue length and solvation model dependency of elastinlike polypeptides

NASA Astrophysics Data System (ADS)

Bilsel, Mustafa; Arkin, Handan

2010-05-01

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell

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 tomore » 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.« less

Excess protons in water-acetone mixtures. II. A conductivity study.

PubMed

Semino, Rocío; Longinotti, M Paula

2013-10-28

In the present work we complement a previous simulation study [R. Semino and D. Laria, J. Chem. Phys. 136, 194503 (2012)] on the disruption of the proton transfer mechanism in water by the addition of an aprotic solvent, such as acetone. We provide experimental measurements of the mobility of protons in aqueous-acetone mixtures in a wide composition range, for water molar fractions, xw, between 0.05 and 1.00. Furthermore, new molecular dynamics simulation results are presented for rich acetone mixtures, which provide further insight into the proton transport mechanism in water-non-protic solvent mixtures. The proton mobility was analyzed between xw 0.05 and 1.00 and compared to molecular dynamics simulation data. Results show two qualitative changes in the proton transport composition dependence at xw ∼ 0.25 and 0.8. At xw < 0.25 the ratio of the infinite dilution molar conductivities of HCl and LiCl, Λ(0)(HCl).Λ(0)(LiCl)(-1), is approximately constant and equal to one, since the proton diffusion is vehicular and equal to that of Li(+). At xw ∼ 0.25, proton mobility starts to differ from that of Li(+) indicating that above this concentration the Grotthuss transport mechanism starts to be possible. Molecular dynamics simulation results showed that at this threshold concentration the probability of interconversion between two Eigen structures starts to be non-negligible. At xw ∼ 0.8, the infinite molar conductivity of HCl concentration dependence qualitatively changes. This result is in excellent agreement with the analysis presented in the previous simulation work and it has been ascribed to the interchange of water and acetone molecules in the second solvation shell of the hydronium ion.

Reactions of Solvated Ions Final Report

DOE R&D Accomplishments Database

Taube, H.

1962-09-24

Brief summaries are presented on isotopic dilution studies on salts dissolved in CH{sub 3}OH, studies on metal and metal salts in solvents of the amine type, and studies on phosphato complexes of the pentammine Co(III) series. A list of papers published on reactions of solvated ions is included. (N.W.R.)

Generalized Born Models of Macromolecular Solvation Effects

NASA Astrophysics Data System (ADS)

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.

PubMed

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.

Solvation and Acid Strength Effects on Catalysis by Faujasite Zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2012-02-01

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

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

PubMed

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.

Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

PubMed

Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

2017-05-10

Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates.

PubMed

Hendler, Richard W; Meuse, Curtis W; Braiman, Mark S; Smith, Paul D; Kakareka, John W

2011-09-01

We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its M(F) and M(S) components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm(-1) for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the M(F) pathway of the parallel cycles model of the photocycle. © 2011 Society for Applied Spectroscopy

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Water-enhanced solvation of organic solutes in ketone and ester solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J.H.; Brunt, V. van; King, C.J.

1994-05-01

Previous research has shown that the solubilities of dicarboxylic acids in certain electron-donor solvents are substantially increased in the presence of water. Information on solubilities, liquid-liquid equilibria and maximum-boiling ternary azeotropes was screened so as to identify other systems where codissolved water appears to enhance solvation of organic solutes in solvents. Several carboxylic acids, an alcohol, diols, and phenols were selected for examination as solutes in ketone and ester solvents. Effects of water upon solute solubilities and volatilities were measured. Results showed that water-enhanced solvation is greatest for carboxylic acids. Solute activity coefficients decreased by factors of 2--3, 6--8, andmore » 7--10 due to the presence of water for mono-, di and tricarboxylic acids, respectively. Activity coefficients decreased by a factor of about 1.5 for ethanol and 1,2-propanediol as solutes. Water-enhanced solvation of phenols is small, when existent.« less

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

NASA Astrophysics Data System (ADS)

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.

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

PubMed

West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

2015-04-16

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marsh, Brett M.; Voss, Jonathan M.; Garand, Etienne, E-mail: egarand@chem.wisc.edu

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 ionsmore » 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.« less

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

DOE PAGES

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

2015-11-24

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 ionsmore » having a shielded charge center or those that do not readily form hydrogen bonds. Finally, infrared photodissociation spectra of D 2-tagged GlyGlyH +·(H 2O) 1–4 are presented. As a result, they display well-resolved spectral features and comparisons with calculations reveal detailed information on the solvation structures of this prototypical peptide.« less

Influence of the Selectivity Filter Properties on Proton Selectivity in the Influenza A M2 Channel.

PubMed

Dudev, Todor; Grauffel, Cédric; Lim, Carmay

2016-10-05

The homotetrameric M2 proton channel of influenza A plays a crucial role in the viral life cycle and is thus an important therapeutic target. It selectively conducts protons against a background of other competing cations whose concentrations are up to a million times greater than the proton concentration. Its selectivity is largely determined by a constricted region of its open pore known as the selectivity filter, which is lined by four absolutely conserved histidines. While the mechanism of proton transport through the channel has been studied, the physical principles underlying the selectivity for protons over other cations in the channel's His 4 selectivity filter remain elusive. Furthermore, it is not known if proton selectivity absolutely requires all four histidines with two of the four histidines protonated and if other titratable amino acid residues in lieu of the histidines could bind protons and how they affect proton selectivity. Here, we elucidate how the competition between protons and rival cations such as Na + depends on the selectivity filter's (1) histidine protonation state, (2) solvent exposure, (3) oligomeric state (the number of protein chains and thus the number of His ligands), and (4) ligand composition by evaluating the free energies for replacing monovalent Na + with H 3 O + in various model selectivity filters. We show that tetrameric His 4 filters are more proton-selective than their trimeric His 3 counterparts, and a dicationic His 4 filter where two of the four histidines are protonated is more proton-selective than tetrameric filters with other charge states/composition (different combinations of His protonation states or different metal-ligating ligands). The [His 4 ] 2+ filter achieves proton selectivity by providing suboptimal binding conditions for rival cations such as Na + , which prefers a neutral or negatively charged filter instead of a dicationic one, and three rather than four ligands with oxygen-ligating atoms.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

Proton transfer from water to ketyl radical anion: Assessment of critical size of hydrated cluster and free energy barrier in solution from first principles simulations

NASA Astrophysics Data System (ADS)

Biswas, Sohag; Dasgupta, Teesta; Mallik, Bhabani S.

2016-09-01

We present the reactivity of an organic intermediate by studying the proton transfer process from water to ketyl radical anion using gas phase electronic structure calculations and the metadynamics method based first principles molecular dynamics (FPMD) simulations. Our results indicate that during the micro solvation of anion by water molecules systematically, the presence of minimum three water molecules in the gas phase cluster is sufficient to observe the proton transfer event. The analysis of trajectories obtained from initial FPMD simulation of an aqueous solution of the anion does not show any evident of complete transfer of the proton from water. The cooperativity of water molecules and the relatively weak anion-water interaction in liquid state prohibit the full release of the proton. Using biasing potential through first principles metadynamics simulations, we report the observation of proton transfer reaction from water to ketyl radical anion with a barrier height of 16.0 kJ/mol.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

PubMed

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

Modeling Free Energies of Solvation in Olive Oil

PubMed Central

Chamberlin, Adam C.; Levitt, David G.; Cramer, Christopher J.; Truhlar, Donald G.

2009-01-01

Olive oil partition coefficients are useful for modeling the bioavailability of drug-like compounds. We have recently developed an accurate solvation model called SM8 for aqueous and organic solvents (Marenich, A. V.; Olson, R. M.; Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 2011) and a temperature-dependent solvation model called SM8T for aqueous solution (Chamberlin, A. C.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2008, 112, 3024). Here we describe an extension of SM8T to predict air–olive oil and water–olive oil partitioning for drug-like solutes as functions of temperature. We also describe the database of experimental partition coefficients used to parameterize the model; this database includes 371 entries for 304 compounds spanning the 291–310 K temperature range. PMID:19434923

Crystal structure and physicochemical characterization of ambazone monohydrate, anhydrous, and acetate salt solvate.

PubMed

Muresan-Pop, Marieta; Braga, Dario; Pop, Mihaela M; Borodi, Gheorghe; Kacso, Irina; Maini, Lucia

2014-11-01

The crystal structures of the monohydrate and anhydrous forms of ambazone were determined by single-crystal X-ray diffraction (SC-XRD). Ambazone monohydrate is characterized by an infinite three-dimensional network involving the water molecules, whereas anhydrous ambazone forms a two-dimensional network via hydrogen bonds. The reversible transformation between the monohydrate and anhydrous forms of ambazone was evidenced by thermal analysis, temperature-dependent X-ray powder diffraction and accelerated stability at elevated temperature, and relative humidity (RH). Additionally, a novel ambazone acetate salt solvate form was obtained and its nature was elucidated by SC-XRD. Powder dissolution measurements revealed a substantial solubility and dissolution rate improvement of acetate salt solvated form in water and physiological media compared with ambazone forms. Also, the acetate salt solvate displayed good thermal and solution stability but it transformed to the monohydrate on storage at elevated temperature and RH. Our study shows that despite the requirement for controlled storage conditions, the acetate salt solvated form could be an alternative to ambazone when solubility and bioavailability improvement is critical for the clinical efficacy of the drug product. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Thin Metallic Films from Solvated Metal Atoms.

DTIC Science & Technology

1987-07-14

platinium , and especially indium are discussed. N, ; ,, -- !, : N) By Dist , , . N S f1 -- ~~r, 821-19 C[ Thin metallic films from solvated metal atoms...metallic films. Cold, palladium, platinium , and especially indium are discussed. 1- INTRQDUCTION In the field of chemistry an active and broad area of

Phase-Equilibria and Nanostructure Formation in Charged Rigid-Rod Polymers and Carbon Nanotubes

DTIC Science & Technology

2002-11-10

or liquid crystalline) and the crystalline polymer state. The form-I crystal solvate, identi- fied as a cocrystal of the protonated polymer and the...dissolution temperature, below 100 °C.12,13 The form-II crystal solvate, considered a polymer-solvent cocrystal in which the polymer is deprotonated,11,12...solvate that is a cocrystal of protonated PBZT and PPA anions. As previously mentioned, the fact that these two extreme cases result in similar

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4) 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 (p K a) 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 p K a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the p K a) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.

PubMed

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

2016-11-01

We predict cyclohexane-water distribution coefficients (log D 7.4 ) 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 (pK a ) 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 pK a model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2-3 for each solvent and two for the pK a ) for training solvation and acidity models. Applying the final models to the log D 7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0-2.1 for the RMSE with the first and 2.2-2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed.

Can a proton be encapsulated in tetraamido/diamino quaternized macrocycles in aqueous solution and electric field?

PubMed

Jiang, Nan; Ma, Jing

2011-09-12

The proton-binding behavior of solvated tetraamido/diamino quaternized macrocyclic compounds with rigid phenyl and flexible phenyl bridges in the absence or presence of an external electric field is investigated by molecular dynamics simulation. The proton can be held through H-bonding interactions with the two carbonyl oxygen atoms in macrocycles containing rigid (phenyl) and flexible (propyl) bridges. The solute-solvent H-bonding interactions cause the macrocyclic backbones to twist to different extents, depending on the different bridges. The macrocycle with the rigid phenyl linkages folds into a cuplike shape due to π-π interaction, while the propyl analogue still maintains the ellipsoidal ringlike shape with just a slight distortion. The potential energy required for proton transfer is larger in the phenyl-containing macrocycle than in the compound with propyl units. When an external electric field with a strength of 2.5 V nm(-1) is exerted along the carbonyl oxygen atoms, a difference in proton encircling is exhibited for macrocycles with rigid and flexible bridges. In contrast to encapsulation of a proton in the propyl analogue, the intermolecular solute-solvent H-bonding and intramolecular π-π stacking between the two rigid phenyl spacers leads to loss of the proton from the highly distorted cuplike macrocycle with phenyl bridges. The competition between intra- and intermolecular interactions governs the behavior of proton encircling in macrocycles. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

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.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

NASA Astrophysics Data System (ADS)

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi

2010-09-01

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

Proton affinities of hydrated molecules

NASA Astrophysics Data System (ADS)

Valadbeigi, Younes

2016-09-01

Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

PubMed Central

2017-01-01

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM’s theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM (MVISM) compares with atomistic VISM (AVISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate MVISM’s suitability to study the solvation properties of an interesting encounter complex, barnase–barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM’s and MARTINI’s applications in the near future. PMID:28613904

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

DOE PAGES

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

2017-07-26

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. In this paper, 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 tomore » 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. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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. In this paper, 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 tomore » 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. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

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

NASA Astrophysics Data System (ADS)

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.

Quantum Monte Carlo studies of solvated systems

NASA Astrophysics Data System (ADS)

Schwarz, Kathleen; Letchworth Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2011-03-01

Solvation qualitatively alters the energetics of diverse processes from protein folding to reactions on catalytic surfaces. An explicit description of the solvent in quantum-mechanical calculations requires both a large number of electrons and exploration of a large number of configurations in the phase space of the solvent. These problems can be circumvented by including the effects of solvent through a rigorous classical density-functional description of the liquid environment, thereby yielding free energies and thermodynamic averages directly, while eliminating the need for explicit consideration of the solvent electrons. We have implemented and tested this approach within the CASINO Quantum Monte Carlo code. Our method is suitable for calculations in any basis within CASINO, including b-spline and plane wave trial wavefunctions, and is equally applicable to molecules, surfaces, and crystals. For our preliminary test calculations, we use a simplified description of the solvent in terms of an isodensity continuum dielectric solvation approach, though the method is fully compatible with more reliable descriptions of the solvent we shall employ in the future.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

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

PubMed Central

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

2017-01-01

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

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

PubMed

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.

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

PubMed

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

2017-03-08

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

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

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

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

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

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.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

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

PubMed

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.

Computing pKa Values in Different Solvents by Electrostatic Transformation.

PubMed

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.

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

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

PubMed

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

2011-06-06

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

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results

Dosimetric and clinical experience in eye proton treatment at INFN-LNS

NASA Astrophysics Data System (ADS)

Cirrone, G. A. P.; Cuttone, G.; Di Rosa, F.; Lojacono, P.; Mongelli, V.; Lo Nigro, S.; Ott, J.; Patti, I. V.; Pittera, S.; Privitera, G.; Raffaele, L.; Reibaldi, A.; Russo, G.; Salamone, V.; Sabini, M. G.; Spatola, C.; Valastro, L. M.

2009-05-01

After six years of activity 155 patients have been treated inside the CATANA (Centro di AdroTerapia ed Applicazioni Nucleari Avanzate) facility. CATANA is the first and unique proton therapy facility in which the 62 MeV proton beams, accelerated by a Superconducting Cyclotron, are used for the radio-therapeutic treatments of choroidal and iris melanomas. Inside CATANA new absolute and relative dosimetric techniques have been developed in order to achieve the best results in terms of treatment precision and dose release accuracy. The follow-up results for 42 patients demonstrated the efficacy of high energy protons in the radiotherapeutic field and encouraged us in our activity in the battle against cancer

Structure of solvates of o-hydroxybenzoic acid in supercritical CO2-cosolvent media, according to molecular dynamics data

NASA Astrophysics Data System (ADS)

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

2015-03-01

Three-component supercritical carbon dioxide-cosolvent (methanol, ethanol, water)- o-hydroxybenzoic acid ( o-HBA) mixtures at a density of 0.7 g/cm3 and temperatures of 318 and 348 K are simulated by means of molecular dynamics. The solvate structures are investigated. It is shown that the solvation mechanism of o-HBA (particularly the o-HBA molecule forming a stable solvate complex with one molecule of a cosolvent via a hydrogen bond through the carboxyl group) does not depend on the temperature or the cosolvent. It is noted that the form of the cosolvent in a supercritical fluid varies: alcohols are distributed in the bulk in the form of monomers and hydrogen-bonded dimers, and water molecules tend to form microclusters along with chained and spatially branched structures by means of hydrogen bonds. It is established that the local molar fraction of cosolvent around the solvate complexes grows. It is concluded that the solvation of o-HBA is determined by the behavior of cosolvent in media of supercritical CO2.

On the aqueous solvation of AsO(OH)3vs. As(OH)3. Born-Oppenheimer molecular dynamics density functional theory cluster studies.

PubMed

Ramírez-Solís, A; Amaro-Estrada, J I; León-Pimentel, C I; Hernández-Cobos, J; Garrido-Hoyos, S E; Saint-Martin, H

2018-06-20

While arsenous acid, As(OH)3, has been the subject of a plethora of studies due to its worldwide ubiquity and its toxicity, pentavalent As in the form of arsenic acid, AsO(OH)3, has recently been found in rivers in central Mexico as the most abundant naturally occurring arsenic species. To better understand the solvation patterns of both toxic acids at the molecular level, we report the results of Born-Oppenheimer molecular dynamics simulations on the aqueous solvation of the AsO(OH)3 and As(OH)3 molecules at room temperature using the cluster microsolvation approach including 30 water molecules at the B3LYP/6-31G** level of theory. We found that the average per-molecule water binding energy is ca. 1 kcal mol-1 larger for the As(v) species as compared to the As(iii) one. To account for the asymmetry of both molecules, the hydration patterns were studied separately for a "lower" hemisphere, defined by the initially protonated oxygens, and for the opposite "upper" hemisphere. Similar lower hydration patterns were found for both As(iii) and As(v), with the same coordination number CN = 7. The upper pattern for As(iii) was found to be of a hydrophobic type, whereas that for As(v) showed the fourth oxygen to be hydrogen-bonded to the water network, yielding CN = 3.7; moreover, a proton "hopped" from the lower to the upper side, through the Grotthuss mechanism. Theoretical EXAFS spectra were obtained that showed good agreement with experimental data for As(iii) and As(v) in liquid water, albeit with somewhat longer As-O distances due to the level of theory employed. Proton transfer processes were also addressed; we found that the singly deprotonated H2AsO3- species largely dominated (99% of the simulation) for the As(iii) case, and that the deprotonated H2AsO4- and HAsO42- species were almost equally present (45% and 55%, respectively) for the As(v) case, which is in line with the experimental data pKa1 = 2.24 and pKa2 = 6.96. Through vibrational analysis the features of

Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein

PubMed Central

Landon, Céline; Berthault, Patrick; Vovelle, Françoise; Desvaux, Hervé

2001-01-01

Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas–protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by ∼12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure. PMID:11274467

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

PubMed

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.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

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

PubMed

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).

Ultrafast Decay of the Solvated Electron in a Neat Polar Solvent: The Unusual Case of Propylene Carbonate.

PubMed

Le Caër, Sophie; Ortiz, Daniel; Marignier, Jean-Louis; Schmidhammer, Uli; Belloni, Jacqueline; Mostafavi, Mehran

2016-01-07

The behavior of carbonates is critical for a detailed understanding of aging phenomena in Li-ion batteries. Here we study the first reaction stages of propylene carbonate (PC), a cyclical carbonate, by picosecond pulse radiolysis. An absorption band with a maximum around 1360 nm is observed at 20 ps after the electron pulse and is shifted to 1310 nm after 50 ps. This band presents the features of a solvated electron absorption band, the solvation lasting up to 50 ps. Surprisingly, in this polar solvent, the solvated electron follows an ultrafast decay and disappears with a half time of 360 ps. This is attributed to the formation of a radical anion PC(-•). The yield of the solvated electron is low, suggesting that the radical anions are mainly directly produced from presolvated electrons. These results demonstrate that the initial electron transfers mechanisms are strongly different in linear compared with cyclical carbonates.

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

NASA Astrophysics Data System (ADS)

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.

Absolute determination of the gelling point of gelatin under quasi-thermodynamic equilibrium.

PubMed

Bellini, Franco; Alberini, Ivana; Ferreyra, María G; Rintoul, Ignacio

2015-05-01

Thermodynamic studies on phase transformation of biopolymers in solution are useful to understand their nature and to evaluate their technological potentials. Thermodynamic studies should be conducted avoiding time-related phenomena. This condition is not easily achieved in hydrophilic biopolymers. In this contribution, the simultaneous effects of pH, salt concentration, and cooling rate (Cr) on the folding from random coil to triple helical collagen-like structures of gelatin were systematically studied. The phase transformation temperature at the absolute invariant condition of Cr = 0 °C/min (T(T)Cr=0) ) is introduced as a conceptual parameter to study phase transformations in biopolymers under quasi-thermodynamic equilibrium and avoiding interferences coming from time-related phenomena. Experimental phase diagrams obtained at different Cr are presented. The T(T)(Cr=0) compared with pH and TT(Cr=0) compared with [NaCl] diagram allowed to explore the transformation process at Cr = 0 °C/min. The results were explained by electrostatic interactions between the biopolymers and its solvation milieu. © 2015 Institute of Food Technologists®

Conical intersections of free energy surfaces in solution: Effect of electron correlation on a protonated Schiff base in methanol solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mori, Toshifumi; Nakano, Katsuhiro; Kato, Shigeki

2010-08-14

The minimum energy conical intersection (MECI) optimization method with taking account of the dynamic electron correlation effect [T. Mori and S. Kato, Chem. Phys. Lett. 476, 97 (2009)] is extended to locate the MECI of nonequilibrium free energy surfaces in solution. A multistate electronic perturbation theory is introduced into the nonequilibrium free energy formula, which is defined as a function of solute and solvation coordinates. The analytical free energy gradient and interstate coupling vectors are derived, and are applied to locate MECIs in solution. The present method is applied to study the cis-trans photoisomerization reaction of a protonated Schiff basemore » molecule (PSB3) in methanol (MeOH) solution. It is found that the effect of dynamic electron correlation largely lowers the energy of S{sub 1} state. We also show that the solvation effect strongly stabilizes the MECI obtained by twisting the terminal C=N bond to become accessible in MeOH solution, whereas the conical intersection is found to be unstable in gas phase. The present study indicates that both electron correlation and solvation effects are important in the photoisomerization reaction of PSB3. The effect of counterion is also examined, and seems to be rather small in solution. The structures of free energy surfaces around MECIs are also discussed.« less

Preferential solvatation of human serum albumin in dimethylsulfoxide-H2O binary solution

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.

2009-12-01

The preferential solvatation of human serum albumin (HSA) in dimethylsulfoxide (DMSO) aqueous solutions were studied using the densitometry method. It has been shown that at DMSO low concentrations HSA undergoes to preferential hydration, but at DMSO higher concentrations preferential binding of DMSO molecules to protein occurs. It has been estimated that DMSO exhibits stabilizing/destabilizing effect on HSA structure which is explained in terms of hydration/solvatation of protein, on the one hand, and the medium structure enhancement/disruption around the protein molecule, on the other hand.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

Differential geometry based solvation model I: Eulerian formulation

PubMed Central

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

2010-01-01

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

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

PubMed

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.

Combined Quantum Chemical/Raman Spectroscopic Analyses of Li+ Cation Solvation: Cyclic Carbonate Solvents - Ethylene Carbonate and Propylene Earbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Joshua L.; Borodin, Oleg; Seo, D. M.

2014-12-01

Combined computational/Raman spectroscopic analyses of ethylene carbonate (EC) and propylene carbonate (PC) solvation interactions with lithium salts are reported. It is proposed that previously reported Raman analyses of (EC)n-LiX mixtures have utilized faulty assumptions. In the present studies, density functional theory (DFT) calculations have provided corrections in terms of both the scaling factors for the solvent's Raman band intensity variations and information about band overlap. By accounting for these factors, the solvation numbers obtained from two different EC solvent bands are in excellent agreement with one another. The same analysis for PC, however, was found to be quite challenging. Commerciallymore » available PC is a racemic mixture of (S)- and (R)-PC isomers. Based upon the quantum chemistry calculations, each of these solvent isomers may exist as multiple conformers due to a low energy barrier for ring inversion, making deconvolution of the Raman bands daunting and inherently prone to significant error. Thus, Raman spectroscopy is able to accurately determine the extent of the EC...Li+ cation solvation interactions using the provided methodology, but a similar analysis of PC...Li+ cation solvation results in a significant underestimation of the actual solvation numbers.« less

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

PubMed

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

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate

PubMed Central

Altavilla, Salvatore F.; Segarra-Martí, Javier; Nenov, Artur; Conti, Irene; Rivalta, Ivan; Garavelli, Marco

2015-01-01

The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ* La and Lb states, whereas the energy of the oxygen lone-pair nπ* state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ* state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region. PMID:25941671

Measurement of inclusive jet and dijet cross-sections in proton-proton collisions at √{s}=13 TeV with the ATLAS detector

NASA Astrophysics Data System (ADS)

Aaboud, M.; Aad, G.; Abbott, B.; Abdinov, O.; Abeloos, B.; Abidi, S. H.; AbouZeid, O. S.; Abraham, N. L.; Abramowicz, H.; Abreu, H.; Abreu, R.; Abulaiti, Y.; Acharya, B. S.; Adachi, S.; Adamczyk, L.; Adelman, J.; Adersberger, M.; Adye, T.; Affolder, A. A.; Afik, Y.; Agatonovic-Jovin, T.; Agheorghiesei, C.; Aguilar-Saavedra, J. A.; Ahlen, S. P.; Ahmadov, F.; Aielli, G.; Akatsuka, S.; Akerstedt, H.; Åkesson, T. P. A.; Akilli, E.; Akimov, A. V.; Alberghi, G. L.; Albert, J.; Albicocco, P.; Alconada Verzini, M. J.; Alderweireldt, S. C.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexopoulos, T.; Alhroob, M.; Ali, B.; Aliev, M.; Alimonti, G.; Alison, J.; Alkire, S. P.; Allbrooke, B. M. M.; Allen, B. W.; Allport, P. P.; Aloisio, A.; Alonso, A.; Alonso, F.; Alpigiani, C.; Alshehri, A. A.; Alstaty, M. I.; Alvarez Gonzalez, B.; Álvarez Piqueras, D.; Alviggi, M. G.; Amadio, B. T.; Amaral Coutinho, Y.; Amelung, C.; Amidei, D.; Amor Dos Santos, S. P.; Amoroso, S.; Amundsen, G.; Anastopoulos, C.; Ancu, L. S.; Andari, N.; Andeen, T.; Anders, C. F.; Anders, J. K.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Angelidakis, S.; Angelozzi, I.; Angerami, A.; Anisenkov, A. V.; Anjos, N.; Annovi, A.; Antel, C.; Antonelli, M.; Antonov, A.; Antrim, D. J.; Anulli, F.; Aoki, M.; Aperio Bella, L.; Arabidze, G.; Arai, Y.; Araque, J. P.; Araujo Ferraz, V.; Arce, A. T. H.; Ardell, R. E.; Arduh, F. A.; Arguin, J.-F.; Argyropoulos, S.; Arik, M.; Armbruster, A. J.; Armitage, L. J.; Arnaez, O.; Arnold, H.; Arratia, M.; Arslan, O.; Artamonov, A.; Artoni, G.; Artz, S.; Asai, S.; Asbah, N.; Ashkenazi, A.; Asquith, L.; Assamagan, K.; Astalos, R.; Atkinson, M.; Atlay, N. B.; Augsten, K.; Avolio, G.; Axen, B.; Ayoub, M. K.; Azuelos, G.; Baas, A. E.; Baca, M. J.; Bachacou, H.; Bachas, K.; Backes, M.; Bagnaia, P.; Bahmani, M.; Bahrasemani, H.; Baines, J. T.; Bajic, M.; Baker, O. K.; Bakker, P. J.; Baldin, E. M.; Balek, P.; Balli, F.; Balunas, W. K.; Banas, E.; Bandyopadhyay, A.; Banerjee, Sw.; Bannoura, A. A. E.; Barak, L.; Barberio, E. L.; Barberis, D.; Barbero, M.; Barillari, T.; Barisits, M.-S.; Barkeloo, J. T.; Barklow, T.; Barlow, N.; Barnes, S. L.; Barnett, B. M.; Barnett, R. M.; Barnovska-Blenessy, Z.; Baroncelli, A.; Barone, G.; Barr, A. J.; Barranco Navarro, L.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Bartoldus, R.; Barton, A. E.; Bartos, P.; Basalaev, A.; Bassalat, A.; Bates, R. L.; Batista, S. J.; Batley, J. R.; Battaglia, M.; Bauce, M.; Bauer, F.; Bawa, H. S.; Beacham, J. B.; Beattie, M. D.; Beau, T.; Beauchemin, P. H.; Bechtle, P.; Beck, H. P.; Beck, H. C.; Becker, K.; Becker, M.; Becot, C.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bedognetti, M.; Bee, C. P.; Beermann, T. A.; Begalli, M.; Begel, M.; Behr, J. K.; Bell, A. S.; Bella, G.; Bellagamba, L.; Bellerive, A.; Bellomo, M.; Belotskiy, K.; Beltramello, O.; Belyaev, N. L.; Benary, O.; Benchekroun, D.; Bender, M.; Benekos, N.; Benhammou, Y.; Benhar Noccioli, E.; Benitez, J.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Bentvelsen, S.; Beresford, L.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Beringer, J.; Berlendis, S.; Bernard, N. R.; Bernardi, G.; Bernius, C.; Bernlochner, F. U.; Berry, T.; Berta, P.; Bertella, C.; Bertoli, G.; Bertram, I. A.; Bertsche, C.; Bertsche, D.; Besjes, G. J.; Bessidskaia Bylund, O.; Bessner, M.; Besson, N.; Bethani, A.; Bethke, S.; Betti, A.; Bevan, A. J.; Beyer, J.; Bianchi, R. M.; Biebel, O.; Biedermann, D.; Bielski, R.; Bierwagen, K.; Biesuz, N. V.; Biglietti, M.; Billoud, T. R. V.; Bilokon, H.; Bindi, M.; Bingul, A.; Bini, C.; Biondi, S.; Bisanz, T.; Bittrich, C.; Bjergaard, D. M.; Black, J. E.; Black, K. M.; Blair, R. E.; Blazek, T.; Bloch, I.; Blocker, C.; Blue, A.; Blumenschein, U.; Blunier, Dr.; Bobbink, G. J.; Bobrovnikov, V. S.; Bocchetta, S. S.; Bocci, A.; Bock, C.; Boehler, M.; Boerner, D.; Bogavac, D.; Bogdanchikov, A. G.; Bohm, C.; Boisvert, V.; Bokan, P.; Bold, T.; Boldyrev, A. S.; Bolz, A. E.; Bomben, M.; Bona, M.; Boonekamp, M.; Borisov, A.; Borissov, G.; Bortfeldt, J.; Bortoletto, D.; Bortolotto, V.; Boscherini, D.; Bosman, M.; Bossio Sola, J. D.; Boudreau, J.; Bouhova-Thacker, E. V.; Boumediene, D.; Bourdarios, C.; Boutle, S. K.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozson, A. J.; Bracinik, J.; Brandt, A.; Brandt, G.; Brandt, O.; Braren, F.; Bratzler, U.; Brau, B.; Brau, J. E.; Breaden Madden, W. D.; Brendlinger, K.; Brennan, A. J.; Brenner, L.; Brenner, R.; Bressler, S.; Briglin, D. L.; Bristow, T. M.; Britton, D.; Britzger, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brooijmans, G.; Brooks, T.; Brooks, W. K.; Brosamer, J.; Brost, E.; Broughton, J. H.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruni, A.; Bruni, G.; Bruni, L. S.; Bruno, S.; Brunt, BH; Bruschi, M.; Bruscino, N.; Bryant, P.; Bryngemark, L.; Buanes, T.; Buat, Q.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Buehrer, F.; Bugge, M. K.; Bulekov, O.; Bullock, D.; Burch, T. J.; Burdin, S.; Burgard, C. D.; Burger, A. M.; Burghgrave, B.; Burka, K.; Burke, S.; Burmeister, I.; Burr, J. T. P.; Büscher, D.; Büscher, V.; Bussey, P.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Butti, P.; Buttinger, W.; Buzatu, A.; Buzykaev, A. R.; Cabrera Urbán, S.; Caforio, D.; Cai, H.; Cairo, V. M.; Cakir, O.; Calace, N.; Calafiura, P.; Calandri, A.; Calderini, G.; Calfayan, P.; Callea, G.; Caloba, L. P.; Calvente Lopez, S.; Calvet, D.; Calvet, S.; Calvet, T. P.; Camacho Toro, R.; Camarda, S.; Camarri, P.; Cameron, D.; Caminal Armadans, R.; Camincher, C.; Campana, S.; Campanelli, M.; Camplani, A.; Campoverde, A.; Canale, V.; Cano Bret, M.; Cantero, J.; Cao, T.; Capeans Garrido, M. D. M.; Caprini, I.; Caprini, M.; Capua, M.; Carbone, R. M.; Cardarelli, R.; Cardillo, F.; Carli, I.; Carli, T.; Carlino, G.; Carlson, B. T.; Carminati, L.; Carney, R. M. D.; Caron, S.; Carquin, E.; Carrá, S.; Carrillo-Montoya, G. D.; Casadei, D.; Casado, M. P.; Casha, A. F.; Casolino, M.; Casper, D. W.; Castelijn, R.; Castillo Gimenez, V.; Castro, N. F.; Catinaccio, A.; Catmore, J. R.; Cattai, A.; Caudron, J.; Cavaliere, V.; Cavallaro, E.; Cavalli, D.; Cavalli-Sforza, M.; Cavasinni, V.; Celebi, E.; Ceradini, F.; Cerda Alberich, L.; Cerqueira, A. S.; Cerri, A.; Cerrito, L.; Cerutti, F.; Cervelli, A.; Cetin, S. A.; Chafaq, A.; Chakraborty, D.; Chan, S. K.; Chan, W. S.; Chan, Y. L.; Chang, P.; Chapman, J. D.; Charlton, D. G.; Chau, C. C.; Chavez Barajas, C. A.; Che, S.; Cheatham, S.; Chegwidden, A.; Chekanov, S.; Chekulaev, S. V.; Chelkov, G. A.; Chelstowska, M. A.; Chen, C.; Chen, C.; Chen, H.; Chen, J.; Chen, S.; Chen, S.; Chen, X.; Chen, Y.; Cheng, H. C.; Cheng, H. J.; Cheplakov, A.; Cheremushkina, E.; Cherkaoui El Moursli, R.; Cheu, E.; Cheung, K.; Chevalier, L.; Chiarella, V.; Chiarelli, G.; Chiodini, G.; Chisholm, A. S.; Chitan, A.; Chiu, Y. H.; Chizhov, M. V.; Choi, K.; Chomont, A. R.; Chouridou, S.; Chow, Y. S.; Christodoulou, V.; Chu, M. C.; Chudoba, J.; Chuinard, A. J.; Chwastowski, J. J.; Chytka, L.; Ciftci, A. K.; Cinca, D.; Cindro, V.; Cioara, I. A.; Ciocio, A.; Cirotto, F.; Citron, Z. H.; Citterio, M.; Ciubancan, M.; Clark, A.; Clark, B. L.; Clark, M. R.; Clark, P. J.; Clarke, R. N.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Colasurdo, L.; Cole, B.; Colijn, A. P.; Collot, J.; Colombo, T.; Conde Muiño, P.; Coniavitis, E.; Connell, S. H.; Connelly, I. A.; Constantinescu, S.; Conti, G.; Conventi, F.; Cooke, M.; Cooper-Sarkar, A. M.; Cormier, F.; Cormier, K. J. R.; Corradi, M.; Corriveau, F.; Cortes-Gonzalez, A.; Costa, G.; Costa, M. J.; Costanzo, D.; Cottin, G.; Cowan, G.; Cox, B. E.; Cranmer, K.; Crawley, S. 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A.; Vazeille, F.; Vazquez Furelos, D.; Vazquez Schroeder, T.; Veatch, J.; Veeraraghavan, V.; Veloce, L. M.; Veloso, F.; Veneziano, S.; Ventura, A.; Venturi, M.; Venturi, N.; Venturini, A.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, A. T.; Vermeulen, J. C.; Vetterli, M. C.; Viaux Maira, N.; Viazlo, O.; Vichou, I.; Vickey, T.; Vickey Boeriu, O. E.; Viehhauser, G. H. A.; Viel, S.; Vigani, L.; Villa, M.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinogradov, V. B.; Vishwakarma, A.; Vittori, C.; Vivarelli, I.; Vlachos, S.; Vogel, M.; Vokac, P.; Volpi, G.; von der Schmitt, H.; von Toerne, E.; Vorobel, V.; Vorobev, K.; Vos, M.; Voss, R.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Wagner, W.; Wagner-Kuhr, J.; Wahlberg, H.; Wahrmund, S.; Walder, J.; Walker, R.; Walkowiak, W.; Wallangen, V.; Wang, C.; Wang, C.; Wang, F.; Wang, H.; Wang, H.; Wang, J.; Wang, J.; Wang, Q.; Wang, R.-J.; Wang, R.; Wang, S. M.; Wang, T.; Wang, W.; Wang, W.; Wang, Z.; Wanotayaroj, C.; Warburton, A.; Ward, C. P.; Wardrope, D. R.; Washbrook, A.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, B. M.; Webb, A. F.; Webb, S.; Weber, M. S.; Weber, S. M.; Weber, S. W.; Weber, S. A.; Webster, J. S.; Weidberg, A. R.; Weinert, B.; Weingarten, J.; Weirich, M.; Weiser, C.; Weits, H.; Wells, P. S.; Wenaus, T.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M. D.; Werner, P.; Wessels, M.; Weston, T. D.; Whalen, K.; Whallon, N. L.; Wharton, A. M.; White, A. S.; White, A.; White, M. J.; White, R.; Whiteson, D.; Whitmore, B. W.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wiglesworth, C.; Wiik-Fuchs, L. A. M.; Wildauer, A.; Wilk, F.; Wilkens, H. G.; Williams, H. H.; Williams, S.; Willis, C.; Willocq, S.; Wilson, J. A.; Wingerter-Seez, I.; Winkels, E.; Winklmeier, F.; Winston, O. J.; Winter, B. T.; Wittgen, M.; Wobisch, M.; Wolf, T. M. H.; Wolff, R.; Wolter, M. W.; Wolters, H.; Wong, V. W. S.; Woods, N. L.; Worm, S. D.; Wosiek, B. K.; Wotschack, J.; Wozniak, K. W.; Wu, M.; Wu, S. L.; Wu, X.; Wu, Y.; Wyatt, T. R.; Wynne, B. M.; Xella, S.; Xi, Z.; Xia, L.; Xu, D.; Xu, L.; Xu, T.; Xu, W.; Yabsley, B.; Yacoob, S.; Yamaguchi, D.; Yamaguchi, Y.; Yamamoto, A.; Yamamoto, S.; Yamanaka, T.; Yamane, F.; Yamatani, M.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, H.; Yang, Y.; Yang, Z.; Yao, W.-M.; Yap, Y. C.; Yasu, Y.; Yatsenko, E.; Yau Wong, K. H.; Ye, J.; Ye, S.; Yeletskikh, I.; Yigitbasi, E.; Yildirim, E.; Yorita, K.; Yoshihara, K.; Young, C.; Young, C. J. S.; Yu, J.; Yu, J.; Yuen, S. P. Y.; Yusuff, I.; Zabinski, B.; Zacharis, G.; Zaidan, R.; Zaitsev, A. M.; Zakharchuk, N.; Zalieckas, J.; Zaman, A.; Zambito, S.; Zanzi, D.; Zeitnitz, C.; Zemaityte, G.; Zemla, A.; Zeng, J. C.; Zeng, Q.; Zenin, O.; Ženiš, T.; Zerwas, D.; Zhang, D.; Zhang, D.; Zhang, F.; Zhang, G.; Zhang, H.; Zhang, J.; Zhang, L.; Zhang, L.; Zhang, M.; Zhang, P.; Zhang, R.; Zhang, R.; Zhang, X.; Zhang, Y.; Zhang, Z.; Zhao, X.; Zhao, Y.; Zhao, Z.; Zhemchugov, A.; Zhou, B.; Zhou, C.; Zhou, L.; Zhou, M.; Zhou, M.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, J.; Zhu, Y.; Zhuang, X.; Zhukov, K.; Zibell, A.; Zieminska, D.; Zimine, N. I.; Zimmermann, C.; Zimmermann, S.; Zinonos, Z.; Zinser, M.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zou, R.; zur Nedden, M.; Zwalinski, L.

2018-05-01

Inclusive jet and dijet cross-sections are measured in proton-proton collisions at a centre-of-mass energy of 13 TeV. The measurement uses a dataset with an integrated luminosity of 3.2 fb-1 recorded in 2015 with the ATLAS detector at the Large Hadron Collider. Jets are identified using the anti- k t algorithm with a radius parameter value of R = 0 .4. The inclusive jet cross-sections are measured double-differentially as a function of the jet transverse momentum, covering the range from 100 GeV to 3.5 TeV, and the absolute jet rapidity up to | y| = 3. The double-differential dijet production cross-sections are presented as a function of the dijet mass, covering the range from 300 GeV to 9 TeV, and the half absolute rapidity separation between the two leading jets within | y| < 3, y ∗, up to y ∗ = 3. Next-to-leading-order, and next-to-next-to-leading-order for the inclusive jet measurement, perturbative QCD calculations corrected for non-perturbative and electroweak effects are compared to the measured cross-sections. [Figure not available: see fulltext.

Synthesis, structural and spectral characterization of a novel NLO crystal N,N‧-diphenylguanidinium picrate: diacetone solvate

NASA Astrophysics Data System (ADS)

Shanmugavadivu, T.; Dhandapani, M.; Naveen, S.; Lokanath, N. K.

2017-09-01

An organic NLO active material N,N‧-diphenylguanidinium picrate: diacetone solvate (C13H14N3+. C6H2N3O7-. 2C3H6O) (DPGPD) was synthesized and single crystals were grown by slow evaporation-solution growth technique at room temperature. DPGPD crystallizes in monoclinic crystal system with noncentrosymmetric space group, Cc confirmed by single crystal X-ray diffraction analysis. The presence of various functional groups was identified from FT-IR spectral analysis and the proton transfer during the formation of compound was confirmed by NMR spectroscopic techniques. The thermal stability was investigated by TG/DTA analyses. Optical transmittance was measured by UV-Vis-NIR spectroscopy and band gap energy was calculated. Photoluminescence spectrum was used to explore its applicability towards laser diodes. Dielectric property of the material was ascertained at different temperatures and it is found that the grown crystal has higher dielectric constant in low frequencies. Photoconductivity study revealed that DPGPD exhibits positive photoconductivity. SHG property was found to be 0.6 times higher than that of KDP.

Proton dose distribution measurements using a MOSFET detector with a simple dose-weighted correction method for LET effects.

PubMed

Kohno, Ryosuke; Hotta, Kenji; Matsuura, Taeko; Matsubara, Kana; Nishioka, Shie; Nishio, Teiji; Kawashima, Mitsuhiko; Ogino, Takashi

2011-04-04

We experimentally evaluated the proton beam dose reproducibility, sensitivity, angular dependence and depth-dose relationships for a new Metal Oxide Semiconductor Field Effect Transistor (MOSFET) detector. The detector was fabricated with a thinner oxide layer and was operated at high-bias voltages. In order to accurately measure dose distributions, we developed a practical method for correcting the MOSFET response to proton beams. The detector was tested by examining lateral dose profiles formed by protons passing through an L-shaped bolus. The dose reproducibility, angular dependence and depth-dose response were evaluated using a 190 MeV proton beam. Depth-output curves produced using the MOSFET detectors were compared with results obtained using an ionization chamber (IC). Since accurate measurements of proton dose distribution require correction for LET effects, we developed a simple dose-weighted correction method. The correction factors were determined as a function of proton penetration depth, or residual range. The residual proton range at each measurement point was calculated using the pencil beam algorithm. Lateral measurements in a phantom were obtained for pristine and SOBP beams. The reproducibility of the MOSFET detector was within 2%, and the angular dependence was less than 9%. The detector exhibited a good response at the Bragg peak (0.74 relative to the IC detector). For dose distributions resulting from protons passing through an L-shaped bolus, the corrected MOSFET dose agreed well with the IC results. Absolute proton dosimetry can be performed using MOSFET detectors to a precision of about 3% (1 sigma). A thinner oxide layer thickness improved the LET in proton dosimetry. By employing correction methods for LET dependence, it is possible to measure absolute proton dose using MOSFET detectors.

Proton dose distribution measurements using a MOSFET detector with a simple dose‐weighted correction method for LET effects

PubMed Central

Hotta, Kenji; Matsuura, Taeko; Matsubara, Kana; Nishioka, Shie; Nishio, Teiji; Kawashima, Mitsuhiko; Ogino, Takashi

2011-01-01

We experimentally evaluated the proton beam dose reproducibility, sensitivity, angular dependence and depth‐dose relationships for a new Metal Oxide Semiconductor Field Effect Transistor (MOSFET) detector. The detector was fabricated with a thinner oxide layer and was operated at high‐bias voltages. In order to accurately measure dose distributions, we developed a practical method for correcting the MOSFET response to proton beams. The detector was tested by examining lateral dose profiles formed by protons passing through an L‐shaped bolus. The dose reproducibility, angular dependence and depth‐dose response were evaluated using a 190 MeV proton beam. Depth‐output curves produced using the MOSFET detectors were compared with results obtained using an ionization chamber (IC). Since accurate measurements of proton dose distribution require correction for LET effects, we developed a simple dose‐weighted correction method. The correction factors were determined as a function of proton penetration depth, or residual range. The residual proton range at each measurement point was calculated using the pencil beam algorithm. Lateral measurements in a phantom were obtained for pristine and SOBP beams. The reproducibility of the MOSFET detector was within 2%, and the angular dependence was less than 9%. The detector exhibited a good response at the Bragg peak (0.74 relative to the IC detector). For dose distributions resulting from protons passing through an L‐shaped bolus, the corrected MOSFET dose agreed well with the IC results. Absolute proton dosimetry can be performed using MOSFET detectors to a precision of about 3% (1 sigma). A thinner oxide layer thickness improved the LET in proton dosimetry. By employing correction methods for LET dependence, it is possible to measure absolute proton dose using MOSFET detectors. PACS number: 87.56.‐v

Measurement of the absolute differential cross section of proton–proton elastic scattering at small angles

DOE PAGES

Mchedlishvili, D.; Chiladze, D.; Dymov, S.; ...

2016-02-03

The differential cross section for proton-proton elastic scattering has been measured at a beam kinetic energy of 1.0 GeV and in 200 MeV steps from 1.6 to 2.8 GeV for centre-of-mass angles in the range from 12°-16° to 25°-30°, depending on the energy. A precision in the overall normalisation of typically 3% was achieved by studying the energy losses of the circulating beam of the COSY storage ring as it passed repeatedly through the windowless hydrogen target of the ANKE magnetic spectrometer. It is shown that the data have a significant impact upon the results of a partial wave analysis.more » Furthermore, after extrapolating the differential cross sections to the forward direction, the results are broadly compatible with the predictions of forward dispersion relations.« less

Accurate Estimation of Solvation Free Energy Using Polynomial Fitting Techniques

PubMed Central

Shyu, Conrad; Ytreberg, F. Marty

2010-01-01

This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem 30: 2297–2304, 2009). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and non-equidistant λ values, the solvation free energy can be estimated with high accuracy without using soft-core scaling and separate simulations for Lennard-Jones and partial charges. The results from our study suggest these polynomial techniques, especially with use of non-equidistant λ values, improve the accuracy for ΔF estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software. PMID:20623657

Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations

NASA Astrophysics Data System (ADS)

Cox, Stephen J.; Geissler, Phillip L.

2018-06-01

Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (1999)]: Long-wavelength solvent response underlying finite size effects should be well described by reduced models like dielectric continuum theory, whose size dependence can be calculated straightforwardly. Applied to an ion in a periodic slab of liquid coexisting with vapor, this approach yields a finite size correction for solvation free energies that differs in important ways from results previously derived for bulk solution. For a model polar solvent, we show that this new correction quantitatively accounts for the variation of solvation free energy with volume and aspect ratio of the simulation cell. Correcting periodic slab results for an aqueous system requires an additional accounting for the solvent's intrinsic charge asymmetry, which shifts electric potentials in a size-dependent manner. The accuracy of these finite size corrections establishes a simple method for a posteriori extrapolation to the thermodynamic limit and also underscores the realism of dielectric continuum theory down to the nanometer scale.

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

NASA Astrophysics Data System (ADS)

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

PubMed Central

Vitalis, Andreas; Pappu, Rohit V.

2009-01-01

A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins: Struct. Func. Genet., 1999, 35: 133-152). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations. PMID:18506808

Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

NASA Astrophysics Data System (ADS)

Kalcher, Immanuel; Schulz, Julius C. F.; Dzubiella, Joachim

2010-10-01

We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

Absolute shielding scales for Al, Ga, and In and revised nuclear magnetic dipole moments of {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antušek, A., E-mail: andrej.antusek@stuba.sk; Holka, F., E-mail: filip.holka@stuba.sk

2015-08-21

We present coupled cluster calculations of NMR shielding constants of aluminum, gallium, and indium in water-ion clusters. In addition, relativistic and dynamical corrections and the influence of the second solvation shell are evaluated. The final NMR shielding constants define new absolute shielding scales, 600.0 ± 4.1 ppm, 2044.4 ± 31.4 ppm, and 4507.7 ± 63.7 ppm for aluminum, gallium, and indium, respectively. The nuclear magnetic dipole moments for {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In isotopes are corrected by combining the computed shielding constants with experimental NMR frequencies. The absolute magnitude of the correction increases alongmore » the series and for indium isotopes it reaches approximately −8.0 × 10{sup −3} of the nuclear magneton.« less

Teaching Absolute Value Meaningfully

ERIC Educational Resources Information Center

Wade, Angela

2012-01-01

What is the meaning of absolute value? And why do teachers teach students how to solve absolute value equations? Absolute value is a concept introduced in first-year algebra and then reinforced in later courses. Various authors have suggested instructional methods for teaching absolute value to high school students (Wei 2005; Stallings-Roberts…

Solvation of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

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).

Variations of water's local-structure induced by solvation of NaCl

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhang, Feng-Shou; Huang, Yu-Gai; Fang, Xia

2010-03-01

The researches on the structure of water and its changes induced by solutes are of enduring interests. The changes of the local structure of liquid water induced by NaCl solute under ambient conditions are studied and presented quantitatively with some order parameters and visualized with 2-body and 3-body correlation functions. The results show that, after the NaCl are solvated, the translational order t of water is decreased for the suppression of the second hydration shells around H2O molecules; the tetrahedral order (q) of water is also decreased and its favorite distribution peak moves from 0.76 to 0.5. In addition, the orientational freedom k and the diffusion coefficient D of water molecules are reduced because of new formed hydrogen-bonding structures between water and solvated ions.

Measurement of the double-differential inclusive jet cross section in proton-proton collisions at √{s} = 13 {TeV}

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; König, A.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Heracleous, N.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-Conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; Mccartin, J.; Poyraz, D.; Salva, S.; Schöfbeck, R.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; Ceard, L.; Visscher, S. De; Delaere, C.; Delcourt, M.; Forthomme, L.; Francois, B.; Giammanco, A.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Nuttens, C.; Piotrzkowski, K.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Hamer, M.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Cheng, T.; Du, R.; Jiang, C. H.; Leggat, D.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Zhao, J.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Micanovic, S.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Finger, M.; Finger, M.; Carrera Jarrin, E.; Elgammal, S.; Mohamed, A.; Mohammed, Y.; Salama, E.; Calpas, B.; Kadastik, M.; Murumaa, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Peltola, T.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Ghosh, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Kucher, I.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Abdulsalam, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Davignon, O.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Miné, P.; Naranjo, I. 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M.; Gunnellini, P.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kalogeropoulos, A.; Karacheban, O.; Kasemann, M.; Keaveney, J.; Kieseler, J.; Kleinwort, C.; Korol, I.; Lange, W.; Lelek, A.; Leonard, J.; Lipka, K.; Lobanov, A.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Placakyte, R.; Raspereza, A.; Roland, B.; Sahin, M. Ö.; Saxena, P.; Schoerner-Sadenius, T.; Seitz, C.; Spannagel, S.; Stefaniuk, N.; Trippkewitz, K. D.; Van Onsem, G. P.; Walsh, R.; Wissing, C.; Blobel, V.; Centis Vignali, M.; Draeger, A. R.; Dreyer, T.; Garutti, E.; Goebel, K.; Gonzalez, D.; Haller, J.; Hoffmann, M.; Höing, R. 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T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; D'imperio, G.; Del Re, D.; Diemoz, M.; Gelli, S.; Jorda, C.; Longo, E.; Margaroli, F.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Costa, M.; Covarelli, R.; Degano, A.; Demaria, N.; Finco, L.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Shchelina, K.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; La Licata, C.; Schizzi, A.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, S.; Lee, S. 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V.; Terkulov, A.; Baskakov, A.; Belyaev, A.; Boos, E.; Dubinin, M.; Dudko, L.; Ershov, A.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Miagkov, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Elumakhov, D.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Cirkovic, P.; Devetak, D.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Ramos, J. P. Fernández; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Yzquierdo, A. Pérez-Calero; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; de Trocóniz, J. 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F.; Chiochia, V.; De Cosa, A.; Galloni, C.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Lange, C.; Ngadiuba, J.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Yang, Y.; Candelise, V.; Doan, T. H.; Jain, Sh.; Khurana, R.; Konyushikhin, M.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Miñano Moya, M.; Paganis, E.; Psallidas, A.; Tsai, J. F.; Tzeng, Y. M.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Cerci, S.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Dumanoglu, I.; Girgis, S.; Gokbulut, G.; Guler, Y.; Gurpinar, E.; Hos, I.; Kangal, E. E.; Onengut, G.; Ozdemir, K.; Sunar Cerci, D.; Tali, B.; Topakli, H.; Turkcapar, S.; Zorbilmez, C.; Bilin, B.; Bilmis, S.; Isildak, B.; Karapinar, G.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Yetkin, E. A.; Yetkin, T.; Cakir, A.; Cankocak, K.; Sen, S.; Grynyov, B.; Levchuk, L.; Sorokin, P.; Aggleton, R.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; Seif El Nasr-Storey, S.; Smith, D.; Smith, V. J.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Calligaris, L.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Bundock, A.; Burton, D.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Della Negra, M.; Dunne, P.; Elwood, A.; Futyan, D.; Haddad, Y.; Hall, G.; Iles, G.; Lane, R.; Laner, C.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Nash, J.; Nikitenko, A.; Pela, J.; Penning, B.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Seez, C.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leslie, D.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Berry, E.; Cutts, D.; Ferapontov, A.; Garabedian, A.; Hakala, J.; Heintz, U.; Jesus, O.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Spencer, E.; Syarif, R.; Breedon, R.; Breto, G.; Burns, D.; De La Barca Sanchez, M. Calderon; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Gardner, M.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Florent, A.; Hauser, J.; Ignatenko, M.; Saltzberg, D.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Malberti, M.; Negrete, M. Olmedo; Paneva, M. I.; Shrinivas, A.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Holzner, A.; Klein, D.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Wood, J.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Heller, R.; Incandela, J.; Mccoll, N.; Mullin, S. D.; Ovcharova, A.; Richman, J.; Stuart, D.; Suarez, I.; West, C.; Yoo, J.; Anderson, D.; Apresyan, A.; Bendavid, J.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Azzolini, V.; Calamba, A.; Carlson, B.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Sun, W.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Apollinari, G.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cremonesi, M.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Field, R. D.; Furic, I. K.; Konigsberg, J.; Korytov, A.; Ma, P.; Matchev, K.; Mei, H.; Milenovic, P.; Mitselmakher, G.; Rank, D.; Shchutska, L.; Sperka, D.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, J. R.; Adams, T.; Askew, A.; Bein, S.; Diamond, B.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Khatiwada, A.; Prosper, H.; Santra, A.; Weinberg, M.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Kurt, P.; O'Brien, C.; Sandoval Gonzalez, l. D.; Turner, P.; Varelas, N.; Wu, Z.; Zakaria, M.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Osherson, M.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Bowen, J.; Bruner, C.; Castle, J.; Kenny, R. P.; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Sanders, S.; Stringer, R.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Khalil, S.; Makouski, M.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Lange, D.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Baty, A.; Bi, R.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Demiragli, Z.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Krajczar, K.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Sumorok, K.; Tatar, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bartek, R.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Knowlton, D.; Kravchenko, I.; Malta Rodrigues, A.; Meier, F.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wang, R.-J.; Wood, D.; Bhattacharya, S.; Hahn, K. A.; Kubik, A.; Low, J. F.; Mucia, N.; Odell, N.; Pollack, B.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Luo, J.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Tully, C.; Zuranski, A.; Malik, S.; Barker, A.; Barnes, V. E.; Benedetti, D.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Jung, K.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Sun, J.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Chou, J. P.; Contreras-Campana, E.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hidas, D.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Nash, K.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Castaneda Hernandez, A.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Juska, E.; Kamon, T.; Krutelyov, V.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Rose, A.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Sharma, A.; Smith, N.; Smith, W. H.; Taylor, D.; Verwilligen, P.; Woods, N.; CMS Collaboration

2016-08-01

A measurement of the double-differential inclusive jet cross section as a function of jet transverse momentum pT and absolute jet rapidity |y | is presented. The analysis is based on proton-proton collisions collected by the CMS experiment at the LHC at a centre-of-mass energy of 13 {TeV}. The data samples correspond to integrated luminosities of 71 and 44 {pb}^ {-1} for |y |<3 and 3.2<|y |<4.7, respectively. Jets are reconstructed with the anti-kt clustering algorithm for two jet sizes, R, of 0.7 and 0.4, in a phase space region covering jet pT up to 2 {TeV} and jet rapidity up to |y | = 4.7. Predictions of perturbative quantum chromodynamics at next-to-leading order precision, complemented with electroweak and nonperturbative corrections, are used to compute the absolute scale and the shape of the inclusive jet cross section. The cross section difference in R, when going to a smaller jet size of 0.4, is best described by Monte Carlo event generators with next-to-leading order predictions matched to parton showering, hadronisation, and multiparton interactions. In the phase space accessible with the new data, this measurement provides a first indication that jet physics is as well understood at √{s}=13 {TeV} as at smaller centre-of-mass energies.

Measurement of the double-differential inclusive jet cross section in proton-proton collisions at √s = 13 TeV

DOE PAGES

Khachatryan, Vardan

2016-08-11

Here, a measurement of the double-differential inclusive jet cross section as a function of jet transverse momentum p T and absolute jet rapidity |y| is presented. The analysis is based on proton-proton collisions collected by the CMS experiment at the LHC at a centre-of-mass energy of 13 TeV. The data samples correspond to integrated luminosities of 71 and 44 inverse picobarns for |y| < 3 and 3.2 < |y| < 4.7, respectively. Jets are reconstructed with the anti-kt clustering algorithm for two jet sizes, R, of 0.7 and 0.4, in a phase space region covering jet p T up tomore » 2 TeV and jet rapidity up to |y| = 4.7. Predictions of perturbative quantum chromodynamics at next-to-leading order precision, complemented with electroweak and nonperturbative corrections, are used to compute the absolute scale and the shape of the inclusive jet cross section. The cross section difference in R, when going to a smaller jet size of 0.4, is best described by Monte Carlo event generators with next-to-leading order predictions matched to parton showering, hadronisation, and multiparton interactions. In the phase space accessible with the new data, this measurement provides a first indication that jet physics is as well understood at √s = 13 TeV as at smaller centre-of-mass energies.« less

Measurement of the double-differential inclusive jet cross section in proton-proton collisions at [Formula: see text].

PubMed

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Raymond, D M; Richards, A; Rose, A; Seez, C; Tapper, A; Uchida, K; Vazquez Acosta, M; Virdee, T; Zenz, S C; Cole, J E; Hobson, P R; Khan, A; Kyberd, P; Leslie, D; Reid, I D; Symonds, P; Teodorescu, L; Turner, M; Borzou, A; Call, K; Dittmann, J; Hatakeyama, K; Liu, H; Pastika, N; Charaf, O; Cooper, S I; Henderson, C; Rumerio, P; Arcaro, D; Avetisyan, A; Bose, T; Gastler, D; Rankin, D; Richardson, C; Rohlf, J; Sulak, L; Zou, D; Benelli, G; Berry, E; Cutts, D; Ferapontov, A; Garabedian, A; Hakala, J; Heintz, U; Jesus, O; Laird, E; Landsberg, G; Mao, Z; Narain, M; Piperov, S; Sagir, S; Spencer, E; Syarif, R; Breedon, R; Breto, G; Burns, D; De La Barca Sanchez, M Calderon; Chauhan, S; Chertok, M; Conway, J; Conway, R; Cox, P T; Erbacher, R; Flores, C; Funk, G; Gardner, M; Ko, W; Lander, R; Mclean, C; Mulhearn, M; Pellett, D; Pilot, J; Ricci-Tam, F; Shalhout, S; Smith, J; Squires, M; Stolp, D; Tripathi, M; Wilbur, S; Yohay, R; Cousins, R; Everaerts, P; Florent, A; Hauser, J; Ignatenko, M; Saltzberg, D; Takasugi, E; Valuev, V; Weber, M; Burt, K; Clare, R; Ellison, J; Gary, J W; Hanson, G; Heilman, J; Jandir, P; Kennedy, E; Lacroix, F; Long, O R; Malberti, M; Negrete, M Olmedo; Paneva, M I; Shrinivas, A; Wei, H; Wimpenny, S; Yates, B R; Branson, J G; Cerati, G B; Cittolin, S; Derdzinski, M; Gerosa, R; Holzner, A; Klein, D; Letts, J; Macneill, I; Olivito, D; Padhi, S; Pieri, M; Sani, M; Sharma, V; Simon, S; Tadel, M; Vartak, A; Wasserbaech, S; Welke, C; Wood, J; Würthwein, F; Yagil, A; Zevi Della Porta, G; Bhandari, R; Bradmiller-Feld, J; Campagnari, C; Dishaw, A; Dutta, V; Flowers, K; Franco Sevilla, M; Geffert, P; George, C; Golf, F; Gouskos, L; Gran, J; Heller, R; Incandela, J; Mccoll, N; Mullin, S D; Ovcharova, A; Richman, J; Stuart, D; Suarez, I; West, C; Yoo, J; Anderson, D; Apresyan, A; Bendavid, J; Bornheim, A; Bunn, J; Chen, Y; Duarte, J; Mott, A; Newman, H B; Pena, C; Spiropulu, M; Vlimant, J R; Xie, S; Zhu, R Y; Andrews, M B; Azzolini, V; Calamba, A; Carlson, B; Ferguson, T; Paulini, M; Russ, J; Sun, M; Vogel, H; Vorobiev, I; Cumalat, J P; Ford, W T; Jensen, F; Johnson, A; Krohn, M; Mulholland, T; Stenson, K; Wagner, S R; Alexander, J; Chaves, J; Chu, J; Dittmer, S; Mirman, N; Nicolas Kaufman, G; Patterson, J R; Rinkevicius, A; Ryd, A; Skinnari, L; Sun, W; Tan, S M; Tao, Z; Thom, J; Tucker, J; Wittich, P; Winn, D; Abdullin, S; Albrow, M; Apollinari, G; Banerjee, S; Bauerdick, L A T; Beretvas, A; Berryhill, J; Bhat, P C; Bolla, G; Burkett, K; Butler, J N; Cheung, H W K; Chlebana, F; Cihangir, S; Cremonesi, M; Elvira, V D; Fisk, I; Freeman, J; Gottschalk, E; Gray, L; Green, D; Grünendahl, S; Gutsche, O; Hare, D; Harris, R M; Hasegawa, S; Hirschauer, J; Hu, Z; Jayatilaka, B; Jindariani, S; Johnson, M; Joshi, U; Klima, B; Kreis, B; Lammel, S; Linacre, J; Lincoln, D; Lipton, R; Liu, T; Lopes De Sá, R; Lykken, J; Maeshima, K; Magini, N; Marraffino, J M; Maruyama, S; Mason, D; McBride, P; Merkel, P; Mrenna, S; Nahn, S; Newman-Holmes, C; O'Dell, V; Pedro, K; Prokofyev, O; Rakness, G; Ristori, L; Sexton-Kennedy, E; Soha, A; Spalding, W J; Spiegel, L; Stoynev, S; Strobbe, N; Taylor, L; Tkaczyk, S; Tran, N V; Uplegger, L; Vaandering, E W; Vernieri, C; Verzocchi, M; Vidal, R; Wang, M; Weber, H A; Whitbeck, A; Acosta, D; Avery, P; Bortignon, P; Bourilkov, D; Brinkerhoff, A; Carnes, A; Carver, M; Curry, D; Das, S; Field, R D; Furic, I K; Konigsberg, J; Korytov, A; Ma, P; Matchev, K; Mei, H; Milenovic, P; Mitselmakher, G; Rank, D; Shchutska, L; Sperka, D; Thomas, L; Wang, J; Wang, S; Yelton, J; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Ackert, A; Adams, J R; Adams, T; Askew, A; Bein, S; Diamond, B; Hagopian, S; Hagopian, V; Johnson, K F; Khatiwada, A; Prosper, H; Santra, A; Weinberg, M; Baarmand, M M; Bhopatkar, V; Colafranceschi, S; Hohlmann, M; Noonan, D; Roy, T; Yumiceva, F; Adams, M R; Apanasevich, L; Berry, D; Betts, R R; Bucinskaite, I; Cavanaugh, R; Evdokimov, O; Gauthier, L; Gerber, C E; Hofman, D J; Kurt, P; O'Brien, C; Sandoval Gonzalez, L D; Turner, P; Varelas, N; Wu, Z; Zakaria, M; Zhang, J; Bilki, B; Clarida, W; Dilsiz, K; Durgut, S; Gandrajula, R P; Haytmyradov, M; Khristenko, V; Merlo, J-P; Mermerkaya, H; Mestvirishvili, A; Moeller, A; Nachtman, J; Ogul, H; Onel, Y; Ozok, F; Penzo, A; Snyder, C; Tiras, E; Wetzel, J; Yi, K; Anderson, I; Blumenfeld, B; Cocoros, A; Eminizer, N; Fehling, D; Feng, L; Gritsan, A V; Maksimovic, P; Osherson, M; Roskes, J; Sarica, U; Swartz, M; Xiao, M; Xin, Y; You, C; Al-Bataineh, A; Baringer, P; Bean, A; Bowen, J; Bruner, C; Castle, J; Kenny, R P; Kropivnitskaya, A; Majumder, D; Mcbrayer, W; Murray, M; Sanders, S; Stringer, R; Tapia Takaki, J D; Wang, Q; Ivanov, A; Kaadze, K; Khalil, S; Makouski, M; Maravin, Y; Mohammadi, A; Saini, L K; Skhirtladze, N; Toda, S; Lange, D; Rebassoo, F; Wright, D; Anelli, C; Baden, A; Baron, O; Belloni, A; Calvert, B; Eno, S C; Ferraioli, C; Gomez, J A; Hadley, N J; Jabeen, S; Kellogg, R G; Kolberg, T; Kunkle, J; Lu, Y; Mignerey, A C; Shin, Y H; Skuja, A; Tonjes, M B; Tonwar, S C; Apyan, A; Barbieri, R; Baty, A; Bi, R; Bierwagen, K; Brandt, S; Busza, W; Cali, I A; Demiragli, Z; Di Matteo, L; Gomez Ceballos, G; Goncharov, M; Hsu, D; Iiyama, Y; Innocenti, G M; Klute, M; Kovalskyi, D; Krajczar, K; Lai, Y S; Lee, Y-J; Levin, A; Luckey, P D; Marini, A C; Mcginn, C; Mironov, C; Narayanan, S; Niu, X; Paus, C; Roland, C; Roland, G; Salfeld-Nebgen, J; Stephans, G S F; Sumorok, K; Tatar, K; Varma, M; Velicanu, D; Veverka, J; Wang, J; Wang, T W; Wyslouch, B; Yang, M; Zhukova, V; Benvenuti, A C; Chatterjee, R M; Evans, A; Finkel, A; Gude, A; Hansen, P; Kalafut, S; Kao, S C; Kubota, Y; Lesko, Z; Mans, J; Nourbakhsh, S; Ruckstuhl, N; Rusack, R; Tambe, N; Turkewitz, J; Acosta, J G; Oliveros, S; Avdeeva, E; Bartek, R; Bloom, K; Bose, S; Claes, D R; Dominguez, A; Fangmeier, C; Gonzalez Suarez, R; Kamalieddin, R; Knowlton, D; Kravchenko, I; Malta Rodrigues, A; Meier, F; Monroy, J; Siado, J E; Snow, G R; Stieger, B; Alyari, M; Dolen, J; George, J; Godshalk, A; Harrington, C; Iashvili, I; Kaisen, J; Kharchilava, A; Kumar, A; Parker, A; Rappoccio, S; Roozbahani, B; Alverson, G; Barberis, E; Baumgartel, D; Chasco, M; Hortiangtham, A; Massironi, A; Morse, D M; Nash, D; Orimoto, T; Teixeira De Lima, R; Trocino, D; Wang, R-J; Wood, D; Bhattacharya, S; Hahn, K A; Kubik, A; Low, J F; Mucia, N; Odell, N; Pollack, B; Schmitt, M H; Sung, K; Trovato, M; Velasco, M; Dev, N; Hildreth, M; Hurtado Anampa, K; Jessop, C; Karmgard, D J; Kellams, N; Lannon, K; Marinelli, N; Meng, F; Mueller, C; Musienko, Y; Planer, M; Reinsvold, A; Ruchti, R; Smith, G; Taroni, S; Valls, N; Wayne, M; Wolf, M; Woodard, A; Alimena, J; Antonelli, L; Brinson, J; Bylsma, B; Durkin, L S; Flowers, S; Francis, B; Hart, A; Hill, C; Hughes, R; Ji, W; Liu, B; Luo, W; Puigh, D; Winer, B L; Wulsin, H W; Cooperstein, S; Driga, O; Elmer, P; Hardenbrook, J; Hebda, P; Luo, J; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Palmer, C; Piroué, P; Stickland, D; Tully, C; Zuranski, A; Malik, S; Barker, A; Barnes, V E; Benedetti, D; Folgueras, S; Gutay, L; Jha, M K; Jones, M; Jung, A W; Jung, K; Miller, D H; Neumeister, N; Radburn-Smith, B C; Shi, X; Sun, J; Svyatkovskiy, A; Wang, F; Xie, W; Xu, L; Parashar, N; Stupak, J; Adair, A; Akgun, B; Chen, Z; Ecklund, K M; Geurts, F J M; Guilbaud, M; Li, W; Michlin, B; Northup, M; Padley, B P; Redjimi, R; Roberts, J; Rorie, J; Tu, Z; Zabel, J; Betchart, B; Bodek, A; de Barbaro, P; Demina, R; Duh, Y T; Ferbel, T; Galanti, M; Garcia-Bellido, A; Han, J; Hindrichs, O; Khukhunaishvili, A; Lo, K H; Tan, P; Verzetti, M; Chou, J P; Contreras-Campana, E; Gershtein, Y; Gómez Espinosa, T A; Halkiadakis, E; Heindl, M; Hidas, D; Hughes, E; Kaplan, S; Kunnawalkam Elayavalli, R; Kyriacou, S; Lath, A; Nash, K; Saka, H; Salur, S; Schnetzer, S; Sheffield, D; Somalwar, S; Stone, R; Thomas, S; Thomassen, P; Walker, M; Foerster, M; Heideman, J; Riley, G; Rose, K; Spanier, S; Thapa, K; Bouhali, O; Castaneda Hernandez, A; Celik, A; Dalchenko, M; De Mattia, M; Delgado, A; Dildick, S; Eusebi, R; Gilmore, J; Huang, T; Juska, E; Kamon, T; Krutelyov, V; Mueller, R; Pakhotin, Y; Patel, R; Perloff, A; Perniè, L; Rathjens, D; Rose, A; Safonov, A; Tatarinov, A; Ulmer, K A; Akchurin, N; Cowden, C; Damgov, J; Dragoiu, C; Dudero, P R; Faulkner, J; Kunori, S; Lamichhane, K; Lee, S W; Libeiro, T; Undleeb, S; Volobouev, I; Wang, Z; Delannoy, A G; Greene, S; Gurrola, A; Janjam, R; Johns, W; Maguire, C; Melo, A; Ni, H; Sheldon, P; Tuo, S; Velkovska, J; Xu, Q; Arenton, M W; Barria, P; Cox, B; Goodell, J; Hirosky, R; Ledovskoy, A; Li, H; Neu, C; Sinthuprasith, T; Sun, X; Wang, Y; Wolfe, E; Xia, F; Clarke, C; Harr, R; Karchin, P E; Lamichhane, P; Sturdy, J; Belknap, D A; Dasu, S; Dodd, L; Duric, S; Gomber, B; Grothe, M; Herndon, M; Hervé, A; Klabbers, P; Lanaro, A; Levine, A; Long, K; Loveless, R; Ojalvo, I; Perry, T; Pierro, G A; Polese, G; Ruggles, T; Savin, A; Sharma, A; Smith, N; Smith, W H; Taylor, D; Verwilligen, P; Woods, N; Collaboration, Authorinst The Cms

2016-01-01

A measurement of the double-differential inclusive jet cross section as a function of jet transverse momentum [Formula: see text] and absolute jet rapidity [Formula: see text] is presented. The analysis is based on proton-proton collisions collected by the CMS experiment at the LHC at a centre-of-mass energy of 13[Formula: see text]. The data samples correspond to integrated luminosities of 71 and 44[Formula: see text] for [Formula: see text] and [Formula: see text], respectively. Jets are reconstructed with the anti-[Formula: see text] clustering algorithm for two jet sizes, R , of 0.7 and 0.4, in a phase space region covering jet [Formula: see text] up to 2[Formula: see text] and jet rapidity up to [Formula: see text] = 4.7. Predictions of perturbative quantum chromodynamics at next-to-leading order precision, complemented with electroweak and nonperturbative corrections, are used to compute the absolute scale and the shape of the inclusive jet cross section. The cross section difference in R , when going to a smaller jet size of 0.4, is best described by Monte Carlo event generators with next-to-leading order predictions matched to parton showering, hadronisation, and multiparton interactions. In the phase space accessible with the new data, this measurement provides a first indication that jet physics is as well understood at [Formula: see text] as at smaller centre-of-mass energies.

Multiply Reduced Oligofluorenes: Their Nature and Pairing with THF-Solvated Sodium Ions

DOE PAGES

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; ...

2016-07-01

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

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

NASA Astrophysics Data System (ADS)

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.

Water-enhanced solvation of organics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jane H.

1993-07-01

Water-enhanced solvation (WES) was explored for Lewis acid solutes in Lewis base organic solvents, to develop cheap extract regeneration processes. WES for solid solutes was determined from ratios of solubilities of solutes in water-sat. and low-water solvent; both were determined from solid-liquid equilibrium. Vapor-headspace analysis was used to determine solute activity coefficients as function of organic phase water concentration. WES magnitudes of volatile solutes were normalized, set equal to slope of log 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,more » 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.« less

Multibody correlations in the hydrophobic solvation of glycine peptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu

2014-12-14

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

Terahertz Absorption and Circular Dichroism Spectroscopy of Solvated Biopolymers

NASA Astrophysics Data System (ADS)

Xu, Jing; Plaxco, Kevin; Allen, S. James

2006-03-01

Biopolymers are expected to exhibit broad spectral features in the terahertz frequency range, corresponding to their functionally relevant, global and sub-global collective vibrational modes with ˜ picosecond timescale. Recent advances in terahertz technology have stimulated researchers to employ terahertz absorption spectroscopy to directly probe these postulated collective modes. However, these pioneering studies have been limited to dry and, at best, moist samples. Successful isolation of low frequency vibrational activities of solvated biopolymers in their natural water environment has remained elusive, due to the overwhelming attenuation of the terahertz radiation by water. Here we have developed a terahertz absorption and circular dichroism spectrometer suitable for studying biopolymers in biologically relevant water solutions. We have precisely isolated, for the first time, the terahertz absorption of solvated prototypical proteins, Bovine Serum Albumin and Lysozyme, and made important direct comparison to the existing molecular dynamic simulations and normal mode calculations. We have also successfully demonstrated the magnetic circular dichroism in semiconductors, and placed upper bounds on the terahertz circular dichroism signatures of prototypical proteins in water solution.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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

2016-12-05

Alkali metal-oxygen batteries are of great interests for energy storage because of their unparalleled theoretical energy densities. Particularly attractive is the emerging Na-O 2 battery because of the formation of superoxide as the discharge product. Dimethyl sulfoxide (DMSO) is a promising solvent for this battery but its instability towards Na makes it impractical in the Na-O 2 battery. Herein we report the enhanced stability of Na in DMSO solutions containing concentrated sodium trifluoromethanesulfonimide (NaTFSI) salts (>3 mol kg -1 ). Raman spectra of NaTFSI/DMSO electrolytes and ab initio molecular dynamics simulation reveal the Na + solvation number in DMSO and the formation of Na(DMSO) 3 (TFSI)-like solvation structure. The majority of DMSO molecules solvating Na + in concentrated solutions reduces the available free DMSO molecules that can react with Na and renders the TFSI anion decomposition, which protects Na from reacting with the electrolyte. Using these concentrated electrolytes, Na-O 2 batteries can be cycled forming sodium superoxide (NaO 2 ) as the sole discharge product with improved long cycle life, highlighting the beneficial role of concentrated electrolytes for Na-based batteries. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

DOE PAGES

He, Mingfu; Lau, Kah Chun; Ren, Xiaodi; ...

2016-11-03

Alkali metal-oxygen batteries are of great interests for energy storage because of their unparalleled theoretical energy densities. Particularly attractive is the emerging Na-O 2 battery because of the formation of superoxide as the discharge product. Dimethyl sulfoxide (DMSO) is a promising solvent for this battery but its instability towards Na makes it impractical in the Na-O 2 battery. Here in this paper, we report the enhanced stability of Na in DMSO solutions containing concentrated sodium trifluoromethanesulfonimide (NaTFSI) salts (>3molkg -1). Raman spectra of NaTFSI/DMSO electrolytes and abinitio molecular dynamics simulation reveal the Na + solvation number in DMSO and themore » formation of Na(DMSO) 3(TFSI)-like solvation structure. The majority of DMSO molecules solvating Na + in concentrated solutions reduces the available free DMSO molecules that can react with Na and renders the TFSI anion decomposition, which protects Na from reacting with the electrolyte. Using these concentrated electrolytes, Na-O 2 batteries can be cycled forming sodium superoxide (NaO 2) as the sole discharge product with improved long cycle life, highlighting the beneficial role of concentrated electrolytes for Na-based batteries.« less

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture

NASA Astrophysics Data System (ADS)

Kasai, Yukako; Yoshida, Norio; Nakano, Haruyuki

2015-05-01

The co-solvent effect on the proton transfer reaction of glycine in a water-acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water-acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is more stable than the neutral form. The reaction free energy is -10.6 kcal mol-1. On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol-1. The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.

Snapshots of Proton Accommodation at a Microscopic Water Surface: Understanding the Vibrational Spectral Signatures of the Charge Defect in Cryogenically Cooled H+(H2O)n=2 – 28 Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Mark A.

In this Article, we review the role of gas-phase, size-selected protonated water clusters, H+(H2O)n, in the analysis of the microscopic mechanics responsible for the behavior of the excess proton in bulk water. We extend upon previous studies of the smaller, two-dimensional sheet-like structures to larger (n≥10) assemblies with three-dimensional cage morphologies which better mimic the bulk environment. Indeed, clusters in which a complete second solvation shell forms around a surface-embedded hydronium ion yield vibrational spectra where the signatures of the proton defect display strikingly similar positions and breadth to those observed in dilute acids. We investigate effects of the localmore » structure and intermolecular interactions on the large red shifts observed in the proton vibrational signature upon cluster growth using various theoretical methods. We show that, in addition to sizeable anharmonic couplings, the position of the excess proton vibration can be traced to large increases in the electric field exerted on the embedded hydronium ion upon formation of the first and second solvation shells. MAJ acknowledges support from the U.S. Department of Energy under Grant No. DE-FG02- 06ER15800 as well as the facilities and staff of the Yale University Faculty of Arts and Sciences High Performance Computing Center, and by the National Science Foundation under Grant No. CNS 08-21132 that partially funded acquisition of the facilities. SMK and SSX acknowledge support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.« less

Electron Emission from Amorphous Solid Water Induced by Passage of Energetic Protons and Fluorine Ions

PubMed Central

Toburen, L. H.; McLawhorn, S. L.; McLawhorn, R. A.; Carnes, K. D.; Dingfelder, M.; Shinpaugh, J. L.

2013-01-01

Absolute doubly differential electron emission yields were measured from thin films of amorphous solid water (ASW) after the transmission of 6 MeV protons and 19 MeV (1 MeV/nucleon) fluorine ions. The ASW films were frozen on thin (1-μm) copper foils cooled to approximately 50 K. Electrons emitted from the films were detected as a function of angle in both the forward and backward direction and as a function of the film thickness. Electron energies were determined by measuring the ejected electron time of flight, a technique that optimizes the accuracy of measuring low-energy electron yields, where the effects of molecular environment on electron transport are expected to be most evident. Relative electron emission yields were normalized to an absolute scale by comparison of the integrated total yields for proton-induced electron emission from the copper substrate to values published previously. The absolute doubly differential yields from ASW are presented along with integrated values, providing single differential and total electron emission yields. These data may provide benchmark tests of Monte Carlo track structure codes commonly used for assessing the effects of radiation quality on biological effectiveness. PMID:20681805

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jurrus, Elizabeth; Engel, Dave; Star, Keith

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 suitemore » 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.« less

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Tuning structure and mobility of solvation shells surrounding tracer additives.

PubMed

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

2015-03-28

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

Real single ion solvation free energies with quantum mechanical simulation

DOE PAGES

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

2017-07-04

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energiesmore » into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.« less

Fluorination, Defluorination, Derivatization and Solvation of Single-Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Margrave, John L.

1999-10-01

Direct fluorination has been used to create fluoronanotubes which have active sites for derivatizing carbon nanotubes. A new technique using hydrazine and its derivatives has been used for defluorination of fluoronanotubes. The products include N2 and HF. Fluorinated species can be derivatized with R-Li or Grignard Reagents to form inorganic fluorides and derivatized products e.g., methyl, butyl or hexyl-nanotubes, (NH2)x-nanotubes, etc. Mass-spectra IR and Raman spectra along with electron microprobe analyses have been utilized, along with AFM, SEM and TEM to characterize the products. ``Fluorotubes" can be solvated as individual tubes in various alcohol solvents via ultrasonication. These solutions persist long enough (over a week) to permit solution phase chemistry to be carried out on the fluorotubes. For example, the solvated fluorotubes can be precipitated out of solution with hydrazine to yield normal, unfluorinated SWNTs or they can be reacted with sodium methoxide to yield methoxylated SWNTs.

Sparingly Solvating Electrolytes for High Energy Density Lithium-Sulfur Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.

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 systemsmore » 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.« less

Real single ion solvation free energies with quantum mechanical simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energiesmore » into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.« less

Sparingly solvating electrolytes for high energy density Lithium–sulfur batteries

DOE PAGES

Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; ...

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 systemsmore » that fundamentally decouple electrolyte volume from reaction mechanism. Furthermore, 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.« less

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NASA Astrophysics Data System (ADS)

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

2008-06-01

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 a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τrot = 2.5 ps) and a fraction of immobilized water molecules ( τrot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement.

PubMed

Cao, Lili; Caldararu, Octav; Ryde, Ulf

2017-09-07

Nitrogenase is the only enzyme that can break the triple bond in N 2 to form two molecules of ammonia. The enzyme has been thoroughly studied with both experimental and computational methods, but there is still no consensus regarding the atomic details of the reaction mechanism. In the most common form, the active site is a MoFe 7 S 9 C(homocitrate) cluster. The homocitrate ligand contains one alcohol and three carboxylate groups. In water solution, the triply deprotonated form dominates, but because the alcohol (and one of the carboxylate groups) coordinate to the Mo ion, this may change in the enzyme. We have performed a series of computational calculations with molecular dynamics (MD), quantum mechanical (QM) cluster, combined QM and molecular mechanics (QM/MM), QM/MM with Poisson-Boltzmann and surface area solvation, QM/MM thermodynamic cycle perturbations, and quantum refinement methods to settle the most probable protonation state of the homocitrate ligand in nitrogenase. The results quite conclusively point out a triply deprotonated form (net charge -3) with a proton shared between the alcohol and one of the carboxylate groups as the most stable at pH 7. Moreover, we have studied eight ionizable protein residues close to the active site with MD simulations and determined the most likely protonation states.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths.

PubMed

Fulfer, K D; Kuroda, D G

2017-09-20

The structure and dynamics of electrolytes composed of lithium hexafluorophosphate (LiPF 6 ) in dimethyl carbonate, ethyl methyl carbonate, and diethyl carbonate were investigated using a combination of linear and two-dimensional infrared spectroscopies. The solutions studied here have a LiPF 6 concentration of X(LiPF 6 ) = 0.09, which is typically found in commercial lithium ion batteries. This study focuses on comparing the differences in the solvation shell structure and dynamics produced by linear organic carbonates of different alkyl chain lengths. The IR experiments show that either linear carbonate forms a tetrahedral solvation shell (coordination number of 4) around the lithium ion irrespective of whether the solvation shell has anions in close proximity to the carbonates. Moreover, analysis of the absorption cross sections via FTIR and DFT computations reveals a distortion in the angle formed by Li + -O[double bond, length as m-dash]C which decreases from the expected 180° when the alkyl chains of the carbonate are lengthened. In addition, our findings also reveal that, likely due to its asymmetric structure, ethyl methyl carbonate has a significantly more distorted tetrahedral lithium ion solvation shell than either of the other two investigated carbonates. IR photon echo studies further demonstrate that the motions of the solvation shell have a time scale of a few picoseconds for all three linear carbonates. Interestingly, a slowdown of the in place-motions of the first solvation shell is observed when the carbonate has a longer alkyl chain length irrespective of the symmetry. In addition, vibrational energy transfer with a time scale of tens of picoseconds is observed between strongly coupled modes arising from the solvation shell structure of the Li + which corroborates the modeling of these solvation shells in terms of highly coupled vibrational states. Results of this study provide new insights into the molecular structure and dynamics of the

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

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

DOEpatents

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

2017-01-24

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

Physical transformation of niclosamide solvates in pharmaceutical suspensions determined by DSC and TG analysis.

PubMed

de Villiers, M M; Mahlatji, M D; Malan, S F; van Tonder, E C; Liebenberg, W

2004-07-01

This study reports the preparation of four niclosamide solvates and the determination of the stability of the crystal forms in different suspension vehicles by DSC and TG analysis. Thermal analysis showed that the niclosamide solvates were extremely unstable in a PVP-vehicle and rapidly changed to monohydrated crystals. A suspension in propylene glycol was more stable and TG analysis showed that crystal transformation was less rapid. In this vehicle, the crystals transformed to the anhydrate, rather than the monohydrate, since the vehicle was non-aqueous. The TEG-hemisolvate was the most stable in suspension and offered the best possibility of commercial exploitation.

Measurement of the inclusive jet cross-sections in proton-proton collisions at $$\\sqrt{s}=8$$ TeV with the ATLAS detector

DOE PAGES

Aaboud, M.; Aad, G.; Abbott, B.; ...

2017-09-05

Inclusive jet production cross-sections are measured in proton-proton collisions at a centre-of-mass energy of √s=8 TeV recorded by the ATLAS experiment at the Large Hadron Collider at CERN. The total integrated luminosity of the analysed data set amounts to 20.2 fb -1. Double-differential cross-sections are measured for jets defined by the anti-k t jet clustering algorithm with radius parameters of R = 0.4 and R = 0.6 and are presented as a function of the jet transverse momentum, in the range between 70 GeV and 2.5 TeV and in six bins of the absolute jet rapidity, between 0 and 3.0.more » The measured cross-sections are compared to predictions of quantum chromodynamics, calculated at next-to-leading order in perturbation theory, and corrected for non-perturbative and electroweak effects. The level of agreement with predictions, using a selection of different parton distribution functions for the proton, is quantified. Tensions between the data and the theory predictions are observed.« less

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study.

PubMed

Kachmar, Ali; Carignano, Marcelo; Laino, Teodoro; Iannuzzi, Marcella; Hutter, Jürg

2017-08-10

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observation of Y(1S) pair production in proton-proton collisions at $$ \\sqrt{s}=8 $$ TeV

DOE PAGES

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; ...

2017-05-03

Pair production of Y(1S) mesons is observed at the LHC in proton-proton collisions at √s = 8 TeV by the CMS experiment in a data sample corresponding to an integrated luminosity of 20.7 fb -1. Both Y(1S) candidates are fully reconstructed via their decays to μ +μ -. The fiducial acceptance region is defined by an absolute Y(1S) rapidity smaller than 2.0. Furthermore, the fiducial cross section for the production of Y(1S) pairs, assuming that both mesons decay isotropically, is measured to be 68.8±12.7 (stat)±7.4 (syst)±2.8 ( BB ) pb, where the third uncertainty comes from the uncertainty in themore » branching fraction of Y(1S) decays to μ +μ -. Assuming instead that the Y(1S) mesons are produced with different polarizations leads to variations in the measured cross section in the range from -38% to +36%.« less

Observation of Y(1S) pair production in proton-proton collisions at √{s}=8 TeV

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; König, A.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rad, N.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Strauss, J.; Waltenberger, W.; Wulz, C.-E.; Dvornikov, O.; Makarenko, V.; Zykunov, V.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; De Wolf, E. A.; Janssen, X.; Lauwers, J.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; De Bruyn, I.; Deroover, K.; Lowette, S.; Moortgat, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Luetic, J.; Maerschalk, T.; Marinov, A.; Randle-conde, A.; Seva, T.; Vander Velde, C.; Vanlaer, P.; Yonamine, R.; Zenoni, F.; Zhang, F.; Cimmino, A.; Cornelis, T.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; Khvastunov, I.; Poyraz, D.; Salva, S.; Schöfbeck, R.; Sharma, A.; Tytgat, M.; Van Driessche, W.; Yazgan, E.; Zaganidis, N.; Bakhshiansohi, H.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Nuttens, C.; Piotrzkowski, K.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Wertz, S.; Beliy, N.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Cheng, T.; Jiang, C. H.; Leggat, D.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Zhao, J.; Ban, Y.; Chen, G.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Micanovic, S.; Sudic, L.; Susa, T.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Tsiakkouri, D.; Finger, M.; Finger, M.; Carrera Jarrin, E.; Ellithi Kamel, A.; Mahmoud, M. 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M.; Fahim, A.; Khakzad, M.; Mohammadi Najafabadi, M.; Naseri, M.; Paktinat Mehdiabadi, S.; Rezaei Hosseinabadi, F.; Safarzadeh, B.; Zeinali, M.; Felcini, M.; Grunewald, M.; Abbrescia, M.; Calabria, C.; Caputo, C.; Colaleo, A.; Creanza, D.; Cristella, L.; De Filippis, N.; De Palma, M.; Fiore, L.; Iaselli, G.; Maggi, G.; Maggi, M.; Miniello, G.; My, S.; Nuzzo, S.; Pompili, A.; Pugliese, G.; Radogna, R.; Ranieri, A.; Selvaggi, G.; Silvestris, L.; Venditti, R.; Verwilligen, P.; Abbiendi, G.; Battilana, C.; Bonacorsi, D.; Braibant-Giacomelli, S.; Brigliadori, L.; Campanini, R.; Capiluppi, P.; Castro, A.; Cavallo, F. R.; Chhibra, S. S.; Codispoti, G.; Cuffiani, M.; Dallavalle, G. M.; Fabbri, F.; Fanfani, A.; Fasanella, D.; Giacomelli, P.; Grandi, C.; Guiducci, L.; Marcellini, S.; Masetti, G.; Montanari, A.; Navarria, F. L.; Perrotta, A.; Rossi, A. M.; Rovelli, T.; Siroli, G. 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M.; Lanza, G.; Lista, L.; Meola, S.; Paolucci, P.; Sciacca, C.; Thyssen, F.; Azzi, P.; Bacchetta, N.; Benato, L.; Bisello, D.; Boletti, A.; Carlin, R.; Checchia, P.; Dall'Osso, M.; De Castro Manzano, P.; Dorigo, T.; Dosselli, U.; Gasparini, F.; Gasparini, U.; Gozzelino, A.; Lacaprara, S.; Margoni, M.; Maron, G.; Meneguzzo, A. T.; Michelotto, M.; Pazzini, J.; Pegoraro, M.; Pozzobon, N.; Ronchese, P.; Simonetto, F.; Zanetti, M.; Zumerle, G.; Braghieri, A.; Magnani, A.; Montagna, P.; Ratti, S. P.; Re, V.; Riccardi, C.; Salvini, P.; Vai, I.; Vitulo, P.; Alunni Solestizi, L.; Bilei, G. M.; Ciangottini, D.; Fanò, L.; Lariccia, P.; Leonardi, R.; Mantovani, G.; Menichelli, M.; Saha, A.; Santocchia, A.; Androsov, K.; Azzurri, P.; Bagliesi, G.; Bernardini, J.; Boccali, T.; Castaldi, R.; Ciocci, M. A.; Dell'Orso, R.; Donato, S.; Fedi, G.; Giassi, A.; Grippo, M. T.; Ligabue, F.; Lomtadze, T.; Martini, L.; Messineo, A.; Palla, F.; Rizzi, A.; Savoy-Navarro, A.; Spagnolo, P.; Tenchini, R.; Tonelli, G.; Venturi, A.; Verdini, P. G.; Barone, L.; Cavallari, F.; Cipriani, M.; Del Re, D.; Diemoz, M.; Gelli, S.; Longo, E.; Margaroli, F.; Marzocchi, B.; Meridiani, P.; Organtini, G.; Paramatti, R.; Preiato, F.; Rahatlou, S.; Rovelli, C.; Santanastasio, F.; Amapane, N.; Arcidiacono, R.; Argiro, S.; Arneodo, M.; Bartosik, N.; Bellan, R.; Biino, C.; Cartiglia, N.; Costa, M.; Cotto, G.; Covarelli, R.; De Remigis, P.; Degano, A.; Demaria, N.; Finco, L.; Kiani, B.; Mariotti, C.; Maselli, S.; Migliore, E.; Monaco, V.; Monteil, E.; Obertino, M. M.; Pacher, L.; Pastrone, N.; Pelliccioni, M.; Pinna Angioni, G. L.; Ravera, F.; Romero, A.; Ruspa, M.; Sacchi, R.; Sola, V.; Solano, A.; Staiano, A.; Traczyk, P.; Belforte, S.; Casarsa, M.; Cossutti, F.; Della Ricca, G.; Zanetti, A.; Kim, D. H.; Kim, G. N.; Kim, M. S.; Lee, S.; Lee, S. W.; Oh, Y. D.; Sekmen, S.; Son, D. C.; Yang, Y. C.; Lee, A.; Kim, H.; Brochero Cifuentes, J. A.; Kim, T. J.; Cho, S.; Choi, S.; Go, Y.; Gyun, D.; Ha, S.; Hong, B.; Jo, Y.; Kim, Y.; Lee, B.; Lee, K.; Lee, K. S.; Lee, S.; Lim, J.; Park, S. K.; Roh, Y.; Almond, J.; Kim, J.; Lee, H.; Oh, S. B.; Radburn-Smith, B. C.; Seo, S. h.; Yang, U. K.; Yoo, H. D.; Yu, G. B.; Choi, M.; Kim, H.; Kim, J. H.; Lee, J. S. H.; Park, I. C.; Ryu, G.; Ryu, M. S.; Choi, Y.; Goh, J.; Hwang, C.; Lee, J.; Yu, I.; Dudenas, V.; Juodagalvis, A.; Vaitkus, J.; Ahmed, I.; Ibrahim, Z. A.; Komaragiri, J. R.; Md Ali, M. A. B.; Mohamad Idris, F.; Wan Abdullah, W. A. T.; Yusli, M. N.; Zolkapli, Z.; Castilla-Valdez, H.; De La Cruz-Burelo, E.; Heredia-De La Cruz, I.; Hernandez-Almada, A.; Lopez-Fernandez, R.; Magaña Villalba, R.; Mejia Guisao, J.; Sanchez-Hernandez, A.; Carrillo Moreno, S.; Oropeza Barrera, C.; Vazquez Valencia, F.; Carpinteyro, S.; Pedraza, I.; Salazar Ibarguen, H. A.; Uribe Estrada, C.; Morelos Pineda, A.; Krofcheck, D.; Butler, P. H.; Ahmad, A.; Ahmad, M.; Hassan, Q.; Hoorani, H. R.; Khan, W. A.; Saddique, A.; Shah, M. A.; Shoaib, M.; Waqas, M.; Bialkowska, H.; Bluj, M.; Boimska, B.; Frueboes, T.; Górski, M.; Kazana, M.; Nawrocki, K.; Romanowska-Rybinska, K.; Szleper, M.; Zalewski, P.; Bunkowski, K.; Byszuk, A.; Doroba, K.; Kalinowski, A.; Konecki, M.; Krolikowski, J.; Misiura, M.; Olszewski, M.; Walczak, M.; Bargassa, P.; Beirão Da Cruz E Silva, C.; Di Francesco, A.; Faccioli, P.; Ferreira Parracho, P. G.; Gallinaro, M.; Hollar, J.; Leonardo, N.; Lloret Iglesias, L.; Nemallapudi, M. V.; Rodrigues Antunes, J.; Seixas, J.; Toldaiev, O.; Vadruccio, D.; Varela, J.; Vischia, P.; Afanasiev, S.; Bunin, P.; Gavrilenko, M.; Golutvin, I.; Gorbunov, I.; Kamenev, A.; Karjavin, V.; Lanev, A.; Malakhov, A.; Matveev, V.; Palichik, V.; Perelygin, V.; Shmatov, S.; Shulha, S.; Skatchkov, N.; Smirnov, V.; Voytishin, N.; Zarubin, A.; Chtchipounov, L.; Golovtsov, V.; Ivanov, Y.; Kim, V.; Kuznetsova, E.; Murzin, V.; Oreshkin, V.; Sulimov, V.; Vorobyev, A.; Andreev, Yu.; Dermenev, A.; Gninenko, S.; Golubev, N.; Karneyeu, A.; Kirsanov, M.; Krasnikov, N.; Pashenkov, A.; Tlisov, D.; Toropin, A.; Epshteyn, V.; Gavrilov, V.; Lychkovskaya, N.; Popov, V.; Pozdnyakov, I.; Safronov, G.; Spiridonov, A.; Toms, M.; Vlasov, E.; Zhokin, A.; Bylinkin, A.; Chistov, R.; Danilov, M.; Rusinov, V.; Andreev, V.; Azarkin, M.; Dremin, I.; Kirakosyan, M.; Leonidov, A.; Rusakov, S. V.; Terkulov, A.; Baskakov, A.; Belyaev, A.; Boos, E.; Dubinin, M.; Dudko, L.; Ershov, A.; Gribushin, A.; Klyukhin, V.; Kodolova, O.; Lokhtin, I.; Miagkov, I.; Obraztsov, S.; Petrushanko, S.; Savrin, V.; Snigirev, A.; Blinov, V.; Skovpen, Y.; Shtol, D.; Azhgirey, I.; Bayshev, I.; Bitioukov, S.; Elumakhov, D.; Kachanov, V.; Kalinin, A.; Konstantinov, D.; Krychkine, V.; Petrov, V.; Ryutin, R.; Sobol, A.; Troshin, S.; Tyurin, N.; Uzunian, A.; Volkov, A.; Adzic, P.; Cirkovic, P.; Devetak, D.; Dordevic, M.; Milosevic, J.; Rekovic, V.; Alcaraz Maestre, J.; Barrio Luna, M.; Calvo, E.; Cerrada, M.; Chamizo Llatas, M.; Colino, N.; De La Cruz, B.; Delgado Peris, A.; Escalante Del Valle, A.; Fernandez Bedoya, C.; Fernández Ramos, J. P.; Flix, J.; Fouz, M. C.; Garcia-Abia, P.; Gonzalez Lopez, O.; Goy Lopez, S.; Hernandez, J. M.; Josa, M. I.; Navarro De Martino, E.; Pérez-Calero Yzquierdo, A.; Puerta Pelayo, J.; Quintario Olmeda, A.; Redondo, I.; Romero, L.; Soares, M. S.; de Trocóniz, J. 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H.; Barney, D.; Bloch, P.; Bocci, A.; Bonato, A.; Botta, C.; Camporesi, T.; Castello, R.; Cepeda, M.; Cerminara, G.; D'Alfonso, M.; d'Enterria, D.; Dabrowski, A.; Daponte, V.; David, A.; De Gruttola, M.; De Roeck, A.; Di Marco, E.; Dobson, M.; Dorney, B.; du Pree, T.; Duggan, D.; Dünser, M.; Dupont, N.; Elliott-Peisert, A.; Fartoukh, S.; Franzoni, G.; Fulcher, J.; Funk, W.; Gigi, D.; Gill, K.; Girone, M.; Glege, F.; Gulhan, D.; Gundacker, S.; Guthoff, M.; Hammer, J.; Harris, P.; Hegeman, J.; Innocente, V.; Janot, P.; Kieseler, J.; Kirschenmann, H.; Knünz, V.; Kornmayer, A.; Kortelainen, M. J.; Kousouris, K.; Krammer, M.; Lange, C.; Lecoq, P.; Lourenço, C.; Lucchini, M. T.; Malgeri, L.; Mannelli, M.; Martelli, A.; Meijers, F.; Merlin, J. A.; Mersi, S.; Meschi, E.; Milenovic, P.; Moortgat, F.; Morovic, S.; Mulders, M.; Neugebauer, H.; Orfanelli, S.; Orsini, L.; Pape, L.; Perez, E.; Peruzzi, M.; Petrilli, A.; Petrucciani, G.; Pfeiffer, A.; Pierini, M.; Racz, A.; Reis, T.; Rolandi, G.; Rovere, M.; Ruan, M.; Sakulin, H.; Sauvan, J. B.; Schäfer, C.; Schwick, C.; Seidel, M.; Sharma, A.; Silva, P.; Sphicas, P.; Steggemann, J.; Stoye, M.; Takahashi, Y.; Tosi, M.; Treille, D.; Triossi, A.; Tsirou, A.; Veckalns, V.; Veres, G. I.; Wardle, N.; Wöhri, H. K.; Zagozdzinska, A.; Zeuner, W. D.; Bertl, W.; Deiters, K.; Erdmann, W.; Horisberger, R.; Ingram, Q.; Kaestli, H. C.; Kotlinski, D.; Langenegger, U.; Rohe, T.; Bachmair, F.; Bäni, L.; Bianchini, L.; Casal, B.; Dissertori, G.; Dittmar, M.; Donegà, M.; Grab, C.; Heidegger, C.; Hits, D.; Hoss, J.; Kasieczka, G.; Lecomte, P.; Lustermann, W.; Mangano, B.; Marionneau, M.; Martinez Ruiz del Arbol, P.; Masciovecchio, M.; Meinhard, M. T.; Meister, D.; Micheli, F.; Musella, P.; Nessi-Tedaldi, F.; Pandolfi, F.; Pata, J.; Pauss, F.; Perrin, G.; Perrozzi, L.; Quittnat, M.; Rossini, M.; Schönenberger, M.; Starodumov, A.; Tavolaro, V. R.; Theofilatos, K.; Wallny, R.; Aarrestad, T. K.; Amsler, C.; Caminada, L.; Canelli, M. F.; De Cosa, A.; Galloni, C.; Hinzmann, A.; Hreus, T.; Kilminster, B.; Ngadiuba, J.; Pinna, D.; Rauco, G.; Robmann, P.; Salerno, D.; Yang, Y.; Zucchetta, A.; Candelise, V.; Doan, T. H.; Jain, Sh.; Khurana, R.; Konyushikhin, M.; Kuo, C. M.; Lin, W.; Lu, Y. J.; Pozdnyakov, A.; Yu, S. S.; Kumar, Arun; Chang, P.; Chang, Y. H.; Chang, Y. W.; Chao, Y.; Chen, K. F.; Chen, P. H.; Dietz, C.; Fiori, F.; Hou, W.-S.; Hsiung, Y.; Liu, Y. F.; Lu, R.-S.; Miñano Moya, M.; Paganis, E.; Psallidas, A.; Tsai, J. f.; Tzeng, Y. M.; Asavapibhop, B.; Singh, G.; Srimanobhas, N.; Suwonjandee, N.; Adiguzel, A.; Damarseckin, S.; Demiroglu, Z. S.; Dozen, C.; Eskut, E.; Girgis, S.; Gokbulut, G.; Guler, Y.; Hos, I.; Kangal, E. E.; Kara, O.; Kayis Topaksu, A.; Kiminsu, U.; Oglakci, M.; Onengut, G.; Ozdemir, K.; Ozturk, S.; Polatoz, A.; Tali, B.; Turkcapar, S.; Zorbakir, I. S.; Zorbilmez, C.; Bilin, B.; Bilmis, S.; Isildak, B.; Karapinar, G.; Yalvac, M.; Zeyrek, M.; Gülmez, E.; Kaya, M.; Kaya, O.; Yetkin, E. A.; Yetkin, T.; Cakir, A.; Cankocak, K.; Sen, S.; Grynyov, B.; Levchuk, L.; Sorokin, P.; Aggleton, R.; Ball, F.; Beck, L.; Brooke, J. J.; Burns, D.; Clement, E.; Cussans, D.; Flacher, H.; Goldstein, J.; Grimes, M.; Heath, G. P.; Heath, H. F.; Jacob, J.; Kreczko, L.; Lucas, C.; Newbold, D. M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; Seif El Nasr-storey, S.; Smith, D.; Smith, V. J.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Calligaris, L.; Cieri, D.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Bundock, A.; Burton, D.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Della Negra, M.; Di Maria, R.; Dunne, P.; Elwood, A.; Futyan, D.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Lane, R.; Laner, C.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Nash, J.; Nikitenko, A.; Pela, J.; Penning, B.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Seez, C.; Summers, S.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leslie, D.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; West, C.; Arcaro, D.; Avetisyan, A.; Bose, T.; Gastler, D.; Rankin, D.; Richardson, C.; Rohlf, J.; Sulak, L.; Zou, D.; Benelli, G.; Berry, E.; Cutts, D.; Garabedian, A.; Hakala, J.; Heintz, U.; Hogan, J. M.; Jesus, O.; Kwok, K. H. M.; Laird, E.; Landsberg, G.; Mao, Z.; Narain, M.; Piperov, S.; Sagir, S.; Spencer, E.; Syarif, R.; Breedon, R.; Breto, G.; Burns, D.; Calderon De La Barca Sanchez, M.; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Flores, C.; Funk, G.; Gardner, M.; Ko, W.; Lander, R.; Mclean, C.; Mulhearn, M.; Pellett, D.; Pilot, J.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Bravo, C.; Cousins, R.; Dasgupta, A.; Everaerts, P.; Florent, A.; Hauser, J.; Ignatenko, M.; Mccoll, N.; Saltzberg, D.; Schnaible, C.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Ghiasi Shirazi, S. M. A.; Hanson, G.; Heilman, J.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Olmedo Negrete, M.; Paneva, M. I.; Shrinivas, A.; Si, W.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Holzner, A.; Klein, D.; Krutelyov, V.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Welke, C.; Wood, J.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Amin, N.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Gran, J.; Heller, R.; Incandela, J.; Mullin, S. D.; Ovcharova, A.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Apresyan, A.; Bendavid, J.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Lawhorn, J. M.; Mott, A.; Newman, H. B.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhu, R. Y.; Andrews, M. B.; Azzolini, V.; Ferguson, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Weinberg, M.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mcdermott, K.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Winn, D.; Abdullin, S.; Albrow, M.; Apollinari, G.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Cremonesi, M.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hare, D.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Das, S.; Field, R. D.; Furic, I. K.; Konigsberg, J.; Korytov, A.; Low, J. F.; Ma, P.; Matchev, K.; Mei, H.; Mitselmakher, G.; Rank, D.; Shchutska, L.; Sperka, D.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Ackert, A.; Adams, J. R.; Adams, T.; Askew, A.; Bein, S.; Diamond, B.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Khatiwada, A.; Prosper, H.; Santra, A.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Jung, K.; Kurt, P.; O'Brien, C.; Sandoval Gonzalez, I. D.; Turner, P.; Varelas, N.; Wang, H.; Wu, Z.; Zakaria, M.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Anderson, I.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Osherson, M.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; Xin, Y.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Bruner, C.; Castle, J.; Forthomme, L.; Kenny, R. P.; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Sanders, S.; Stringer, R.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Khalil, S.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Toda, S.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Calvert, B.; Eno, S. C.; Ferraioli, C.; Gomez, J. A.; Hadley, N. J.; Jabeen, S.; Kellogg, R. G.; Kolberg, T.; Kunkle, J.; Lu, Y.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Apyan, A.; Barbieri, R.; Baty, A.; Bi, R.; Bierwagen, K.; Brandt, S.; Busza, W.; Cali, I. A.; Demiragli, Z.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Krajczar, K.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Sumorok, K.; Tatar, K.; Varma, M.; Velicanu, D.; Veverka, J.; Wang, J.; Wang, T. W.; Wyslouch, B.; Yang, M.; Zhukova, V.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Finkel, A.; Gude, A.; Hansen, P.; Kalafut, S.; Kao, S. C.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bartek, R.; Bloom, K.; Claes, D. R.; Dominguez, A.; Fangmeier, C.; Gonzalez Suarez, R.; Kamalieddin, R.; Kravchenko, I.; Malta Rodrigues, A.; Meier, F.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Alyari, M.; Dolen, J.; George, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Kaisen, J.; Kharchilava, A.; Kumar, A.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wang, R.-J.; Wood, D.; Bhattacharya, S.; Hahn, K. A.; Kubik, A.; Kumar, A.; Mucia, N.; Odell, N.; Pollack, B.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Smith, G.; Taroni, S.; Wayne, M.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Hughes, R.; Ji, W.; Liu, B.; Luo, W.; Puigh, D.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Lange, D.; Luo, J.; Marlow, D.; Mc Donald, J.; Medvedeva, T.; Mei, K.; Mooney, M.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Tully, C.; Zuranski, A.; Malik, S.; Barker, A.; Barnes, V. E.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Miller, D. H.; Neumeister, N.; Schulte, J. F.; Shi, X.; Sun, J.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Chen, Z.; Ecklund, K. M.; Geurts, F. J. M.; Guilbaud, M.; Li, W.; Michlin, B.; Northup, M.; Padley, B. P.; Redjimi, R.; Roberts, J.; Rorie, J.; Tu, Z.; Zabel, J.; Betchart, B.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Agapitos, A.; Chou, J. P.; Contreras-Campana, E.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hidas, D.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Nash, K.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Foerster, M.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Juska, E.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Rose, A.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; De Guio, F.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Sun, X.; Wang, Y.; Wolfe, E.; Xia, F.; Clarke, C.; Harr, R.; Karchin, P. E.; Sturdy, J.; Belknap, D. A.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.

2017-05-01

Pair production of Y(1S) mesons is observed at the LHC in proton-proton collisions at √{s}=8 TeV by the CMS experiment in a data sample corresponding to an integrated luminosity of 20.7 fb-1. Both Y(1S) candidates are fully reconstructed via their decays to μ + μ -. The fiducial acceptance region is defined by an absolute Y(1S) rapidity smaller than 2.0. The fiducial cross section for the production of Y(1S) pairs, assuming that both mesons decay isotropically, is measured to be 68.8±12.7 (stat)±7.4 (syst)±2.8 ( B ) pb, where the third uncertainty comes from the uncertainty in the branching fraction of Y(1S) decays to μ + μ -. Assuming instead that the Y(1S) mesons are produced with different polarizations leads to variations in the measured cross section in the range from -38% to +36%. [Figure not available: see fulltext.

Observation of Y(1S) pair production in proton-proton collisions at $$ \\sqrt{s}=8 $$ TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.

Pair production of Y(1S) mesons is observed at the LHC in proton-proton collisions at √s = 8 TeV by the CMS experiment in a data sample corresponding to an integrated luminosity of 20.7 fb -1. Both Y(1S) candidates are fully reconstructed via their decays to μ +μ -. The fiducial acceptance region is defined by an absolute Y(1S) rapidity smaller than 2.0. Furthermore, the fiducial cross section for the production of Y(1S) pairs, assuming that both mesons decay isotropically, is measured to be 68.8±12.7 (stat)±7.4 (syst)±2.8 ( BB ) pb, where the third uncertainty comes from the uncertainty in themore » branching fraction of Y(1S) decays to μ +μ -. Assuming instead that the Y(1S) mesons are produced with different polarizations leads to variations in the measured cross section in the range from -38% to +36%.« less

Easy Absolute Values? Absolutely

ERIC Educational Resources Information Center

Taylor, Sharon E.; Mittag, Kathleen Cage

2015-01-01

The authors teach a problem-solving course for preservice middle-grades education majors that includes concepts dealing with absolute-value computations, equations, and inequalities. Many of these students like mathematics and plan to teach it, so they are adept at symbolic manipulations. Getting them to think differently about a concept that they…

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

PubMed

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.

Kamlet-Taft solvent parameters, NMR spectroscopic analysis and thermoelectrochemistry of lithium-glyme solvate ionic liquids and their dilute solutions.

PubMed

Black, Jeffrey J; Dolan, Andrew; Harper, Jason B; Aldous, Leigh

2018-06-06

Solvate ionic liquids are a relatively new class of liquids produced by combining a coordinating solvent with a salt. They have a variety of uses and their suitability for such depends upon the ratio of salt to coordinating solvent. This work investigates the Kamlet-Taft solvent parameters of, NMR chemical shifts of nuclei in, and thermoelectrochemistry of a selected set of solvate ionic liquids produced from glymes (methyl terminated oligomers of ethylene glycol) and lithium bis(trifluoromethylsulfonyl)imide at two different compositions. The aim is to improve the understanding of the interactions occurring in these ionic liquids to help select suitable solvate ionic liquids for future applications.

Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

NASA Astrophysics Data System (ADS)

Reif, Maria M.; Hünenberger, Philippe H.

2011-04-01

The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is

Directing the Lithium-Sulfur Reaction Pathway via Sparingly Solvating Electrolytes for High Energy Density Batteries.

PubMed

Lee, Chang-Wook; Pang, Quan; Ha, Seungbum; Cheng, Lei; Han, Sang-Don; Zavadil, Kevin R; Gallagher, Kevin G; Nazar, Linda F; Balasubramanian, Mahalingam

2017-06-28

The lithium-sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium-sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium-sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparingly solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium-sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. This discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation-dissolution chemistries, lithium-sulfur and beyond.

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

PubMed

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

2014-12-07

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

Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory★

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-80329-7.

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

PubMed

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.

Absolutely relative or relatively absolute: violations of value invariance in human decision making.

PubMed

Teodorescu, Andrei R; Moran, Rani; Usher, Marius

2016-02-01

Making decisions based on relative rather than absolute information processing is tied to choice optimality via the accumulation of evidence differences and to canonical neural processing via accumulation of evidence ratios. These theoretical frameworks predict invariance of decision latencies to absolute intensities that maintain differences and ratios, respectively. While information about the absolute values of the choice alternatives is not necessary for choosing the best alternative, it may nevertheless hold valuable information about the context of the decision. To test the sensitivity of human decision making to absolute values, we manipulated the intensities of brightness stimuli pairs while preserving either their differences or their ratios. Although asked to choose the brighter alternative relative to the other, participants responded faster to higher absolute values. Thus, our results provide empirical evidence for human sensitivity to task irrelevant absolute values indicating a hard-wired mechanism that precedes executive control. Computational investigations of several modelling architectures reveal two alternative accounts for this phenomenon, which combine absolute and relative processing. One account involves accumulation of differences with activation dependent processing noise and the other emerges from accumulation of absolute values subject to the temporal dynamics of lateral inhibition. The potential adaptive role of such choice mechanisms is discussed.

A solvated electron lithium electrode for secondary batteries

NASA Astrophysics Data System (ADS)

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.

Measurements of proton energy spectra using a radiochromic film stack

NASA Astrophysics Data System (ADS)

Filkins, T. M.; Steidle, Jessica; Ellison, D. M.; Steidle, Jeffrey; Freeman, C. G.; Padalino, S. J.; Fiksel, G.; Regan, S. P.; Sangster, T. C.

2014-10-01

The energy spectrum of protons accelerated from the rear-side of a thin foil illuminated with ultra-intense laser light from the OMEGA EP laser system at the University of Rochester's Laboratory for Laser Energetics (LLE) was measured using a stack of radiochromic film (RCF). The film stack consisted of four layers of Gafchromic HD-V2 film and four layers of Gafchromic MD-V2-55 film. Aluminum foils of various thicknesses were placed between each piece of RCF in the stack. This arrangement allowed protons with energies of 30 MeV to reach the back layer of RCF in the stack. The stack was placed in the detector plane of a Thomson parabola ion energy (TPIE) spectrometer. Each piece of film in the stack was scanned using a commercially available flat-bed scanner (Epson 10000XL). The resulting optical density was converted into proton fluence using an absolute calibration of the RCF obtained at the SUNY Geneseo 1.7 MV Pelletron accelerator laboratory. In these calibration measurements, the sensitivity of the radiochromic film was measured using monoenergetic protons produced by the accelerator. Details of the analysis procedure and the resulting proton energy spectra will be presented. Funded in part by a grant from the DOE through the Laboratory for Laser Energetics.

Reactivity between biphenyl and precursor of solvated electrons in tetrahydrofuran measured by picosecond pulse radiolysis in near-ultraviolet, visible, and infrared.

PubMed

Saeki, Akinori; Kozawa, Takahiro; Ohnishi, Yuko; Tagawa, Seiichi

2007-02-22

The initial decrease of solvated electrons in tetrahydrofuran (THF) upon addition of biphenyl was investigated by picosecond pulse radiolysis. Transient absorption spectra derived from the biphenyl radical anion (centered at 408 and 655 nm) and solvated electrons of THF (infrared) were successfully measured in the wavelength region from 400 to 900 nm by the extension of a femtosecond continuum probe light to near-ultraviolet using a second harmonic generation of Ti:sapphire laser and a CaF2 plate. From the analysis of kinetic traces at 1300 nm considering the overlap of primary solvated electrons and partial biphenyl radical anion, C37, which is defined by the solute concentration to reduce the initial yield of solvated electrons to 1/e, was found to be 87 +/- 3 mM. The rate constant of solvated electrons with biphenyl was determined as 5.8 +/- 0.3 x 10(10) M(-1) s(-1). We demonstrate that the kinetic traces at both 408 nm mainly due to biphenyl radical anion and 1300 nm mainly due to solvated electrons are reproduced with high accuracy and consistency by a simple kinetic analysis. Much higher concentrations of biphenyl (up to 2 M) were examined, showing further increase of the initial yield of biphenyl radical anion accompanying a fast decay component. This observation is discussed in terms of geminate ion recombination, scavenging, delayed geminate ion recombination, and direct ionization of biphenyl at high concentration.

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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.

Enhancement of proton transfer in ion channels by membrane phosphate headgroups.

PubMed

Wyatt, Debra L; de Godoy, Carlos Marcelo G; Cukierman, Samuel

2009-05-14

The transfer of protons (H+) in gramicidin (gA) channels is markedly distinct in monoglyceride and phospholipid membranes. In this study, the molecular groups that account for those differences were investigated using a new methodology. The rates of H+ transfer were measured in single gA channels reconstituted in membranes made of plain ceramides or sphingomyelins and compared to those in monoglyceride and phospholipid bilayers. Single-channel conductances to protons (gH) were significantly larger in sphingomyelin than in ceramide membranes. A novel and unsuspected finding was that H+ transfer was heavily attenuated or completely blocked in ceramide (but not in sphingomyelin) membranes in low-ionic-strength solutions. It is reasoned that H-bond dynamics at low ionic strengths between membrane ceramides and gA makes channels dysfunctional. The rate of H+ transfer in gA channels in ceramide membranes is significantly higher than that in monoglyceride bilayers. This suggests that solvation of the hydrophobic surface of gA channels by two acyl chains in ceramides stabilizes the gA channels and the water wire inside the pore, leading to an enhancement of H+ transfer in relation to that occurring in monoglyceride membranes. gH values in gA channels are similar in ceramide and monoglyceride bilayers and in sphingomyelin and phospholipid membranes. It is concluded that phospho headgroups in membranes have significant effects on the rate of H+ transfer at the membrane gA channel/solution interfaces, enhancing the entry and exit rates of protons in channels.

Influence of Spin-Orbit Quenching on the Solvation of Indium in Helium Droplets

NASA Astrophysics Data System (ADS)

Meyer, Ralf; Pototschnig, Johann V.; Ernst, Wolfgang E.; Hauser, Andreas W.

2017-06-01

Recent experimental interest of the collaborating group of M. Koch on the dynamics of electronic excitations of indium in helium droplets triggered a series of computational studies on the group 13 elements Al, Ga and In and their indecisive behavior between wetting and non wetting when placed onto superfluid helium droplets. We employ a combination of multiconfigurational self consistent field calculations (MCSCF) and multireference configuration interaction (MRCI) to calculate the diatomic potentials. Particularly interesting is the case of indium with an Ancilotto parameter λ close to the threshold value of 1.9. As shown by Reho et al. the spin-orbit splitting of metal atoms solvated in helium droplets is subject to a quenching effect. This can drastically change the solvation behavior. In this work we extend the approach presented by Reho et al. to include distance dependent spin-orbit coupling. The resulting potential surfaces are used to calculate the solvation energy of the ground state and the first excited state with orbital-free helium density functional theory. F. Ancilotto, P. B. Lerner and M. W. Cole, Journal of Low Temperature Physics, 1995, 101, 1123-1146 J. H. Reho, U. Merker, M. R. Radcliff, K. K. Lehmann and G. Scoles, The Journal of Physical Chemistry A, 2000, 104, 3620-3626

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

PubMed

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.

TH-C-BRD-04: Beam Modeling and Validation with Triple and Double Gaussian Dose Kernel for Spot Scanning Proton Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirayama, S; Takayanagi, T; Fujii, Y

2014-06-15

Purpose: To present the validity of our beam modeling with double and triple Gaussian dose kernels for spot scanning proton beams in Nagoya Proton Therapy Center. This study investigates the conformance between the measurements and calculation results in absolute dose with two types of beam kernel. Methods: A dose kernel is one of the important input data required for the treatment planning software. The dose kernel is the 3D dose distribution of an infinitesimal pencil beam of protons in water and consists of integral depth doses and lateral distributions. We have adopted double and triple Gaussian model as lateral distributionmore » in order to take account of the large angle scattering due to nuclear reaction by fitting simulated inwater lateral dose profile for needle proton beam at various depths. The fitted parameters were interpolated as a function of depth in water and were stored as a separate look-up table for the each beam energy. The process of beam modeling is based on the method of MDACC [X.R.Zhu 2013]. Results: From the comparison results between the absolute doses calculated by double Gaussian model and those measured at the center of SOBP, the difference is increased up to 3.5% in the high-energy region because the large angle scattering due to nuclear reaction is not sufficiently considered at intermediate depths in the double Gaussian model. In case of employing triple Gaussian dose kernels, the measured absolute dose at the center of SOBP agrees with calculation within ±1% regardless of the SOBP width and maximum range. Conclusion: We have demonstrated the beam modeling results of dose distribution employing double and triple Gaussian dose kernel. Treatment planning system with the triple Gaussian dose kernel has been successfully verified and applied to the patient treatment with a spot scanning technique in Nagoya Proton Therapy Center.« less

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

PubMed

Perrin, Elsa; Schoen, Martin; Coudert, François-Xavier; Boutin, Anne

2018-04-26

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Precision Luminosity of LHC Proton-Proton Collisions at 13 TeV Using Hit Counting With TPX Pixel Devices

NASA Astrophysics Data System (ADS)

Sopczak, André; Ali, Babar; Asawatavonvanich, Thanawat; Begera, Jakub; Bergmann, Benedikt; Billoud, Thomas; Burian, Petr; Caicedo, Ivan; Caforio, Davide; Heijne, Erik; Janeček, Josef; Leroy, Claude; Mánek, Petr; Mochizuki, Kazuya; Mora, Yesid; Pacík, Josef; Papadatos, Costa; Platkevič, Michal; Polanský, Štěpán; Pospíšil, Stanislav; Suk, Michal; Svoboda, Zdeněk

2017-03-01

A network of Timepix (TPX) devices installed in the ATLAS cavern measures the LHC luminosity as a function of time as a stand-alone system. The data were recorded from 13-TeV proton-proton collisions in 2015. Using two TPX devices, the number of hits created by particles passing the pixel matrices was counted. A van der Meer scan of the LHC beams was analyzed using bunch-integrated luminosity averages over the different bunch profiles for an approximate absolute luminosity normalization. It is demonstrated that the TPX network has the capability to measure the reduction of LHC luminosity with precision. Comparative studies were performed among four sensors (two sensors in each TPX device) and the relative short-term precision of the luminosity measurement was determined to be 0.1% for 10-s time intervals. The internal long-term time stability of the measurements was below 0.5% for the data-taking period.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and their Complexes with Proteins

PubMed Central

Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry; Simmerling, Carlos

2016-01-01

The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures, or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software. PMID:26574454

Infrared spectroscopy of protonated trimethylamine-(benzene)(n) (n = 1-4) as model clusters of the quaternary ammonium-aromatic ring interaction.

PubMed

Shishido, Ryunosuke; Kawai, Yuki; Fujii, Asuka

2014-09-04

The essence of the molecular recognition of the neurotransmitter acetylcholine has been attributed to the attractive interaction between a quaternary ammonium and aromatic rings. We employed protonated trimethylamine-(benzene)n clusters (n = 1-4) in the gas phase as a model to study the recognition mechanism of acetylcholine at the microscopic level. We applied size-selective infrared spectroscopy to the clusters and observed the NH and CH stretching vibrational regions. We also performed density functional theory calculations of stable structures, charge distributions, and infrared spectra of the clusters. It was shown that the methyl groups of protonated trimethylamine are solvated by benzene one at a time in the n > 1 clusters, and the validity of these clusters as a model system of the acetylcholine recognition was demonstrated. The nature of the interactions between a quaternary ammonium and aromatic rings is discussed on the basis of the observed infrared spectra and the theoretical calculations.

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

PubMed

Levy, Ronald M; Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki

2017-04-20

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

Tuning structure and mobility of solvation shells surrounding tracer additives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmer, James; Jain, Avni; Bollinger, Jonathan A.

2015-03-28

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

Directing the Lithium–Sulfur Reaction Pathway via Sparingly Solvating Electrolytes for High Energy Density Batteries

PubMed Central

2017-01-01

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparingly solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. This discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond. PMID:28691072

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2014-12-07

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

Directing the lithium–sulfur reaction pathway via sparingly solvating electrolytes for high energy density batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Chang -Wook; Pang, Quan; Ha, Seungbum

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparinglymore » solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. Finally, this discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond.« less

Directing the lithium–sulfur reaction pathway via sparingly solvating electrolytes for high energy density batteries

DOE PAGES

Lee, Chang -Wook; Pang, Quan; Ha, Seungbum; ...

2017-05-25

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparinglymore » solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. Finally, this discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond.« less

Theoretical analysis of co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasai, Yukako; Yoshida, Norio, E-mail: noriwo@chem.kyushu-univ.jp; Nakano, Haruyuki

2015-05-28

The co-solvent effect on the proton transfer reaction of glycine in a water–acetonitrile mixture was examined using the reference interaction-site model self-consistent field theory. The free energy profiles of the proton transfer reaction of glycine between the carboxyl oxygen and amino nitrogen were computed in a water–acetonitrile mixture solvent at various molar fractions. Two types of reactions, the intramolecular proton transfer and water-mediated proton transfer, were considered. In both types of the reactions, a similar tendency was observed. In the pure water solvent, the zwitterionic form, where the carboxyl oxygen is deprotonated while the amino nitrogen is protonated, is moremore » stable than the neutral form. The reaction free energy is −10.6 kcal mol{sup −1}. On the other hand, in the pure acetonitrile solvent, glycine takes only the neutral form. The reaction free energy from the neutral to zwitterionic form gradually increases with increasing acetonitrile concentration, and in an equally mixed solvent, the zwitterionic and neutral forms are almost isoenergetic, with a difference of only 0.3 kcal mol{sup −1}. The free energy component analysis based on the thermodynamic cycle of the reaction also revealed that the free energy change of the neutral form is insensitive to the change of solvent environment but the zwitterionic form shows drastic changes. In particular, the excess chemical potential, one of the components of the solvation free energy, is dominant and contributes to the stabilization of the zwitterionic form.« less

Absolute biological needs.

PubMed

McLeod, Stephen

2014-07-01

Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb 'need' has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of 'normative' are distinguished. On two of these, to describe a phenomenon or claim as 'normative' is to describe it as value-dependent. A description of a phenomenon or claim as 'normative' in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses. © 2013 John Wiley & Sons Ltd.

Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds

PubMed Central

Delgado, Eduardo J.; Jaña, Gonzalo A.

2009-01-01

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. PMID:19399236

Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.

PubMed

Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

2013-05-16

Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

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

NASA Astrophysics Data System (ADS)

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.

Solvent effect on the self-assembly of salt solvates of an antihypertensive drug azilsartan and 2-methylimidazole

NASA Astrophysics Data System (ADS)

Zhang, Xian-Rui; Zhang, Lei

2017-06-01

Three salt solvates of azilsartan (AZ) with 2-methylimidazole (2MI) (namely AZ-2MI-H2O, AZ-2MI-ACE and AZ-2MI-THF) and one azilsartan solvate (AZ-DIO, ACE = acetone, THF = tetrahydrofuran, and DIO = 1,4-dioxane) were manufactured by solvent-controlled self-assembly in aqueous-organic solutions. The experimental result of AZ-DIO shows that AZ is high affinity to DIO molecule, which has a unique ability to prevent salt formation between AZ and 2MI. Thermal studies of three salt solvates exhibit poor thermodynamic stability in environmental conditions. Solubility experiments show that AZ-2MI-ACE and AZ-2MI-THF are unstable and convert to AZ-2MI-H2O in aqueous solution, and that AZ-2MI-H2O exhibits increased solubility and retention stability in an aqueous medium compared with the commercial AZ-A crystalline form.

Proton-Proton and Proton-Antiproton Colliders

NASA Astrophysics Data System (ADS)

Scandale, Walter

In the last five decades, proton-proton and proton-antiproton colliders have been the most powerful tools for high energy physics investigations. They have also deeply catalyzed innovation in accelerator physics and technology. Among the large number of proposed colliders, only four have really succeeded in becoming operational: the ISR, the SppbarS, the Tevatron and the LHC. Another hadron collider, RHIC, originally conceived for ion-ion collisions, has also been operated part-time with polarized protons. Although a vast literature documenting them is available, this paper is intended to provide a quick synthesis of their main features and key performance.

Proton-Proton and Proton-Antiproton Colliders

NASA Astrophysics Data System (ADS)

Scandale, Walter

2014-04-01

In the last five decades, proton-proton and proton-antiproton colliders have been the most powerful tools for high energy physics investigations. They have also deeply catalyzed innovation in accelerator physics and technology. Among the large number of proposed colliders, only four have really succeeded in becoming operational: the ISR, the SppbarS, the Tevatron and the LHC. Another hadron collider, RHIC, originally conceived for ion-ion collisions, has also been operated part-time with polarized protons. Although a vast literature documenting them is available, this paper is intended to provide a quick synthesis of their main features and key performance.

Proton-Proton and Proton-Antiproton Colliders

NASA Astrophysics Data System (ADS)

Scandale, Walter

2015-02-01

In the last five decades, proton-proton and proton-antiproton colliders have been the most powerful tools for high energy physics investigations. They have also deeply catalyzed innovation in accelerator physics and technology. Among the large number of proposed colliders, only four have really succeeded in becoming operational: the ISR, the SppbarS, the Tevatron and the LHC. Another hadron collider, RHIC, originally conceived for ion-ion collisions, has also been operated part-time with polarized protons. Although a vast literature documenting them is available, this paper is intended to provide a quick synthesis of their main features and key performance.

Solvation-controlled lithium-ion complexes in a nonflammable solvent containing ethylene carbonate: structural and electrochemical aspects.

PubMed

Sogawa, Michiru; Kawanoue, Hikaru; Todorov, Yanko Marinov; Hirayama, Daisuke; Mimura, Hideyuki; Yoshimoto, Nobuko; Morita, Masayuki; Fujii, Kenta

2018-02-28

The structural and electrochemical properties of lithium-ion solvation complexes in a nonflammable organic solvent, tris(2,2,2-trifluoroethyl)phosphate (TFEP) containing ethylene carbonate (EC), were investigated using vibrational spectroscopic and electrochemical measurements. Based on quantitative Raman and infrared (IR) spectral analysis of the Li bis(trifluoromethanesulfonyl)amide (TFSA) salt in TFEP + EC electrolytes, we successfully evaluated the individual solvation numbers of EC (n EC ), TFEP (n TFEP ), and TFSA - (n TFSA ) in the first solvation sphere of the Li-ion. We found that the n EC value linearly increased with increasing EC mole fraction (x EC ), whereas the n TFEP and n TFSA values gradually decreased with increasing n EC . The ionic conductivity and viscosity (Walden plots) indicated that mainly Li + TFSA - ion pairs formed in neat TFEP (x EC = 0). This ion pair gradually dissociated into positively charged Li-ion complexes as x EC increased, which was consistent with the Raman/IR spectroscopy results. The redox reaction corresponding to an insertion/desertion of Li-ion into/from the graphite electrode occurred in the LiTFSA/TFEP + EC system at x EC ≥ 0.25. The same was not observed in the lower x EC cases. We discussed the relation between Li-ion solvation and electrode reaction behaviors at the molecular level and proposed that n EC plays a crucial role in the electrode reaction, particularly in terms of solid electrolyte interphase formation on the graphite electrode.

Electron- and proton-induced ionization of pyrimidine

NASA Astrophysics Data System (ADS)

Champion, Christophe; Quinto, Michele A.; Weck, Philippe F.

2015-05-01

The present work describes a quantum-mechanically based model of the electron- and proton-induced ionization of isolated pyrimidine molecules. The impact energies range from the target ionization threshold up to ~1 keV for electrons and from 10 keV up to 10 MeV for protons. The cross-section calculations are performed within the 1st Born approximation in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered projectiles are both described by plane waves. The pyrimidine target is described using the Gaussian 09 software package. The theoretical predictions obtained are in good agreement with experimental absolute total cross sections, while large discrepancies are observed between existing semi-empirical models and the present calculations. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

Investigation of Solvation Effects on Optical Rotatory Dispersion Using the Polarizable Continuum Model

NASA Astrophysics Data System (ADS)

Aharon, Tal; Lemler, Paul M.; Vaccaro, Patrick; Caricato, Marco

2017-06-01

The Optical Rotatory Dispersion (ORD) of a chiral solute is heavily affected by solvation, but this effect does not follow the usual correlation with the solvent polarity, i.e., larger solvent polarity does not imply a larger change in the solute's property. Therefore, a great deal of experimental and theoretical effort has been directed towards correlating the solvation effect on the ORD and the solvent properties. This discovery followed from the development of cavity ring down polarimetry (CRPD), which allows measurements of gas-phase ORD. In order to investigate this phenomenon, we chose a set of five rigid molecules to limit the effect of molecular vibrations and isolate the role of solvation. The latter was investigated with the Polarizable Continuum Model (PCM), and compared to experimental results. We used Bondi radii to build the PCM cavity, and performed extensive calculations at multiple frequencies using density functional theory (DFT) with two functionals: B3LYP and CAM-B3LYP, together with the aug-cc-pVDZ basis set. We also performed coupled cluster singles and doubles (CCSD/aug-cc-pVDZ) calculations at the wavelengths where gas-phase data are available, all of which are augmented with zero point vibrational corrections. These results are compared to experimental data and seem to indicate that PCM does not entirely account for the environmental effects on the ORD.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 coarse grained models of electrolyte solution. Here, we provide rigorous 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 (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the 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 (CHA) 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. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

PubMed Central

Knight, Jennifer L.

2011-01-01

Implicit solvent models are powerful tools in accounting for the aqueous environment at a fraction of the computational expense of explicit solvent representations. Here, we compare the ability of common implicit solvent models (TC, OBC, OBC2, GBMV, GBMV2, GBSW, GBSW/MS, GBSW/MS2 and FACTS) to reproduce experimental absolute hydration free energies for a series of 499 small neutral molecules that are modeled using AMBER/GAFF parameters and AM1-BCC charges. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, most implicit solvent models demonstrate reasonable agreement with extensive explicit solvent simulations (average difference 1.0-1.7 kcal/mol and R2=0.81-0.91) and with experimental hydration free energies (average unsigned errors=1.1-1.4 kcal/mol and R2=0.66-0.81). Chemical classes of compounds are identified that need further optimization of their ligand force field parameters and others that require improvement in the physical parameters of the implicit solvent models themselves. More sophisticated nonpolar models are also likely necessary to more effectively represent the underlying physics of solvation and take the quality of hydration free energies estimated from implicit solvent models to the next level. PMID:21735452

Electromagnetic waves with frequencies near the local proton gyrofrequency: ISEE-3 1 AU observations

NASA Technical Reports Server (NTRS)

Tsurutani, Bruce T.; Arballo, John K.; Mok, John; Smith, Edward J.; Mason, Glenn M.; Tan, Lun C.

1994-01-01

Low Frequency (LF) electromagnetic waves with periods near the local proton gyrofrequency have been detected in interplanetary space by the magnetometer onboard International-Sun-Earth-Explorer-3 (ISEE-3). Transverse peak-to-peak amplitudes as large as delta vector B/absolute value of B approximately 0.4 have been noted with compressional components (Delta absolute value of B/absolute value of B) typically less than or = 0.1. Generally, the waves have even smaller amplitudes, or are not detectable within the solar wind turbulence. The waves are elliptically/linearly polarized and are often, but not always, found to propagate nearly along vector B(sub zero). Both right- and left-hand polarizations in the spacecraft-frame have been detected. The waves are observed during all orientations of the interplanetary magnetic field, with the Parker spiral orientation being the most common case. Because the waves are detected at and near the local proton cyclotron frequency, the generation mechanism must almost certainly be solar wind pickup of freshly created hydrogen ions. Possible sources for the hydrogen are the Earth's atmosphere, coronal mass ejections from the Sun, comets and interstellar neutral atoms. At this time it is not obvious which potential source is the correct one. Statistical tests employing over one year of ISEE-3 data will be done in the near future to eliminate/confirm some of these possibilities.

Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin.

PubMed

Harris, Michael J; Woo, Hyung-June

2008-11-01

Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

Correlation of electron and proton irradiation-induced damage in InP solar cells

NASA Technical Reports Server (NTRS)

Walters, Robert J.; Summers, Geoffrey P.; Messenger, Scott R.; Burke, Edward A.

1996-01-01

The measured degradation of epitaxial shallow homojunction n(+)/p InP solar cells under 1 MeV electron irradiation is correlated with that measured under 3 MeV proton irradiation based on 'displacement damage dose'. The measured data is analyzed as a function of displacement damage dose from which an electron to proton dose equivalency ratio is determined which enables the electron and proton degradation data to be described by a single degradation curve. It is discussed how this single curve can be used to predict the cell degradation under irradiation by any particle energy. The degradation curve is used to compare the radiation response of InP and GaAs/Ge cells on an absolute damage energy scale. The comparison shows InP to be inherently more resistant to displacement damage deposition than the GaAs/Ge.

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

PubMed

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

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

NASA Astrophysics Data System (ADS)

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

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

NASA Astrophysics Data System (ADS)

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.

Water Interfaces, Solvation, and Spectroscopy

NASA Astrophysics Data System (ADS)

Geissler, Phillip L.

2013-04-01

Liquid water consistently expands our appreciation of the rich statistical mechanics that can emerge from simple molecular constituents. Here I review several interrelated areas of recent work on aqueous systems that aim to explore and explain this richness by revealing molecular arrangements, their thermodynamic origins, and the timescales on which they change. Vibrational spectroscopy of OH stretching features prominently in these discussions, with an emphasis on efforts to establish connections between spectroscopic signals and statistics of intermolecular structure. For bulk solutions, the results of these efforts largely verify and enrich existing physical pictures of hydrogen-bond network connectivity, dynamics, and response. For water at interfaces, such pictures are still emerging. As an important example I discuss the solvation of small ions at the air-water interface, whose surface propensities challenge a basic understanding of how aqueous fluctuations accommodate solutes in heterogeneous environments.

Jasminum flexile flower absolute from India--a detailed comparison with three other jasmine absolutes.

PubMed

Braun, Norbert A; Kohlenberg, Birgit; Sim, Sherina; Meier, Manfred; Hammerschmidt, Franz-Josef

2009-09-01

Jasminum flexile flower absolute from the south of India and the corresponding vacuum headspace (VHS) sample of the absolute were analyzed using GC and GC-MS. Three other commercially available Indian jasmine absolutes from the species: J. sambac, J. officinale subsp. grandiflorum, and J. auriculatum and the respective VHS samples were used for comparison purposes. One hundred and twenty-one compounds were characterized in J. flexile flower absolute, with methyl linolate, benzyl salicylate, benzyl benzoate, (2E,6E)-farnesol, and benzyl acetate as the main constituents. A detailed olfactory evaluation was also performed.

Proton-proton correlations observed in two-proton radioactivity of 94Ag.

PubMed

Mukha, Ivan; Roeckl, Ernst; Batist, Leonid; Blazhev, Andrey; Döring, Joachim; Grawe, Hubert; Grigorenko, Leonid; Huyse, Mark; Janas, Zenon; Kirchner, Reinhard; La Commara, Marco; Mazzocchi, Chiara; Tabor, Sam L; Van Duppen, Piet

2006-01-19

The stability and spontaneous decay of naturally occurring atomic nuclei have been much studied ever since Becquerel discovered natural radioactivity in 1896. In 1960, proton-rich nuclei with an odd or an even atomic number Z were predicted to decay through one- and two-proton radioactivity, respectively. The experimental observation of one-proton radioactivity was first reported in 1982, and two-proton radioactivity has now also been detected by experimentally studying the decay properties of 45Fe (refs 3, 4) and 54Zn (ref. 5). Here we report proton-proton correlations observed during the radioactive decay of a spinning long-lived state of the lightest known isotope of silver, 94Ag, which is known to undergo one-proton decay. We infer from these correlations that the long-lived state must also decay through simultaneous two-proton emission, making 94Ag the first nucleus to exhibit one- as well as two-proton radioactivity. We attribute the two-proton emission behaviour and the unexpectedly large probability for this decay mechanism to a very large deformation of the parent nucleus into a prolate (cigar-like) shape, which facilitates emission of protons either from the same or from opposite ends of the 'cigar'.

Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Bin; Pettitt, Bernard M.

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLSAA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirmsmore » that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.« less

Determination of lipid bilayer affinities and solvation characteristics by electrokinetic chromatography using polymer-bound lipid bilayer nanodiscs.

PubMed

Penny, William M; Palmer, Christopher P

2018-03-01

Styrene-maleic acid polymer-bound lipid bilayer nanodiscs have been investigated and characterized by electrokinetic chromatography. Linear solvation energy relationship analysis was employed to characterize the changes in solvation environment of nanodiscs of varied belt to lipid ratio, belt polymer chemistry and molecular weight, and lipid composition. Increases in the lipid to belt polymer ratio resulted in smaller, more cohesive nanodiscs with greater electrophoretic mobility. Nanodisc structures with belt polymers of different chemistry and molecular weight were compared and showed only minor changes in solvent characteristics and selectivity consistent with changes in structure of the lipid bilayer. Seven phospholipid and sphingomyelin nanodiscs of different lipid composition were characterized. Changes in lipid head group structure had a significant effect on bilayer-solute interactions. In most cases, changes in alkyl tail structure had no discernible effect on solvation environment aside from those explained by changes in the gel-liquid transition temperature. Comparison to vesicles of similar lipid composition show only minor differences in solvation environment, likely due to differences in lipid composition and bilayer curvature. Together these results provide evidence that the dominant solute-nanodisc interactions are with the lipid bilayer and that head group chemistry has a greater impact on bilayer-solute interactions than alkyl tail or belt polymer structure. Nanodisc electrokinetic chromatography is demonstrated to allow characterization of solute interactions with lipid bilayers of varied composition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Absolute nuclear material assay

DOEpatents

Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

2012-05-15

A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

Absolute nuclear material assay

DOEpatents

Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

2010-07-13

A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3).

PubMed

Klyne, Johanna; Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

2018-01-31

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA + , N-phenylacetamide), AA + -(H 2 O) n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν OH , ν NH , ν CH , amide A, 2800-3800 cm -1 ) and fingerprint (amide I-II, 1000-1900 cm -1 ) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA + -(H 2 O) n structures, the H 2 O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H 2 O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH 3 ) on the shape of the intermolecular potential and the structure of the hydration shell.

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

PubMed

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.

Observation of $$\\Upsilon(\\mathrm{1S})$$ pair production in proton-proton collisions at $$\\sqrt{s} = $$ 8 TeV

DOE PAGES

Khachatryan, Vardan

2017-05-03

Here, pair production ofmore » $$\\Upsilon(\\mathrm{1S})$$ mesons is observed at the LHC in proton-proton collisions at $$ \\sqrt{s} = $$ 8 TeV by the CMS experiment in a data sample corresponding to an integrated luminosity of 20.7 fb$$^{-1}$$. Both $$\\Upsilon(\\mathrm{1S})$$ candidates are fully reconstructed via their decays to $$\\mu^{+}\\mu^{- } $$. The fiducial acceptance region is defined by an absolute $$\\Upsilon(\\mathrm{1S})$$ rapidity smaller than 2.0. The fiducial cross section for the production of $$\\Upsilon(\\mathrm{1S})$$ pairs, assuming that both mesons decay isotropically, is measured to be 68.8 $$\\pm$$ 12.7 (stat) $$\\pm$$ 7.4 (syst) $$\\pm$$ 2.8 ($$\\mathcal{B}$$) pb, where the third uncertainty comes from the uncertainty in the branching fraction of $$\\Upsilon(\\mathrm{1S})$$ decays to $$\\mu^{+}\\mu^{-}$$. Assuming instead that the $$\\Upsilon(\\mathrm{1S})$$ mesons are produced with different polarizations leads to variations in the measured cross section in the range from $$-38\\%$$ to $$+36\\%$$.« less

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

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

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.

Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model

PubMed Central

Sharma, Ity; Kaminski, George A.

2012-01-01

We have computed pKa values for eleven substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pKa values of propanoic and butanoic acids within ca. 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it employs either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of employing the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent. PMID:22815192

Pion, Kaon, Proton and Antiproton Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.; Blattnig, Steve R.

2008-01-01

Inclusive pion, kaon, proton, and antiproton production from proton-proton collisions is studied at a variety of proton energies. Various available parameterizations of Lorentz-invariant differential cross sections as a function of transverse momentum and rapidity are compared with experimental data. The Badhwar and Alper parameterizations are moderately satisfactory for charged pion production. The Badhwar parameterization provides the best fit for charged kaon production. For proton production, the Alper parameterization is best, and for antiproton production the Carey parameterization works best. However, no parameterization is able to fully account for all the data.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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.

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

PubMed

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.

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

PubMed Central

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

Ultrafast studies of excess electrons in liquid acetonitrile: revisiting the solvated electron/solvent dimer anion equilibrium.

PubMed

Doan, Stephanie C; Schwartz, Benjamin J

2013-04-25

We examine the ultrafast relaxation dynamics of excess electrons injected into liquid acetonitrile using air- and water-free techniques and compare our results to previous work on this system [Xia, C. et al. J. Chem. Phys. 2002, 117, 8855]. Excess electrons in liquid acetonitrile take on two forms: a "traditional" solvated electron that absorbs in the near-IR, and a solvated molecular dimer anion that absorbs weakly in the visible. We find that excess electrons initially produced via charge-transfer-to-solvent excitation of iodide prefer to localize as solvated electrons, but that there is a subsequent equilibration to form the dimer anion on an ~80 ps time scale. The spectral signature of this interconversion between the two forms of the excess electron is a clear isosbestic point. The presence of the isosbestic point makes it possible to fully deconvolute the spectra of the two species. We find that solvated molecular anion absorbs quite weakly, with a maximum extinction coefficient of ~2000 M(-1)cm(-1). With the extinction coefficient of the dimer anion in hand, we are also able to determine the equilibrium constant for the two forms of excess electron, and find that the molecular anion is favored by a factor of ~4. We also find that relatively little geminate recombination takes place, and that the geminate recombination that does take place is essentially complete within the first 20 ps. Finally, we show that the presence of small amounts of water in the acetonitrile can have a fairly large effect on the observed spectral dynamics, explaining the differences between our results and those in previously published work.

25Mg NMR and Computational Modeling Studies of the Solvation Structures and Molecular Dynamics in Magnesium Based Liquid Electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian Z.; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are

25 Mg NMR and computational modeling studies of the solvation structures and molecular dynamics in magnesium based liquid electrolytes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Jian Zhi; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Broad-Band Pump-Probe Spectroscopy Quantifies Ultrafast Solvation Dynamics of Proteins and Molecules.

PubMed

Jumper, Chanelle C; Arpin, Paul C; Turner, Daniel B; McClure, Scott D; Rafiq, Shahnawaz; Dean, Jacob C; Cina, Jeffrey A; Kovac, Philip A; Mirkovic, Tihana; Scholes, Gregory D

2016-11-17

In this work, we demonstrate the use of broad-band pump-probe spectroscopy to measure femtosecond solvation dynamics. We report studies of a rhodamine dye in methanol and cryptophyte algae light-harvesting proteins in aqueous suspension. Broad-band impulsive excitation generates a vibrational wavepacket that oscillates on the excited-state potential energy surface, destructively interfering with itself at the minimum of the surface. This destructive interference gives rise to a node at a certain probe wavelength that varies with time. This reveals the Gibbs free-energy changes of the excited-state potential energy surface, which equates to the solvation time correlation function. This method captures the inertial solvent response of water (∼40 fs) and the bimodal inertial response of methanol (∼40 and ∼150 fs) and reveals how protein-buried chromophores are sensitive to the solvent dynamics inside and outside of the protein environment.

Thermochemical characteristics of nicotinamide protolytic equilibria in water-dimethylsulfoxide mixtures

NASA Astrophysics Data System (ADS)

Grazhdan, K. V.; Gamov, G. A.; Dushina, S. V.; Sharnin, V. A.

2012-04-01

The heat effects of nicotinamide protonation in water-dimethylsulfoxide (DMSO) solutions over the concentration range 0-0.75 DMSO mole fractions were determined calorimetrically at 25.00 ± 0.01°C and ionic strength 0.25 (NaClO4). Changes in the enthalpy of protonation as the content of DMSO increased were found to be described by an S-shaped curve. This curve shape was caused by the dynamics of reagent solvation contributions as the concentration of DMSO grew with the predominance of the nicotinamide solvation contribution.

Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction

NASA Astrophysics Data System (ADS)

Sulea, Traian; Hogues, Hervé; Purisima, Enrico O.

2012-05-01

We carried out a prospective evaluation of the utility of the SIE (solvation interaction energy) scoring function for virtual screening and binding affinity prediction. Since experimental structures of the complexes were not provided, this was an exercise in virtual docking as well. We used our exhaustive docking program, Wilma, to provide high-quality poses that were rescored using SIE to provide binding affinity predictions. We also tested the combination of SIE with our latest solvation model, first shell of hydration (FiSH), which captures some of the discrete properties of water within a continuum model. We achieved good enrichment in virtual screening of fragments against trypsin, with an area under the curve of about 0.7 for the receiver operating characteristic curve. Moreover, the early enrichment performance was quite good with 50% of true actives recovered with a 15% false positive rate in a prospective calculation and with a 3% false positive rate in a retrospective application of SIE with FiSH. Binding affinity predictions for both trypsin and host-guest complexes were generally within 2 kcal/mol of the experimental values. However, the rank ordering of affinities differing by 2 kcal/mol or less was not well predicted. On the other hand, it was encouraging that the incorporation of a more sophisticated solvation model into SIE resulted in better discrimination of true binders from binders. This suggests that the inclusion of proper Physics in our models is a fruitful strategy for improving the reliability of our binding affinity predictions.

Molecular dynamics simulation of Bu4N+ in dimethylformamide: Solvation-induced volume changes

NASA Astrophysics Data System (ADS)

Kiselev, M. G.; Safonova, L. P.

2011-06-01

The structure of the Bu4N+-dimethylformamide system in the condensed and gas phases was studied by molecular dynamics simulation and quantum-chemical calculations. The calculation results were used to reveal the role played by steric effects in the volumetric characteristics of ion solvation.

Three new defined proton affinities for polybasic molecules in the gas-phase: Proton microaffinity, proton macroaffinity and proton overallaffinity

NASA Astrophysics Data System (ADS)

Salehzadeh, Sadegh; Bayat, Mehdi

2006-08-01

A theoretical study on complete protonation of a series of tetrabasic molecules with general formula N[(CH 2) nNH 2][(CH 2) mNH 2][(CH 2) pNH 2] (tren, pee, ppe, tpt, epb and ppb) is reported. For first time, three kinds of gas-phase proton affinities for each polybasic molecule are defined as: 'proton microaffinity (PA n, i)', 'proton macroaffinity (PA)' and 'proton overall affinity ( PA)'. The variations of calculated logPA in the series of these molecules is very similar to that of their measured log Kn. There is also a good correlation between the calculated gas-phase proton macroaffinities and proton overallaffinities with corresponding equilibrium macroconstants and overall protonation constants in solution.

Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.

PubMed

Li, Bo; Zhao, Yanxiang

2013-01-01

Central in a variational implicit-solvent description of biomolecular solvation is an effective free-energy functional of the solute atomic positions and the solute-solvent interface (i.e., the dielectric boundary). The free-energy functional couples together the solute molecular mechanical interaction energy, the solute-solvent interfacial energy, the solute-solvent van der Waals interaction energy, and the electrostatic energy. In recent years, the sharp-interface version of the variational implicit-solvent model has been developed and used for numerical computations of molecular solvation. In this work, we propose a diffuse-interface version of the variational implicit-solvent model with solute molecular mechanics. We also analyze both the sharp-interface and diffuse-interface models. We prove the existence of free-energy minimizers and obtain their bounds. We also prove the convergence of the diffuse-interface model to the sharp-interface model in the sense of Γ-convergence. We further discuss properties of sharp-interface free-energy minimizers, the boundary conditions and the coupling of the Poisson-Boltzmann equation in the diffuse-interface model, and the convergence of forces from diffuse-interface to sharp-interface descriptions. Our analysis relies on the previous works on the problem of minimizing surface areas and on our observations on the coupling between solute molecular mechanical interactions with the continuum solvent. Our studies justify rigorously the self consistency of the proposed diffuse-interface variational models of implicit solvation.

DESTRUCTION OF HALOGENATED HYDROCARBONS WITH SOLVATED ELECTRONS IN THE PRESENCE OF WATER. (R826180)

EPA Science Inventory

Model halogenated aromatic and aliphatic hydrocarbons and halogenated phenols were dehalogenated in seconds by solvated electrons generated from sodium in both anhydrous liquid ammonia and ammonia/water solutions. The minimum sodium required to completely dehalogenate these mo...

Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

NASA Astrophysics Data System (ADS)

Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

2015-06-01

The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering.

PubMed

Loschen, Christoph; Klamt, Andreas

2015-06-01

The fact that novel drug candidates are becoming increasingly insoluble is a major problem of current drug development. Computational tools may address this issue by screening for suitable solvents or by identifying potential novel cocrystal formers that increase bioavailability. In contrast to other more specialized methods, the fluid phase thermodynamics approach COSMO-RS (conductor-like screening model for real solvents) allows for a comprehensive treatment of drug solubility, solvate and cocrystal formation and many other thermodynamics properties in liquids. This article gives an overview of recent COSMO-RS developments that are of interest for drug development and contains several new application examples for solubility prediction and solvate/cocrystal screening. For all property predictions COSMO-RS has been used. The basic concept of COSMO-RS consists of using the screening charge density as computed from first principles calculations in combination with fast statistical thermodynamics to compute the chemical potential of a compound in solution. The fast and accurate assessment of drug solubility and the identification of suitable solvents, solvate or cocrystal formers is nowadays possible and may be used to complement modern drug development. Efficiency is increased by avoiding costly quantum-chemical computations using a database of previously computed molecular fragments. COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use. © 2015 Royal

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

NASA Astrophysics Data System (ADS)

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.

Changes in the distribution of low-energy trapped protons associated with the April 17, 1965, magnetic storm.

NASA Technical Reports Server (NTRS)

Burns, A. L.; Krimigis, S. M.

1972-01-01

The absolute intensity of geomagnetically trapped protons in the energy ranges from 0.52 to 4.0 MeV and from 0.90 to 1.8 MeV has been measured with the solid-state proton detector on the satellite Injun 4 for the period from Mar. 1 to May 31, 1965. A study of the temporal variations of these fluxes associated with the Apr. 17, 1965, magnetic storm shows a general redistribution of these protons for L greater than 2.5. The effect of the sudden commencement was a general depression in the intensities and a hardening of the energy spectra, although the intensities recovered to their prestorm level during the initial phase. The major redistribution was apparently initiated by the polar substorm. During the recovery phase, a secondary peak developed in the intensity profile at L of about 3.5 for 0.52-MeV protons that had no counterpart at this energy at the equator. No such peak was observed for 0.9-MeV protons.

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

NASA Astrophysics Data System (ADS)

Delgado, Alain; Corni, Stefano; Pittalis, Stefano; Rozzi, Carlo Andrea

2015-10-01

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Delgado, Alain; Centro de Aplicaciones Tecnológicas y Desarrollo Nuclear, Calle 30 # 502, 11300 La Habana; Corni, Stefano

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 aremore » 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.« less

Solid-State Characterization of Novel Propylene Glycol Ester Solvates Isolated from Lipid Formulations.

PubMed

Chakravarty, Paroma; Kothari, Sanjeev; Deese, Alan; Lubach, Joseph W

2015-07-06

The purpose of this study was to identify and characterize precipitates obtained from a liquid formulation of GNE068.HCl, a Genentech developmental compound, and lipophilic excipients, such as propylene glycol monocaprylate, and monolaurate. Precipitates were characterized using powder X-ray diffractometry (PXRD), differential scanning calorimetry, thermogravimetry, microscopy, nuclear magnetic resonance spectroscopy (NMR; solution and solid-state) and water sorption analysis. PXRD and NMR revealed the precipitates to be crystalline solvates of propylene glycol esters. The solvates (capryolate and lauroglycolate) were isomorphic and stable up to 70 °C, beyond which melting of the lattice occurred with subsequent dissolution of the active ingredient in the melt (microscopy and variable temperature PXRD). They were found to be mechanically stable (no change in PXRD pattern upon compression) and were nonhygroscopic up to ∼70% RH (25 °C). Our results highlight the outcome of inadvertent drug-excipient interactions in two separate lipid solution formulations with good solid-state properties and, thus, potential for further development.

Atomistic Structure and Dynamics of the Solvation Shell Formed by Organic Carbonates around Lithium Ions via Infrared Spectroscopies

NASA Astrophysics Data System (ADS)

Kuroda, Daniel; Fufler, Kristen

Lithium-ion batteries have become ubiquitous to the portable energy storage industry, but efficiency issues still remain. Currently, most technological and scientific efforts are focused on the electrodes with little attention on the electrolyte. For example, simple fundamental questions about the lithium ion solvation shell composition in commercially used electrolytes have not been answered. Using a combination of linear and non-linear IR spectroscopies and theoretical calculations, we have carried out a thorough investigation of the solvation structure and dynamics of the lithium ion in various linear and cyclic carbonates at common battery electrolyte concentrations. Our studies show that carbonates coordinate the lithium ion tetrahedrally. They also reveal that linear and cyclic carbonates have contrasting dynamics in which cyclic carbonates present the most ordered structure. Finally, our experiments demonstrate that simple structural modifications in the linear carbonates impact significantly the microscopic interactions of the system. The stark differences in the solvation structure and dynamics among different carbonates reveal previously unknown details about the molecular level picture of these systems.

Estimating the absolute wealth of households.

PubMed

Hruschka, Daniel J; Gerkey, Drew; Hadley, Craig

2015-07-01

To estimate the absolute wealth of households using data from demographic and health surveys. We developed a new metric, the absolute wealth estimate, based on the rank of each surveyed household according to its material assets and the assumed shape of the distribution of wealth among surveyed households. Using data from 156 demographic and health surveys in 66 countries, we calculated absolute wealth estimates for households. We validated the method by comparing the proportion of households defined as poor using our estimates with published World Bank poverty headcounts. We also compared the accuracy of absolute versus relative wealth estimates for the prediction of anthropometric measures. The median absolute wealth estimates of 1,403,186 households were 2056 international dollars per capita (interquartile range: 723-6103). The proportion of poor households based on absolute wealth estimates were strongly correlated with World Bank estimates of populations living on less than 2.00 United States dollars per capita per day (R(2)  = 0.84). Absolute wealth estimates were better predictors of anthropometric measures than relative wealth indexes. Absolute wealth estimates provide new opportunities for comparative research to assess the effects of economic resources on health and human capital, as well as the long-term health consequences of economic change and inequality.

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

PubMed

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

2016-11-01

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

On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils.

PubMed

Gross, Adam S; Chu, Jhih-Wei

2010-10-28

Biomass recalcitrance is a fundamental bottleneck to producing fuels from renewable sources. To understand its molecular origin, we characterize the interaction network and solvation structures of cellulose microfibrils via all-atom molecular dynamics simulations. The network is divided into three components: intrachain, interchain, and intersheet interactions. Analysis of their spatial dependence and interaction energetics indicate that intersheet interactions are the most robust and strongest component and do not display a noticeable dependence on solvent exposure. Conversely, the strength of surface-exposed intrachain and interchain hydrogen bonds is significantly reduced. Comparing the interaction networks of I(β) and I(α) cellulose also shows that the number of intersheet interactions is a clear descriptor that distinguishes the two allomorphs and is consistent with the observation that I(β) is the more stable form. These results highlight the dominant role of the often-overlooked intersheet interactions in giving rise to biomass recalcitrance. We also analyze the solvation structures around the surfaces of microfibrils and show that the structural and chemical features at cellulose surfaces constrict water molecules into specific density profiles and pair correlation functions. Calculations of water density and compressibility in the hydration shell show noticeable but not drastic differences. Therefore, specific solvation structures are more prominent signatures of different surfaces.

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

PubMed Central

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

2014-01-01

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 the 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 means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the 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 are discussed in detail in this unit. PMID:18428877

Probing solvation decay length in order to characterize hydrophobicity-induced bead-bead attractive interactions in polymer chains.

PubMed

Das, Siddhartha; Chakraborty, Suman

2011-08-01

In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.

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

PubMed

Calvo, F; Yurtsever, E

2016-06-14

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

Volume Exclusion and H-Bonding Dominate the Thermodynamics and Solvation of Trimethylamine-N-oxide in Aqueous Urea

PubMed Central

2012-01-01

Trimethylamine-N-oxide (TMAO) and urea represent the extremes among the naturally occurring organic osmolytes in terms of their ability to stabilize/destabilize proteins. Their mixtures are found in nature and have generated interest in terms of both their physiological role and their potential use as additives in various applications (crystallography, drug formulation, etc.). Here we report experimental density and activity coefficient data for aqueous mixtures of TMAO with urea. From these data we derive the thermodynamics and solvation properties of the osmolytes, using Kirkwood–Buff theory. Strong hydrogen-bonding at the TMAO oxygen, combined with volume exclusion, accounts for the thermodynamics and solvation of TMAO in aqueous urea. As a result, TMAO behaves in a manner that is surprisingly similar to that of hard-spheres. There are two mandatory solvation sites. In plain water, these sites are occupied with water molecules, which are seamlessly replaced by urea, in proportion to its volume fraction. We discuss how this result gives an explanation both for the exceptionally strong exclusion of TMAO from peptide groups and for the experimentally observed synergy between urea and TMAO. PMID:22280147

Solvation dynamics of tryptophan in water-dimethyl sulfoxide binary mixture: in search of molecular origin of composition dependent multiple anomalies.

PubMed

Roy, Susmita; Bagchi, Biman

2013-07-21

Experimental and simulation studies have uncovered at least two anomalous concentration regimes in water-dimethyl sulfoxide (DMSO) binary mixture whose precise origin has remained a subject of debate. In order to facilitate time domain experimental investigation of the dynamics of such binary mixtures, we explore strength or extent of influence of these anomalies in dipolar solvation dynamics by carrying out long molecular dynamics simulations over a wide range of DMSO concentration. The solvation time correlation function so calculated indeed displays strong composition dependent anomalies, reflected in pronounced non-exponential kinetics and non-monotonous composition dependence of the average solvation time constant. In particular, we find remarkable slow-down in the solvation dynamics around 10%-20% and 35%-50% mole percentage. We investigate microscopic origin of these two anomalies. The population distribution analyses of different structural morphology elucidate that these two slowing down are reflections of intriguing structural transformations in water-DMSO mixture. The structural transformations themselves can be explained in terms of a change in the relative coordination number of DMSO and water molecules, from 1DMSO:2H2O to 1H2O:1DMSO and 1H2O:2DMSO complex formation. Thus, while the emergence of first slow down (at 15% DMSO mole percentage) is due to the percolation among DMSO molecules supported by the water molecules (whose percolating network remains largely unaffected), the 2nd anomaly (centered on 40%-50%) is due to the formation of the network structure where the unit of 1DMSO:1H2O and 2DMSO:1H2O dominates to give rise to rich dynamical features. Through an analysis of partial solvation dynamics an interesting negative cross-correlation between water and DMSO is observed that makes an important contribution to relaxation at intermediate to longer times.

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Molecular Simulations of Carbon Dioxide and Water: Cation Solvation and Wettability

NASA Astrophysics Data System (ADS)

Criscenti, L. J.; Bracco, J.; Cygan, R. T.

2010-12-01

Proposed carbon dioxide sequestration scenarios in sedimentary basins require investigation into the interaction between supercritical carbon dioxide, brines, and the mineral phases found in the basin and overlying caprock. Classical molecular dynamics (MD) simulations can be used to investigate some of these interactions such as the partitioning of metal cations between aqueous solutions and supercritical carbon dioxide, and the relative wettability of basin and caprock minerals with different fluid phases including water, carbon dioxide, and oil. Initial research has lead to the development of a new flexible carbon dioxide force field that successfully reproduces the vibrational properties of carbon dioxide, and a methodology for extracting contact angle information from large-scale MD simulations. Molecular simulations were performed to compare the solvation of alkali and alkaline metal cations in water and liquid carbon dioxide at 300K, using a flexible simple point charge (SPC) model for water and the new carbon dioxide force field. Solvation energies for Na+, Cs+, Mg2+, and Ba2+ are larger in water than in carbon dioxide, suggesting that these cations will partition preferentially into water. In both solutions, the solvation energy for the cations decreases with ion size and increases with ion charge. However, changes in solvation energy with increasing ionic radii are smaller in carbon dioxide than in water. Therefore, the overall partitioning of cations into carbon dioxide is predicted to increase with ion size. Molecular dynamics simulations are also useful to examine the relative wettability of minerals with different fluid phases. Large-scale MD simulations involving between 100,000 and 200,000 atoms have been conducted to establish a dynamic equilibrium between a drop of liquid water, water vapor, and kaolinite surfaces. The water drops consisted of at least 1700 molecules. Simulations were performed for five nanoseconds. The contact angle calculated

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

PubMed

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

2015-04-07

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

The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

PubMed

Wan, Liwen F; Prendergast, David

2014-10-15

The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition.

Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

NASA Astrophysics Data System (ADS)

Aguilar, M.; Ali Cavasonza, L.; Alpat, B.; Ambrosi, G.; Arruda, L.; Attig, N.; Aupetit, S.; Azzarello, P.; Bachlechner, A.; Barao, F.; Barrau, A.; Barrin, L.; Bartoloni, A.; Basara, L.; Başeǧmez-du Pree, S.; Battarbee, M.; Battiston, R.; Bazo, J.; Becker, U.; Behlmann, M.; Beischer, B.; Berdugo, J.; Bertucci, B.; Bindi, V.; Boella, G.; de Boer, W.; Bollweg, K.; Bonnivard, V.; Borgia, B.; Boschini, M. J.; Bourquin, M.; Bueno, E. F.; Burger, J.; Cadoux, F.; Cai, X. D.; Capell, M.; Caroff, S.; Casaus, J.; Castellini, G.; Cernuda, I.; Cervelli, F.; Chae, M. J.; Chang, Y. H.; Chen, A. I.; Chen, G. M.; Chen, H. S.; Cheng, L.; Chou, H. Y.; Choumilov, E.; Choutko, V.; Chung, C. H.; Clark, C.; Clavero, R.; Coignet, G.; Consolandi, C.; Contin, A.; Corti, C.; Coste, B.; Creus, W.; Crispoltoni, M.; Cui, Z.; Dai, Y. M.; Delgado, C.; Della Torre, S.; Demirköz, M. B.; Derome, L.; Di Falco, S.; Dimiccoli, F.; Díaz, C.; von Doetinchem, P.; Dong, F.; Donnini, F.; Duranti, M.; D'Urso, D.; Egorov, A.; Eline, A.; Eronen, T.; Feng, J.; Fiandrini, E.; Finch, E.; Fisher, P.; Formato, V.; Galaktionov, Y.; Gallucci, G.; García, B.; García-López, R. J.; Gargiulo, C.; Gast, H.; Gebauer, I.; Gervasi, M.; Ghelfi, A.; Giovacchini, F.; Goglov, P.; Gómez-Coral, D. M.; Gong, J.; Goy, C.; Grabski, V.; Grandi, D.; Graziani, M.; Guerri, I.; Guo, K. H.; Habiby, M.; Haino, S.; Han, K. C.; He, Z. H.; Heil, M.; Hoffman, J.; Hsieh, T. H.; Huang, H.; Huang, Z. C.; Huh, C.; Incagli, M.; Ionica, M.; Jang, W. Y.; Jinchi, H.; Kang, S. C.; Kanishev, K.; Kim, G. N.; Kim, K. S.; Kirn, Th.; Konak, C.; Kounina, O.; Kounine, A.; Koutsenko, V.; Krafczyk, M. S.; La Vacca, G.; Laudi, E.; Laurenti, G.; Lazzizzera, I.; Lebedev, A.; Lee, H. T.; Lee, S. C.; Leluc, C.; Li, H. S.; Li, J. Q.; Li, J. Q.; Li, Q.; Li, T. X.; Li, W.; Li, Z. H.; Li, Z. Y.; Lim, S.; Lin, C. H.; Lipari, P.; Lippert, T.; Liu, D.; Liu, Hu; Lu, S. Q.; Lu, Y. S.; Luebelsmeyer, K.; Luo, F.; Luo, J. Z.; Lv, S. S.; Majka, R.; Mañá, C.; Marín, J.; Martin, T.; Martínez, G.; Masi, N.; Maurin, D.; Menchaca-Rocha, A.; Meng, Q.; Mo, D. C.; Morescalchi, L.; Mott, P.; Nelson, T.; Ni, J. Q.; Nikonov, N.; Nozzoli, F.; Nunes, P.; Oliva, A.; Orcinha, M.; Palmonari, F.; Palomares, C.; Paniccia, M.; Pauluzzi, M.; Pensotti, S.; Pereira, R.; Picot-Clemente, N.; Pilo, F.; Pizzolotto, C.; Plyaskin, V.; Pohl, M.; Poireau, V.; Putze, A.; Quadrani, L.; Qi, X. M.; Qin, X.; Qu, Z. Y.; Räihä, T.; Rancoita, P. G.; Rapin, D.; Ricol, J. S.; Rodríguez, I.; Rosier-Lees, S.; Rozhkov, A.; Rozza, D.; Sagdeev, R.; Sandweiss, J.; Saouter, P.; Schael, S.; Schmidt, S. M.; Schulz von Dratzig, A.; Schwering, G.; Seo, E. S.; Shan, B. S.; Shi, J. Y.; Siedenburg, T.; Son, D.; Song, J. W.; Sun, W. H.; Tacconi, M.; Tang, X. W.; Tang, Z. C.; Tao, L.; Tescaro, D.; Ting, Samuel C. C.; Ting, S. M.; Tomassetti, N.; Torsti, J.; Türkoǧlu, C.; Urban, T.; Vagelli, V.; Valente, E.; Vannini, C.; Valtonen, E.; Vázquez Acosta, M.; Vecchi, M.; Velasco, M.; Vialle, J. P.; Vitale, V.; Vitillo, S.; Wang, L. Q.; Wang, N. H.; Wang, Q. L.; Wang, X.; Wang, X. Q.; Wang, Z. X.; Wei, C. C.; Weng, Z. L.; Whitman, K.; Wienkenhöver, J.; Willenbrock, M.; Wu, H.; Wu, X.; Xia, X.; Xiong, R. Q.; Xu, W.; Yan, Q.; Yang, J.; Yang, M.; Yang, Y.; Yi, H.; Yu, Y. J.; Yu, Z. Q.; Zeissler, S.; Zhang, C.; Zhang, J.; Zhang, J. H.; Zhang, S. D.; Zhang, S. W.; Zhang, Z.; Zheng, Z. M.; Zhu, Z. Q.; Zhuang, H. L.; Zhukov, V.; Zichichi, A.; Zimmermann, N.; Zuccon, P.; AMS Collaboration

2016-08-01

A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49 ×1 05 antiproton events and 2.42 ×1 09 proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ˜60 to ˜500 GV , the antiproton p ¯, proton p , and positron e+ fluxes are found to have nearly identical rigidity dependence and the electron e- flux exhibits a different rigidity dependence. Below 60 GV, the (p ¯/p ), (p ¯/e+), and (p /e+) flux ratios each reaches a maximum. From ˜60 to ˜500 GV , the (p ¯/p ), (p ¯/e+), and (p /e+) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

Calculating Free Energy Changes in Continuum Solvation Models

DOE PAGES

Ho, Junming; Ertem, Mehmed Z.

2016-02-27

We recently showed for a large dataset of pK as and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKmore » a calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol -1 and 25 kJ mol -1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less

Estimating the absolute wealth of households

PubMed Central

Gerkey, Drew; Hadley, Craig

2015-01-01

Abstract Objective To estimate the absolute wealth of households using data from demographic and health surveys. Methods We developed a new metric, the absolute wealth estimate, based on the rank of each surveyed household according to its material assets and the assumed shape of the distribution of wealth among surveyed households. Using data from 156 demographic and health surveys in 66 countries, we calculated absolute wealth estimates for households. We validated the method by comparing the proportion of households defined as poor using our estimates with published World Bank poverty headcounts. We also compared the accuracy of absolute versus relative wealth estimates for the prediction of anthropometric measures. Findings The median absolute wealth estimates of 1 403 186 households were 2056 international dollars per capita (interquartile range: 723–6103). The proportion of poor households based on absolute wealth estimates were strongly correlated with World Bank estimates of populations living on less than 2.00 United States dollars per capita per day (R2 = 0.84). Absolute wealth estimates were better predictors of anthropometric measures than relative wealth indexes. Conclusion Absolute wealth estimates provide new opportunities for comparative research to assess the effects of economic resources on health and human capital, as well as the long-term health consequences of economic change and inequality. PMID:26170506

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yadav, Hari O. S., E-mail: cyz108802@chemistry.iitd.ac.in, E-mail: hariyadav.iitd@gmail.com; Shrivastav, Gourav; Agarwal, Manish

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,more » 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

Role of Solvation Effects in Protein Denaturation: From Thermodynamics to Single Molecules and Back

PubMed Central

England, Jeremy L.; Haran, Gilad

2011-01-01

Protein stability often is studied in vitro through the use of urea and guanidinium chloride, chemical cosolvents that disrupt protein native structure. Much controversy still surrounds the underlying mechanism by which these molecules denature proteins. Here we review current thinking on various aspects of chemical denaturation. We begin by discussing classic models of protein folding and how the effects of denaturants may fit into this picture through their modulation of the collapse, or coil-globule transition, which typically precedes folding. Subsequently, we examine recent molecular dynamics simulations that have shed new light on the possible microscopic origins of the solvation effects brought on by denaturants. It seems likely that both denaturants operate by facilitating solvation of hydrophobic regions of proteins. Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition. PMID:21219136

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

NASA Astrophysics Data System (ADS)

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.

Measurements of Cosmic-Ray Proton and Helium Spectra from the BESS-Polar Long-Duration Balloon Flights Over Antarctica

NASA Technical Reports Server (NTRS)

Abe, K.; Fuke, H.; Haino, S.; Hams, T.; Hasegawa, M.; Horikoshi, A.; Itazaki, A.; Kim, K. C.; Kumazawa, T.; Kusumoto, A.;

20 CFR 404.1205 - Absolute coverage groups.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Absolute coverage groups. 404.1205 Section... Covered § 404.1205 Absolute coverage groups. (a) General. An absolute coverage group is a permanent... are not under a retirement system. An absolute coverage group may include positions which were...

Protons and how they are transported by proton pumps.

PubMed

Buch-Pedersen, M J; Pedersen, B P; Veierskov, B; Nissen, P; Palmgren, M G

2009-01-01

The very high mobility of protons in aqueous solutions demands special features of membrane proton transporters to sustain efficient yet regulated proton transport across biological membranes. By the use of the chemical energy of ATP, plasma-membrane-embedded ATPases extrude protons from cells of plants and fungi to generate electrochemical proton gradients. The recently published crystal structure of a plasma membrane H(+)-ATPase contributes to our knowledge about the mechanism of these essential enzymes. Taking the biochemical and structural data together, we are now able to describe the basic molecular components that allow the plasma membrane proton H(+)-ATPase to carry out proton transport against large membrane potentials. When divergent proton pumps such as the plasma membrane H(+)-ATPase, bacteriorhodopsin, and F(O)F(1) ATP synthase are compared, unifying mechanistic premises for biological proton pumps emerge. Most notably, the minimal pumping apparatus of all pumps consists of a central proton acceptor/donor, a positively charged residue to control pK(a) changes of the proton acceptor/donor, and bound water molecules to facilitate rapid proton transport along proton wires.

Dosimetric study of uniform scanning proton therapy planning for prostate cancer patients with a metal hip prosthesis, and comparison with volumetric‐modulated arc therapy

PubMed Central

Cheng, ChihYao; Zheng, Yuanshui; Hsi, Wen; Zeidan, Omar; Schreuder, Niek; Vargas, Carlos; Larson, Gary

2014-01-01

The main purposes of this study were to 1) investigate the dosimetric quality of uniform scanning proton therapy planning (USPT) for prostate cancer patients with a metal hip prosthesis, and 2) compare the dosimetric results of USPT with that of volumetric‐modulated arc therapy (VMAT). Proton plans for prostate cancer (four cases) were generated in XiO treatment planning system (TPS). The beam arrangement in each proton plan consisted of three fields (two oblique fields and one lateral or slightly angled field), and the proton beams passing through a metal hip prosthesis was avoided. Dose calculations in proton plans were performed using the pencil beam algorithm. From each proton plan, planning target volume (PTV) coverage value (i.e., relative volume of the PTV receiving the prescription dose of 79.2 CGE) was recorded. The VMAT prostate planning was done using two arcs in the Eclipse TPS utilizing 6 MV X‐rays, and beam entrance through metallic hip prosthesis was avoided. Dose computation in the VMAT plans was done using anisotropic analytical algorithm, and calculated VMAT plans were then normalized such that the PTV coverage in the VMAT plan was the same as in the proton plan of the corresponding case. The dose‐volume histograms of calculated treatment plans were used to evaluate the dosimetric quality of USPT and VMAT. In comparison to the proton plans, on average, the maximum and mean doses to the PTV were higher in the VMAT plans by 1.4% and 0.5%, respectively, whereas the minimum PTV dose was lower in the VMAT plans by 3.4%. The proton plans had lower (or better) average homogeneity index (HI) of 0.03 compared to the one for VMAT (HI = 0.04). The relative rectal volume exposed to radiation was lower in the proton plan, with an average absolute difference ranging from 0.1% to 32.6%. In contrast, using proton planning, the relative bladder volume exposed to radiation was higher at high‐dose region with an average absolute difference ranging from 0

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajput, Nav Nidhi; Murugesan, Vijayakumar; Shin, Yongwoo

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 asmore » 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.« less

Solvation of apolar compounds in protic ionic liquids: the non-synergistic effect of electrostatic interactions and hydrogen bonds.

PubMed

Sedov, I A; Magsumov, T I; Salikov, T M; Solomonov, B N

2017-09-27

The solvation properties of protic ionic liquids such as alkylammonium salts are still virtually uncharacterized. Both electrostatic interactions between charged particles and hydrogen bond networks in a solvent are known to hinder the solubility of apolar species. Protic ionic liquids can be a priori expected to dissolve hydrocarbons worse than aprotic ionic liquids which do not form hydrogen bonds between the ions. We measured the limiting activity coefficients of several alkanes and alkylbenzenes in propylammonium and butylammonium nitrates at 298 K. Surprisingly, we observed the tendency of higher solubility than for the same compounds in aprotic ionic liquids with a similar molar volume. The calculations of the excess Gibbs free energies using test particle insertions into the snapshots of molecular dynamics trajectories reproduced lower values in protic rather than in aprotic ionic liquids for both methane molecules and hard sphere solutes. This can be explained by the favorable solvation of apolar species in the apolar domain of nanostructured PILs. For the first time, we point out at the essential difference between the solvation properties of two types of ionic liquids and prove that it arises from the cavity formation term.

Probing the solvation structure and dynamics in ionic liquids by time-resolved infrared spectroscopy of 4-(dimethylamino)benzonitrile.

PubMed

Ando, Rômulo A; Brown-Xu, Samantha E; Nguyen, Lisa N Q; Gustafson, Terry L

2017-09-20

In this work we demonstrate the use of the push-pull model system 4-(dimethylamino)benzonitrile (DMABN) as a convenient molecular probe to investigate the local solvation structure and dynamics by means of time-resolved infrared spectroscopy (TRIR). The photochemical features associated with this system provide several advantages due to the high charge separation between the ground and charge transfer states involving the characteristic nitrile bond, and an excited state lifetime that is long enough to observe the slow solvation dynamics in organic solvents and ionic liquids. The conversion from a locally excited state to an intramolecular charge transfer state (LE-ICT) in ionic liquids shows similar kinetic lifetimes in comparison to organic solvents. This similarity confirms that such conversion depends solely on the intramolecular reorganization of DMABN in the excited state, and not by the dynamics of solvation. In contrast, the relative shift of the ν(CN) vibration during the relaxation of the ICT state reveals two distinct lifetimes that are sensitive to the solvent environment. This study reveals a fast time component which is attributed to the dipolar relaxation of the solvent and a slower time component related to the rotation of the dimethylamino group of DMABN.

Preferential solvation bromophenol blue in water-alcohol binary mixture.

PubMed

Dangui, Anayana Z; Santos, Vanessa M S; Gomes, Benhur S; de Castilho, Taiane S; Nicolini, Keller P; Nicolini, Jaqueline

2018-05-29

In this study, the perichromic behavior of bromophenol blue (BPB) in various binary solvent mixtures was investigated. The binary mixtures considered were comprised of water and methanol (MeOH), ethanol (EtOH), n-propanol (n-PrOH), isopropanol (iso-PrOH) or t-butanol (t-BuOH). The investigation of a preferential solvation model that considers the addition of small quantities of alcohol to water in the presence of bromophenol blue (BPB) is described in this paper. The data obtained were employed to study the preferential solvation (PS) of the probe. It was observed that with increases in the molar fraction of water the spontaneity of the system decreases. This can be explained by the high solubility of BPB in ethanol, with ∆G>0 at higher wavelengths (region rich in water with violet solution) and ∆G<0 at lower wavelengths (region rich in alcohol with yellow solution). The pK of the binary mixture changed in all solvents and for all ratios, and the higher the water ratio is the lower the pK In will be. In binary mixture, an increase in the hydrogen bond acceptor (HBA) nature of the solvents tested resulted in a bathochromic effect on the absorption band of BPB (Δλ=12nm). All of the data obtained showed a good nonlinear fit with the mathematical model (SD≤6.6×10 -3 ), suggesting that BPB has other potential applications besides its use as a pH indicator. Copyright © 2017. Published by Elsevier B.V.

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

PubMed

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.

A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected Traditional Chemical Warfare Agents and Simulants II: COSMO RS and COSMOTherm

DTIC Science & Technology

2017-04-01

A COMPARISON OF PREDICTIVE THERMO AND WATER SOLVATION PROPERTY PREDICTION TOOLS AND EXPERIMENTAL DATA FOR...4. TITLE AND SUBTITLE A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected...1  2.  EXPERIMENTAL PROCEDURE

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

PubMed

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

2016-09-14

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

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Photoproduction of $$ \\pi^{0}$$-pairs off protons and off neutrons

DOE PAGES

Dieterle, M.; Oberle, M.; Ahrens, J.; ...

2015-11-04

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of π 0π 0 pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. Themore » results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final-state invariant masses up to ≈1550 MeV), where both reactions are dominated by the N(1520)3/2 –→Δ(1232)3/2 +π decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an N*→Nσ decay for the proton, while the reaction is dominated by a sequential decay via a Δπ intermediate state for the neutron. Here, the data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled-channel analysis.« less

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

NASA Astrophysics Data System (ADS)

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.

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

PubMed

Klähn, Marco; Lim, Geraldine S; Seduraman, Abirami; Wu, Ping

2011-01-28

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme

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

NASA Astrophysics Data System (ADS)

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+.

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

PubMed

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

2009-05-07

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous

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

NASA Astrophysics Data System (ADS)

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.

Absolute prompt-gamma yield measurements for ion beam therapy monitoring

NASA Astrophysics Data System (ADS)

Pinto, M.; Bajard, M.; Brons, S.; Chevallier, M.; Dauvergne, D.; Dedes, G.; De Rydt, M.; Freud, N.; Krimmer, J.; La Tessa, C.; Létang, J. M.; Parodi, K.; Pleskač, R.; Prieels, D.; Ray, C.; Rinaldi, I.; Roellinghoff, F.; Schardt, D.; Testa, E.; Testa, M.

2015-01-01

Prompt-gamma emission detection is a promising technique for hadrontherapy monitoring purposes. In this regard, obtaining prompt-gamma yields that can be used to develop monitoring systems based on this principle is of utmost importance since any camera design must cope with the available signal. Herein, a comprehensive study of the data from ten single-slit experiments is presented, five consisting in the irradiation of either PMMA or water targets with lower and higher energy carbon ions, and another five experiments using PMMA targets and proton beams. Analysis techniques such as background subtraction methods, geometrical normalization, and systematic uncertainty estimation were applied to the data in order to obtain absolute prompt-gamma yields in units of prompt-gamma counts per incident ion, unit of field of view, and unit of solid angle. At the entrance of a PMMA target, where the contribution of secondary nuclear reactions is negligible, prompt-gamma counts per incident ion, per millimetre and per steradian equal to (124 ± 0.7stat ± 30sys) × 10-6 for 95 MeV u-1 carbon ions, (79 ± 2stat ± 23sys) × 10-6 for 310 MeV u-1 carbon ions, and (16 ± 0.07stat ± 1sys) × 10-6 for 160 MeV protons were found for prompt gammas with energies higher than 1 MeV. This shows a factor 5 between the yields of two different ions species with the same range in water (160 MeV protons and 310 MeV u-1 carbon ions). The target composition was also found to influence the prompt-gamma yield since, for 300/310 MeV u-1 carbon ions, a 42% greater yield ((112 ± 1stat ± 22sys) × 10-6 counts ion-1 mm-1 sr-1) was obtained with a water target compared to a PMMA one.

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

PubMed

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

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

PubMed Central

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

2012-01-01

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

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

NASA Astrophysics Data System (ADS)

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 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural

On the nature of the solvated electron in ice Ih.

PubMed

de Koning, Maurice; Fazzio, Adalberto; da Silva, Antônio José Roque; Antonelli, Alex

2016-02-14

The water-solvated excess electron (EE) is a key chemical agent whose hallmark signature, its asymmetric optical absorption spectrum, continues to be a topic of debate. While nearly all investigation has focused on the liquid-water solvent, the fact that the crystalline-water solvated EE shows a very similar visible absorption pattern has remained largely unexplored. Here, we present spin-polarized density-functional theory calculations subject to periodic boundary conditions of the interplay between an EE and a number of intrinsic lattice defects in ice Ih. Our results show that the optical absorption signatures in the presence of three unsaturated hydrogen bonds (HB) are very similar to those observed experimentally. Its low-energy side can be attributed to transitions between the EE ground state and a single localized excited level, in a picture that is different from that for the liquid solvent, where this portion has been associated with hydrogen-like s → p excitations. The blue tail, on the other hand, relates to transitions between the EE ground state and delocalized excited states, which is in line with the bound-to-continuum transition interpretations for the EE in liquid water. Finally, we find that, depending on the number of dangling HBs participating in the EE trap, its charge density may spontaneously break the spin degeneracy through exchange interactions with the surrounding electrons, displaying the many-electron quantum nature of the EE problem in ice Ih.

Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

PubMed

Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

2015-02-14

We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

Occipital cortical proton MRS at 4 Tesla in human moderate MDMA polydrug users

PubMed Central

Cowan, Ronald L.; Bolo, Nicolas R.; Dietrich, Mary; Haga, Erica; Lukas, Scott E.; Renshaw, Perry F.

2007-01-01

The recreational drug MDMA (3,4, methylenedioxymethamphetamine; sold under the street name of Ecstasy) is toxic to serotonergic axons in some animal models of MDMA administration. In humans, MDMA use is associated with alterations in markers of brain function that are pronounced in occipital cortex. Among neuroimaging methods, magnetic resonance spectroscopy (MRS) studies of brain metabolites N-acetylaspartate (NAA) and myoinositol (MI) at a field strength of 1.5 Tesla (T) reveal inconsistent results in MDMA users. Because higher field strength proton MRS has theoretical advantages over lower field strengths, we used proton MRS at 4.0 T to study absolute concentrations of occipital cortical NAA and MI in a cohort of moderate MDMA users (n = 9) versus non-MDMA using (n = 7) controls. Mean NAA in non-MDMA users was 10.47 mM (± 2.51), versus 9.83 mM (± 1.94) in MDMA users. Mean MI in non-MDMA users was 7.43 mM (± 1.68), versus 6.57 mM (± 1.59) in MDMA users. There were no statistical differences in absolute metabolite levels for NAA and MI in occipital cortex of MDMA users and controls. These findings are not supportive of MDMA-induced alterations in NAA or MI levels in this small sample of moderate MDMA users. Limitations to this study suggest caution in the interpretation of these results. PMID:17574394

Occipital cortical proton MRS at 4 Tesla in human moderate MDMA polydrug users.

PubMed

Cowan, Ronald L; Bolo, Nicolas R; Dietrich, Mary; Haga, Erica; Lukas, Scott E; Renshaw, Perry F

2007-08-15

The recreational drug MDMA (3,4, methylenedioxymethamphetamine; sold under the street name of Ecstasy) is toxic to serotonergic axons in some animal models of MDMA administration. In humans, MDMA use is associated with alterations in markers of brain function that are pronounced in occipital cortex. Among neuroimaging methods, magnetic resonance spectroscopy (MRS) studies of brain metabolites N-acetylaspartate (NAA) and myoinositol (MI) at a field strength of 1.5 Tesla (T) reveal inconsistent results in MDMA users. Because higher field strength proton MRS has theoretical advantages over lower field strengths, we used proton MRS at 4.0 T to study absolute concentrations of occipital cortical NAA and MI in a cohort of moderate MDMA users (n=9) versus non-MDMA using (n=7) controls. Mean NAA in non-MDMA users was 10.47 mM (+/-2.51), versus 9.83 mM (+/-1.94) in MDMA users. Mean MI in non-MDMA users was 7.43 mM (+/-.68), versus 6.57 mM (+/-1.59) in MDMA users. There were no statistical differences in absolute metabolite levels for NAA and MI in occipital cortex of MDMA users and controls. These findings are not supportive of MDMA-induced alterations in NAA or MI levels in this small sample of moderate MDMA users. Limitations to this study suggest caution in the interpretation of these results.

Solvation effects on like-charge attraction.

PubMed

Ghanbarian, Shahzad; Rottler, Jörg

2013-02-28

We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.

Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station.

PubMed

Aguilar, M; Ali Cavasonza, L; Alpat, B; Ambrosi, G; Arruda, L; Attig, N; Aupetit, S; Azzarello, P; Bachlechner, A; Barao, F; Barrau, A; Barrin, L; Bartoloni, A; Basara, L; Başeǧmez-du Pree, S; Battarbee, M; Battiston, R; Bazo, J; Becker, U; Behlmann, M; Beischer, B; Berdugo, J; Bertucci, B; Bindi, V; Boella, G; de Boer, W; Bollweg, K; Bonnivard, V; Borgia, B; Boschini, M J; Bourquin, M; Bueno, E F; Burger, J; Cadoux, F; Cai, X D; Capell, M; Caroff, S; Casaus, J; Castellini, G; Cernuda, I; Cervelli, F; Chae, M J; Chang, Y H; Chen, A I; Chen, G M; Chen, H S; Cheng, L; Chou, H Y; Choumilov, E; Choutko, V; Chung, C H; Clark, C; Clavero, R; Coignet, G; Consolandi, C; Contin, A; Corti, C; Coste, B; Creus, W; Crispoltoni, M; Cui, Z; Dai, Y M; Delgado, C; Della Torre, S; Demirköz, M B; Derome, L; Di Falco, S; Dimiccoli, F; Díaz, C; von Doetinchem, P; Dong, F; Donnini, F; Duranti, M; D'Urso, D; Egorov, A; Eline, A; Eronen, T; Feng, J; Fiandrini, E; Finch, E; Fisher, P; Formato, V; Galaktionov, Y; Gallucci, G; García, B; García-López, R J; Gargiulo, C; Gast, H; Gebauer, I; Gervasi, M; Ghelfi, A; Giovacchini, F; Goglov, P; Gómez-Coral, D M; Gong, J; Goy, C; Grabski, V; Grandi, D; Graziani, M; Guerri, I; Guo, K H; Habiby, M; Haino, S; Han, K C; He, Z H; Heil, M; Hoffman, J; Hsieh, T H; Huang, H; Huang, Z C; Huh, C; Incagli, M; Ionica, M; Jang, W Y; Jinchi, H; Kang, S C; Kanishev, K; Kim, G N; Kim, K S; Kirn, Th; Konak, C; Kounina, O; Kounine, A; Koutsenko, V; Krafczyk, M S; La Vacca, G; Laudi, E; Laurenti, G; Lazzizzera, I; Lebedev, A; Lee, H T; Lee, S C; Leluc, C; Li, H S; Li, J Q; Li, J Q; Li, Q; Li, T X; Li, W; Li, Z H; Li, Z Y; Lim, S; Lin, C H; Lipari, P; Lippert, T; Liu, D; Liu, Hu; Lu, S Q; Lu, Y S; Luebelsmeyer, K; Luo, F; Luo, J Z; Lv, S S; Majka, R; Mañá, C; Marín, J; Martin, T; Martínez, G; Masi, N; Maurin, D; Menchaca-Rocha, A; Meng, Q; Mo, D C; Morescalchi, L; Mott, P; Nelson, T; Ni, J Q; Nikonov, N; Nozzoli, F; Nunes, P; Oliva, A; Orcinha, M; Palmonari, F; Palomares, C; Paniccia, M; Pauluzzi, M; Pensotti, S; Pereira, R; Picot-Clemente, N; Pilo, F; Pizzolotto, C; Plyaskin, V; Pohl, M; Poireau, V; Putze, A; Quadrani, L; Qi, X M; Qin, X; Qu, Z Y; Räihä, T; Rancoita, P G; Rapin, D; Ricol, J S; Rodríguez, I; Rosier-Lees, S; Rozhkov, A; Rozza, D; Sagdeev, R; Sandweiss, J; Saouter, P; Schael, S; Schmidt, S M; Schulz von Dratzig, A; Schwering, G; Seo, E S; Shan, B S; Shi, J Y; Siedenburg, T; Son, D; Song, J W; Sun, W H; Tacconi, M; Tang, X W; Tang, Z C; Tao, L; Tescaro, D; Ting, Samuel C C; Ting, S M; Tomassetti, N; Torsti, J; Türkoğlu, C; Urban, T; Vagelli, V; Valente, E; Vannini, C; Valtonen, E; Vázquez Acosta, M; Vecchi, M; Velasco, M; Vialle, J P; Vitale, V; Vitillo, S; Wang, L Q; Wang, N H; Wang, Q L; Wang, X; Wang, X Q; Wang, Z X; Wei, C C; Weng, Z L; Whitman, K; Wienkenhöver, J; Willenbrock, M; Wu, H; Wu, X; Xia, X; Xiong, R Q; Xu, W; Yan, Q; Yang, J; Yang, M; Yang, Y; Yi, H; Yu, Y J; Yu, Z Q; Zeissler, S; Zhang, C; Zhang, J; Zhang, J H; Zhang, S D; Zhang, S W; Zhang, Z; Zheng, Z M; Zhu, Z Q; Zhuang, H L; Zhukov, V; Zichichi, A; Zimmermann, N; Zuccon, P

2016-08-26

A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49×10^{5} antiproton events and 2.42×10^{9} proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ∼60 to ∼500  GV, the antiproton p[over ¯], proton p, and positron e^{+} fluxes are found to have nearly identical rigidity dependence and the electron e^{-} flux exhibits a different rigidity dependence. Below 60 GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios each reaches a maximum. From ∼60 to ∼500  GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calvo, F., E-mail: florent.calvo@univ-grenoble-alpes.fr; Yurtsever, E.

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 asmore » 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.« less

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

NASA Astrophysics Data System (ADS)

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

2016-03-01

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

Forecasting Error Calculation with Mean Absolute Deviation and Mean Absolute Percentage Error

NASA Astrophysics Data System (ADS)

Khair, Ummul; Fahmi, Hasanul; Hakim, Sarudin Al; Rahim, Robbi

2017-12-01

Prediction using a forecasting method is one of the most important things for an organization, the selection of appropriate forecasting methods is also important but the percentage error of a method is more important in order for decision makers to adopt the right culture, the use of the Mean Absolute Deviation and Mean Absolute Percentage Error to calculate the percentage of mistakes in the least square method resulted in a percentage of 9.77% and it was decided that the least square method be worked for time series and trend data.

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

PubMed

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.

A molecular dynamics computer simulation study of room-temperature ionic liquids. II. Equilibrium and nonequilibrium solvation dynamics.

PubMed

Shim, Y; Choi, M Y; Kim, Hyung J

2005-01-22

The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M. Y. Choi and H. J. Kim, J. Chem. Phys. 122, 044510 (2005)] is extended to investigate dynamic properties of these liquids. Solvent fluctuation dynamics near equilibrium are studied via MD and associated time-dependent friction is analyzed via the generalized Langevin equation. Nonequilibrium solvent relaxation following an instantaneous change in the solute charge distribution and accompanying solvent structure reorganization are also investigated. Both equilibrium and nonequilibrium solvation dynamics are characterized by at least two vastly different time scales--a subpicosecond inertial regime followed by a slow diffusive regime. Solvent regions contributing to the subpicosecond nonequilibrium relaxation are found to vary significantly with initial solvation configurations, especially near the solute. If the solvent density near the solute is sufficiently high at the outset of the relaxation, subpicosecond dynamics are mainly governed by the motions of a few ions close to the solute. By contrast, in the case of a low local density, solvent ions located not only close to but also relatively far from the solute participate in the subpicosecond relaxation. Despite this difference, linear response holds reasonably well in both ionic liquids. (c) 2005 American Institute of Physics.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2009-04-30

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which amore » few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91

Proton Affinities of Anionic Bases:  Trends Across the Periodic Table, Structural Effects, and DFT Validation.

PubMed

Swart, Marcel; Bickelhaupt, F Matthias

2006-03-01

We have carried out an extensive exploration of the gas-phase basicity of archetypal anionic bases across the periodic system using the generalized gradient approximation of density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities:  BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 1.6 kcal/mol for the proton affinity at 0 K with respect to high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the anionic conjugate bases of all main-group-element hydrides of groups 14-17 and periods 2-6. We have also studied the effect of stepwise methylation of the protophilic center of the second- and third-period bases.

Impact of the NTCP modeling on medical decision to select eligible patient for proton therapy: the usefulness of EUD as an indicator to rank modern photon vs proton treatment plans.

PubMed

Chaikh, Abdulhamid; Calugaru, Valentin; Bondiau, Pierre-Yves; Thariat, Juliette; Balosso, Jacques

2018-06-07

The aim of this study is to evaluate the impact of normal tissue complication probability (NTCP)-based radiobiological models on the estimated risk for late radiation lung damages. The second goal is to propose a medical decision-making approach to select the eligible patient for particle therapy. 14 pediatric patients undergoing cranio-spinal irradiation were evaluated. For each patient, two treatment plans were generated using photon and proton therapy with the same dose prescriptions. Late radiation damage to lung was estimated using three NTCP concepts: the Lyman-Kutcher-Burman, the equivalent uniform dose (EUD) and the mean lung dose according to the quantitative analysis of normal tissue effects in the clinic QUANTEC review. Wilcoxon paired test was used to calculate p-value. Proton therapy achieved lower lung EUD (Gy). The average NTCP values were significantly lower with proton plans, p < 0.05, using the three NTCP concepts. However, applying the same TD 50/5 using radiobiological models to compare NTCP from proton and photon therapy, the ΔNTCP was not a convincing method to measure the potential benefit of proton therapy. Late radiation pneumonitis estimated from the mean lung dose model correlated with QUANTEC data better. treatment effectiveness assessed on NTCP reduction depends on radiobiological predictions and parameters used as inputs for in silico evaluation. Since estimates of absolute NTCP values from LKB and GN models are imprecise due to EUD ≪ TD 50/5 , a reduction of the EUD value with proton plans would better predict a reduction of dose/toxicity. The EUD concept appears as a robust radiobiological surrogate of the dose distribution to select the optimal patient's plan.

Measurement of the differential and double-differential Drell-Yan cross sections in proton-proton collisions at sqrt{s} = 7 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chatrchyan, Serguei; et al.,

2013-12-01

Measurements of the differential and double-differential Drell-Yan cross sections are presented using an integrated luminosity of 4.5(4.8) inverse femtobarns in the dimuon (dielectron) channel of proton-proton collision data recorded with the CMS detector at the LHC at sqrt{s} = 7 TeV. The measured inclusive cross section in the Z-peak region (60-120 GeV) is \\sigma(\\ell \\ell) = 986.4 +/- 0.6 (stat.) +/- 5.9 (exp. syst.) +/- 21.7 (th. syst.) +/- 21.7 (lum.) pb for the combination of the dimuon and dielectron channels. Differential cross sectionsmore » $$d\\sigma/dm$$ for the dimuon, dielectron, and combined channels are measured in the mass range 15 to 1500 GeV and corrected to the full phase space. Results are also presented for the measurement of the double-differential cross section d^2\\sigma/dm d |y| in the dimuon channel over the mass range 20 to 1500 GeV and absolute dimuon rapidity from 0 to 2.4. These measurements are compared to the predictions of perturbative QCD calculations at next-to-leading and next-to-next-to-leading orders using various sets of parton distribution functions.« less

The solvation structure of alprazolam.

PubMed

Sridhar, Akshay; Johnston, Andrew J; Varathan, Luxmmi; McLain, Sylvia E; Biggin, Philip C

2016-08-10

Alprazolam is a benzodiazepine that is commonly prescribed for the treatment of anxiety and other related disorders. Like other benzodiazepines, it is thought to exert its effect through interaction with GABAA receptors. However, it has also been described as a potent and selective protein interaction inhibitor of bromodomain and extra-terminal (BET) proteins. Indeed, the only crystal structure of alprazolam bound to a protein is a complex between alprazolam and the BRD4 bromodomain. The structure shows that the complex also involves many water interactions that mediate contacts between the drug and the protein, a scenario that exists in many drug-protein complexes. How such waters relate to solvation patterns of small molecules may improve our understanding of what dictates their appearance or absence in bridging positions within complexes and thus will be important in terms of future rational drug-design. Here, we use neutron diffraction in conjunction with molecular dynamics simulations to provide a detailed analysis of how water molecules interact with alprazolam in methanol/water mixtures. The agreement between the neutron diffraction and the molecular dynamics is extremely good. We discuss the results in the context of drug design.

Effect of solvation-related interaction on the low-temperature dynamics of proteins

NASA Astrophysics Data System (ADS)

Zuo, Guanghong; Wang, Jun; Qin, Meng; Xue, Bin; Wang, Wei

2010-03-01

The effect of solvation-related interaction on the low-temperature dynamics of proteins is studied by taking into account the desolvation barriers in the interactions of native contacts. It is found out that about the folding transition temperature, the protein folds in a cooperative manner, and the water molecules are expelled from the hydrophobic core at the final stage in the folding process. At low temperature, however, the protein would generally be trapped in many metastable conformations with some water molecules frozen inside the protein. The desolvation takes an important role in these processes. The number of frozen water molecules and that of frozen states of proteins are further analyzed with the methods based on principal component analysis (PCA) and the clustering of conformations. It is found out that both the numbers of frozen water molecules and the frozen states of the protein increase quickly below a certain temperature. Especially, the number of frozen states of the protein increases exponentially following the decrease in the temperature, which resembles the basic features of glassy dynamics. Interestingly, it is observed that the freezing of water molecules and that of protein conformations happen at almost the same temperature. This suggests that the solvation-related interaction performs an important role for the low-temperature dynamics of the model protein.

Necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation

PubMed Central

Vaikuntanathan, Suriyanarayanan; Rotskoff, Grant; Hudson, Alexander; Geissler, Phillip L.

2016-01-01

Modern theories of the hydrophobic effect highlight its dependence on length scale, emphasizing the importance of interfaces in the vicinity of sizable hydrophobes. We recently showed that a faithful treatment of such nanoscale interfaces requires careful attention to the statistics of capillary waves, with significant quantitative implications for the calculation of solvation thermodynamics. Here, we show that a coarse-grained lattice model like that of Chandler [Chandler D (2005) Nature 437(7059):640–647], when informed by this understanding, can capture a broad range of hydrophobic behaviors with striking accuracy. Specifically, we calculate probability distributions for microscopic density fluctuations that agree very well with results of atomistic simulations, even many SDs from the mean and even for probe volumes in highly heterogeneous environments. This accuracy is achieved without adjustment of free parameters, because the model is fully specified by well-known properties of liquid water. As examples of its utility, we compute the free-energy profile for a solute crossing the air–water interface, as well as the thermodynamic cost of evacuating the space between extended nanoscale surfaces. These calculations suggest that a highly reduced model for aqueous solvation can enable efficient multiscale modeling of spatial organization driven by hydrophobic and interfacial forces. PMID:26957607

Registration of pencil beam proton radiography data with X-ray CT.

PubMed

Deffet, Sylvain; Macq, Benoît; Righetto, Roberto; Vander Stappen, François; Farace, Paolo

2017-10-01

Proton radiography seems to be a promising tool for assessing the quality of the stopping power computation in proton therapy. However, range error maps obtained on the basis of proton radiographs are very sensitive to small misalignment between the planning CT and the proton radiography acquisitions. In order to be able to mitigate misalignment in postprocessing, the authors implemented a fast method for registration between pencil proton radiography data obtained with a multilayer ionization chamber (MLIC) and an X-ray CT acquired on a head phantom. The registration was performed by optimizing a cost function which performs a comparison between the acquired data and simulated integral depth-dose curves. Two methodologies were considered, one based on dual orthogonal projections and the other one on a single projection. For each methodology, the robustness of the registration algorithm with respect to three confounding factors (measurement noise, CT calibration errors, and spot spacing) was investigated by testing the accuracy of the method through simulations based on a CT scan of a head phantom. The present registration method showed robust convergence towards the optimal solution. For the level of measurement noise and the uncertainty in the stopping power computation expected in proton radiography using a MLIC, the accuracy appeared to be better than 0.3° for angles and 0.3 mm for translations by use of the appropriate cost function. The spot spacing analysis showed that a spacing larger than the 5 mm used by other authors for the investigation of a MLIC for proton radiography led to results with absolute accuracy better than 0.3° for angles and 1 mm for translations when orthogonal proton radiographs were fed into the algorithm. In the case of a single projection, 6 mm was the largest spot spacing presenting an acceptable registration accuracy. For registration of proton radiography data with X-ray CT, the use of a direct ray-tracing algorithm to compute

Photo-induced water oxidation at the aqueous GaN (101¯0) interface: Deprotonation kinetics of the first proton-coupled electron-transfer step

DOE PAGES

Ertem, Mehmed Z.; Kharche, Neerav; Batista, Victor S.; ...

2015-03-12

Photoeclectrochemical water splitting plays a key role in a promising path to the carbon-neutral generation of solar fuels. Wurzite GaN and its alloys ( e.g., GaN/ZnO and InGaN) are demonstrated photocatalysts for water oxidation, and they can drive the overall water splitting reaction when coupled with co-catalysts for proton reduction. In the present work, we investigate the water oxidation mechanism on the prototypical GaN (101¯0) surface using a combined ab initio molecular dynamics and molecular cluster model approach taking into account the role of water dissociation and hydrogen bonding within the first solvation shell of the hydroxylated surface. The investigationmore » of free-energy changes for the four proton-coupled electron-transfer (PCET) steps of the water oxidation mechanism shows that the first PCET step for the conversion of –Ga-OH to –Ga-O˙⁻ requires the highest energy input. We further examine the sequential PCETs, with the proton transfer (PT) following the electron transfer (ET), and find that photo-generated holes localize on surface –NH sites is thermodynamically more favorable than –OH sites. However, proton transfer from –OH sites with subsequent localization of holes on oxygen atoms is kinetically favored owing to hydrogen bonding interactions at the GaN (101¯0)–water interface. We find that the deprotonation of surface –OH sites is the limiting factor for the generation of reactive oxyl radical ion intermediates and consequently for water oxidation.« less

Chiral aldehydes in hydrocarbons: diastereoselective nucleophilic addition, NMR, and CD spectroscopy reveal dynamic solvation effects.

PubMed

Cainelli, Gianfranco; Galletti, Paola; Pieraccini, Silvia; Quintavalla, Arianna; Giacomini, Daria; Piero Spada, Gian

2004-01-01

Temperature-dependent studies on the diastereoselective nucleophilic addition of n- BuLi to alpha-chiral aldehydes as (S)-O-(t-butyl-dimethylsilyl)lactal, (S)-O-(t-butyl-dimethylsilyl) mandelic aldehyde, and (R)-2-phenylpropanal in n-decane and n-dodecane reveal dynamic solvation phenomena with the presence of inversion temperatures (T(inv)) in the Eyring plots of ln (anti/syn) vs. 1/ T. These dynamic solvent effects were disclosed by temperature-dependent studies of the (13)C NMR, CD, and UV spectra of the starting aldehydes in solution of n-decane and n-dodecane. The concomitant presence of three peculiar temperatures T(CD), T(UV), and T(NMR), whose values are identical and match T(inv), clearly confirms our earlier interpretation of the solvent-dependent nature of T(inv). The inversion temperature, as well as T(CD), T(UV), and T(NMR) represents the interconversion temperature of two different solvation clusters which act as two different supramolecules with different stereoselectivities. Copyright 2003 Wiley-Liss, Inc.

20 CFR 404.1205 - Absolute coverage groups.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 20 Employees' Benefits 2 2014-04-01 2014-04-01 false Absolute coverage groups. 404.1205 Section... INSURANCE (1950- ) Coverage of Employees of State and Local Governments What Groups of Employees May Be Covered § 404.1205 Absolute coverage groups. (a) General. An absolute coverage group is a permanent...

20 CFR 404.1205 - Absolute coverage groups.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 20 Employees' Benefits 2 2013-04-01 2013-04-01 false Absolute coverage groups. 404.1205 Section... INSURANCE (1950- ) Coverage of Employees of State and Local Governments What Groups of Employees May Be Covered § 404.1205 Absolute coverage groups. (a) General. An absolute coverage group is a permanent...

20 CFR 404.1205 - Absolute coverage groups.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 20 Employees' Benefits 2 2012-04-01 2012-04-01 false Absolute coverage groups. 404.1205 Section... INSURANCE (1950- ) Coverage of Employees of State and Local Governments What Groups of Employees May Be Covered § 404.1205 Absolute coverage groups. (a) General. An absolute coverage group is a permanent...

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

PubMed

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.

PubMed

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.

Crystal structure and habit of dirithromycin acetone solvate: A combined experimental and simulative study

NASA Astrophysics Data System (ADS)

Yi, Qinhua; Chen, Jianfeng; Le, Yuan; Wang, Jiexin; Xue, Chunyu; Zhao, Hong

2013-06-01

Dirithromycin (DIR) was crystallized from acetone solvent in the form of an acetone solvate. Its crystal structure belongs to monoclinic, space group P21, with the unit cell parameters a=14.688(3) Å, b=11.6120(12) Å, c=14.9129(12) Å, β=94.794(10)°, and Z=2. Results of X-ray diffraction (XRD) and thermogravimetry-differential scanning calorimetry (TG-DSC) indicated that the solvent molecules could enter the crystal lattice and thus the solvate is formed. The molecular dynamics (MD) simulation method was applied to study the solvent effect. It revealed that the relative growth rates of the main crystal habit faces changed a lot, which made the most morphologically important habit face shift from (001) face to (100) face due to polar groups or atoms exposure and hence a large solvent interaction. The prism habit predicted by a modified attachment energy (AE) model agreed well with the observed experimental morphology grown from the acetone solution. This prediction method may help for a solvent selection to improve the morphology in the drug crystallization process.

On the Basicity of 8-Phenylsulfanyl Quipazine Derivatives: New Potential Serotonergic Agents.

PubMed

Pieńko, T; Taciak, P P; Mazurek, A P

2015-07-09

A protonation state of serotonergic ligands plays a crucial role in their pharmacological activity. In this research, the basicity of 8-phenylsulfanyl quipazine derivatives as new potential serotonergic agents was studied. The most favorable protonation sites were determined in the gas and aqueous phases. In water, a solvation effect promoting the protonation of the N3 atom overcomes a positive charge delocalization phenomenon favoring a N1 atom protonation. The most stable conformations of neutral and protonated molecules in gas and water were found. It was demonstrated that a diprotonation reaction may occur. The most favorable among the diprotonated structures is the molecule with the N1 and N3 atoms protonated. A calculation of the pKa and pKa2 in water of a set of monosubstituted 8-phenylsulfanyl quipazine derivatives was performed using B3LYP/6-31G(d) and the SMD continuum solvation model. Enthalpic and entropic contributions to the pKa and pKa2 in gas and water were separated for a rationalization of a substituent effect on values of the pKa and pKa2. The relationship of the proton affinity and the solvation enthalpy in water with some reactivity descriptors, such as the Fukui function, the molecular electrostatic potential (MEP), and the global softness, was investigated. The order of the pKa values is the most controlled by the entropy. The diprotonation reaction, despite having an unfavorable enthalpy in water, is driven entropically. Final state effects in the diprotonated species were analyzed with the triadic formula. Results of a calculation of the theoretical basicity of the 8-phenylsulfanyl quipazines indicate that they should be monoprotonated on the N3 atom in the CNS environment. Diprotonation of the studied compounds may occur in very acidic body fluids such as the gastric juice.

Joint Estimation of Cardiac Toxicity and Recurrence Risks After Comprehensive Nodal Photon Versus Proton Therapy for Breast Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stick, Line B., E-mail: line.bjerregaard.stick@regionh.dk; Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen; Yu, Jen

Purpose: The study aims to perform joint estimation of the risk of recurrence caused by inadequate radiation dose coverage of lymph node targets and the risk of cardiac toxicity caused by radiation exposure to the heart. Delivered photon plans are compared with realistic proton plans, thereby providing evidence-based estimates of the heterogeneity of treatment effects in consecutive cases for the 2 radiation treatment modalities. Methods and Materials: Forty-one patients referred for postlumpectomy comprehensive nodal photon irradiation for left-sided breast cancer were included. Comparative proton plans were optimized by a spot scanning technique with single-field optimization from 2 en face beams.more » Cardiotoxicity risk was estimated with the model of Darby et al, and risk of recurrence following a compromise of lymph node coverage was estimated by a linear dose-response model fitted to the recurrence data from the recently published EORTC (European Organisation for Research and Treatment of Cancer) 22922/10925 and NCIC-CTG (National Cancer Institute of Canada Clinical Trials Group) MA.20 randomized controlled trials. Results: Excess absolute risk of cardiac morbidity was small with photon therapy at an attained age of 80 years, with median values of 1.0% (range, 0.2%-2.9%) and 0.5% (range, 0.03%-1.0%) with and without cardiac risk factors, respectively, but even lower with proton therapy (0.13% [range, 0.02%-0.5%] and 0.06% [range, 0.004%-0.3%], respectively). The median estimated excess absolute risk of breast cancer recurrence after 10 years was 0.10% (range, 0.0%-0.9%) with photons and 0.02% (range, 0.0%-0.07%) with protons. The association between age of the patient and benefit from proton therapy was weak, almost non-existing (Spearman rank correlations of −0.15 and −0.30 with and without cardiac risk factors, respectively). Conclusions: Modern photon therapy yields limited risk of cardiac toxicity in most patients, but proton therapy can reduce

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baer, Marcel D.; Mundy, Christopher J.

2016-03-03

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

Variance computations for functional of absolute risk estimates.

PubMed

Pfeiffer, R M; Petracci, E

2011-07-01

We present a simple influence function based approach to compute the variances of estimates of absolute risk and functions of absolute risk. We apply this approach to criteria that assess the impact of changes in the risk factor distribution on absolute risk for an individual and at the population level. As an illustration we use an absolute risk prediction model for breast cancer that includes modifiable risk factors in addition to standard breast cancer risk factors. Influence function based variance estimates for absolute risk and the criteria are compared to bootstrap variance estimates.

Variance computations for functional of absolute risk estimates

PubMed Central

Pfeiffer, R.M.; Petracci, E.

2011-01-01

We present a simple influence function based approach to compute the variances of estimates of absolute risk and functions of absolute risk. We apply this approach to criteria that assess the impact of changes in the risk factor distribution on absolute risk for an individual and at the population level. As an illustration we use an absolute risk prediction model for breast cancer that includes modifiable risk factors in addition to standard breast cancer risk factors. Influence function based variance estimates for absolute risk and the criteria are compared to bootstrap variance estimates. PMID:21643476

Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

PubMed

Chakravorty, Arghya; Jia, Zhe; Li, Lin; Zhao, Shan; Alexov, Emil

2018-02-13

Typically, the ensemble average polar component of solvation energy (ΔG polar solv ) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG polar solv ) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG polar solv (⟨ΔG polar solv ⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.

Design, performance, and calculated error of a Faraday cup for absolute beam current measurements of 600-MeV protons

NASA Technical Reports Server (NTRS)

Beck, S. M.

1975-01-01

A mobile self-contained Faraday cup system for beam current measurments of nominal 600 MeV protons was designed, constructed, and used at the NASA Space Radiation Effects Laboratory. The cup is of reentrant design with a length of 106.7 cm and an outside diameter of 20.32 cm. The inner diameter is 15.24 cm and the base thickness is 30.48 cm. The primary absorber is commercially available lead hermetically sealed in a 0.32-cm-thick copper jacket. Several possible systematic errors in using the cup are evaluated. The largest source of error arises from high-energy electrons which are ejected from the entrance window and enter the cup. A total systematic error of -0.83 percent is calculated to be the decrease from the true current value. From data obtained in calibrating helium-filled ion chambers with the Faraday cup, the mean energy required to produce one ion pair in helium is found to be 30.76 + or - 0.95 eV for nominal 600 MeV protons. This value agrees well, within experimental error, with reported values of 29.9 eV and 30.2 eV.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dibya, Pooja Arora

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 themore » 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

Halo structure of 8B determined from intermediate energy proton elastic scattering in inverse kinematics

NASA Astrophysics Data System (ADS)

Korolev, G. A.; Dobrovolsky, A. V.; Inglessi, A. G.; Alkhazov, G. D.; Egelhof, P.; Estradé, A.; Dillmann, I.; Farinon, F.; Geissel, H.; Ilieva, S.; Ke, Y.; Khanzadeev, A. V.; Kiselev, O. A.; Kurcewicz, J.; Le, X. C.; Litvinov, Yu. A.; Petrov, G. E.; Prochazka, A.; Scheidenberger, C.; Sergeev, L. O.; Simon, H.; Takechi, M.; Tang, S.; Volkov, V.; Vorobyov, A. A.; Weick, H.; Yatsoura, V. I.

2018-05-01

The absolute differential cross section for small-angle proton elastic scattering on the proton-rich 8B nucleus has been measured in inverse kinematics for the first time. The experiment was performed using a secondary radioactive beam with an energy of 0.7 GeV/u at GSI, Darmstadt. The active target, namely hydrogen-filled time projection ionization chamber IKAR, was used to measure the energy, angle and vertex point of the recoil protons. The scattering angle of the projectiles was simultaneously determined by the tracking detectors. The measured differential cross section is analyzed on the basis of the Glauber multiple scattering theory using phenomenological nuclear-density distributions with two free parameters. The radial density distribution deduced for 8B exhibits a halo structure with the root-mean-square (rms) matter radius Rm = 2.58 (6) fm and the rms halo radius Rh = 4.24 (25) fm. The results on 8B are compared to those on the mirror nucleus 8Li investigated earlier by the same method. A comparison is also made with previous experimental results and theoretical predictions for both nuclei.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu; Mewes, Jan-Michael

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 failsmore » 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.« less

Formation of solvate structures by the ortho-, meta-, and para-isomers of hydroxybenzoic acid in supercritical fluid

NASA Astrophysics Data System (ADS)

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

2017-04-01

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid ( o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm3 and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.

Optimization of Pore Structure of Cathodic Carbon Supports for Solvate Ionic Liquid Electrolytes Based Lithium-Sulfur Batteries.

PubMed

Zhang, Shiguo; Ikoma, Ai; Li, Zhe; Ueno, Kazuhide; Ma, Xiaofeng; Dokko, Kaoru; Watanabe, Masayoshi

2016-10-04

Lithium-sulfur (Li-S) batteries are a promising energy-storage technology owing to their high theoretical capacity and energy density. However, their practical application remains a challenge because of the serve shuttle effect caused by the dissolution of polysulfides in common organic electrolytes. Polysulfide-insoluble electrolytes, such as solvate ionic liquids (ILs), have recently emerged as alternative candidates and shown great potential in suppressing the shuttle effect and improving the cycle stability of Li-S batteries. Redox electrochemical reactions in polysulfide-insoluble electrolytes occur via a solid-state process at the interphase between the electrolyte and the composite cathode; therefore, creating an appropriate interface between sulfur and a carbon support is of great importance. Nevertheless, the porous carbon supports established for conventional organic electrolytes may not be suitable for polysulfide-insoluble electrolytes. In this work, we investigated the effect of the porous structure of carbon materials on the Li-S battery performance in polysulfide-insoluble electrolytes using solvate ILs as a model electrolyte. We determined that the pore volume (rather than the surface area) exerts a major influence on the discharge capacity of S composite cathodes. In particular, inverse opal carbons with three-dimensionally ordered interconnected macropores and a large pore volume deliver the highest discharge capacity. The battery performance in both polysulfide-soluble electrolytes and solvate ILs was used to study the effect of electrolytes. We propose a plausible mechanism to explain the different porous structure requirements in polysulfide-soluble and polysulfide-insoluble electrolytes.

Proton Radiography Imager:Generates Synthetic Proton Radiographs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilks, Scott C.; Black, Mason R.

ProRad is a computer program that is used to generate synthetic images of proton (or other charged particles) radiographs. The proton radiographs arc images that arc obtained by sending energetic protons (or electrons or positrons, for example) through 11 plasma where electric and/or magnetic fields alter the particles trajectory, Dnd the variations me imaged on RC film, image plate, or equivalent

Absolute Summ

NASA Astrophysics Data System (ADS)

Phillips, Alfred, Jr.

Summ means the entirety of the multiverse. It seems clear, from the inflation theories of A. Guth and others, that the creation of many universes is plausible. We argue that Absolute cosmological ideas, not unlike those of I. Newton, may be consistent with dynamic multiverse creations. As suggested in W. Heisenberg's uncertainty principle, and with the Anthropic Principle defended by S. Hawking, et al., human consciousness, buttressed by findings of neuroscience, may have to be considered in our models. Predictability, as A. Einstein realized with Invariants and General Relativity, may be required for new ideas to be part of physics. We present here a two postulate model geared to an Absolute Summ. The seedbed of this work is part of Akhnaton's philosophy (see S. Freud, Moses and Monotheism). Most important, however, is that the structure of human consciousness, manifest in Kenya's Rift Valley 200,000 years ago as Homo sapiens, who were the culmination of the six million year co-creation process of Hominins and Nature in Africa, allows us to do the physics that we do. .

Water network-mediated, electron-induced proton transfer in [C5H5N ṡ (H2O)n]- clusters

NASA Astrophysics Data System (ADS)

DeBlase, Andrew F.; Wolke, Conrad T.; Weddle, Gary H.; Archer, Kaye A.; Jordan, Kenneth D.; Kelly, John T.; Tschumper, Gregory S.; Hammer, Nathan I.; Johnson, Mark A.

2015-10-01

The role of proton-assisted charge accommodation in electron capture by a heterocyclic electron scavenger is investigated through theoretical analysis of the vibrational spectra of cold, gas phase [Py ṡ (H2O)n=3-5]- clusters. These radical anions are formed when an excess electron is attached to water clusters containing a single pyridine (Py) molecule in a supersonic jet ion source. Under these conditions, the cluster ion distribution starts promptly at n = 3, and the photoelectron spectra, combined with vibrational predissociation spectra of the Ar-tagged anions, establish that for n > 3, these species are best described as hydrated hydroxide ions with the neutral pyridinium radical, PyH(0), occupying one of the primary solvation sites of the OH-. The n = 3 cluster appears to be a special case where charge localization on Py and hydroxide is nearly isoenergetic, and the nature of this species is explored with ab initio molecular dynamics calculations of the trajectories that start from metastable arrangements of the anion based on a diffuse, essentially dipole-bound electron. These calculations indicate that the reaction proceeds via a relatively slow rearrangement of the water network to create a favorable hydration configuration around the water molecule that eventually donates a proton to the Py nitrogen atom to yield the product hydroxide ion. The correlation between the degree of excess charge localization and the evolving shape of the water network revealed by this approach thus provides a microscopic picture of the "solvent coordinate" at the heart of a prototypical proton-coupled electron transfer reaction.

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