Journal articles: 'Solvation entropies'

1

Golden, Sidney, and Thomas R. Tuttle. "Entropies of solvation of solvated electrons." Journal of Physical Chemistry 95, no. 10 (May 1991): 4109–13. http://dx.doi.org/10.1021/j100163a039.

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2

Waibl, Franz, Johannes Kraml, Monica L. Fernández-Quintero, Johannes R. Loeffler, and Klaus R. Liedl. "Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures." Journal of Computer-Aided Molecular Design 36, no. 2 (January 15, 2022): 101–16. http://dx.doi.org/10.1007/s10822-021-00429-y.

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AbstractHydration thermodynamics play a fundamental role in fields ranging from the pharmaceutical industry to environmental research. Numerous methods exist to predict solvation thermodynamics of compounds ranging from small molecules to large biomolecules. Arguably the most precise methods are those based on molecular dynamics (MD) simulations in explicit solvent. One theory that has seen increased use is inhomogeneous solvation theory (IST). However, while many applications require accurate description of salt–water mixtures, no implementation of IST is currently able to estimate solvation properties involving more than one solvent species. Here, we present an extension to grid inhomogeneous solvation theory (GIST) that can take salt contributions into account. At the example of carbazole in 1 M NaCl solution, we compute the solvation energy as well as first and second order entropies. While the effect of the first order ion entropy is small, both the water–water and water–ion entropies contribute strongly. We show that the water–ion entropies are efficiently approximated using the Kirkwood superposition approximation. However, this approach cannot be applied to the water–water entropy. Furthermore, we test the quantitative validity of our method by computing salting-out coefficients and comparing them to experimental data. We find a good correlation to experimental salting-out constants, while the absolute values are overpredicted due to the approximate second order entropy. Since ions are frequently used in MD, either to neutralize the system or as a part of the investigated process, our method greatly extends the applicability of GIST. The use-cases range from biopharmaceuticals, where many assays require high salt concentrations, to environmental research, where solubility in sea water is important to model the fate of organic substances.

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3

Marcus, Y. "The solvation number of ions obtained from their entropies of solvation." Journal of Solution Chemistry 15, no. 4 (April 1986): 291–306. http://dx.doi.org/10.1007/bf00648884.

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4

Irwin, Benedict W. J., and David J. Huggins. "On the accuracy of one- and two-particle solvation entropies." Journal of Chemical Physics 146, no. 19 (May 21, 2017): 194111. http://dx.doi.org/10.1063/1.4983654.

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5

Abe, Takehiro. "Theoretical Estimation of the Entropies of Solvation of Univalent Ions." Bulletin of the Chemical Society of Japan 64, no. 9 (September 1991): 2844–45. http://dx.doi.org/10.1246/bcsj.64.2844.

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6

Hefter, Glenn. "Ion solvation in aqueous–organic mixtures." Pure and Applied Chemistry 77, no. 3 (January 1, 2005): 605–17. http://dx.doi.org/10.1351/pac200577030605.

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The importance of ion solvation in determining the properties of electrolyte solutions in aqueous–organic solvent mixtures is discussed. Solubility measurements are shown to be particularly useful for determining the Gibbs energies of transfer of ions between solvents, which reflect differences in the overall solvation of the ions in different solvent mixtures. Solubility measurements can also be used to determine the other thermodynamic parameters of transfer, but such quantities are usually better obtained by more direct methods. The inadequacy of current theories of ion solvation to quantitatively account for the thermodynamics of ion transfer is discussed by reference to measurements on some simple model systems. Although donor/acceptor interactions can explain many of the observed effects between pure solvents, the situation is more complex in aqueous–organic mixtures because selective solvation and even solvent–solvent interactions may become significant. This is illustrated by consideration of ion transfer from water to water + t-butanol solutions, where spectacular effects are observed in the enthalpies and entropies and especially in the heat capacities and volumes.

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7

Reinhard, Friedemann, and Helmut Grubmüller. "Estimation of absolute solvent and solvation shell entropies via permutation reduction." Journal of Chemical Physics 126, no. 1 (January 7, 2007): 014102. http://dx.doi.org/10.1063/1.2400220.

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8

Singh, Nidhi, and Arieh Warshel. "Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects." Journal of Physical Chemistry B 113, no. 20 (May 21, 2009): 7372–82. http://dx.doi.org/10.1021/jp811063v.

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9

Ashbaugh, Henry S. "Assessment of scaled particle theory predictions of the convergence of solvation entropies." Fluid Phase Equilibria 530 (February 2021): 112885. http://dx.doi.org/10.1016/j.fluid.2020.112885.

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Heinz, Leonard P., and Helmut Grubmüller. "Calculation of Absolute Solvation Shell Entropies from MD Trajectories via Permutation Reduction." Biophysical Journal 114, no. 3 (February 2018): 677a. http://dx.doi.org/10.1016/j.bpj.2017.11.3652.

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11

Duignan, Timothy T., Drew F. Parsons, and Barry W. Ninham. "A Continuum Solvent Model of the Partial Molar Volumes and Entropies of Ionic Solvation." Journal of Physical Chemistry B 118, no. 11 (March 5, 2014): 3122–32. http://dx.doi.org/10.1021/jp410956m.

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12

Solis, JS, PM May, and G. Hefter. "Cyanide Thermodynamics. III. Enthalpies and Entropies of Ionization of Water and Hydrogen Cyanide." Australian Journal of Chemistry 49, no. 6 (1996): 651. http://dx.doi.org/10.1071/ch9960651.

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The heats (enthalpy changes) associated with the ionization of water and of hydrogen cyanide have been determined by titration calorimetry at 25�C as a function of ionic strength up to 5 M in both NaCl and NaClO4 media. The enthalpy changes for both reactions exhibit a 'medium effect' with ?H being more positive in NaCl than in NaClO4 and with the difference becoming more pronounced with increasing ionic strength. This is attributed to the greater solvation of Cl- cf. CN- in aqueous solution. The present ?H values are similar to previous published results at high ionic strengths, and are in excellent agreement with the well established literature values at infinite dilution. The present ?H values were combined with literature stability constant data to calculate the corresponding entropies for the ionization of H2O and HCN as a function of ionic strength.

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13

Hefter, GT, and PJ Mclay. "Solvation of Fluoride Ions. II. Enthalpies and Entropies of Transfer From Water to Aqueous Methanol." Australian Journal of Chemistry 41, no. 12 (1988): 1971. http://dx.doi.org/10.1071/ch9881971.

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Enthalpies of transfer of potassium fluoride from water to water-methanol mixtures over the whole composition range have been determined by calorimetry. Combination of these values with literature data has enabled calculation of the enthalpies and entropies of transfer for the individual ions through the tetraphenylarsonium tetrapbenylborate ( tatb ) assumption. The values of ΔtH°(F-) and ΔtS°(F-) show a complex dependence on solvent composition which closely parallels the dependence of the other halide ions. These effects are discussed in terms of ion-solvent and solvent-solvent interactions. The halide ions appear to be (weakly) preferentially solvated by H2O, and the alkali metal ions by MeOH.

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14

Glover, Stephen A., and Meredith Adams. "Reaction of N-Acyloxy-N-alkoxyamides with Biological Thiol Groups." Australian Journal of Chemistry 64, no. 4 (2011): 443. http://dx.doi.org/10.1071/ch10470.

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Mutagenic N-acyloxy-N-alkoxyamides 1 react with thiols by an SN2 process at nitrogen with displacement of carboxylate. They react with glutathione 4 in [D6]DMSO/D2O and methyl and ethyl esters of cysteine hydrochloride, 11 and 12, in [D4]methanol but the intermediate N-alkoxy-N-(alkylthio)amides undergo a rapid substitution reaction at sulfur by a second thiol molecule to give hydroxamic esters and disulfides. Arrhenius activation energies and entropies of activation obtained for a series of different N-benzyloxy-N-(4-substitutedbenzoyloxy)benzamides 13–17 were similar to those found for the SN2 reaction of the same series with N-methylaniline. Entropies of activation were strongly negative in keeping with polar separation and attendant solvation in the transition state, and in keeping with this, bimolecular reaction rate constants at 298 K correlated with Hammett σ constants with a positive ρ-value of 1.1. The structure of model N-methoxy-N-(methylthio)acetamide has been computed at the B3LYP/6–31G(d) level and exhibits properties atypical of other anomeric amides with more electronegative atoms at nitrogen. Relative to N,N-bisoxyl substitution, the combination of a sulfur and an oxygen atom at the amide nitrogen results in a relatively small reduction in amide resonance.

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15

Salem, Shereen E., Esam A. Gomaa, Mohamed M. El-Defrawy, and Noha M. Ebrahem. "Studies on the Complexation of Succinic Hydrazide with Copper Chloride Salt." European Journal of Advanced Chemistry Research 2, no. 1 (February 11, 2021): 14–20. http://dx.doi.org/10.24018/ejchem.2021.2.1.40.

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The electrochemical behavior of the complexation between copper chloride salt and succinic hydrazide can be explained using cyclic voltammetric measurements. The complex is formed through the interaction with nitrogen and hydroxyl group or carbonyl group of succinic hydrazides. This interaction can be observed by decreasing in the height peak of current and measuring the (anodic/cathodic) shift of the potentials. All the solvation and thermodynamic parameters for the interaction of copper ions with succinic hydrazide as stability constant, Gibbs free energies, enthalpies and entropies of interaction were calculated. Finally, the activity of the formed complex was compared with the succinic hydrazide by comparing their effects on different types of gram-negative bacteria and fungi indicating high activity of the formed complex and its ability to be used in different medical applications.

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16

de Namor, Angela F. Danil. "Linear correlation between entropies of complexation of cryptand 222 with metal ions in non-aqueous solvents and entropies of solvation of these ions in these solvents." Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases 84, no. 7 (1988): 2441. http://dx.doi.org/10.1039/f19888402441.

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17

de Namor, Angela F. Danil, and Franz Fernandez Salazar. "Thermodynamic parameters for the complexation process between metal(I) cations and dibenzocryptand 222 in dipolar, aprotic solvents. Linear correlation between entropies of complexation and entropies of solvation of cations." Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases 84, no. 10 (1988): 3539. http://dx.doi.org/10.1039/f19888403539.

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18

Florián, Jan, and Arieh Warshel. "Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model." Journal of Physical Chemistry B 103, no. 46 (November 1999): 10282–88. http://dx.doi.org/10.1021/jp992041r.

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19

Reif, Maria M., and Philippe H. Hünenberger. "Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions." Journal of Chemical Physics 134, no. 14 (April 14, 2011): 144103. http://dx.doi.org/10.1063/1.3567020.

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20

Menezes, Filipe, and Grzegorz Maria Popowicz. "How to Catch the Ball: Fullerene Binding to the Corannulene Pincer." Molecules 27, no. 12 (June 15, 2022): 3838. http://dx.doi.org/10.3390/molecules27123838.

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The corannulene pincer (also known in the literature as the buckycatcher) is a fascinating system that may encapsulate, among other molecules, the C60 and C70 fullerenes. These complexes are held together by strong π-stacking interactions. Although these are quantum mechanical effects, their description by quantum chemical methods has proved very hard. We used three semi-empirical methods, PM6-D3H4X, PM6-D3H+ and GFN2-xTB, to model the interactions. Binding to fullerenes was extended to all open conformations of the buckycatcher, and with the proper choice of solvation model and partition functions, we obtained Gibbs free energies of binding that deviated by 1.0–1.5 kcal/mol from the experimental data. Adding three-body dispersion to PM6-D3H+ led to even better agreement. These results agree better with the experimental data than calculations using higher-level methods at a significantly lower fraction of the computational cost. Furthermore, the formation of adducts with C60 was studied using dynamical simulations, which helped to build a more complete picture of the behavior of the corannulene pincer with fullerenes. We also investigated the use of exchange-binding models to recover more information on this system in solution. Though the final Gibbs free energies in solution were worsened, gas-phase enthalpies and entropies better mirrored the experimental data.

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21

Schweitzer-Stenner, Reinhard, Bridget Milorey, and Harald Schwalbe. "Randomizing of Oligopeptide Conformations by Nearest Neighbor Interactions between Amino Acid Residues." Biomolecules 12, no. 5 (May 11, 2022): 684. http://dx.doi.org/10.3390/biom12050684.

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Flory’s random coil model assumes that conformational fluctuations of amino acid residues in unfolded poly(oligo)peptides and proteins are uncorrelated (isolated pair hypothesis, IPH). This implies that conformational energies, entropies and solvation free energies are all additive. Nearly 25 years ago, analyses of coil libraries cast some doubt on this notion, in that they revealed that aromatic, but also β-branched side chains, could change the 3J(HNHCα) coupling of their neighbors. Since then, multiple bioinformatical, computational and experimental studies have revealed that conformational propensities of amino acids in unfolded peptides and proteins depend on their nearest neighbors. We used recently reported and newly obtained Ramachandran plots of tetra- and pentapeptides with non-terminal homo- and heterosequences of amino acid residues to quantitatively determine nearest neighbor coupling between them with a Ising type model. Results reveal that, depending on the choice of amino acid residue pairs, nearest neighbor interactions either stabilize or destabilize pairs of polyproline II and β-strand conformations. This leads to a redistribution of population between these conformations and a reduction in conformational entropy. Interactions between residues in polyproline II and turn(helix)-forming conformations seem to be cooperative in most cases, but the respective interaction parameters are subject to large statistical errors.

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22

Alghaith, Adel F., Wael A. Mahdi, Nazrul Haq, Sultan Alshehri, and Faiyaz Shakeel. "Solubility and Thermodynamic Properties of Febuxostat in Various (PEG 400 + Water) Mixtures." Materials 15, no. 20 (October 19, 2022): 7318. http://dx.doi.org/10.3390/ma15207318.

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The solubility of the poorly soluble medicine febuxostat (FXT) (3) in various {polyethylene glycol 400 (PEG 400) (1) + water (H2O) (2)} mixtures has been examined at 298.2–318.2 K and 101.1 kPa. FXT solubility was measured using an isothermal method and correlated with “van’t Hoff, Apelblat, Buchowski–Ksiazczak λh, Yalkowsky–Roseman, Jouyban–Acree, and Jouyban–Acree-van’t Hoff models”. FXT mole fraction solubility was enhanced via an increase in temperature and PEG 400 mass fraction in {(PEG 400 (1) + H2O (2)} mixtures. Neat PEG 400 showed the highest mole fraction solubility of FXT (3.11 × 10–2 at 318.2 K), while neat H2O had the lowest (1.91 × 10–7 at 298.2 K). The overall error value was less than 6.0% for each computational model, indicating good correlations. Based on the positive values of apparent standard enthalpies (46.72–70.30 kJ mol−1) and apparent standard entropies (106.4–118.5 J mol−1 K−1), the dissolution of FXT was “endothermic and entropy-driven” in all {PEG 400 (1) + H2O (2)} mixtures examined. The main mechanism for FXT solvation in {PEG 400 (1) + H2O (2)} mixtures was discovered to be an enthalpy-driven process. In comparison to FXT-H2O, FXT-PEG 400 showed the strongest molecular interactions. In conclusion, these results suggested that PEG 400 has considerable potential for solubilizing a poorly soluble FXT in H2O.

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23

Nevěčná, Taťjana, Vojtěch Bekárek, and Oldřich Pytela. "A Study of Effects of Temperature and Medium on Reaction of Triethylamine with Ethyl Bromide." Collection of Czechoslovak Chemical Communications 59, no. 6 (1994): 1384–91. http://dx.doi.org/10.1135/cccc19941384.

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The rate constants of reaction of triethylamine with ethyl bromide have been measured in 13 solvents at the temperatures of 293, 313, 333, and 373 K. The activation entropies in the individual solvents increase when going from nonpolar to dipolar aprotic and polar protic solvents, which is explained by dominant solvation of the basic triethylamine and by formation of highly ordered associates without solvent in the activated complex in nonpolar solvent media. No isokinetic relationship has been found between the activation entropy and activation enthalpy, which indicates different solvent effects on the two quantities. The activation enthalpy and entropy of the reaction investigated are close to those of the reaction of triethylamine with ethyl iodide. Three methods have been used to evaluate the effect of medium at all the temperatures, their success being decreased in the order: Pytela's method - Kamlet-Taft - Koppel-Palm. Irrespective of the temperature, all the methods indicate that the reaction is accelerated by the solvent polarity, the significance of other effects being reflected differently depending on the temperature and the correlation equation used. A complex evaluation involving also the interpretation of the entropy and enthalpy components by means of empiric solvent parameters has shown that the resulting Gibbs energy represents a superposition of different effects of solvents on the two thermodynamic quantities, the solvent effect upon the activation entropy being predominant at the higher temperatures.

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24

Ohtsu, Kumiko, Kazuhiko Ozutsumi, Makoto Kurihara, and Takuji Kawashima. "Thermodynamics of Complexation of Sodium Ion with 12-Crown-4 and 18-Crown-6 in Pyridine." Zeitschrift für Naturforschung B 50, no. 4 (April 1, 1995): 529–35. http://dx.doi.org/10.1515/znb-1995-0410.

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The complexation of sodium ion with 1,4,7,10-tetraoxacyclododecane (12-crown-4) and 1,4,7,10,13,16-hexaoxacyclooctadecane (18-crown-6) has been studied by titration calorimetry in pyridine (PY) containing 0.1 mol dm-3 (C2H5)4NClO4 as a constant ionic medium at 25 °C. The calorimetric titration data were well explained in terms of the formation of the [Na(12-crown-4)]+, [Na(12-crown-4)2]+, and [Na(18-crown-6)]+ complexes, and their formation constants, reaction enthalpies, and entropies were determined. The formation of [Na(18-crown-6)]+ is much pronounced in PY over N,N-dimethylformamide (DMF) and water, and the stability order is PY > DMF > water. The enthalpy values for the formation of [Na(18-crown-6)]+ are all negative in PY, DMF, and water, and increase in the order PY < DMF < water. The complexation is the least exothermic in water, though sodium ion is the most weakly solvated in water. This is because 18-crown-6 is much stabilized in water by forming hydrogen bonds with water molecules. Despite the stronger electron pair-donating ability of PY than DMF, the complexation is more exothermic in PY than in DMF. This is ascribed to the different solvation number of the sodium ion in P Y and DMF, i.e., the sodium ion is coordinated with a smaller number of solvent molecules in the former solvent than in the latter.

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25

Maham, Yadollah, and Gordon R. Freeman. "Effect of solvent structure on electron reactivity: 2-propanol/water mixtures." Canadian Journal of Chemistry 66, no. 7 (July 1, 1988): 1706–11. http://dx.doi.org/10.1139/v88-276.

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The reactivity of solvated electrons [Formula: see text] with efficient (nitrobenzene, acetone) and inefficient (phenol, toluene) scavengers is affected greatly by the solvent composition in 2-propanol/water mixed solvents. 2-Propanol is the only secondary alcohol that is completely miscible with water. The variation of the nitrobenzene rate constant k2 with solvent composition displays four viscosity zones, as in primary and tertiary alcohol/water mixtures. In zone (c), where the Stokes–Smoluchowski equation applies, the nitrobenzene k2 values in the secondary alcohol/water mixtures are situated between those in the primary and tertiary alcohols, due to the relative values of the dielectric permittivity ε. The charge–dipole attraction energy varies as ε−1.The two water-rich zones (c) and (d) are characterized by a large change of viscosity η and a small change in [Formula: see text] solvation energy (trap depth) Er; here k2 for all the scavengers correlates with the inverse of the viscosity. In the two alcohol-rich zones (a) and (b) the change of η is small but that of Er is large; here k2 of inefficient scavengers correlates with the inverse of Er, due to the difficulty of electron transfer out of deeper traps. Activation energies E2 and entropies [Formula: see text] also show composition zone behaviour. The value of [Formula: see text] is more negative for less efficient scavengers; E2 varies less and does not correlate with reactivity or Er. Electron transfer from solvent to inefficient scavenger is driven by solvent rearrangement around the reaction center, reflected in [Formula: see text].

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26

Inada, Y., Y. Tsutsui, H. Wasada, and S. Funahashi. "Solvation Structure of Solvated Cu(I) Ions in Non-Aqueous Solvents as Studied by EXAFS and ab initio Molecular Orbital Methods." Zeitschrift für Naturforschung B 54, no. 2 (February 1, 1999): 193–99. http://dx.doi.org/10.1515/znb-1999-0207.

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The structure parameters around the Cu(I) ion in pyridine (PY), 4-methylpyridine (4MPY), 2-methylpyridine (2MPY), 2,6-dimethylpyridine (26DMPY), and acetonitrile (AN) were determined by the extended X-ray absorption fine structure (EXAFS) method. The solvation structures of the Cu(I) ion in PY, 4MPY, and AN are 4-coordinate tetrahedral with Cu-N bond lengths of 205, 205, and 200 pm, respectively. In the case of 2MPY and 26DMPY, the Cu(I) ion has a 3-coordinate triangular structure with a Cu-N bond length of 201 pm. Such a decrease in the coordination number was interpreted in terms of the bulkiness of the solvent molecules. In order to clarify the most stable solvation structure of the Cu(I) ion, we carried out ab initio molecular orbital calculations for the solvation system of [Cu(NCH)n]+ (n = 1 - 6 ) where the steric effect is negligible. The Gibbs free energy of solvation was the smallest in the case of n = 4 and the 4-coordinate tetrahedral solvation of the Cu(I) ion was theoretically evaluated as most stable. The enthalpy of solvation monotonously decreases with increasing n, while the entropy of solvation proportionally increases. Although a larger gain of enthalpy is observed for the octahedral structure rather than the tetrahedral one, the entropic loss for the former overcomes the enthalpic gain.

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27

Giesen, David J., Christopher J. Cramer, and Donald G. Truhlar. "Entropic Contributions to Free Energies of Solvation." Journal of Physical Chemistry 98, no. 15 (April 1994): 4141–47. http://dx.doi.org/10.1021/j100066a038.

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28

Mikheev, Yu A., and G. E. Zaikov. "The Entropic Mechanism of Water Solvation of Polymers." International Journal of Polymeric Materials and Polymeric Biomaterials 46, no. 3-4 (July 2000): 511–32. http://dx.doi.org/10.1080/00914030008033893.

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Mikheev, Yu A., and G. E. Zaikov. "The Entropic Mechanism of Water Solvation by Polymers." Polymers and Polymer Composites 9, no. 1 (January 2001): 51–61. http://dx.doi.org/10.1177/096739110100900107.

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30

Mukadam, A. A., and A. L. L. East. "Challenges in predicting Δ_rxnG in solution: The chelate effect." Journal of Chemical Physics 157, no. 3 (July 21, 2022): 034109. http://dx.doi.org/10.1063/5.0097291.

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Gibbs energies for reactions involving aqueous ions are challenging to predict due to the large solvation energies of such ions. A stringent test would be the ab initio reproduction of the aqueous-phase chelate effect, an entropic effect in reactions of very small enthalpy changes. This paper examines what is required to achieve such a reproduction for the paradigmatic reaction M(NH3)42+ + 2 en → M( en)22+ + 4 NH3 ( en = 1,2-ethylenediamine), for which ΔrxnG* and ΔrxnH* are −2.3 and +1.6 kcal mol−1, respectively, if M = Zn. Explicit solvation via simulation was avoided in order to allow sufficiently accurate electronic structure models; this required the use of continuum solvation models (CSMs), and a great deal of effort was made in attempting to lower the relative errors of ΔsolvG*[M(NH3)42+] vs ΔsolvG*[M( en)22+] from the CSMs available in Gaussian software. CSMs in ADF and JDFTx software were also tested. A uniform 2.2 kcal mol−1 accuracy in ΔrxnG* for all three metal-atom choices M = {Zn, Cd, Hg} was eventually achieved, but not from any of the known CSMs tested, nor from cavity size reoptimization, nor from semicontinuum modeling: post facto solvation energy corrections [one per solute type, NH3, en, M(NH3)42+, M( en)22+] were needed. It is hoped that this study will aid (and encourage) further CSM development for coordination-complex ions.

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Hou, Kevin J., and Jian Qin. "Solvation and Entropic Regimes in Ion-Containing Block Copolymers." Macromolecules 51, no. 19 (September 17, 2018): 7463–75. http://dx.doi.org/10.1021/acs.macromol.8b01616.

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32

ZHAN, JIN-HUI, XI ZHAO, XU-RI HUANG, and CHIA-CHUNG SUN. "INTERACTIONS BETWEEN HUMAN SLINGSHOT PHOSPHATASE 2 AND PHOSPHO-COFILIN: A MOLECULAR DYNAMICS STUDY." Journal of Theoretical and Computational Chemistry 08, no. 02 (April 2009): 233–50. http://dx.doi.org/10.1142/s0219633609004770.

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Human slingshot phosphatase 2 (SSH2) is one of the dual specificity protein tyrosine phosphatases, which can activate cofilin substrate by binding its phosphorylation state. Because the interaction model of SSH2 and phospho-cofilin (P-cofilin) was unknown, we obtained the complex through macromolecular docking method. The molecular dynamics studies were used to investigate the complex dynamics in an aqueous solution. To understand the binding specificity, the free energy was calculated with the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) approach and the interaction mode in active site was analyzed. The results indicated that the interaction of the P-loop of SSH2 with phosphoserine of human P-cofilin was stabilized by molecular mechanics energy and nonpolar solvation energy components, while polar solvation energy and the entropic contributions were unfavorable for the combination of the two proteins. In addition, the electrostatic contributions were negative for the formation of the complex on the whole, but seen from the active local, the Coulomb interaction between the phosphoserine and the P-loop residues could play an important role in determining substrate specificity.

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33

Tundo, Pietro, Fabio Aricò, Anthony E. Rosamilia, Maurizio Rigo, Andrea Maranzana, and Glauco Tonachini. "Reaction of dialkyl carbonates with alcohols: Defining a scale of the best leaving and entering groups." Pure and Applied Chemistry 81, no. 11 (October 31, 2009): 1971–79. http://dx.doi.org/10.1351/pac-con-08-12-02.

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A series of dialkyl and methyl alkyl carbonates has been synthesized and their reactivity investigated. The behavior of preferential leaving and entering groups for the newly synthesized carbonates has been accurately investigated. Both experimental and computational studies agreed that the scale of leaving groups follows the trend: PhCH2O–, MeO– ≥ EtO–, CH3(CH2)2O–, CH3(CH2)7O– > (CH3)2CHO– > (CH3)3CO–. Accordingly, the scale of the entering group has the same trend, with t-butoxide being the worst entering group. A preliminary attempt to rationalize the nucleofugality trends, limited to the (CH3)3CO– and CH3O– groups, has indicated that a likely origin of the observed trends lies in the different entropic contributions and solvation effects.

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34

Goethe, Martin, Ignacio Fita, and J. Rubi. "Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen." Entropy 20, no. 8 (August 7, 2018): 580. http://dx.doi.org/10.3390/e20080580.

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Popcoen is a method for configurational entropy estimation of proteins based on machine-learning. Entropy is predicted with an artificial neural network which was trained on simulation trajectories of a large set of representative proteins. Popcoen is extremely fast compared to other approaches based on the sampling of a multitude of microstates. Consequently, Popcoen can be incorporated into a large class of protein software which currently neglects configurational entropy for performance reasons. Here, we apply Popcoen to various conformations of the Cas4 protein SSO0001 of Sulfolobus solfataricus, a protein that assembles to a decamer of known toroidal shape. We provide numerical evidence that the native state (NAT) of a SSO0001 monomer has a similar structure to the protomers of the oligomer, where NAT of the monomer is stabilized mainly entropically. Due to its large amount of configurational entropy, NAT has lower free energy than alternative conformations of very low enthalpy and solvation free-energy. Hence, SSO0001 serves as an example case where neglecting configurational entropy leads to incorrect conclusion. Our results imply that no refolding of the subunits is required during oligomerization which suggests that configurational entropy is employed by nature to largely enhance the rate of assembly.

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Pizio and Sokolowski. "Entropic solvation force between surfaces modified by grafted chains: a density functional approach." Condensed Matter Physics 13, no. 1 (2010): 13602. http://dx.doi.org/10.5488/cmp.13.13602.

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Das, Bedamati, and Hagai Meirovitch. "Solvation parameters for predicting the structure of surface loops in proteins: Transferability and entropic effects." Proteins: Structure, Function, and Genetics 51, no. 3 (May 15, 2003): 470–83. http://dx.doi.org/10.1002/prot.10356.

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Self, Julian, Helen K. Bergstrom, Kara D. Fong, Bryan D. McCloskey, and Kristin A. Persson. "A Theoretical Model for Computing Freezing Point Depression of Lithium-Ion Battery Electrolytes." Journal of The Electrochemical Society 168, no. 12 (December 1, 2021): 120532. http://dx.doi.org/10.1149/1945-7111/ac3e47.

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Reliable prediction of freezing point depression in liquid electrolytes will accelerate the development of improved Li-ion batteries which can operate in low temperature environments. In this work we establish a computational methodology to calculate activity coefficients and liquidus lines for battery-relevant liquid electrolytes. Electronic structure methods are used in conjuction with classical molecular dynamics simulations and theoretical expressions for Born solvation energy, ion-atmosphere effects from Debye-Hückel theory and solvent entropic effects. The framework uses no a priori knowledge beyond neat solvent properties and the concentration of salt. LiPF6 in propylene carbonate (PC), LiPF6 in dimethyl carbonate (DMC) and LiClO4 in DMC are investigated up to 1 molal with accuracy better than 3 °C when compared to experimental freezing point measurements. We find that the difference in freezing point depression between the propylene carbonate-based electrolyte and the dimethyl carbonate electrolytes originates from the difference in the solvent dielectric constant.

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Mitrasinovic, Petar M. "Small-Molecule Interaction with G-Quadruplex DNA." Croatica chemica acta 92, no. 1 (2019): 43–57. http://dx.doi.org/10.5562/cca3456.

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Targeting G-quadruplex (G4) DNA structures by small molecules is a potential strategy for directing gene therapy of cancer disease. Herein, novel insights into non-covalent interactions between a structurally diversified spectrum of ligands and a G-quadruplex DNA (formed in the c-Myc oncogene promoter region) are reported. Solvation-induced effects on and entropic contributions to the binding free energy are explored. In addition, the correlation of G4 domain motions and active site rearrangements with the binding of highest affinity ligands, being associated with the fundamentally distinguishable modes of interaction (external stacking: BRACO-19, TMPyP4, and CX-3543; groove binding: Sanguinarine, Tetrahydropalmatine, and Hoechst 33258), is quantitatively evaluated and elaborated by observing thermodynamic consequences of the receptor conformational flexibility changes in the asymptotic regime (t → ∞) of molecular dynamics (MD) simulation. BRACO-19 and Tetrahydropalmatine are identified as unique (thermodynamically favorable and highly selective) G4-DNA binders. Implications of the present study for experimental research are elucidated.

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Zhou, Yucheng, Etienne Le Calvez, Sun Woong Baek, Matevž Frajnkovič, Camille Douard, Olivier Crosnier, Thierry Brousse, and Laurent Pilon. "Effect of Particle Size on Thermodynamics and Lithium Ion Transport in Ti₂Nb₂O₉ Electrodes Synthesized By Solid State or Sol-Gel Method." ECS Meeting Abstracts MA2022-01, no. 2 (July 7, 2022): 258. http://dx.doi.org/10.1149/ma2022-012258mtgabs.

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Ti2Nb2O9 has been identified as a promising lithium-ion battery anode material with large specific capacity, small cycling degradation, and good capacity retention at large currents. This study aims to gain insight into the charging mechanisms as well as the thermodynamics and ion transport in Ti2Nb2O9 synthesized by the solid state or the sol-gel method and formed by particles of different sizes using potentiometric entropy and operando isothermal calorimetric measurements. First, electrochemical testing showed that Ti2Nb2O9 electrodes made by sol-gel synthesis exhibited larger specific capacity, smaller polarization between lithiation/delithiation, and better capacity retention at large currents compared to those made by solid state synthesis. The measured open-circuit voltage and entropic potential revealed that the same solid solution charging mechanism prevailed and was independent of particle size, as confirmed by in situ XRD measurements. In other words, particle size had no influence on the quasi-equilibrium thermodynamics behavior of Ti2Nb2O9. However, Ti2Nb2O9 electrodes made by sol-gel synthesis featured smaller overpotential and faster lithium diffusion. In fact, operando isothermal calorimetry revealed smaller instantaneous heat generation rates and smaller time-averaged irreversible heat generation rates at Ti2Nb2O9 electrodes made by sol-gel synthesis compared to those made by solid state synthesis at any given C-rate. These observations highlight the smaller resistive losses and the larger electrical conductivity of Ti2Nb2O9 synthesized by the sol-gel method. Furthermore, time-averaged reversible heat generation rates at Ti2Nb2O9 electrodes made by both synthesis methods featured significant contributions from entropic changes, ion adsorption/desorption, and ion solvation/desolvation accompanied by ion-pairing.

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Morgon, Nelson H., Srijit Biswas, Surajit Duari, and Aguinaldo R. de Souza. "Solvent Effects in the Regioselective N-Functionalization of Tautomerizable Heterocycles Catalyzed by Methyl Trifluoromethanesulfonate: A Density Functional Theory Study with Implicit Solvent Model." Computation 10, no. 10 (September 26, 2022): 172. http://dx.doi.org/10.3390/computation10100172.

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Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections.

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Ortiz, Claudia Patricia, Rossember Edén Cardenas-Torres, Fleming Martínez, and Daniel Ricardo Delgado. "Solubility of Sulfamethazine in the Binary Mixture of Acetonitrile + Methanol from 278.15 to 318.15 K: Measurement, Dissolution Thermodynamics, Preferential Solvation, and Correlation." Molecules 26, no. 24 (December 14, 2021): 7588. http://dx.doi.org/10.3390/molecules26247588.

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Solubility of sulfamethazine (SMT) in acetonitrile (MeCN) + methanol (MeOH) cosolvents was determined at nine temperatures between 278.15 and 318.15 K. From the solubility data expressed in molar fraction, the thermodynamic functions of solution, transfer and mixing were calculated using the Gibbs and van ’t Hoff equations; on the other hand, the solubility data were modeled according to the Wilson models and NRTL. The solubility of SMT is thermo-dependent and is influenced by the solubility parameter of the cosolvent mixtures. In this case, the maximum solubility was achieved in the cosolvent mixture w0.40 at 318.15 K and the minimum in pure MeOH at 278.15 K. According to the thermodynamic functions, the SMT solution process is endothermic in addition to being favored by the entropic factor, and as for the preferential solvation parameter, SMT tends to be preferentially solvated by MeOH in all cosolvent systems; however, δx3,1<0.01, so the results are not conclusive. Finally, according to mean relative deviations (MRD%), the two models could be very useful tools for calculating the solubility of SMT in cosolvent mixtures and temperatures different from those reported in this research.

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Israelachvili, Jacob. "Differences between non-specific and bio-specific, and between equilibrium and non-equilibrium, interactions in biological systems." Quarterly Reviews of Biophysics 38, no. 4 (November 2005): 331–37. http://dx.doi.org/10.1017/s0033583506004203.

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Biological interactions are ‘processes’ 331Intermolecular forces involved 332Synergy between different forces occurring at different locations 333Non-equilibrium, rate and time-dependent interactions 335Reversible and irreversible interactions 337The interaction forces between biological molecules and surfaces are much more complex than those between non-biological molecules or surfaces, such as colloidal particle surfaces. This complexity is due to a number of factors: (i) the simultaneous involvement of many different molecules and different non-covalent forces – van der Waals, electrostatic, solvation (hydration, hydrophobic), steric, entropic and ‘specific’, and (ii) the flexibility of biological macromolecules and fluidity of membranes. Biological interactions are better thought of as ‘processes’ that evolve in space and time and, under physiological conditions, involve a continuous input of energy. Such systems are, therefore, not at thermodynamic equilibrium, or even tending towards equilibrium. Recent surface forces apparatus (SFA) and atomic force microscopy (AFM) measurements on supported model membrane systems (protein-containing lipid bilayers) illustrate these effects. It is suggested that the major theoretical challenge is to establish manageable theories or models that can describe the spatial and time evolution of systems consisting of different molecules subject to certain starting conditions or energy inputs.

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Jakhar, Ritu, Mehak Dangi, Alka Khichi, and Anil Kumar Chhillar. "Relevance of Molecular Docking Studies in Drug Designing." Current Bioinformatics 15, no. 4 (June 11, 2020): 270–78. http://dx.doi.org/10.2174/1574893615666191219094216.

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Molecular Docking is used to positioning the computer-generated 3D structure of small ligands into a receptor structure in a variety of orientations, conformations and positions. This method is useful in drug discovery and medicinal chemistry providing insights into molecular recognition. Docking has become an integral part of Computer-Aided Drug Design and Discovery (CADDD). Traditional docking methods suffer from limitations of semi-flexible or static treatment of targets and ligand. Over the last decade, advances in the field of computational, proteomics and genomics have also led to the development of different docking methods which incorporate protein-ligand flexibility and their different binding conformations. Receptor flexibility accounts for more accurate binding pose predictions and a more rational depiction of protein binding interactions with the ligand. Protein flexibility has been included by generating protein ensembles or by dynamic docking methods. Dynamic docking considers solvation, entropic effects and also fully explores the drug-receptor binding and recognition from both energetic and mechanistic point of view. Though in the fast-paced drug discovery program, dynamic docking is computationally expensive but is being progressively used for screening of large compound libraries to identify the potential drugs. In this review, a quick introduction is presented to the available docking methods and their application and limitations in drug discovery.

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Saini, Jagmohan S., Nadine Homeyer, Simone Fulle, and Holger Gohlke. "Determinants of the species selectivity of oxazolidinone antibiotics targeting the large ribosomal subunit." Biological Chemistry 394, no. 11 (November 1, 2013): 1529–41. http://dx.doi.org/10.1515/hsz-2013-0188.

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Abstract Oxazolidinone antibiotics bind to the highly conserved peptidyl transferase center in the ribosome. For developing selective antibiotics, a profound understanding of the selectivity determinants is required. We have performed for the first time technically challenging molecular dynamics simulations in combination with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculations of the oxazolidinones linezolid and radezolid bound to the large ribosomal subunits of the eubacterium Deinococcus radiodurans and the archaeon Haloarcula marismortui. A remarkably good agreement of the computed relative binding free energy with selectivity data available from experiment for linezolid is found. On an atomic level, the analyses reveal an intricate interplay of structural, energetic, and dynamic determinants of the species selectivity of oxazolidinone antibiotics: A structural decomposition of free energy components identifies influences that originate from first and second shell nucleotides of the binding sites and lead to (opposing) contributions from interaction energies, solvation, and entropic factors. These findings add another layer of complexity to the current knowledge on structure-activity relationships of oxazolidinones binding to the ribosome and suggest that selectivity analyses solely based on structural information and qualitative arguments on interactions may not reach far enough. The computational analyses presented here should be of sufficient accuracy to fill this gap.

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Dangles, Olivier, and Raymond Brouillard. "Polyphenol interactions. The copigmentation case: thermodynamic data from temperature variation and relaxation kinetics. Medium effect." Canadian Journal of Chemistry 70, no. 8 (August 1, 1992): 2174–89. http://dx.doi.org/10.1139/v92-273.

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Copigmentation of malvin (a common anthocyanic pigment) with a series of naturally occurring colourless organic molecules (copigments) has been investigated by UV–visible absorption. The temperature-dependence of the visible spectrum of the copigmented solutions yields the copigmentation enthalpy and entropy changes. The experiments are carried out at pH 3.5 (malvin flavylium cation copigmentation) and pH 5.5 (copigmentation of the malvin quinonoidal bases). Copigmentation appears to be clearly enthalpically driven (exothermic process with unfavourable entropy change) in the case of chlorogenic acid and (+)-catechin. Concerning caffeine and tryptophan, favourable entropy changes, probably arising from solvation effects, have been recorded. Similar experiments in water–ethanol binary solvents have shown that the dramatic weakening of copigmentation on cosolvent addition is essentially entropic in origin. Salt effects on copigmentation have been investigated as well. Most of the results are discussed with a view to pointing out the major contributions to the magnitude of the copigmentation. Finally, relaxation kinetic measurements on the malvin–rutin system give striking evidence of the strong slowing down that a good copigment causes to the anthocyanin fading process (hydration). From the decrease in the apparent first-order rate constant of hydration on copigment addition, a general method for a quick determination of the copigmentation stability constants is proposed.

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Komarov, Pavel V., Pavel G. Khalatur, and Alexei R. Khokhlov. "Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport." Beilstein Journal of Nanotechnology 4 (September 26, 2013): 567–87. http://dx.doi.org/10.3762/bjnano.4.65.

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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.

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Luan, Chi-Hao, John Jaggard, R. Dean Harris, and Dan W. Urry. "On the source of entropic elastomeric force in polypeptides and proteins: Backbone configurational vs. side-chain solvational entropy." International Journal of Quantum Chemistry 36, S16 (June 19, 2009): 235–44. http://dx.doi.org/10.1002/qua.560360718.

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Fianchini, Mauro, Lluis Llorens, and Miquel A. Pericàs. "Separating Enthalpic, Configurational, and Solvation Entropic Components in Host–Guest Binding: Application to Cucurbit[7]uril Complexes through a Full In Silico Approach via Water Nanodroplets." Journal of Physical Chemistry B 124, no. 46 (November 9, 2020): 10486–99. http://dx.doi.org/10.1021/acs.jpcb.0c08507.

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Warshel, Arieh, and William W. Parson. "Dynamics of biochemical and biophysical reactions: insight from computer simulations." Quarterly Reviews of Biophysics 34, no. 4 (November 2001): 563–679. http://dx.doi.org/10.1017/s0033583501003730.

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1. Introduction 5632. Obtaining rate constants from molecular-dynamics simulations 5642.1 General relationships between quantum electronic structures and reaction rates 5642.2 The transition-state theory (TST) 5692.3 The transmission coefficient 5723. Simulating biological electron-transfer reactions 5753.1 Semi-classical surface-hopping and the Marcus equation 5753.2 Treating quantum mechanical nuclear tunneling by the dispersed-polaron/spin-boson method 5803.3 Density-matrix treatments 5833.4 Charge separation in photosynthetic bacterial reaction centers 5844. Light-induced photoisomerizations in rhodopsin and bacteriorhodopsin 5965. Energetics and dynamics of enzyme reactions 6145.1 The empirical-valence-bond treatment and free-energy perturbation methods 6145.2 Activation energies are decreased in enzymes relative to solution, often by electrostatic effects that stabilize the transition state 6205.3 Entropic effects in enzyme catalysis 6275.4 What is meant by dynamical contributions to catalysis? 6345.5 Transmission coefficients are similar for corresponding reactions in enzymes and water 6365.6 Non-equilibrium solvation effects contribute to catalysis mainly through Δg[Dagger], not the transmission coefficient 6415.7 Vibrationally assisted nuclear tunneling in enzyme catalysis 6485.8 Diffusive processes in enzyme reactions and transmembrane channels 6516. Concluding remarks 6587. Acknowledgements 6588. References 658Obtaining a detailed understanding of the dynamics of a biochemical reaction is a formidable challenge. Indeed, it might appear at first sight that reactions in proteins are too complex to analyze microscopically. At room temperature, even a relatively small protein can have as many as 1034 accessible conformational states (Dill, 1985). In many cases, however, we have detailed structural information about the active site of an enzyme, whereas such information is missing for corresponding chemical systems in solution. The atomic coordinates of the chromophore in bacteriorhodopsin, for example, are known to a resolution of 1–2 Å. In addition, experimental studies of biological processes such as photoisomerization and electron transfer have provided a wealth of detailed information that eventually may make some of these processes classical problems in chemical physics as well as biology.

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Leckband, Deborah, and Jacob Israelachvili. "Intermolecular forces in biology." Quarterly Reviews of Biophysics 34, no. 2 (May 2001): 105–267. http://dx.doi.org/10.1017/s0033583501003687.

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0. Abbreviations 1061. Introduction: overview of forces in biology 1081.1 Subtleties of biological forces and interactions 1081.2 Specific and non-specific forces and interactions 1131.3 van der Waals (VDW) forces 1141.4 Electrostatic and ’double-layer‘ forces (DLVO theory) 1221.4.1 Electrostatic and double-layer interactions at very small separation 1261.5 Hydration and hydrophobic forces (structural forces in water) 1311.6 Steric, bridging and depletion forces (polymer-mediated and tethering forces) 1371.7 Thermal fluctuation forces: entropic protrusion and undulation forces 1421.8 Comparison of the magnitudes of the major non-specific forces 1461.9 Bio-recognition 1461.10 Equilibrium and non-equilibrium forces and interactions 1501.10.1 Multiple bonds in parallel 1531.10.2 Multiple bonds in series 1552. Experimental techniques for measuring forces between biological molecules and surfaces 1562.1 Different force-measuring techniques 1562.2 Measuring forces between surfaces 1612.3 Measuring force–distance functions, F(D) 1612.4 Relating the forces between different geometries: the ‘Derjaguin Approximation’ 1622.5 Adhesion forces and energies 1642.5.1 An example of the application of adhesion mechanics of biological adhesion 1662.6 Measuring forces between macroscopic surfaces: the surface forces apparatus (SFA) 1672.7 The atomic force microscope (AFM) and microfiber cantilever (MC) techniques 1732.8 Micropipette aspiration (MPA) and the bioforce probe (BFP) 1772.9 Osmotic stress (OS) and osmotic pressure (OP) techniques 1792.10 Optical trapping and the optical tweezers (OT) 1812.11 Other optical microscopy techniques: TIRM and RICM 1842.12 Shear flow detachment (SFD) measurements 1872.13 Cell locomotion on elastically deformable substrates 1893. Measurements of equilibrium (time-independent) interactions 1913.1 Long-range VDW and electrostatic forces (the two DVLO forces) between biosurfaces 1913.2 Repulsive short-range steric–hydration forces 1973.3 Adhesion forces due to VDW forces and electrostatic complementarity 2003.4 Attractive forces between surfaces due to hydrophobic interactions: membrane adhesion and fusion 2093.4.1 Hydrophobic interactions at the nano- and sub-molecular levels 2113.4.2 Hydrophobic interactions and membrane fusion 2123.5 Attractive depletion forces 2133.6 Solvation (hydration) forces in water: forces associated with water structure 2153.7 Forces between ‘soft-supported’ membranes and proteins 2183.8 Equilibrium energies between biological surfaces 2194. Non-equilibrium and time-dependent interactions: sequential events that evolve in space and time 2214.1 Equilibrium and non-equilibrium time-dependent interactions 2214.2 Adhesion energy hysteresis 2234.3 Dynamic forces between biomolecules and biomolecular aggregates 2264.3.1 Strengths of isolated, noncovalent bonds 2274.3.2 The strengths of isolated bonds depend on the activation energy for unbinding 2294.4 Simulations of forced chemical transformations 2324.5 Forced extensions of biological macromolecules 2354.6 Force-induced versus thermally induced chemical transformations 2394.7 The rupture of bonds in series and in parallel 2424.7.1 Bonds in series 2424.7.2 Bonds in parallel 2444.8 Dynamic interactions between membrane surfaces 2464.8.1 Lateral mobility on membrane surfaces 2464.8.2 Intersurface forces depend on the rate of approach and separation 2494.9 Concluding remarks 2535. Acknowledgements 2556. References 255While the intermolecular forces between biological molecules are no different from those that arise between any other types of molecules, a ‘biological interaction’ is usually very different from a simple chemical reaction or physical change of a system. This is due in part to the higher complexity of biological macromolecules and systems that typically exhibit a hierarchy of self-assembling structures ranging in size from proteins to membranes and cells, to tissues and organs, and finally to whole organisms. Moreover, interactions do not occur in a linear, stepwise fashion, but involve competing interactions, branching pathways, feedback loops, and regulatory mechanisms.

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Journal articles on the topic 'Solvation entropies'

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