Solvation Energy Difference Research Articles

Calculation of Electron Affinities of Polycyclic Aromatic Hydrocarbons and Solvation Energies of Their Radical Anion

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

Effect of solvation on the kinetic parameters of the reactions of phenoxyl radicals with phenols and semiquinone radicals with hydroquinones

Experimental rate constants of the reactions of semiquinone radicals with hydroquinones in chlorobenzene at ∼300 K are by almost an order of magnitude higher than the rate constants of the reactions of phenoxyl radicals with phenols, which are equivalent to the former ones by heat effects. To reveal differences in the rate constants of these groups of reactions, we performed quantum chemical calculations of the energy profiles of the reactions and dissociation energies by the B3LYP density functional theory using the GAMESS and GAUSSIAN-03 programs in the 6-31+G* basis set. The solvation energies were calculated in all stationary points on the reaction coordinate by the method of polarized continuum model. In terms of the intersecting parabolas method, the reactions of semiquinone radicals with hydroquinones and phenoxyl radicals with phenols can be attributed to the same class of reactions only in the gas phase. In solvents this class of reactions is divided into two subclasses due to differences in solvation energies of the preliminary complexes and transition states of these reactions.

Thermochemical Properties of the Ammonia−Water Ionized Dimer Probed by Ion−Molecule Reactions

The thermochemical properties of some small clusters such as the (H2O)2*+ dimer have already been investigated by both experimental and theoretical methods. The recent method to selectively prepare the ammonia-water ionized dimer [NH3, H2O]*+ (and not its proton transfer isomer [NH4+, OH*]) allowed us to study its chemical reactivity. This study focuses on the charge and proton transfer pathways: Ion-molecule reactions in the cell of an FT-ICR mass spectrometer were carried out with a range of organic compounds. Examination of the reactivity of the [NH3, H2O]*+ ionized dimer versus ionization energy and proton affinity of the neutral reagents shows a threshold in the reactivity in both instances. This leads to a bracketing of thermochemical properties related to the dimer. From these experiments and in agreement with ab initio calculations, the adiabatic recombination energy of the [NH3, H2O]*+ dimer was evaluated at -9.38 +/- 0.04 eV. The proton affinity bracketing required the reevaluation of two reference gas-phase basicity values. The results, in good agreement with the calculation, lead to an evaluation of the proton affinity of the [NH2*, H2O] dimer at 204.4 +/- 0.9 kcal mol(-1). These two experimental values are respectively related to the ionization energy of NH3*+ and to the proton affinity of NH2* by the difference in single water molecule solvation energies of ionized ammonia, of neutral ammonia, and of the NH2* radical.

Water Dimer Proton Affinity from the Kinetic Method: Dissociation Energy of the Water Dimer

The proton affinity of water dimer was measured, using the kinetic method with nitrile reference bases, to be 808 +/- 6 kJ mol(-1). The difference between the measured value and the proton affinity of a single water molecule (690 +/- 4 kJ mol(-1)) reflects the difference in solvation energy for two neutral water molecules (the hydrogen bond energy of water dimer), and the energy for solvation of hydronium cation and water. Using the measured proton affinity of the dimer along with ancillary data yields an experimental value of the hydrogen bond energy of neutral water dimer, 18 +/- 9 kJ mol(-1), in good agreement with previous experimental and theoretical values. The proton affinity of the dimer measured by using alcohol references is ca 100 kJ mol(-1) too low, likely because the structure of the protonated cluster is not well-suited for kinetic method measurements. These results highlight the importance of choosing reference bases that form cluster ions consisting of a proton bound complex between the water dimer and the reference base.

Fast accurate evaluation of protein solvent exposure.

Protein solvation energies are often taken to be proportional to solvent-accessible surface areas. Computation of these areas is numerically demanding and may become a bottleneck for folding and design applications. Fast graph-based methods, such as dead-end elimination (DEE), become possible if all energies, including solvation energies, are expressed as single-residue and pair-residue terms. To this end, Street and Mayo originated a pair-residue approximation for solvent-accessible surface areas (Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253-258). The dominant source of error in this method is the overlapping burial of side-chain surfaces in the protein core. Here we report a new pair-residue approximation, which greatly reduces this overlap error by the use of optimized generic side-chains. We have tested the generic-side-chain method for the ten proteins studied by Street and Mayo and for 377 single-domain proteins from the CATH database (Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108). With little additional cost in computation, the new method consistently reduces error for total areas and residue-by-residue areas by more than a factor of two. For example, the residue-by-residue error (for buried area) is reduced from 7.42 A(2) to 3.70 A(2). This difference translates into a solvation energy difference of approximately 0.2 kcal/mol per residue, amounting to a reduction in root-mean-square energy error of 2 kcal/mol for a 100 residue chain, a potentially critical difference for both protein folding and design applications.

Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking.

A novel method for fast and accurate evaluation of the generalized Born radii in macromolecular solvation electrostatics calculations is proposed, based on the solvent accessibility of the first two solvation layers around an atom. The reverse generalized Born radii calculated by the method have correlation coefficient of 98.7% and RMSD of 0.031 A(-1) with the values obtained using a precise but significantly slower numerical boundary element solution. The method is applied to derive an estimate of the free solvation energy difference between octanol and water and to predict LogP octanol-water. A nine-parameter model is optimized on an 81 compound training set and applied to predict LogP(ow) for an external evaluation set of 19 drug molecules with RMSD of 0.9. The new GB approximation is also tested in Monte Carlo docking simulations of the fully flexible p53 peptide fragment to MDM2. The best energy solution found in the simulations has RMSD of 2.8 A to the X-ray structure.

A weak, short metal-metal bond in a chromium(II) amidinate complex.

Treatment of chromium(II) chloride with 2 equiv of Li[tBuNC(CH3)NtBu], Li[iPrNC(CH3)NiPr], or Li[tBuNC(CH3)NEt] (prepared from the corresponding carbodiimides and methyllithium) afforded Cr[tBuNC(CH3)NtBu]2 (1, 50%), Cr[iPrNC(CH3)NiPr]2 (2, 54%), and [Cr(tBuNC(CH3)NEt)2]2 (3, 58%) as deep blue, purple, and amber or metallic green crystals, respectively. Cr[tBuNC(CH3)NtBu]2 and Cr[iPrNC(CH3)NiPr]2 possess monomeric structures in the solid state with tetrahedral and square planar geometries about the chromium centers, respectively. [Cr(tBuNC(CH3)NEt)2]2 exists as a dimer in the solid state, with two mu2-amidinate ligands, two eta2-amidinate ligands, and a chromium-chromium bond length of 1.9601(12) A. [Cr(tBuNC(CH3)NEt)2]2 is diamagnetic in the solid state, as determined by magnetic susceptibility measurement and CP/MAS 13C NMR spectroscopy. However, [Cr(tBuNC(CH3)NEt)2]2 dissociates into paramagnetic monomers in solution, as determined by observation of extremely broad peaks in the 1H NMR spectra in cyclohexane-d12 and benzene-d6, a solution magnetic moment measurement, and by solution molecular weight measurements in benzene. The combined results suggest that the chromium-chromium bond strength in [Cr(tBuNC(CH3)NEt)2]2 is weak and cannot exceed the difference in solvation energies between the dimer and two monomers, plus any increase in metal-nitrogen bond strengths in the monomers.

Prediction of the 1-octanol/H2O partition coefficient, log P, by ab initio MO calculations: hydrogen-bonding effect of organic solutes on log P.

To predict the 1-octanol/H2O partition coefficient, log P, based on molecular structures, we calculated the solvent accessible surface area and the solvation energy difference of 166 organic molecules between 1-octanol and water environments with the ab initio molecular orbital self-consistent reaction field method, and then analyzed the relationships among the measured log P values with these two structural quantities by multiple linear-regression analyses. Physicochemically meaningful correlations were obtained, suggesting that non-hydrogen bonding and hydrogen-acceptor molecules behave similarly to each other in partitioning, but that hydrogen-donor molecules behave differently from the former molecules. The results provide a new computational approach for predicting log P.

Density dependence of solvation properties in polar dumbbell fluids from gaseous to liquid densities

The solvent density dependence of the solvation energy difference associated with a charge transfer process in a polar dumbbell fluid is studied from the gaslike to the liquidlike densities by means of two types of the integral equation theories and the Monte Carlo simulation. The polar dumbbell fluid model including the Coulombic interaction explicitly has succeeded in a qualitative reproduction of quite a larger density dependence of the solvation energy in the low-density region than that in the higher-density region. The origin of the density dependence has been attributed to the difference in the reaction field response at various densities. At the low density, the reaction field shows a highly enhanced nonlinear response to the solute dipole moment. The nonlinear enhancement is an intrinsic nature in the gaseous dielectric solvation, and is due to the enhanced local density around the solute molecule with increasing the solute charge. On the other hand, the reaction field at the high density responds almost linearly to the solute dipole moment. The analysis based on the integral equation has clarified that the high linearity at the liquid density is closely related to the invariance of the radial distribution between cores in spite of the charging on the solute, which reflects the highly packed structure at the high density. When the solute dipole moment is quite large, we observe the dielectric saturation at the high density, where the enhanced local density around the solute does not result in the increase of the reaction field because of the saturation in the orientational correlation between the solute and solvent dipoles. Even when the solute dipole moment is small enough not to cause the nonlinear response, the reaction field is induced nonlinearly to the solvent density, which is interpreted not only by the local density but also by the contribution per solvent molecule at various densities. This study demonstrates that the following two properties often neglected so far have significant effect on the evaluation of the solvation energy difference at various densities: one is the nonlinearly enhanced field response at the gaseous density, and the other is the density variation of the reaction field induced per solvent molecule.

Simple kinetic models of ion transfer across an interface between two immiscible electrolyte solutions.: A comparison with experimental data

The Nernst–Planck equation is used to examine the kinetic behavior of three simple models of ion transfer, which all assume that the potential of mean force acting on the ion can be obtained as a superposition of the solvation potential and the electrical double layer potential. A comparison is made with the experimental kinetic data for 21 ion transfer reactions at the water/nitrobenzene interface. It is shown that only the models which account in an explicit way for the effect of the electrical double layer can provide a plausible description of experimental behavior. In particular, the absence of a correlation between the apparent standard rate constant or the apparent charge transfer coefficient and the standard Gibbs energy of ion transfer across the water/nitrobenzene interface can be due to the mutual compensation of the effect of electrical double layer and the effect of the difference in solvation energy on the ion transfer rate. It is concluded that a double layer correction is necessary to obtain true kinetic parameters of ion transfer across the interface.

Binding energetics of phosphorus-containing inhibitors of thermolysin.

The importance of a specific hydrogen bond between thermolysin and a phosphonamidate inhibitor, Z-NHCH2-PO(O-)-Leu-Leu (1) [Bartlett, P. A., & Marlowe, C. K. (1987) Science (Washington D.C.) 235, 569-571], has been reevaluated. We have determined the inhibition constants (binding free energies) for thermolysin of phosphonamidate n-hexyl-P(O)(O-)-Leu-Trp-NHMe (4), phosphonate n-hexyl-P-(O)(O-)OCH(iBu)CO-Trp-NHMe (5), and phosphinates n-hexyl-P(O)(O-)CH2CH(iBu)CO-Trp-NHMe (6) and Z-NHCH2PO(O-)CH2CH(iBu)CO-Leu (3). Replacement of the P-NH group by P-CH2 (1----3 and 4----6) weakens the overall binding free energy by about 1.5 kcal/mol. A negligible difference in solvation energy has been measured for these pairs, and the basicity of the P-O- ligand for zinc in each pair remains nearly unchanged as determined by pH titration of their 31P NMR resonances. Therefore, this value of 1.5 kcal/mol can be assigned to the specific hydrogen bond known to exist between the P-NH of 1 and thermolysin [Tronrud, D. E., Holden, H. M., & Matthews, B. W. (1987) Science (Washington, D.C.) 235, 871-574] and inferred to exist between 4 and the enzyme. Substitution of P-O for P-NH (1----2 [Bartlett, P. A., & Marlowe, C. K. (1987) Science (Washington, D.C.) 235, 569-571] and 4----5) weakens the overall binding free energy by 4.1 kcal/mol for each pair as the basicity of the P-O- ligand decreases by about 1.6 pH units. The measured solvation energy difference between 4 and 5 (and by inference between 1 and 2) is negligible.(ABSTRACT TRUNCATED AT 250 WORDS)

Why is gramicidin valence selective? A theoretical study

Calculations contrasting the channel solvation energy for cesium ions and chloride ions associated with water in gramicidin-like channels are presented. The energy profile for the cation exhibits a deep well at the channel entrance; within the single file region the solvation energy is roughly constant. The anion exhibits a totally different energy profile. There is an energy barrier at the channel entrance; if the ion could surmount this barrier, it would be quite stable within the channel. At the channel entrance, the calculated solvation energy difference between anion and cation is approximately 15 kcal mol-1. This is completely consistent with the observation that chloride neither permeates nor blocks the channel since the estimated rate of ion entry would be approximately 0.01-10(-5) s-1, far slower than the rate at which the channel dimer dissociates into monomers.

Offcenter Molecular Charge Distribution Corrections to Born Equation Electrostatic Solvation Energies

AbstractUse of simple model charge distributions and classical multipolar dielectric theory has allowed investigation of the corrections appropriate to the Born equation for structured ion solutes. Among the results obtained for centrosymmetric charge distributions, but presumably of general consequence, are the demonstration of nonlinear dependence and great sensitivity of polarization to charge‐cavity boundary proximity, rapid falloff of effects upon continued subdivision of charge, and the significance of solvation energy differences for 2‐ and 3‐dimensional charge distributions. That 50% or greater corrections to the Born energy may readily be obtained in real ion systems, and the lack of sensitivity of such corrections to the dielectric of the medium for ε > 10 are also results of general interest. Analytical approximations for the electrostatic work equations appropriate to high dielectric solvation are included, and how uncertainties in charge magnitude and position for real ions might affect the analysis are also briefly considered.

Molecular-mechanical studies of hormone-protein interactions: the interaction of T4 and T3 with prealbumin.

AbstractWe present molecular‐mechanical calculations on the interactions of L‐thyroxine (T4) and 3,5,3′‐triiodo‐L‐thyronine (T3) with the binding site of human serum prealbumin. Energy refinement with restraints on the movement of the iodine atoms leads to reasonably low‐energy structures with the iodines within 0.2 Å of their x‐ray determined positions; removal of these restraints leads to larger (∼1.0 Å) deviations from these positions. However the relative energies of T3 and T4 complexation are similar in both cases, and the relative calculated energies for these complexes, when corrected by a simple empirical method for the solvation energy differences of the hormones, are in reasonable qualitative agreement with experiment.

Pyrophosphate of high and low energy. Contributions of pH, Ca2+, Mg2+, and water to free energy of hydrolysis.

The equilibrium between inorganic pyrophosphate and inorganic orthophosphate was determined at pH values varying between 6.0 and 8.0, in the presence of different concentrations of MgCl2, mixtures of MgCl2 and CaCl2, and different organic solvents. The reactions were catalyzed by yeast inorganic pyrophosphatase. It was found that at 35 degrees C, depending on the conditions used, the observed equilibrium constant of pyrophosphate hydrolysis vary from a value higher than 4 X 10(3) M (delta Goobs more negative than -5.1 kcal/mol) to a value as low as 3 M (delta Goobs -0.7 kcal/mol). The experimental data were used to compute the equilibrium constants of the reactions involving different ionic species. The data presented are interpreted according to the concept that the Keq of hydrolysis of a high energy compound depends on the difference in solvation energy of reactants and products.

Role of Water on the Free Energy of Hydrolysis of Pyrophosphate

This chapter discusses the role of water on the free energy of hydrolysis of pyrophosphate. The energy of hydrolysis of pyrophosphate and other compounds is determined by the difference in solvation energies of reactant and products. The chapter discusses the experiment where 32Piwas obtained from the Brazilian Institute of Atomic Energy and purified and the synthesis of pyrophosphate was assayed by measuring the formation of radioactive pyrophosphate from 32Pi. The specific activity was 500 units/mg of enzyme. The data presented in the chapter can be interpreted according to the concept of solvation energy. The finding that in mixed solvents there is a significant decrease in the Kobsfor pyrophosphate hydrolysis strongly suggests that organization of water around reactants and products plays a major role in determining the thermodynamic parameters of pyrophosphate hydrolysis. Water possesses the most cooperative structure of all common solvents, but it is destroyed by organic cosolvents. The chemical reactivity of water molecules is scarcely affected by cosolvents. However, the reactions that depend on solvent structure change markedly with cosolvent addition.

Ab initio MO calculation of hydration energies of ammonium ions and their solvation effect

The hydration energies for the NH + 4 and CH 3NH + 3 ions were calculated by an ab initio MO method. The aqueous solvation energy difference between these two ions was found to be accounted for by the interactions of the ions with a few solvent molecules.

Theoretical consideration on the aqueous solvation effect in the proton transfer reaction: NH4++OH2=NH3+OH3+.

The hydration energies for the NH4+ and OH3+ ions were calculated by an ab initio MO method with the 3-21G and 6-31G* basis sets. 6-31G* values were found to be in good agreement with the experimental ones. The aqueous solvation energy difference between these two ions could be accounted for by the interactions of the corresponding ion with a few solvent molecules, as suggested by Kebarle, Hehre and Taft. On the basis of the calculated results, the aqueous solvation effect on the proton transfer reaction, NH4+ + OH2 = NH3 + OH3+, was studided. The most part of the aqueous solvation effect upon the proton transfer reaction can be accounted for by the aqueous solvation energy difference between two ions (NH4+ and OH3+); the aqueous solvation energy difference between two neutral molecules (NH3 and OH2) is really quite small.

Dielectric and raman spectroscopic studies on the rotational isomerism of t-butyl formate

Static dielectric constants, refractive indices and densities have been measured for t-butyl formate and acetate in cyclohexane at increasing concentrations and at two temperatures, 20°C and 60°C. The Δ H value for the cis-trans equilibrium of t-butyl formate and the dipole moment of the trans conformation has been calculated from the dielectric measurements taking the Δ S value calculated from the sum-over-states for the cis and trans conformations and assuming the dipole moment of the cis conformation to be equal to 1.94 D as found for t-butyl acetate, which has the cis conformation only. The relative intensities of the Raman bands corresponding to specific vibrations modes of the cis and trans conformations of t-butyl formate are measured in cyclohexane and acetonitrile at various concentrations. The enthalpy difference Δ H is also measured in the liquid state and in acetonitrile by variation of the intensity ratio of the bands with temperature. All thermodynamic quantities obtained from dielectric or Raman intensity measurements are compared with each other and with the theoretical values. The solvation energy difference between cis and trans conformations in cyclohexane and acetonitrile as well as in the liquid state are also compared with theoretical values. The large deviation of solvation energy difference between the experimental value and Onsager's model value are well described by an additional term, which considers dipole-dipole interaction.

Stability of sodium and potassium complexes of valinomycin

Stability constants of sodium and potassium complexes of valinomycin in some alcohols and water—organic solvent mixtures have been determined by titration, using circular dichroism to monitor complex formation. Constants range from 10 1 to 10 6 M −1. Stability of the potassium and sodium complexes increases with decreasing dielectric constant, but the ratio of the constants remains about 10 3–10 4. As others have shown, a similar selectivity for K + is observed in a number of other types of measurements involving valinomycin. These include the permeability and conductance ratios which characterize the selectivity of cation transport through membranes and the ratio of salt extraction equilibrium constants. On the basis of data presented here, and elsewhere, it is suggested that conformational constraints within the depsipeptide part of the complexes aid ion selectivity and that differences in cation solvation and carbonyl ligand binding energies make an important, roughly equal, contribution.