A microsolvation approach to the prediction of the relative enthalpies and free energies of hydration for ammonium ions

Hartree–Fock (HF) and second-order Møller–Plesset (MP2) calculations were used to investigate the structures and thermochemistry of methylammonium–water clusters (Me_4-m NH _m ⁺ (H₂O) _n , m=1–4, n=1–4). Water molecules were treated ab initio and with effective fragment potentials (EFP). In addition to a thorough phase-space search, the importance of basis set, electron correlation, and thermodynamic effects was systematically examined. Cluster structures resulted from hydrogen bond formation between the ammonium group and water molecules; upon saturation of the hydrogen bonding sites of the ammonium group, water molecules entered the second hydration shell. With only four water molecules, the experimental relative enthalpies of hydration were well reproduced at the HF level, while the MP2 relative free energies were in best agreement with experiment. Absolute energies of hydration were calculated using an empirical correction. These results strongly suggest that a HF-based microsolvation approach employing a small number of water molecules can be used to compute relative enthalpies of hydration.     

Alchemical free energy calculations via metadynamics: Application to the theophylline-RNA aptamer complex

We propose a computational workflow for robust and accurate prediction of both binding poses and their affinities at early stage in designing drug candidates. Small, rigid ligands with few intramolecular degrees of freedom, for example, fragment-like molecules, have multiple binding poses, even at a single binding site, and their affinities are often close to each other. We explore various structures of ligand binding to a target through metadynamics using a small number of collective variables, followed by reweighting to obtain the atomic coordinates. After identifying each binding pose by cluster analysis, we perform alchemical free energy calculations on each structure to obtain the overall value. We applied this protocol in computing free energy of binding for the theophylline-RNA aptamer complex. Of the six (meta)stable structures found, the most favorable binding structure is consistent with the structure obtained by NMR. The overall free energy of binding reproduces the experimental values very well.     

Thermodynamic quantities relative to solution processes of Naproxen in aqueous media at pH 1.2 and 7.4

Based on van’t Hoff and Gibbs equations, the thermodynamic functions Gibbs free energy, enthalpy, and entropy of solution, mixing and solvation of naproxen (NAP) in water at pH 1.2 and 7.4, were evaluated from solubility values determined at several temperatures. The solubility at pH 7.4 and 25.0°C was almost 150 times higher with respect to pH 1.2. The enthalpies of solution were positive and greater for pH 1.2, while the entropies of solution were both negative, thereby implying a greater molecular organization at pH 7.4. The results were discussed in terms of solute–solvent interactions.     

Application of Ab initio calculations to nuclear internal conversion: Repulsion energies of highly charged HBr ions

Ab initio MO calculations were applied to the evaluation of repulsion energies in highly charged HBr ions. Net charges of H and Br atoms were obtained from the Mulliken atomic population, and repulsion energies were estimated by a simplified model based on the Coulomb repulsion. The repulsion energy of HBr⁸⁺ was calculated to be 71.5 eV.     

Coordination properties of 1-allyl-2-methylimidazole relative to some metal ions in the solid state and aqueous solution

Cobalt(II) and copper(II) complexes with 1-allyl-2-methylimidazole (L), of general formula [ML₂(NO₃)₂], have been prepared in the solid state. The compounds were characterised by structural, spectroscopic and magnetic measurements. The metal ions in both six coordinate complexes are surrounded by two nitrogen atoms of the imidazole rings and four oxygen atoms of the chelating nitrato group (the CoN₂O₄ and CuN₂O₄ chromophores). The structure of both chromophores is described by a very distorted tetragonal bipyramid. The formation of successive complexes of the azole with Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺ and Cd²⁺ in aqueous solution was followed potentiometrically. An irregularity in the K_n constants of successive Co²⁺ and Zn²⁺ complexes suggests a change in the coordination sphere of the central ions from octahedral to tetrahedral. With the Co²⁺–1-allyl-2-methylimidazole system, the change has been proven by inspection of the visible absorption spectra.     

Thermodynamic characteristics of complex formation in the zinc(II)-glycylglycine system in aqueous solution

The heats of reaction of zinc(II) with glycylglycine at temperatures 288.15, 298.15, and 308.15 K and ionic strengths 0.25, 0.50, and 0.75 (potassium nitrate as a supporting electrolyte) were determined by calorimetry. The thermochemical results were processed with inclusion of stepwise equilibria. In addition to complexation reactions, “side” protolytic processes were considered. Standard heats of complexation in the system were found by extrapolation to the zero ionic strength by an equation with one individual parameter. The influence of the supporting electrolyte concentration and temperature on the thermodynamic characteristics of the complexation reactions in the glycylglycine-zinc(II) system was considered. The standard enthalpies of formation of ZnGlyGly⁺, Zn(GlyGly)₂, and Zn(GlyGly)₃⁻ species in aqueous solution were calculated.     

Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton

Thermochemical cycles that involve pKa, gas-phase acidities, aqueous solvation free energies of neutral species, and gas-phase clustering free energies have been used with the cluster pair approximation to determine the absolute aqueous solvation free energy of the proton. The best value obtained in this work is in good agreement with the value reported by Tissandier et al. (Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. J.; Earhart, A. D.; Coe, J. V. J. Phys. Chem. A 1998, 102, 7787), who applied the cluster pair approximation to a less diverse and smaller data set of ions. We agree with previous workers who advocated the value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton. Considering the uncertainties associated with the experimental gas-phase free energies of ions that are required to use the cluster pair approximation as well as analyses of various subsets of data, we estimate an uncertainty for the absolute aqueous solvation free energy of the proton of no less than 2 kcal/mol. Using a value of -265.9 kcal/mol for the absolute aqueous solvation free energy of the proton, we expand and update our previous compilation of absolute aqueous solvation free energies; this new data set contains conventional and absolute aqueous solvation free energies for 121 unclustered ions (not including the proton) and 147 conventional and absolute aqueous solvation free energies for 51 clustered ions containing from 1 to 6 water molecules. When tested against the same set of ions that was recently used to develop the SM6 continuum solvation model, SM6 retains its previously determined high accuracy; indeed, in most cases the mean unsigned error improves when it is tested against the more accurate reference data.     

A calculation of the relative protonation energies of amines in solution

Relative protonation energies in the primary, secondary and tertiary aliphatic series of amines are calculated by a semiempirical method employing the virtual charge model. The method accounts quite well for the observed differences between the gas-phase protonation affinities and the protonation enthalpies in solution, but when allowance is made for steric shielding from the bulk solvent for “non-edge” atoms, some anomalies in the uncorrected model are removed. The calculated solute-solvent interactions are related to experimental enthalpies of solution and to trends expected from the Born model.     

Thermodynamic study on the complexation of Am(III) and Eu(III) with tetradentate nitrogen ligands: a probe of complex species and reactions in aqueous solution

A thermodynamic investigation has been performed to study the complexation of trivalent metal (M) ions (M = Am(III), Eu(III)) with tetradentate ligands (L), 6,6'-bis(5,6-dialkyl-1,2,4-triazin-3-yl)-2,2'-bipyridines (BTBPs), by using relativistic quantum mechanical calculations. The structures and stabilities of the inner-sphere BTBPs complexes were explored in the presence of various counterions such as NO(3)(-), Cl(-), and ClO(4)(-). According to our calculations, Am(III) and Eu(III) can chelate eight or nine water molecules at most, whereas more stable species like M(NO(3))(3)(H(2)O)(4) tend to be formed in the presence of nitrate ions. The inner sphere of the BTBPs complexes can accommodate four water molecules or three nitrate ions based on our calculations, forming species such as [ML(H(2)O)(4)](3+) and ML(NO(3))(3). Compared with Eu(III) complexes, the Am(III) counterparts have obviously lower binding energies in both the gas phase and solution. In addition, the solvent effect significantly decreases the binding energies of the BTBPs complexes. It has been found that the complexing reactions, in which products and reactants possess the same or close number of nitrate ions, are more favorable for formation of the BTBPs complexes. In short, the reactions of M(NO(3))(3)(H(2)O)(4) → ML(NO(3))(3) and [M(NO(3))(H(2)O)(7)](2+) → [ML(2)(NO(3))](2+) are probably the dominant ones in the Am(III)/Eu(III) separation process.     

The thermodynamic characteristics of complex formation between calcium ions and L-leucine in aqueous solution

Complex formation of L-leucine with calcium ions in aqueous solution was studied by potentiometric titration at 298.15 K and ionic strength values I = 0.5, 1.0, and 1.5 (KNO₃). The formation of the CaL⁺ and CaHL²⁺ complex particles was established and their stability constants were determined. The enthalpies of protolytic equilibria of leucine and formation of calcium ion complexes with leucine were determined calorimetrically at 298.15 K and I = 0.5 (KNO₃). The thermodynamic characteristics of complex formation between calcium ions and L-leucine were calculated.     

Thermodynamic properties of the benzene-phenol dimer in dilute aqueous solution

Precise vapor pressure-solubility measurements have been obtained for dilute solutions of benzene and phenol in water at 15, 25, 35 and 45°C. All of the results are consistent with a mass action model that attributes deviations from ideal solution behavior to the formation of benzene dimers and hetero-dimers between benzene and phenol. The benzene-phenol dimer forms endothermically at 25°C, with a very large negative heat capacity, and a formation constant that reaches a maximum value of 0.66 l-mol^?1 at approximately 35°C. Thermodynamic properties of the benzene-phenol dimer are reported and compared with those of other aggregates that are believed to be stabilized primarily by hydrophobic interactions.     

Changes in hydration of lanthanide ions on binding to DNA in aqueous solution

The interaction of the trivalent lanthanides Ce(III), Eu(III), and Tb(III) with sodium deoxyribonucleic acid (DNA) in aqueous solution has been studied using their luminescence spectra and decays. Complexation with DNA is indicated by changes in luminescence intensity. In the system terbium(III)-DNA, changes in luminescence with pH are suggested to be due to the protonation of phosphate groups. The degree of hydration of Tb(III) on binding to DNA is followed by luminescence lifetime measurements in water and deuterium oxide solutions, and it is found that the lanthanide ion loses at least one hydration water on binding to long double stranded DNA at pH 4.7 and pH 7. Rather different behavior is observed on binding to long or short single stranded DNA, where six water molecules are lost, independent of pH. It is suggested that in this case the lanthanide probably binds to the bases of the DNA backbone. The DNA conformation seems to be an important factor in the binding. In addition, the isotopic effect on terbium luminescence lifetime may provide a useful method to distinguish between single and double stranded DNA. DSC results are consistent with cleavage of the double helix of DNA at pH 9 in the presence of terbium.     

Interactions between ions and free or immobilized ligands. Application of the competition method

Application of a competition method to determine affinities of ligands for ionic species in low polarity media is described. A soluble ligand, L, and a network-immobilized ligand, N, are allowed to interact with the counterion of an ionic chromophore A” according to the reaction NM⁺A⁻ + L → LM⁺A⁻ + N (K). K values were determined in toluene and in ether-type solvents for linear and macrocyclic polyethers and polyamines, as well as for other cation-complexing agents, by varying either N or L. In solvents such as dioxane, binding constants of M⁺A⁻ to N can be determined directly. Combined with K values they yield the complex formation constant, K_L, of the reaction M⁺A⁻ + L → LM+A⁻.     

On the relation between core electron binding energies of ions in solution and their solvation energies

Experimental and computational results from the study of positive and negative ions in solution are presented. The importance of short-range interactions between ion and solvent is studied with regard to core ionization of the ion. Exchange repulsion is found to be a significant factor in the interpretation of data for both cations and anions. Experimental results are presented for the core ionization of the OH^? ion in solution. The data show a strong similarity with corresponding data for the F^? ion, resulting in a large negative solvation energy for the final core hole state. The Be²⁺ ion shows large solvation energies for both ground- and core-ionized states, which is interpreted as due to charge transfer effects between solvent and ion.     

Thermodynamic characteristics of complex formation in the nickel(II) ion-β-alanine systems in aqueous solution

Heats of reactions between a nickel(II) ion and β-alanine were measured calorimetrically at 288.15, 298.15, and 308.15 K and ionic strengths of 0.5, 1.0, and 1.5 (KNO₃). Thermochemical data were processed with account for stepwise equilibria; attendant protolytic processes were taken into account together with complexing reactions. Extrapolation to the zeroth ionic strength with the use of a one-parameter equation gave standard thermodynamic characteristics of complex formation in the system. The influence of the supporting electrolyte and temperature on the heats of complex formation reactions was considered. Standard enthalpies of formation were calculated for NiAla⁺, NiAla₂, and NiAla₃⁻ species. Original Russian Text ? L.A. Kochergina, O.V. Platonycheva, O.M. Drobilova, V.V. Chernikov, 2009, published in Zhurnal Neorganicheskoi Khimii, 2009, Vol. 54, No. 2, pp. 377–384.     

Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules

The aqueous solvation free energies of ionized molecules were computed using a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1, MNDO, and PM3 semiempirical molecular orbital methods for the solute molecule and the TIP3P molecular mechanics model for liquid water. The present work is an extension of our model for neutral solutes where we assumed that the total free energy is the sum of components derived from the electrostatic/polarization terms in the Hamiltonian plus an empirical “nonpolar” term. The electrostatic/polarization contributions to the solvation free energies were computed using molecular dynamics (MD) simulation and thermodynamic integration techniques, while the nonpolar contributions were taken from the literature. The contribution to the electrostatic/polarization component of the free energy due to nonbonded interactions outside the cutoff radii used in the MD simulations was approximated by a Born solvation term. The experimental free energies were reproduced satisfactorily using variational parameters from the vdW terms as in the original model, in addition to a parameter from the one-electron integral terms. The new one-electron parameter was required to account for the short-range effects of overlapping atomic charge densities. The radial distribution functions obtained from the MD simulations showed the expected H-bonded structures between the ionized solute molecule and solvent molecules. We also obtained satisfactory results by neglecting both the empirical nonpolar term and the electronic polarization of the solute, i.e., by implementing a nonpolarization model. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1028–1038, 1999     

17O-NMR spectroscopy to study the coordination of oxygen-based ligands to lanthanide ions in solution

The number of oxygen-based ligands coordinated to lanthanide ions influences the physical and chemical properties of lanthanide complexes, making this number important to study. We used peak shifts in ¹⁷O-NMR spectroscopy to determine the number of individual nonhydroxyl-oxygen-based ligands coordinated to Dy³⁺. Oxygen-containing organic solvents were used as models to represent oxygen-based ligands to explore the scope of the technique because they contain a range of functional groups that have different electron-donating abilities and steric bulk. The measured coordination numbers of dimethylformamide, dimethyl sulfoxide, acetone, diethyl ether, tetrahydrofuran, di-isopropyl ketone, and hexamethyl acetone were consistent with reasonable values, indicating that ¹⁷O-NMR spectroscopy is a useful technique to study the coordination chemistry of nonhydroxyl ligands to lanthanide ions in solution.