Thermodynamics of solute transfer between chloroform and water

The apparent enthalpies, free energies and entropies of transfer from water saturated chloroform to chloroform saturated aqueous buffer (pH 7) were determined for five primary alcohols and six other organic nonelectrolytes using an isoperibol flow microcalorimeter. A linear relationship between the enthalpies and free energies of transfer is found for the homologous series of alcohols indicating that the occurrence of enthalpy-entropy compensation in solute transfer is not restricted to solvent systems of low mutual solubility. The apparent thermodynamics of transfer from chloroform to aqueous buffer were compared with those from 2,2,4-trimethylpentane to aqueous buffer and were rationalized in terms of solvation interactions.     

The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff

Using tRNA molecule as an example, we evaluate the applicability of the Poisson-Boltzmann model to highly charged systems such as nucleic acids. Particularly, we describe the effect of explicit crystallographic divalent ions and water molecules, ionic strength of the solvent, and the linear approximation to the Poisson-Boltzmann equation on the electrostatic potential and electrostatic free energy. We calculate and compare typical similarity indices and measures, such as Hodgkin index and root mean square deviation. Finally, we introduce a modification to the nonlinear Poisson-Boltzmann equation, which accounts in a simple way for the finite size of mobile ions, by applying a cutoff in the concentration formula for ionic distribution at regions of high electrostatic potentials. We test the influence of this ionic concentration cutoff on the electrostatic properties of tRNA.     

Gas to olive oil partition coefficients: a linear free energy analysis

Literature values of gas to olive oil partition coefficients at 37 degrees C have been assembled for 218 compounds. Application of an Abraham linear free energy equation correlates 215 compounds with R2=0.981 and a standard deviation, SD, of 0.196 log units. One hundred and eight compounds were then used as a training set, and the resulting equation was used to predict the remaining 107 compounds with an average error of 0.025, an absolute average error of 0.150, and a standard deviation of 0.224 log units. The linear free energy equation shows that as a solvent olive oil is not very polar but is reasonably basic, although with a weaker hydrogen bond base than ethyl acetate or acetone, and has no hydrogen bond acidity. The coefficients for partition from the gas phase to biological phases such as blood and brain lie between those for water and olive oil, which explains why gas to biological phase partition can be described in an empirical way by a combination of gas to olive oil and gas to saline coefficients.     

Partition of Neutral Molecules and Ions from Water to <Emphasis Type="Italic">o</Emphasis>-Nitrophenyl Octyl Ether and of Neutral Molecules from the Gas Phase to <Emphasis Type="Italic">o</Emphasis>-Nitrophenyl Octyl Ether

We have set out an equation for partition of 87 neutral molecules from water to o-nitrophenyl octyl ether, NPOE, an equation for partition of the 87 neutral molecules and 21 ionic species from water to NPOE, and an equation for partition of 87 neutral molecules from the gas phase to NPOE. Comparison with equations for partition into other solvents shows that, as regards partition of neutral (nonelectrolyte) compounds, NPOE would be a good model for 1,2-dichloroethane and for nitrobenzene. In terms of partition of ions and ionic species, NPOE is quite similar to 1,2-dichloroethane and not far away from other aprotic solvents such as nitrobenzene.     

A method for calculating the Gibbs energy of nonspecific solvation

A method for calculating the Gibbs energy of nonspecific solvation of nonelectrolytes was suggested. The new equation for the Gibbs energy of nonspecific solvation contains one solvent parameter that characterize nonspecific solvent-solute interactions and two experimental Gibbs energies of solvation in two standard solvents. The method is applicable to a wide range of solutes and solvents. It was successfully used to describe some 800 Gibbs energies of solvation for systems without specific solvent-solute interactions.     

Incorporating the excluded solvent volume and surface charges for computing solvation free energy

Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near‐solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near‐solute dielectric polarization from MD simulations, the first‐shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model. © 2013 Wiley Periodicals, Inc.     

Die Reaktion von wässerigem Epichlorhydrin mit Hydroxid- und Phenolat-Ionen

The reactions of epichlorhydrin with hydroxide and phenolate ions in water are shown to proceed by the same mechanism as the reactions of other epoxides with nucleophilic reagents, and not by direct attack on the halogen-substituted carbon. The effect of solvent composition on the linear free energy correlations, like the equation of SWAIN & SCOTT , is discussed on the basis of recent literature data.     

Facilitated transport of salts by neutral anion carriers

Partitioning of ions from water to the membrane solvent (NPOE) can be quantified by Gibbs free energies of transfer, deltaG(tr,NPOE)(ion). These were derived from transport studies of lipophilic salts through supported liquid membranes (SLMs) in the absence of the carrier. Partition coefficients Kp for various salts can now be calculated. The neutral anion receptors uranyl sal(oph)enes 1-5 transport Cl- and H2PO4- as tetrapropylammonium salts. The transport is diffusion-limited and can be described by two transport parameters Dm and K(ex). From the extraction constants K(ex) and the partition coefficients Kp of the transported salts, the association constants Ka of the anion receptors for Cl- and H2PO4- in NPOE were determined. Competitive transport with carriers 3 and 4 of NPr4H2PO4 and NPr4Cl demonstrated highly selective transport of H2PO4- even in the presence of excess of Cl-.     

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

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

Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3-benzazepines for the D1receptor

We computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1–SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson–Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1–SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D₁ dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.     

A solvolysis model for 2-chloro-2-methyladamantane based on the linear solvation energy approach

Solvolysis/dehydrohalogenation rates of 2-chloro-2-methyladamantane (CMA) in 15 hydrogen-bond acidic and/or basic solvents are studied. The rates of reaction in these solvents have been correlated with the solvation equation developed by Kamlet, Abraham, and Taft. The linear solvation energy relationship (LSER) derived from this study is given by the following equation: log k = -5.409 + 2.219 + 2.505alpha(1) - 1.823beta(1) where , alpha(1), and beta(1) are the solvation parameters that measure the solvent dipolarity/polarizability, hydrogen-bond acidity (electrophilicity), and hydrogen-bond basicity (nucleophilicity). A high correlation coefficient (r = 0.996, SD = 0.191) was achieved. The cavity term, which includes the Hildebrand parameter for solvent cohesive energy density, delta(H), was not found to be statistically significant for this reaction substrate. The resulting equation allows calculated rates of reaction in other solvents and provides insight into the reaction pathway. In a previously reported correlation for another tertiary chloride, tert-butyl chloride (TBC), the coefficients for alpha(1) and are significantly larger and the coefficient for is statistically significant. In addition, the coefficient for beta(1) in the TBC correlation is positive, rather than negative, indicating that the transition states for TBC and CMA are significantly different. These results demonstrate why the uses of simple solvolytic correlation methods may be invalid even for comparisons of similar type substrates, e.g., tertiary chlorides. Also, these results provide confidence in the use of multiple linear regression analysis for predicting solvolytic rates in additional solvents.     

Thermodynamic parameters of solvation of nonelectrolytes in aqueous solutions with hydrogen bond networks

The contributions from interaction and reorganization to the enthaplies of solvation of polar and nonpolar nonelectrolytes in aqueous solutions of formamide, ethanediol, and 1,2-propanediol, forming 3D-associated structures in the entire composition range, were calculated. The enthalpy terms of the solvation of nonelectrolytes in aqueous solutions of methyl-and dimethylformamide were estimated. The data were compared considering the thermodynamic characteristics of these aqueous systems that we determined previously. It was found that the shape of the concentration dependences of the enthalpies of solvation of nonelectrolytes in all the examined solutions is determined by the reorganization term. The fact that the solvation of nonelectrolytes in water is the most exothermic compared to the aqueous-organic systems under consideration is due to the lowest value of the reorganization term in water, despite the fact that nonelectrolytes interact with water more weakly than with the nonaqueous components.     

The performance of ANI-ML potentials for ligand-n(H2O) interaction energies and estimation of hydration free energies from end-point MD simulations

Here, we investigate the performance of “Accurate NeurAl networK engINe for Molecular Energies” (ANI), trained on small organic compounds, on bulk systems including non-covalent interactions and applicability to estimate solvation (hydration) free energies using the interaction between the ligand and explicit solvent (water) from single-step MD simulations. The method is adopted from ANI using the Atomic Simulation Environment (ASE) and predicts the non-covalent interaction energies at the accuracy of wb97x/6-31G(d) level by a simple linear scaling for the conformations sampled by molecular dynamics (MD) simulations of ligand-n(H₂O) systems. For the first time, we test ANI potentials' abilities to reproduce solvation free energies using linear interaction energy (LIE) formulism by modifying the original LIE equation. Our results on ~250 different complexes show that the method can be accurate and have a correlation of R² = 0.88–0.89 (MAE <1.0 kcal/mol) to the experimental solvation free energies, outperforming current end-state methods. Moreover, it is competitive to other conventional free energy methods such as FEP and BAR with 15-20 × fold reduced computational cost.     

Quantum chemistry in solution by combining 3D integral equation theory with a cluster embedding approach

Free energy changes associated with chemical reactions in solution are treated by integral equation theory in the form of the 3D reference interaction site model (RISM) in combination with quantum-chemical calculations via an embedded cluster approach (EC-RISM). The electronic structure of the solute is computed self-consistently with the solvent structure by mapping the charge distribution of the solvent onto a set of discrete background point charges that are added to the molecular Hamiltonian. The EC-RISM procedure yields chemical accuracy in free energy predictions for several benchmark systems without adjusting empirical parameters. We apply the method to the standard reaction free energy for the gauche-trans equilibrium of 1,2-dichloroethane in water and to pKa shift calculations for trifluoroacetic acid/acetic acid and 4-nitroaniline/aniline in water.     

Free energy of an inhomogeneous polymer–polymer–solvent system. II

A complete expression for the enthalpy of mixing of inhomogeneous polymer–polymer–solvent systems applicable for small as well as large concentration fluctuations has been developed. This is used to express the free energy of inhomogeneous polymer–polymer–solvent systems in an extended form of the Landau-Ginzburg functional. The gradient energy parameters obtained here are consistent with the published results. The free energy functional has been applied to develop a generalized continuity equation for spinodal decomposition in polymer–polymer systems. A linearized version of this continuity equation has been used to study the effect of the gradient terms on the dominant wavelength during spinodal decomposition.     

Universal model based on the mobile order and disorder theory for predicting lipophilicity and partition coefficients in all mutually immiscible two-phase liquid systems

The quantitative thermodynamic development of the mobile order and disorder theory in H-bonded liquids has been extended in order to predict partition coefficients. The model enables "a priori" estimation of the partition coefficient (log P) of neutral solutes, not only in the conventional 1-octanol/water reference but also in all mutually saturated two-phase systems made up of largely immiscible solvents. The model is obtained from the thermodynamic treatment of the various physicochemical free energy processes encoded in the overall distribution process and accordingly provides a useful tool for better understanding both the origin and the factors, such as the solute molar volume, that determine the partition coefficient of nonelectrolytes in a given system. From the comparison of the relative magnitude of the processes contributing to the log P value, a lot of information can also be gained regarding the variation in log P of the same substance partitioned between different solvent systems. As a demonstration, the model has been successfully applied to predict the log P of a great number of chemicals of varying structure, size, and chemical nature partitioned in a large set of essentially immiscible solvent pairs, differing either by their nonpolar or by their polar phase. In the systems involving water as the polar phase, the hydrophobic effect is always the driving force that governs the distribution process irrespective of the interacting or noninteracting nature of the substances studied. In the other two-phase systems, the partitioning of complexing solutes in particular appears to be ruled rather by their hydrogen-bonding capabilities than by their hydrophobicities.     

Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation

The relationship is investigated for QM/MM (quantum-mechanical/molecular-mechanical) systems between the fluctuations of the electronic state of the QM subsystem and of the solvation effect due to the QM-MM interaction. The free-energy change due to the electron-density fluctuation around its average is highlighted, and is evaluated through an approximate functional formulated in terms of distribution functions of the many-body coupling (pairwise non-additive) part of the QM-MM interaction energy. A set of QM/MM simulations are conducted in MM water solvent for QM water solute in ambient and supercritical conditions and for QM glycine solute in the neutral and zwitterionic forms. The variation of the electronic distortion energy of the QM solute in the course of QM/MM simulation is then shown to be compensated by the corresponding variation of the free energy of solvation. The solvation free energy conditioned by the electronic distortion energy is further analyzed with its components. It is found that the many-body contribution is essentially equal between the free energy and the average sum of solute-solvent interaction energy.