Universal solvation model based on conductor‐like screening model

Atomic surface tensions are parameterized for use with solvation models in which the electrostatic part of the calculation is based on the conductor‐like screening model (COSMO) and the semiempirical molecular orbital methods AM1, PM3, and MNDO/d. The convergence of the calculated polarization free energies with respect to the numerical parameters of the electrostatic calculations is first examined. The accuracy and precision of the calculated values are improved significantly by adjusting two parameters that control the segmentation of the solvent‐accessible surface that is used for the calculations. The accuracy of COSMO calculations is further improved by adopting an optimized set of empirical electrostatic atomic radii. Finally, the electrostatic calculation is combined with SM5‐type atomic surface tension functionals that are used to compute the nonelectrostatic portions of the solvation free energy. All parameterizations are carried out using rigid (R) gas‐phase geometries; this combination (SM5‐type surface tensions, COSMO electrostatics, and rigid geometries) is called SM5CR. Six air–water and 76 water–solvent partition coefficients are added to the training set of air–solvent data points previously used to parameterize the SM5 suite of solvation models, thereby bringing the total number of data points in the training set to 2266. The model yields free energies of solvation and transfer with mean unsigned errors of 0.63, 0.59, and 0.61 kcal/mol for AM1, PM3, and MNDO/d, respectively, over all 2217 data points for neutral solutes in the training set and mean unsigned errors of 3.0, 2.7, and 3.1 kcal/mol, respectively, for 49 data points for the ions. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 340–366, 2000     

气相和溶液中金属离子与腺嘌呤配位选择性的理论研究

在B3LYP/6-31G(d,p)水平,全优化Mg2+、Ca2+、Mn2+、Co2+、Zn2+、Cu2+、Ni2+、Cd2+ (用有效实势(ECP) 方法处理)与腺嘌呤(A) N(1)、N(7)位点配位的两类配合物气相结构,通过相互作用能和自由能分析分别得出两位点对所研究金属离子的选择性顺序;后采用Onsager模型,优化其在水溶液(=78.39)中的结构,讨论溶剂效应对上述顺序的影响;通过相对自由能分析分别得出气相和溶液中,同种金属对两位点的选择性规律。溶液中金属离子与N(7)位配位的相对优选顺序为:Co2+ > Mg2+ > Cd2+ > Ca2+ > Zn2+ > Mn2+ > Ni2+ > Cu2+。     

Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets,protocols, and force fields

The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 769–780, 1998     

Estimating relative free energies from a single ensemble: Hydration free energies

The ability to determine the free energy of solvation for a number of small organic molecules with varying sizes and properties from the coordinate trajectory of a single simulation of a given reference state was investigated. The relative free energies were estimated from a single step perturbation using the perturbation formula. The reference state consisted of a cavity surrounded by solvent. To enhance sampling a soft-core interaction was used for the cavity. The effect of the size of the cavity, the effective core height, and the length of simulation on the ability to reproduce results obtained from thermodynamic integration calculations was considered. The results using a single step perturbation from an appropriately chosen initial state were comparable to results from thermodynamic integration calculations for a wide range of compounds. Using a large number of compounds the computational efficiency was potentially increased by 2–3 orders of magnitude over traditional free energy approaches. Factors determining the efficiency of the approach are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1604–1617, 1999     

Theoretical evaluation of some interactions in the system of acetylene-alkali metal hydroxide-DMSO

Within the ab initio approach and with the use of density functional theory the formation of solvation shells of nondissociated alkali metals hydroxides of the corresponding cations and the hydroxide ion in dimethyl sulfoxide (DMSO) is studied. Complexes in which the alkali metal environment contains the coordinated acetylene molecule along with solvent molecules are considered. The coordination number of the hydroxide ion in DMSO is shown to be 4. It is demonstrated that solvated cations of alkali metals cannot form π-complexes with the acetylene molecule, whereas the introduction of molecular acetylene into the solvation sphere of nondissociated NaOH and KOH is possible.     

Partitioning behaviour of organic compounds between ionic liquids and supercritical fluids

Applications and prospects of two-phase, tuneable solvent systems composed of ionic liquids (ILs) and supercritical fluids with an emphasis on supercritical carbon dioxide (scCO(2)) are reviewed. The IL-scCO(2) biphasic systems have increasingly been used in diverse fields of chemistry and technology, and some examples of these applications are mentioned here. Rational design of such applications can obviously benefit from pertinent data on phase equilibria including the partition coefficients of the prospective products and reactants between the two phases. Therefore, a reliable technique to measure the limiting partition coefficients would be of value. Here, the pros and cons of supercritical fluid chromatography in this respect are discussed. An overview of methods for predictive thermodynamic modelling of binary (IL-scCO(2)) and ternary (solute-IL-scCO(2)) systems is also included.     

On-line preferential solvation studies of polymers by coupled chromatographic-Fourier transform infrared spectroscopic flow-cell technique

Qualitative and quantitative comparison between liquid chromatography (LC) and LC coupled with Fourier transform infrared spectroscopy (LC-FTIR) to evaluate preferential solvation phenomenon of polymers in a mixed solvent has been performed. These studies show that LC-FTIR technique leads to detailed structural information without the requirement for determination of additional parameters for quantitative analysis except calibration. Appropriate experimental conditions for preferential solvation study have been established by variation of polymer concentration, molar mass and eluent content.     

A comparative theoretical study of dipeptide solvation in water

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).     

Heuristic molecular lipophilicity potential (HMLP): lipophilicity and hydrophilicity of amino acid side chains

Heuristic molecular lipophilicity potential (HMLP) is applied in the study of lipophilicity and hydrophilicity of 20 natural amino acids side chains. The HMLP parameters, surface area S(i), lipophilic indices L(i), and hydrophilic indices H(i) of amino acid side chains are derived from lipophilicity potential L(r). The parameters are correlated with the experimental data of phase-transferring free energies of vapor-to-water, vapor-to-cyclohexane, vapor-to-octanol, cyclohexane-to-water, octanol-to-water, and cyclohexane-to-octanol through a linear free energy equation DeltaG(0)(tr,i) = b(0) + b(1)S(i) (+) + b(2)S(i) (-) + b(3)L(i) + b(4)H(i). For all above six phase-transfer free energies, the HMLP parameters of 20 amino acid side chains give good calculation results using linear free energy equation. HMLP is an ab initio quantum chemical approach and a structure-based technique. Except for atomic van der Waals radii, there are no other empirical parameters used. The HMLP has clear physical and chemical meaning and provides useful lipophilic and hydrophilic parameters for the studies of proteins and peptides.     

Splay-bend textures involving tetrahedratic order

We show that defect-free splay-bend textures are less energetic compared to uniform states in liquid-crystalline phases that possess both quadrupolar (nematic) and octupolar (tetrahedratic) order. This is because, in such systems, there is a symmetry-allowed linear gradient term in the energy. Another unusual feature of these splay-bend textures is the fact that they have a non-homogeneous, space-dependent free-energy density. These results may help clarify some mysterious features noted for the B7 liquid-crystal phase formed by achiral banana-shaped molecules.