Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

Cu(II) in liquid ammonia: an approach by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulation.

To investigate the solvation structure of the Cu(II) ion in liquid ammonia, ab initio quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold-coordinated species was found to be predominant in the HF case whereas five- and sixfold-coordinated complexes were obtained in a ratio 2:1 from the B3 LYP simulation. In contrast to hydrated Cu(II), which exhibits a typical Jahn-Teller distortion, the geometrical arrangement of ligand molecules in the case of ammonia can be described as a [2 + 4] ([2 + 3]) configuration with 4 (3) elongated copper-nitrogen bonds. First shell solvent exchange reactions at picosecond rate took place in both HF and B3 LYP simulations, again in contrast to the more stable sixfold-coordinated hydrate. NH3 ligands apparently lead to strongly accelerated dynamics of the Cu(II) solvate due to the "inverse" [2 + 4] structure with its larger number of elongated copper-ligand bonds. Several dynamical properties, such as mean ligand residence times or ion-ligand stretching frequencies, prove the high lability of the solvated complex.     

Selective solvation of Ag(I) iodate in methanol-dimethyl sulphoxide mixtures

The selective solvation of silver(I) iodate was studied in methanoldimethyl sulohoxide mixtures at 30° C by solubility and EMF measurements. The solubility of the salt increases continuously with the addition of dimethyl sulphoxide after a slight decrease into X_DMSO =0.1. The Gibbs energy of transfer of silver cation (determined on the basis of ferrocene reference method) decreases continuously while that of the iodate ion increases with the addition of dimethyl sulphoxide. The solvent transport number passes through a maximum (Δ = 2.0) around X_DMSO = 0.5. These results were interpreted as arising due to a heteroselective solvation of the salt, the silver ions being preferentially solvated by dimethyl sulphoxide and the iodate ion by methanol in these mixtures.     

水热法合成的MoVTeNbOx多组分氧化物催化剂上异丁烷的选择氧化

采用水热法合成了MoVTeNbOx多组分氧化物催化剂, 并用XRD, ICP, BET和SEM等方法对催化剂进行了表征, 考察了MoVTeNbOx多组分氧化物催化剂的组成、反应温度和空速对异丁烷选择氧化反应性能的影响. 其中组成为MoV0.3Te0.17Nb0.12Ox的催化剂显示出最好的催化活性和选择性, 在673 K下, 异丁烷的转化率为10.8%, 甲基丙烯醛(MAL)和甲基丙烯酸(MAA)的收率累积达到6.5%.     

A stannylene strategy for regioselective acylation and phosphorylation of 1,2-cyclohexylidene-myo-inositol. Its convenient resolution and phosphatidylinositol synthesis

The bis(dibutylstannylene) derivative of 1,2-cyclohexylidene-myo-inositol reacted with (S)-O-acetylmandeloyl chloride and diphosphate tetraesters to give 3,6-dimandelate and 3-phosphate, respectively. Using the stannylene methodology for the optical resolution and regioselective phosphorylation of the ketal, a concise synthesis of phosphatidylinositol with the natural configuration was accomplished.     

Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins

The classical simplex method is extended into the Semiglobal Simplex (SGS) algorithm. Although SGS does not guarantee finding the global minimum, it affords a much more thorough exploration of the local minima than any traditional minimization method. The basic idea of SGS is to perform a local minimization in each step of the simplex algorithm, and thus, similarly to the Convex Global Underestimator (CGU) method, the search is carried out on a surface spanned by local minima. The SGS and CGU methods are compared by minimizing a set of test functions of increasing complexity, each with a known global minimum and many local minima. Although CGU delivers substantially better success rates in simple problems, the two methods become comparable as the complexity of the problems increases. Because SGS is generally faster than CGU, it is the method of choice for solving optimization problems in which function evaluation is computationally inexpensive and the search region is large. The extreme simplicity of the method is also a factor. The SGS method is applied here to the problem of finding the most preferred (i.e., minimum free energy) solvation sites on a streptavidin monomer. It is shown that the SGS method locates the same lowest free energy positions as an exhaustive multistart Simplex search of the protein surface, with less than one-tenth the number of minizations. The combination of the two methods, i.e.. multistart simplex and SGS, provides a reliable procedure for predicting all potential solvation sites of a protein.     

Enthalpies of solvation for N-alkylamides in water and in carbon tetrachloride at 25°C

Molar enthalpies of solution at infinite dilution have been determined at 25°C for several N-alkyl and N,N-dialkylamides in water and in carbon tetrachloride, using a Calvet-type rotating calorimeter, and solution concentrations below 5×10^–2 molal. Relevant enthalpies of transfer between the two solvents also have been derived. Molar enthalpies of solvation have been obtained by adding enthalpies of vaporization to solution values. Results are compared with those of other laboratories on other substituted amides, and their dependence on the number of carbon atoms in the chain is discussed. A possible computation of solvation enthalpies of functional groups is suggested and results for hydration of peptide or similar groups present in the compounds examined are discussed in terms of current models of their hydration and hydrogen bond formation.Presented at the sixth Italian meeting on Calorimetry and Thermal Analysis (AICAT) held in Naples, December 4–7, 1984.     

Solvation of Cobalt(II) Ion in N,N-Dimethylformamide–Methanol Mixed Solvent: Calorimetry and VIS Spectroscopy Studies

The enthalpies of solution of Co(II) and Na(I) trifluoromethanesulfonates (triflates) in N,N-dimethylformamide (DMF)–methanol (MeOH) mixtures have been measured over the whole range of solvent composition. From these data the enthalpies of transfer of Co(II) and triflate ions from methanol to the mixed solvent have been determined usingliterature values of the enthalpies of transfer of the Na⁺ ion. The results have been analyzed by means of the theory of preferential solvation. The analysis revealed the preference of DMF for solvating the Co(II) ion in the MeOH-rich region of solvent composition and the lack of preference of any component in the DMF-rich region. Visible absorption spectra of the Co(II) ion in DMF–MeOH mixtures have been also measured in the whole range of solvent composition and analyzed using the partial least-squares method. The mean composition of the solvation sphere of the Co(II) ion versus solvent composition has been determined on the basis of both analyses. The results were found to be consistent with each other and with those obtained previously from FT-IR spectra.     

Proton magnetic relaxation study of water orientation around I− and Li+

Proton relaxation time measurements are performed for 6m aqueous solutions of⁷LiI and⁶LiI in D₂O containing small amounts of H₂O. The measurements are done at low temperatures and yield maxima of the relaxation rate plotted against 1/T. From the maxima of the relaxation rates, proteon-I^– and proton-Li⁺ distances in the first coordination sphere of the ions are determined, and from the knowledge of the ion-water oxygen distance it is shown that for iodide a somewhat broadened H-bonded configuration is valid and that for Li⁺ the electric dipole orientation deviates from the radial direction. In order to test the reliability of the method a proton-¹²⁷I interaction study is also performed in KI solution in glycerol. The I-H distance obtained is in satisfactory agreement with that found in the aqueous system.