Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.     

Interval estimation of the critical value in a general linear model

Summary This paper concerns interval estimation of the critical value θ which satisfies under the general linear model,Y _i =μ(x _i )+ε _i (i=1,2,···), where for and the functional forms off _j ^′ s are known. From an asymptotic expansion it is shown that, under reasonable conditions, the limiting distribution of is normal. Thus in the large-sample case a confidence interval for θ can be obtained. Such a result is useful when one is interested in carrying out a retrospective analysis rather than designing the experiment (as in the Kiefer-Wolfowitz procedure). In Section 3 a sequential procedure is considered for confidence intervals with fixed width 2d. It is shown that, for a given stopping variableN, is also asymptotically normal asd→0. Thus the coverage probability converges to 1−α (preassigned) asd→0. An example of application in estimating the phase parameter in circadian rhythms is given for the purpose of illustration. Research partially supported by the NSF Grant DMS-8502346.     

Compressibility and Volume Effects of Mixing of 1-Propanol with Heavy Water

Speed of sound and density of 1-propanol + heavy water were measured in the whole concentration range at temperatures from 293 to 313 K. Isentropic compressibility was calculated from the Laplace formula. The partial molar volume of 1-propanol reaches a minimum at the mole fraction of 1-propanol x ₁ 0.03. At the same concentration, the compressibility isotherms intersect one another. These features of the investigated system are similar to those of 1-propanol + H₂O, that points to essential similarity of the two mixtures. A clathrate-like structure was suggested to explain the experimental results for dilute solutions of the alcohol. Somewhat more pronounced hydrophobic hydration in D₂O than in H₂O is manifested by an effect similar to that resulting from the elongation of the alcohol molecule.     

Density and Speed of Sound for Binary Mixtures of a Cyclic Ether with a Butanol Isomer

Densities and speeds of sound of the binary mixtures 1,3-dioxolane + 1-butanol, 1,3-dioxolane + 2-butanol, 1,4-dioxane + 1-butanol, and 1,4-dioxane + 2-butanol have been measured at 25 and 40°C. The excess molar volumes and excess isentropic compressibility coefficients were calculated from experimental data and fitted to a Redlich–Kister polynomial function. Results were analyzed in terms of molecular interactions and compared with literature data.     

Polyparametric modification equation for estimating thermodynamic properties of energetic nitro compounds

Calculation methods, based on hybrid density-functional theory with the basis sets of B3LYP/ 6-311+G (2d, p)//B3LYP/6-31G(d, p)and B3LYP/6-31+G(d)//B3LYP/6-31G(d, p), were applied to determine the thermodynamic characteristics of various energetic nitro compounds. A parametric modification equation and the least-squares approach were used to identify 21 of the energetic research compounds. The atomization energies of these 21 compounds have an average relative error of 0.21–0.25% of the experimental values. The enthalpy (H _f) and the Gibbs energy (G _f) of formation have mean absolute errors of 10.8–11.4 kJ/ mol (2.6–2.7 kcal/mol) and 10.0–10.3 kJ/mol (2.4 kcal/ mol), respectively. The enthalpy and the Gibbs energy of formation obtained exceed those in the literature obtained by semiempirical calculations. The calibrated least-squares parameters and parametric equations were used to predict H _f and G _f for the five newly developed energetic nitro compounds for further applications.Acknowledgements. The authors would like to thank the National Science Council of the Republic of China for financial support of this work under grant no. NSC-91-2113-M-014-003. The National Center for High-Performance Computing providing the computation facility is also acknowledged.     

Aldol condensations over reconstructed Mg-Al hydrotalcites: structure-activity relationships related to the rehydration method

Two different rehydration procedures in the liquid or gas phase have been applied to reconstruct mixed oxides derived from calcined hydrotalcite-like materials to be used as catalysts for aldol condensation reactions. The as-synthesized hydrotalcite, its decomposition product, as well as the reconstructed solids upon rehydration were characterized by XRD, N(2) adsorption, He pycnometry, FTIR, SEM, TEM, (27)Al MAS-NMR and CO(2)-TPD (TPD=temperature-programmed desorption). Compared to the Mg-Al mixed oxide rehydrated in the gas phase (HT-rg), that rehydrated in the liquid phase (HT-rl) exhibits a superior catalytic performance with respect to the aldol condensation of citral with ketones to yield pseudoionones and in the self-aldolization of acetone. The textural properties of HT-rl and HT-rg differ strongly and determine the catalytic behavior. A memory effect led to a higher degree of reconstruction of the lamellar structure when the mixed oxide was rehydrated in the gas phase rather than in the liquid phase, although liquid-phase rehydration under fast stirring produced a surface area that was 26 times greater. This contrasts to typical statements in the literature claiming a higher degree of reconstruction in the presence of large amounts of water in the medium. CO(2)-TPD shows that the number of OH(-) groups and their nature are very similar in HT-rg and HT-rl, and cannot explain the markedly different catalytic behavior. Accordingly, only a small fraction of the available basic sites in the rehydrated samples is active in liquid-phase aldol condensations. Our results support the model in which only basic sites near the edges of the hydrotalcite platelets are partaking in aldol reactions. Based on this, reconstructed materials with small crystallites (produced by exfoliation during mechanical stirring), that is, possessing a high external surface area, are beneficial in the reactions compared to larger crystals with a high degree of intraplatelet porosity.     

病态分析体系有偏估计的研究

运用广义岭估计和Ｌｉｕｋｅｊｉａｎ提出的有偏估计，对病态分析体系进行了数值模拟和实际光度测定，结果表明，广义岭估计显优于最小二乘估计，Ｌｉｕｋｅｊｉａｎ法有功效，可和为解析病态分析体系的化学计量学方法。     

Design and fabrication of 2 kHz nematic liquid crystal variable retarder with reflection mode

ABSTRACT

This study proposes a simple method of designing a high-speed liquid crystal variable retarder (LCVR) with reflection mode. First, a series of simple formulas is provided for analysing the effects of tilt incidence and birefringence of the liquid crystal on the phase retardation and response time of the LCVR. Then, a reflective LCVR is fabricated to validate the theoretical analysis. Measured results show that the response speed can reach 2.7 kHz with a phase retardation of 1 λ. Furthermore, the theoretical curve is close to the measured curve while the incident angle is less than 10°. However, the theoretical and measured values show a considerable difference under a large incident angle. This problem is discussed, and a modified method is given. This work is helpful for the design and fabrication of high-speed LCVR.     

Speed of Sound, Isentropic Compressibilities, and Excess Molar Volumes of Binary Mixtures Containing p-Dioxane

The speed of sound u in and densities of eight binary mixtures of p-dioxane (p-C₄H₈O₂) with methylcyclohexane (c-C₆H₁₁CH₃), 1-chlorohexane (C₆H₁₃C1), 1-bromohexane (C₆H₁₃Br), p-xylene [C₆H₄(CH₃)₂], propylbenzene (C₆H₅C₃H₇), methyl acetate CH₃COOCH₃), butyl acetate (CH₃COOC₄H₉), and amyl acetate (CH₃COOC₅H₁₁) were measured over the whole composition range at 30°C. Isentropic compressibilities (K _S), Rao's molar sound functions (R), excess molar volumes (V ^E), excess isentropic compressibilities (K _S ^E ) together with relative change in volume V/₁₂ values, have been obtained for all measured mole fractions. The excess partial molar volume (V₁-V ₁ ⁰ ) of p-dioxane in different solvents have also been estimated. The experimental results have been analyzed in terms of the Prigogine–Flory–Patterson theory of solutions.     

色谱技术在中药指纹图谱研究中的应用

 介绍了气相色谱、高效液相色谱、超临界流体色谱和高速逆流色谱等几种色谱技术在中药指纹图谱研究中的应用现状,以及使用模糊聚类分析和人工神经网络分析指纹图谱对中药进行模式识别和质量鉴定的方法。