A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

The modified characteristic finite difference fractional steps method for the coupled system of fluid dynamics in porous media and its analysis

For the coupled system of multilayer fluid dynamics in porous media, the modified characteristic finite difference fractional steps method applicable to parallel arithmetic is put forward and two‐dimensional and three‐dimensional schemes are used to form a complete set. Some techniques, such as calculus of variations, energy method, piecewise biquadratic interpolation, multiplicative commutation rule of difference operators, decomposition of high order difference operators and prior estimates are adopted. Optimal order estimates in L² norm are derived to determine the error in the approximate solution. This method has already been applied to the numerical simulation of multilayer fluid dynamics in porous media. © 2003 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 19: 665–681, 2003.     

LB技术制备大面积超薄PMMA抗蚀层的研究

采用自行研制的ＬＢ自动提膜装置，制备出大面积（１０×８ｃｍ２）、高质量的ＰＭＭＡ超薄抗蚀剂膜，并将其用于高分辨率铬掩模版的研制。通过电子束曝光，湿法蚀刻，制作了分辨率优于０．５μｍ，特征线宽０．３８μｍ的４（１００ｍｍ）铬掩模版。     

Cyclizations via Palladium-Catalyzed Allylic Alkylations [New Synthetic Methods (79)]

The history of ring systems in organic chemistry parallels their synthetic accessibility. Transition-metal-catalyzed cyclizations offer a new opportunity to create carbo- and heterocyclic compounds with great facility. Among these methods, allylic alkylations catalyzed by palladium have proven unusually productive because of the extraordinary chemo-, regio-, and diastereoselectivity and the continuing possibility for the development of enantioselectivity. The rules for ring closure differ from those for non-transition-metal-catalyzed reactions. A major benefit is the ability to generate medium (eight-, nine-, ten-, and eleven-membered) and large rings in preference to normal (five-, six- and seven-membered) rings. With the appropriate substrate, efficient macrocyclizations are possible under conditions of normal concentrations. A second major benefit derives from the complementary stereochemistry of the metalcatalyzed substitution (net retention of configuration) compared to non-metal-catalyzed reactions (inversion of configuration). Further, the requirement for the substrate to conform to the transition-metal template may impose a stereochemical preference in the intermediate that ultimately translates into the thermodynamically less stable organic product regardless of the stereochemistry of the starting material. While more work has focused on carbocyclic synthesis, the possibilities for heterocyclic synthesis are just beginning to be tapped. In addition to forming heterocycles by C? C bond formation, use of a heteroatom as a nucleophile has already proven effective for oxygen and nitrogen, with other nucleophiles awaiting investigation. New dimensions for cyclization via allylic alkylation arise by generating the requisite π-allylpalladium intermediates by methods other than palladium(0)-initiated allylic ionizations. In addition, metals other than palladium will clearly expand the possibilities, but as yet remain untapped.     

Structure analytical methods for quantitative reference applications

The analytical methods mass spectrometry, UV/Vis, IR, Raman, Fluorometry, XRD, Mössbauer, and NMR used to elucidate chemical structure are evaluated regarding their capabilities to be used as primary analytical techniques in quantitative measurements, considering the criteria in the CCQM definition of primary methods. This includes a review of the respective measurement equations, the evaluation of the measurement uncertainty, and a discussion of evidence for the “highest metrological level”, as obtained from intercomparisons in contest with other methods. It is shown that only few methods fulfill the CCQM criteria. Quantitative NMR spectroscopy is one of them and may be considered as a potential primary method as recommended by CCQM because of being free of empirical factors in the uncertainty budget.     

Recent Applications of α-Metalated Isocyanides in Organic Synthesis

Being both nucleophilic and electrophilic, α-metalated isocyanides can add to polar double bonds, forming heterocycles. They are also synthons for α-metalated primary amines. This article describes recent or improved procedures for their use in organic synthesis: (1) In heterocyclic syntheses to give 2-oxazolines, 2-imidazolines, 2-thiazolines, oxazoles and oligooxazoles, thiazoles, triazoles, imidazolinones, pyrroles, 5,6-dihydro-1,3-oxazines and -thiazines, and (via cycloaddition with nitrones) 2-imidazolidinones. (2) In the field of formylaminomethylenation, for example transformation of estrone methyl ether and a keto sugar into the corresponding α-formylaminoacrylic esters, and the conversion of aldehydes and ketones by 3- and 4-pyridyl-methyl isocyanides into N-(1-pyridyl-1-alkenyl)formamides and their hydrolysis to 3- and 4-acylpyridines. (3) In connection with the use of α-metalated isocyanides as synthons for α-metalated primary amines, the author demonstrates how they may be used for preparation of 1,2- and 1,3-amino alcohols, 1,2-diamines, 2,3-diaminoalkanoic acids and for synthesis of higher amino acids starting from simple amino acids.     

Comparison of path-complete Lyapunov functions via template-dependent lifts

This paper investigates, in the context of discrete-time switched systems, the problem of comparison for path-complete stability certificates. We introduce and study abstract operations on path-complete graphs, called lifts, which allow us to recover previous results in a general framework. Moreover, this approach highlights the existing relations between the analytical properties of the chosen set of candidate Lyapunov functions (the template) and the admissibility of certain lifts. This provides a new methodology for the characterization of the ordering relation of path-complete Lyapunov functions criteria, when a particular template is chosen. We apply our results to specific templates, notably the sets of primal and dual copositive norms, providing new stability certificates for positive switched systems. These tools are finally illustrated with the aim of numerical examples.     

High-Resolution,Higher-Order UV/VIS Derivative Spectrophotometry

Derivative spectrophotometry has gained increasing importance in the past two years and is currently experiencing vigorous development. Following and introduction the present article provides a review of this extremely effective method. In particular, the advantages of higher-order derivative spectrophotometry (HODS method, n > 2) are discussed on the basis of practical examples from a wide range of analytical fields. The results are achieved with the aid of a newly developed analog computer unit, whereby for the first time readily reproducible, low-noise, on-line spectra can be obtained up to the 7th order and even, in favorable cases, up to the 9th order. In practice it has proved valuable to work with spectra of the 3rd to 5th order; but even higher derivations could be profitable for the separation of strongly superposed signals or for “fingerprinting”.     

Modern Analysis

The important advances being made in modern analytical methods are indicative of the fundamental changes that are occuring in the theory and practice of “analytical chemistry”. “Information optimization” demands a new approach in teaching and research, and calls for the intergration of chemistry with other scientific and technical disciplines.     

Catalyzed Addition of Aldehydes to Activated Double Bonds—A New Synthetic Approach

In the presence of cyanide ions as catalyst, aromatic and heterocyclic aldehydes can be smoothly added to α,β-unsaturated ketones, esters, and nitriles in aprotic solvents to form γ-diketones, 4-oxo carboxylic esters, and 4-oxo nitriles. Thiazolium salts in the presence of bases are also suitable catalysts; they permit not only addition of aromatic and heterocyclic aldehydes but also the addition of aliphatic aldehydes.