Computers & chemistry最新文献

The molecular geometries and internal rotational barriers of the nitro group of 3-nitrotoluene (3-NT), 4-nitrotoluene (4-NT), 3-nitrophenol (3-NP), 4-nitrophenol (4-NP), 3-nitroaniline (3-NA), and 4-nitroaniline (4-NA) were calculated by five different types of density functional theory (DFT) methods with three different levels of basis sets. Analyses of the torsional angles of the nitro, methyl, amino, and hydroxyl groups indicate that 3-NP, and 4-NP are planar molecules, but 3-NT, 4-NT, 3-NA, and 4-NA are not planar molecules. Internal rotational barriers of the nitro group were calculated as the V₂ barrier, and the NO₂ torsional potentials for each molecule were given. The heights of the V₂ barrier vary with the DFT methods, the basis sets, and the kinds and positions of substituents. The average values of the V₂ barriers for 3-NT, 4-NT, 3-NP, 4-NP, 3-NA, and 4-NA are 6.44, 6.92, 6.64, 7.93, 6.38, and 9.13 kcal/mol, respectively. Torsional potentials of the OH and NH₂ groups of nitrophenol and nitroaniline derivatives were also studied by a B3LYP/6-31G* approach. Except for the OH group in 2-NP, these derivatives have the V₂ barrier.

The function of a protein is closely correlated to its subcellular location. Is it possible to utilize a bioinformatics method to predict the protein subcellular location? To explore this problem, proteins are classified into 12 groups (Protein Eng. 12 (1999) 107–118) according to their subcellular location: (1) chloroplast, (2) cytoplasm, (3) cytoskeleton, (4) endoplasmic reticulum, (5) extracellular, (6) Golgi apparatus, (7) lysosome, (8) mitochondria, (9) nucleus, (10) peroxisome, (11) plasma membrane and (12) vacuole. In this paper, the neural network method was proposed to predict the subcellular location of a protein according to its amino acid composition. Results obtained through self-consistency, cross-validation and independent dataset tests are quite high. Accordingly, the present method can serve as a complement tool for the existing prediction methods in this area.

Libraries of cyclic peptides are being synthesized using combinatorial chemistry for high throughput screening in the drug discovery process. This paper describes the min_syn_steps.cpp program (available at http://www.imb.uq.edu.au/groups/smythe/tran), which after inputting a list of cyclic peptides to be synthesized, removes cyclic redundant sequences and calculates synthetic strategies which minimize the synthetic steps as well as the reagent requirements. The synthetic steps and reagent requirements could be minimized by finding common subsets within the sequences for block synthesis. Since a brute-force approach to search for optimum synthetic strategies is impractically large, a subset-orientated approach is utilized here to limit the size of the search.

The computer package CST (Conversions, Standardization and Transformations) is useful for general manipulations of the zero-field splitting (ZFS) and crystal field (CF) parameters for various systems, especially for transition ions at orthorhombic and lower symmetry sites in crystals. The ZFS parameters are extensively used in the EMR and related spectroscopic and magnetic studies (e.g. magnetic susceptibility, magnetic anisotropy, Mössbauer spectroscopy), whereas the CF parameters in optical absorption spectroscopy, inelastic neutron scattering, and infrared spectroscopy. An extended version of the CST package developed recently is presented in this paper. The standardization, including the standardization errors, for the five possible non-standard ranges of the ‘rhombicity’ parameter for monoclinic and triclinic symmetry in the local axis system has been worked out. The handling of the border points in the standardization module has been improved. The rotational invariants used before only for the transformations of the CF parameters have been incorporated into the standardization module for the CF and ZFS parameters expressed in any of the major tensor operator notations. The input option in the Euler angles has been added into the transformation module, and the newest physical constants in the unit conversions module have been adopted. Specific applications of the CST package for the CF and ZFS parameters will be presented elsewhere.

In this paper we present the results of a computational study that analyses the relationship between the noise associated with the optical transmittance of a system of particles and the morphology of such particles. Computational algorithms have been developed in order to represent the different morphologies within a wide range of sizes. By using this methodology, it has been possible to study the morphology of particles in a virtual system, therefore avoiding the distortions that would inevitably be present in a real system. As a consequence of this study, a classification of the morphologies observed has been made according to the amount of noise they would add to the transmittance of a system of particles. The theoretical results obtained are in good agreement with the available experimental data obtained in real systems.

It is necessary to generate the automorphism group of a chemical graph in computer-aided structure elucidation. In this paper, an algorithm was developed by the all-paths topological symmetry algorithm to build the automorphism group of a chemical graph. A comparison of several topological symmetry algorithms reveals that the all-paths algorithm (APA) could yield the correct class of a chemical graph. It lays a foundation for the ESESOC system in computer-aided structure elucidation.

Information agents integrate multiple distributed heterogeneous information sources. The challenging yet unsolved problem that remains, is to ensure the semantic consistency of the integrated data. In this paper we set out to develop a general approach to inconsistency management for information agents. It is implemented as part of the EDITtoTrEMBL system and applied on a large real-world problem in the domain of bioinformatics.