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Molecular Representation (molecular + representation)
Selected AbstractsA case of structure determination using pseudosymmetryACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Sergei Radaev Here, a case is presented of an unusual structure determination which was facilitated by the use of pseudosymmetry. Group A streptococcus uses cysteine protease Mac-1 (also known as IdeS) to evade the host immune system. Native Mac-1 was crystallized in the orthorhombic space group P21212. Surprisingly, crystals of the inactive C94A mutant of Mac-1 displayed monoclinic symmetry with space group P21, despite the use of native orthorhombic Mac-1 microcrystals for seeding. Attempts to solve the structure of the C94A mutant by MAD phasing in the monoclinic space group did not produce an interpretable map. The native Patterson map of the C94A mutant showed two strong peaks along the (1 0 1) diagonal, indicating possible translational pseudosymmetry in space group P21. Interestingly, one-third of the monoclinic reflections obeyed pseudo-orthorhombic P21212 symmetry similar to that of the wild-type crystals and could be indexed and processed in this space group. The pseudo-orthorhombic and monoclinic unit cells were related by the following vector operations: am = bo,co, bm = ao and cm = ,2co,bo. The pseudo-orthorhombic subset of data produced good SAD phases, leading to structure determination with one monomer in the asymmetric unit. Subsequently, the structure of the Mac-1 mutant in the monoclinic form was determined by molecular replacement, which showed six molecules forming three translationally related dimers aligned along the (1 0 1) diagonal. Knowing the geometric relationship between the pseudo-orthorhombic and the monoclinic unit cells, all six molecules can be generated in the monoclinic unit cell directly without the use of molecular replacement. The current case provides a successful example of the use of pseudosymmetry as a powerful phase-averaging method for structure determination by anomalous diffraction techniques. In particular, a structure can be solved in a higher pseudosymmetry subcell in which an NCS operator becomes a crystallographic operator. The geometrical relationships between the subcell and parental cell can be used to generate a complete molecular representation of the parental asymmetric unit for refinement. [source] The Study of Molecular Modeling for Heavy Oil Thermal CrackingCHEMICAL ENGINEERING & TECHNOLOGY (CET), Issue 9 2007L. Yan Abstract The tighter specifications for refining products have gradually led refineries to focus on the molecular modeling of petroleum processing. In this work, a systematic methodology is presented for the molecular modeling of heavy oil thermal cracking (HOTC). This research which is based on a microscopic understanding provides a basis to achieve better design, management, optimization, and control of HOTC. The molecular information of HOTC product streams is represented in the form of a MTHS (molecular type homologous series) matrix. From consideration of the complexity of structural isomers in heavy petroleum fractions, the heavy molecules in a homologous series are grouped to reduce the dimension of the MTHS matrix. Transformation correlations are developed to capture the molecular properties of each homologous series in the MTHS matrix and to interrelate the molecular composition and bulk properties of the product streams. The HOTC process model was built on the basis of the molecular representation provided by the MTHS matrix and the transformation correlations. Two case studies are illustrated for validation of the proposed model and methodology. [source] Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolutionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2009Ramon Carbó-Dorca Abstract Classical quantitative structure-properties relationship (QSPR) statistical techniques unavoidably present an inherent paradoxical computational context. They rely on the definition of a Gram matrix in descriptor spaces, which is used afterwards to reduce the original dimension via several possible kinds of algebraic manipulations. From there, effective models for the computation of unknown properties of known molecular structures are obtained. However, the reduced descriptor dimension causes linear dependence within the set of discrete vector molecular representations, leading to positive semi-definite Gram matrices in molecular spaces. To resolve this QSPR dimensionality paradox (QSPR DP) here is proposed to adopt as starting point the quantum QSPR (QQSPR) computational framework perspective, where density functions act as infinite dimensional descriptors. The fundamental QQSPR equation, deduced from employing quantum expectation value numerical evaluation, can be approximately solved in order to obtain models exempt of the QSPR DP. The substitution of the quantum similarity matrix by an empirical Gram matrix in molecular spaces, build up with the original non manipulated discrete molecular descriptor vectors, permits to obtain classical QSPR models with the same characteristics as in QQSPR, that is: possessing a certain degree of causality and explicitly independent of the descriptor dimension. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Prediction of Polymer Properties from their Structure by Recursive Neural Networks,MACROMOLECULAR RAPID COMMUNICATIONS, Issue 9 2006Celia Duce Abstract Summary: We propose a new approach for predicting polymer properties from structured molecular representations based on recursive neural networks. To this aim, a structured representation is designed for the modeling of polymer structures. This representation can also account for average macromolecule characteristics. Preliminarily, this model is applied to the calculation of the Tg of (meth)acrylic polymers with different stereoregularity. Representation of poly(methyl methacrylate) as a chemical tree and unfolding of the encoding process through its structure. [source] | ||||||||||