We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

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The Amber biomolecular simulation programs

Chitin and chitosan: Properties and applications

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

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Cellulose nanomaterials review: structure, properties and nanocomposites

Fundamental features of microbial cellulose utilization are examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of cellulolytic microorganisms, ecological aspects of cellulase-degrading communities, and rate-limiting factors in nature. The methodological basis for studying microbial cellulose utilization is considered relative to quantification of cells and enzymes in the presence of solid substrates as well as apparatus and analysis for cellulose-grown continuous cultures. Quantitative description of cellulose hydrolysis is addressed with respect to adsorption of cellulase enzymes, rates of enzymatic hydrolysis, bioenergetics of microbial cellulose utilization, kinetics of microbial cellulose utilization, and contrasting features compared to soluble substrate kinetics. A biological perspective on processing cellulosic biomass is presented, including features of pretreated substrates and alternative process configurations. Organism development is considered for "consolidated bioprocessing" (CBP), in which the production of cellulolytic enzymes, hydrolysis of biomass, and fermentation of resulting sugars to desired products occur in one step. Two organism development strategies for CBP are examined: (i) improve product yield and tolerance in microorganisms able to utilize cellulose, or (ii) express a heterologous system for cellulose hydrolysis and utilization in microorganisms that exhibit high product yield and tolerance. A concluding discussion identifies unresolved issues pertaining to microbial cellulose utilization, suggests approaches by which such issues might be resolved, and contrasts a microbially oriented cellulose hydrolysis paradigm to the more conventional enzymatically oriented paradigm in both fundamental and applied contexts.

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Microbial cellulose utilization: fundamentals and biotechnology.

A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

Crystals of the disaccharide, (2,3,4,6-tetra- O -acetyl- α - d -glucopyranosyl) (2,3,4,6–tetra- O -acetyl- β - d -glucopyranosyl)amine belong to the space group P2 1 with a =14.848(2), b =21.838(3), c =11.534(2) A, and β =113.72(4)° and Z=4. The crystal structure was solved by direct methods and refined by the full-matrix least squares procedure to an R value of 0.049 ( Rw =0.46) for 4262 observed reflections. This work provides the first crystalline features in the diglycosylamine series and this molecule can be considered as a N -analogue of peracetylated α , β -trehalose. The conformational features of the two independent diglycosylamine molecules do not display any major significant differences. The d –glucopyranose residues have the usual 4 C 1 chair conformations, whereas all the primary and secondary acetate groups display usual orientations. In the crystal structure the hydrogen atom covalently linked to the nitrogen at the glycosidic linkage could be located; its configuration is ( R ) providing the priority is given to the ( R ) carbon neighbor (C-1 β ). The torsional angles at the glycosidic linkages Φα (O-5–C-1 α –N-1–C-1 β ), Φβ (C-1 α –N-1–C-1 β –O-5) of the two molecules have values of (57.6°,−78.8°) and (59.8°,−85.9°), respectively, slightly different from the conformation found in α , β -trehalose monohydrate. These conformations have been rationalized through the use of molecular mechanics calculations. The packing mode is highly anisotropic, with the existence of chains of molecules along the c axis, stabilized by numerous van der Waals contacts and by a strong hydrogen bond, involving the NH group of the glycosidic linkage and the carbonyl group of one acetate.

The Crystal and Molecular Structure of a Diglycosylamine: The N-Analogue of Peracetylated α,β-Trehalose.

The title compound, C6H8N2O3S2·H2O, was synthesized from l-erythrulose and the structure of the enantiopure (4R,9S) diastereo­isomer has been determined. The structure is a hydrate and the water mol­ecules establish a hydrogen-bond network that involves the hydroxy­methyl group as well as one N and one S atom.

(4R,9S)-4-Hydroxymethyl-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dithione monohydrate

The application of molecular modelling methods to the realistic description of cell wall polysaccharides is described. In a first section, the basic principles and tools are presented; they provide a consistent description of the levels of structural organization of polysaccharides, from the basic monomeric components to the more complex assemblies of macromolecular chains and their interactions. The second section provides a comprehensive illustration which includes the application of these methods to the elucidation of the structural features of the plant cell wall polysaccharides, pectins. The ordered and disordered states of both the `smooth' and the `hairy' regions of the pectin components are described, along with a discussion of the role of some key structural moieties such as the degree of esterification or acetylation. The stereochemical and electrostatic requirements for ionic binding to the polysaccharide chain are also presented. In an effort to provide a more global view, a `canonical' structure of pectin has been constructed and described; it corresponds to a hypothetical model having a molecular mass of 50 kDa. The main structural features of rhamnogalacturonan II, which have been determined to date, are also reported.

The Three‐Dimensional Structures of the Pectic Polysaccharides

Conformational studies of oligomethylene glycol derivatives and related compounds. part ii. crystal and molecular structure of ethylene glycol di(parachlorobenzoate), c16h12o4cl2

The present report assesses the capability of a soluble glycosyltransferase to modify glycolipids organized in two synthetic membrane systems that are attractive models to mimic cell membranes: giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs). The objective was to synthesize the Gb3 antigen (Galα1,4Galβ1,4Glcβ-Cer), a cancer biomarker, at the surface of these membrane models. A soluble form of LgtC that adds a galactose residue from UDP-Gal to lactose-containing acceptors was selected. Although less efficient than with lactose, the ability of LgtC to utilize lactosyl–ceramide as an acceptor was demonstrated on GUVs and SLBs. The reaction was monitored using the B-subunit of Shiga toxin as Gb3-binding lectin. Quartz crystal microbalance with dissipation analysis showed that transient binding of LgtC at the membrane surface was sufficient for a productive conversion of LacCer to Gb3. Molecular dynamics simulations provided structural elements to help rationalize experimental data.

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Serge Pérez

Papers

The Crystal and Molecular Structure of a Diglycosylamine: The N-Analogue of Peracetylated α,β-Trehalose.

(4R,9S)-4-Hydroxymethyl-3,8-dioxa-1,6-diazaspiro[4.4]nonane-2,7-dithione monohydrate

The Three‐Dimensional Structures of the Pectic Polysaccharides

Conformational studies of oligomethylene glycol derivatives and related compounds. part ii. crystal and molecular structure of ethylene glycol di(parachlorobenzoate), c16h12o4cl2

Enzymatic Glyco-Modification of Synthetic Membrane Systems