Model carbohydrates

Carbohydrate hydroxyls represented by external atoms (CHEAT) is a force field designed specifically for modeling carbohydrates. 

The choice of solvent can also be beneficial in another respect. This possibility was highlighted by the findings of Cioffi on the Raney Nickel catalyzed hydrogen-deuterium exchange of a model carbohydrate [l-0-methyl-/l-D-galactopyranoside] but under ultrasonic irradiation (Tab. 13.2) [43], Extensive deuteration at C-4 position occurred for a series of ethereal solvents, the C-3 position was deuterated by seven solvent systems and the C-2 position deuterated less extensively, also by seven solvent systems. For l,4-dioxane-D20 no labeling at the C-2 position occurred and for l,2-dimethoxyethane-D20 no C-3 labeling was observed. 

Tab. 13.2 Pattern of labeling for a model carbohydrate under ultrasonic irradiation.

Molecular dynamics (MD) simulations are a class of molecular mechanics calculation which directly model the motions of molecular systems, often providing considerable information which cannot be obtained by any other technique, theoretical or experimental. MD simulations have only recently been applied to problems of carbohydrate conformation and motions, but it is likely that this technique will be widely used for modeling carbohydrates in the future. This paper introduces the basic techniques of MD simulations and illustrates the types of information which can be gained from such simulations by discussing the results of several simulations of sugars. The importance of solvation in carbohydrate systems will also be discussed, and procedures for including solvation in molecular dynamics simulations will be introduced and again illustrated from carbohydrate studies. 

The modeling of carbohydrates is undergoing rapid development. For example, the first comprehensive conformational mappings of disaccharides with flexible residues and the first molecular dynamics studies of carbohydrates have only recently been published. At the same time, interest in carbohydrates has been increasing dramatically, and there is a need for a publication that gently introduces the uninitiated and provides an overview of current research in the area. We feel that Computer Modeling ( Carbohydrate Molecules meets these needs. 

Bertoft, E. (2004). On the nature of categories of chains in amylopectin and their connection to the super helix model. Carbohydr. Polym., 57, 211-224. 

M. Bosco, A. Segre, S. Miertus, A. Cesaro, and S. Paoletti, The disordered conformation of K-carra-geenan in solution as determined by NMR experiments and molecular modeling, Carbohydr. Res., 340 (2005) 943-958. 

Iyer RN, Goldstein IJ. Quantitative studies on the interaction of concanavalin A, the carbohydrate-binding protein of the jack bean, with model carbohydrate-protein conjugates. Immunochemistry 1973 10 313-322. 

Table 16.2.3. Percentage of volatiles detected in the pyrograms of three model carbohydrates and of lignin [47],...

Titanium-based catalysts, would seem particularly attractive candidates, but the pore size of e.g. TS-1, is much too small to admit even a monosaccharide. Recently a number of synthetic approaches towards mesoporous titanium containing catalysts of the MCM-41 type have appeared in the literature . In the present paper we will deseribe the use of Ti-MCM-41 materials in the oxidation of the model mono- and disaccharides methyl a-D-glucopyranoside, sucrose and a,a-trehalose, and we will discuss the effect of the zeolite synthesis on the effectiveness in these reactions. Several preparative approaches of Ti-MCM-41 have been compared in the oxidation of these model carbohydrates. 

In this paper, we have compared two commonly used permethylation methods [4, 5] and have applied them to a model carbohydrate compound. The completeness of the methylation steps was established by matrix-assisted laser desorption/ionization tlme-of-flight mass spectrometry (MALDI-TOF MS). The methylated carbohydrate products were acid-hydrolyzed and converted to methylated partially acelylated aldononitrile derivatives (Me PAANs) for linkage analysis by gas chromatography-mass spectrometry (GC-MS) [11]. 

Cioffi et al., who previously has studied the Raney Nickel catalyzed hydrogen-deuterium exchange of a model carbohydrate (l-O-methyl-yS-n-galactopyranoside) under ultrasonic irradiation, have extended their investigations into the microwave area [58]. Using a D20-tetrahydrofuran (THF) solvent mixture the above compound could rapidly (<10 min) be deuterated with 86% incorporation at one site and an even better incorporation (91%) for sucrose other sites were labeled less extensively. 

Woodcock HL, Moran D, Pastor RW, McKerell AD Jr, Brooks BR (2007) Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate 2-ethoxy tetrahydropyran. Biophys J 93 1-10... 

One of the most powerful theoretical tools for modeling carbohydrate solution systems on a microscopic scale and evaluating the degree of flexibility of these molecules is the molecular dynamics technique (MD) which has become popular over the last two decades. The first reported works of MD carbohydrate simulation appeared in 1986 and since then an in-... 

Fig. 2 (a) Diverse biomolecules that contain glycerol, (b) Enantioselective acylation of glycerol by a peptide catalyst [49]. (c) Reactivity modulation in model carbohydrates [50]... 

In this paper we have studied amylose as a model carbohydrate, whieh is one of the typical representatives of polysaccharides, constituent part of starch [10]. It is convenient to use because it has a small molecular weight and its ability to dissolve in widespread solvents, including hot water. 

CA Rubin, JM Wasylyk, JG Baust. Investigation of vitrificaiton by nuclear magnetic resonance and differential scanning calorimetry in honey a model carbohydrate system. J Agric Food Chem 38 1824 1827, 1990. 

In order to increase the yield of the respective C-glycosyl compounds, the conditions (nature of the base, time, temperature, solvent) of the reaction were modified. Xylose was chosen as a model carbohydrate (Scheme 5), due to its potential interest in the activation of GAGs biosynthesis, as seen before. 

K. Azuma, T. Osaki, S. Ifuku, H. Saimoto, T. Tsuka, T. Imagawa, Y. Okamoto, and S. Minami, a-Chitin nanofibrils improve inflammatory and fibrosis responses in inflammatory bowel disease mice model, Carbohydr. Polym., 90 (1), 197-200,2012. 

Labropoulos KC, Niesz DE, Danforth SC, Kevrekidis PG. Dynamic rheology of agar gels theory and experiments part I development of a rheological model. Carbohydr Polym 2002 50 393 06. 

Yu, Z., Jin, C., Xin, M. and Jiamnin, H. 2009. Effect of Aloe vera polysaccharides on immunity and antioxidant activities in oral ulcer animal models. Carbohydrate polymers, 75(2),pp. 307-311. 

Woodcock, H. L., Moran, D., Pastor, R. W, MacKerell, A. D., Brooks, B. R. (2007). Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate, 2-Ethoxy Tetrahydropyran, Biophys, J 93,1-10. 

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