Spatial Models of Sugars and Their Compounds

Spatial Models of Sugars and Their Compounds

Gennadiy Vladimirovich Zhizhin
Copyright: © 2021 |Pages: 14
DOI: 10.4018/IJARB.2021070102
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Abstract

The images of saccharide and polysaccharide molecules in spaces of various dimensions are considered. A method has been developed for obtaining simplified three-dimensional images of sugar molecules and their chains based on their images in spaces of higher dimensions. It was found that three-dimensional images of furanose and pyranose molecules fundamentally differ from each other to form convex and, accordingly, non-convex bodies. This leads to fundamental differences in the structure of polysaccharides from these molecules.
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Introduction

Sugar molecules are widespread in nature and play an important role in all living organisms. Sugars are found in nucleic acids, in fruit sikes (“grape sugar”), as well as in human and animal blood (“blood sugar”). They are part of many glycolipids and glycoproteins. Sugars are used by plants to transport and store carbohydrates in soluble form. Sugarcane and sugar beets are rich in sugars (cane and beet sugar). Bees using sugar from flower nectar produce honey. This class of compounds includes simple sugars (monosaccharides) and their polymers - oligosaccharides and polysaccharides. The classification of monosaccharides is based on the number of carbon atoms in the molecule (pentoses, hexoses, etc.), as well as on the chemical nature of the carbonyl group (aldoses and ketoses). A small fraction of sugar molecules (less than 0.1%) in living organisms is linear. The vast majority of monosaccharide molecules are present in living organisms with the formation of rings of carbon atoms containing one oxygen atom in the ring (pyranoses are rings with five carbon atoms and one oxygen atom, furanoses are rings with four carbon atoms and one oxygen atom). The linear forms of monosaccharides are usually depicted in the form of Fischer projections, and the cyclic forms of monosaccharides are depicted in the form of Haworth projections (Metzler, 1980; Lehninger, 1982; Koolman and Roehm, 2013). Neither projection gives a spatial image of monosaccharide molecules. Although it is clear that spatial images of molecules allow us to understand their structure, location in space and the possibility of their participation in various chemical reactions in living organisms. Speaking about spatial models of molecules, we mean the definition of which spatial forms are formed by the atoms of molecules in the form of a convex body or a set of convex bodies. The structure of these bodies determines their dimension in accordance with the Euler - Poincaré equation (Poincaré, 1895). Given the large dimensionality of molecules, it is often useful for ease of use to construct their three - dimensional images based on their images of higher dimensionality, without forgetting that their complete models have higher dimensionality (Zhizhin, 2019 c). In this paper, these approaches are used to analyze spatial models of molecules of various sugars and their compounds.

Methods

The structure of monosaccharides and polysaccharides (pyranoses and furanoses) is studied by constructing closed convex polytopes of higher dimension and their chains. For the convenience of practical use, a general method is being developed for obtaining approximate three -dimensional images of figures based on polytopes of higher dimension. This method is used to geometrically describe saccharides and their compounds.

Results

Using this method, an approximate three - dimensional image is obtained from a complete spatial model of a pyranose molecule in the form of a polytope of dimension 15 in the form of a connected pentagonal prism and a pyramid with hexagonal and pentagonal bases. An approximate three - dimensional image is obtained from the complete spatial model of furanose in the form of a polytope of dimension 12 in the form of a connected quadrangular prism and a quadrangular pyramid. The resulting three - dimensional image of the pyranose molecule allows changes taking into account possible conformations of the molecule. Three - dimensional images of saccharide molecules are used to build chains of saccharide molecules. It was found that the obtained three - dimensional image of the pyranose molecule unambiguously leads to the twisting of the polysaccharide depending on the valence angle of the oxygen bonding atom in this molecule. A three - dimensional image of the furanose molecule using the example of the D - ribose molecule was constructed in the author's previous works (Zhizhin, 2016, 2018, 2019 a, b, c, 2020 a, b). This three - dimensional image made it possible to establish the existence of a degree of freedom of arrangement of nitrogen bases in nucleic acids hidden in space of higher dimension. From which a one - correspondence of the number of possible locations of nucleotides and amino acids follows.

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