Carbohydrates three-center bonds

Three-center bonding in the carbohydrates and the amino acids is therefore a result of excess acceptors over donors, or of proton deficiency. Hence the analogy with the three-center electron bond from electron deficiency in the boron hydrides [76]. 

Three-center hydrogen bonds in the nucleic acid constituents occur as frequently as in the carbohydrates (see Thble 2.3). Because there are virtually no neutron diffraction studies available for this class of compounds, the analysis of the three-center bonds has to rely on data where the X-H bond lengths are normalized and are therefore to some extent less reliable than those of the carbohydrates (Table 8.3) which are based on neutron diffraction data. 

Since nucleic acid constituents exhibit a wider range of donor and acceptor types, the three-center hydrogen bonds have more variation than in+the carbohydrates. It is clear from the data summarized in Thble 8.5 that - NH3 (and NH4), O—H and — NH2 groups tend to form more three-center bonds than OwH... 

The proportion of three-center bonds in the pyrimidine, purine, and barbiturate crystal structures of about 30% is comparable to the number observed in the carbohydrate crystal structures (Thble 2.3). There is also a small proportion, about 1 %, of four-center bonds. A particular feature of the three-center bonds in these crystal structures is the occurrence of chelation, where both acceptor atoms are covalently bonded to the same atom(s), as in Fig. 15.7. 

The crystal structure of 5-chloro-2-deoxyuridine [CLDOUR] has a very simple pattern with two infinite chains (Fig. 17.21). One is through the O -H groups, and the other through the minor component of a three-center bond formed by 0(30-H. It strongly resembles a carbohydrate hydrogen-bonding pattern. A very simple scheme is also formed by 2-chloro-2 -deoxyuridine [CDURID] with a short finite chain and a separate link from the primary alcohol (Fig. 17.22). 

An analysis of the water molecule configurations in hydrates of the amino adds, peptides, carbohydrates, purines, pyrimidines, nucleosides and nucleotides is presented in Ihble 22.1. The key to the 12 different observed configurations is given in Ihble 22.2. The water molecules, which are involved only in two-center bonds constitute 63% of the total number of bonds, the others are donors or acceptors of three-center bonds. Similar proportions are observed in all three different classes of molecules. Thq only possibly significant difference is a trend toward more three-coordinated pyramidal configurations with the nucleosides and nucleotides. 

Three-center hydrogen bonds in the carbohydrate crystal structures. The first systematic study which suggested that three-center hydrogen bonds are more widespread than originally thought came from the examination of the results of the neutron diffraction crystal structures of the pyranose and pyranoside sugars referred to in Chapter 7 [58]. 

Table 8.3. Geometries of three-center hydrogen bonds from the neutron diffraction analyses of carbohydrates ...

The three-center hydrogen bonds observed in the crystal structures of the amino acids are described in Thble 8.6. They range from symmetrical to unsymmet-rical, as found for the carbohydrates and nucleic acid constituents, but there is a significantly greater tendency to form more unsymmetrical bonds. A particular feature are the chelated three-center hydrogen bonds discussed below. 

From among the variety of non-carbohydrate precursors, acetylenes and alkenes have found wide application as substrates for the synthesis of monosaccharides. Although introduction of more than three chiral centers having the desired, relative stereochemistry into acyclic compounds containing multiple bonds is usually difficult, the availability of such compounds, as well as the choice of methods accessible for their functionalization, make them convenient starting-substances for the synthesis. In this Section is given an outline of all of the synthetic methods that have been utilized for the conversion of acetylenic and olefinic precursors into carbohydrates. Only reactions leading from dialkenes to hexitols are omitted, as they have already been described in this Series.7... 

The shift in the two tensors is expected to be effective for carbohydrate molecules bearing a number of polar groups and hydrogen-bonding centers. Hence, serious difficulty for quantitative analysis may arise if the molecule does not contain three or more nonequivalent C—H vectors that relax predominantly via the overall motion. If this fact is ignored, qualitative treatment may lead to an erroneous motional description. Thus, one should be very cautious in interpreting the relaxation data for overall motion, especially when discrepancies well outside the experimental error are observed for the T, values. When the relaxation times are nearly similar and within the experimental error, isotropic motion may be considered as a first approximation to the problem. 

Most organic molecules in living organisms contain asymmetrical centers (i.e., they are chiral). (The terminology of stereochemistry has been reviewed by Moss.1) For example, amino acids that are incorporated into proteins are L and sugars in carbohydrates are D. It is understandable that the three-dimensional structures of the receptors in proteins for small molecules will favor only one optical isomer (i.e., the one that fits sterically, hydrogen bonds properly, and so on). Most compounds made for use by plants and animals will have to be single optical isomers. 

Chemists use two-dimensional representations called Fischer projections to show the configuration of molecules with multiple chiral centers, especially carbohydrates. To write a Fischer projection, draw a three-dimensional representation of the molecule oriented so that the vertical bonds from the chiral center are directed away from you and the horizontal bonds from the chiral center are directed toward you. Then write the molecule as a two-dimensional figure with the chiral center indicated by the point at which the bonds cross. 

Emil Fischer devised a simplified system for drawing stereoisomers that shows the arrangements of the atoms around the chiral centers. Fischer received the Nobel Prize in Chemistry in 1902 for his contributions to carbohydrate and protein chemistry. Now we use his model, called a Fischer projection, to represent a three-dimensional structure of enantiomers. Vertical lines represent bonds that project backward from a carbon atom and horizontal lines represent bonds that project forward. In this model, the most highly oxidized carbon is placed at the top and the intersections of vertical and horizontal lines represent a carbon atom that is usually chiral. 

---