Homodromic hydrogen bond cycle

Figure 7.12 Crystal structures of (a) J -octyl-D-gluconamide (head-to-tail homodromic intralayer hydrogen bond cycle) and (b) bi-octyl-i>gulonamide (tail-to-tail interlayer hydrogen bonds)P...

H3C)2C OH C OH (CH3)2, in which three different conformers occur in the same crystal [485]. One is centrosymmetric, one has twofold axial symmetry, and one is asymmetric. The hydroxyl groups of all three different conformers are hydrogen-bonded to form the four-member homodromic cycle shown in Fig. 13.3. 

Fig. 13.10. Hydrogen-bonding pattern in the crystal structure of methyl 1,5-dithio-a-D-ribopyra-noside quarterhydrate. Four molecules form a hydrogen-bonded cluster around the water molecule. The perimeter of the cluster is hydrophobic and the packing of the 4(C6H1203S2)-H20 clusters is van der Waals. Note the eight-membered homodromic cycle and the homodromic spiral involving the water molecule. The swivel indicates hydrogen bonding to the next asymmetric unit [MDTRPY20]...

The hydrogen bonding in melibiose monohydrate includes a homodromic cycle. Cyclic hydrogen-bonding schemes are not common in mono- and disaccharides, but in the crystal structure of the epimeric a,yS-melibiose monohydrate, 6-0-a-D-galactopyranosyl-cr,/ -D-glucopyranose-H20 [MELIBM01] (Fig. 13.49),... 

Cyclic Trimer Configuration. The a-cytidine [ACYTID] crystal structure contains two cyclic trimer configurations (Fig. 17.32). In one, N(H)H is engaged in a three-center bond, the other is a homodromic cycle stabilized by a- and w-cooperativity. A comparable situation is found in the crystal structure of a-pseudouridine monohydrate [APSURD] (Fig. 17.13). The glycosyl link is to uracil C(6) instead of N(l), and therefore the N(1)H group is free to donate a hydrogen bond in a homodromic cycle. 

Cyclic Pentamers. In uridine-3 -phosphate monohydrate [URIDMP10], the cyclic pentamer configuration involves )NH OH, OH- -OC CH 0(H)P, P-OH- OwH and OwH- -0=C hydrogen bonds, all of which are short (Fig. 17.11 a). It is a homodromic cycle if we include the polarizability of the ribose-0(4 )-CH-component, and probably stabilized by the strong donor/acceptor p-OH of the neutral phosphate group. 

In the crystal structure of guanosine 5 -phosphate 3H20 [GUANPH01] (Fig. 17.56) the free acid of the nucleotide is in the zwitterion form with N(7) pro-tonated. There is a four-membered cycle formed by two water molecules and two phosphate groups which is part of an infinite, homodromic chain. The N(l)-H and amino N(2)-H form a chelated bifurcated hydrogen bond with a phosphate oxygen, and N(2)-H is further involved in a three-center bond with another phosphate oxygen atom. 

Fig. 18.7a-e. Cyclic and chain-like hydrogen-bonding patterns O-H- -O observed in a a-cyclo-dextrin-6H20, form I b a-cyclodextrin 6 H20, form II , intramolecular c,d,e a-cyclodextrin-7.57 H20. Infinite homodromic chains are marked chain, and cycles are indicated by round arrows with one (homodromic) and two (antidromic) heads. Only atoms of water molecules and of hydroxyl groups are drawn, the former denoted by W and the latter by the nomenclature described in Fig. 18.1. Each of the pictures a to e shows only a section of the respective crystal structure [78, 109, 575]...

The ribbon is linked to another component of the hydrogen-bond structure (X in Fig. 18.5c) through a bond which connects W(4)-H W(2). This component consists of four- and five-membered homodromic cycles m and IV (Fig. 18.7d) linked by a chain of three hydrogen bonds -O-H- -O-H -O-H . 

The water W(5) in cycle IV (Fig. 18.5 c) is disordered and the hydrogen atoms could not be located. Since W(5) 0(6)2 is 2.7 A, a hydrogen bond is likely to complete the homodromic cycle. The hydrogen-bond lengths and angles are... 

Hydrogen-bonding patterns in crystal structures of the cydodextrins and the simpler carbohydrates differ. The infinite, homodromic chains are common both in the low molecular-weight carbohydrates and in the cydodextrins. The principal difference lies in the frequency of occurrence of the homodromic and antidromic cycles, which are common in the cyclodextrin crystal structures and rare in the mono-, di-, and trisaccharides. The cyclic patterns are the rule in the clathrate hydrates and in the ices. From this point of view, the hydrogen-bonding patterns of the hydrated cydodextrins lie between those of the simpler hydrated carbohydrates and those of the hydrate inclusion compounds, discussed in Part IV, Chapter 21. 

These calculations also predict that the formation of chains or cycles of O-H - 0 hydrogen bonds causes polarization such that the charges on oxygen become more negative while those on the hydrogen atoms become more positive (Thble 18.3). The polarization is calculated to be greater for homodromic than for antidromic arrangements. 

Fig. 18.16. The quadrilateral flip-flop cycle and its deconvolution into two cycles with homodromic O-H- -O hydrogens bond in clockwise and anticlockwise orientation hydrogen atom positions a, b are only half occupied...

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