Hydrogen, acceptors bonding

Water forms hydrogen-bonded clusters with itself and with other proton donors or acceptors. Hydrogen bonds account for the surface tension, viscosity, liquid state at room temperature, and solvent power of water. 

P2j Z = 2 D = 1.57 R = 0.048 for 931 intensities. The base exists in the thioxo form, with C-8=S and N-7 protonated. The 8-thio substituent causes the base to assume the syn (—102.6°) orientation. The o-ribosyl group is 2T3 (174.8 °, 44.1 °). The exocyclic, C-4 -C-5 bond orientation is trans (—173.2°). This does not favor intramolecular hydrogen-bonding of 0-5 to N-3 of the syn base. The C=S distance is 166.8 pm. The S atom is involved in a weak, acceptor hydrogen-bond to a water molecule, S H-O(w) = 361 pm. The bases are stacked head-to-tail, with overlap of the C=S bonds and the purine ring, in contrast to the known, related structure l-/ -D-ribofuranosyl-2-thioxo-3ff-benzimidazole,197 where similar head-to-tail stacking of the bases involves overlap of the base rings only. 

In these three ligands the and atoms are suitable for covalent coordination with the metal center (see Scheme 3.5 for labeling). Although also possesses an electron pair, this will not be the preferred position for metal coordination because normally it is involved in the formation of donor-acceptor hydrogen bonds together with one or two hydrogen atoms of the amino groups. Very few examples of the coordination of an N atom with two vicinal NH2 functions have been reported... 

Basicity (including the abilities as proton acceptor, hydrogen-bond acceptor, electron pair donor, and electron donor)a)... 

The MOLECULAR COMPLEX may include all non-covalent interactions (donor-acceptor, hydrogen bonding,. ..). 

M. W. Deprotonation of arylnitromethanes. Higher intrinsic rate constants with thiolate ions than with oxyanions or amines as the proton acceptors. Hydrogen bonding in the transition state and desolvation of the base as competing factors in proton transfer at carbon. 

The distinction between hydrogen-bond donors, i.e., N-H, and nondonors, i.e., C-H, is often not apparent in deformation density maps. This distinction appears much more clearly on the electrostatic potential maps, such as illustrated in Fig. 3.4 [218]. Such maps may therefore provide a more effective means of quantitatively analyzing the electronic differences between the different donor-acceptor hydrogen-bond combinations which is manifested by the different mean bond lengths described in Part IB, Chapter 7 [222- 226]. It has been suggested that hydrogen-bond strengths can be at least qualitatively compared from the values of the electrostatic potentials at fixed distances from the donor and acceptor atoms, i.e., 2.0 A [227]. 

Bifurcated (acceptor) hydrogen bonds as defined by Pimentel and McClelland [28] can be formed by -NH2 and H20, but were never observed in the crystal structures of small biological molecules except if in combination with three-center bonds, where they adopt configurations of the type ... 

Fig. 21.3. The (H2O)20 pentagonal dodecahedron. This shows one of the ordered arrangements of the hydrogen atoms. In the gas hydrates, the hydrogen atoms are twofold disordered across the 0-(yH) (-i-H)-O edges. This unit of structure has 10 donor/10 acceptor hydrogen-bond functionality...

Scheme 12 Top LC copolymers containing mesogenic side groups and carboxylic side groups capable of hydrogen bonding. Bottom Azobenzene-containing dopants with pyridine ring and with a primary amine group ensuring the formation of donor-acceptor hydrogen bonds. Reprinted from [23,252]. 2003, with permission from Elsevier...

Another type of hydrogen bond involves 7i-facial interactions of the type illustrated in Figure 2.5.As an approximation, such arrangements can be considered to bear a relationship to both a classical donor-acceptor hydrogen bond as well as to a n-n bonded system (see below). Interactions of this type tend to be quite weak (1-5 kJ mol" ). However, they often act in a co-operative manner with other intermolecular interactions such that, for example, they help to dictate a precise orientation within a given supramolecular architecture. 

Figure 2.4 The four potential functions that may be used to classify donor-acceptor hydrogen bonds...

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