Ordered molecules, hydrogen bonds

Figure 1.7 Effects of hydration on a drug molecule A drug molecule does not exist in a vacuum it is hydrated. In order to interact with its receptor, it must be dehydrated. Water molecules hydrogen-bond to the functional groups of the drug molecule. Additional water molecules then hydrogen-bond to these inner water molecules. The overall result consists of many layers of hydration.

Fig. 23.3. Contact areas of main-chain N-H top) and C=0 (bottom) groups in human lysozyme. Circles indicate ordered water molecules hydrogen-bonded to the appropriate groups, a and P mark a-helical and yff-pleated sheet regions [625]...

We have to consider the structure of water in order to estimate whether the vinyl double bond of an acrylonitrile molecule, hydrogen-bonded to a water molecule via its nitrogen lone pair orbital, may come into reaction distance (say 300 pm = 3 A) to the radical site of a growing chain coordinated to the same species. For an estimate of the geometry of the possible reaction complexes we use literature data of bond lengths and bond an es, as summarized in Table 6. 

In molecules containing no hydrogen, the order of hydrogen bond perturbing ( breaking ) potency was found to be Cl < Br < I. 

The conversion of the information in DNA into proteins begins in the nucleus of cells with the synthesis of mRNA by transcription of DNA. Several turns of the DNA double helix unwind, forming a bubble and exposing the bases of the two strands. Ribonucleotides line up in the proper order by hydrogen bonding to their complementary bases on DNA, bond formation occurs in the 5 —> 3 direction, and the growing RNA molecule unwinds from DNA (Figure 28.9, p. 1170). 

Continuing with the adsorption process, further hydration results in highly ordered layers of wafer molecules hydrogen-bonded fo each... 

This is an aromaticity index calculated from molecular topology. It is defined in terms ofthe first-order —> valence connectivity index divided by the number B of bonds of the molecule (hydrogen bonds excluded), and normalized on the benzene molecule [Kier and Hall, 1986] ... 

The quadruplexes, similar to duplex DNA have grooves contain a network of water molecules ordered about hydrogen bonding donors and acceptors, the exocyclic amino groups N2, and heterocyclic N3 atoms for quadruplexes. The... 

As described above, the two vicinal cysteines in Dx, Cys 28 and Cys 29, impose structural constraints in the polypeptide chain fold while the Cys 9-X-X-Cys 12 pattern allows the rubredoxin knuckle to be maintained. As a result, the coordination around the metal in Dx, although geometrically not very different, lacks the pseudo two-fold symmetry and has a different local environment in comparison to Rd. The second coordination spheres of the Dx and Rd centers also show some structural differences. In contrast to Rd, Dx has several polar residues and one internal ordered water molecule, hydrogen bonded to a more exposed water molecule (Figures 20-4 and 20-5B). These differences in the local environment around the metal centers may lead to differences in the electrostatic potentials at the iron site which will contribute to the distinctly observed spectroscopic properties of Dx and Rd [31, 34, 35]. 

The molecular models adopt a statistical mechanical treatment of the adsorbed layer. In most cases a lattice structure is assumed and the differences of the various models lie in the effects on which the emphasis is put. There are two main molecular approaches one has been developed by Guidelli and his colleagues and the other is based on the LBS theory. Guidelli s approach emphasizes local order and hydrogen bonding among adsorbed water (solvent) molecules, whereas the models based on the LBS theory disregard local order and focus their attention on the polarizability of the adsorbed molecules. 

In addition, the structure shows the presence of a fourth water molecule hydrogen-bonded to the other three water/hydroxide ligands and to a sulfate ion from the crystallization buffer. Given the importance of water in the reaction that is catalyzed, the presence of an ordered and fully occupied array of water (hydroxide) in the cavity is likely to be relevant to the catalytic mechanism. 

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