Acceptor hydrogen bonds

Two ligands may be able to position a hydrogen-bond acceptor in different locations in space yet still vith the same hydrogen-bond donor. 

Fig. 10. Pharmacophores for angiotension-converting enzyme. Distances in nm. (a) The stmcture of a semirigid inhibitor and distances between essential atoms from which one pharmacophore was derived (79). (b) In another pharmacophore, atom 1 is a potential zinc ligand (sulfhydryl or carboxylate oxygen), atom 2 is a neutral hydrogen bond acceptor, atom 3 is an anion (deprotonated sulfur or charged oxygen), atom 4 indicates the direction of a hydrogen bond to atom two, and atom 5 is the central atom of a carboxylate, sulfate, or phosphate of which atom 3 is an oxygen, or atom 5 is an unsaturated carbon when atom 3 is a deprotonated sulfur. The angle 1- -2- -3- -4 is —135 to —180° or 135 to 180°, and 1- -2- -3- -5 is —90 to 90°.

Figure 7.7 Color codes for the recognition patterns at the edges of the base pairs in the major (a) and minor (b) grooves of B-DNA. Hydrogen-bond acceptors are red hydrogen-bond donors are blue. The methyl group of thymine is yellow, while the corresponding H atom of cytosine is white.

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

Query 2 an aromatic group and a hydrogen-bond acceptor center. R1 is a complex generic group (not detailed here) which delimits the search to all groups that provides lone-pair electrons to the hydrogen bond. 

If the cation has been unchanged, its ability to act as a hydrogen-bond donor has been unchanged, so why is an effect seen at all I propose that there is competition between the anion and the Reichardt s dye solute for the proton. Thus, the values of the ionic liquids are controlled by the ability of the liquid to act as a hydrogen bond donor (cation effect) moderated by its hydrogen bond acceptor ability (anion effect). This may be described in terms of two competing equilibria. The cation can hydrogen bond to the anion [Equation (3.5-2)] ... 

Coleman et al. have performed a preliminary structure/activity study for a series of analogues of 77 [149]. They found that removal of the naphthoate moiety (88 Scheme 11.11) dramatically reduced the yield of DNA alkylation, while replacement of the NH2 group with O-benzyl (89 and 90) abolished DNA alkylation completely. Compound 91 alkylated DNA with reduced efficiency, so this effect is not simply due to a requirement for a hydrogen bond donor at this position. Perhaps the amide is required at this position to increase the ability of the C=0 to act as a hydrogen bond acceptor. Importantly, they found a strong correlation between the extent of in vitro DNA alkylation and cell culture cytotoxicity. 

Thus it seems clear that, in the absence of interactions with the reaction medium, SOR groups behave as — R substituents and activate electrophilic substitution. However, they are prone to protonation or at least to act as hydrogen bond acceptors, in which condition they behave as + R substituents, deactivate electrophilic substitution and are metadirecting. 

Recently, Kamlet and Taft introduced new elaborate parameters in order to explain the linear energy relationship for the formation of the hydrogen bond between HBA (hydrogen bond acceptor) and HBD (hydrogen bond donor). They treated several sulphoxides as HBA. The detailed presentations and actual treatments of these parameters have been described in their recent review article72. 

A similar quantitative treatment of sulphoxides as hydrogen bonding acceptors has been obtained by comparing the IR frequency shift AvOH of the C—I bond in an acetylenic iodide such as IC=CI (Avc j) due to formation of a C—T complex with phenol in various bases. This investigation suggests that sulphoxides belong to the same family as carbonyls, phosphine oxides, arsine oxides and their derivatives90. 

Hydrogen bond acceptor (HBA) 552 Hydrogen bond donor (HBD) 552 Hydrogen bonding 461, 544-567 influence on the conformation and configuration of sulphoxides 562-565... 

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