Hydrogen common bonding patterns

In Chapter 3, you learned to draw Lewis structures for many common molecules by trying to give each atom its most common bonding pattern (Table 12.2). For example, to draw a Lewis structure for methanol, CH3OH, you would ask yourself how you can get one bond to each hydrogen atom, four bonds to the carbon atom, and two bonds and two lone pairs for the oxygen atom. The structure below shows how this can be done. 

Shortcut The shortcut to drawing Lewis structures described in Section 3.3 can often be used for uncharged molecules such as CH3Br. Carbon atoms usually have four bonds and no lone pairs, hydrogen atoms always have one bond, and bromine atoms most commonly have one bond and three lone pairs. The only way to give these atoms their most common bonding patterns is with the following Lewis structure, which is the same Lewis structure we arrived at with the stepwise procedure. 

Based on your knowledge of the most common bonding patterns for the nonmetallic elements, predict the formulas with the lowest subscripts for the compounds that would form from the following pairs of elements. (For example, hydrogen and oxygen can combine to form H2O and H2O2, but H2O has lower subscripts.)... 

An unusual photochemical reaction of 2-pyridones, 2-aminopyridinium salts and pyran-2-ones is photodimerization to give the so-called butterfly dimers. These transformations are outlined in equations (13) and (14). Photodimerization by [2+2] cyclization is also a common and important reaction with these compounds. It has been the subject of particular study in pyrimidines, especially thymine, as irradiation of nucleic acids at ca. 260 nm effects photodimerization (e.g. equation 15) this in turn changes the regular hydrogen bonding pattern between bases on two chains and hence part of the double helix structure is disrupted. The dimerization is reversed if the DNA binds to an enzyme and this enzyme-DNA complex is irradiated at 300-500 nm. Many other examples of [2+2] photodimerization are known and it has recently been shown that 1,4-dithiin behaves similarly (equation 16) (82TL2651). 

Matrix metalloproteinase structural studies of the P -side inhibitors to date show a common set of inhibitor-enzyme interactions. This can be attributed primarily to the strong directional zinc-binding forces. Further stabilizing forces from the backbone hydrogen-bonding patterns common to a (3 sheet allow for minor adjustments due to the zinc interactions to be made while maintaining a common pharmacophore. 

Cyclic hydrogen-bond patterns involving 4, 5, 6 and 7 bonds are commonly observed in the ices and the clathrate hydrates, described in Part IV. Similar cyclic systems are also observed in the hydrates of strong acids and salts which contain the so-called hydrated proton, for example, (H20)nH + in HBr -4 H20 [112, 113]. 

The fact that hydrates are more common in the disaccharides provides an opportunity to study the way in which the inclusion of water molecules may influence the hydrogen-bonding patterns of oligo- and polysaccharides. The crystal structures of several compounds have been studied in both the anhydrous and hydrated forms. 

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. 

Formation of alternative hydrogen bonding patterns. Although less common than the R2(8) motif, carboxylic acids can adopt the C(4) motif. This has been shown to be important for sterically hindered 2,6-disubstituted benzoic acids... 

Fig. 8 Common hydrogen bonding patterns observed for amides a the tape structure formed by primary amides involving i (8) and C(4) motifs b chains formed by non-cyclic secondary amides c the dimer formed by cyclic amides [62]...

The third group of conformations is reverse turns. These are important and common conformational elements in globular proteins that enable the chain to reverse direction and fold back on itself. Proline is often used to cause the structure to reverse direction. Reverse turns can also be stabilized by hydrogen bonding between the first and the third residue. The chain can fold in six different ways to make this hydrogen bond, two of which are like part of a modified a-helix called a 310 helix (310 bends). Some other forms have been called b-bends because the H-bonding pattern resembles that in a b-sheet (Fig. 3.7). 

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