Crystal structure acids

Wang, W. Wang, S. Ma, X. Gong, J. Crystal Structures, Acid-Base Properties, and... 

Fig. 1. Superposition of three crystal structures of cAMP-dependent protein kinase that show the protein in a closed conformation (straight line), in an intermediate conformation (dashed line), and in an open conformation (broken line). The structures were superimposed on the large lobe. In three locations, arrows identify corresponding amino acid positions in the small lobe.

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

The lac repressor monomer, a chain of 360 amino acids, associates into a functionally active homotetramer. It is the classic member of a large family of bacterial repressors with homologous amino acid sequences. PurR, which functions as the master regulator of purine biosynthesis, is another member of this family. In contrast to the lac repressor, the functional state of PurR is a dimer. The crystal structures of these two members of the Lac I family, in their complexes with DNA fragments, are known. The structure of the tetrameric lac repressor-DNA complex was determined by the group of Mitchell Lewis, University of Pennsylvania, Philadelphia, and the dimeric PurR-DNA complex by the group of Richard Brennan, Oregon Health Sciences University, Portland. 

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

The crystal structure of the adduct of titanium tetrachloride and the ester formed from ethyl 2-hydroxypropanoate (ethyl lactate) and acrylic acid has been solved. It is a chelated structure with the oxygen donor atoms being incorporated into the titanium coordination sphere along with the four chloride anions. 

The NMR spectrum of this compound shows a diamagnetic ring current of the type expected in an aromatic system. X-ray crystal structures of 1 and its carboxylic acid derivative 2 are shown in Fig. 9.2. Both reveal a pattern of bond lengths very similar to that in naphthalene (see p. 534). ... 

Fig. 9.4. (A) X-ray crystal structure of j> n-tricyclo[8.4.1.F ]hexadeca-2,4,6,8,10,12,14-heptaene. iB) X-ray crystal structure of anti stereoisomer of tricyclo[8.4.1.1 ]hexadeca-2,4,6,8,10,12,14-heptaene-5-carboxylic acid. (Reproduced from Ref 63 by permission of Wiley-VCH.)...

The formation of acyl halide-Lewis acid complexes have been observed by several methods. For example, both 1 1 and 1 2 complexes of acetyl chloride, with AICI3 can be observed by NMR spectroscopy. The existence of acylium ions has been demonstrated by X-ray diffraction studies on crystalline salts. For example, crystal structure determinations have been reported for /i-methylphenylacylium and acetylium ions as SbFg salts. There is also a good deal of evidence from NMR measurements which demonstrates that acylium ions can exist in nonnucleophilic solvents. " The positive charge on acylium ions is delocalized onto the oxygen atom. This delocalization is demonstrated in particular by the short O—C bond lengths in acylium ions, which imply a major contribution from the structure having a triple bond ... 

The crystal structure of many compounds is dominated by the effect of H bonds, and numerous examples will emerge in ensuing chapters. Ice (p. 624) is perhaps the classic example, but the layer lattice structure of B(OH)3 (p. 203) and the striking difference between the a- and 6-forms of oxalic and other dicarboxylic acids is notable (Fig. 3.9). The more subtle distortions that lead to ferroelectric phenomena in KH2PO4 and other crystals have already been noted (p. 57). Hydrogen bonds between fluorine atoms result in the formation of infinite zigzag chains in crystalline hydrogen fluoride... 

Addition of the appropriate amount of water to anhydrous H3PO4, or crystallization from a concentrated aqueous solution of syrupy phosphoric acid, yields the hemihydrale 2H3PO4.H2O as a congruently melting compound (mp 29.3 "). The crystal structure shows the presence of 2 similar H3P()4 molecules which, together with the H2O molecule, are linked into... 

Figure 17.4 The phase diagrams of the systems (a) HF/H2O and (b) HCI/H2O. Note that for hydrofluoric acid all the solvates contain >1HF per H2O, whereas for hydrochloric acid they contain <1HC1 per H2O. This is because the H bonds F-H F and F-H O are stronger than O-H O, whereas C1-H---C1 and C1-H---0 are weaker than 0-H---0. Accordingly the solvates in the former system have the crystal structures [HsOJ+F , [H30]+[HF2] and [H30] [H3F4], whereas the latter are [H30]+C1 , [H502]" C1 and [H502]" CP. H2O. The structures of HCI.6H2O and the metastable HCI.4H2O are not known.

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