X-ray crystal structure of

Diederich F, Jonas U, Gramlich V, Herrmann A, Ringsdorf H and Thilgen C 1993 Synthesis of a fullerene derivative of benzo[18]crown-6 by Diels-Alder reaction complexation ability, amphiphilic properties, and x-ray crystal structure of a dimethoxy-1,9-(methano[1, 2]benzomethano)fullerene[60] benzene clathrate Helv. Chim. Acta 76 2445-53... 

Bode, W., Papamokos, E., Musil, D. The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Eur. J. Biochem. 166 (1987) 673-692... 

D, H W Hoeffken, D Crosse, J Stuerzebecher, P D Martin, B F P Edwards and W Bode 1992. Refined 2.3 Angstroms X-Ray Crystal Structure of Bovine Thrombin Complexes Formed witli he 3 Benzamidine and Arginine-Based Thrombin Inhibitors NAPAP, 4-TAPAP and MQPA A Starting Point for Improving Antithrombotics. Journal of Molecular Biology 226 1085-1099. 

D, J Sturzebecher and WBode 1991. Geometry of Binding of the N-Alpha-Tosylated Piperidides of weffl-Amidino-Phenylalanine, Para Amidino-Phenylalanine and para-Guanidino-Phenylalanine to Thrombin and Trypsin - X-ray Crystal Structures of Their Trypsin Complexes and Modeling of their Thrombin Complexes. FEBS Letters 287 133-138. 

An impressive example of the application of structure-based methods was the design of a inhibitor of the HIV protease by a group of scientists at DuPont Merck [Lam et al. 1994 This enzyme is crucial to the replication of the HIV virus, and inhibitors have bee shown to have therapeutic value as components of anti-AIDS treatment regimes. The star1 ing point for their work was a series of X-ray crystal structures of the enzyme with number of inhibitors boimd. Their objective was to discover potent, novel leads whid were orally available. Many of the previously reported inhibitors of this enzyme possessei substantial peptide character, and so were biologically unstable, poorly absorbed am rapidly metabolised. 

Picot, D., Loll, P.J., Garavito, R.M. The x-ray crystal structure of the membrane protein prostaglandin H2 synthase-1. Nature 367 243-249, 1994. 

Figure 17.12 Ribbon diagram of EMPl bound to the extracellular domain of the erythropoietin receptor (EBP). Binding of EMPl causes dimerization of erythropoietin receptor. The x-ray crystal structure of the EMPl-EBP complex shows a nearly symmetrical dimer complex in which both peptide monomers interact with both copies of EBP. Recognition between the EMPl peptides and EBP utilizes more than 60% of the EMPl surface and four of six loops in the erythropoietin-binding pocket of EBP.

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). ... 

The syn isomer can achieve a conjugated system with angles of up to 35° between adjacent p orbitals. The anti isomer is much more twisted. An X-ray crystal structure of the syn isomer shows C—C bond lengths between 1.368 and 1.418 A for the conjugated system (Fig. 9.3). ° The spectroscopic properties of the syn isomer are consistent with considering it to be a delocalized annulene. B3LYP calculations indicate that both the syn and anti structures are stabilized by delocalization, the syn (17.6kcal/mol) more so than the anti (8.1 kcal). ... 

The NMR spectrum of the syn isomer shows evidence of a diamagnetic ring current, based on both the relatively low-field position of the vinylic hydrogens and the upfield shift of the methylene hydrogens. The anti isomer shows much less pronounced shifts. The X-ray crystal structure of the syn isomer shows a moderate level of bond alternation, ranging ftom 1.36 to 1.45 A (Fig. 9.4A). In the anti isomer, bond alternation is more pronounced, vith the double bond in the center ring being essentially a localized double bond (Fig. 9.4B). 

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.)...

Reductive coupling reaction of fluonnated vinyl iodides or bromides has been used as a route to fluorinated dienes [246, 247, 248, 249, 250. Generally, the vinyl iodide is heated with copper metal in DMSO or DMF no 1 ntermediate perfluorovmy I-copper reagent is detected. Typical examples are shown m equations 163-165 [246, 247, 249. The X-ray crystal structure of perfluorotetracyclobutacyclooctatetraene, prepared via coupling of tetrafluoro-l,2-diiodocyclobutene with copper, is planar... 

P Fluonnation always strongly stabilizes carbamons both by induction and by negative (anionic) hyperconjugaQon, 7 The latter "no-bond resonance has been controversial, but its importance is now well established both theoretically [133, 134] and expenmentally [67] The X-ray crystal structures of salts 8 [fi5] and 9 [136] provide cogent evidence for negative hyperconjugation... 

Renatns, M., Engh, R. A., Stubbs, M. T, et al., 1997. Lysine-156 promotes the anomalons proenzyme activity of tPA X-ray crystal structure of singlechain human tPA. EMBO Journal 16 4797-4805. 

The X-ray crystal structures of many of these complexes have now been determined representative examples are. shown in Fig. 4.11 from which it is clear that, at least for the larger cations, coordinative saturation and bond rhrectionality are far less significant factors than in many transition element complexes. Further interest in these ligands stems from their use in biochemical modelling since they sometimes mimic the behaviour of naturally occurring, neutral, macrocydic antibiotics such as valinomycin, monactin, nonactin, nigericin... 

An X-ray crystal structure of the Pr N-derivative shows the presence of a bent, 2-coordinate P atom, equal P- N distances, and accurately planar 3-coordinaie N atoms as in (c) above.In liquid ammonia ammonolysis also occurs ... 

The first X-ray crystal structure of a species containing an S-I bond was of the curious and unexpected cation [87 ]+ which was found in the dark-orange compound [S7l)+[SbF6] formed when iodine and sulfur react in SbF5 solution.The structure of the cation is shown in Fig. 15.22a and features an 87 ring with alternating 8-8 distances and a pendant iodine atom the conformation of the ring is the same as in 87, 8g, and 8sO (p. 696). The same cation was... 

Conversely, when A-alkyl tryptophan methyl esters were condensed with aldehydes, the trans diastereomers were observed as the major products." X-ray-crystal structures of 1,2,3-trisubstituted tetrahydro-P-carbolines revealed that the Cl substituent preferentially adopted a pseudo-axial position, forcing the C3 substituent into a pseudo-equatorial orientation to give the kinetically and thermodynamically preferred trans isomer." As the steric size of the Cl and N2 substituents increased, the selectivity for the trans isomer became greater. A-alkyl-L-tryptophan methyl ester 42 was condensed with various aliphatic aldehydes in the presence of trifluoroacetic acid to give predominantly the trans isomers. ... 

A limited number of non-transition-metal derivatives of thiophene will be considered in this subsection. There are no short-range contacts between the lithium atoms originating from the (LiO)6 cores and the sulfur atoms in [Li—O—EMc2 (2-C4H3S)]6 (E = C, Si) (97OM5032), and evidence for Tr-interactions can be found in the X-ray crystal structures of these compounds. Theoretical computations show that a- (S ) Li" " interactions are weak, whereas Tr-Li" contributions are considerable, in accord with the general reasoning on the electronic characteristics of uncomplexed thiophene. 

Fig. 3.4 X- ray crystal structure of the 18-crown-6-ICH2Znl adduct 31. [Charette, A.B. Marcoux, ).F. B4langer-Gari4py, F. J. Am. Chem. Soc. 1996, 7 78, 6792. Reprinted with permission from The American Chemical Society]...

Fig. 3.24 X-ray crystal structure of the 131b-bipy zinc complex. [Denmark, S.E. O Connor, S.O. Wilson, S.R. Angew. Chem., int. Ed. Eng. 1998, 37, 1149. Reprinted with permission from Wiley-VCH ...

Figure 5.9 Models of hexo-kinase in space-filling and wireframe formats, showing the cleft that contains the active site where substrate binding and reaction catalysis occur. At the bottom is an X-ray crystal structure of the enzyme active site, showing the positions of both glucose and ADP as well as a lysine amino acid that acts as a base to deprotonate glucose.

Figure 26.9 X-ray crystal structure of citrate synthase. Part (a) is a space-filling model and part (b) is a ribbon model, which emphasizes the a-helical segments of the protein chain and indicates that the enzyme is dimeric that is, it consists of two identical chains held together by hydrogen bonds and other intermolecular attractions. Part (cl is a close-up of the active site in which oxaloacetate and an unreactive acetyl CoA mimic are bound.

Protein Data Bank and, 1048-1049 rate acceleration of, 1041 specificity of. 1041 substrate of, 1041 turnover number of, 1041 X-ray crystal structures of,... 

The X-ray crystal structure of rapamycin reveals the constitution of the major isomer, compound 1, although in solution at least four isomers are detectable. The most abundant isomers are 1 (major) and the isomeric seven-membered hemiketal (mixture of stereoisomers). For the purposes of this chapter, we will restrict ourselves to structure 1. 

Dimethyl 2,7-dimethyl-4//-azepine-3,6-dicarboxylate, which was the first 4//-azepine to be isolated and characterized,29 on heating, or on treatment with sodium ethoxide in ethanol, rearranges quantitatively to the 3//-isomer. The X-ray crystal structure of dimethyl 7-(dimethylamino)-6-methyl-4//-azepine-2,3-dicarboxylate has been determined.42... 

Similar problems arise with the four isomeric dibenzazepines 4-7. since only 5//-dibenz-[6,d]azepine (4) and 5//-dibenz[/>,./]azepine (7) can be drawn as fully benzenoid ring structures. Even so, 5//-dibenz[/ ,t/]azepines are rare and are known only as the 7-oxo derivatives.4 In contrast, 5//-dibenz[6,e azepine (5) and 6//-dibenz[r,t>]azepine (6) exist only as the 11//- 5a and 5H- 6a isomers, respectively. In fact, there is no chemical or spectrosopic evidence for the isomerization of 5//-dibenz[e,e]azepine,5 or its 6-oxide,6 to the 6//-dibenz[r, e]azcpinc isomer (6). In addition, an X-ray crystal structure of 7-methoxy-5//-dibenz[e,e]azepine supports unequivocally the benzenoid rather than the quinonoid form.7 9//-Tribenz[6,d /]azepine (8) has only recently been prepared.8... 

An X-ray crystal structure of 7-methoxy-5//-dibenz[c,c]azepine reveals that the seven-mem-bered ring is in the boat conformation.7 Likewise, X-ray structural determinations of 2-morpho-lino-5H-d benz.[A/]azepi ne,7 and 5//-dibenz[/>, /]azepi ne.1 " 11 and its 5-acyl derivatives,12 in-... 

AMJnsubstituted compounds are, in general, too unstable to be isolated. The X-ray crystal structure of 1-tosyl-l //-1,2-diazepine shows that the molecule adopts a boat conformation with localized double bonds.69... 

The x-ray crystal structures of the hexaethyl- and hexabutenylbenzene complexes show noteworthy conformational effects [78] (Fig. 6). The hexaethylbenzene complex has four distal chains [76] contrary to all the previous conformations of C6Et6 and (M)C6Et6 of C3 symmetry. This conformation also depends on the counter-anion as the three conformations with four, five, and six distal ET groups have close energies and can be observed by low-temperature 1H NMR. The hexabutenyl benzene complex has five distal chains [77]. 

In a similar manner, treatment of anhydrous rare-earth chlorides with 3 equivalents of lithium 1,3-di-ferf-butylacetamidinate (prepared in situ from di-ferf-butylcarbodiimide and methyllithium) in THF at room temperature afforded LnlMeCfNBuOils (Ln = Y, La, Ce, Nd, Eu, Er, Lu) in 57-72% isolated yields. X-ray crystal structures of these complexes demonstrated monomeric formulations with distorted octahedral geometry about the lanthanide(III) ions (Figure 20, Ln = La). The new complexes are thermally stable at >300°C, and sublime... 

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