Crystal structure analyses

The purpose of this book is to introduce the reader to the methods of molecular structure determination by X-ray diffraction of crystals. This will enable the reader to appreciate those results published in the scientific literature not only in terms of the structural parameters derived, but also in terms of their precision. We will also demonstrate how useful these results can be to the chemist and biochemist. 

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Wang, D., Bode, W., Huber, R. Bovine chymotrypsinogen A. X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution. /. Mol. Biol. 

Quantitative compositional analysis from EDS or EELS, and crystal structure analysis from CBED... 

In spite of the slow development of crystal structure analysis, once it did take olT it involved a huge number of investigators tens of thousands of crystal structures were determined, and as experimental and interpretational techniques became more sophisticated, the technique was extended to extremely complex biological molecules. The most notable early achievement was the structure analysis, in 1949, of crystalline penicillin by Dorothy Crowfoot-Hodgkin and Charles Bunn this analysis achieved something that traditional chemical examination had not been able to do. By this time, the crystal structure, and crystal chemistry, of a huge variety of inorganic compounds had been established, and that was most certainly a prerequisite for the creation of modern materials science. 

The crystal structure analysis of the parent 1,2,3-triazole in the solid state unambiguously demonstrated that it crystallizes as a 1 1 molecular complex of both possible tautomers 24a and 24b, linked by a N-H - N hydrogen bond [97AX(C)1846]. 

The alkaloid Nigellicine proved to be the pyridazino[l,2-u]indazolium-l 1-carboxylate (234) and forms yellow crystals (Scheme 77). It was isolated from the widely distributed herbaceous plant Nigella saliva L., which is used as a spice and for the treatment of various diseases (85TL2759). The structure was determined by an X-ray crystal structure analysis. The carboxylate bond distances are essentially equal (123.3 and 125.6 pm). An intramolecular hydrogen bond was found between the carboxylate oxygen atom and the hydroxy group. In mass spectrometry, the molecular peak was found at mjz —246 (20) and the base peak at mjz —202 which corresponds... 

Compounds of the same stoichiometry type usually have the same type crystal structure within the row of alkali metals K - Rb - Cs rarely the same type structure with sodium-containing analogues and never ciystallize similarly with lithium-containing compounds. The crystal structure analysis of different fluoride and oxyfluoride compounds clearly indicates that the steric similarity between all cations and tantalum or niobium must be taken into account when calculating the X Me ratio. 

Precipitated K—salt crystals are carefully filtrated and washed so as to separate them from the mother solution. Drying of filtrated K-salt is also a very delicate and important process that must be performed under conditions that avoid hydrolysis of the material. Potassium heptafluorotantalate is sensitive to water, basic compounds and alcohols, especially at elevated temperatures. The main product of K-salt hydrolysis is Marignac s salt. For a long time it was believed that the composition of Marignac s salt is K/Ta Fg. However, X-ray crystal structure analysis and precise chemical analysis of the... 

Imidazo[l,5-t/)[l, 2,4]triazin-l(2//)-ones 504 were prepared (78-USP4115572 79JHC277 88USP4743586) by the cyclization of hydrazide 503 with triethyl orthoesters. l,2,3,4-Tetrahydro-2,4,4-trimethyl-8-nitroimidazo[ 1,5-t/J[ 1,2,4]triazin-1 -one 506 was isolated as a byproduct during the course of purification of hydrazide 505, whose structure was determined (91MI4) by crystal structure analysis. They had antiasthmatic... 

The absolute (25,1 i ) configuration of these products was established by chemical correlation and X-ray crystal structure analysis of a prehydrolysis adduct30. 

Glusker, J. P., Trueblood, W. T. (1972) Crystal Structure Analysis. Oxford University Press, London [4.2]. 

The novel highly substituted spiro[4.4]nonatrienes 98 and 99 are produced by a [3+2+2+2] cocyclization with participation of three alkyne molecules and the (2 -dimethylamino-2 -trimethylsilyl)ethenylcarbene complex 96 (Scheme 20). This transformation is the first one ever observed involving threefold insertion of an alkyne and was first reported in 1999 by de Meijere et al. [81]. The structure of the product was eventually determined by X-ray crystal structure analysis of the quaternary ammonium iodide prepared from the regioisomer 98 (Ar=Ph) with methyl iodide. Interestingly, these formal [3+2+2+2] cycloaddition products are formed only from terminal arylacetylenes. In a control experiment with the complex 96 13C-labeled at the carbene carbon, the 13C label was found only at the spiro carbon atom of the products 98 and 99 [42]. 

Reaction of Ph2PLi with Pr N = C = NPr in THF proceeds via insertion of the carbodiimide into the Li-P bond, affording the lithium phosphaguanidinate salt Li[Ph2PC(NPr )2] in 72% yield. The preparation and reactivity of this new ligand are summarized in Scheme 217. An X-ray crystal structure analysis of the product obtained after removal of the solvent from the reaction mixture revealed the presence of a mono-solvated, centrosymmetric dimer in the solid state (Figure... 

As was suggested in the preceding discussion, most of the arene complexes isolated by metal-atom techniques are benzene derivatives. However, heterocyclic ligands are also known to act as 5- or 6-electron donors in transition-metal 7r-complexes (79), and it has proved possible to isolate heterocyclic complexes via the metal-atom route. Bis(2,6-di-methylpyridine)Cr(O) was prepared by cocondensation of Cr atoms with the ligand at 77 K (79). The red-brown product was isolated in only 2% yield the stoichiometry was confirmed by mass spectrometry, and the structure determined by X-ray crystal-structure analysis, which supported a sandwich formulation. 

The molecular mechanism of the enantioselective protonation reaction by antibody 14D9 was revealed by a crystal structure analysis [19[. A catalytic carboxyl group AspH 101 was found at the bottom of the catalytic pocket and found to be necessary for catalysis by mutagenesis to Asn or Ala. The mechanism or protonation involves an overall syn addition of water to the enol ether in a chiral binding pocket ensuring complete enantioselectivity (Figure 3.4). 

The research work described here was carried out by an able group of students of Yamaguchi University and Ube Techinical College, and in collaboration with our laboratory staffs and industrial colleagues. In particular, Dr. S. Fujisaki and Dr. T. Okamoto made significant contributions. We thank them all, and also Dr. H. Tsuzuki of Central Analytical Center of Kyushu University undertook X-ray crystal structure analysis of BTMA Br3. Furthermore, we wish to thank Professor M. Tashiro of Kyushu University for useful discussions. Finally, we are grateful to Professor Y. Sasson of The Hebrew University of Jerusalem, Chairman of the Scientific Committee of Orgabrom 93, for the invitation to present this work in Jerusalem. 

This review presents an overview of the discovery of the Fepr protein, the spectroscopy that led to the suggestion that it contained a [6Fe-6S] cluster, and the subsequent crystal structure analysis that disproved this hypothesis, yet uncovered what is at a present a unique Fe-S cluster in biology. 

The absolute configuration of (—)-29 was established by X-ray crystal structure analysis of the bromolactone (89), which was prepared from (—)-29 by bromolactonization with hypobromous acid. It was found that ( )-29 belongs to the d series of carba-sugars, and hence, (+)-29 corresponds to the L series. - ... 

From crystal-structure analysis of hen-egg lysozyme and of its complex with the competitive inhibitor tri-Af-acetylchitotriose, the following conclusions were drawn the active site consists of a cleft containing six sub-sites, A to F, of which each could accommodate a) -( 1 — 4)-linked A-acetylglucosa-... 

Crystal-structure analysis of Taka amylase A gave similar results, in that it showed that it had an extended cleft which could accommodate six, or possibly seven, a-( 1 — 4)-linked glucose units and two oppositely placed acidic amino acids (Asp-206 and Glu-230) which could interact with the bound substrate similarly to Asp-52 and Glu-35 in lysozyme. 

Similar behaviour has been observed in the photoreaction of methyl a-cyano-4-[2-(2-pyridyl)ethenyl]cinnamate (7 OMe) crystals in which the yield of [2.2] paracyclophane reached 65% on irradiation at — 78°C (see Scheme 10 p. 153) (Hasegawa et al., 1989b). From the crystal structure analysis of the same type of [2.2] paracyclophane, which is topochemically derived from alkyl a-cyano-4-[2-(4-pyridyl)ethenyl]cinnamate crystals, a highly strained molecular shape is confirmed in which two phenylene rings are severely bent (Maekawa et al., 1991b). 

The crystal of 2 OPr recrystallized from EtOH/H20 solution, and the mixed crystal of the same ethyl and propyl cinnamate derivatives (2 OEt and 2 OPr), on photoirradiation for 2h at room temperature with a 500 W super-high-pressure Hg lamp, afforded the highly strained tricyclic [2.2] paracyclophane (2 OEt-2 OPr-cyclo) crystal quantitatively (Maekawa et ai, 1991b). A crystal structure analysis was carried out of a single crystal of the complex of 2 OEt-2 OPr-cyclo with HFIP (recrystallization solvent) in a 1 2 molar ratio. Fig. 13 shows the molecular structure of 2 OEt-2 OPr-cyclo viewed along the phenylene planes. The short non-bonded distances and deformation of the benzene rings, as seen in Fig. 13, are common to those of [2.2] paracyclophanes, as previously reported (Hope et ai, 1972a,b). 

Photoirradiation of both neat and benzene solutions of 2-cyclohexenone (66b) gives a complex mixture of photodimers [40]. However, photoirradiation of a 1 1 complex of 66b with the chiral host (S,S)-(-)-l,4-bis[3-(o-chlorophenyl)-3-hydroxy-3-phenylprop-l-ynyl]benzene (167) in the solid state (Scheme 24) gave (-)-anf/-head-to-head dimer 168 of 46% ee in 75% yield [40]. This reaction was found to proceed in a single crystal-to-single crystal manner. The mechanism of the reaction was studied by X-ray crystal structural analysis [41]. 

However, the nature of these compounds could not be determined until in 1963 Danielsen et al. made a crystal structure analysis of the manganese compound (77). Later on these dichlorophosphates, in analogy to reaction (26), were prepared from dichlorophosphoric anhydride too ... 

An interesting Mossbauer study has been reported on the dinuclear SCO complex [Fe2 (PMAT)2](BF4)4-DMF (PMAT 4-amino-3,5-bis [(2-pyridylmethyl) amino]methyl -4H-1,2,4-triazole), where thermal ST occurs from [HS-HS] to the stable endproduct [HS-LS] [32]. The molecular structure and magnetic behavior of this complex was reported earlier by Brooker et al. [33, 34] (Fig. 8.15). At ca. 225 K, the complex undergoes a sharp half ST from the HS state, T2, to a state containing 50% HS and 50% LS, Af, isomers. The single-crystal structural analysis... 

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