Crystals structure determination

The first, and earliest, application of CSP was to aid in crystal structure determination of an nncharacterized material, combined with experimental observations that, on their own, are insufficient to provide a structure. The idea is that CSP calculations can provide a set of plausible, energetically feasible structures that could be used as starting models to refine against experimental data. Under the assumption that the set of predicted structures is complete, and sufficiently accurate that the experimental 

Developments in electronic structure methods have led to accurate methods for predicted NMR chemical shifts from a crystal structure [100]. This has contributed to the development of methods for determining structures from solid-state NMR. The assigned H chemical shifts have been shown to provide enough information to select the observed crystal structure of many drug-like molecules from sets of CSP-generated structures [101, 102], and this combination of CSP with soUd-state NMR was recently used to determine the structure of a polymorph of 4-[4-(2-adamantyl-carbamoyl)-5-tert-butyl-pyrazol-l-yl]benzoic acid, a pharmaceutical compound developed for the treatment of Type 2 diabetes [38]. 

Structure solution from X-ray powder diffraction began as a means of characterising inorganic products of solid state synthesis [36] but has been more widely used in recent years for the study of organic compounds [34b, 37], particularly of pharmaceutical importance. There have been some notable recent successes in the area of organometallic compounds [38], but structure determination of coordination framework materials is very much in its infancy [39]. 

From the diffraction pattern, the crystal structure can be determined mathematically and the compound identified. While the discussion of the details is beyond the scope of this text, small, benchtop automated single-crystal XRD systems have come into use. These instruments possess a variety of powerful data processing programs and libraries that permit the determination of high-resolution crystal structures of small molecules rapidly and automatically. Systems include the Rigaku XtaLAB mini and the Bruker X2S. 

In cases of metastable polymorphs (susceptible toward crystal growth conditions), twinned crystals, and materials of extreme insolubility, electron diffraction or X-ray powder data can be used as a basis for structure determination. 

Electron diffraction has been used to investigate bulk structures of pigments [29, 30, 79] as well as thin layers [11, 80]. A strength of this method is the spatial resolution which allows the structural characterization of single microcrystals even in mixtures of polymorphs. Even more striking, the occurrence of two polymorphs in the same sub-micron crystal may be analyzed, as in the case of a/p copper phthalocyanine [29]. 

Despite such restrictions, real-space crystallographic methods based on genetic algorithms [32], Monte-Carlo methods [33], or simulated annealing techniques [34] have proved to be powerful means for structure solutions from X-ray powder patterns. Provided with the unit cell, the composition and configuration of the 

were found to be lower in energy, which may be explainable by inadequacies in the force field. 

The minimization of the packing energy allows the determination of crystal structures even from nonindexable, lowquality X-ray powder diagrams (see Sections 8.4.2 and 20.3.3.1) [74, 82]. 

09-0-01 - Localisation of K ions in (Na,K)-LSX and K-LSX zeolites by Rietveld analysis and NMR spectroscopy. A new cationic site in the orthorhombic dehydrated K-LSX at room temperature 

A LSX zeolite sample was studied under its as-made form and its fully exchanged potassium form. Upon dehydration, a lowering of the symmetry is observable at room temperature. This phenomenon was confirmed by MAS NMR spectroscopy. The structure reveals for the first time a simultaneous occupancy of sites 1 and T by potassium cations. This is due to a shift of site 1 from the centre of the D6R unit. wide line NMR spectroscopy confirms the Rietveld analysis, especially the absence of ions on site I in the as-made Na72,K24-LSX sample. 

RMN et Chimie du Solide, UMR 7510 ULP-Bruker-CNRS, Universite Louis Pasteur, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France, e-mail taulelle chimie.u-strasbg.fr 

09-0-03 - FOS-5, a novel zeotype with 3D interconnected 12- ring channels 

Structural Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden 

---

The crystal structure determines not only the arrangement of atoms in the lattice but also the external form of the crystal. 

Small-Molecule Single-Crystal Structure Determination... 

Figure 9.3 Comparison of the consensus nucleotide sequence of the TATA box (a) and the sequences of the DNA fragments used in the crystal structure determinations of the TATA box-binding proteins from yeast (b) and the plant Arabidopsis thaliana (c).

Crystallography is a very broad science, stretching from crystal-structure determination to crystal physics (especially the systematic study and mathematical analysis of anisotropy), crystal chemistry and the geometrical study of phase transitions in the solid state, and stretching to the prediction of crystal structures from first principles this last is very active nowadays and is entirely dependent on recent advances in the electron theory of solids. There is also a flourishing field of applied crystallography, encompassing such skills as the determination of preferred orientations, alias textures, in polycrystalline assemblies. It would be fair to say that... 

Perhaps the last general overview of crystallography in all its many aspects, including crystal chemistry and crystal physics and the history of crystallographic concepts, as well as the basics of crystal structure determination, was a famous book... 

One of the structural implications of the delocalization of the negative charge, the identity of the two C—O bond lengths, intermediate between those of single and double bonds, has been verified by many crystal structure determinations. 

Only the bisected conformation aligns the cyclopropyl C—C orbitals for effective overlap. Crystal structure determinations on two cyclopropylmethyl cabons with additional stabilizing substituents, C and D, have confirmed file preference for the bisected geometry. The crystal structures of C and D are shown in Fig. 5.8. 

X-r crystal structure determinations have been completed on two salts containing bicyclo[2.2.1]heptyl cations (Fig. 5.12). Both are more stable than the 2-norbomyl cation itself 18 is tertiary whereas 19 contains a stabilizing methoxy group. The crystal structure of 18 shows an extremely long (1.74 A) C—C bond between C-1 and C-6. The C(1)—C(2) bond is shortened to 1.44 A. The distance between C-2 and C-6 is shortened from 2.5 A in norbomane to 2.09 AThese structural changes can be depicted as a partially bridged structure. 

In the case of phenyllithium, it has been possible to demonstrate by NMR studies that the compound is tetrameric in 1 2 ether-cyclohexane but dimeric in 1 9 TMEDA-cyclohexane. X-ray crystal structure determinations have been done on both dimeric and tetrameric structures. A dimeric structure crystallizes from hexane containing TMEDA. This structure is shown in Fig. 7.1 A. A tetrameric structure incorporating four ether molecules forms from ether-hexane solution. This structure is shown in Fig. 7.IB. There is a good correspondence between the structures that crystallize and those indicated by the NMR studies. 

Crystal structure determination has also been done with -butyllithium. A 4 1 n-BuLi TMEDA complex is a tetramer accommodating two TMEDA molecules, which, rather than chelating a lithium, link the tetrameric units. The 2 2 -BuLi TMEDA complex has a structure similar to that of [PhLi]2 [TMEDA]2. Both 1 1 -BuLi THF and 1 1 -BuLi DME complexes are tetrameric with ether molecules coordinated at each lithium (Fig. 7.2). These and many other organolithium structures have been compared in a review of this topic. ... 

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 ... 

M. Jansen and M. Voss, Angew. Chem. Int. Edn. Engl. 20, 100-1, 965 (1981), and references therein to crystal structure determinations on the other members of the series P406+ . See also M. Jansen and M. Moebs, Inorg. Chem. 23, 4486-8 (1984). 

X-Ray crystal structure determinations of l-(aminocarbonyl)-3-methyl-4-methoxy-l//-pyrazol-5(2H)-one 107 (R = H) and l-(phenylaminocar-bonyl)-3-methyl-4-methoxy-l//-pyrazol-5(2H)-one 107 (R = Ph) demonstrated that both molecules exist in the crystal exclusively as NH-CO tautomers (97T5617). The tautomeric form similar to 104b is realized in the crystal of 4,4-dichloro-substituted pyrazolone 108 (93BSB735). 

Among the variety of nitrogen-containing fulvalenes emerging from types 7-14, X-ray structural determinations have been performed on about 20 representative examples. Tire first crystal structure determination was carried out by application of the folding-molecule method on 3,3 -diphenyl-l,l -bi-isoindolylidene 64 (R = FI) (71CB3108). Tire dimeric isoindolenine system... 

Kashiwagi et al.10) determined the second moment anisotropy for the one-way drawn polyethylene terephthalate sheets discussed above. The three lattice sums S00, S2q and S4o were calculated from the crystal structure determination of Daubeny et al., the proton positions being calculated on the basis of known bond angles and lengths. The isotropic lattice sum S00 was adjusted to a value consistent with the measured isotropic second moment of 10.3G2. The values for P200, P220 etc. were then used to predict the optical anisotropy. The predicted refractive indices for the sheets of draw ratio 2 1 and 2.5 1 are shown in Fig. 10, together with the experimental... 

Bis(dicyclohexylammonium) bis(2,6-pyridinedicarboxylato)dibutylstannate is concluded to have sevenfold coordination at the Sn on the basis of its Sn CP/ MAS NMR chemical shift ((5 = —424.9 ppm). The assignment has been corroborated by crystal structure determination of its monohydrate, in which the Sn atom has frflMS-C2SnN04 PBP geometry (Sn-C = 204.0,206.7pm, C-Sn-C = 168.9°). One 2,6-pyiidinedicarboxylato group chelates to the Sn atom (Sn-O = 223.4,226.0 pm Sn-N = 227.9 pm), whereas the other binds through only one carboxyl end (Sn-O = 241.6, 244.1pm). The anhydrous compound displays higher in vitro antitumor activity than those of cisplatin and carboplatin (Table 7). ... 

A crystal-structure determination on [Ni(PhCH2CS2)2] showed evidence of a Ni-Ni bond (Ni—Ni distance, 256 pm) in a bridging, acetate-cage, binuclear complex (363). Each nickel atom is 5-coordinate and is in a tetragonally distorted, square-pyramid spectroscopic evidence for a Ni-Ni bond has been obtained (364). The polarized crystal spectra showed more bands than predicted for a mononuclear, diamagnetic, square-planar nickel(Il), and the spectra are indicative of substantial overlap of the d-orbitals between the two nickel atoms. The bis(dithiobenzation)nickeKII) complex was found to exhibit unusual spectrochemical behavior (365). 

An X-ray crystal-structure determination (370) revealed that mixed, nickel coordination exists in the trimeric complex, [Ni(S2CPh)2]3. The trimeric structure is similar to that found (371) in [Pd(PhCS2>]. The structure contains one molecule of type A linked centrosymmetrically through short Ni-S bridges to two molecules of type B, the three molecules being closely parallel (XXVII). Bonamico and co-workers (372)... 

For a review of crystal-structure determinations of triarylmethyl cations and other carbocations that can be isolated in stable solids, see SundaraUngam, M. Chwang, A.K. in Olah Schleyer, Ref. 2, vol. 5, p. 2427. 

To date, the crystal structures of more than 200 mesogenic compounds are known. In this review, we wish to present a general overview of the crystal structures of mesogenic compounds up to the end of 1997. Unfortunately, it is not possible to consider the crystal structure determinations of carbohydrate liquid crystals [13, 14], metallomesogens [15-18], phasmid and biforked mesogens [19-22], perfluorinated mesogenic compounds [23-27], benzoic acids [6, 28-31], cinnamic acids [7, 32, 33], dicarboxylic acids [34, 35], cinnamate compounds [8, 36-40], and discotic liquid crystals [41-43] due to the lack of space. 

In 1986, Walz and Haase [148] presented the crystal structure of the mesogenic hydrocarbon compound l,2-bis-(4 -pentylcyclohexyl)ethane. The compound exhibits a smectic B phase over a remarkably broad range of temperature. To our knowledge, this is the only crystal structure determination of a mesogenic hydrocarbon compound up to now. Since this compound does not contain any polar groups, the arrangement in the crystalline state is... 

---