Asymmetric units of crystals

Association constant. See Formation constant Astacin 627 Asthma 26, 385 Asymmetric unit of crystal 134 Asymmetry of molecules 41-43 handedness 41-43 in oligomers 344 Ataxia telangiectasia 566, 574 Atomic force microscope 131 diagram of 131... 

C and N NMR SS NMR experiments to distinguish between poly-morphs/solvatomorphs of Leu-enkephalin were published by Saito and coworkers [164,165]. The SS NMR spectra of various crystaUine forms of Leu-enkephalin revealed different amount of molecules and solvents in the asymmetric unit of crystal lattice and due to that the assignments of signals were ambiguous. On the basis of REDOR NMR experiment and relaxation studies, the differences in dynamics of the backbone and side chains for polymorphs have been shown. Based on that, authors also proved the less-restricted molecular motion of side residues in more hydrated sample. Dynamics of phenylalanine ring of enkephalin crystals have heen examined utihzing sohd-state NMR patterns (Fig. 2.28) and relaxation time (T ) measurements [166]. Results obtained for HsPhe-labelled samples were consistent with data from previous studies. 

M03S7X4 (X = Cl, Br), monoclinic (P2i/c). Figure 24 shows the asymmetrical unit of the crystal structure. The three, independent molybdenum atoms form an almost equilateral triangle. Six of the seven sulfur atoms occur in three S2 groups, each one bridging one Mo-Mo... 

Fig. 2 A 1.4 A crystal structure reveals that intercalating phi ligands do not disrupt the DNA re-stack. Shown are a the five A-a-[Rh(R,R-dimethyltrien)phi]3+-DNA octamers stacked end-to-end in the asymmetric unit of the crystal, and b a view from the major groove of A-a-[Rh(R,R-dimethyltrien)phi]3+ intercalated in the DNA duplex, 5 -G-dIU-TGCAAC-3. The intercalator is inserted as an additional DNA base step with minimal perturbation of DNA re-stack. Adapted from [51]...

On intuition, a minute amount of water was added to the solvent (ethyl acetate) in the first crystallization experiment containing a molar excess of imidazole corresponding to 1, Regularly shaped crystals were formed within one hour. Such a crystal, subjected to X-ray analysis, has the structure as shown in Fig. 41 U1). Apart from the formation of the expected salt-type associate (carboxylate-imidazolium ion pair, cf. Sect. 4.2.2), two water molecules are present in the asymmetric unit of the crystal structure. This fact called our attention again to the family of serine protease enzymes, where water molecules are reported as being located in the close vicinity of the active sites 115-120),... 

The equivalent of the tryptic fragment of human transferrin receptor has been expressed in Chinese hamster ovary cells and its structure determined at a resolution of 0.32 nm (Lawrence et ah, 1999). The asymmetric unit of the crystals contains four transferrin receptor dimers. Interpretable electron density is found for the entire tryptic fragment except for Arg-121 at the amino terminus, and density is also seen for the first N-acetylglucosamine residue at each of the N-glycosylation sites. The transferrin receptor monomer is made up of three distinct domains, organized such that the dimer is butterfly shaped (Figure 5.10, Plate 7). The likely orientation of the dimer with respect to the plasma membrane has been assigned on the basis of the... 

Information content in a powder diffraction pattern is reduced as compared to that in single crystal diffraction, due to the collapse of the three dimensional reciprocal space into a one dimensional space where the only independent variable is the scattering angle. The poorer the resolution of the diffraction method, the less the information content in the pattern (Altomare et al. 1995 David 1999). As a consequence, structure of less complex phases can be determined from power diffraction alone (fewer atoms in the asymmetric unit of the unit cell). However, refinement of the structure is not limited so seriously with resolution issues, so powder diffraction data are used in Rietveld refinement more frequently than in structure determination. Electron powder diffraction patterns can be processed and refined using public domain computer programs. The first successful applications of electron diffraction in this field were demonstrated on fairly simple structures. 

There are six subunits in the asymmetric unit of the Panuliris structure, arranged in a particle best described as a trimer of dimers. The 3-2 symmetry was good enough to be useful in a phase extension technique commonly used in the structure determination of highly symmetric viruses. Unfortunately, these crystals diffract only to 3.2 A, so that there cannot be a high level of detail available for description of the active site. Nevertheless, because there are six independent copies of the molecule in the asymmetric unit, there is more information than might normally be available at this resolution. The structure has been carefully refined at this resolution, with and without the 3-2 symmetry restraint. The estimated coordinate error is —0.35 A. The overall R is 0.201 for data between 8 and 3.2 A. Surprisingly, while the overalls for subunits 1 and... 

Fig. 7. Molecular structures of KCPh3.L. L = PMDTA, 11, diglyme, 12, and the asymmetric unit and crystal packaging of KCPh,.THF, 13. (Reprinted with permission from H. Viebrock ef al., J. Organomet. Chem. 1995, 491, 19. Copyright 1995 Elsevier Science SA.)...

Explanatory comments on crystal structures of lepidopterenes dimethyllepidopterene, and the stable phase of tetrachlorolepidopterene are centrosymmetric, i.e., the asymmetric unit consists of a molecular half. The stable phase of L, and the metastable phase of tetrachlorolepidopterene also are centrosymmetric, but the asymmetric unit consists of two half-molecules. The asymmetric unit of the metastable phase of lepidopterene consists of the three independent, complete molecules L-l, L-2, and L-3. bReprinted with permission from Ref. 33. 

Fig. 15. A schematic drawing showing the difference in the arrangement of subunits found in the asymmetric unit of BI and BII crystals. From Anderson et at. (70).

Perspective view of the asymmetric unit t crystal coordinates)... 

The parameter Z is used to denote the number of molecules or formula units in the asymmetric unit of a crystal structure, i.e. the number of molecules that cannot be related to one another by the symmetry operations defined by the crystal space group. Of course, Z is therefore crucially dependent on the somewhat subjective definition of what constitutes the formula unit . Strictly Z is defined as the number of formula units in the unit cell divided by the number of independent general positions. The... 

To describe the contents of a unit cell, it is sufficient to specify the coordinates of only one atom in each equivalent set of atoms, since the other atomic positions in the set are readily deduced from space group symmetry. The collection of symmetry-independent atoms in the unit cell is called the asymmetric unit of the crystal structure. In the International Tables, a portion of the unit cell (and hence its contents) is designated as the asymmetric unit. For instance, in space group P2 /c, a quarter of the unit cell within the boundaries 0asymmetric unit. Note that the asymmetric unit may be chosen in different ways in practice, it is preferable to choose independent atoms that are connected to form a complete molecule or a molecular fragment. It is also advisable, whenever possible, to take atoms whose fractional coordinates are positive and lie within or close to the octant 0 < x < 1/2,0 < y < 1/2, and 0 < z < 1 /2. Note also that if a molecule constitutes the asymmetric unit, its component atoms may be related by non-crystallographic symmetry. In other words, the symmetry of the site at which the molecule is located may be a subgroup of the idealized molecular point group. 

Crystals, however, are not always so perfectly ordered. Atomic mobility exists within the crystal lattice however, it is greatly reduced relative to the amorphous state. Partial loss of solvent from the lattice can result in static disorder within the lattice where the atomic positions of a given atom can deviate slightly within one asymmetric unit of the unit cell relative to another. Lattice strain and defects occur for many reasons. Solvents can be present within channels of the lattice in sites not described by the symmetry of the crystal structure itself, resulting in disordered solvent molecules or incommensurate structures and potentially nonstoichiometric solvates or hydrates. 

The crystal structures of acetylcholine bromide and acetylcholine iodide have both been investigated by Sorum [6, 7]. The structure was solved in the P2i space group, with two crystallographically different molecules in the asymmetric unit. The crystal structure of acetylcholine chloride was reported by Allen [8],... 

In molecular crystals, the asymmetric unit of the unit cell may be composed of a part of the chemical unit, of the chemical unit itself, or even of more than one chemical unit. The chemical unit is understood as the single molecule or the formula unit of the substance. For the free molecule (or formula unit) we can define "chemically equivalent"sites within the molecule. 

NQR spectroscopy also gives some hint about the numer of molecules in the asymmetric unit of the crystal. Let us consider 2,4-dichloro-3,5-dimethyl-phenetole (see Table III.2). At 77 °K six 3SC1 NQR lines have been found 126) and it therefore follows that there are three formula units in the asymmetric crystallographic unit. 

There are two molecules A, B in the crystal asymmetric unit of inosine (orthorhombic) [INOSIN11] (Fig. 17.59). They are both in the syn conformation which is stabilized by intramolecular hydrogen bonds 0(5 )-H N(3) indicated by ( ). Oxygen atoms 0(4 ) and 0(6) of molecule A and the 0(50-H of molecule B are not engaged as hydrogen-bond acceptors. 

Replacement of the oxygen ring atom in 30 by sulfur affords a thia-analog with two different solid-state conformations (see 31,32 in Figs. 14 and 15). X-ray crystallography of the crystals showed spontaneous resolution had occurred in which the conglomerate of enantiomorphic chiral crystals contained two symmetry independent molecules of identical configuration in the asymmetric unit of each chiral crystal.1 This is similar to the case for the chiral crystals of 27, but now there are two different conformations instead of only one. One of the chiral crystals showed both... 

Fig. 9. Non-covalent semaphorin dimerization mediated by the sema domains. (A) The Sema3A-65K dimer in the asymmetric unit of the crystals. (B) The interacting sema domains in the Sema4D dimer viewed in the same orientation as in (A). The expansive dimerization interface (total buried area of approximately 3000 A ) is generated by the approximation of four protruding loops from each monomer. These loops, located at the top face of the fi propeller are also implicated in interactions with the semaphorin receptors.

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