Crystal structures, molecules

Figure 4. Helix axis projection of the chondroitin 4-sulfate crystal structure. Molecules with full and open bonds indicate up- and down-pointing chains. The large and small filled circles represent potassium ions and water molecules respectively. (Reproduced with permission from ref. 18. Copyright 1983 Academic Press Inc.)...

In the case of the fluorescein-binding variant FluA, crystals were obtained in the presence of the hgand at pH 8.1 with two FluA fluorescein complexes in the asymmetric unit, which were refined to a resolution of 2.0 A [52]. The two molecules were highly similar in structure, with a root mean square difference (rmsd) of 0.33 A for 173 mutually superimposed positions. The overall topology of the //-barrel with the a-hehx attached to it, both of which are characteristic features of the lipocahn architecture (see Section 8.2), was found to be conserved (Fig. 8.4). Both disulfide bonds of the BBP scaffold, one between Cys and fJys and one between Cys" and Cys, were also clearly visible. Upon superposition with the BBP crystal structure (molecule A from the Protein Data Base entry IBBP [32]), an rmsd of 1.2 A was calculated for 159 superimposed positions. 

Tautomerism of sulfonamides proved an important issue in the development of computational methods for prediction of crystal structures. Molecule VI, 6-amino-2-(pheylsulfonylimino)-l,2-dihydropyiridine (R = phenyl on Scheme... 

To enable an atomic interpretation of the AFM experiments, we have developed a molecular dynamics technique to simulate these experiments [49], Prom such force simulations rupture models at atomic resolution were derived and checked by comparisons of the computed rupture forces with the experimental ones. In order to facilitate such checks, the simulations have been set up to resemble the AFM experiment in as many details as possible (Fig. 4, bottom) the protein-ligand complex was simulated in atomic detail starting from the crystal structure, water solvent was included within the simulation system to account for solvation effects, the protein was held in place by keeping its center of mass fixed (so that internal motions were not hindered), the cantilever was simulated by use of a harmonic spring potential and, finally, the simulated cantilever was connected to the particular atom of the ligand, to which in the AFM experiment the linker molecule was connected. 

Table 2 shows the results of our preliminary calculations of the pKa of the Cys403 residue, for several different models of the enzyme, based on two structures available from the PDB. In the case of the YPT structure, a crystal water molecule is close to Cys403 and was included in some of the calculations as part of the protein (i.e. it was treated with the same internal dielectric as that of the protein). Simulations denoted as -I-H2O in Table 2, include a crystallographically resolved, buried water molecule, situated 3.2lA from... 

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

The two major databases containing information obtained from X-ray structure analysis of small molecules are the Cambridge Structural Database (CSD) [25] and the Inorganic Crystal Structure Database (ICSD) [26] both are available as in-house versions. CSD provides access to organic and organometallic structures (mainly X-ray structures, with some structures from neutron diffraction), data which are mostly unpublished. The ICSD contains inorganic structures. 

Fig. 9.35 Some typical molecules tested using the PROMET approach to predicting crystal structures.

Karfunkel H R and R J Gdanitz 1992. Ah initio Prediction of Possible Crystal Structures for General Organic Molecules. Journal of Computational Chemistry 13 1171-1183. 

The next step is to obtain geometries for the molecules. Crystal structure geometries can be used however, it is better to use theoretically optimized geometries. By using the theoretical geometries, any systematic errors in the computation will cancel out. Furthermore, the method will predict as yet unsynthesized compounds using theoretical geometries. Some of the simpler methods require connectivity only. 

WebLab Viewer gives a very-high-quality display suitable for publication and presentation. Molecules can be displayed as lines, sticks, ball and stick, CPK, and polyhedrons. In addition, different atoms within the same structure may be displayed in different ways. Text can be added to the display as well as labeling parts of the structure in a variety of ways. The user has control over colors, radii, and display quality. The program can also replicate a unit cell to display a crystal structure. Several types of molecular surfaces can be displayed. 

A description of Pasteur s work as part of a broader discussion concerning crystal structure can be found in the article Molecules Crys tals and Chirality in the July 1997 issue of the ioc/rna/ of Chemical Education pp 800-806... 

The polymers compared all have similar crystal structures but are different from polyethylene, which excludes the possibility for also including the latter in this series. Also note that the isotactic structure of these molecules permits crystallinity in the first place. With less regular microstructure, crystallization would not occur at all. 

Crystal structure of solids. The a-crystal form of TiCla is an excellent catalyst and has been investigated extensively. In this particular crystal form of TiCla, the titanium ions are located in an octahedral environment of chloride ions. It is believed that the stereoactive titanium ions in this crystal are located at the edges of the crystal, where chloride ion vacancies in the coordination sphere allow coordination with the monomer molecules. 

Fig. 18. Crystal structures of recent clathrate design (a) coordinatoclathrate between host (39) (Fig. 17) and / -butanol (host—guest hydrogen bonding in the shaded area) (b) perspective view of the hehcal inclusion channel formed by diol host (43) (Fig. 17 all except one host molecule are represented...

Small-Molecule Single-Crystal Structure Determination... 

Syntheses, crystallization, structural identification, and chemical characterization of high nuclearity clusters can be exceedingly difficult. Usually, several different clusters are formed in any given synthetic procedure, and each compound must be extracted and identified. The problem may be compounded by the instabiUty of a particular molecule. In 1962 the stmcture of the first high nuclearity carbide complex formulated as Fe (CO) C [11087-47-1] was characterized (40,41) see stmcture (12). This complex was originally prepared in an extremely low yield of 0.5%. This molecule was the first carbide complex isolated and became the foremnner of a whole family of carbide complexes of square pyramidal stmcture and a total of 74-valence electrons (see also Carbides, survey). 

The pyrimidine ring is virtually flat. Its corrected bond lengths, as determined by a least-squares analysis of the crystal structure data for a unit cell of four molecules, are shown in formula (2) (60AX80), and the bond angles derived from these data show good agreement with those (3) derived by other means (63JCS5893) for comparison, each bond... 

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