Water molecules crystal structure

One of the most important peroxo complexes synthesized after 1983 is the rhenium species formed from methyltrioxorhenium (MTO) precursor. The synthesis of this complex is achieved in the way indicated in equation 2, by reacting hydrogen peroxide with MTO . The isolated peroxo complex 1 contains in the coordination sphere two /7 -peroxide bridges, a direct metal carbon bond and a molecule of water. The crystal structure of the peroxo rhenium derivative, however, was obtained by substitution of the water molecule with other ligands " more details on this aspect are enclosed in the structural characterization paragraph. 

As in the small molecule crystal structures the water molecules are three- and four-coordinated (see Part IV, Chap. 21). 

Because internal water molecules are in mostly apolar environments, their hydrogen bonds are often strong and well defined. The average O- -O distance is 2.89 0.21 A for the internal water molecules in lysozyme, carboxypeptidase, cytochrome c, actinidin, and penicillopepsin. As with the small molecule crystal structures, the water molecules are involved in three or four hydrogen bonds, with 48% engaged in three and 37% in four interactions. 

An alternate interpretation is that hydrogen bonding is dynamic and that the water molecule is satisfying all acceptor sites by rotating into two positions [596]. A distinction between these two hypotheses is difficult for small molecule crystal structures, and impossible for proteins. 

If distances between main-chain C=0 and N-H groups and hydrogen-bonded water molecules are compared (Thble 23.5 and Fig. 23.5 a), it is apparent that the distribution is narrower about the N-H groups. The reason is that the C=0 groups are more exposed and, in most cases, accessible to more than one or two hydrogen-bond donors. Where this results in overcrowding the C=0 0W distances may be beyond the 3.5 A cut-off limit used in the analysis [596]. In the major parts of both C=0 Ow and N-H ow distribution, the peaks in Fig. 23.5a are at 2.89 A (2.94 A in Thble 23.5a) and 2.97 A respectively, as expected from the data for the hydrogen bonds in small molecule crystal structures. 

When an aqueous solution of the A-fraction is cooled in contact with butyl alcohol, it satisfies its associative tendencies through the formation of an alcoholate. Since butyl alcohol is probably adsorbed via its hydroxyl group, the alcoholate then presents a hydrophobic surface to the medium and precipitates from solution." The crystalline precipitate can be washed with cold water saturated with butyl alcohol, since this will not dissolve alcohol from the alcoholate and therefore does not disturb the crystal lattice. When the crystals are dried in the absence of water, the crystal structure is frozen without the establishment of intermolecular bonding. Consequently, the product can be dissolved in hot water. With cold water, the molecules immediately associate to give an insoluble gel. 

A class of hydrates (compounds containing water) with crystal structures composed of a molecular-water framework that encloses (or enclathrates) other molecules, such as gases. An example is the compound methane hydrate, CH4 nH20 (where n is about 6) that occurs in abundance on Earth in marine sediments and under arctic permafrost. 

All ten of the parent phenanthrolines are solids (see Table I). Most of the crystal structure work so far reported has been concerned with 1,10-phenanthroline and its derivatives. Crystal structure data and X-ray powder work on 1,10-phenanthroline hydrate confirm, as expected, that it exists as the monomer (12) with hydrogen bonding between the nitrogen atoms and the hydrogens of a water molecule. Crystal data on 2,9-dimethyl-1,10-phenanthroline have also been described. ... 

Geometrical aspects of the nucleophilic approach have been derived from structure correlation [107, 108] on small molecule crystal structures. The addition of amine to carbonyl has been shown to proceed via an approach of the nucleophile from above and behind the C = 0 group, in a local mirror plane of the R2C=0 fragment [109]. A more recent study is based on structural data of 31 N... R2C = 0 fragments [110]. In Figure 13.24, these are superimposed by matching the three atoms directly bound to the central carbon, and the observed positions of N are indicated (-h). These results were compared with a computer simulation of a model reaction in which the attack of NH3 on H2C=0 is assisted by a water molecule [110]. 

One observation raises the question of whether enough is known about the carbonium-ion lifetime in enzymic sites to be certain that it is always as short as estimated for reactions in water. The crystal structure of soybean beta-amylase complexed either with /8-maltose or maltal shows features strongly suggesting that the reaction center is shielded from solvent.101 A mechanism involving a carbonium-ion transition state with C-l unsubstituted and subject to attack by a structurally positioned water molecule, to form a product of /3-configurat.ion, is likely for the inverting reactions... 

As molecular dynamics simulations imply considerable demands on computation time and expertise, a collection of empirical and implicit methods for investigating water-induced effects on ligand binding have been developed. SuperStar, for example, uses information derived from experimental data to identify interaction sites in proteins [85, 86]. It generates propensity maps representing the distribution of one functional group around another found in small-molecule crystal structures. Success rates reported for the prediction of water positions around proteins are promising, in particular for those water positions that are well defined in the X-ray structure [86]. 

Add missing hydrogens using AMBER 3.1 to the x-ray crystal structure including crystallographic water molecules. The structure included 145 residues, 7 calcium ions, and was electrically neutral. 

Hydrates are solid structures composed of water molecules joined as crystals that have a system of cavities. The structure is stable only if at least one part of the cavities contains molecules of small molecular size. These molecules interact weakly with water molecules. Hydrates are not chemical compounds rather, they are clathrates . 

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. 

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