Oxygen molecule crystal structure

The great majority of Ca ligands in small-molecule crystal structures are oxygen atoms. In protein crystal structures oxygen atoms are the only Ca ligands observed to date. Of the 182 ligands in the 27 sites of Table... 

As observed for the N- H O interactions between main-chain and side-chain groups, the N-ft Ow angles are almost linear, 156(15)°, if the all-a-helix proteins are omitted from the sampling, see Ihble 19.6d. The distribution of these angles is 140° to 180° for 90% of the data, and consistent also with small molecule crystal structures [75, 382, 475]. The spread of hydrogen-bond distances is broad, and wider for C=0 than for N-H, probably because the C=0 oxygen is more readily accessible and multiple C=0- -HOw interactions are frequently observed. 

Figure 7. Crystal structures of (a) hollandite, (b) romanechite (psilomelane), and (c) todorokite. The structures arc shown as three-dimensional arrangements of the MnO() octahedra (the tunnel-tilling cations and water molecules, respectively, are not shown in these plots) and as projections along the short axis. Small, medium, and large circles represenl the manganese atoms, oxygen atoms, and the foreign cations or water molecules, respectively. Open circles, height z. = 0 fdled circles, height z = Vi.

Thus, l,6-methano[10]annulene (77) and its oxygen and nitrogen analogs 78 and 79 have been prepared and are stable compounds that undergo aromatic substitution and are diatropic. For example, the perimeter protons of 77 are found at 6.9-7.3 5, while the bridge protons are at —0.5 5. The crystal structure of 77 shows that the perimeter is nonplanar, but the bond distances are in the range 1.37-1.42A. It has therefore been amply demonstrated that a closed loop of 10 electrons is an aromatic system, although some molecules that could conceivably have such a system are too distorted from planarity to be aromatic. A small distortion from planarity (as in 77) does not prevent aromaticity, at least in part because the s orbitals so distort themselves as to maximize the favorable (parallel) overlap of p... 

Z = 8 Dx = 3.09 R = 0.076 for 1,253 intensities. The crystal structure contains two symmetry-independent molecules. The two l-ascorbate ions differ significantly only in the orientations of the terminal hydroxyl groups of the side chains, with C-6 - 0-6 to C-5 - 0-5 gauche and trans, respectively. The unprotonated oxygen-atoms are 0-1 and 0-3, with C-O distances ofbetween 127 and 133 pm. One Tl+atom has four oxygen atoms at distances of 258 to 298 pm the other has three, at distances of 258,268, and 300 pm. The 0-3 atoms have two Tl+ contacts,... 

Incorporation of the position of water molecules that are firmly bound to the protein can impart affinity and novelty to the designed ligand. A prime example is the design of a class of HIV protease cyclic urea inhibitors by DuPont scientists that incorporated a water molecule bound to both flaps of the enzyme into their ligand [32]. The crystal structure of the HIV protease-cyclic urea complex [32] shows the urea carbonyl oxygen substituting for the position of the water molecule. 

Fig. 43. Packing in the crystal structure of the 1 imidazole 2 H,() associate viewed from the c direction1111. Observe the layer-like arrangement of water molecules near x = 0 (H-bonds are indicated as broken lines only relevant H atoms are shown O atoms of the host are dotted water oxygen as a bold circle N atoms are hatched the hatched segments signify the imidazole rings)...

A number of chemical elements, mainly oxygen and carbon but also others, such as tin, phosphorus, and sulfur, occur naturally in more than one form. The various forms differ from one another in their physical properties and also, less frequently, in some of their chemical properties. The characteristic of some elements to exist in two or more modifications is known as allotropy, and the different modifications of each element are known as its allotropes. The phenomenon of allotropy is generally attributed to dissimilarities in the way the component atoms bond to each other in each allotrope either variation in the number of atoms bonded to form a molecule, as in the allotropes oxygen and ozone, or to differences in the crystal structure of solids such as graphite and diamond, the allotropes of carbon. 

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