Coordinate data

Coordinate atomic coordinate data MODEL, AEOM, SIC ATOM... 

The atomie coordinate data section shown in Figure 2-114 is constructed mostly... 

Figure 2-114. Atomic coordinate data section of the analy2ed PD B file.

CWG van Gelder, EJJ Leusen, JAM Leunissen, JH Noordik. A molecular dynamics approach for the generation of complete protein structures from limited coordinate data. Proteins 18 174-185, 1994. 

Fig. 7 Chromaticity diagram presented in terms of the x and y coordinates. (Data adapted from Ref. 39.)...

New Brunswick privacy regulations prohibit the distribution of these water quality data by any method which identifies the individual well owner or associated property. These data can only be provided to researchers and other interested parties in aggregate form with all identifying coordinate data removed. 

To compile the data for this table with rectangular coordinates the plotting was done in two scales, the lower values of responses from 1 to 45 response area units and the overall scale for responses greater than 45 area units. For extended range data, however, analysts often use log-log coordinates. Data was thus obtained using this method. Because difficulties were seen in either of these methods, the response versus amount values were plotted after they had been independently transformed as found in Kurtz work ( 2 ). Data from the use of all of these plotting methods are shown in the table. 

This program can run in batch or interactively. As input data, it requires the structure of the compound and this can be provided as a set of coordinate data from X-ray measurements, it can be entered interactively in the form of a connection table or the program can simply be provided with a CAS registry number, and if the corresponding connection table is in the files of the CIS, it will use that. 

The authors are honored by the invitation of Karl A, Gschneidner, Jr, to present this paper at the Second Chemical Congress of the North American Continent, They are also indebted to Joseph G, Cannon of Molycorp, Inc, and H, Holt Apgar of Rhone-Poulenc, Inc, for discussions relating to the market for rare earths. We acknowledge with thanks Wayne Person of GTE Sylvania, Towanda, PA, who provided the brightness and color coordinate data in Table I,... 

Sheridan RP Rusinko A, Nilkantan R, Venkatraghavan R. Searching for pharmacophores in large coordinate data bases and its use in dmg design. Proc Natl Acad Sci USA 1989 86 8165-8169. 

The most obvious data in a typical 3D structure record are the atomic coordinate data, the locations in space of the atoms of a molecule represented by (x, y, z) triples, and distances along each axis to some arbitrary origin in space. The coordinate data for each atom are attached to a list of labeling information in the structure record such as that derived from the protein or nucleic acid sequence. 

These data provide a useful mean of checking the reliability of the thermodynamic parameters associated with the solution and complexation processes. Indeed, coordination data should be the same (within the experimental error) independently of the solvent used in the solution process. This statement is now corroborated by representative examples involving the fluoride anion and 1. Thus in fulfilling the requirements of equation (6), the enthalpies of solution of the reactants (Bu4NF and 1) and product (Bu4N1F) are combined with the enthalpies of complexation of the fluoride anion and 1 in acetonitrile (MeCN) (equation (7)) and N,N- dimethylformamide (DMF) (equation (8)) to derive the enthalpy of coordination for this system in the solid state. 

It can be concluded that for the fluoride-1 system, both Acoord/-/° values (equations (7) and (8)) derived from acetonitrile (Acoord/-/° = -11.7 kJ mol-1) and A/,A/-dimethylformamide (Acoord/-/° = — 11.6 kJ mol-1) are in good agreement. For further details regarding the applicability of coordination data readers are referred to literature [18,44],... 

Figure 6.1 Ionic radii of the lanthanide cations in oxides. (a) Eight-fold coordination (b) octahedral coordination (data from Shannon, 1976).

From the coordinate data stored in the trajectory files, the mean-square displacements for all tiie movable atoms were calculated, and the diffusion coefficient, D sd, computed using Einstein s relation... 

Fig. 8.11. EX AES data for various alkali-metal-iron glasses and melts along with model compounds having mainly Fe + in tetrahedral (hercynite) and octahedral (magnesiowustite) coordination. Data are the Fourier transforms of the weighted EXAFS functions (after Waychunas et al., 1988).

Tel. 800-232-2224, 203-335-0906, fax 203-336-2481 Display and manipulation of 3D models using keyboard input. Molecular Animator for creating and displaying 3D models. Molecular Graphics for display and manipulation of atomic coordinate data. ChemFile II for creating databases of 2D chemical structures with associated text. PCs and Macintosh. 

The file Figure2.19f.in contains a list of the polar coordinates of the vertices on the unit sphere, arranged so that the 9, (p) values of each decagon are read in during execution of the programme in the sequence that all the 0 - values are read before the 4> - values. This order is convenient because most of the coordinate data for the structures were calculated on spreadsheets and so could be copied and then pasted [PASTESPECIAL command] into a NOTEPAD file as unformatted text. 

All the FORTRAN programmes in the BonusPack require formatted input. For the coordinate data input file, for example, Figure2.19f.in, the formal requirement is that the (0, (p) values be in F18.4 format. ... 

Control File [Figure 2.15b.in] Coordinate data file [Connections list]... 

Coordinate data file starts with list of 2 4 18 2... 

Figure 7 Migration path for benzene between sites Sn and W in faujasite and the energy profile along the migration path (reaction coordinate). Data from Ref. 50.

Much of our current knowledge of bonding geometry of atoms has been derived from crystal structure determinations. Atomic coordinate data that have been published are included in databases, as will be described in more detail in Chapter 16. For organic compounds the Cambridge Structural Database " can be accessed by computer. Similar data for inorganic compounds are found in the Inorganic Crystal Structure Database. Comparisons with other experimental methods, such as... 

The results calculated are in reasonable agreement with the seawater speciation data from Turner et al. (1981) quoted in Table 6.5 and with the qualitative features of the Garrels and Thompson model. Of course, the selection of different suites of stability constants leads to somewhat different speciation pictures. For example, the calculations made by Garrels and Thompson, Dickson et al., and in Tableau 6.6 are based on the assumption that chloride complexes with the major cations are unimportant. This assumption may be wrong and ion pairs with CP may represent nonnegligible fractions of the major cation concentration. Then, of course, a different speciation picture would result however, the extension of these results to trace metals (see the column for seawater in Table 6.5) would require a reinterpretation of the original experimental coordination data with equilibrium constants with the CP ion pairing model. 

The benzobicyclo[2.2.1]heptene and 1,2,3,4-tetra-hydro-1,4-epoxynaphthalene systems were constructed from the coordinate data for benzobicyclo[2.2.1]heptene-syn- and -anti-bromobenzenesulfonates (147). Positions for the exo and endo amino groups were selected by using a standard C-N bond length with the bond angles and dihedral angles calculated from a crystallographic study of 2-exo-aminonorbornane-2-carboxylic acid (148). 

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