Molecules viewing

Fi re 12.8 Schematic diagram of the trimerlc porin molecule viewed from the extracellular space. Blue regions illustrate the walls of the three porin barrels, the loop regions that constrict the channel are red and the calcium atoms are orange. 

Figure 3. Two stereo stick views of the Mo2(OCH2CMe3)6(py)2 molecule viewed perpendicular to the Mo-Mo bond (top) and down the Mo-Mo bond (bottom).

Figure 1. (a) A schematic representation of the overall organization of the molecule of human ceruloplasmin. Domains 2,4, and 6 contain mononuclear copper centers, while the trinuclear copper cluster is located at the interface of domains 1 and 6. (b) An a-carbon ribbon diagram of the human ceruloplasmin molecule viewed along the pseudo threefold axis highlighting the triplication of the structure. Domains 1, 3, and 5 are depicted by striped motifs, whereas domains 2, 4, and 6 are dark shaded. The copper... 

Fig. 28 Results of a molecular dynamics study of an Mg3Al - Cl LDH the structure viewed along the (010) direction is shown on the left and the arrangement of interlayer Cl" and H2O molecules viewed along the (001) direction is shown on the right. Dashed lines represent hydrogen bonding. Reprinted with permission from [223], Copyright Mineralogical Society of America...

This chapter highlights recent work that shows the relevance of a smaU-molecule view of SP mechanical properties, in which reversible and specific intermolecular... 

Fig. 14 Crystal structure of BTCA, with the three crystallographically independent molecules displayed in different colours (A, greerv, B, blue, C, red) (a) a hydrogen-bonded chain of A and C molecules viewed approximately along the c-axis, and (b) the complete crystal structure viewed along the b-axis (the AC chains run into the page, with adjacent AC chains cross-linked by hydrogen bonding to B molecules)...

Figure 7. (Top) The pentagonal bipy-ramidal geometry of H4Os(PMe2Ph)3 as determined by neutron diffraction. Hydrogen atoms on the methyl and phenyl groups have been omitted for clarity. (Bottom) The central core of the molecule, viewed normal to the equatorial H4OsP plane. Note the slight bending of the phosphorus-osmium-phosphorus axis (69)...

Apart from the original idea of Arrhenius about active molecules, views of this sort have been put forward by Marcelin, Rice,f Trautz, Kruger, and others. 

Fig. 25. The arrangement of two neighboring molecules viewed perpendicular to the 6c plane (84 ...

Fig. 26. (a) The arrangement of the polymer chains in the unit cell viewed roughly perpendicular to the fiber axis, (b) The packing of the molecules viewed down the fiber axis (5-/)... 

FIGURE 8. Tetrakis(l-methylcyclopropyl)-ethene (40) molecule viewed along an axis of approximate two-fold symmetry. Drawn after Reference 83... 

A model of the structure of porin from the outer membrane of Rhodobacter capsulatus. Part (a) shows the a-carbon backbones of a trimer of porin molecules viewed along an axis approximately perpendicular to the plane of the membrane. Each molecule forms a tube that passes across the membrane. Part (b) shows an individual porin monomer, enlarged slightly from (a) and viewed along an axis approximately in the plane of the membrane. The molecule folds as a jS-barrel with 16 antiparallel jS strands. (From M. S. Weiss, et al.. The three-dimensional structure of porin from Rhodobacter capsulatus at 3 A resolution, FEES Lett. 267 268, 1990. Copyright 1990 Elsevier Science Publishers BV, Amsterdam, Netherlands. Reprinted by permission.)... 

Fio. 18. The dibenzophenanthrene molecule viewed along the twofold axis. 

Figure 121. The relationship between enantiomeric pairs of Ga(S2COEt)3 (a) two molecules viewed down the crystallographic threefold axis (along the c axis), and (b) two molecules viewed normal to the threefold axis.

Soloway (6l) suggested that the cyclodienes and lindane have in common two electronegative centres separated by a similar distance and pointed out the similarity between the profiles of these molecules viewed perpendicular to their plane of symmetry. 

STM image of Langmuir-Blodgett monolayer of y-C16H33-Q-3CNQ (structure is shown in Fig 11.31) on HOPG The 0.6x 1.2-nm shape is consistent with the molecules viewed "end-on" from the dicya-nomethylene end [27]. 

Newman diagram, molecule viewed along C(6)—C(5) bond (also applies to formulae 38 and 39). 

Because the Bemal-Folwer ice rules [34] constrain the allowable orientations of the nearest neighbour water molecules, viewed from a central (i.e. a target) molecule, the electric field generated by each molecule cannot cancel as illustrated in the lower diagram of Fig. 9. This produces a strong effective field... 

Newman projection A projection of a molecule viewed down the bond between two atoms. A circle represents these atoms, the larger circle for the more distant atom. Lines from the center to the exterior of the circles represent bonds to the nearer atoms. Lines representing bonds to the further atom do not penetrate the inner circle. When two bonds are coincident, they are drawn at a small angle to each other. 

FIG. 25.19. The helical AUF3 molecule viewed along its length. 

Fig. 1 Schematic of molecular self-assembly process of surfactant molecules. (View this art in color at www.dekker.com.)...

Figure 21, Images (a,c) and Fourier transforms (b,d) of helical crystals of streptavidin formed on lipid tubules containing DODA-EOa-biotin (50). (a,c) Stain striations extend along the tubules. Protein densities are particularly visible at tube edges, corresponding to streptavidin molecules viewed edge-on. Scale bar 40 nm. (b,d) Distribution of Fourier transform amplitudes from the tubes shown in (a,c) corresponding to about 1700 streptavidin molecules. The fine spacing between layer lines indicates a helical repeat of 47 nm. Visible diffraction peaks extend up to 1.7 nm (arrowhead in (b)]. Reproduced from ref. 242 (Ringler et al., Chem. Eur. J. 1997, 3, 620) with permission ofWiley-VCH.

The water molecule viewed as the overlap of 2pv and 2pz orbitals of the oxygen atom with hydrogen Is orbitals to produce an expected bond angle of 90°. This is not entirely satisfactory. See Fig. 21. The shaded 2px orbital constitutes the lone pair. 

Fig. 5.7. The C o molecule viewed down a threefold rotation-inversion axis. The upper half of the molecule is identified with filled, the lower half with unfilled bond lines. Molecular twofold axes are also shown. The unfilled bond lines also represent the upper half of the second orientation of Cgo found in the crystal...

Figure 9.4 (a) The NH3 molecule in its coordinate axes, with symmetry elements shown (after Levine), (b) The NH3 molecule viewed from the positive z axis (after Levine). 

As we select the relevant entry in the tree, the possible commands are shown in the lower part of the toolbox, that is, project-systems-system. The command tab line now shows the possible commands, for example, show, add, and delete. As we wantto add a molecule, we select the add tab. A subtab within the add command now displays the items that can be added, that is, forceJidd, molecule, and view. On selecting the molecule tab by clicking with the mouse, we can set important parameters for the molecule in a subtab, for example, the name of the molecule write Co(III)(NH3)6. On the lower right side of the toolbox, we can now proceed by selecting the confirm button. The molecule is added, and an empty molecule view for [Co(NH3)6] is automatically added to the graphics area. 

We now navigate to molecule-add and choose molecule-add-atom to create the cobalt(III) center. In the symbol subtab, we set the atom type to C03 and press confirm. The atom appears in the molecule view. The first nitrogen atoms are now added by changing the atom type and position to NT and (1.95,0,0), respectively. For the second nitrogen atom, we choose (0, 1.95, 0), and so on. 

Likewise, the molecule can be displayed by adding a molecule view in the job result-add section. In the graphical display, you can follow the changes in the geometry by selecting the molecular structure for the desired step. 

Now you are ready to submit the molecule for geometry optimization via calc-queue-add and to visualize the results in the results calc-result section, as described above. To be able to determine which conformer was optimized, you may choose the wireframe or tubes render options, which you will find in molecule-views-view-render, you may also want to deactivate the display of hydrogen atoms in molecule-views. 

Newman projections illustrate the conformation of molecules viewed along the length of a bond. See p. 364 if you need reminding of how to draw and interpret them. 

Fig. 3 A DCA molecule and CPK model of the DCA host substructure Channels are formed between corrugated host bilayers constructed from hydrogen-bonded DCA molecules (View this art m colot at vcm m dekker com )...

Fig. 13 The (EF)4 embrace between a pair of Ph4E molecules View this art in coloi at wwn dekkei com)...

Fig. 5 Channel-type molecular-sieve structure based on the self-assembly via coordination of MTPyP building blocks. View down the channel axis. The width of the parallel onedimensional channels is 0.6 nm. suitable for the storage and transport of small molecules.(View this art in color at WWW. dekker. com.)...

Very similar ideas apply to Ihc structures of /c/a and amc////ocap[es. Wliereas doso species with / cage atoms require 77+ 1) skeletal pairs, nido and aradino species with u cage atoms have /7 + 2 and u + 3 skeletal bonding orbitals, respectively that is. an identical number of electrons as the parent doso species. Some examples are shown in 22.23 and 22.24 and include some rather unusual species as well as traditional molecules viewed in a rather different light. The scries in 22.23 is iso-... 

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