Capped Sticks Model

The capped sticks model can be seen as a variation of the wire frame model, where the structure is represented by thicker cylindrical bonds (figure 2-123b). The atoms are shi unk to the diameter of the cylinder and ai e used only for smoothing or closing the ends of the tubes. With its thicker bonds, the capped sticks model conveys an improved 3D impression of a molecule when compared with the wire frame model. 

Figure 2 Capped-stick model of the photoactive assembly 2(bpp-34-crown-10)-2(amm-stilb).

Figure 23 (a) Schematic and (b) capped-stick model of two propiolic acids and (c) schematic and (d) capped-stick model of anthracene... 

Fig. 10.6 Packing of TATP as capped-stick model alraig the crystaiiographic screw axis in a perpendicular view [13]. Reprinted with permission frran Dubnikova et al., Decompositirai of TATP Is an Entropic Explosion, J. Am. Chem. Soc. 2005, 127, 1146-1159. Copyright (2005) American Chemical Society...

A more comfortable representation for the human visual perception is the balls and sticks model. Here, the molecule is depicted as a composition of two types of objects, small spheres defining the atoms and cylinders for bonds (single, double, triple). Hidden lines are removed allowing proper intersection of bonds and atoms to give some indication of the depth of the molecule. However, the balls and sticks model cannot represent the shape of the molecule because the radii are chosen arbitrarily (see Figure lb). If the spheres of the atoms are not explicitly drawn or placed at the end of the cylinders in order to close the cylinders the representation is referred as sticks or capped sticks, respectively (see Figure Ic). 

Figure 1 Structure models of the amino acid tryptophane color coded by atom types (black or green, carbon white, hydrogen red, oxygen blue, nitrogen) (a) wire frame (b) balls and sticks (c) capped sticks and (d) CPK-model...

Figure 34 Mixed representation of the p53 DNA complex. The p53 protein and the DNA is shown as capped stick model, the protein backbone is represented as ribbon model. Parts of the molecular surface indicate the p53 protein DNA interface region. The surfaces are color coded with respect to the electrostatic potential calculated by a finite difference algorithm solving the Poisson-Boltzmann equation - (blue, negative gray, neutral red. positive). The electropositive parts of the p53 protein fit perfectly in the major and minor groove of the almost electronegative DNA...

Fig. 9. Ball-and-stick model for a 19.2° fullerene cone. The back part of the cone is identical to the front part displayed in the figure, due to the mirror symmetry. The network is in armchair and zigzag configurations, at the upper and lower sides, respectively. The apex of the cone is a fullerene-type cap containing five pentagons.

Get an NMR tube. They are about 180 mm long, 5 mm wide, and about a buck apiece for what is euphemistically called the inexpensive model. The tubes are not precision ground, and some may stick in the NMR probe. This should not be your worry, though. They also have matching, color coordinated designer caps (Fig. 134). 

Fig. 6 The colchicine and vinblastine sites, a Ribbon representation of RB3-SLD and of the two tubulin a 3 heterodimers. The nucleotides (GTP on a, GDP on P), colchicine (Col, yellow) and vinblastine (Vlb, cyan) are shown as ball-and-stick models. The dashed line shows the location of the RB3-SLD linker between the N-terminal cap and the C-terminal helix, which is the least ordered part of RB3-SLD. The sulfur atom of Cys 12 of the P subunit contacting vinblastine is highlighted as a yellow sphere. b,c Illustration of the interfacial interference of destabilizing molecules with MT assembly schematic representation of the (Tc)2R-vinblastine complex (b) and of a straight protofilament (c). Longitudinal MT-specific contacts (black rectangles in c) cannot be established between vinblastine- or colchicine-bound monomers...

Fig. 2. (A) Atomic resolution STM image of a carbon tube, 35 A in diameter. In addition to the atomic honeycomb structure, a zigzag superpattern along the tube axis can be seen. (B) "Ball-and-stick" structural model of a Cg(,-based carbon tube. The upper part is closed by a Cgo hemisphere cap. (C) Structural model of a giant superpattern produced by two misoriented graphitic sheets. The carbon atoms in the first layer are shaded, and the second layer atoms are open. Between the two dashed lines, we highlight those first layer atoms with white that do not overlap with second layer atoms. Because of their higher local density of states at the Fermi level, these atoms (p-type atoms) appear particularly bright in STM images (16,21). [ results in a zigzag superpattern along the tube axis within the two white dashed lines as indicated.

A simple macrobicycle can be considered to arise by addition of another chain or strap of atoms to a macromonocycle, to provide three chains joined at two capping carbon atoms (top), effectively two fused macromonocycles. This example offers six donor groups to a metal ion, as exemplified with ball and stick and space-filling models the latter shows the small central cavity able to accommodate only a single cation. These readily form very stable octahedral complexes with a range of metal ions the best-known example has L = NH (called sarcophagine ). 

Therefore, a new phase was constructed based on dimethylpentylsilane. It consisted of 991 atoms, 1051 bonds and 15 193 connectors, containing 171 silicons, 328 oxygens, 143 carbons and 349 hydrogens. Twenty dimethyl-pentylsilanes and one trimethylsilane were bonded within 900 A2 on the polysilicondioxide phase. The trimethylsilane was considered an end-capped molecule. The optimized structure of a complex of this model phase and iopanoic acid is shown in Figure 6.27. The upper view of the space-filled structure indicates how a molecule fits in the pocket. The trimethylsilane is the center of the pocket. The atomic size is 1 instead of 0.2 for the stick and... 

Figure 5. The structure of the activation complex (left) with the activation domain enclosing the cobalamin and part of the Bj binding domain, and the cap domain at the lower right. The cobalamin cofactor, with its side chain protruding into the B 12-binding domain, is shown in ball-and-stick mode. AdoMet has been included at the site where it binds in the isolated activation domain 4). From cross-linking experiments 49), it is known that flavodoxin binds to this face of the gactivation complex. On the right is a model for the structure of the [649-1227] fragment in its cap-on conformation. The motions of the activation and cap domains that occur in the interconversion of conformations involve rotations around axes that are not parallel to one another.

The manufacture specifies a number of physical parameters on the specification sheet. The user has no option but to accept these figures. However, they will be critical when setting up mathematical models such as MCNP programs and ISOCS (see Chapter 7, Section 7.7). The measurements will have been made with the detector at room temperature and un-mounted. Therefore, some laboratories have found it necessary to X-ray their detector while cooled in order to measure the physical parameters at operating temperature. There have been surprises detectors mounted off-centre, for example A useful trick when making such measurements is to stick a small piece of carefully measured platinum wire to the side of the detector cap. The image of this will be very clear on the X-ray and provide a reference distance. 

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