Sticking model

Fig. 7. Snapshots of rupture taken (A) at the start of the simulation (zcant = 0), (li) at ZcB.nl = 2.8 A, (C) at Zcnm = 4.1 A, (D) at Zcnm = 7.1 A, and (E) at Zcant = 10.5 A. The biotin molecule is drawn as a ball-and-stick model within the binding )ocket (lines). The bold dashed lines show hydrogen bonds, the dotted lines show selected water bridges.

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. 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

The earliest ball and stick models were exactly that wooden balls in which holes were drilled to ac commodate dowels that connected the atoms Plastic versions including relatively inexpensive student sets became available in the 1960s and proved to be a valuable learning aid Precisely scaled stainless steel framework and plastic space filling models although relatively expensive were standard equipment in most research laboratories... 

Ball and stick model (Section 1 10) Type of molecular model in which balls representing atoms are connected by sticks representing bonds Similar to ball and spoke models of Learning By Modeling... 

Thermodynamic properties such as heats of reaction and heats of formation can be computed mote rehably by ab initio theory than by semiempirical MO methods (55). However, the Hterature of the method appropriate to the study should be carefully checked before a technique is selected. Finally, the role of computer graphics in evaluating quantum mechanical properties should not be overlooked. As seen in Figures 2—6, significant information can be conveyed with stick models or various surfaces with charge properties mapped onto them. Additionally, information about orbitals, such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), which ate important sites of reactivity in electrophilic and nucleophilic reactions, can be plotted readily. Figure 7 shows representations of the HOMO and LUMO, respectively, for the antiulcer dmg Zantac. 

Fig. 2. X-ray structure of dearniaooxytociii (a) space-filling model (b) equivalent stick model. Numbers and amino acids refer to positions indicated in...

Fig. 1. Methods for representing SiO and AlO tetrahedra by means of (a) baH-and-stick model, (b) soHd tetrahedron, (c) skeletal tetrahedron, and (d) spare-filling of packed spheres (1). (e) Linking of four tetrahedra in a four-membered ring, (f) Secondary building unit called tmncated octahedron as...

The use of graphic displays as an essential element of computer-based instmctional systems has been exploited in a number of ways. Molecular modeling and visualization techniques have supplemented the traditional set of stick models in courses on organic and inorganic chemistry, and animation of molecular motion and of the progress or mechanism of chemical reactions has been a useful classroom tool. 

Panel 1.1 The 20 different amino acids that occur in proteins. Only side chains are shown, except for the first amino acid, alanine, where all atoms are shown. The bond from the side chain to Ca is red. A ball-and stick model, the chemical formula, the full name, and the three-letter and one-letter codes are given for each amino acid. 

All pictorial representations of molecules are simplified versions of our current model of real molecules, which are quantum mechanical, probabilistic collections of atoms as both particles and waves. These are difficult to illustrate. Therefore we use different types of simplified representations, including space-filling models ball-and-stick models, where atoms are spheres and bonds are sticks and models that illustrate surface properties. The most detailed representation is the ball-and-stick model. However, a model of a protein structure where all atoms are displayed is confusing because of the sheer amount of information present (Figure 2.9a). 

Figure S.22 Chemical formula for sialic acid (a-5-n-acetylneuramlnlc acid) drawn In approximately the same orientation as the ball and stick models in Figure 5.24. Ri and Rz which are H atoms in sialic acid, denote substituents introduced to design tightly bound inhibitors. These are large and hydrophobic as shown in Figure 5.24.

Figure 14.1 Each polypeptide chain in the collagen molecule folds into an extended polyproline type II helix with a rise per turn along the helix of 9.6 A comprising 3.3 residues. In the collagen molecule three such chains are supercoiled about a common axis to form a 3000-A-long rod-like molecule. The amino acid sequence contains repeats of -Gly-X-Y- where X is often proline and Y is often hydroxyproline. (a) Ball and stick model of two turns of one polypeptide chain.

Figure 15.16 Detailed views of the environment of Gin 121 in the lysozyme-antilysozyme complex. Gin 121 in lysozyme is colored green both in the space-filling representation to the left and in the ball and stick model to the right. This side chain of the antigen fits into a hole between CDR3 regions of both the heavy (Tyr 101) and the light (Trp 92) chains as well as CDRl from the light chain (Tyr 32). (After A.G. Amit et al.. Science 233 747-753, 1986.)...

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.

Let s return to bromochlorofluoromethane as a simple example of a chiral molecule. The two enantiomers of BrCIFCH are shown as ball-and-stick models, as wedge-and-dash drawings, and as Fischer projections in Figure 7.6. Fischer projections are always generated the same way the molecule is oriented so that the vertical bonds at the chirality center are directed away from you and the horizontal bonds point toward you. A projection of the bonds onto the page is a cross. The chirality center lies at the center of the cross but is not explicitly shown. 

Figure Three represernarions of the structure of Cm- (a) normal ball-and-stick model (b) the polyhedron derived by truncating the 12 vertices of an icosahedron to form 12 symmetrically separated pentagonal faces (c) a conventional bonding model.

Bell-end-stick models of water (H20), ammonia (NHj), and methane (CH4). The... 

Benzene ball-and-stick model, showing double bonds. 

Species type Orientation of electron pairs Predicted bond angles Example Ball and stick model... 

FORMULA BALL -AND-STICK MODEL SPACE-FILLING MODEL... 

The next most important aspect of a molecular compound is its shape. The pictorial representations of molecules that most accurately show their shapes are images based on computation or software that represents atoms by spheres of various sizes. An example is the space-filling model of an ethanol molecule shown in Fig. C.2a. The atoms are represented by colored spheres (they are not the actual colors of the atoms) that fit into one another. Another representation of the same molecule, called a ball-and-stick model, is shown in Fig. C.2b. Each ball represents the location of an atom, and the sticks represent the bonds. Although this kind of model does not represent the actual molecular shape as well as a space-filling model does, it shows bond lengths and angles more clearly. It is also easier to draw and interpret. 

Below are ball-and-stick models of two molecules. In each case, indicate whether or not there must be, may be, or cannot be one or more lone pairs of electrons on the central atom ... 

Fig. 3 Sialidase inhibitor Neu5Ac2en 4 bound in the active site of influenza A virus sialidase (from PDB structure IfSb (Smith et al, 2001)), Left Stick model of 4 surrounded by some important active site residues. Right Electrostatic potential surface rendering of the active site (blue -positive, red - negative), (Amino acid numbering for influenza A/N2 sialidase is used throughout this review)...

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

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