Atomic colorings molecular modeling

In order to represent 3D molecular models it is necessary to supply structure files with 3D information (e.g., pdb, xyz, df, mol, etc.. If structures from a structure editor are used directly, the files do not normally include 3D data. Indusion of such data can be achieved only via 3D structure generators, force-field calculations, etc. 3D structures can then be represented in various display modes, e.g., wire frame, balls and sticks, space-filling (see Section 2.11). Proteins are visualized by various representations of helices, / -strains, or tertiary structures. An additional feature is the ability to color the atoms according to subunits, temperature, or chain types. During all such operations the molecule can be interactively moved, rotated, or zoomed by the user. 

C03-0005. Determine the molecular formula, stmctural formula, and line stmcture for each compound whose ball-and-stick model follows (see Figure for atom colors) ... 

Figure 7. Interactions of Nation s side chains and a Pt nanoparticle. A light brown color indicates Pt atoms at distances closer than 6.79A° from an S atom. Atoms that are in regions around the sulfonic groups have been enlarged to improve visualization. Color codes are white and red for H and O in water, respectively, green for F, gray for C, and yellow for S 73 Reprinted from Electrochim Acta, Vol. 50, Balbuena et al., Molecular modeling studies of polymer electrolytes for power sources, p. 3788, Copyright (2005), with permission from Elsevier.

Figure 11 Molecular model of the complex between Ru-65-c) t bs and Cc. The geometry of the complex is the same as that of the complex involving native cytochrome bs proposed by Salemme. The heme groups (red), and the ruthenimn complex (green) are highhghted. The atoms forming an electron-transfer pathway between the ruthenimn complex and the heme group of Ru-65-c) t bs are colored yellow. The lysine and arginine residues are blue, while aspartate and glutamate residues are red ...

We will begin to represent molecules with models having balls for atoms and sticks for bonds, as in the ball-and-stick model of acetylene just shown. These representations are analogous to a set of molecular models. Balls are color-coded using accepted conventions carbon (black), hydrogen (white or gray), oxygen (red), and so forth. 

TABLE A-6 KEY OF ATOM COLORS USED IN MOLECULAR MODELS IN HOLT CHEMISTRY... 

You can now identify atoms that bond covalently and name the molecular compounds formed through covalent bonding. In order to predict the arrangement of atoms in each molecule, a model, or representation is used. Several different models can be used, as shown in Figure 9-10. Note that in the ball-and-stick and space-filling molecular models, atoms of each specific element are represented by spheres of a representative color, as shown in Table C-1 in Appendix C. These colors are used for identification of the atoms if the chemical symbol of the element is not present. 

Fig. 2 The mechanical molecular model considers atoms as spheres and bonds as springs. The mathematics of spring deformation can be used to describe the ability of bonds to stretch, bend, and twist. (View this art in color at www.

FIGURE 301. Cutouts for paper or cardboard molecular models from the first German edition of van t Hoff s The Arrangement of Atoms in Space (Die Lagerung Der Atome Im Raume, 1877). Color photographs of the assembled models are found in Heilbonner and Dunitz, Reflections on Symmetry, 1993). 

Note and record the color used to represent each of the following atoms in the molecular model kit hydrogen (H), oxygen (O), phosphorus (P), carbon (C), fluorine (F), sulfur (S), and nitrogen (N). 

Brumlik Uuiversal Molecular Model Kit (ISBN 0-13-931700-7) This scientifically accurate molecular model set demonstrates the framework of a molecule, the space filling capacity of a molecule, and molecular orbitals. This kit features color-coded atomic valence spheres and connectors. Its parts are fully interchangeable with the Brumlik Framework Molecular Model Kit... 

At this point you should convince yourself that there are no other stereoisomers by writing other structural formulas. You will find that rotation about the single bonds, or of the entire structure, or of any other arrangement of the atoms will cause the structure to become superposable with one of the structures that we have written here. Better yet, using different colored balls, make molecular models as you work this out. 

As described earlier in this chapter, polymers are long chains of atoms linked together. They may be flexible and bendable. To explain this, one may visual them as ball-and-stick model. In chemistry, the ball-and-stick model is a molecular model of a chemical substance which aims to display both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods which represent the bonds. Double and triple bonds are usually represented by two or three curved rods, respectively. The chemical element of each atom is often indicated by the sphere s color and size. The top of Figure 1.6 shows a drawing of a ball-and-stick model of a molecule. Figure 1.6 also indicates that there is free rotation around the single bonds. If there was a double or triple bond, there would not be any rotation possible around those bonds. 

The molecular model shown here represents guanine, a component of a DNA molecule. Only the connections between the atoms are shown in this model. Draw a complete Lewis structure of the molecule, showing all the multiple bonds and lone pairs. (For color code, see inside back endpaper.)... 

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