Representative atoms

Fig. 1. Structure adapted hierarchical description of Coulomb interactions in biological macromolecules. Filled circles (level 0) represent atoms, structural units (li vel 1) are surrounded by a single-line border, and clusters (level 2) are surrounded by a double-line border.

The HETATM records (Figure 2-115) represent atomic coordinates for atoms within non-.standard grotips (water molecules and atoms presented in HET... 

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... 

The initial configuration is set up by building the field 0(r) for a unit cell first on a small cubic lattice, A = 3 or 5, analogously to a two-component, AB, molecular crystal. The value of the field 0(r) = at the point r = (f, 7, k)h on the lattice is set to 1 if, in the molecular crystal, an atom A is in this place if there is an atom B, 0, is set to —1 if there is an empty place, j is set to 0. Fig. 2 shows the initial configuration used to build the field 0(r) for the simple cubic-phase unit cell. Filled black circles represent atoms of type A and hollow circles represent atoms of type B. In this case all sites are occupied by atoms A or B. 

Using squares to represent atoms of one element (or cations) and circles to represent the atoms of die other element (or anions), represent die principal spedes in die following pictorially. (You may represent die hydroxide anion as a single drde.)... 

Molecular modeling helps students understand physical and chemical properties by providing a way to visualize the three-dimensional arrangement of atoms. This model set uses polyhedra to represent atoms, and plastic connectors to represent bonds (scaled to correct bond length). Plastic plates representing orbital lobes are included for indicating lone pairs of electrons, radicals, and multiple bonds—a feature unique to this set. 

A.5 In the containers below, the green spheres represent atoms of one element, the pink spheres the atoms of a second element. In each case, the pictures show either a physical or chemical change identify the type of change. 

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. 

The drawing below shows a tiny section of a flask containing two gases. The orange spheres represent atoms of neon and the blue spheres represent atoms of argon, (a) If the partial pressure of neon in this mixture is 420. Torr, what is the partial pressure of argon (b) What is the total pressure ... 

A range of symbolic conventions is used in representing atomic and molecular stractures at the electronic level. So for example double and triple lines are used for multiple bonds. This seems a clear convention, which helps keep check of valency rales. However the symbol = for a double bond is not intended to imply two equal bonds (which the symmetry of the symbol could seem to suggest) as u and TT components have different geometries, contributions to bond strength , and consequences for chemical properties. The novice learner may well find interpreting such representations a considerable challenge. 

This is a qualitative problem requiring you to visualize and represent molecules, hi molecular pictures, circles represent atoms, and different colors or shadings identify different elements. The problem does not state how many atoms and molecules to draw, so we can start with any convenient amounts. However, the numbers of atoms of each element must not change during the reaction. 

A chemical formula describes the composition of a substance by giving the relative numbers of atoms of each element. When a substance contains discrete molecules, a chemical formula is also a molecular formula. A chemical formula contains elemental symbols to represent atoms and subscripted numbers to indicate the number of atoms of each type. The simplest chemical formulas describe pure elements. The chemical formulas of most elements are their elemental symbols helium is He, silicon is Si, copper is Cu. However, seven elements occur naturally as diatomic molecules (Figure 3-lT so their chemical formulas take the form X2 A few other elements occur as atomic clusters, notably P4 and Sg. ... 

In a ball-and-stick model, balls represent atoms, and sticks represent chemical bonds. The balls are labeled with elemental symbols or with different colors to distinguish among different elements. Figure includes ball-and-stick models, and Figure 3A shows a ball-and-stick model of propane. 

Fig. 80.—Minimum energy forms for ethane (a) and for a section of a polymethylene chain (b) as viewed along the axis of the C—C bond about which hindrance to rotation is under consideration. Dotted portions in each figure represent atoms or substituents attached to the lower carbon of the bond.

Figure 9.11 Several minimum energy paths for O2 dissociation on PtsCo) 11) (labeled by respective initial states), generating ML of atomic O, compared with equilibrium and 2% compressed Pt(lll). The points on each path are the images or states used to discretize the path with the climbing-image nudged elastic band method. The zero of the energy axis corresponds to an O2 molecule and the respective clean surfaces at infinite separation. The points located on the right vertical axis represent atomic O at ML. (Reproduced with permission from Xu et al. [2004].)...

To study covalent molecules, chemists find the use of models and drawings of structures helpful. In models, colored wooden or plastic balls are used to represent atoms. These balls have holes drilled in them according to the number of covalent bonds they will form. The holes are bored at angles that approximate the accepted bond angles. 

Look at your ball-and-stick model sets. Identify the different pieces that represent atoms, single bonds, double bonds, and triple bonds... 

FIGURE 5.3 A representation of the cyclohexane molecule. Filled circles represent atoms above the plane of the page and open circles represent atoms below the page. 

A few representative atomic refractivities and bond contributions are given in Table 18.1 below ... 

Figure 7.4a. cPl -Po unit cell. Open circles represent atoms on the paper plane, dashed circles atoms on other parallel planes. 

Figure 7.25. oS8-CrB structure type. Sections of a few cells (four cells are outlined) along the x/y (a) and the z/y (b) planes and (c) a projection on the z/y plane. Notice that this projection, in which the CrgB prisms parallel to the x axis have been evidenced, corresponds to the superposition of the two sections shown in (b), where the larger circles represent atoms in the x = A layer and smaller circles represent atoms in the x = 0 layer. 

Figure 7.36. Projections on characteristic planes of the unit cells of AlB2-derivative structures (binary deformation variants). Open circles represent atoms on the projection plane, dashed circles atoms on other parallel planes. For A1B2 compare with Fig. 7.5 and, for KHg2, with 7.33. (Adapted from Gladyshevskii et al. 1992)...

Figure 7.50. tI10-BaAl4 type structure. Perspective view (a) and projection of a few adjacent cells on the plane x, z (b) (open and filled circles represent atoms withy1 = 0 andy = / ). 

Pour the pennies onto a table. Remove all the pennies that are "heads-up." These pennies represent atoms of the radioisotope that have undergone radioactive decay. 

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