Simplified structural drawings

With practice writing structural formulas for organic molecules soon becomes rou tine and can be simplified even more For example a chain of carbon atoms can be rep resented by drawing all of the C—C bonds while omitting individual carbons The result mg structural drawings can be simplified still more by stripping away the hydrogens... 

Each energy level in the band is called a state. The important quantity to look at is the density of states (DOS), the number of states at a given energy. We like to simplify and draw the DOS of transition metals as the smooth curves of Fig. A.6, but in reality DOS curves show complicated structure, due to crystal structure and symmetry [6, 15]. The bands are filled with valence electrons of the atoms up to the Fermi level. In a molecule one would call this level the Highest Occupied Molecular Orbital or HOMO. 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

The closo structures of the B9H92 (a) and B10H102 (b) ions. In each case, there is one hydrogen atom attached to each boron atom, but the hydrogen atoms have been omitted to simplify the drawing. 

This cumbersome structure can be simplified by drawing a simple triangle. Each comer or bend" in the drawing represents a carbon atom and the single lines tell that the carbon atoms are single bonded. (See Figure 11.4.)... 

Example 11.5 draws attention to the fact that the crystalline and noncrystalline regions, particularly the crystalline regions, are likely to be highly anisotropic and that this must be taken into account in applying the models. A further complication is that, for many polymer samples, the structures illustrated schematically in fig. 11.9 are too simplified. Structures such as those shown in fig. 11.10, which allow for amorphous material both... 

Previously fatal infections have been rendered harmless by antibiotics such as the one above. Amoxicillin is not a large compound, yet drawing this compound is time consuming. To deal with this problem, organic chemists have developed an efficient drawing style that can be used to draw molecules very quickly. Bond-line structures not only simplify the drawing process but also are easier to read. The bond-line structure for amoxicillin is... 

An important factor for a simplified structure of the fuel cell and fuel power plant is that of supplying fuel as the only reactant while drawing the other... 

A simplified structure called the skeletal formula shows the carbon skeleton in which carbon atoms are represented as the end of each line or as comers. The hydrogen atoms are not shown, but each carbon is understood to have bonds to four atoms. For example, in the skeletal formula of hexane, each line in the zigzag drawing represents a single bond. The carbon atoms on the ends are bonded to three hydrogen atoms. However the carbon atoms in the middle of the carbon chain are each bonded to two carbons and two hydrogen atoms (see Figure 11.2). 

Figure 11.10 A schematic of the diffiaction patterns in a RHEED experiment resulting from different surface structures. To simplify the drawing the broad rods of the rough surface are drawn as constant in width. Properly, for a two-level surface they have two non-zero Fourier coefficients and should oscillate as sine waves perpendicular to the surface. Therefore the rods should be wdder and narrower along their length. See Figure 11.11 for a more accurate representation.

Imagine, now, a solid held together by such little springs, linking atoms between two planes within the material as shown in Fig. 6.1. For simplicity we shall put atoms at the comers of cubes of side Tq. To be correct, of course, we should draw out the atoms in the positions dictated by the crystal structure of a particular material, but we shall not be too far out in our calculations by making our simplifying assumption - and it makes drawing the physical situation considerably easier ... 

Figure 5. Structure of LiC6. (a) Left schematic drawing showing the AA layer stacking sequence and the aa interlayer ordering of the intercalated lithium. Right Simplified representation [21. (b) In-plane distribution of Li in LiC6. (c) In-plane distribution of Li in LiC,.

The six-carbon sugar a-galactose is identical to a-glucose except at carbon atom number 4, where the orientations are different. Draw the molecular structure of a-galactose. Simplify the stmcture by using flat rings rather than the true three-dimensional forms. 

Figure 29-4 Structure of 23S-28S ribosomal RNAs. (A) The three-dimensional structure of RNA from the 50S subunit of ribosomes of Halocirculci marismortui. Both the 5S RNA and the six structural domains of the 23S RNA are labeled. Also shown is the backbone structure of protein LI. From Ban et al.17 Courtesy of Thomas A. Steitz. (B) The corresponding structure of the 23S RNA from Thermus thermophilus. Courtesy of Yusupov et al.33a (C) Simplified drawing of the secondary structure of E. coli 23S RNA showing the six domains. The peptidyltransferase loop (see also Fig. 29-14) is labeled. This diagram is customarily presented in two halves, which are here connected by dashed lines. Stem-loop 1, which contains both residues 1 and 2000, is often shown in both halves but here only once. From Merryman et al.78 Similar diagrams for Haloarcula marismortui17 and for the mouse79 reveal a largely conserved structure with nearly identical active sites. (D) Cryo-electron microscopic (Cryo-EM) reconstruction of a 50S subunit of a modified E. coli ribosome. The RNA has been modified genetically to have an...

Figure 29-6 Some protein-RNA interactions within the ribosome. (A) A space-filling model of the 23S and 5S RNA with associated proteins from the ribosome of Haloarcula marismortui. The CCA ends of bound tRNA molecules in the A, P, and E sites are also included. The view is looking into the active site cleft. The proteins with e after the number are related to eukaryotic ribosomal proteins more closely than to those of E. coli.17 Courtesy of T. A. Steitz. (B) Three-dimensional structure of a 70S ribosome from Thermus thermophilus. The 30S subunit is to the right of the 50S subunit. Courtesy of Yusupov et al.33a (C) Stereoscopic view of the helix 21 to helix 23b region of the 16S RNA with associated proteins S6 (upper left), S18 (upper center, front), and S15 (lower back) from T. thermophilus. Courtesy of Agalarov et at.31 (D) Simplified in vitro assembly map of the central domain of the 30S bacterial ribosome. Courtesy of Gloria Culver. (E) Contacts of proteins with the central (platform) domain of the 16S RNA component. The sequence shown is that of Thermus thermophilus. Courtesy of Agalarov et al. (F) Three drawings showing alternative location of the four copies of protein L7/L12. The N-terminal and C-terminal...

Methane has a tetrahedral structure with each C-H bond 109 pm and all the bond angles 109.5°. To simplify tilings, we shall draw a molecule of methane enclosed in a cube. It is possible to do this since the opposite corners of a cube describe a perfect tetrahedron. The carbon atom is at the centre of the cube and the four hydrogen atoms are at four of the corners. 

The whole concept of modern chemistry is based on the usage of drawings or other visual models of molecular structures. These simplified models of real molecules provide us with a framework that helps us understand the behavior of chemical compounds. With the development of computers, scientists had to face the problem of transferring molecular models into computer language. 

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