Molecular representations bond-line structures

Chemists have historically employed various means of representating molecular structure. Two-dimensional drawings of atoms connected by lines are some of the most common molecular representations. Each line represents a chemical bond that, in the simplest case, is a pair of electrons shared between the connected atoms, resulting in a very strong attractive interatomic force. The various interatomic forces define the structure or shape of a molecule, while its chemistry is dependent on the distribution of electrons. A chemical reaction involves a change in the electron distribution, i.e., a change in bonding. 

The molecular representations in Figure 15.5 are known as line drawings. The corners, where two lines meet, represent carbon atoms, and the end of any line that does not have a symbol attached also represents a carbon atom. We assume that each carbon has enough hydrogen atoms attached to yield four bonds total. Compare the line drawings in Figure 15.5 to the more complete Lewis structures in Figure 15.6. 

In Summary Determination of organic structures relies on the use of several experimental techniques, including elemental analysis and various forms of spectroscopy. Molecular models are useful aids for the visualization of the spatial arrangements of the atoms in structures. Condensed and bond-line notations are useful shorthand approaches to drawing two-dimensional representations of molecules, whereas hashed-wedged fine formulas provide a means of depicting the atoms and bonds in three dimensions. 

Condensed and bond-line formulas are abbreviated representations of molecules. Hashed-wedged line drawings illustrate molecular structures in three dimensions. 

The most well-known and at the same time the earliest computer model for a molecular structure representation is a wire frame model (Figure 2-123a). This model is also known under other names such as line model or Drciding model [199]. It shows the individual bonds and the angles formed between these bonds. The bonds of a molecule are represented by colored vector lines and the color is derived from the atom type definition. This simple method does not display atoms, but atom positions can be derived from the end and branching points of the wire frame model. In addition, the bond orders between two atoms can be expressed by the number of lines. 

Fig. 11.2. Schematic representation of the primary structure of secreted AChE B of N. brasiliensis in comparison with that of Torpedo californica, for which the three-dimensional structure has been resolved. The residues in the catalytic triad (Ser-His-Glu) are depicted with an asterisk, and the position of cysteine residues and the predicted intramolecular disulphide bonding pattern common to cholinesterases is indicated. An insertion of 17 amino acids relative to the Torpedo sequence, which would predict a novel loop at the molecular surface, is marked with a black box. The 14 aromatic residues lining the active-site gorge of the Torpedo enzyme are illustrated. Identical residues in the nematode enzyme are indicated in plain text, conservative substitutions are boxed, and non-conservative substitutions are circled. The amino acid sequence of AChE C is 90% identical to AChE B, and differs only in the features illustrated in that Thr-70 is substituted by Ser.

Figure 45 (a) ORTEP view of the molecular adduct 39 35 (H-bonds are represented by thin lines), (b) ORTEP view of the inclusion complex between benzene and adduct 39 35. (c) Side view of the H-bonding network of adduct 39 35. (d) Simplified representation of the view in (c) showing the right-handed helical motif of the ribbon like H-bonded core of the assembly, (e) Single strand for H-bonded units extracted from the triple-stranded heli-cate structure in 39 35 showing left-handed helicity. (f) Stereoview of the inclusion complex between benzene and adduct 39 35 [60],... 

To avoid any misinterpretations concerned with the digit style of numbers, the decimal point is used throughout the book instead of a comma (i.e. computer notation 1.03 instead of 1,03, except for some graphical representations). In representative molecular structures, spin-paired non-bonding electrons around an atom of a molecule are represented (if necessary) by a bold line —in accord with commonly used leivis-structures. Single electrons are represented by a dot A full arrow (-> ) indicates shifts of electron pairs, whereas single electron shifts are... 

Fig. 18. Redox-coupled conformational change in a loop between helices I and II of subunit I. A stereoview (A, see color insert) and a schematic representation of the hydrogen bond network connecting Asp-51 with the matrix space (B). (A) The molecular surface on the intermembrane side is shown by small dots. Maroon and green sticks represent the structures in the fully oxidized and reduced states. (B) Dotted lines show hydrogen bonds. The rectangle represents a cavity near heme a. The two dotted lines connecting the matrix surface and the cavity represent the water path. The dark balls show the positions of the fixed water molecules.

FIGURE 1 Molecular structures of I, II, and a-cyclodextrin (a-CD) alkoxide. Schematic representation of the inclusion complexes and reaction intermediates involved in the hydrolysis of I affording acetic acid and m-ferf-butyl phenol. The inset shows the CAChe-minimized structure of the ternary catalytic complex I C a-CD alkoxide-ll proposed by Bender et al. (7S). The putative hydrogen bond between the alkoxide of a-CD and II is indicated by a solid line. a-CD alkoxide is shown in stick representation, and only polar hydrogen atoms are specified. I is shown in CPK representation and II in ball and stick. (See Color Insert in the back of this book.)... 

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