Three-dimensional bond-line structures

Bond-line structures with wedges and dashes to indicate three dimensionality. 

Three-Dimensional Bond-Line Structures (Section 2.6)... 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Methane is a tetrahedral molecule its four hydrogens occupy the corners of a tetra hedron with carbon at its center We often show three dimensionality m structural for mulas by using a solid wedge ) to depict a bond projecting from the paper toward you and a dashed wedge (i 111 ) for one receding away from you A simple line (—)... 

The two individual line-bond structures for acetate are called resonance forms, and their special resonance relationship is indicated by the doubleheaded arrow between them. The only difference between resonance forms is the placement of the r and nonbonding valence electrons. The atoms themselves occupy exactly the same place in both resonance forms, the connections between atoms are the same, and the three-dimensional shapes of the resonance forms are the same. 

A note on good practice Dashed and solid wedge-shaped bonds are commonly used when displaying organic structures to convey a sense of the three-dimensional shapes. The dashed wedge-shaped bonds go into the page and the solid wedge-shaped bonds come toward us. The thin lines are in the plane of the paper. 

Finally, we should note that the lines that are often drawn in illustrations of three-dimensional ionic crystal structures to better show the relative arrangement of the ions do not represent shared pairs of electrons, that is, they are not bond 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 11.12 The three-dimensional tetrahedral structure of carbon (e.g., in methane, CH4), with an angle between the bonds of 109.5°. The simple straight lines are in the plane of the paper, the solid tapered line points towards the observer and the dashed line is into the paper.

Fig. 3.2-1. Electron-rich (A, B) and electron-precise (C) planar aromatics as well as three dimensional structures D—L as a result of less skeletal electrons (SE). Lines in electron-deficient corn-pounds indicate connectivities not 2c2e bonds.

Fig. 2.8 Cleavage in the amphiboles. (A) Schematic representation of the characteristic stacked amphibole I-beams in the three-dimensional structure. A tetrahedral portion of an I-beam is labeled "silica ribbon." The octahedral portion is labeled "cation layer" and represented by solid circles. One of the possible cleavage directions (110) along planes of structural weakness is indicated by the line A-A stepped around the I-beams in the lower part of the diagram. (B) Cross section of the stacked I-beams with the directions of easy cleavage indicated. There is a lower density of bonds between I-beams in the crystallographic directions (110) and (110). These directions, parallel to the c axis and the length of the chains, are the planes of cleavage. The minimum thickness of a rhombic fragment produced through cleavage is 0.84 nm.

Fig. 7 Crystal structure of (CHC )(TCNQ) salt, (a) Uniform segregated stacks of CHC and TCNQ. (b) CHC ribbons by complementary hydrogen bonds and TCNQ form a layer within a bc-plane (hydrogen bonds red dotted lines), (c) Formation of three-dimensional structure (//a) between hemiprotonated cytosine pair and RTCNQ species...

DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types deoxyadenylate (A), deoxyguanylate (G), deoxycytidy-late (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but non-covalently with one other nucleotide in the complementary chain A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. 

Figure 19-17 Aptamer that specifically binds citrulline within a pocket in a short stretch of RNA. Long straight lines represent hydrogen-bonded nucleotide bases. The three-dimensional structure was deduced from nuclear magnetic resonance. 

It is called an a-amino acid because the amino group is attached to the a (or number 2) carbon atom. To indicate its three-dimensional structure on a flat piece of paper, the bonds that project out of the plane of the paper and up toward the reader are often drawn as elongated triangles, while bonds that lie behind the plane of the paper are shown as dashed lines. The isomer of alanine having the configuration about the a-carbon atom shown in the following structural formulas is called S-alanine or L-alanine. The isomer which is a mirror image of S-alanine is R-alanine or D-alanine. Pairs of R and S compounds (see Section B for definitions) are known as enantiomorphic forms or enantiomers. 

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