Structures Drawing Conventions

Draw conventional structures for the contributors to the resonance hybrid of an allyl cation. 

Fig. 1. Consensus structure prediction for three tRNA sequences in different representations. Top row conventional secondary structure drawing as produced by RNAalifold (left) and colorrna.pl (right). Second row dot plot and mountain representation. Bottom alignment with consensus structure in bracket format, and conservation curve as produced by coloraln.pl. In this black and white version, red (no variation) is replaced by light gray, ochre (two types of pairs) by medium gray, and green (three types of pairs) by dark gray. Color versions of all figures can be found in the electronic supplement.

When referring to a particular enantiomer, we would like to be able to specify which configuration we mean without having to draw the structure. A convention for doing this is known as the R-S or Cahn-lngold-Prelog system. Here is how it works. 

How many stereoisomers are possible for each of the following structures Draw them, and name each by the R-S and E-Z conventions. (See Problem 5.41.)... 

The commercial 2D structure editor. Chemistry 4D-Draw, from Chemlnnovativc Software Inc., includes two additional special modules besides conventional chemical drawing tools. NamExpert provides the interpretation ofa compound name according to the lUPAC nomenclature to create the corresponding chemical structure. The latter can be represented in three different styles the shorthand. Kckulc. or semi-structural formula. In contrast to NamExpert, the Nomenclature module assigns lUPAC names to drawn structures. 

The editor provides two modes for drawing the structure and the draw mode. This distinction is important for differentiating chemical information from conventional drawings. Both modes are switchable and provide an extensive set of features in the menu bar to create chemical structures and reactions, or just drawings. The number of options can be quite confusing for beginners however, one becomes accustomed to them after a short period of vocational adjustment. 

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. 

Testosterone, conformation of, 129 molecular model of, 129 structure and function of, 1082 Tetracaine, structure of, 967 Tetrahedral geometry, conventions for drawing. 8... 

Student drawings and descriptions of their conceptions of structures and processes at the molecular level often reveal misconceptions not detectable in conventional equation-writing questions (p. 155). 

The primary structure of a polypeptide is its sequence of amino acids. It is customary to write primary structures of polypeptides using the three-letter abbreviation for each amino acid. By convention, the structure is written so that the amino acid on the left bears the terminal amino group of the polypeptide and the amino acid on the right bears the terminal carboxyl group. Figure 13-35 shows the two dipeptides that can be made from glycine and serine. Although they contain the same amino acids, they are different molecules whose chemical and physical properties differ. Example shows how to draw the primary stmcture of a peptide. 

Fig. 1 (a) Ball and stick structure of faujasite (FAU). (b) Conventional stick drawing of faujasite (FAU). 

Lavastre s approach is valid, but the use of (a) less reactive brominated arenes and (b) the obvious lack of solubilizing groups restricts the value of this approach. Perhaps all of the 96 polymers would have to be made in a conventional approach and compared to the polymers obtained by the high-through-put method to draw further conclusions. In addition, the fluorescence was measured in situ, in a THF/diisopropylamine mixture in the presence of the Pd-Cu catalyst. That approach may have an intrinsic problem too, because it is known that PAEs are solvatochromic, and as a consequence, the obtained fluorescence data might be biased. However, with some tweaking this is a powerful method to obtain a cornucopia of different structures quickly and without too much synthetic effort, if the monomers are easily available. 

Do appreciate that there is no strict convention for how you orientate the structure on paper. In fact, we will turn structures around, as appropriate, to suit our needs. For example, the amino acid tyrosine has three functional groups, i.e. a carboxylic acid, a primary amine, and a phenol. How we draw tyrosine will... 

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