Numbering side chains

Rule 5 Form the above types of names for all hydrocarbon terpene radicals derived from menthane-type monocyclic hydrocarbons regardless of the position of the point or points of attachment that is, the H or H s may be removed from carbons in the ring or from carbons in the numbered side chains. Use position numbers to designate the position of the point or points of attachment in the radicals. 

The term vitamin K2 was applied to 2-methyl-3-difarnesyl-l,4-naphthoquinone, m.p. 54 C, isolated from putrefied fish meal. It now includes a group of related natural compounds ( menaquinones ), differing in the number of isoprene units in the side chain and in their degree of unsaturation. These quinones also appear to be involved in the electron transport chain and oxidative phosphorylation. 

Similar ligand-ligand interactions have been reported for a large number of ternary -amino acid complexes, built up of two different amino acid.s. A compilation of 72 examples is presented in reference 39. The extra stabilisation due to ligand-ligand interactions in these complexes depends on the character of the amino-acid side chains and amounts to 0.34 - 0.57 kJ/mole for combinations of aromatic and aliphatic side chains and 0.11 - 6.3 kJ/mole when arene - arene interactions are possible. ... 

The best-known equation of the type mentioned is, of course, Hammett s equation. It correlates, with considerable precision, rate and equilibrium constants for a large number of reactions occurring in the side chains of m- and p-substituted aromatic compounds, but fails badly for electrophilic substitution into the aromatic ring (except at wi-positions) and for certain reactions in side chains in which there is considerable mesomeric interaction between the side chain and the ring during the course of reaction. This failure arises because Hammett s original model reaction (the ionization of substituted benzoic acids) does not take account of the direct resonance interactions between a substituent and the site of reaction. This sort of interaction in the electrophilic substitutions of anisole is depicted in the following resonance structures, which show the transition state to be stabilized by direct resonance with the substituent ... 

Electrophoresis is used primarily to analyze mix tures of peptides and proteins rather than individual ammo acids but analogous principles apply Because they incorporate different numbers of ammo acids and because their side chains are different two pep tides will have slightly different acid-base properties and slightly different net charges at a particular pH Thus their mobilities m an electric field will be differ ent and electrophoresis can be used to separate them The medium used to separate peptides and proteins is typically a polyacrylamide gel leading to the term gel electrophoresis for this technique... 

If the same alkyl group occurs more than once as a side chain, this is indicated by the prefixes di-, tri-, tetra-, etc. Side chains are cited in alphabetical order (before insertion of any multiplying prefix). The name of a complex radical (side chain) is considered to begin with the first letter of its complete name. Where names of complex radicals are composed of identical words, priority for citation is given to that radical which contains the lowest-numbered locant at the first cited point of difference in the radical. If two or more side chains are in equivalent positions, the one to be assigned the lowest-numbered locant is that cited first in the name. The complete expression for the side chain may be enclosed in parentheses for clarity or the carbon atoms in side chains may be indicated by primed locants. 

Monocyclic Aliphatic Hydrocarbons. Monocyclic aliphatic hydrocarbons (with no side chains) are named by prefixing cyclo- to the name of the corresponding open-chain hydrocarbon having the same number of carbon atoms as the ring. Radicals are formed as with the alkanes, alkenes, and alkynes. Examples ... 

Radicals derived from monocyclic substituted aromatic hydrocarbons and having the free valence at a ring atom (numbered 1) are named phenyl (for benzene as parent, since benzyl is used for the radical C5H5CH2—), cumenyl, mesityl, tolyl, and xylyl. All other radicals are named as substituted phenyl radicals. For radicals having a single free valence in the side chain, these trivial names are retained ... 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

Hydrogenation of polybutadiene converts both cis and trans isomers to the same linear structure and vinyl groups to ethyl branches. A polybutadiene sample of molecular weight 168,000 was found by infrared spectroscopy to contain double bonds consisting of 47.2% cis, 44.9% trans, and 7.9% vinyl. After hydrogenation, what is the average number of backbone carbon atoms between ethyl side chains ... 

Unit sales prices of from 800 to 900 fine chemicals are fisted weekly in the Chemical Marketing Reporter. This number reflects those fine chemicals produced and sold in industrial quantities. Some market studies on fine chemicals, fisting important product families, such as side chains for P-lactam antibiotics (qv). A/- and A-heterocycfic compounds, fluoroaromatics, etc, do exist (14,15). 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

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