Conformations, of hydrocarbons

With spectroscopic methods it is possible to obtain information about the conformation of hydrocarbon-DNA complexes. The fluorescence quantum yields of aromatic hydrocarbons are greatly reduced when they bind to DNA in intercalated conformations. Figure 3 shows how the intensity of the emission spectrum of DMA decreases with increasing concentrations of DNA in 15% methanol. (In Figure 3 and throughout this discussion DNA concentrations and association constants have been reported in terms of PO molarity unless otherwise indicated. The solution content of organic solvents is given in percent volume.)... 

In the last two decades, there has been a large accumulation of experimental evidence as well as of theoretical interpretations of intramolecular reactions. One notes, however, that attention has been focused on the phenomena of immediate interest to the various specialists. As a consequence of the fact that specialisation implies intensification of knowledge on the one hand but limitation on the other, there has still been insufficient communication and cross-fertilisation between the different schools. This situation is well exemplified by the two most extensive reviews on intramolecular phenomena, namely, that of Kirby (1980), entitled Effective Molarities for Intramolecular Reactions , and that of Winnik (1981a), entitled Cyclisation and the Conformation of Hydrocarbon Chains , which present different approaches and apparently unrelated facts and theories. 

Mono-, di-, and trifluoro derivatives of fatty acids have been prepared in regio- and stereoselective manners, in order to evaluate the gauche effect induced by fluorine atoms on the conformation of hydrocarbon chains and for enzymatic studies. 

For reviews of the cyclization of acyclic molecules, sec Nakagaki Sakuragi Mutai J. Phys. Org. Chem. 1989 2, 187-204 Mandolini Adv. Phys. Org. Chem. 1986, 22. Mil. For a review of the cyclization and conformation of hydrocarbon chains, see Winnik Chem. Rev. 1981,5/. 491-524. Fora review of steric and electronic effects in heterolytic ring closures, sec Valters Russ. Chem. Rev. 1982 51, 788-801. 

Difference in energy of trans and gauche conformations of hydrocarbon chains. 

Figure 3.3 3D and cross-sectional models of SDS micelles with a statistical conformation of hydrocarbon chains of 60 molecules. (SDS = sodium dodecyl sulfate). 

Since gas-phase reactions are free from complications arising from solvation effects, a convenient starting point for a meaningful analysis of structural effects on reactivity would be the study of cyclisation reactions in the gas phase. Unfortunately, quantitative evidence of this sort is scanty. A section in Winnik s review (Winnik, 1981a) is devoted to cyclisation and the gas-phase conformation of hydrocarbon chains. From the numerous references therein one obtains a substantial body of evidence pointing to a general resemblance of cyclisation reactions in the gas phase with cyclisation reactions in solution. However, as Winnik has pointed out, gas-phase reactions have not been studied so far with the same kind of detail that is possible for reactions in solution. As a result, any attempt at understanding the relations between structure and reactivity in the area of cyclisation reactions must still rely heavily upon solution chemistry data. 

When methyl groups are added, as in butane, two additional conformations are possible. There are two staggered conformations, called anti and gauche, and two eclipsed conformations, one with methyl-methyl eclipsing and the other with two hydrogen-methyl alignments. In the methyl-methyl eclipsed conformation, van der Waals repulsions come into play. The barrier for this conformation increases to about 6 kcal/mol, as shown in Figure 1.35. We pursue the conformation of hydrocarbons further in Section 2.2.1. 

Extensive discussions have focused on the conformation of the alkyl chains in the interior ". It has been has demonstrated that the alkyl chains of micellised surfactant are not fully extended. Starting from the headgroup, the first two or three carbon-carbon bonds are usually trans, whereas gauche conformations are likely to be encountered near the centre of tlie chain ". As a result, the methyl termini of the surfactant molecules can be located near the surface of the micelle, and have even been suggested to be able to protrude into the aqueous phase "". They are definitely not all gathered in the centre of tire micelle as is often suggested in pictorial representations. NMR studies have indicated that the hydrocarbon chains in a micelle are highly mobile, comparable to the mobility of a liquid alkane ... 

We can relate the conformational preference for an equatorial methyl group m methylcyclohexane to the conformation of a noncyclic hydrocarbon we discussed ear her butane The red bonds m the following structural formulas trace paths through four carbons beginning at an equatorial methyl group The zigzag arrangement described by each path mimics the anti conformation of butane... 

The conformations of simple hydrocarbons can be interpreted by extensions of the principles illustrated in the analysis of rotational equilibria in ethane and butane. The staggered... 

Although the —CH2— group could be inserted in other places, the free rotation about single C—C bonds in hydrocarbons allows the resulting molecules to be twisted into one or the other of these two isomers. Both compounds are gases, but butane (24) condenses at —1CC, whereas methylpropane (25) condenses at — 12°C. Two molecules that differ only by rotation about one or more bonds may look different on paper, but they are not isomers of each other they are different conformations of the same molecule. Example 18.3 illustrates how to tell if two molecules are different isomers or different conformations of the same isomer. 

A modification of the united-atom approach, called the anisotropic united-atom (AUA) model was the focus of extensive work by Karabomi et al. [362-365]. As in the other models of hydrocarbon chains described so far, the AUA approach to monolayers was preceded by work on alkanes [367]. hi the AUA model the interaction site is located at the geometrical mean of the valence electrons of the atoms it represents, while the pseudoatom itself is located at the carbon atom position. The movement of each interaction center depends on the conformation of the molecule as a whole. 

Allinger NL, Miller MA, Van Catledge FA, Hirsch JA. Conformational analysis. LVII. The calculation of the conformational structures of hydrocarbons... 

The two O -alkylated guanosine derivatives (117) shown in Figure 28, do not demonstrate a perpendicularity of hydrocarbon and base, presumably because the hydrocarbon is much smaller. However, again the nucleoside has the syn-conformation. This perpendicularity, however, is found for the acetylamino fluorine derivative. 

The major goals of recent studies of the physical binding to DNA of BP and DMBA metabolites and metabolite models are to determine (1) the magnitudes of the binding constants, (2) the conformations of physical complexes which are formed and the nature of DNA binding sites, (3) how DNA structure and environment influence physical binding, (4) how the structure of hydrocarbon metabolites influences physical binding properties, (5) whether the... 

When rationalizing the significant difference of the hydrocarbon- and ether-bridged radical anions, the main aspect will certainly be the conformation of the oxyethylene chain, which brings the electrophores into closer contact. An additional aspect follows from the ability of the oxygen centres along the chain to chelate the counterion and thus to fix the cation between the electrophores. It is not possible from the available experimental evidence to discriminate between the two effects. The role of ion pairing and the relative position of the counterion and carbanion will be dealt with below. 

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