Conformer gauche

Many of the torsional terms in the AMBER force field contain just one term from the cosine series expansion, but for some bonds it was found necessary to include more than one term. For example, to correctly model the tendency of O-C—C-O bonds to adopt a gauche conformation, a torsional potential with two terms was used for the O—C—C—O contribution ... 

With all-atom simulations the locations of the hydrogen atoms are known and so the order parameters can be calculated directly. Another structural property of interest is the ratio of trans conformations to gauche conformations for the CH2—CH2 bonds in the hydrocarbon tail. The trans gauche ratio can be estimated using a variety of experimental techniques such as Raman, infrared and NMR spectroscopy. 

The trans conformation corresponds to a torsion angle of 180°, the gauche(+) conformation to oni + 60° and the gauche -) conformation to -60°. These approximately correspond to the torsion anj of the three minimum energy conformations of butane. 

Figure 4-18 The Potential Energy for Rotation of n-Butane About its Central Bond Axis. The anti conformer in the center is slightly lower in energy than the two gauche conformers.

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 ... 

FIGURE 3 6 The gauche and anti conformations of butane shown as ball and spoke mod els left) and as Newman projections right) The gauche conformation is less stable than the anti because of the van der Waals strain between the methyl groups... 

Higher alkanes having unbranched carbon chains are like butane most stable m then-all anti conformations The energy difference between gauche and anti conformations is similar to that of butane and appreciable quantities of the gauche conformation are pres ent m liquid alkanes at 25°C In depicting the conformations of higher alkanes it is often more helpful to look at them from the side rather than end on as m a Newman projec tion Viewed from this perspective the most stable conformations of pentane and hexane... 

We have seen that alkanes are not locked into a single conformation Rotation around the central carbon-carbon bond m butane occurs rapidly mterconvertmg anti and gauche conformations Cyclohexane too is conformationally mobile Through a process known as ring inversion, chair-chair mterconversion, or more simply ring flipping, one chair conformation is converted to another chair... 

When the methyl group is axial each path mimics the gauche conformation of butane... 

Example Ethane is stable in the staggered (gauche) conformation. The transition state for rotating a methyl group in ethane has the eclipsed conformation. Ageometry optimization starting from an eclipsed conformation yields the transition state. 

The potential energy shows secondary minima after rotation through 120°. These are called gauche conformations, and for polyethylene they are on the order of 4 kJ mol higher in energy than the trans conformation. 

In addition to existing as helices in crystals, there is evidence that certain vinyl polymers also show some degree of regular alternation between trans and gauche conformations in solution. In solution, the chain is free from the sort of environmental constraints that operate in a crystal, so the length of the helical sequence in a dissolved isotactic vinyl polymer may be relatively short. 

In a class of reahstic lattice models, hydrocarbon chains are placed on a diamond lattice in order to imitate the zigzag structure of the carbon backbones and the trans and gauche bonds. Such models have been used early on to study micelle structures [104], monolayers [105], and bilayers [106]. Levine and coworkers have introduced an even more sophisticated model, which allows one to consider unsaturated C=C bonds and stiffer molecules such as cholesterol a monomer occupies several lattice sites on a cubic lattice, the saturated bonds between monomers are taken from a given set of allowed bonds with length /5, and torsional potentials are introduced to distinguish between trans and "gauche conformations [107,108]. 

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