Comparing molecular conformation

Let us consider first the case of comparing molecular conformations (i.e., OD models) encountered along a trajectory. Their root-mean-square (rms) standard deviation is given simply as follows ... 

Partial Least Squares (PLS) regression (Section 35.7) is one of the more recent advances in QSAR which has led to the now widely accepted method of Comparative Molecular Field Analysis (CoMFA). This method makes use of local physicochemical properties such as charge, potential and steric fields that can be determined on a three-dimensional grid that is laid over the chemical stmctures. The determination of steric conformation, by means of X-ray crystallography or NMR spectroscopy, and the quantum mechanical calculation of charge and potential fields are now performed routinely on medium-sized molecules [10]. Modem optimization and prediction techniques such as neural networks (Chapter 44) also have found their way into QSAR. 

Firstly charge density despite the fact that polyelectrolytes of comparable molecular weight are adsorbed in a flatter conformation and thus to a lesser extent as their charge density increases (see above), charge neutralisation is still achieved at a lower addition level for high than for low charge density polyelectrolytes (Figure 6.13). 

The geometry of the cis-alkylcyclohexanol is favorable for trans elimination since the hydroxyl and the neighboring trans hydrogen are coplanar, but this is not true for the l,i-trans isomer hence the molecular conformation has to flip over, to set the hydroxyl group in the axial position for the trans elimination to occur. This would require a few kilocalories of energy and for frans-lert-butylcyclohexanol it would be more difficult to achieve than for IroMs-methylcyclohexanol. It is, therefore, possible that the trans elimination from a boat conformation, or possibly even an epimerization from the trans to the cis isomer which then undergoes a trans elimination reaction. Such an epimerization was found to occur under conditions of dehydration of certain alcohols over alumina, as will be seen under 1,4-cyclohexanediol. The more facile elimination of the cis-i-tert-butylcyclohexanol system as compared with the trans system in solution was also reported in the literature 63). 

It has been mentioned in Sect. 3.1 that the molecular conformation can be altered strongly compared to that in solution if the side chains of a brush molecule are specifically adsorbed on the substrate or tend to spread on the surface to minimize the interfacial energy (Fig. 27). Moreover, the substrate changes the dimensionality of the system and breaks its symmetry [169,170]. Depending on the interfacial interactions and distribution of the side chains we can discuss a number of distinct conformations (a) stretched brush, (b) two-dimensional helix [170], and (c) globule state. 

Although the molecular conformation of organic solids profoundly affects their properties, In the case of coals this characteristic has been little studied compared to their chemical composition and functionality Studies of coal at any level of structure are difficult because of the complex heterogeneity of any particular coal and the great variability of coal types that occur ... 

Molecules in the gas phase provide an electron diffraction pattern which can be analyzed in order to obtain relative interatomic distances in molecules. Some of the distances depend on molecular conformation and, in principle, it is possible to extract conformational data (conformer structure and population). Rough estimates of energy barriers may also be obtained from the peak widths by comparing calculated and experimental distribution functions. Uncertainties on populations are rather high ( 10-15%). 

A general theory of quantitatively comparing molecular shapes using common overlap steric volume(33-36) and, more recently, descriptors derived from superimposed molecular potential energy fields of pairs of molecules(37) has been derived and tested. This theory allows a "marriage between Hansch analysis and conformational analysis. 

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