Conformation measurement rotational potentials

An additional advantage of the force field method 32) is its power to predict the energy levels of conformations which are not populated and even complete rotational potentials of bonds. Again, statisfying agreement with results from dynamic nmr-measurements for a series of crowed hydrocarbons was found 36). Knowledge of the shape of rotational potentials proved to be helpful for the interpretation of entropy effects in these series of compounds and in their thermolysis reactions. 

Van der Waals complexes ean be observed speetroseopieally by a variety of different techniques, including microwave, infrared and ultraviolet/visible speetroseopy. Their existence is perhaps the simplest and most direct demonstration that there are attractive forees between stable moleeules. Indeed the spectroscopic properties of Van der Waals complexes provide one of the most detailed sourees of information available on intermolecular forces, especially in the region aroimd the potential minimum. The measured rotational constants of Van der Waals complexes provide information on intermoleeular distances and orientations, and the frequencies of bending and stretching vibrations provide information on how easily the complex can be distorted from its equilibrium conformation. In favourable cases, the whole of the potential well can be mapped out from spectroscopic data. 

Simple hydrocarbons represent rather well-behaved extensions of the conformational principles illustrated previously in the analysis of rotational equilibria in ethane and n-butane. The staggered conformations correspond to potential energy minima, the eclipsed conformations to potential energy maxima. Of the staggered conformations, anti forms are more stable than gauche. The magnitudes of the barriers to rotation of many small organic molecules have been measured. Some representative examples are listed in Table 3.3. The experimental techniques used to study rotational isomerism include microwave spectroscopy, electron diffraction, ultrasonic absorption, and infrared spectroscopy. ... 

PPII helix-forming propensities have been measured by Kelly et al. (2001) and A. L. Rucker, M. N. Campbell, and T. P. Creamer (unpublished results). In the simulations the peptide backbone was constrained to be in the PPII conformation, defined as (0,VO = ( — 75 25°, +145 25°), using constraint potentials described previously (Yun and Hermans, 1991 Creamer and Rose, 1994). The AMBER/ OPLS potential (Jorgensen and Tirado-Rives, 1988 Jorgensen and Severance, 1990) was employed at a temperature of 298° K, with solvent treated as a dielectric continuum of s = 78. After an initial equilibration period of 1 x 104 cycles, simulations were run for 2 x 106 cycles. Each cycle consisted of a number of attempted rotations about dihedrals equal to the total number of rotatable bonds in the peptide. Conformations were saved for analysis every 100 cycles. Solvent-accessible surface areas were calculated using the method of Richmond (1984) and a probe of 1.40 A radius. 

Let US first examine current practice in nomenclature of the phenom-menon of internal rotation. Standard textbooks on conformational analysis on the one hand and those on spectroscopy on the other hand deal differently with the basic definitions. Internal rotation is measured by one or more torsion angles (dihedral angles, azimuthal angles). In the simple cases of e.g. a 1,2-disubstituted ethane the potential energy associated with the internal rotation may be written in a formal sense as a truncated Fourier expansion ... 

If the variability in conformation from crystal structure to crystal structure is extremely small, it is probably due to molecular vibrations and rotations, that is, the dynamics of molecular motion within the crystal. If the variability is large, however, this is not likely to be the case. There may be appreciable potential energy barriers between the various possible conformers, so that each of these conformers can exist as a separate entity in the crystal, as described in Chapter 13. Some measure of the probability of the relative proportions of the various conformers in solution may be derived from the percentage of times each conformer is seen in the total of crystal structures of that compound or ion. This argument hinges, however, on the assumption that the sampling in the crystal structures studied is random, an assumption that merits investigation in each analysis. 

---