Conformational minima

There are two additive terms to the energy, POP and TORS, that have not been mentioned yet because they are zero in minimal ethylene. The POP term comes from higher-energy conformers. If the energy at the global minimum is not too far removed from one or more higher conformational minima, molecules will be distributed over the conformers according to the Boltzmann distribution... 

Relative molecular enthalpies then result simply as the sum of the minimum potential energy V°, Z/yj, and the rotational and translational enthalpy contributions (= 3 RT). By experience, the // -contributions of different conformational minima of a molecule rarely differ by more than 1 kcal mole"-1 (see also Section 6.2.4.). Vibrational entropy contributions may be evaluated in a similar way as//vibr. 

Figure 8.20 Structure and phase sequence of prototypical bent-core mesogen NOBOW (8) are given, along with space-filling model showing one of many conformational minima obtained using MOPAC with AMI force field. With observation by Tokyo Tech group of polar EO switching for B2 smectic phases formed by mesogens of this type, banana LC field was bom. Achiral, polar C2v layer structure, with formation of macroscopic spontaneous helix in polarization field (and concomitant chiral symmetry breaking), was proposed to account for observed EO behavior.

The prediction of the partition properties of peptide molecules is difficult, owing to their conformational flexibility, and the possible presence of multiple intramolecular hydrogen bonds and ionizable groups. Richards and coworkers (40-42) were the first to consider explicitly the effects of the population of accessible conformational minima in both phases. These types of calculation are, however, computationally intensive. The introduction of the solvent-accessible surface area in the prediction of log Poct for steric isomers (43,44) also constitutes a promising approach. 

For CH3SC50 four local conformational minima are obtained by molecular mechanics calculations using the MMX force field (Figure 6.4) [7]. Thereby, as shown in Figure 6.4, the asymmetric conformation for this radical is preferred. 

Figure 6.4 Structures of the preferred local conformational minima of the radical CHjSC q" obtained by molecular mechanics calculations [7. ...

We now turn to several examples where these techniques have been applied to peptide hormones, and show how we can study the conformational properties, including conformational minima and fluctuations, dynamics, and energetics of these molecules, and how these properties can in turn be used to design analogs. 

To molecules of relatively large size, methods from molecular mechanics and force fields are also applied (84MI1 85JMC1301), and they have provided information on the conformational minima occurring in systems with several internal degrees of molecular mobility. 

J. Dale, Exploratory Calculations of Medium and Large Rings. Part 1. Conformational Minima of Cycloalkanes, Acta Chem. Scand. 27, 1115 (1973). 

The resulting species can be viewed as a molecular assembly, in which two allyl moieties are linked to a four-carbon spacer , each group attached to two adjacent carbon atoms. The resulting structure has three conformational minima the... 

One advantage of the NAMFIS approach is that it does not rely on the calculated energies of the conformers, which have proven to provide unreliable values at least with highly polar molecules like PTX [65], Instead, NAMFIS uses all reasonable conformational minima proposals regardless of their energies and selects them on the basis of their fitting to the experimental NMR data. 

Initially, the conformational minima for each isolated monomer were calculated by rotating the

results obtained at the two computational levels considered here are almost identical. The [SL conformation is the most stable one for all cases except for glycine and alanine where it shows a relative energy of 0.4 and 3.6 kJ mol-1, respectively. The presence of fluorine atoms as XI or X2 substituents tends to destabilize the y and 8 conformations and favors the presence of and a ones that are absent in the rest of the cases. The intramolecular HB formed in each case is responsible for these tendencies. While the y and 8 conformations present an intramolecular HB that is disrupted by the presence of fluorine atoms at XI and X2, new HBs are formed in the and a conformation, stabilizing their relative energies. 

The conformational minima of a series of chiral ethers have been studied by means of DFT (B3LYP/6-31+G ) and ab initio (MP2/6-311+G ) methods [40]. The protonation of these compounds produces diasteromeric systems depending on the protonated lone pair. The relative energy of the conformers has been analyzed using the QTAIM and NBO methods (Fig. 3.21). 

Butadiene, the parent conjugated diene, can in principle attain two planar conformations, namely s-frans-butadiene and. v-m-butadiene. In reality, the majority of the acyclic 1,3-butadiene derivatives exhibit global conformational minima that are at least close to the s-trans-diene situation.1,2 For butadiene itself the s-trans-C4H6 conformer is more stable than the i-cw-isomer by ca. 3 4 kcal mol-1, although the s-trans- - s-cis-butadiene interconversion is kinetically rapid (AG 7 kcal mol-1). Consequently, reactions via the less favorable conformations are not uncommon (e.g., the Diels-Alder reaction) (Scheme 1). 

Okoronkwo, T. Nguyen, P. T Castro, C. Karney, W. L. [14]Annulene cis/trans isomerization via two-twist and nondegenerate planar bond shifting and Mobius conformational minima, Org. Lett. 2010,12, 972-975. 

These comparisons show that variation of the Si-O-Si bond angle significantly alters the values of the potential barriers between conformational minima and the relative energies of these minima. Relaxation of adjacent bonds has an important effect on bond torsions it modifies the potential barriers, as well as the energies and positions of the minima. 

Taylor, R. The Cambridge Structural Database in molecular graphics techniques for the rapid identification of conformational minima. J. Molec. Graphics 4, 123-131 (1986). 

The torsional angles of gauche conformers of a number of molecules are included in this study. However, the prediction of torsional potential energy functions for these molecules are not included although geometrical structures at conformation minima are indeed related to torsional potentials. Further systematic study of these problems is required. 

R. Taylor,/. Mol. Graphics, 4,123 (1986). The Cambridge Structural Database in Molecular Graphics Techniques for the Rapid Identification of Conformational Minima. 

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