Single-bond torsions

Fully relaxed single-bond torsional potentials of oligothiophenes 16 (n = 0-2) under the interaction of the parallel external electric field (EF) constructed by point charges have been evaluated with semi-empirical AMI and PM3 calculations <2004SM(145)253>. Consistent evolutions of the torsional potential surfaces have been observed for three lineal oligothiophenes (Figure 43) as the EF increases. In particular, the equilibrium molecular geometries are deformed toward planar conformations, and the torsional barriers around the central bond are elevated. These... 

The first step applies rigorously to overall molecular rotations. At temperatures where internal barriers can be neglected (typically <10 kT e.g. for most single-bond torsions at room temperature), the algorithm can be extended to include internal rotations. A simple example illustrates the use of the algorithm the unimolecular dissociation of ionized isopropyl... 

According to the authors, the poor charge redistribution (delocalization) ability is responsible for the unfavorable TICT-forming process and facilitates the competition of the single-bond torsional reaction. In contrast, the quinoidal character of a molecule in the PICT state kinetically favors both fluorescence and photoisomerization but disfavors the single-bond torsion. The concept of thermodynamically allowed, but kinetically inhibited, TICT formation was formulated. 

Figure 4.13 Potential energy surfaces for c s-stilbene along (a) the double-bond torsion coordinate ( ) and (b) the single-bond torsion coordinate (p) [46], (Reproduced with permission from Elsevier.)...

A. Karpfen, C. H. Choi, and M. Kertesz,/. Phys. Ghent. A, 101, 7426 (1997). Single-Bond Torsional Potentials in Conjugated Systems A Comparison of Ab Initio and Density Functional Results. 

An sp sp- single bond where each of the central atoms is in Group VIA (for example, hydrogen peroxide) has a two fold barrier with optirn iitn torsional an glc of 90 degrees, as described by V2=-2,0 kcal/tnol. 

An sp3-sp2 or sp -sp - single bond where the atom con-nected to the central sp (sp - ) atom is another sp (sp - ) atom, as in the H-C-C-double bond 0 torsion of acetic acid, is described by the MM-t parameters of acetic acid, Vl=-0.167 kcal/mol and V3=-0.1 kcal/mol. 

Torsional Asymmetry. Rotation about single bonds of most acyclic compounds is relatively free at ordinary temperatures. There are, however, some examples of compounds in which nonbonded... 

A chiral axis is present in chiral biaryl derivatives. When bulky groups are located at the ortho positions of each aromatic ring in biphenyl, free rotation about the single bond connecting the two rings is inhibited because of torsional strain associated with twisting rotation about the central single bond. Interconversion of enantiomers is prevented (see Fig. 1.16). 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

The torsional strain is a sinusoidal function of the torsion angle. Torsional strain results from the barrier to rotation about single bonds as described for ethane on p. 56. For molecules with a threefold barrier such as ethane, the form of the torsional barrier is... 

One way of reducing the number of parameters is to reduce the dependence on atom types. Torsional parameters, for example, can be taken to depend only on the types of the two central atoms. All C-C single bonds would then have the same set of torsional parameters. This does not mean that the rotational barriers for all C-C bonds are identical, since van der Waals and/or electrostatic tenns also contribute. Such a reduction replaces all tetra-atomic parameters with diatomic constants, i.e. 

In Fig. 4-11, two different samples are displayed in their original conformations and conformations fitted to the query as they are highlighted by the CFS search process. The CFS process rotates single bonds between two atoms to find the maximum and minimum difference possible with the distance and angle constraints. Then, using a torsional fitter, it attempts to minimize in those conformations the deviations between measured values of 3D constraints and the values that are specified in the 3D-search query. 

If one rotates about a C-C single bond in a compound of type X-C-C-Y, at each step of this torsional motion there are electron redistributions, and the bond lengths and angles will change. This phenomenon is the basis of the local nature of molecular structure. Several examples are illustrated in Figs. 7.6 and 7.7. 

The energetical description of rotations around bonds with high torsional barriers (e.g. the C=C double bond) demands the evaluation of the influence of higher cosine terms. Rotations around single bonds with sixfold symmetric torsional potentials have very low barriers (18) they occur in alkylsubstituted aromatic compounds (e.g. toluene), in nitro-alkanes and in radicals, for example. 

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