Conformer pairs

The distances between neighboring atoms in all conformations give rise to favorable (attractive) interactions. These attractions are particularly strong in the two most compact conformational pairs, 90°, 90°, and in none of the conformations are there severe steric overlaps. These circumstances are very different from those in typical organic polymers. These conformational preferences should make sulfur chains extremely compact, with very small unperturbed dimensions. Conformational analyses, in fact, indicate that the characteristic ratio of polymeric sulfur should be less than unity (which is the freely jointed value).52... 

Su, Borho and Xu have applied rotational spectroscopic and high-level ab initio studies to the 1 1 chiral molecular adduct of propylene oxide dimer [117], Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two 6- or 5-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. 

In some early applications [96] to ETs involving compounds with quin-one-like compounds Q, QA Q -A Q=, it was necessary to examine some data on the formation constants of the semiquinone QH, Q + QH2 — 2QH (The H is typically attached to an O or an N.) My impression, after looking at available data, was that the equilibrium constant was approximately the same, provided all three species had the same charge. Looking at the structures, one could see that every atom in a molecule on the left in this reaction corresponded to one on the right that had the same nearest and next nearest neighbor. I then looked at many examples of other pairs of compounds, which I termed conformal pairs and found that the total of heat of combustion of a pair was approximately the same as its conformal pair [97]. 

Only certain , y conformation pairs are observed. This is usually described in terms of the Ramachandran diagram, as shown in Figure 5.8, with as the horizontal axis and y as the vertical axis. In Figure 5.8, the experimentally determined backbone dihedral angles for the alanine, glycine, and proline residues of 699 proteins are depicted. There are three basic... 

Table VI. Conformer pairs between the substructures I(SS) and III( ) which passed criteria 1 and 2...

Figure 9.6 contains two challenging cases, paracetamol [57] and indomethacin, based on the experimental data from reference [60], for which the original screening via gave the worst results with AUC 0.5. The figure demonstrates the obtained emichment, that is, how many hits are found successively if one follows the A// ordered list of drug-conformer pairs. 

An anchor, as defined above, contains stable molecules, conformers, all pairs of radicals and biradicals formed by a simple bond fission in which no spin re-pairing took place, ionic species, and so on. Figure 1 shows some examples of species belonging to the same anchor. Thus, an anchor is a more general and convenient temi used in the discussion of spin re-pairing. 

The probability of finding a nucleic acid unit in the certain conformation according to our results is never equal to the unit. It agrees with the idea that NAs are not static but fluctuating, breathing , objects [23]. For example, in RNA molecule with 10 base pairs at the room temperature about 510 base pairs do not take part in the stacking and are not connected with H -bonds [2]. 

One way to describe the conformation of a molecule other than by Cartesian or intern coordinates is in terms of the distances between all pairs of atoms. There are N(N - )/ interatomic distances in a molecule, which are most conveniently represented using a N X N S5munetric matrix. In such a matrix, the elements (i, j) and (j, i) contain the distant between atoms i and and the diagonal elements are all zero. Distance geometry explort conformational space by randomly generating many distance matrices, which are the converted into conformations in Cartesian space. The crucial feature about distance geometi (and the reason why it works) is that it is not possible to arbitrarily assign values to ti... 

A cluster analysis requires a measure of the similarity (or dissimilarity) between pairs of objects. When comparing conformations, the RMSD would be an obviou.s measure to use. 

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