Nonbonded intramolecular

Homoconjugational interactions and nonbonding intramolecular contacts of the four ji-systems are responsible for the observed distribution of bond angles at the central atom, which are also significantly inequivalent [105.1(1)° to 111.8(1)°]. 

The polydihalophosphazenes are examined by conformational analysis using nonbonding intramolecular interactions based on a 6-12 Lennard-Jones potential and a Coulombic term. The results provide an insight into the reasons for the low glass transition temperatures, the high chain flexibilities, and the conformational preferences of these molecules. Minimum energy conformations are discussed. 

Interactions between the nonbonded atoms of a molecule play an important role in determining conformational energies and geometries as well as barriers to internal rotation. It seems reasonable that such interactions are of the same type as those between atoms in different molecules, and thus the theory to describe nonbonded intramolecular interactions is the same as that used to describe intermolecular forces. The physical origins of such forces, which are all of the electromagnetic type, are... 

The external potential energy accounts for all interactions with other molecules and for all the nonbonded intramolecular interactions. In addition, interactions with any external field that may be present are also included in... 

In what follows we shall denote a chain in the absence of the external interactions as the ideal chain. Note that this is a purely fictitious concept, as real chains always have nonbonded intramolecular interactions. 

Close intramolecular contacts (clashes). A rough measure has been proposed and implemented in the program CONCORD [4,11] - the close contact ratio (CCR). The CCR of a 3D stracture is defined as the ratio of the smallest nonbonded distance to the smallest acceptable value for this distance. Normally, structures with CCR>0.8 are acceptable. Some programs as CORINA [5] or CONCORD [4, 11] have fallback procedures for attempting to relax close contacts in structures with unacceptably low CCR. 

Fig. 2.5. Possible applications of a coupling parameter, A, in free energy calculations, (a) and (b) correspond, respectively, to simple and coupled modifications of torsional degrees of freedom, involved in the study of conformational equilibria (c) represents an intramolecular, end-to-end reaction coordinate that may be used, for instance, to model the folding of a short peptide (d) symbolizes the alteration of selected nonbonded interactions to estimate relative free energies, in the spirit of site-directed mutagenesis experiments (e) is a simple distance separating chemical species that can be employed in potential of mean force (PMF) calculations and (f) corresponds to the annihilation of selected nonbonded interactions for the estimation of e.g., free energies of solvation. In the examples (a), (b), and (e), the coupling parameter, A, is not independent of the Cartesian coordinates, x. Appropriate metric tensor correction should be considered through a relevant transformation into generalized coordinates...

Functions and partly also constants for nonbonded interactions within single molecules (intramolecular interactions) have been taken over in many cases from investigations of interactions between different molecules (intermolecular interactions) (7,3). The derivation of parameters for nonbonded interactions presents further difficulties, e.g. the problem of the anisotropy of such interactions (8, 23) and parameter correlations (Section 2.4.). There is no agreement on the question whether pairs of atoms separated by a chain of only three bonds should be counted as nonbonded interactions. Some authors include these pairs,... 

In contrast, substrates 149 all furnished [4 + 3]-cycloadducts 150 and 151 in yields ranging from 10-79% (Scheme 34)68. In all cases, exclusive approach of the furan from the zwitterion face opposite the epoxide ring was seen. In most cases, the exo diastereomer 151 was the major product or was formed to the exclusion of the endo diastereomer 150. The contrasting diastereoselectivity seen in inter- and intramolecular cycloadditions may result from unfavorable nonbonding interactions in the endo transition state between the tether atoms and the alkyl groups at C-2 and C-5. 

An even stronger case of intramolecular RAHB coupling is provided by the maleate ion (HOOCCH=CHCOO-), whose H-bonded and open conformers are shown in Fig. 5.22. Skeletal bond lengths and bond orders of these conformers are compared in Table 5.18. As shown in Fig. 5.22, the H-bonded conformer is favored in this case by more than 26 kcalmol-1, which is indicative of a powerful intramolecular no aoH interaction (estimated second-order stabilization 104 kcalmol-1) that is sufficient to overcome the severe steric repulsion of the extremely short H- -O nonbonded distance ( 1.3 A).56... 

Just like any other valence-shell empty orbital, the empty Zr orbital may interact with any proximal electrons, including (i) nonbonding electron pair donors, abbreviated here as n-donors or n-electron pair for simplicity, (ii) 7t-bonds or 7t-electrons, or (iii) a-bonds or o-electrons. Such interactions may be intermolecular or intramolecular. Some of the significant examples are listed in a generalized manner in Scheme 1.3. 

The observed low barrier of conformational interconversion in manxane (18, 12 2 kcal/mol) was satisfactorily reproduced by the Schleyer force field (125). This molecule also involves a number of close intramolecular nonbonded H H contacts (126). The flipping of one methylene bridge is transmitted readily through space to the... 

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