Strain energy, theoretical calculations

Theoretical calculation at the HF/6-31G level99,102 on some S-S dications and their precursors have shown that the electronic structure of 1,4-dithionia-bicyclo[2.2.0]hexane and the sp-sp conformation of the tetramethyldisulfonium dication, the difference in the energy levels of [S] — [S] and [S] + n[S]103 is decreased owing to steric strain and the order of orbitals thus corresponds to case B. In the less strained systems (l,5-dithioniabicyclo[3.3.0]octane, 1,4-dithioniabicyclo[3.2.0]heptane), the order of orbitals corresponds to case C. Interestingly, ap-ap conformer of tetramethyldisulfonium dication was reported to correspond to case A. 

All these methods have found applications in theoretical considerations of numerous problems more or less directly related to solvent extraction. The MM calculated structures and strain energies of cobalt(III) amino acid complexes have been related to the experimental distribution of isomers, their thermodynamic stability, and some kinetic data connected with transition state energies [15]. The influence of steric strain upon chelate stability, the preference of metal ions for ligands forming five- and six-membered chelate rings, the conformational isomerism of macrocyclic ligands, and the size-match selectivity were analyzed [16] as well as the relation between ligand structures, coordination stereochemistry, and the thermodynamic properties of TM complexes [17]. 

A recent theoretical study on the effect of substituents on the strain energies of small ring compounds has provided some valuable insight into the differences between 1,2-dioxetanes and 1,3-dioxetanes <2002JOC2588>. The C-H bonds within 1,2-dioxetane have been calculated to be stronger than those within 1,3-dioxetane by some 8 kcal mol-1 at the G2 level of theory. Calculations at the same level of theory indicate that 1,2-dioxetane is more strained than 1,3-dioxetane by some 6 kcal mol-1. Somewhat surprising is that this study has also shown that 1,2-dioxetanes are more strained than dioxiranes by some 7-12 kcal mol-1, which is in stark contrast to the case for the parent hydrocarbons and our expectations. The vibrational frequencies and the moments of inertia have also been calculated for the parent 1,2- and 1,3-dioxetanes <1997PGA2471>. 

Because of the strict stereochemical requirements, it is not easy to find optimal sites for the introduction of disulfide bonds into proteins. Introduction of disulfide bonds into T4 lysozyme has been engineered by theoretical calculations and computer modeling.4 7 The results obtained from the mutant lysozymes illustrate several points relevant to the use of disulfide bonds for improving protein stability.6 (i) Introduction of the cysteine(s) should minimize the disruption or loss of interactions that stabilize the native structure, (ii) The size of the loop formed by the crosslink should be as large as possible, (iii) The strain energy introduced by the disulfide bond should be kept as low as possible. For this purpose, a location within the flexible part of the molecule is desirable. 

Stacking faults are characterised by a fault plane and a fault displacement vector. On one side of the fault plane, the atoms that are located fer from the fault are displaced by a vector R in relation to the positions they would occupy in the absence of the fault. Strain fields emanating from any reconstructive bonding that is present near the fault plane will lead to additional displacements for atoms near the fault plane. Thus, the specification of R determines the positions of the atoms that are sufficiently distant so that the strain field generated by the fault is below some specified tolerance. For a planar fault, R may be determined experimentally by analysis of the diffraction contrast obtained with different diffraction vectors g. The positions of atoms near the fault may be determined theoretically by total energy minimisation calculations. Knowledge of these positions is essential to determine the electronic structure of the fault. 

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