Nonbonded energy

The switching function used by HyperChem, called switch below, alters the nonbonded energy (van der Waals, hydrogen bond, and electrostatic) in the following way ... 

HyperChem can also use a shifted nonbonded potential, where the nonbonded energy is modified by ... 

For large systems, the computation of the energy can require 98% or more of the total computational effort, and within the energy computation, the pair interaction energy (van der Waals and electrostatic terms) can represent more than 90% of the total effort. For this reason, the aspects of the program that deal with the generation of the nonbond list and the computation of the nonbond energy are of critical importance. 

An area of development is the inclusion of code necessary for free energy perturbation calculations for internal, van der Waals and electrostatic energy terms ( ). Another area of development is the option to use lookup tables for both nonbond energies and for constraint energy terms such as a solvent boundary energy term (16). Other features and options are routinely added as needed to aid in the execution of current projects underway within the NIH. 

Molecular modeling studies relative to both preinsertion intermediates and insertion states indicate that for all the metallocenes from 1 to 39 of Scheme 1.2 (independent of their structure and symmetry), when a substantial stereoselectivity is calculated for primary monomer insertion, this is mainly due to nonbonded energy interactions of the methyl group of the chirally coordinated monomer with the chirally oriented growing chain. 

Calculated Nonbonded Energy Contributions to Enantioselectivity for Preinsertion Intermediates (A enant) and Approximated Transition States (A fnant)... 

Molecular mechanics calculations similar to those described in the previous sections allow us to evaluate energy differences between catalytic models (preinsertion intermediates and transition states) suitable for primary and secondary insertions. This energy difference, in the framework of the assumed mechanism, can give a rough estimate of the nonbonded energy contribution... 

Nonbonded energy interactions are able to rationalize not only the stereospecificities observed for different metallocene-based catalytic systems (isospecific, syndiospecific, hemi-isospecific, and with oscillating stereocontrol) but also the origin of particular stereodefects and their dependence on monomer concentration as well as stereostructures associated with regioirregular insertions. Nonbonded energy analysis also allowed to rationalize the dependence of regiospecificity on the type of stereospecificity of metallocene-based catalysts. 

E()init and E()dyn very similar except for sites A and B. In the initial structure, the energy ()init for B is higher than that of any other site, while the average structure energy E()dyn of site B is lower than that of A, E and F. E()dyn of site B is decreased because of the more favorable intermolecular nonbond energy obtained in the dynamic calculation (compare Figures lb and Ic). 

Now we know that nonbonded energies differ somewhat from case to case in comparisons between structural isomers. On the other hand, the NeeSe and terms are also structure-dependent. For these reasons, a minor readjustment... 

This handy energy formula requires only the NMR spectra of the molecules under semtiny. A comparison made for a group of 19 molecules indicated a root-mean-square deviation of 0.25 kcal/mol relative to experimental data, whereas the rms deviation amounts to 0.21 kcal/mol for calculations made with the theoretical Ai and A2 parameters, with nonbonded energies deduced directly from Eq. (10.3). 

The nonbonded energy (van der Waals) is computed for isolated helical amylose chains as a function of the dihedral angles (, relative orientations of the glucose residues in the polysaccharide chain. In conformity with x-ray data, different helical conformations ere proposed for different crystalline modifications of amylose. 

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