Dihedral angle deformation energy

Another important point deals with selectivity in the abstraction of -protons on equally substituted carbons. In a iyw-periplanar transition state as described above, the minimization of energy concept implies proton abstraction with a maximum of orbital overlap and a minimum of molecular deformation. Consequently, conformations possessing the more acute dihedral angles for bonds H —C—C—O wiU be favored (Scheme 2l/. 

A mathematical method is developed to provide a solution to two problems hitherto arising in conformational energy calculations of oligomers and polymers, when bond length and bond angles are maintained fixed. The two problems are the calculation of the sets of dihedral angles which lead to (a) exact ring closure in cyclic molecules and Ibl local conformational deformations of linear or cyclic molecules. Most of the emphasis is placed on polypeptide chain molecules. 

Cyclodecene is the smallest cycloalkene, which can accommodate a trans double bond without significant deformation of bond angles and/or dihedral angles. The strain energies and structures of smaller fraws-cycloalkenes have been the subjects of considerable research over the years. 

The simulations were performed with the modified AMBER5.0 software (35) where the potential energy is described by a sum of bond, angle and dihedral deformation energies, and pairwise additive 1-6-12 (electrostatic + van der Waals) interactions between non-bonded atoms. 

The energy is calculated as the sum of two sets of contributions, bonded and non-bonded interactions [1-6]. The energy required to deform the geometry of chemically bonded structures is obtained as the sum of error terms proportional to the square of the difference of each bondlength, each bondangle and fixed dihedral angle and the corresponding nonstrained equilibrium value. 

An introduction to the modeling methods can be found in refs. [22,231. The classical MD simulations reported here were performed with the modified AMBER software/241 in which the potential energy consists of harmonic deformations of bond and angles, dihedral energies, plus non-bonded interactions represented by a sum of pair wise additive coulombic and van der Waals contributions ... 

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