Molecular mechanics distortions

The distorted structure can be replaced by a more reasonable structure using an empir ical molecular mechanics calculation This calculation which is invoked m Spartan Build by clicking on Minimize, automatically finds the structure with the smallest strain energy (m this case a structure with realistic bond distances and a boat conformation for the SIX membered ring)... 

The monoketone bis(2,2, /V,/V -bipyridyl)ketone forms a [CoinL2]+ complex on reaction with [Co(NH3)4(C03)]+ in water.981 As reported for a quite different Co11 complex, the ketone is hydrated to form the gem diol which binds as a monodeprotonated O-donor along with the two pyridine groups in a tridentate chelate, with very little distortion from octahedral observed in the complex. This appears to represent a facile route for this type of inherently poor donor to achieve coordination. Chelated /3-diketonate anions are long-studied examples of O-donor chelates, and continue to be examined. A simple example is the m-[Co(acac)2(NH 3)2]1 (acac = 2,4-pentane-dionate), structurally characterized and utilized to produce molecular mechanics force field parameters for /3-diketones bound to Co111.982... 

The functionalization of zinc porphyrin complexes has been studied with respect to the variation in properties. The structure and photophysics of octafluorotetraphenylporphyrin zinc complexes were studied.762 Octabromoporphyrin zinc complexes have been synthesized and the effects on the 11 NMR and redox potential of 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetraarylporphyrin were observed.763 The chiral nonplanar porphyrin zinc 3,7,8,12,13,17,18-heptabromo-2-(2-methoxyphenyl)-5,10,15,20-tetraphenylporphyrin was synthesized and characterized.764 X-ray structures for cation radical zinc 5,10,15,20-tetra(2,6-dichlorophenyl)porphyrin and the iodinated product that results from reaction with iodine and silver(I) have been reported.765 Molecular mechanics calculations, X-ray structures, and resonance Raman spectroscopy compared the distortion due to zinc and other metal incorporation into meso dialkyl-substituted porphyrins. Zinc disfavors ruffling over doming with the total amount of nonplanar distortion reduced relative to smaller metals.766 Resonance Raman spectroscopy has also been used to study the lowest-energy triplet state of zinc tetraphenylporphyrin.767... 

TABLE 2. Structural (molecular mechanics) and spectral parameters of selected distorted dienes0... 

Since the complete GVFF is rarely available for compounds of unknown structure, exact molecular mechanics simulation of small distortions is not... 

In order to examine the nature of the unusual geometric distortions observed in the X-ray structures of complexes 3 and 4, we have performed a series of density functional theory (DFT) and combined quantum mechanics and molecular mechanics (QM/MM) calculations [22-27], Although the computational resources to wholly treat both 3 and 4 at the DFT level are available, we have employed the combined QM/MM method to unravel the... 

The deformed-chair conformation of ring A in a 4,4-dimethyl-3-oxo-5or-steroid has been confirmed by an X-ray study of a 17 -benzoyloxyandrostane derivative. The results agree with those of an earlier study of the 17-iodoacetate, and with the geometry indicated by force-field calculations. Dipole moments calculated by the application of molecular mechanics to 5a-androstane-3,17-dione and its distorted 4,4-dimethyl derivative are larger than those observed the reasons for these deviations are not yet clear. 

The molecular mechanics energy of a molecule is described in terms of a sum of contributions arising from distortions from ideal bond distances ( stretch contributions ), bond angles ( bend contributions ) and torsion angles ( torsion contributions ), together with contributions due to non-bonded (van der Waals and Coulombic) interactions. It is commonly referred to as a strain energy , meaning that it reflects the strain inherent to a real molecule relative to some idealized form. 

Force Field. The set of rules underlying Molecular Mechanics Models. Comprises terms which account for distortions from ideal bond distances and angles and for Non-Bonded van der Waals and Coulombic Interactions. 

Molecular Mechanics Models. Methods for structure, conformation and strain energy calculation based on bond stretching, angle bending and torsional distortions, together with Non-Bonded Interactions, and parameterized to fit experimental data. 

The mechanism of the regulation of electron transfer in metalloproteins has been investigated 61) and two relevant examples have been discussed in the first one the molecular mechanism controlling the electron transfer reactions is restricted to the immediate chemical environment of the metal center (azurin), while in the second one it involves a conformational transition of the whole quaternary structure of the enzyme. The power of the kinetic approach in detecting significant intermediates was emphasized 6t>. The Cu metal complex site of azurin has a distorted tetrahedral... 

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