Molecular mean geometry

Molecular Modeling Studies and Conformational Energy Calculations on Dithiopeptides Mean Geometry of the Thiopeptide Unit and Conformational Flexibility of Peptide-Thiopeptides and Dithiopeptides. ... 

When constructing more general molecular wave functions there are several concepts that need to be defined. The concept of geometry is inhoduced to mean a (time-dependent) point in the generalized phase space for the total number of centers used to describe the END wave function. The notations R and P are used for the position and conjugate momenta vectors, such that... 

NMR calculations are based on a given molecular geometry, which means that an experimental 3D structure must be available, or it has to be previously calculated. Because a rigid structure is used for the calculations, different chemical... 

The presence of the q B term with its implied distance dependency means that the charges depend upon the molecular geometry. Thus, should the conformation of a molecule change the atomic charges will also change. Just three parameters are required for each atom in the system (the electronegativity, the idempotential and the covalent radius). 

In Chapter 2, a brief discussion of statistical mechanics was presented. Statistical mechanics provides, in theory, a means for determining physical properties that are associated with not one molecule at one geometry, but rather, a macroscopic sample of the bulk liquid, solid, and so on. This is the net result of the properties of many molecules in many conformations, energy states, and the like. In practice, the difficult part of this process is not the statistical mechanics, but obtaining all the information about possible energy levels, conformations, and so on. Molecular dynamics (MD) and Monte Carlo (MC) simulations are two methods for obtaining this information... 

Heats of formation, molecular geometries, ionization potentials and dipole moments are calculated by the MNDO method for a large number of molecules. The MNDO results are compared with the corresponding MINDO/3 results on a statistical basis. For the properties investigated, the mean absolute errors in MNDO are uniformly smaller than those in MINDO/3 by a factor of about 2. Major improvements of MNDO over MINDO/3 are found for the heats of formation of unsaturated systems and molecules with NN bonds, for bond angles, for higher ionization potentials, and for dipole moments of compounds with heteroatoms. 

The VSEPR model is readly extended to species in which double or triple bonds are present A simple principle applies Insofar as molecular geometry is concerned, a multiple bond behaves like a single bond. This makes sense. The four electrons in a double bond, or the six electrons in a triple bond, must be located between the two atoms, as are the two electrons in a single bond. This means that the electron pairs in a multiple bond must occupy the same region of space as those in a single bond. Hence the extra electron pairs in a multiple bond have no effect on geometry. 

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