Molecular geometry mechanics

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

Some properties, such as the molecular size, can be computed directly from the molecular geometry. This is particularly important, because these properties are accessible from molecular mechanics calculations. Many descriptors for quantitative structure activity or property relationship calculations can be computed from the geometry only. 

Use the HyperChem Model Builder to construct an approximate geometry. If you want to look at the relative energies of a set of molecules, you may want to carry out the calculations using fully optimized molecular geometries. These geometry optimization calculations can use either molecular mechanics or quantum mechanics to further refine the molecular geometry beyond that given by the Model Builder. 

Force field methods, also called molecular mechanics, are empirical approaches to calculate molecular geometries and energies. The general aim of a force field... 

The fragmentation can be concerted or stepwise. The concerted mechanism is restricted to molecular geometry that is appropriate for continuous overlap of the participating... 

The molecular mechanics method is usually limited to the determination of molecular geometry and thermodynamic quantities. However, it is sometimes employed to estimate vibrational frequencies - at least in those cases in which 7r electrons are not involved in the determination of the molecular geometry. It should be emphasized that this method, as well as those presented in Chapter 12, are applicable only to isolated molecules, as intermolecular forces are not included in the model. 

Schafer, L. 1983. The Ab Initio Gradient Revolution in Structural Chemistry the Importance of Local Molecular Geometries and the Efficacy of Joint Quantum Mechanical and Experimental Procedures. J. Mol. Struct. 100, 51-73. 

Spin relaxation in NMR is known to provide information about the dynamics of molecular entities and possibly about molecular geometry or electron distribution. Generally, dynamical information is obtained if the tensor of the relevant relaxation mechanism is known from independent determinations. Conversely, if parameters describing the dynamics of the considered molecule have been deduced beforehand, geometrical parameters may be derived. Only in particular situations, one can hope to access both types of parameters (dynamical and geometrical). For... 

Evidence on the mechanism of reactions can also come from examining the exact molecular geometry of the overall process, its stereochemistry. For example, if a reactant with defined handedness (chirality) is converted to a product that is an equal mixture of the left- and right-handed forms, the loss of handedness indicates that a particular geometry must have been involved along the path. If a right-handed molecule is converted only to a left-handed product, we say that an inversion of configuration has occurred, and this also tells us a lot about how the reaction occurred. 

Levy, M. and Perdew, J. P. Success of quantum mechanical approximations for molecular geometries and electron-nuclear attraction expectation values gift of the Coulomb potential , J. Chem. Phys., 84 (1986), 4519-4523... 

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