Specifying Molecular Geometry

A somewhat dilferent way to define a molecule is as a simplified molecular input line entry specification (SMILES) structure. It is a way of writing a single text string that defines the atoms and connectivity. It does not define the exact bond lengths, and so forth. Valid SMILES structures for ethane are CC, C2, and H3C-CH3. SMILES is used because it is a very convenient way to describe molecular geometry when large databases of compounds must be maintained. There is also a very minimal version for organic molecules called SSMILES. 

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The following procedure is commonly used to do an SCF calculation at a specified molecular geometry. 

Another approach to calculating molecular geometry and energy is based on density functional theory (DFT). DFT focuses on the electron cloud corresponding to a molecule. The energy of a molecule is uniquely specified by the electron density functional. The calculation involves the construction of an expression for the electron density. The energy of the system is then expressed as... 

The molecular geometry is quite different when one or more unshared pairs are present. In describing molecular geometry, we refer only to the positions of the bonded atoms. These positions can be determined experimentally positions of unshared pairs cannot be established by experiment. Hence, the locations of unshared pairs are not specified in describing molecular geometry. 

The chemist s knowledge of molecular geometry extends beyond typical values of bond distances. He will also be able to predict many bond angles fairly accurately. This is equivalent to specifying a 1-3 nonbonded interatomic distance. The chemist s sketch portrays cis and trans isomerization, syn and anti, and gauche conformations which specify either torsion angles, or indirectly, a 1-4 nonbonded distance. 

An input structure (a molecular geometry) must be specified and submitted to calculation. The geometry can be specified in Cartesian coordinates (probably the usual way nowadays) or as bond lengths, angles and dihedrals (internal... 

Difficulty arises when we attempt to specify bond force constants in polyatomic molecules. It was mentioned in Chapter 1 that molecular geometry of itself does not imply the existence of chemical bonds. Now force constants are the measure of the resistance of the molecule to infinitesimal displacements from the equilibrium configuration that is, to infinitesimal alterations in molecular geometry. And just as molecular geometry does not require the structure of the molecule to be stated in terms of bonds, so the force constants which express its resistance to change do not need to be stated in terms of bonds. Indeed, it is often inconvenient to do so. 

Point (2) is both hardware and software specific. It is not well suited to a textbook, as the information rapidly becomes out of date. The average lifetime of computer hardware is a few years, the time between new versions of software is even less. Problems of type (2) need to be solved on location . I have made one exception, however, and have included a short discussion of how to make Z-matrices. A Z-matrix is a convenient way of specifying a molecular geometry in terms of internal coordinates, and it is used by many electronic structure programs. Furthermore, geometry optimizations are often... 

Since the cartesian displacement coordinates of the nuclei (in the molecule fixed Eckart axis system) are related to the normal coordinates by a strictly linear transformation, the average values specify the displacements of the average nuclear positions from the equilibrium positions. At the r molecular geometry the value of the observable O is... 

When the calculation menu appears, you want to specify Equilibrium Geometry with Molecular Mechanics using MMFF. Have the computer start from initial geometry, neutral total charge and singlet multiplicity. Click on Submit (not OK). If you have not already saved the file, the program will have you do so now. 

The molecular Hamiltonian is invariant under all orthogonal transformations (rotation-reflections) of the particle variables in the frame fixed in the laboratory. The usual potential energy surface is similarly invariant so it is sensible to separate as far as possible the orientational motions of the system from its purely internal motions because it is in terms of the internal motions that the potential energy surface is expressed. The internal motions comprise dilations, contractions and deformations of a specified configuration of particle variables so that the potential energy surface is a function of the molecular geometry only. 

The Winsor R parameter and the Mitchell-Ninham VH /lca0 parameter are related to each other in that both specify that when the value of the parameter exceeds 1, normal micelles in aqueous media in the presence of excess nonpolar solvent will be converted into reverse micelles in nonpolar solvent in the presence of excess aqueous phase. The former concept bases this on molecular interactions, the latter on molecular geometry. 

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