Geometry, molecular input

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. 

SMILES (simplified molecular-input line-entry specification) a way of specifying a molecular formula and connectivity, but not the three-dimensional geometry... 

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. 

To go from a semiempirical calculation in the GAUSSIAN implementation (File 9-1) to an ab initio calculation, one need only change PM3 in the route section of the input file to sto-3g for a single point calculation or sto-3g opt for an optimization. We have made this change in File 10-1 along with the substitution of h for f in the second line of the geometry section to calculate the molecular... 

In most programs, it is still possible to input a geometry manually in an ASCII input file. If the geometry is already in a file but of the wrong format, there are several utilities for converting molecular structure files. The most popular of these is the Babel program, which is described in Appendix A. 

Band structure calculations have been done for very complicated systems however, most of software is not yet automated enough or sufficiently fast that anyone performs band structures casually. Setting up the input for a band structure calculation can be more complex than for most molecular programs. The molecular geometry is usually input in fractional coordinates. The unit cell lattice vectors and crystallographic angles must also be provided. It may be nee-... 

AMPAC can also be run from a shell or queue system using an ASCII input file. The input file format is easy to use. It consists of a molecular structure defined either with Cartesian coordinates or a Z-matrix and keywords for the type of calculation. The program has a very versatile set of options for including molecular geometry and symmetry constraints. 

All calculations need as input a molecular geometry. This is commonly given by one of the following three methods. 

The E-state is based solely on atom connectivity information obtained from the molecular graph, without any input from the molecular geometry or sophisticated quantum calculations. We start this chapter with a brief presentation of the relevant notions of graph theory and continue with the definitions of a couple of important graph matrices. Then the molecular connectivity indices are mentioned... 

A dynamical study of molecular collision requires a detailed knowledge of the interaction potential as an input. Ab initio potential energy (PE) values for a chemical reaction for different geometries are usually reported in the form of table of numbers resulting from sophisticated electronic structure calculations. However, for use in dynamical calculations, the PES must be known in some convenient analytical or numerically interpolated form, which is capable of generating potential and its derivatives accurately and efficiently at any arbitrary geometry. 

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