The Molecule Specification Section

All molecule specifications require that the charge and spin multiplicity be specified (as two integers) on the first line of this section. The structure of the molecule follows, in either Cartesian coordinates, internal coordinates (a Z-matrix), or a combination of the two. 

The spin multiplicity for a molecule is given by the equation 2S + 1, where S is the total spin for the molecule. Paired electrons contribute nothing to this quantity. They have a net spin of zero since an alpha electron has a spin of +Vi and a beta electron has a spin of -Vi. Each unpaired electron contributes +Vi to S. Thus, a singlet—a system with no unpaired electrons—has a spin multiplicity of 1, a doublet (one unpaired electron) has a spin multiplicity of 2, a triplet (two unpaired electrons of like spin) has a spin multiplicity of 3, and so on. 

The structure of the molecular system to be investigated follows the initial charge and spin multiplicity line in the molecule specification section. The structure may be obtained in a variety of ways from the coordinates generated by or converted from a drawing program (as demonstrated in the Quick Start), by constructing a Z-matrix by hand (see Appendix B), from the experimental literature, from the results of a previous calculation, and so on. 

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These items form the route section, the title section, and the molecule specification section of the input file, respectively. We ll look at each of them again briefly as we set up an input file for an energy calculation on formaldehyde. 

Note that the inner carbon atoms are the first two atoms listed for each compound. The predicted NMR shielding values will appear in the output in the same order as the atoms are listed in the molecule specification section. 

The Optimized Parameters are the predicted bond lengths (named Rn), bond angles (An) and dihedral angles (Dn) for the optimized structure. The applicable atom numbers are in parentheses. Atoms in the molecule are numbered according to their order in the molecule specification section. These center numbers also appear in the Cartesian coordinates for the optimized strucmre expressed in the standard orientation which follows the listing of the optimized parameters. 

Because of the nature of the computations involved, firequency calculations are valid only at stationary points on the potential energy surface. Thus, frequency calculations must be performed on optimized structures. For this reason, it is necessary to run a geometry optimization prior to doing a frequency calculation. The most convenient way of ensuring this is to include both Opt and Freq in the route section of the job, which requests a geometry optimization followed immediately by a firequency calculation. Alternatively, you can give an optimized geometry as the molecule specification section for a stand-alone frequency job. 

The center numbers for the atoms of interest. Gaussian s numbering scheme assigns each atom the number corresponding to its input line within the molecule specification section, where the charge and multiplicity line is line 0. Thus, the first atom listed is center number 1, and so on. 

The SCRf keyword in the route section of a Gaussian job requests a calcuJation in the presence of a solvent. SCRF calculations generally require an additional input line following the molecule specification section s terminating blank line, having the following form ... 

Blank line ending the molecule specification section Starts a new job step... 

This information makes up the molecule specification section, in this case for water. The first line of the molecule specification gives the charge and spin multiplicity for the molecule as two free-format integers. In this case, our molecule is neutral (charge 0), and has spin multiplicity 1 (a singlet). Spin multiplicity is discussed in Chapter 2, and molecule specifications in general are discussed in Appendix B. 

The Molecule Specification section holds the type and positions of each of the atoms ip the molecule. For this job, we ll enter our water molecule s structure in Cartesian coordinates. 

Enter the following data into the Molecule Specification section ... 

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