Gaussian 03W Bonding: How Does It Work?

[dreamzndigita]

I'm a new Gaussian 03W user and I have what I assume is a pretty basic question.

How does Gaussian "know" how atoms are bonded to each other when a molecule is specified in an input file. An example molecule specification in Cartesian coordinates follows:

0 1
C 0.00 0.00 0.00
C 0.00 0.00 1.52
H 1.02 0.00 -0.39
H -0.51 -0.88 -0.39
H -0.51 0.88 -0.39
H -1.02 0.00 1.92
H 0.51 -0.88 1.92
H 0.51 0.88 1.92

I know that the geom=connect option can be used to explicitly set up bonds but it doesn't seem to be necessary. Thanks!

 

[chemisttree]

It probably calculates distances between each atom and all of the other atoms. Only one will be within bonding distance and it chooses that one. A set of definitions may prevent H-H bonds in favor of C-H or O-H, etc...

In the case of the two carbons,

C 0.00 0.00 0.00
C 0.00 0.00 1.52

you will notice that one carbon lies at the center of the coordinate system (0.00, 0.00, 0.00) and one lies 1.52 (angstroms?) along the Z-axis. These two carbons are 1.52 angstroms(?) apart. A lookup table for C-C bonds is likely used to determine that these two are within bonding distance from each other.

 

[Blueshift5]

Gaussian 03W is a computational chemistry software package that uses quantum mechanical methods to calculate molecular properties and behavior. When a molecule is specified in an input file, Gaussian uses a combination of algorithms and parameters to determine the bonding between atoms.

One of the key components in determining bonding is the molecular geometry, which is specified in the input file in Cartesian coordinates. From the positions of the atoms, Gaussian can calculate the distances between them and determine which atoms are close enough to form bonds.

Gaussian also uses a set of predefined bond lengths and angles for different types of bonds (e.g. C-C, C-H, H-H) based on experimental data and theoretical calculations. These parameters are stored in a library and are used to compare with the distances and angles calculated from the input file.

In addition, Gaussian takes into account the electronic structure of the molecule, specifically the distribution of electrons and their energies. This information is used to determine the type and strength of bonds between atoms.

Overall, Gaussian uses a combination of geometry, bond parameters, and electronic structure to determine bonding in a molecule. This information is then used to perform calculations and simulations on the molecule. The geom=connect option is available for users to explicitly specify bonds, but it is not necessary as Gaussian is able to determine bonding automatically based on the input file.