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Gaussian 03W Bonding

  1. Feb 6, 2009 #1
    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!
     
  2. jcsd
  3. Feb 9, 2009 #2

    chemisttree

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    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.
     
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