Molecular Structure Laboratory/Idealized Geometry Database/benzene

Benzene



Symmetry: D6h
Optimization program: Gaussian03
Level of theory: b3lyp/6-311+G(d)
Date: April 15, 2010
Contributor: Ilia A. Guzei

FRAG command for the INS file, idealized molecular geometry presented with and without H atoms

FRAG 17
C1 1  0.000517 0.000000  0.000299
C2 1  0.000517 0.000000  1.394692
C3 1  1.208097 0.000000  2.091889
C4 1  2.415677 0.000000  1.394692
C5 1  2.415677 0.000000  0.000299
C6 1  1.208097 0.000000 -0.696898
H1 2 -0.939430 0.000000 -0.542380
H2 2 -0.939430 0.000000  1.937371
H3 2  1.208097 0.000000  3.177246
H4 2  3.355625 0.000000  1.937371
H5 2  3.355625 0.000000 -0.542380
H6 2  1.208097 0.000000 -1.782255
FEND

or

FRAG 17
C1 1  0.000517 0.000000  0.000299
C2 1  0.000517 0.000000  1.394692
C3 1  1.208097 0.000000  2.091889
C4 1  2.415677 0.000000  1.394692
C5 1  2.415677 0.000000  0.000299
C6 1  1.208097 0.000000 -0.696898
FEND

Template for the molecule to be idealized (replace the coordinates as necessary)

Caution. The first AFIX command will require some additional work because the H atoms do not immediately follow the C atoms they are attached to. After the first rigid group refinement these 12 atoms should be reordered (C1,H1,C2,H2...) in order for the H atoms' thermal displacement coefficient to reference proper C atoms.

AFIX 173
C1 1  0.000517 0.000000  0.000299 11.0 0.05
C2 1  0.000517 0.000000  1.394692 11.0 0.05
C3 1  1.208097 0.000000  2.091889 11.0 0.05
C4 1  0.000000 0.000000  0.000000 11.0 0.05
C5 1  0.000000 0.000000  0.000000 11.0 0.05
C6 1  0.000000 0.000000  0.000000 11.0 0.05
H1 2  0.000000 0.000000  0.000000 11.0 -1.2
H2 2  0.000000 0.000000  0.000000 11.0 -1.2
H3 2  0.000000 0.000000  0.000000 11.0 -1.2
H4 2  0.000000 0.000000  0.000000 11.0 -1.2
H5 2  0.000000 0.000000  0.000000 11.0 -1.2
H6 2  0.000000 0.000000  0.000000 11.0 -1.2
AFIX 0

or

AFIX 173
C1 1  0.000517 0.000000  0.000299 11.0 0.05
C2 1  0.000517 0.000000  1.394692 11.0 0.05
C3 1  1.208097 0.000000  2.091889 11.0 0.05
C4 1  0.000000 0.000000  0.000000 11.0 0.05
C5 1  0.000000 0.000000  0.000000 11.0 0.05
C6 1  0.000000 0.000000  0.000000 11.0 0.05
AFIX 0

Alternative representation of the geometry with restraints

DFIX 1.3944 0.001 C1 C2 C2 C3 C3 C4 C4 C5 C5 C6 C6 C1
DFIX 1.0854 0.020 C1 H1 C2 H2 C3 H3 C4 H4 C5 H5 C6 H6

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