I have this simple molecule I'm studying: H2SCl
The Gaussian 2009 (G09) input file is this:
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#ub2plyp/6-31g(d,p) freq OPT
adducto H2S--Cl
0 2
Cl
S, 1, r1
H, 2, r2, 1, a1
H, 2, r3, 1, a2, 3, d1
Variables:
r1=1.9
r2=1.0
r3=1.0
a1=120.0
a2=120.0
d1=120.0
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After running g09, I get these internal coordinate values in the output
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! Name Definition Value Derivative Info.
--------------------------------------------------------------------------------
! R1 R(1,2) 2.7341 -DE/DX = 0.0
! R2 R(2,3) 1.3401 -DE/DX = -0.0001
! R3 R(2,4) 1.3401 -DE/DX = -0.0001
! A1 A(1,2,3) 89.758 -DE/DX = 0.0
! A2 A(1,2,4) 89.758 -DE/DX = 0.0
! A3 A(3,2,4) 93.213 -DE/DX = 0.0
! D1 D(1,2,4,3) -89.744 -DE/DX = 0.0
--------------------------------------------------------------------------------
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It's easy to see that G09 is not printing the same internal coordinates
I used in the input
If I redefine the initial internal coordinates, putting sulphur as
the first atom:
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#ub2plyp/6-31g(d,p) freq OPT
adducto H2S--Cl
0 2
S
Cl, 1, r1
H, 1, r2, 2, a1
H, 1, r3, 2, a2, 3, d1
Variables:
r1=2.9
r2=1.0
r3=1.0
a1=120.0
a2=120.0
d1=120.0
---------- cut here -------------
...I get these final internal coordinates:
---------- cut here -------------
! Name Definition Value Derivative Info.
--------------------------------------------------------------------------------
! R1 R(1,2) 2.7349 -DE/DX = 0.0
! R2 R(1,3) 1.3399 -DE/DX = 0.0
! R3 R(1,4) 1.3399 -DE/DX = 0.0
! A1 A(2,1,3) 89.7451 -DE/DX = 0.0
! A2 A(2,1,4) 89.7451 -DE/DX = 0.0
! A3 A(3,1,4) 93.2202 -DE/DX = 0.0
! D1 D(2,1,4,3) -89.7303 -DE/DX = 0.0
---------- cut here -------------
Distances and bond angles are no problem. The problem I'm having is with
the dihedral angle.
In both cases the numbering in the dihedral angle is different from the
one I used in the input file.
In the first case the dihedral angle in the input is numbered: 4,2,1,3 but
in the output I get: 1,2,4,3
In the second case the dihedral angle in the input numbered: 4,1,2,3 but
in the output I get: 2,1,4,3
For a different calculation I need to take these internal coordinates
results from G09 output and recreate the geometry in internal coordinates
but with the original numbering. As I said, distances and bond angles are
no problem. The problem is getting the original dihedral angle from the
internal coordinates data provided in the output.
I was wondering whether I could do this with openbabel?
I haven't been able to find a way that works for all cases: depending on
the atomic numbers, G09 displays different numbering of dihedral angles.
Apparently it lists atoms from the highest to lowest atomic number.
Maybe there's a way I can use the internal coordinates in the output to
convert to cartesian coordinates and from there calculate the internal
coordinates with the original numbering.
Maybe there's a simple way to convert dihedral angles based on their
numbering, but I haven't been able to come up with a solution, nor have I
found any literature on this topic.
If someone could provide me with some guidance or has any idea, I'd be
very grateful. Thanks in advance.
Best regards
Kenneth
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