Experimental geometries to Z-matrix
- From: jkl' at
\`ccl.net
- Subject: Experimental geometries to Z-matrix
- Date: Fri, 14 Aug 1992 04:58:56 -0400
Dear Netters,
I enclose 2 short programs which I found useful in converting
experimental geometries to Z-matrix. They relate to my previous posting.
You will have to draw a picture to follow my variable names. Cut them and use
them if you need them, or change them back to C if you did not buy the
overpriced Fortran Compiler for your workstation (or use a CRAY, it always has
FORTRAN, -:) )
The two short programs are followed by the example.
I will put them in Comp.Chem.List archives as methyl.f and amino.f
============= PROGRAM METHYL ==============
C Jan Labanowski, Aug 13, 1992
C This "program" calculates geometrical parameters of the methyl
group rotor
C suitable for constructing Z-matrix
C The experimental data from microwave spectroscopy for CH3--something
C are frequently given as a C--H bond lengths and H--C--H angle for
C an equilateral methyl piramid (idealized), and the deviation of the
C the C--something bond from the rotation axis of the CH3 (so called
C methyl group tilt). These data have to be converted to other parameters
C to be used in construction of the Z-matrix for the molecule.
C
C Input:
C d = C--H bond length and theta = angle H--C--H
C
C Output:
C a = distance H....H (the side of the equilateral triangle formed by 3 H's)
C h = the height of the equilateral triangle formed by 3 H atoms
C v = height of the isosceles H--C--H
C alpha = angle between the C--H bond and the height of the CH3 pyramid
C Hp = the height of the pyramid formed by CH3
C beta = angle between height of the H--C--H isosceles (v) and the
C height of pyramid (Hp)
C Sorry for FORTRAN ugliness, but it is a translation of the C original
PROGRAM METHYL
DOUBLE PRECISION d, theta, alpha, h, Hp, a, v, deg, beta
WRITE(*,*)
1 ' Enter C--H bond length and H--C--H angle (in deg):'
READ(*,*)d,theta
WRITE(*,*)
deg = 3.1415926536D0/180.0D0
a = 2.0D0*d*dsin(0.5D0*theta*deg)
v = d*dcos(0.5D0*theta*deg)
h = 0.5D0*a*dsqrt(3.0D0)
Hp = dsqrt(d*d - a*a/3.0D0)
alpha = dacos(Hp/d)/deg
beta = dacos(Hp/v)/deg
100 FORMAT(1X,A,F10.5)
WRITE(*,100) 'C--H bond length = ', d
WRITE(*,100) 'H--C--H angle = ', theta
WRITE(*,100) 'Height of the H--C--H isosceles =', v
WRITE(*,100) 'H....H distance = ', a
WRITE(*,100) 'Height of pyramid base (h)= ', h
h = 2.0D0*h/3.0D0
WRITE(*,100) '2/3*h = ',h
WRITE(*,100) 'Angle between C--H bond and pyramid height = ',
1 alpha
WRITE(*,100) 'Pyramid height = ', Hp
WRITE(*,100) 'Angle between wall height and pyramid height =',
1 beta
STOP
END
================= end of methyl.f ============
=================beginning of amino.f =========
C Jan Labanowski, Aug 13, 1992
C This "program" calculates geometrical parameters of the amino
group
C suitable for constructing Z-matrix
C The experimental data from microwave spectroscopy for something-C-NH2
C are frequently given as a N--H bond lenth, C--N--H angle and H--N--H
C angle. Depending where you start, you need some dummy atoms to build
C the molecule. This programs gives you a few parameters you might use.
C
C Input:
C d = N--H bond length, thCNH angle C--N--H, thHNH angle H--N--H
C
C Output:
C a = distance H....H (the base of the H--N--H isosceles)
C v = the height of the H--N--H isosceles (i.e., v is the bisector of
C the H--N--H angle). It starts at C and ends at point Y. Point Y
C is located half way between H atoms.
C l = distance N--X (X is the projection of Y on the line passing through
C C--N). l is a projection of v on the C--N line.
C h = is the distance from Y to X. (h and l are perpendicular,
C h is a bisector of the H--X--H angle).
C b = H--X distance, i.e. distance of the point half way between H atoms
C and C--N line
C alpha = C--N--Y angle (angle between C--N bond and v).
C beta = half of H--X--H angle, i.e. half of the dihedral angle between
C two CNH planes, i.e., H--X--Y angle.
PROGRAM AMINO
DOUBLE PRECISION d, thCNH, thHNH, alpha, h, l, a, v, deg, beta
WRITE(*,*)
1 ' Enter N--H bond length, C--N--H angle, H--N--H angle (in deg):'
READ(*,*)d,thCNH,thHNH
WRITE(*,*)
deg = 3.1415926536D0/180.0D0
a = 2.0D0*d*dsin(0.5D0*thHNH*deg)
C v = d*dcos(0.5D0*thHNH*deg)
v = dsqrt(d*d - a*a/4.0D0)
b = d*dsin((180.0D0-thCNH)*deg)
h = dsqrt(b*b - a*a/4.0D0)
l = dsqrt(v*v - h*h)
alpha = 180.0D0 - dasin(h/v)/deg
beta = acos(h/b)/deg
100 FORMAT(1X,A,F10.5)
WRITE(*,100) 'N--H bond length = ', d
WRITE(*,100) 'C--N--H angle = ', thCNH
WRITE(*,100) 'H--N--H angle = ', thHNH
WRITE(*,100) 'Height of the H--N--H isosceles =', v
WRITE(*,100) 'H...H distance = ', a
WRITE(*,100)
1 'Projection of H--N--H bisector on the C--N line = ', l
WRITE(*,100)
1 'Distance between H...H midpoint and C--N line = ', h
WRITE(*,100)
1 'Angle between C--N bond and bisector of H--N--H = ', alpha
WRITE(*,100)
1 'Half of dihedral angle between C--N--H planes = ',beta
WRITE(*,100)
1 'Distance between H atom and C--N line = ', b
STOP
END
====================== end of amino.f =========
Now I ran them for experimental data for CH3NH2 from Landolt-Boernstein,
Group II, Vol. 7, Neue Serie. They were:
dNH=1.0096 dCN=1.4714 dCH=1.0987
aHCN=108.0 aHCN=110.3 aHNH=107.1
Methyl group tilt was 2.9
The results were of methyl were:
---------------------
Enter C--H bond length and H--C--H angle (in deg):
1.0987 108.0
C--H bond length = 1.09870
H--C--H angle = 108.00000
Height of the H--C--H isosceles = 0.64580
H....H distance = 1.77773
Height of pyramid base (h)= 1.53956
2/3*h = 1.02638
Angle between C--H bond and pyramid height = 69.09484
Pyramid height = 0.39204
Angle between wall height and pyramid height = 52.62263
Results of amino were:
----------------
Enter N--H bond length, C--N--H angle, H--N--H angle (in deg):
1.0096 110.3 107.1
N--H bond length = 1.00960
C--N--H angle = 110.30000
H--N--H angle = 107.10000
Height of the H--N--H isosceles = 0.59982
H...H distance = 1.62420
Projection of H--N--H bisector on the C--N line = 0.35027
Distance between H...H midpoint and C--N line = 0.48693
Angle between C--N bond and bisector of H--N--H = 125.72869
Half of dihedral angle between C--N--H planes = 59.05317
Distance between H atom and C--N line = 0.94689
===============================================================
Based on these, I made a Z-matrix for CH3NH2 for G9X. It is not meant to
be used for geometry optimization. I needed it to measure angles and
such. You could probably make a better Z-matrix for CH3NH2
----------
%chk=something
# HF/STO-3G
Methylamine Geometry from Landolt-Bornstein
0 1
X
C 1 dCX
H 2 dCH 1 aHCX
H 2 dCH 1 aHCX 3 t120
H 2 dCH 1 aHCX 4 t120
X 2 dCV 1 aVCX 3 t180
N 2 dCN 1 aNCH 3 t180
X 7 dNY 2 aCNY 3 t0
H 7 dNH 2 aCNH 8 tYXH
H 7 dNH 2 aCNH 8 tmYXH
dCX=0.39204
dCH=1.09870
dCN=1.4714
dCV=0.64580
dNH=1.00960
dNY=0.59982
aHCX=69.09484
aVCX=52.62263
aNCH=177.1
aCNH=110.3
aCNY=125.72869
t120=120.0
t180=180.0
t0=0.0
tYXH=59.05317
tmYXH=-59.05317
===================
I converted it to cartesians using xmol program which was announced on the
list on 92/06/03 (it is a really nice piece of software, use it, when it
is still available...).
10
Methylamine Geometry from Landolt-Bornstein
X 0.000000 0.000000 0.000000
C 0.392040 0.000000 0.000000
H -0.000000 1.026375 0.000000
H -0.000000 -0.513188 0.888867
H -0.000000 -0.513188 -0.888867
X -0.000001 -0.513188 -0.000000
N 1.861556 -0.074442 -0.000000
X 2.236006 0.394142 -0.000000
H 2.236009 0.394145 0.812098
H 2.236009 0.394145 -0.812098
Sorry for the long message, but if someone have sent me this a week ago,
I would be younger...
Jan Labanowski
Ohio Supercomputer Center
jkl' at \`ccl.net