Note
This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.
VDWM¶
In `MOZYME <mozyme.html>`__, the
`LEWIS <Lewis_structures.html>`__ structure is constructed from the
topology of the system. Atoms are considered to be connected if they
are within 10% of the addition of the two radii, or within twice the
heavy-atom radius if one of the atoms is hydrogen. Values for all radii
used are shown in the Table below.
The criterion of whether atoms are connected or not can be changed by
modifying the radii. using the VDWM keyword. The format of the
command is:
VDWM(<chemical symbol1>=n.nn;<chemical symbol2>=n.nn;<chemical symbol3>=n.nn;…)
For example, if a hydrogen atom should be regarded as connected to a
nitrogen, but the N-H distance is 1.62 Angstroms, then VDWM(N=0.85)
would override the default values of the van der Waals radii of nitrogen
(0.75), and result in the hydrogen being connected (the N-H distance of
1.62 being less than 2*0.85).
If a fluorine atom should be connected to a bromine, but the F-Br
distance is 2.1 Angstroms, i.e., it is too large for the two atoms to be
regarded as being connected (2.1 > 1.1(0.71 + 1.14), then either the F
radius, or the Br radius, or both, could be increased. One possible
change would be to use keyword VDWM(F=0.75;Br=1.2)
Entries for different elements should be separated by a colon, a comma, or a semi-colon.
** Table 1:** Default radii (Angstroms) used in MOZYME
I
II
Transition Metals
III
IV
V
VI
VII
VIII
H
0.37
He
0.32
Li
1.34
Be
0.90
B
0.82
C
0.77
N
0.75
O
0.73
F
0.71
Ne
0.69
Na
1.54
Mg
1.30
Al
1.18
Si
1.11
P
1.06
S
1.02
Cl
0.99
Ar
0.97
K
1.96
Ca
1.74
Sc
1.44
Ti
1.36
V
1.25
Cr
1.27
Mn
1.39
Fe
1.25
Co
1.26
Ni
1.21
Cu
1.38
Zn
1.31
Ga
1.26
Ge
1.22
As
1.19
Se
1.16
Br
1.14
Kr
1.10
Rb
2.11
Sr
1.92
Y
1.62
Zr
1.48
Nb
1.37
Mo
1.45
Tc
1.56
Ru
1.26
Rh
1.35
Pd
1.31
Ag
1.53
Cd
1.48
In
1.44
Sn
1.41
Sb
1.38
Te
1.35
I
1.33
Xe
1.30
Cs
2.25
Ba
1.98
La
1.69
Hf
1.50
Ta
1.38
W
1.46
Re
1.59
Os
1.28
Ir
1.37
Pt
1.28
Au
1.44
Hg
1.49
Tl
148
Pb
1.47
Bi
1.46
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