after trying to obtain a minimum structure of a complex with several explicit water molecules, the solvent tends to react with the complex's ligand. Is there a way to avoid this during optimization by using some Gaussian09 controls in the input file?
Dear Francis,
You should freeze all variable of the water molecules. This can be done by placing all water variables (bond distance, torsion angle and dihedral angle) below the word "constants"). Alternatively, you can freeze ONLY the dihedral angles of the water molecules.
An example for freezing variables:
%chk=TranexamicAcidProD3CoWB3LYPGMa
# B3LYP/6-31G(d,p)Freq Opt=(Z-matrix,MaxCycle=300,CalcFC) GFINPUT IOP(6/7=3)
RECATION COORDINATE FOR
0 1
c
c 1 cc2
c 2 cc3 1 ccc3
c 3 cc4 2 ccc4 1 dih4
c 4 cc5 3 ccc5 2 dih5
c 5 cc6 4 ccc6 3 dih6
c 3 cc7 2 ccc7 1 dih7
n 7 nc8 3 ncc8 2 dih8
c 8 cn9 7 cnc9 3 dih9
o 9 oc10 8 ocn10 7 dih10
c 6 cc11 5 ccc11 4 dih11
o 11 oc12 6 occ12 5 dih12
o 11 oc13 6 occ13 5 dih13
c 9 cc14 8 ccn14 7 dih14
c 14 cc15 9 ccc15 8 dih15
c 15 cc16 14 ccc16 9 dih16
o 16 oc17 15 occ17 14 dih17
o 16 oc18 15 occ18 14 dih18
h 2 hc19 3 hcc19 4 dih19
h 2 hc20 3 hcc20 4 dih20
h 3 hc21 2 hcc21 1 dih21
h 4 hc22 3 hcc22 2 dih22
h 4 hc23 3 hcc23 2 dih23
h 5 hc24 4 hcc24 3 dih24
h 5 hc25 4 hcc25 3 dih25
h 6 hc26 5 hcc26 4 dih26
h 1 hc27 2 hcc27 3 dih27
h 1 hc28 2 hcc28 3 dih28
h 7 hc29 3 hcc29 2 dih29
h 7 hc30 3 hcc30 2 dih30
h 8 hn31 7 hnc31 3 dih31
h 12 ho32 11 hoc32 6 dih32
c 14 cc33 9 ccc33 8 dih33
c 15 cc34 14 ccc34 9 dih34
h 18 ho35 16 hoc35 15 dih35
h 17 ho36 16 hoc36 15 dih36
o 36 oh37 17 oho37 16 dih37
h 37 ho38 17 hoo38 16 dih38
h 34 hc39 15 hcc39 14 dih39
h 34 hc40 15 hcc40 14 dih40
h 34 hc41 15 hcc41 14 dih41
h 33 hc42 14 hcc42 9 dih42
h 33 hc43 14 hcc43 9 dih43
h 33 hc44 14 hcc44 9 dih44
variables:
cc2 1.535363
cc3 1.540437
ccc3 111.764
cc5 1.537035
ccc5 112.290
dih5 54.163
cc6 1.538186
ccc6 112.675
dih6 -53.601
cc7 1.536228
ccc7 110.120
dih7 -180.716
nc8 1.464168
ncc8 112.531
dih8 -172.751
cn9 1.355500
cnc9 128.583
dih9 -145.712
oc10 1.242932
ocn10 120.155
dih10 197.360
cc11 1.522848
ccc11 111.701
dih11 -72.998
oc12 1.356431
occ12 111.663
dih12 -178.183
oc13 1.212885
occ13 126.446
dih13 0.825
cc14 1.507437
ccn14 118.883
dih14 20.798
cc15 1.352469
ccc15 123.173
dih15 -123.436
cc16 1.514007
ccc16 125.237
dih16 3.134
oc17 1.220526
occ17 120.091
dih17 147.447
oc18 1.332171
occ18 119.659
dih18 -34.474
hc19 1.096821
hcc19 110.213
dih19 -177.357
hc20 1.099804
hcc20 109.134
dih20 66.218
hc21 1.102923
hcc21 107.337
dih21 62.575
hc22 1.095772
hcc22 109.941
dih22 176.370
hc23 1.096335
hcc23 109.319
dih23 -66.498
hc24 1.093784
hcc24 109.656
dih24 -176.343
hc25 1.097617
hcc25 109.521
dih25 66.420
hc26 1.098311
hcc26 109.487
dih26 171.038
hc27 1.093202
hcc27 110.581
dih27 178.806
hc28 1.097297
hcc28 109.143
dih28 -63.808
hc29 1.092454
hcc29 110.411
dih29 65.751
hc30 1.099003
hcc30 109.308
dih30 -51.324
hn31 1.014587
hnc31 116.343
dih31 55.553
ho32 0.972302
hoc32 106.143
dih32 -180.957
cc33 1.517006
ccc33 115.592
dih33 60.114
cc34 1.511242
ccc34 121.205
dih34 -180.293
ho35 0.992008
hoc35 112.355
dih35 3.418
ho36 1.981132
hoc36 113.199
dih36 190.584
oh37 0.972284
oho37 177.000
dih37 151.820
ho38 0.964944
hoo38 104.724
dih38 -29.504
hc39 1.089689
hcc39 109.523
dih39 203.647
hc40 1.092627
hcc40 112.194
dih40 324.767
hc41 1.098325
hcc41 110.551
dih41 84.608
hc42 1.093972
hcc42 110.389
dih42 128.735
hc43 1.098100
hcc43 112.130
dih43 248.135
hc44 1.090852
hcc44 111.577
dih44 8.800
constants:
cc4 1.538137
ccc4 110.555
dih4 -55.256
The last three variables (bolded) are frozen (restricted).
Hoping this will be helpful,
Rafik
Just bear in mind that there may be some vital chemical information included in the fact, that water reacts with your complex. Perhaps it's not stable in water? Or very reactive? There's a reason it behaves in such manner...
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