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Program and scripts to prepare and process NICS calculations.
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ElenaKusevska/NICS_prepare_input
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Program and scripts to prepare and process NICS calculations.
(Using geometries optimized with Gaussian 16 followed by Gaussian 16 NMR calculation)
I originally wanted to write this program in Fortran 95, but I realized that
because of the varying lenght of the filenames, C++ would be more convenient.
I'm saving the Fortran program to read from input because, who knows,
it might come in handy some time in the future.
The general workflow for calculating the NICS values is the following:
1) Get optimized geometry coordinates
2) Realign so that the z-axis is perpendicular to ring
I considered two approaches to perform this step,
implemented in "using_inertia_tensor" and
"using_regression_plane". The method in
"using_regression_plane" gives much better results
3) Place Bq in center of ring, at +1 z, and at -1 z.
4) Run NMR NBO (NLMO or NCO) NCS calculation
5) Get NICS(1), NICS(-1), and NICS(0) values
6) Get NICS(1)zz, NICS(-1)zz, and NICS(0)zz values
7) Get NLMO or CMO pi-contributions to NICS(1)zz, NICS(-1)zz, NICS(0)zz,
to get NICS(1)pi-zz, NICS(-1)pi-zz, NICS(0)pi-zz
The only way to get NBO to use CMO with NCS clacluations is by
installing NBO 5 or higher. The version of NBO currently installed is 3.1
Gaussian output:
Calculating GIAO nuclear magnetic shielding tensors.
SCF GIAO Magnetic shielding tensor (ppm):
1 C Isotropic = 51.9784 Anisotropy = 145.4443
XX= 14.2024 YX= -27.1885 ZX= -0.0235
XY= -45.1857 YY= -7.2084 ZY= -0.0047
XZ= 0.0429 YZ= -0.0100 ZZ= 148.9413
Eigenvalues: -34.2404 41.2344 148.9413
2 H Isotropic = 24.6004 Anisotropy = 4.1248
XX= 27.1477 YX= -0.0250 ZX= -0.0014
XY= -1.4330 YY= 24.7263 ZY= -0.0025
XZ= 0.0053 YZ= 0.0023 ZZ= 21.9271
Eigenvalues: 21.9271 24.5238 27.3503
Natural Chemical Shielding Analysis:
Contributions to Atom 1 Sigma-XX ( 14.2026 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 -28.3302 -40.7407 12.4105 -40.7407 12.4105
2 -16.1242 -28.9125 12.7882 -28.9125 12.7882
3 10.9138 -7.1945 18.1083 -7.1945 18.1083
4 -141.8520 -146.1417 4.2897 -146.1417 4.2897
5 -3.0937 -5.2055 2.1117 -5.2055 2.1117
6 4.5384 3.3109 1.2275 3.3109 1.2275
7 -6.8138 -7.3401 0.5263 -7.3401 0.5263
8 -4.7364 -4.4878 -0.2486 -4.4878 -0.2486
9 -8.0675 -9.5787 1.5112 -9.5787 1.5112
10 -0.9251 -1.6400 0.7150 -1.6400 0.7150
12 203.6884 0.0057 203.6827 0.0057 203.6827
22 4.0166 -0.0340 4.0506 -0.0340 4.0506
Sum 13.2142 -247.9589 261.1731 -247.9589 261.1731
Contributions to Atom 1 Sigma-YX ( -27.1884 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 63.5003 61.6134 1.8869 61.6134 1.8869
2 -59.6707 -56.3388 -3.3319 -56.3388 -3.3319
3 -9.0658 -10.3160 1.2502 -10.3160 1.2502tom
4 -17.1701 -16.0594 -1.1107 -16.0594 -1.1107
5 -13.2449 -13.7078 0.4630 -13.7078 0.4630
6 7.9660 8.0235 -0.0575 8.0235 -0.0575
7 -1.0182 -0.5771 -0.4411 -0.5771 -0.4411
9 1.2649 1.8561 -0.5912 1.8561 -0.5912
11 -1.1023 -1.3948 0.2924 -1.3948 0.2924
Sum -28.5407 -26.9008 -1.6399 -26.9008 -1.6399
All contributions to Atom 1 Sigma-ZX are negligible.
Contributions to Atom 1 Sigma-XY ( -45.1856 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 57.6278 57.0559 0.5719 57.0558 0.5719
2 -72.9230 -68.1608 -4.7622 -68.1608 -4.7622
3 -6.2281 -7.8789 1.6507 -7.8789 1.6507
4 -14.1467 -12.9203 -1.2265 -12.9203 -1.2265
5 -2.4559 -2.0263 -0.4295 -2.0263 -0.4295
6 -7.0269 -6.9370 -0.0899 -6.9370 -0.0899
7 -7.2461 -8.1587 0.9127 -8.1587 0.9127
8 4.7310 4.3386 0.3923 4.3386 0.3923
9 3.3212 3.8401 -0.5188 3.8401 -0.5188
11 1.3135 0.5729 0.7406 0.5729 0.7406
22 -1.2063 -1.1075 -0.0988 -1.1075 -0.0988
Sum -44.2396 -41.3821 -2.8575 -41.3821 -2.8575
Contributions to Atom 1 Sigma-YY ( -7.2082 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 -73.3797 -86.1719 12.7922 -86.1719 12.7922
2 -127.3288 -132.6558 5.3271 -132.6558 5.3270
3 -9.9095 -30.3052 20.3957 -30.3052 20.3957
4 12.5314 -1.4188 13.9502 -1.4188 13.9502
5 -4.9759 -5.7700 0.7940 -5.7700 0.7940
6 -14.0864 -13.3393 -0.7470 -13.3393 -0.7470
7 0.7421 -1.2019 1.9440 -1.2019 1.9440
8 -0.4412 -1.6376 1.1964 -1.6376 1.1964
9 3.8520 -0.2296 4.0816 -0.2296 4.0816
11 -1.9507 -1.7287 -0.2220 -1.7287 -0.2220
12 203.6538 -0.0217 203.6755 -0.0217 203.6755
21 -2.0846 -3.3458 1.2613 -3.3458 1.2613
22 6.8097 6.2021 0.6075 6.2021 0.6075
Sum -6.5677 -271.6242 265.0566 -271.6242 265.0565
All contributions to Atom 1 Sigma-ZY are negligible.
All contributions to Atom 1 Sigma-XZ are negligible.
All contributions to Atom 1 Sigma-YZ are negligible.
Contributions to Atom 1 Sigma-ZZ ( 148.9417 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 -28.2619 -24.6142 -3.6478 -39.1506 10.8887
2 -17.8880 -29.8116 11.9236 -20.4814 2.5934
3 9.4961 0.9275 8.5686 0.8509 8.6452
4 -10.5196 -22.4627 11.9431 -13.8493 3.3296
5 -3.3088 -4.9363 1.6276 -4.4358 1.1270
6 -0.8747 -0.7140 -0.1607 -1.2073 0.3326
7 -3.2164 -4.9693 1.7530 -4.0760 0.8596
8 1.6597 0.3577 1.3020 0.6934 0.9663
9 3.5881 0.4837 3.1045 1.4597 2.1284
11 -4.5031 -5.7491 1.2460 -9.2584 4.7553
12 203.6453 -0.0064 203.6518 -0.0340 203.6793
21 -1.9862 -1.9156 -0.0706 -1.3854 -0.6008
22 3.3759 2.1749 1.2010 1.8689 1.5070
Sum 151.2066 -91.2355 242.4421 -89.0052 240.2118
Contributions to Isotropic shielding for atom 1 ( 51.9787 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 -43.3239 -50.5089 7.1850 -55.3544 12.0305
2 -53.7803 -63.7933 10.0130 -60.6832 6.9029
3 3.5002 -12.1907 15.6909 -12.2162 15.7164
4 -46.6134 -56.6744 10.0610 -53.8033 7.1898
5 -3.7928 -5.3039 1.5111 -5.1371 1.3443
6 -3.4742 -3.5808 0.1066 -3.7452 0.2710
7 -3.0960 -4.5038 1.4078 -4.2060 1.1100
8 -1.1726 -1.9225 0.7499 -1.8107 0.6380
9 -0.2091 -3.1082 2.8991 -2.7829 2.5737
11 -1.8610 -2.3646 0.5036 -3.5344 1.6733
12 203.6625 -0.0075 203.6700 -0.0167 203.6792
21 -1.2046 -1.7917 0.5871 -1.6149 0.4103
22 4.7340 2.7810 1.9530 2.6790 2.0551
Sum 53.3686 -202.9694 256.3380 -202.2259 255.5945
Contributions to Atom 2 Sigma-XX ( 27.1478 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 28.2757 1.6108 26.6649 1.6108 26.6649
2 0.5285 -1.4660 1.9946 -1.4660 1.9946
3 4.4091 -0.3416 4.7507 -0.3416 4.7507
4 -6.2982 -6.9141 0.6158 -6.9141 0.6158
9 -0.8096 -1.0406 0.2310 -1.0406 0.2310
22 1.0395 -0.1408 1.1803 -0.1408 1.1803
Sum 27.1452 -8.2922 35.4373 -8.2922 35.4373
Contributions to Atom 2 Sigma-YX ( -0.0250 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 0.6742 -2.3515 3.0257 -2.3515 3.0257
2 -1.1555 -2.8460 1.6904 -2.8460 1.6904
3 -1.6199 -2.2884 0.6685 -2.2884 0.6685
5 -0.3643 -1.4235 1.0592 -1.4235 1.0592
6 1.2114 1.1275 0.0839 1.1275 0.0839
9 1.0063 0.6925 0.3138 0.6925 0.3138
Sum -0.2478 -7.0894 6.8416 -7.0894 6.8416
All contributions to Atom 2 Sigma-ZX are negligible.
Contributions to Atom 2 Sigma-XY ( -1.4330 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 0.9118 -2.6630 3.5748 -2.6630 3.5748
2 -3.6650 -3.6514 -0.0136 -3.6514 -0.0136
3 0.5343 -0.9332 1.4674 -0.9332 1.4674
4 1.2352 -0.6658 1.9010 -0.6658 1.9010
7 -0.2779 -1.5268 1.2490 -1.5268 1.2490
Sum -1.2615 -9.4402 8.1787 -9.4402 8.1787
Contributions to Atom 2 Sigma-YY ( 24.7263 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 27.3769 3.8924 23.4846 3.8924 23.4846
2 -6.4266 -6.1013 -0.3253 -6.1013 -0.3253
3 3.2288 -0.5571 3.7858 -0.5571 3.7858
4 1.3096 0.1829 1.1266 0.1829 1.1266
6 -1.8562 -1.4872 -0.3690 -1.4872 -0.3690
9 1.1435 -0.0715 1.2150 -0.0715 1.2150
Sum 24.7759 -4.1418 28.9177 -4.1418 28.9177
All contributions to Atom 2 Sigma-ZY are negligible.
All contributions to Atom 2 Sigma-XZ are negligible.
All contributions to Atom 2 Sigma-YZ are negligible.
Contributions to Atom 2 Sigma-ZZ ( 21.9272 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 24.3297 1.8301 22.4996 2.4584 21.8713
2 -0.8422 0.4826 -1.3248 -0.4925 -0.3497
3 -2.9758 -0.1602 -2.8156 -5.5685 2.5927
4 -0.3309 1.0132 -1.3441 0.1280 -0.4589
5 -0.3649 -0.4003 0.0354 -2.5203 2.1555
7 -0.1215 -0.3286 0.2071 -1.8831 1.7616
11 0.1846 -0.5202 0.7047 -3.3011 3.4857
12 1.6444 1.0104 0.6340 2.1767 -0.5323
Sum 21.5235 2.9271 18.5964 -9.0023 30.5257
Contributions to Isotropic shielding for atom 2 ( 24.6004 ppm):
Standard Origin Atomic Origin
NLMO Total Paramagnetic Diamagnetic Paramagnetic Diamagnetic
1 26.6608 2.4444 24.2164 2.6539 24.0069
2 -2.2467 -2.3616 0.1148 -2.6866 0.4399
3 1.5540 -0.3530 1.9070 -2.1557 3.7097
4 -1.7732 -1.9060 0.1328 -2.2010 0.4279
5 -0.1584 -0.5719 0.4134 -1.2785 1.1201
7 -0.1835 -0.4951 0.3116 -1.0132 0.8297
11 -0.0585 -0.3312 0.2727 -1.2582 1.1997
12 1.0068 0.6535 0.3533 1.0423 -0.0355
Sum 24.8013 -2.9207 27.7220 -6.8972 31.6985
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