Tip
All input files can be downloaded: Files.
Semi-empirical Quantum Chemistry Methods
This tutorial will lead you step by step to do semi-empirical quantum chemistry calculations using Qbics. There are two semi-empirical methods implemented in Qbics: xTB and NDDO (neglect of diatomic differential overlap). While xTB is a modern one with better accuracy and speed, NDDO is a traditional semi-empirical method, which is still widely used in many fields. Note that NDDO is a series of methods, including AM1, PM3, PM6, etc, which are all available in Qbics.
xTB can be applied for elements from H to Rn (Z=86), while NDDO is only for elements from H to Cl (Z=17). xTB is more accurate than NDDO in general, but NDDO has some special parameterizations for specific systems, such as biomolecules. You can choose either one according to your needs.
Example: xTB for Ligand-protecing Gold Clusters
We will use xTB to calculate the binding energy of a ligand-protecting gold cluster, Au18(C6H11S)14, which is a model for gold nanoparticles:
The input file is:
1mol
2 Au 6.95958 2.87913 2.94614
3 S 9.08599 3.67339 2.88510
4 S 4.89113 1.81941 3.01855
5 Au 5.82923 4.53162 5.05796
6 Au 4.13669 3.38239 1.49897
7 Au 5.79250 5.99300 2.82997
8 Au 8.65595 5.47861 4.26420
9 S 3.33616 4.66634 -0.18204
10 Au 3.45811 5.08053 3.76279
11 S 8.56081 7.20090 5.75077
12 Au 6.24304 7.42405 5.38760
13 S 7.04744 3.53845 6.81588
14 Au 3.89147 6.19365 6.32206
15 Au 6.56834 5.22532 8.23897
16 S 6.65568 7.45648 1.19187
17 Au 3.92517 7.94284 4.15361
18 Au 3.18725 6.66426 1.06638
19 Au 6.51959 9.17260 2.68377
20 S 1.11550 4.78967 4.09094
21 Au 0.97656 6.80219 5.13736
22 S 3.01320 8.66765 2.07979
23 S 6.26671 7.02193 9.67527
24 Au 5.18561 8.18601 7.95848
25 Au 5.18171 9.94301 5.85487
26 S 3.00776 5.17778 8.25337
27 Au 2.88045 8.79374 6.73399
28 S 0.61480 8.81770 6.18653
29 S 6.59196 10.92950 4.17781
30 Au 3.60146 10.47321 8.93384
31 Au 2.73505 7.19691 9.38807
32 S 3.42541 8.93876 10.69319
33 S 4.56391 11.83306 7.37982
34 C 4.95046 0.19661 2.19906
35 C 4.13304 0.27617 0.92539
36 C 6.43827 -0.19882 1.91962
37 H 4.54937 -0.47352 2.79236
38 C 4.32830 -1.08837 0.26931
39 H 4.45695 0.98625 0.34829
40 H 3.19681 0.43452 1.12181
41 C 5.75611 -1.40758 -0.15592
42 H 4.03232 -1.77426 0.88894
43 H 3.75560 -1.14070 -0.51433
44 C 6.56085 -1.57337 1.12181
45 H 5.78086 -2.22375 -0.68037
46 H 6.11951 -0.68416 -0.69252
47 H 7.48911 -1.76356 0.91526
48 H 6.20590 -2.30489 1.65233
49 H 6.91097 -0.27514 2.76401
50 H 6.86172 0.50545 1.40529
51 C 9.82213 2.61150 4.17741
52 C 11.27211 3.02202 4.31713
53 C 9.74817 1.08389 3.77445
54 H 9.35450 2.75237 5.02585
55 C 10.56493 0.41654 4.92663
56 H 8.83144 0.76495 3.75825
57 H 10.15792 0.92343 2.90981
58 C 12.02599 0.81419 4.94688
59 H 10.16185 0.65719 5.77507
60 H 10.50409 -0.54817 4.83551
61 C 12.15597 2.23072 5.30934
62 H 12.50229 0.26663 5.59080
63 H 12.41786 0.66328 4.07414
64 H 13.08043 2.51488 5.23847
65 H 11.85571 2.37597 6.22055
66 H 11.29164 3.95583 4.58037
67 H 11.68263 2.96345 3.44034
68 C 4.66625 4.65474 -1.39922
69 C 4.08243 5.21781 -2.70732
70 C 5.34316 3.30509 -1.70701
71 H 5.36069 5.27536 -1.09143
72 C 5.11020 5.41339 -3.85747
73 H 3.66929 6.07468 -2.51697
74 H 3.38482 4.61959 -3.01510
75 C 5.75779 4.03509 -4.14096
76 H 4.66354 5.74193 -4.65326
77 H 5.78875 6.05533 -3.59626
78 C 6.40351 3.59895 -2.71947
79 H 6.44382 4.10772 -4.82336
80 H 5.09199 3.38992 -4.43052
81 H 6.95572 2.81229 -2.84501
82 H 6.97114 4.31314 -2.39345
83 H 5.73476 2.93101 -0.90109
84 H 4.69806 2.67321 -2.06137
85 C 8.43376 7.22633 1.27772
86 C 8.75735 8.28980 0.28956
87 C 8.35307 5.81798 0.56900
88 H 8.85999 7.27198 2.15856
89 C 9.69198 5.73389 -0.12554
90 H 8.24574 5.10410 1.21495
91 H 7.62278 5.78581 -0.06682
92 C 9.96941 6.72193 -1.21293
93 H 10.38502 5.82694 0.54673
94 H 9.77560 4.84353 -0.50420
95 C 10.00162 8.16508 -0.53458
96 H 9.27489 6.68456 -1.88925
97 H 10.82171 6.53031 -1.63411
98 H 10.78731 8.25471 0.02835
99 H 10.02631 8.85607 -1.21293
100 H 8.80872 9.13067 0.77149
101 H 8.00761 8.35930 -0.32196
102 C 6.50278 1.84108 7.01432
103 C 7.28044 0.78458 6.26712
104 C 5.01755 1.78217 6.64983
105 H 6.57149 1.62563 7.96806
106 C 4.62585 0.27870 6.86447
107 H 4.87778 2.04901 5.72850
108 H 4.49708 2.36180 7.22896
109 C 5.32148 -0.69994 6.03831
110 H 4.78156 0.05322 7.79391
111 H 3.67418 0.18804 6.70046
112 C 6.86575 -0.64443 6.40482
113 H 5.19434 -0.49612 5.09875
114 H 4.97170 -1.58883 6.20840
115 H 7.00953 -0.95193 7.31401
116 H 7.37939 -1.20492 5.80342
117 H 7.24906 1.00744 5.32351
118 H 8.20707 0.84878 6.54251
119 C 0.20628 5.07898 2.57975
120 C -1.17788 5.60632 2.82071
121 C 0.12299 3.68230 1.96215
122 H 0.70535 5.68323 1.99050
123 C -2.09672 5.44393 1.59766
124 H -1.12354 6.54642 3.05358
125 H -1.56781 5.13549 3.57398
126 C -2.13396 4.00151 1.13800
127 H -2.99320 5.73375 1.82850
128 H -1.77409 6.00689 0.87679
129 C -0.77977 3.40755 0.79984
130 H -2.70051 3.94240 0.35234
131 H -2.54195 3.46517 1.83458
132 H -0.85827 2.45198 0.65607
133 H -0.42430 3.81421 -0.00607
134 H 1.02042 3.43820 1.69081
135 H -0.13232 3.07325 2.67289
136 C 1.22368 8.95953 2.26183
137 C 1.12729 10.21342 3.03333
138 C 0.58490 8.92423 0.89906
139 H 0.84462 8.23475 2.80046
140 C -0.33067 10.76335 3.01510
141 H 1.72744 10.87617 2.65264
142 H 1.40251 10.05251 3.94859
143 C -0.94306 10.81773 1.64018
144 H -0.88199 10.20064 3.58208
145 H -0.33207 11.65642 3.39579
146 C -0.86444 9.45049 0.98209
147 H -0.46965 11.47057 1.09953
148 H -1.87007 11.09632 1.70701
149 H -1.23397 9.50606 0.08707
150 H -1.40292 8.82297 1.48832
151 H 0.58426 8.01529 0.56293
152 H 1.09749 9.47365 0.28551
153 C 9.36023 8.74574 5.21214
154 C 10.86188 8.70547 5.36199
155 C 8.95878 10.12481 5.70825
156 H 9.21073 8.77731 4.24423
157 C 11.60848 10.07555 4.97725
158 H 11.21015 7.99337 4.80108
159 H 11.07472 8.48276 6.28130
160 C 11.02957 11.31196 5.49158
161 H 12.52433 10.01664 5.29314
162 H 11.64061 10.13767 4.00934
163 C 9.64347 11.22271 4.97928
164 H 11.48770 12.09264 5.14127
165 H 11.04890 11.33807 6.46152
166 H 9.64988 11.03765 4.02756
167 H 9.17822 12.06083 5.12507
168 H 8.00026 10.23061 5.60903
169 H 9.16848 10.19519 6.65186
170 C 1.34521 4.56248 7.90731
171 C 1.40899 3.18816 7.18441
172 C 0.54823 4.35183 9.30855
173 H 0.86252 5.20662 7.34641
174 C -0.07413 2.78935 7.12974
175 H 1.78534 3.27425 6.29547
176 H 1.92910 2.54705 7.69267
177 C -0.80128 2.46805 8.41759
178 H -0.55555 3.50944 6.69438
179 H -0.14563 2.01082 6.55264
180 C -0.86288 3.76310 9.11619
181 H -1.69120 2.12632 8.23940
182 H -0.31186 1.81328 8.94002
183 H -1.28564 3.64254 9.98083
184 H -1.40450 4.38118 8.59983
185 H 1.06264 3.75719 9.87755
186 H 0.47489 5.20576 9.76213
187 C -0.54610 8.85187 7.55700
188 C -1.42383 7.61911 7.56712
189 C 0.13609 9.11399 8.90357
190 H -1.14205 9.61310 7.39500
191 C -0.81332 9.13457 10.11650
192 H 0.59493 9.96753 8.85497
193 H 0.80788 8.42822 9.04734
194 C -1.61822 7.79848 10.15294
195 H -1.42237 9.88711 10.04562
196 H -0.30118 9.23490 10.93456
197 C -2.33420 7.77525 8.81447
198 H -1.02569 7.03632 10.24407
199 H -2.25370 7.79342 10.88596
200 H -2.83653 8.60120 8.72538
201 H -2.97165 7.04481 8.82257
202 H -0.88524 6.81500 7.63597
203 H -1.95664 7.57099 6.75918
204 C 5.66496 11.91514 3.03738
205 C 4.48325 12.57713 3.69345
206 C 6.75652 13.09456 3.09408
207 H 5.50202 11.51720 2.15654
208 C 4.01247 13.67426 2.75186
209 H 4.74047 12.95485 4.54999
210 H 3.77295 11.93342 3.84127
211 C 4.95307 14.81578 2.67492
212 H 3.89878 13.30013 1.86293
213 H 3.14769 13.99831 3.04953
214 C 6.28899 14.17196 2.16059
215 H 5.07738 15.22261 3.54563
216 H 4.63300 15.48946 2.05529
217 H 6.14907 13.79575 1.27772
218 H 6.97282 14.85592 2.09174
219 H 6.83302 13.43874 3.99719
220 H 7.62357 12.76089 2.81666
221 C 7.95025 7.70554 9.46245
222 C 9.08324 7.19276 10.30481
223 C 7.56261 9.04330 10.05575
224 H 8.19986 7.78177 8.51883
225 C 8.71371 9.99070 9.74796
226 H 7.43198 8.96562 11.01353
227 H 6.73901 9.36744 9.65481
228 C 10.01359 9.54163 10.38176
229 H 8.83261 10.04465 8.78612
230 H 8.49169 10.87665 10.06992
231 C 10.17136 8.09472 9.87755
232 H 9.95824 9.57114 11.34967
233 H 10.75522 10.09727 10.09017
234 H 10.20460 8.10323 8.90762
235 H 11.01530 7.73984 10.19749
236 H 8.89533 7.28281 11.25247
237 H 9.28629 6.26536 10.10435
238 C 3.58120 8.97738 12.45325
239 C 3.87228 7.63942 12.91696
240 C 4.76190 9.97412 12.52412
241 H 2.77621 9.34003 12.88051
242 C 5.22516 10.02524 13.96587
243 H 5.48641 9.67955 11.95107
244 H 4.47681 10.85355 12.23254
245 C 4.31547 9.13888 14.84873
246 H 5.19805 10.94040 14.28378
247 H 6.14155 9.71264 14.02459
248 C 4.30411 7.70335 14.37287
249 H 4.62974 9.17209 15.76602
250 H 3.41121 9.49129 14.83051
251 H 3.69312 7.18421 14.91758
252 H 5.19018 7.32063 14.46602
253 H 4.58019 7.25029 12.37833
254 H 3.08262 7.08128 12.82989
255 C 6.12615 12.74745 7.11152
256 C 5.69265 14.15817 6.96775
257 C 6.88685 12.44111 8.39531
258 H 6.60533 12.43112 6.31775
259 C 8.18621 13.33378 8.61401
260 H 7.14883 11.50780 8.38721
261 H 6.29036 12.57167 9.15061
262 C 7.69055 14.76319 8.40949
263 H 8.54378 13.21441 9.50699
264 H 8.87278 13.10822 7.96603
265 C 7.19952 14.81323 6.96572
266 H 8.41121 15.39975 8.54921
267 H 6.97027 14.96791 9.02506
268 H 7.78915 14.30147 6.38862
269 H 7.16999 15.72812 6.64578
270 H 5.15832 14.46117 7.72102
271 H 5.21541 14.31654 6.13753
272end
273
274xtb
275 chrg 0
276 uhf 0
277 gfn 1
278end
279
280task
281 energy xtb
282end
Then run it:
$ qbics aulig.inp -n 4 > aulig.out
Here, -n 4 means Qbics will use 4 CPU cores for parallization. xTB is controlled by the xtb block:
chrganduhfkeywords define the charge and number of unpaired electrons of the system, respectively.gfnkeyword defines which version of xTB will be used. Currently, Qbics supports GFN1-xTB (gfn 1) and GFN2-xTB (gfn 2). You can choose one of them according to your needs. In this example, we use GFN1-xTB (gfn 1). According to our experience, for systems NOT containing too many metallic atoms, GFN1-xTB is is much better. For other systems, GFN2-xTB is better.
You can also use implicit solvent model in xTB calculations with gbsa:
1xtb
2 chrg 0
3 uhf 0
4 gfn 1
5 gbsa h2o
6end
So the solvent h2o will be used in the xTB calculation. The list of all supported solvents can be found in xtb. Without giving gbsa, the xTB calculation will be done in gas phase.
In aulig.out, you will find the energy:
1xTB Iteration ... done (3.087 seconds)
2Total xTB energy: -382.97973634 Hartree
3
4Final total energy: -382.97973634 Hartree
In aulig.inp, you can change energy to opt to do geometry optimization, or md to do molecular dynamics simulation. For more information, please refer to Geometry Optimization and Standard Molecular Dynamics Simulations, respectively.
Hint
Qbics only supports a part of the xTB functions. Some functions like GFN0-xTB are not supported. If you want to use these functions, please use the original xTB program: https://xtb-docs.readthedocs.io/en/latest/.
Example: AM1 and PM3 for An Organic Anion
We will use NDDO to calculate the energy of an organi anion, C11H17SO3-:
We will first use AM1. The input file is:
1mol
2 C -0.05133195 0.13820273 -0.07408260
3 H 1.06386427 0.23393150 -0.04053791
4 H -0.48221807 1.16269423 -0.21129857
5 C -0.55764462 -0.46814486 1.23108862
6 H -0.25721997 0.18955243 2.08945318
7 C -0.45901605 -0.75614552 -1.24106425
8 H -0.08318986 -0.31245213 -2.20112418
9 C 0.13909675 -2.14772780 -1.05064293
10 H 1.25634763 -2.07769530 -1.02321562
11 H -0.14484400 -2.80323400 -1.91285383
12 C 0.04667328 -1.85701716 1.40913664
13 H -0.28851614 -2.29736205 2.38206320
14 H 1.16439595 -1.78130414 1.43736333
15 C -0.37460514 -2.75694197 0.25288279
16 H 0.05838753 -3.78596700 0.40210267
17 C -1.90186350 -2.87990458 0.16288292
18 H -2.14499703 -3.44910342 -0.78452731
19 C -2.50285637 -3.65508897 1.30500807
20 C -2.07739083 -0.58718463 1.18573116
21 H -2.53453817 0.42961535 1.07690940
22 H -2.44934230 -1.03769263 2.14165477
23 C -1.98072027 -0.85710196 -1.28599969
24 H -2.42386255 0.16167103 -1.42776124
25 H -2.29241214 -1.49373089 -2.15289033
26 C -2.49210287 -1.47123081 0.01543189
27 H -3.61168946 -1.54021627 -0.01947598
28 S -2.36143038 -5.42667342 1.13627320
29 O -2.91083500 -5.72787974 -0.13380691
30 O -3.12407542 -5.92344897 2.22190957
31 O -0.97593034 -5.70753864 1.23827617
32 H -3.59090253 -3.41118657 1.38165847
33 H -2.04104042 -3.35568384 2.27489529
34end
35
36nddo
37 charge -1
38 spin2p1 1
39end
40
41task
42 energy am1
43end
The usage of NDDO is similar to DFT. The mol section defines the molecule, and the nddo section defines the charge (charge) and spin multiplicity (spin2p1) of the system.
To use PM3, you can change the method to PM3 by replacing am1 with pm3 in the task section:
1task
2 energy pm3
3end
Of course, you can change energy to opt to do geometry optimization, or md to do molecular dynamics simulation. For more information, please refer to Geometry Optimization and Standard Molecular Dynamics Simulations, respectively.