.. tip:: All input files can be downloaded: :download:`Files `. .. tip:: For more information of this section, please refer to these pages: - :doc:`../keywords/xtb` - :doc:`../keywords/nddo` - :doc:`../keywords/mol` Semi-empirical Quantum Chemistry Methods ========================================= .. contents:: :local: 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, Au\ :sub:`18`\ (C\ :sub:`6`\ H\ :sub:`11`\ S)\ :sub:`14`, which is a model for gold nanoparticles: .. image:: ./figs/a14.jpg The input file is: .. code-block:: :caption: aulig.inp :linenos: mol Au 6.95958 2.87913 2.94614 S 9.08599 3.67339 2.88510 S 4.89113 1.81941 3.01855 Au 5.82923 4.53162 5.05796 Au 4.13669 3.38239 1.49897 Au 5.79250 5.99300 2.82997 Au 8.65595 5.47861 4.26420 S 3.33616 4.66634 -0.18204 Au 3.45811 5.08053 3.76279 S 8.56081 7.20090 5.75077 Au 6.24304 7.42405 5.38760 S 7.04744 3.53845 6.81588 Au 3.89147 6.19365 6.32206 Au 6.56834 5.22532 8.23897 S 6.65568 7.45648 1.19187 Au 3.92517 7.94284 4.15361 Au 3.18725 6.66426 1.06638 Au 6.51959 9.17260 2.68377 S 1.11550 4.78967 4.09094 Au 0.97656 6.80219 5.13736 S 3.01320 8.66765 2.07979 S 6.26671 7.02193 9.67527 Au 5.18561 8.18601 7.95848 Au 5.18171 9.94301 5.85487 S 3.00776 5.17778 8.25337 Au 2.88045 8.79374 6.73399 S 0.61480 8.81770 6.18653 S 6.59196 10.92950 4.17781 Au 3.60146 10.47321 8.93384 Au 2.73505 7.19691 9.38807 S 3.42541 8.93876 10.69319 S 4.56391 11.83306 7.37982 C 4.95046 0.19661 2.19906 C 4.13304 0.27617 0.92539 C 6.43827 -0.19882 1.91962 H 4.54937 -0.47352 2.79236 C 4.32830 -1.08837 0.26931 H 4.45695 0.98625 0.34829 H 3.19681 0.43452 1.12181 C 5.75611 -1.40758 -0.15592 H 4.03232 -1.77426 0.88894 H 3.75560 -1.14070 -0.51433 C 6.56085 -1.57337 1.12181 H 5.78086 -2.22375 -0.68037 H 6.11951 -0.68416 -0.69252 H 7.48911 -1.76356 0.91526 H 6.20590 -2.30489 1.65233 H 6.91097 -0.27514 2.76401 H 6.86172 0.50545 1.40529 C 9.82213 2.61150 4.17741 C 11.27211 3.02202 4.31713 C 9.74817 1.08389 3.77445 H 9.35450 2.75237 5.02585 C 10.56493 0.41654 4.92663 H 8.83144 0.76495 3.75825 H 10.15792 0.92343 2.90981 C 12.02599 0.81419 4.94688 H 10.16185 0.65719 5.77507 H 10.50409 -0.54817 4.83551 C 12.15597 2.23072 5.30934 H 12.50229 0.26663 5.59080 H 12.41786 0.66328 4.07414 H 13.08043 2.51488 5.23847 H 11.85571 2.37597 6.22055 H 11.29164 3.95583 4.58037 H 11.68263 2.96345 3.44034 C 4.66625 4.65474 -1.39922 C 4.08243 5.21781 -2.70732 C 5.34316 3.30509 -1.70701 H 5.36069 5.27536 -1.09143 C 5.11020 5.41339 -3.85747 H 3.66929 6.07468 -2.51697 H 3.38482 4.61959 -3.01510 C 5.75779 4.03509 -4.14096 H 4.66354 5.74193 -4.65326 H 5.78875 6.05533 -3.59626 C 6.40351 3.59895 -2.71947 H 6.44382 4.10772 -4.82336 H 5.09199 3.38992 -4.43052 H 6.95572 2.81229 -2.84501 H 6.97114 4.31314 -2.39345 H 5.73476 2.93101 -0.90109 H 4.69806 2.67321 -2.06137 C 8.43376 7.22633 1.27772 C 8.75735 8.28980 0.28956 C 8.35307 5.81798 0.56900 H 8.85999 7.27198 2.15856 C 9.69198 5.73389 -0.12554 H 8.24574 5.10410 1.21495 H 7.62278 5.78581 -0.06682 C 9.96941 6.72193 -1.21293 H 10.38502 5.82694 0.54673 H 9.77560 4.84353 -0.50420 C 10.00162 8.16508 -0.53458 H 9.27489 6.68456 -1.88925 H 10.82171 6.53031 -1.63411 H 10.78731 8.25471 0.02835 H 10.02631 8.85607 -1.21293 H 8.80872 9.13067 0.77149 H 8.00761 8.35930 -0.32196 C 6.50278 1.84108 7.01432 C 7.28044 0.78458 6.26712 C 5.01755 1.78217 6.64983 H 6.57149 1.62563 7.96806 C 4.62585 0.27870 6.86447 H 4.87778 2.04901 5.72850 H 4.49708 2.36180 7.22896 C 5.32148 -0.69994 6.03831 H 4.78156 0.05322 7.79391 H 3.67418 0.18804 6.70046 C 6.86575 -0.64443 6.40482 H 5.19434 -0.49612 5.09875 H 4.97170 -1.58883 6.20840 H 7.00953 -0.95193 7.31401 H 7.37939 -1.20492 5.80342 H 7.24906 1.00744 5.32351 H 8.20707 0.84878 6.54251 C 0.20628 5.07898 2.57975 C -1.17788 5.60632 2.82071 C 0.12299 3.68230 1.96215 H 0.70535 5.68323 1.99050 C -2.09672 5.44393 1.59766 H -1.12354 6.54642 3.05358 H -1.56781 5.13549 3.57398 C -2.13396 4.00151 1.13800 H -2.99320 5.73375 1.82850 H -1.77409 6.00689 0.87679 C -0.77977 3.40755 0.79984 H -2.70051 3.94240 0.35234 H -2.54195 3.46517 1.83458 H -0.85827 2.45198 0.65607 H -0.42430 3.81421 -0.00607 H 1.02042 3.43820 1.69081 H -0.13232 3.07325 2.67289 C 1.22368 8.95953 2.26183 C 1.12729 10.21342 3.03333 C 0.58490 8.92423 0.89906 H 0.84462 8.23475 2.80046 C -0.33067 10.76335 3.01510 H 1.72744 10.87617 2.65264 H 1.40251 10.05251 3.94859 C -0.94306 10.81773 1.64018 H -0.88199 10.20064 3.58208 H -0.33207 11.65642 3.39579 C -0.86444 9.45049 0.98209 H -0.46965 11.47057 1.09953 H -1.87007 11.09632 1.70701 H -1.23397 9.50606 0.08707 H -1.40292 8.82297 1.48832 H 0.58426 8.01529 0.56293 H 1.09749 9.47365 0.28551 C 9.36023 8.74574 5.21214 C 10.86188 8.70547 5.36199 C 8.95878 10.12481 5.70825 H 9.21073 8.77731 4.24423 C 11.60848 10.07555 4.97725 H 11.21015 7.99337 4.80108 H 11.07472 8.48276 6.28130 C 11.02957 11.31196 5.49158 H 12.52433 10.01664 5.29314 H 11.64061 10.13767 4.00934 C 9.64347 11.22271 4.97928 H 11.48770 12.09264 5.14127 H 11.04890 11.33807 6.46152 H 9.64988 11.03765 4.02756 H 9.17822 12.06083 5.12507 H 8.00026 10.23061 5.60903 H 9.16848 10.19519 6.65186 C 1.34521 4.56248 7.90731 C 1.40899 3.18816 7.18441 C 0.54823 4.35183 9.30855 H 0.86252 5.20662 7.34641 C -0.07413 2.78935 7.12974 H 1.78534 3.27425 6.29547 H 1.92910 2.54705 7.69267 C -0.80128 2.46805 8.41759 H -0.55555 3.50944 6.69438 H -0.14563 2.01082 6.55264 C -0.86288 3.76310 9.11619 H -1.69120 2.12632 8.23940 H -0.31186 1.81328 8.94002 H -1.28564 3.64254 9.98083 H -1.40450 4.38118 8.59983 H 1.06264 3.75719 9.87755 H 0.47489 5.20576 9.76213 C -0.54610 8.85187 7.55700 C -1.42383 7.61911 7.56712 C 0.13609 9.11399 8.90357 H -1.14205 9.61310 7.39500 C -0.81332 9.13457 10.11650 H 0.59493 9.96753 8.85497 H 0.80788 8.42822 9.04734 C -1.61822 7.79848 10.15294 H -1.42237 9.88711 10.04562 H -0.30118 9.23490 10.93456 C -2.33420 7.77525 8.81447 H -1.02569 7.03632 10.24407 H -2.25370 7.79342 10.88596 H -2.83653 8.60120 8.72538 H -2.97165 7.04481 8.82257 H -0.88524 6.81500 7.63597 H -1.95664 7.57099 6.75918 C 5.66496 11.91514 3.03738 C 4.48325 12.57713 3.69345 C 6.75652 13.09456 3.09408 H 5.50202 11.51720 2.15654 C 4.01247 13.67426 2.75186 H 4.74047 12.95485 4.54999 H 3.77295 11.93342 3.84127 C 4.95307 14.81578 2.67492 H 3.89878 13.30013 1.86293 H 3.14769 13.99831 3.04953 C 6.28899 14.17196 2.16059 H 5.07738 15.22261 3.54563 H 4.63300 15.48946 2.05529 H 6.14907 13.79575 1.27772 H 6.97282 14.85592 2.09174 H 6.83302 13.43874 3.99719 H 7.62357 12.76089 2.81666 C 7.95025 7.70554 9.46245 C 9.08324 7.19276 10.30481 C 7.56261 9.04330 10.05575 H 8.19986 7.78177 8.51883 C 8.71371 9.99070 9.74796 H 7.43198 8.96562 11.01353 H 6.73901 9.36744 9.65481 C 10.01359 9.54163 10.38176 H 8.83261 10.04465 8.78612 H 8.49169 10.87665 10.06992 C 10.17136 8.09472 9.87755 H 9.95824 9.57114 11.34967 H 10.75522 10.09727 10.09017 H 10.20460 8.10323 8.90762 H 11.01530 7.73984 10.19749 H 8.89533 7.28281 11.25247 H 9.28629 6.26536 10.10435 C 3.58120 8.97738 12.45325 C 3.87228 7.63942 12.91696 C 4.76190 9.97412 12.52412 H 2.77621 9.34003 12.88051 C 5.22516 10.02524 13.96587 H 5.48641 9.67955 11.95107 H 4.47681 10.85355 12.23254 C 4.31547 9.13888 14.84873 H 5.19805 10.94040 14.28378 H 6.14155 9.71264 14.02459 C 4.30411 7.70335 14.37287 H 4.62974 9.17209 15.76602 H 3.41121 9.49129 14.83051 H 3.69312 7.18421 14.91758 H 5.19018 7.32063 14.46602 H 4.58019 7.25029 12.37833 H 3.08262 7.08128 12.82989 C 6.12615 12.74745 7.11152 C 5.69265 14.15817 6.96775 C 6.88685 12.44111 8.39531 H 6.60533 12.43112 6.31775 C 8.18621 13.33378 8.61401 H 7.14883 11.50780 8.38721 H 6.29036 12.57167 9.15061 C 7.69055 14.76319 8.40949 H 8.54378 13.21441 9.50699 H 8.87278 13.10822 7.96603 C 7.19952 14.81323 6.96572 H 8.41121 15.39975 8.54921 H 6.97027 14.96791 9.02506 H 7.78915 14.30147 6.38862 H 7.16999 15.72812 6.64578 H 5.15832 14.46117 7.72102 H 5.21541 14.31654 6.13753 end xtb chrg 0 uhf 0 gfn 1 end task energy xtb end Then run it: .. code-block:: bash $ 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: - ``chrg`` and ``uhf`` keywords define the charge and number of unpaired electrons of the system, respectively. - ``gfn`` keyword 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``: .. code-block:: :linenos: xtb chrg 0 uhf 0 gfn 1 gbsa h2o end So the solvent ``h2o`` will be used in the xTB calculation. The list of all supported solvents can be found in :doc:`../keywords/xtb`. Without giving ``gbsa``, the xTB calculation will be done in gas phase. In ``aulig.out``, you will find the energy: .. code-block:: :caption: aulig.out :linenos: xTB Iteration ... done (3.087 seconds) Total xTB energy: -382.97973634 Hartree Final 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 :doc:`opt` and :doc:`md`, 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: ``_. Example: AM1 and PM3 for An Organic Anion ------------------------------------------------- We will use NDDO to calculate the energy of an organi anion, C\ :sub:`11`\ H\ :sub:`17`\ SO\ :sub:`3`\ :sup:`-`: .. image:: ./figs/a15.jpg We will first use AM1. The input file is: .. code-block:: :caption: c11h17so3-1.inp :linenos: mol C -0.05133195 0.13820273 -0.07408260 H 1.06386427 0.23393150 -0.04053791 H -0.48221807 1.16269423 -0.21129857 C -0.55764462 -0.46814486 1.23108862 H -0.25721997 0.18955243 2.08945318 C -0.45901605 -0.75614552 -1.24106425 H -0.08318986 -0.31245213 -2.20112418 C 0.13909675 -2.14772780 -1.05064293 H 1.25634763 -2.07769530 -1.02321562 H -0.14484400 -2.80323400 -1.91285383 C 0.04667328 -1.85701716 1.40913664 H -0.28851614 -2.29736205 2.38206320 H 1.16439595 -1.78130414 1.43736333 C -0.37460514 -2.75694197 0.25288279 H 0.05838753 -3.78596700 0.40210267 C -1.90186350 -2.87990458 0.16288292 H -2.14499703 -3.44910342 -0.78452731 C -2.50285637 -3.65508897 1.30500807 C -2.07739083 -0.58718463 1.18573116 H -2.53453817 0.42961535 1.07690940 H -2.44934230 -1.03769263 2.14165477 C -1.98072027 -0.85710196 -1.28599969 H -2.42386255 0.16167103 -1.42776124 H -2.29241214 -1.49373089 -2.15289033 C -2.49210287 -1.47123081 0.01543189 H -3.61168946 -1.54021627 -0.01947598 S -2.36143038 -5.42667342 1.13627320 O -2.91083500 -5.72787974 -0.13380691 O -3.12407542 -5.92344897 2.22190957 O -0.97593034 -5.70753864 1.23827617 H -3.59090253 -3.41118657 1.38165847 H -2.04104042 -3.35568384 2.27489529 end nddo charge -1 spin2p1 1 end task energy am1 end 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: .. code-block:: :caption: c11h17so3-2.inp :linenos: task energy pm3 end 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 :doc:`opt` and :doc:`md`, respectively.