# Claisen Rearrangement with GFN1-xTB This report summarizes a GFN1-xTB workflow for the Claisen rearrangement of `C=CC(CCCC)C1C=CC(C)=CC1=O`. The workflow consisted of reactant optimization with normal modes, a one-dimensional PES scan of the carbonyl oxygen to terminal vinyl carbon distance, a transition-state search started from the highest-energy scan point, and a product optimization from the shortest-distance scan structure. ## Conclusions - Reaction free energy barrier from Gibbs free energies: `17.61 kcal/mol` - Reaction free energy from Gibbs free energies: `-16.51 kcal/mol` - Transition-state verification: `1` imaginary frequency/frequencies - Imaginary frequency values (cm^-1): `-523.87` ## Scan Profile ![Energy vs distance](scan_energy_vs_distance.png) The PES scan used the directly identified carbonyl oxygen and terminal vinyl carbon and sampled the O...C distance across `17` points, ending at `1.500 Angstrom`. ### Representative scan structures Shortest-distance structure (`1.500 Angstrom`, `-45.070213 Eh`) ![Shortest scan structure](scan_shortest_distance.png) Longest-distance structure (`4.736 Angstrom`, `-45.043347 Eh`) ![Longest scan structure](scan_longest_distance.png) Highest-energy structure (`1.904 Angstrom`, `-45.020033 Eh`) ![Highest-energy scan structure](scan_highest_energy.png) ## Optimized stationary points | Stationary Point | Electronic Energy (Eh) | Relative Electronic (kcal/mol) | Gibbs Free Energy (Eh) | Relative Gibbs (kcal/mol) | |:-------------------|-------------------------:|---------------------------------:|-------------------------:|----------------------------:| | Reactant | -45.043346 | 0.000000 | -44.789812 | 0.000000 | | TS | -45.017765 | 16.052713 | -44.761746 | 17.611167 | | Product | -45.073091 | -18.665161 | -44.816126 | -16.512827 | Optimized reactant ![Reactant](reactant_optimized.png) Optimized transition state ![Transition state](ts_optimized.png) Optimized product ![Product](product_optimized.png) ## Job provenance - `reactant_opt`: Optimized reactant with normal modes for the reference Gibbs free energy. - `pes_scan`: Constrained PES scan used to generate the scan profile and TS starting geometry. - `ts_search`: Transition-state search with initial Hessian and normal-mode verification. - `product_opt`: Optimized product candidate taken from the shortest-distance scan structure. ## Calculation inputs ### `reactant_opt` ```ams Properties NormalModes yes End Task GeometryOptimization System Atoms C 0.0352835768 -1.2634200451 2.0295182868 C -0.0415942574 -0.1145626957 1.3513671875 C 0.3768358030 -0.0107622019 -0.1023946895 C 1.3482601493 1.1778757204 -0.3037836994 C 2.7043903423 1.0005137599 0.4064036347 C 3.6037073244 -0.0421656093 -0.2748047891 C 4.9927169421 -0.0650315668 0.3569733474 C -0.8639092594 0.0835558950 -1.0353753505 C -1.6167867797 -1.2320759497 -1.0242134522 C -2.8481006207 -1.3596284649 -0.5174591373 C -3.5920200469 -0.2007888095 0.0203302547 C -4.9621855196 -0.4060955913 0.5962914008 C -3.0923854072 1.0353581165 -0.0982955957 C -1.7693748858 1.2549099789 -0.7024024375 O -1.3979590243 2.4318691017 -0.9545350183 H -0.2932245841 -1.3055311163 3.0627223262 H 0.4201319644 -2.1657625412 1.5646403918 H -0.4547906310 0.7594326185 1.8469683919 H 0.9219001025 -0.9336388195 -0.3976829884 H 0.8826924392 2.1060815765 0.0912568365 H 1.5283912179 1.3393815818 -1.3892591926 H 3.2253886735 1.9831444015 0.3897766333 H 2.5489641777 0.7270983739 1.4724197858 H 3.7064446671 0.1953577571 -1.3559394825 H 3.1616795189 -1.0552978497 -0.1752916690 H 4.9208180589 -0.3155000900 1.4369243466 H 5.6171362308 -0.8337967696 -0.1451860994 H 5.4865795359 0.9232818198 0.2413060231 H -0.5128916286 0.2263228659 -2.0809303623 H -1.1176209481 -2.1146362083 -1.4056763567 H -3.3119945930 -2.3382881694 -0.5095056928 H -5.0700115595 -1.4398065936 0.9877091215 H -5.7246495708 -0.2382537447 -0.1928669653 H -5.1447217319 0.2985644575 1.4359193845 H -3.6670996767 1.8922948115 0.2337513069 End BondOrders 1 2 2.0 1 16 1.0 1 17 1.0 2 3 1.0 2 18 1.0 3 4 1.0 3 8 1.0 3 19 1.0 4 5 1.0 4 20 1.0 4 21 1.0 5 6 1.0 5 22 1.0 5 23 1.0 6 7 1.0 6 24 1.0 6 25 1.0 7 26 1.0 7 27 1.0 7 28 1.0 8 9 1.0 8 14 1.0 8 29 1.0 9 10 2.0 9 30 1.0 10 11 1.0 10 31 1.0 11 12 1.0 11 13 2.0 12 32 1.0 12 33 1.0 12 34 1.0 13 14 1.0 13 35 1.0 14 15 2.0 End End Engine DFTB Model GFN1-xTB EndEngine ``` ### `pes_scan` ```ams PESScan ScanCoordinate Distance 15 1 4.735989 1.500000 nPoints 17 End End Task PESScan System Atoms C 0.0828356678 -1.2361609693 1.8600638635 C 0.0230169857 -0.1005602292 1.1840009238 C 0.3826447205 0.0205084136 -0.2724822300 C 1.3521611871 1.1876495589 -0.5166034737 C 2.6460120158 1.0536430092 0.2949181241 C 3.5226812171 -0.1192578462 -0.1586482087 C 4.8440952630 -0.1487866778 0.6087729338 C -0.9228364398 0.1942082855 -1.1223234263 C -1.6417212509 -1.1113136883 -1.1603288968 C -2.8348664870 -1.3002647840 -0.5845342490 C -3.5290877878 -0.2152724185 0.0761825981 C -4.8363082077 -0.5304791294 0.7410256425 C -3.0099669152 1.0319921635 0.0677756390 C -1.7445286569 1.3573294302 -0.5816422387 O -1.3421283198 2.4993510190 -0.6786401890 H -0.1867739182 -1.2949537692 2.9060301868 H 0.4054485891 -2.1640373293 1.4040032539 H -0.3132648021 0.8147181482 1.6634827407 H 0.8526673855 -0.9130807246 -0.6103291960 H 0.8652795062 2.1269807927 -0.2427291012 H 1.5917222736 1.2336264690 -1.5839435535 H 3.2135209300 1.9836685557 0.1837301315 H 2.4029556447 0.9387983613 1.3567719686 H 3.7270456881 -0.0291243509 -1.2313367049 H 2.9958873621 -1.0655744537 0.0032020358 H 4.6610192136 -0.2577301258 1.6789699085 H 5.4540419485 -0.9882669028 0.2733338621 H 5.4025750367 0.7741601198 0.4448678964 H -0.5977984126 0.4596345834 -2.1362258221 H -1.1214637929 -1.9293767174 -1.6486896873 H -3.3158183859 -2.2722781899 -0.6066649463 H -4.6890376443 -1.2952553745 1.5059415186 H -5.5423337805 -0.9250234583 0.0077423503 H -5.2667892044 0.3561142097 1.2052954354 H -3.5308866291 1.8644140190 0.5276865919 End BondOrders 1 2 2.0 1 16 1.0 1 17 1.0 2 3 1.0 2 18 1.0 3 4 1.0 3 8 1.0 3 19 1.0 4 5 1.0 4 20 1.0 4 21 1.0 5 6 1.0 5 22 1.0 5 23 1.0 6 7 1.0 6 24 1.0 6 25 1.0 7 26 1.0 7 27 1.0 7 28 1.0 8 9 1.0 8 14 1.0 8 29 1.0 9 10 2.0 9 30 1.0 10 11 1.0 10 31 1.0 11 12 1.0 11 13 2.0 12 32 1.0 12 33 1.0 12 34 1.0 13 14 1.0 13 35 1.0 14 15 2.0 End End Engine DFTB Model GFN1-xTB EndEngine ``` ### `ts_search` ```ams GeometryOptimization InitialHessian Type Calculate End End Properties NormalModes yes End Task TransitionStateSearch System Atoms C -0.1883855639 0.8849440844 2.8380677896 C 0.5627428136 1.3021798440 1.7761149239 C 0.2952333107 0.7218491339 0.4570370534 C 1.3447101401 1.0740177929 -0.5988077995 C 2.7398580096 0.5677441272 -0.2063178575 C 2.8468332670 -0.9605979608 -0.2429802578 C 4.2721905153 -1.4211851135 0.0591373277 C -1.1747522277 1.3440766657 -0.0038150205 C -1.5207378757 0.8630891391 -1.3508859600 C -2.3683829623 -0.1681694771 -1.5433814212 C -3.0696805006 -0.7696212742 -0.4470282606 C -3.9924790716 -1.9182697347 -0.7364163010 C -2.9158147501 -0.2700241146 0.8113791419 C -2.0845178261 0.8661991276 1.0809153734 O -1.9403895618 1.3267279730 2.2360511787 H -0.1493070037 1.4294235569 3.7730952063 H -0.4767901508 -0.1543179245 2.9358426632 H 0.9713072494 2.3092268737 1.7869621609 H 0.1389341018 -0.3610438632 0.4980558820 H 1.3877309740 2.1612653470 -0.7201423987 H 1.0669049571 0.6375254770 -1.5627741289 H 3.4679284037 0.9925994395 -0.9055578088 H 2.9913397275 0.9283248842 0.7965107426 H 2.5493453999 -1.3238854757 -1.2328140760 H 2.1656346027 -1.3999529135 0.4928224177 H 4.5804954685 -1.0829907202 1.0494557149 H 4.3281249818 -2.5097136723 0.0308707210 H 4.9691052791 -1.0181568941 -0.6771753844 H -1.0207148970 2.4248273894 0.0189637741 H -1.0450925835 1.3493498217 -2.1957393948 H -2.5748585113 -0.5292833208 -2.5455309316 H -3.4370217067 -2.7390101685 -1.1940103991 H -4.7684533300 -1.6087508459 -1.4392993575 H -4.4676411820 -2.2800376390 0.1748340102 H -3.4833994970 -0.6683595645 1.6452363582 End BondOrders 1 2 2.0 1 16 1.0 1 17 1.0 2 3 1.0 2 18 1.0 3 4 1.0 3 8 1.0 3 19 1.0 4 5 1.0 4 20 1.0 4 21 1.0 5 6 1.0 5 22 1.0 5 23 1.0 6 7 1.0 6 24 1.0 6 25 1.0 7 26 1.0 7 27 1.0 7 28 1.0 8 9 1.0 8 14 1.0 8 29 1.0 9 10 2.0 9 30 1.0 10 11 1.0 10 31 1.0 11 12 1.0 11 13 2.0 12 32 1.0 12 33 1.0 12 34 1.0 13 14 1.0 13 35 1.0 14 15 2.0 End End System final Atoms C -1.0451269478 2.0735889566 2.2034291742 C 0.3809633753 1.9201215848 1.7721373932 C 1.1744665724 0.9376768117 2.1784859003 C 2.5918951088 0.7657262339 1.7151237820 C 2.7112172482 -0.4246946392 0.7469721264 C 1.9541349796 -0.1700007854 -0.5601651801 C 2.0736467518 -1.3557249519 -1.5155867636 C -2.6204936975 1.4665200110 -1.1058903775 C -2.7938208214 0.4675898504 -2.0476039400 C -2.3983555033 -0.8358684068 -1.7758915240 C -1.8296740847 -1.1465175506 -0.5444949898 C -1.4268441422 -2.5633638543 -0.2308997241 C -1.6530482167 -0.1460785668 0.4082593299 C -2.0439493279 1.1630869836 0.1305154182 O -1.9305596711 2.1983235634 0.9990828078 H -1.2003629359 3.0217346306 2.7262971868 H -1.3943747537 1.2462085997 2.8296833104 H 0.7319447437 2.6783949005 1.0785449878 H 0.8086725407 0.1766513728 2.8640131241 H 3.2361043614 0.5779133975 2.5800608176 H 2.9429714280 1.6751678780 1.2168056076 H 3.7705997359 -0.5934415113 0.5290325792 H 2.3197285611 -1.3262388519 1.2303528490 H 2.3530861556 0.7287477483 -1.0429599793 H 0.8970543304 0.0117095184 -0.3400784601 H 1.6755236766 -2.2602423039 -1.0532884067 H 1.5119163852 -1.1570786327 -2.4287278953 H 3.1172183154 -1.5327563377 -1.7801746401 H -2.9237811573 2.4862797052 -1.3082386669 H -3.2380402552 0.7066147322 -3.0077839698 H -2.5339668703 -1.6104563479 -2.5222966220 H -1.0206620652 -3.0537871017 -1.1160991236 H -2.2983720908 -3.1326597682 0.1005183787 H -0.6800413687 -2.5911646697 0.5628480847 H -1.2196703602 -0.4019821983 1.3666930871 End BondOrders 1 2 1.0 1 15 1.0 1 16 1.0 1 17 1.0 2 3 2.0 2 18 1.0 3 4 1.0 3 19 1.0 4 5 1.0 4 20 1.0 4 21 1.0 5 6 1.0 5 22 1.0 5 23 1.0 6 7 1.0 6 24 1.0 6 25 1.0 7 26 1.0 7 27 1.0 7 28 1.0 8 9 1.5 8 14 1.5 8 29 1.0 9 10 1.5 9 30 1.0 10 11 1.5 10 31 1.0 11 12 1.0 11 13 1.5 12 32 1.0 12 33 1.0 12 34 1.0 13 14 1.5 13 35 1.0 14 15 1.0 End End Engine DFTB Model GFN1-xTB EndEngine ``` ### `product_opt` ```ams Properties NormalModes yes End Task GeometryOptimization System Atoms C -1.0451269478 2.0735889566 2.2034291742 C 0.3809633753 1.9201215848 1.7721373932 C 1.1744665724 0.9376768117 2.1784859003 C 2.5918951088 0.7657262339 1.7151237820 C 2.7112172482 -0.4246946392 0.7469721264 C 1.9541349796 -0.1700007854 -0.5601651801 C 2.0736467518 -1.3557249519 -1.5155867636 C -2.6204936975 1.4665200110 -1.1058903775 C -2.7938208214 0.4675898504 -2.0476039400 C -2.3983555033 -0.8358684068 -1.7758915240 C -1.8296740847 -1.1465175506 -0.5444949898 C -1.4268441422 -2.5633638543 -0.2308997241 C -1.6530482167 -0.1460785668 0.4082593299 C -2.0439493279 1.1630869836 0.1305154182 O -1.9305596711 2.1983235634 0.9990828078 H -1.2003629359 3.0217346306 2.7262971868 H -1.3943747537 1.2462085997 2.8296833104 H 0.7319447437 2.6783949005 1.0785449878 H 0.8086725407 0.1766513728 2.8640131241 H 3.2361043614 0.5779133975 2.5800608176 H 2.9429714280 1.6751678780 1.2168056076 H 3.7705997359 -0.5934415113 0.5290325792 H 2.3197285611 -1.3262388519 1.2303528490 H 2.3530861556 0.7287477483 -1.0429599793 H 0.8970543304 0.0117095184 -0.3400784601 H 1.6755236766 -2.2602423039 -1.0532884067 H 1.5119163852 -1.1570786327 -2.4287278953 H 3.1172183154 -1.5327563377 -1.7801746401 H -2.9237811573 2.4862797052 -1.3082386669 H -3.2380402552 0.7066147322 -3.0077839698 H -2.5339668703 -1.6104563479 -2.5222966220 H -1.0206620652 -3.0537871017 -1.1160991236 H -2.2983720908 -3.1326597682 0.1005183787 H -0.6800413687 -2.5911646697 0.5628480847 H -1.2196703602 -0.4019821983 1.3666930871 End BondOrders 1 2 1.0 1 15 1.0 1 16 1.0 1 17 1.0 2 3 2.0 2 18 1.0 3 4 1.0 3 19 1.0 4 5 1.0 4 20 1.0 4 21 1.0 5 6 1.0 5 22 1.0 5 23 1.0 6 7 1.0 6 24 1.0 6 25 1.0 7 26 1.0 7 27 1.0 7 28 1.0 8 9 1.5 8 14 1.5 8 29 1.0 9 10 1.5 9 30 1.0 10 11 1.5 10 31 1.0 11 12 1.0 11 13 1.5 12 32 1.0 12 33 1.0 12 34 1.0 13 14 1.5 13 35 1.0 14 15 1.0 End End Engine DFTB Model GFN1-xTB EndEngine ```