# GFN1-xTB Claisen rearrangement profile ## Summary The neutral, closed-shell molecule `C=CC(CCCC)C1C=CC(C)=CC1=O` was treated in the gas phase with GFN1-xTB. The carbonyl oxygen and terminal vinyl carbon were identified from the `ChemicalSystem.bonds` graph as atoms 15 and 1, respectively. All thermochemical values are ideal-gas rigid-rotor/harmonic-oscillator results at the AMS default temperature of 298.15 K. For the explicitly scanned direction—supplied dienone → short O–C aryl-ether endpoint—the reaction free-energy barrier is **18.06 kcal/mol**, and the reaction free energy is **-14.96 kcal/mol**. The requested O–C contraction is the retro-Claisen direction. For the opposite, conventional aryl ether → dienone Claisen direction, the same stationary points give ΔG‡ = **33.02 kcal/mol** and ΔG = **14.96 kcal/mol**. The transition state has exactly one imaginary frequency, **-522.65 cm⁻¹**, and AMS classifies it as a transition state. ## Stationary points | Reactant | Transition state | Product | |:--:|:--:|:--:| | ![Optimized reactant](figures/reactant_optimized.png) | ![Optimized transition state](figures/ts_optimized.png) | ![Optimized product](figures/product_optimized.png) | | Structure | Electronic energy (Hartree) | Electronic energy (kcal/mol) | Relative electronic energy (kcal/mol) | Gibbs free energy (Hartree) | Gibbs free energy (kcal/mol) | Relative Gibbs free energy (kcal/mol) | PES point character | Negative frequencies | Lowest frequency (cm^-1) | |:------------|------------------------------:|-------------------------------:|----------------------------------------:|------------------------------:|-------------------------------:|----------------------------------------:|:----------------------|-----------------------:|---------------------------:| | Reactant | -45.0435 | -28265.2 | 0 | -44.7908 | -28106.7 | 0 | local minimum | 0 | 21.5804 | | TS | -45.018 | -28249.2 | 15.9885 | -44.7621 | -28088.6 | 18.0607 | transition state | 1 | -522.655 | | Product | -45.0708 | -28282.3 | -17.1168 | -44.8147 | -28121.6 | -14.9631 | local minimum | 1 | -14.1897 | Electronic and Gibbs energies use identical GFN1-xTB settings. Relative values are referenced to the optimized reactant. The reactant has no negative frequencies and is classified as a local minimum. The product is classified as a local minimum by AMS; its lowest mode is -14.19 cm⁻¹. The small negative value is below the AMS PES-point-character tolerance and represents a very soft conformational mode rather than a chemically significant unstable mode. ## Relaxed O–C distance scan The optimized reactant O···C distance is 4.758 Å. To preserve an exact 0.2 Å grid ending at 1.5 Å, the relaxed scan begins at 4.9 Å, requiring a 0.142 Å adjustment at its first constrained point. The only scan warning records this difference between the initial geometry and first requested constraint. All 18 constrained optimizations converged. Point 16, at 1.90 Å, has the highest scan energy and was used directly as the TS-search starting structure. ![Electronic energy versus O-C distance](figures/energy_vs_distance.png) Five representative relaxed-scan geometries, displayed in scan order in one row: ![Five representative three-dimensional scan structures](figures/scan_structures_one_row.png) | Point | O-C distance (angstrom) | Electronic energy (Hartree) | Relative electronic energy (kcal/mol) | Converged | |--------:|--------------------------:|------------------------------:|----------------------------------------:|:------------| | 1 | 4.9 | -45.0433 | 0 | True | | 2 | 4.7 | -45.0434 | -0.0994 | True | | 3 | 4.5 | -45.0429 | 0.2206 | True | | 4 | 4.3 | -45.042 | 0.8207 | True | | 5 | 4.1 | -45.0408 | 1.5587 | True | | 6 | 3.9 | -45.0397 | 2.281 | True | | 7 | 3.7 | -45.0387 | 2.8487 | True | | 8 | 3.5 | -45.0382 | 3.1937 | True | | 9 | 3.3 | -45.0379 | 3.3608 | True | | 10 | 3.1 | -45.0406 | 1.6597 | True | | 11 | 2.9 | -45.0401 | 1.9894 | True | | 12 | 2.7 | -45.0393 | 2.4763 | True | | 13 | 2.5 | -45.0376 | 3.585 | True | | 14 | 2.3 | -45.0338 | 5.9742 | True | | 15 | 2.1 | -45.0274 | 9.947 | True | | 16 | 1.9 | -45.0201 | 14.5278 | True | | 17 | 1.7 | -45.0427 | 0.3462 | True | | 18 | 1.5 | -45.0676 | -15.2562 | True | ## Frequency and TS verification - Reactant: 99 vibrational modes; 0 negative frequencies; AMS character `local minimum`. - Transition state: 99 vibrational modes; 1 negative frequency (-522.65 cm⁻¹); AMS character `transition state`. - Product: 99 vibrational modes; 1 formally negative frequency (-14.19 cm⁻¹); AMS character `local minimum`. The TS calculation explicitly used `GeometryOptimization InitialHessian Type Calculate`, requested final normal modes, and followed the O–C distance reaction coordinate. ## Conclusion At the GFN1-xTB/RRHO level, the requested O–C contraction has ΔG‡ = **18.06 kcal/mol** and ΔG = **-14.96 kcal/mol** at 298.15 K; the opposite conventional Claisen direction has ΔG‡ = **33.02 kcal/mol** and ΔG = **14.96 kcal/mol**. The stationary-point classification and one-imaginary-frequency requirement are satisfied for the transition state. Because the molecule is conformationally flexible and only one UFF-generated starting conformer was refined, these values are a single-conformer estimate. ## Calculation inputs and provenance ### Reactant GFN1-xTB reactant geometry optimization and harmonic normal modes. ```ams Properties NormalModes yes End Task GeometryOptimization System Atoms C -1.0262011744 3.6046926978 -0.2030752582 C -0.9035269429 2.3901008178 0.3408609206 C -0.4009428537 1.2066229963 -0.4627217180 C -0.7776227692 -0.1290248391 0.2282156809 C -2.2934811062 -0.3814086734 0.2142972611 C -2.6329822843 -1.7213596794 0.8772441541 C -4.1372958777 -1.9767897946 0.8660277936 C 1.1303217520 1.3264778198 -0.7117340959 C 1.9147614601 1.2390177228 0.5837038809 C 2.7911117108 0.2612237981 0.8372508888 C 3.0893435188 -0.7949325961 -0.1531566567 C 4.0845233772 -1.8654105033 0.1865977012 C 2.5469104038 -0.7480427923 -1.3759398575 C 1.5967756662 0.3149579130 -1.7373095423 O 1.1622136995 0.3767158868 -2.9184606990 H -1.3934559320 4.4326652206 0.3943984043 H -0.7656343746 3.7807957810 -1.2422634043 H -1.1854283646 2.2565790784 1.3818262125 H -0.9131945896 1.2302176134 -1.4518142013 H -0.2836357033 -0.9723523125 -0.3009606569 H -0.4109781544 -0.1302659874 1.2786173024 H -2.6546413428 -0.3910944354 -0.8377006564 H -2.8155520622 0.4353890465 0.7582495012 H -2.1243020036 -2.5481141441 0.3349578458 H -2.2765053910 -1.7192668188 1.9304560262 H -4.5155582378 -2.0082479091 -0.1780047553 H -4.6686812035 -1.1773474916 1.4251395814 H -4.3522897820 -2.9522077118 1.3510970272 H 1.3437069086 2.3280134690 -1.1451953696 H 1.7442874387 1.9920817558 1.3433076540 H 3.3012697072 0.2515915366 1.7926076621 H 3.7924960109 -2.8332928298 -0.2746686918 H 5.0872692461 -1.5710654156 -0.1877819966 H 4.1396520738 -2.0134731165 1.2858798231 H 2.8072671761 -1.4934461026 -2.1185896705 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 ``` ### Scan Relaxed O···C distance scan used to locate the TS-search starting geometry. ```ams PESScan ScanCoordinate Distance 15 1 4.90000000 1.50000000 nPoints 18 End End Task PESScan System Atoms C -1.4768962046 3.3710010886 -0.2660432725 C -0.8296109555 2.3624709099 0.2961452241 C -0.3377937283 1.1663138274 -0.4704503129 C -0.7704424781 -0.1458215069 0.2019805372 C -2.2957998312 -0.2814957815 0.2172593734 C -2.7278659743 -1.5958743579 0.8740081402 C -4.2491691452 -1.7358265259 0.8921579647 C 1.2128063406 1.2071055728 -0.6238353582 C 1.9299248920 1.0488976744 0.6730242660 C 2.8783337450 0.1243084812 0.8695632889 C 3.2648423695 -0.7950246192 -0.1789700821 C 4.3330466113 -1.7989335531 0.1390641408 C 2.6730234977 -0.7366904386 -1.3921352589 C 1.6162085544 0.2158540618 -1.7110405145 O 1.0613123584 0.2371809325 -2.7903580823 H -1.8175944810 4.2229704893 0.3068512941 H -1.6997487234 3.3941933878 -1.3251316790 H -0.6234882257 2.3661804894 1.3635572560 H -0.7439678812 1.1959660877 -1.4902927828 H -0.3358807825 -0.9877830167 -0.3462227052 H -0.3864165134 -0.1798846428 1.2276025489 H -2.6736173859 -0.2443523661 -0.8100739464 H -2.7320444638 0.5617590728 0.7636889629 H -2.2916595664 -2.4376602013 0.3254447428 H -2.3468119479 -1.6328085660 1.9005115271 H -4.6462444652 -1.7222330553 -0.1238116543 H -4.7019471101 -0.9161880419 1.4520715443 H -4.5336535981 -2.6770264334 1.3634989034 H 1.4513187962 2.2023624136 -1.0251106476 H 1.6566840656 1.7355824043 1.4675685922 H 3.3848767268 0.0450999542 1.8255347799 H 4.5370334805 -2.4431666072 -0.7153282093 H 5.2531081374 -1.2852080866 0.4233120913 H 4.0233983384 -2.4176524126 0.9832343894 H 2.9447355481 -1.4236166349 -2.1859169701 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 GFN1-xTB transition-state search from the highest scan-energy geometry, with calculated initial Hessian and final normal modes. ```ams GeometryOptimization InitialHessian Type Calculate End End Properties NormalModes yes End Task TransitionStateSearch TransitionStateSearch ReactionCoordinate Distance 15 1 1.0 End End System Atoms C -0.2316361456 2.2807559308 -1.8136617243 C -0.8062612953 1.7962127505 -0.6720971478 C -0.2476286605 0.5848606872 -0.0655132351 C -1.1099093178 0.0011651211 1.0537746448 C -2.4664420638 -0.4512211188 0.4993192587 C -3.3468024410 -1.0411145964 1.6050450534 C -4.6987018997 -1.4955174275 1.0569713563 C 1.2253041465 1.0449807669 0.5534669286 C 1.8602850707 -0.0932119963 1.2364711661 C 2.8173403506 -0.8364210099 0.6439142663 C 3.3495585122 -0.4793093645 -0.6383245763 C 4.4087265074 -1.3575073499 -1.2396883518 C 2.9163345891 0.6536650062 -1.2596842803 C 1.9522482407 1.5273339028 -0.6590874280 O 1.5526154261 2.5693553880 -1.2278659562 H -0.4929889574 3.2691829894 -2.1701340678 H 0.1202716719 1.6052348215 -2.5835685232 H -1.2952987071 2.4927581086 0.0038486361 H -0.0165980772 -0.1890842204 -0.8056381492 H -0.6069241543 -0.8594886862 1.5042741873 H -1.2641485972 0.7520512383 1.8357332091 H -2.3067775443 -1.2028827579 -0.2816042846 H -2.9759075223 0.4024920705 0.0403466936 H -2.8345249453 -1.8941520050 2.0632058006 H -3.5048270930 -0.2883756821 2.3848834899 H -4.5632298755 -2.2615722115 0.2920855003 H -5.2335913464 -0.6542588237 0.6138978311 H -5.3082418828 -1.9105357725 1.8600806243 H 0.9756127232 1.8514023568 1.2459650093 H 1.5120182939 -0.3389269411 2.2338722957 H 3.2405737404 -1.6948630701 1.1550947815 H 4.7413122793 -0.9696206675 -2.2019627016 H 5.2682634275 -1.4224562927 -0.5697016981 H 4.0207741768 -2.3678486307 -1.3823132687 H 3.3492013700 0.9769174860 -2.2000472489 End End Engine dftb Model GFN1-xTB EndEngine ``` ### Product GFN1-xTB geometry optimization and harmonic normal modes from the 1.5 Å scan endpoint. ```ams Properties NormalModes yes End Task GeometryOptimization System Atoms C 0.2727454588 2.1733276750 -1.0949727072 C -0.4695956457 1.2742361392 -0.1540261068 C -1.1050803480 0.1756719103 -0.5401584839 C -1.8905843685 -0.7033492757 0.3887482533 C -3.3850787001 -0.6737164224 0.0313866413 C -4.1961134004 -1.5791287731 0.9628849611 C -5.6828852851 -1.5498643388 0.6118206344 C 3.6347404396 2.4047543696 0.4997113073 C 4.7159874530 1.6134167929 0.8457288890 C 4.7229710234 0.2576382213 0.5459763762 C 3.6364681225 -0.3139508997 -0.1107070676 C 3.6444542523 -1.7844534637 -0.4364030571 C 2.5468038488 0.4764607905 -0.4637857683 C 2.5403640294 1.8364356512 -0.1580102199 O 1.5320352160 2.6887349682 -0.4636687950 H -0.2977883956 3.0870756354 -1.2888412653 H 0.5183303018 1.6865500278 -2.0448223826 H -0.4668920139 1.5929689500 0.8839305572 H -1.1024816973 -0.1288932529 -1.5843745396 H -1.5245023888 -1.7327522204 0.3050965334 H -1.7543895805 -0.3770701537 1.4249711427 H -3.5166476048 -1.0011852344 -1.0054349599 H -3.7523887280 0.3552197272 0.1064017382 H -3.8241708482 -2.6065881731 0.8866697873 H -4.0604518958 -1.2506900076 1.9989161859 H -5.8410768346 -1.8937321509 -0.4113769329 H -6.0770378574 -0.5365996323 0.7018128823 H -6.2396700042 -2.2003106131 1.2868003253 H 3.6183660932 3.4629726241 0.7296482927 H 5.5634886637 2.0571999453 1.3567825361 H 5.5730897941 -0.3557799202 0.8227697574 H 2.7198414984 -2.0824863798 -0.9307355173 H 4.4829563934 -2.0209507218 -1.0941816440 H 3.7575440930 -2.3730567026 0.4758730382 H 1.7066489154 0.0218949082 -0.9730723006 End End Engine dftb Model GFN1-xTB EndEngine ```