├── .gitignore ├── AaronDriver.pm ├── AaronInit.pm ├── AaronOutput.pm ├── Constants.pm ├── G09Job.pm ├── G_Key.pm ├── LICENSE ├── README.md ├── TS_geoms ├── Allylation │ ├── NN-dioxide │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── NN-dioxide_example │ │ ├── R │ │ │ └── ts2.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ └── ts3.xyz │ │ ├── Structures │ │ └── readme │ └── Templates ├── Dearomatization │ ├── Templates │ └── thiourea │ │ ├── R │ │ ├── TS1 │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── TS2 │ │ │ └── ts1.xyz │ │ ├── int2 │ │ │ ├── min1.xyz │ │ │ ├── min2.xyz │ │ │ ├── min3.xyz │ │ │ ├── min4.xyz │ │ │ └── min5.xyz │ │ └── int3 │ │ │ ├── min1.xyz │ │ │ ├── min2.xyz │ │ │ ├── min3.xyz │ │ │ ├── min4.xyz │ │ │ └── min5.xyz │ │ ├── S │ │ ├── TS1 │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── TS2 │ │ │ ├── ts1.xyz │ │ │ └── ts2.xyz │ │ ├── int2 │ │ │ ├── min1.xyz │ │ │ ├── min2.xyz │ │ │ ├── min3.xyz │ │ │ ├── min4.xyz │ │ │ └── min5.xyz │ │ └── int3 │ │ │ ├── min1.xyz │ │ │ ├── min2.xyz │ │ │ ├── min3.xyz │ │ │ ├── min4.xyz │ │ │ └── min5.xyz │ │ ├── Structures │ │ └── readme ├── Enamide_Hydrogenation │ ├── BIBOP │ │ ├── Structures │ │ ├── TS1 │ │ │ ├── R │ │ │ │ ├── tsa1.xyz │ │ │ │ └── tsb1.xyz │ │ │ └── S │ │ │ │ ├── tsa1.xyz │ │ │ │ └── tsb1.xyz │ │ ├── TS2 │ │ │ ├── R │ │ │ │ ├── tsa1.xyz │ │ │ │ ├── tsa2.xyz │ │ │ │ ├── tsb1.xyz │ │ │ │ └── tsb2.xyz │ │ │ └── S │ │ │ │ ├── tsa1.xyz │ │ │ │ ├── tsa2.xyz │ │ │ │ ├── tsb1.xyz │ │ │ │ └── tsb2.xyz │ │ └── readme │ └── Templates ├── Heck_Allenylation │ ├── 2-t-BuPyrOx │ │ ├── R │ │ │ ├── ts1 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ ├── ts2 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ ├── ts3 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ └── ts4 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ ├── S │ │ │ ├── ts1 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ ├── ts2 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ ├── ts3 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ │ └── ts4 │ │ │ │ ├── Cf1.xyz │ │ │ │ └── Cf2.xyz │ │ ├── Structures │ │ └── readme │ └── Templates ├── Indole_CH_functionalization │ ├── CH3 │ │ ├── Structures │ │ ├── readme │ │ ├── ts2.xyz │ │ └── ts3.xyz │ ├── Ph │ │ ├── Structures │ │ ├── readme │ │ ├── ts2.xyz │ │ └── ts3.xyz │ └── Templates ├── Propargylation │ ├── 2a │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── 3a │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── 4a │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── 5a │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── 6a │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ ├── NN-dioxide │ │ ├── R │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── S │ │ │ ├── ts1.xyz │ │ │ ├── ts2.xyz │ │ │ ├── ts3.xyz │ │ │ ├── ts4.xyz │ │ │ └── ts5.xyz │ │ ├── Structures │ │ └── readme │ └── Templates ├── Reactions └── Vinyl_boronic_acid_addition │ ├── BINOL │ ├── R │ │ ├── ts1.xyz │ │ ├── ts2.xyz │ │ ├── ts3.xyz │ │ └── ts4.xyz │ ├── S │ │ ├── ts1.xyz │ │ ├── ts2.xyz │ │ ├── ts3.xyz │ │ └── ts4.xyz │ ├── Structures │ └── readme │ └── Templates ├── bin ├── Aaron └── print_SI ├── images ├── Allylation_RTS2.png ├── COOH.png ├── Et.png ├── Ir-Indole.JPG ├── Ir-indole.png ├── Mes.png ├── Ph.png ├── Ph_full_numbering.png ├── isoquinoline.JPG ├── isoquinoline.png ├── libadd_substitute-example.png ├── make_conf.gif ├── methane-1-{34-OMe-Ph}Me.png ├── readme.md ├── substitute_tutorial │ ├── example.png │ ├── methane.png │ ├── methanol.png │ ├── no-m.png │ ├── tBuOH.png │ └── with-m.png ├── ts1.png ├── ts2.png └── ts3.png ├── pod_ref └── test ├── environment_setup └── environment_setup.t ├── job_setup ├── job_setup.t └── test.com └── test_full_install.t /.gitignore: -------------------------------------------------------------------------------- 1 | .aaronrc 2 | template.job 3 | test/job_setup/test.* 4 | -------------------------------------------------------------------------------- /Constants.pm: -------------------------------------------------------------------------------- 1 | package Aaron::Constants; 2 | 3 | use strict; 4 | use Cwd qw(cwd); 5 | use base 'Exporter'; 6 | 7 | our @EXPORT = (); 8 | our @EXPORT_OK = ('INFO', 'MAXSTEP', 'OTHERS'); 9 | #Code Information 10 | use constant INFO => { 11 | VERSION => 1.0, 12 | YEAR => 2018, 13 | LASTUPDATE => '7/11/18', 14 | AUTHORS => ["Yanfei Guan", "Victoria M. Ingman", "Benjamin J. Rooks", "Steven E. Wheeler"], 15 | CONTRIBUTORS => ["Tony Schaefer"], 16 | }; 17 | 18 | use constant MAXSTEP => { 19 | TS => 5, 20 | INT => 4, 21 | TS_SINGLE => 3, 22 | }; 23 | 24 | use constant OTHERS => { 25 | MAX_LAUNCH_FAILED => 5, 26 | MAX_CYCLE => 4, 27 | SLEEP_TIME => 300, 28 | TS_LIB=>'TS_geoms', 29 | }; 30 | 31 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Aaron 2 | AARON 1.0, An Automated Reaction Optimizer for New catalysts 3 | 4 | We are currently merging several development branches of AARON and AaronTools, to be released soon as along with accompanying documentation. 5 | 6 | Installation instructions and basic tutorials are available here. 7 | 8 | AARON is a computational toolkit to automate the QM-based geometry optimization of transition state and intermediate structures for homogeneous catalytic reactions. It is built using AaronTools. 9 | 10 | AARON does not implement new electronic structure methods or geometry optimization algorithms. Instead, it is essentially an interface to Gaussian (G09 or G16) that automates computations. Briefly, given a set of TS and intermediate geometries for a given catalytic reaction, AARON can automatically compute analogous structures for similar catalysts/ligands and substrates. In this way, users can screen potential catalysts and substrates for a given reaction by predicting the activity and selectivity of a given catalyst/substrate combination. 11 | 12 | ## TS Library 13 | Information about the TS library packaged with AARON is available here. 14 | 15 | ## Citation 16 | If you use AARON, please cite the following papers: 17 | 18 | 1. "AARON: An Automated Reaction Optimizer for New Catalysts", J. Chem. Theory Comput. 14, 5249 (2018) 19 | 20 | 2. "QChASM: Quantum Chemistry Automation and Structure Manipulation" WIREs Comp. Mol. Sci. (in press, 2021) 21 | 22 | ## Contact 23 | If you have any questions, feel free to contact us at qchasm@uga.edu 24 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.041866 -1.759728 0.179377 4 | C -0.571446 -2.685376 -0.534815 5 | C -0.544788 -4.062042 0.015877 6 | H -0.471208 -2.615228 -1.620129 7 | C -0.349727 -4.302713 1.385457 8 | C -0.720936 -5.140348 -0.865417 9 | C -0.322356 -5.612604 1.861953 10 | H -0.216213 -3.463399 2.060809 11 | C -0.691649 -6.449708 -0.384643 12 | H -0.873408 -4.947174 -1.924633 13 | C -0.494182 -6.687781 0.980210 14 | H -0.166653 -5.798722 2.921116 15 | H -0.820098 -7.281715 -1.071315 16 | H -0.472553 -7.707084 1.356113 17 | C -2.551092 -2.342063 -0.401614 18 | C -2.504937 -1.053656 -0.921173 19 | H -2.944932 -3.146733 -1.015094 20 | H -2.637569 -2.469833 0.674941 21 | C -2.082418 0.075313 -0.152647 22 | H -2.400160 0.047480 0.889484 23 | Cl -0.098971 0.206239 2.279482 24 | Cl 0.209913 -0.082128 -2.291962 25 | H -2.595561 -0.937199 -1.998953 26 | H -2.266004 1.037394 -0.630561 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.232600 -0.004245 -1.779187 4 | C -0.416322 -0.658900 -2.711947 5 | C 0.146040 -0.587109 -4.078725 6 | H -1.505932 -0.674547 -2.647877 7 | C 1.472917 -0.184856 -4.305256 8 | C -0.683469 -0.903899 -5.166791 9 | C 1.958157 -0.096803 -5.609002 10 | H 2.106126 0.064250 -3.459762 11 | C -0.193701 -0.814227 -6.469524 12 | H -1.710535 -1.212957 -4.987136 13 | C 1.128608 -0.412748 -6.692842 14 | H 2.983083 0.219170 -5.783766 15 | H -0.840368 -1.053915 -7.308826 16 | H 1.510995 -0.343479 -7.707537 17 | C -0.109026 -2.662310 -2.344277 18 | C -0.647435 -2.606075 -1.069262 19 | H -0.681931 -3.109048 -3.150752 20 | H 0.971338 -2.644469 -2.467517 21 | C 0.059516 -2.080067 0.059595 22 | H 1.130364 -2.289782 0.054876 23 | Cl -2.234822 0.141722 -0.142501 24 | Cl -0.026570 0.145276 2.252676 25 | H -1.716248 -2.781131 -0.961488 26 | H -0.412965 -2.304403 1.015041 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.232244 -0.034975 -1.781210 4 | C -0.498844 -0.025941 -2.866841 5 | C -0.216079 -1.031286 -3.914796 6 | H -0.783777 0.957375 -3.256507 7 | C 0.471157 -2.221174 -3.624353 8 | C -0.635141 -0.765564 -5.229406 9 | C 0.739400 -3.129829 -4.647090 10 | H 0.786362 -2.416997 -2.604931 11 | C -0.363161 -1.676791 -6.248358 12 | H -1.168460 0.157310 -5.446067 13 | C 0.322971 -2.862293 -5.957618 14 | H 1.274113 -4.049177 -4.424826 15 | H -0.682215 -1.465430 -7.265051 16 | H 0.534318 -3.574640 -6.750486 17 | C -2.434975 -0.624409 -2.407625 18 | C -2.551577 0.327070 -1.411738 19 | H -2.890234 -0.453735 -3.377651 20 | H -2.220827 -1.654748 -2.135599 21 | C -2.064934 0.132252 -0.079688 22 | H -2.304856 -0.849258 0.333309 23 | Cl -0.138442 0.180781 2.260133 24 | Cl 0.039977 -2.257115 0.098255 25 | H -2.862432 1.329891 -1.706295 26 | H -2.312591 0.944956 0.601467 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O -0.088229 -1.773756 0.109715 4 | C 0.790295 -2.668740 -0.286099 5 | C 0.402932 -4.091421 -0.154209 6 | H 1.844058 -2.454858 -0.095061 7 | C -0.941241 -4.482837 -0.044495 8 | C 1.417647 -5.061612 -0.132368 9 | C -1.260521 -5.832800 0.093778 10 | H -1.720565 -3.727371 -0.058910 11 | C 1.093715 -6.411201 0.007011 12 | H 2.456919 -4.752616 -0.218424 13 | C -0.246483 -6.799207 0.118278 14 | H -2.300295 -6.134328 0.185502 15 | H 1.882431 -7.157955 0.031483 16 | H -0.500278 -7.850152 0.226705 17 | C 0.862164 -2.557693 -2.326867 18 | C 1.168332 -1.204685 -2.381205 19 | H 1.626282 -3.290934 -2.566462 20 | H -0.168437 -2.867732 -2.480829 21 | C 0.202643 -0.188187 -2.108210 22 | H -0.811588 -0.445397 -2.409853 23 | Cl -0.077964 0.144872 2.235149 24 | Cl -2.209705 0.235571 -0.180965 25 | H 2.217043 -0.917945 -2.433695 26 | H 0.503873 0.796147 -2.462362 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O -1.742315 0.258667 -0.178123 4 | C -2.622466 -0.491954 -0.812171 5 | C -4.002666 0.044753 -0.904183 6 | H -2.553662 -1.570816 -0.655467 7 | C -4.271496 1.415643 -0.765334 8 | C -5.055609 -0.853582 -1.137770 9 | C -5.584132 1.877663 -0.852907 10 | H -3.452985 2.103908 -0.578441 11 | C -6.367584 -0.387429 -1.224613 12 | H -4.841528 -1.914466 -1.243932 13 | C -6.633865 0.979397 -1.084822 14 | H -5.792425 2.937868 -0.737463 15 | H -7.180363 -1.087335 -1.397240 16 | H -7.655412 1.343534 -1.152214 17 | C -2.148675 -0.433104 -2.766385 18 | C -0.859681 -0.925356 -2.603070 19 | H -2.911984 -1.070628 -3.201940 20 | H -2.286030 0.638146 -2.896530 21 | C 0.210743 -0.127382 -2.100098 22 | H 0.171682 0.903393 -2.450006 23 | Cl -0.187325 0.240321 2.214751 24 | Cl -0.012044 -2.242587 0.181935 25 | H -0.712874 -2.001628 -2.658452 26 | H 1.195918 -0.577145 -2.222419 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.039000 -1.767861 0.038359 4 | C -0.688023 -2.602390 0.758649 5 | C -0.610224 -4.034013 0.377927 6 | H -0.737866 -2.410514 1.833121 7 | C -0.233425 -4.431733 -0.914795 8 | C -0.925843 -5.002611 1.343754 9 | C -0.165842 -5.788064 -1.230546 10 | H 0.008158 -3.675811 -1.655551 11 | C -0.855817 -6.358822 1.023929 12 | H -1.219688 -4.688206 2.342540 13 | C -0.477649 -6.753672 -0.264379 14 | H 0.130553 -6.095501 -2.229679 15 | H -1.093416 -7.105545 1.776450 16 | H -0.424415 -7.809676 -0.514889 17 | C -2.619502 -2.274624 0.306829 18 | C -2.625080 -0.937354 0.686746 19 | H -3.110741 -3.006742 0.940632 20 | H -2.556731 -2.519511 -0.750859 21 | C -2.077230 0.102125 -0.127273 22 | H -2.247875 -0.030582 -1.195673 23 | Cl -0.092409 0.199918 2.288872 24 | Cl 0.210585 -0.094075 -2.283235 25 | H -2.861934 -0.705717 1.723164 26 | H -2.302510 1.108790 0.225390 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.056842 -0.002939 -1.805016 4 | C 0.934990 -0.545673 -2.613587 5 | C 0.630237 -0.506209 -4.058141 6 | H 1.991295 -0.449672 -2.354601 7 | C -0.677461 -0.303433 -4.530209 8 | C 1.689064 -0.646772 -4.970159 9 | C -0.916119 -0.236475 -5.901732 10 | H -1.490225 -0.193514 -3.819144 11 | C 1.445646 -0.577231 -6.341544 12 | H 2.699625 -0.803328 -4.599816 13 | C 0.142354 -0.373898 -6.809734 14 | H -1.926995 -0.076667 -6.266405 15 | H 2.268126 -0.680440 -7.043684 16 | H -0.048718 -0.321811 -7.878049 17 | C 0.798864 -2.599650 -2.313388 18 | C 1.046880 -2.527570 -0.953164 19 | H 1.569964 -2.964434 -2.984528 20 | H -0.227603 -2.680143 -2.662058 21 | C 0.070170 -2.083400 -0.003132 22 | H -0.956296 -2.342641 -0.265881 23 | Cl -2.228254 0.143992 -0.114536 24 | Cl -0.014337 0.132973 2.251388 25 | H 2.077370 -2.626776 -0.616056 26 | H 0.316392 -2.323105 1.030578 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.205872 0.016851 -1.787569 4 | C -0.363342 -0.778729 -2.668396 5 | C -0.115051 -0.508227 -4.103805 6 | H -0.427000 -1.836342 -2.407359 7 | C 0.473445 0.686053 -4.546360 8 | C -0.459432 -1.498575 -5.039808 9 | C 0.706487 0.890044 -5.906150 10 | H 0.765097 1.435648 -3.822177 11 | C -0.226196 -1.292346 -6.398455 12 | H -0.907600 -2.428305 -4.697478 13 | C 0.353065 -0.094750 -6.835975 14 | H 1.170033 1.814049 -6.241278 15 | H -0.491718 -2.063686 -7.115794 16 | H 0.535240 0.066092 -7.894966 17 | C -2.362447 -0.359166 -2.610676 18 | C -2.503760 -0.688427 -1.270562 19 | H -2.749566 -1.032646 -3.368488 20 | H -2.272100 0.686583 -2.894727 21 | C -2.077851 0.159920 -0.201361 22 | H -2.213683 1.226639 -0.386333 23 | Cl -0.157534 0.257219 2.248285 24 | Cl 0.021324 -2.233313 0.173433 25 | H -2.760847 -1.717656 -1.026942 26 | H -2.443780 -0.151493 0.775569 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.093467 -1.768131 0.117716 4 | C -0.656751 -2.669300 -0.484466 5 | C -0.270429 -4.088408 -0.291792 6 | H -1.731810 -2.478658 -0.507397 7 | C 1.033459 -4.456240 0.076544 8 | C -1.245882 -5.078569 -0.487167 9 | C 1.351055 -5.802050 0.255153 10 | H 1.783821 -3.685925 0.225721 11 | C -0.924395 -6.424156 -0.307149 12 | H -2.254259 -4.788654 -0.772966 13 | C 0.375159 -6.788652 0.062598 14 | H 2.359226 -6.084873 0.545639 15 | H -1.685048 -7.186207 -0.452094 16 | H 0.626837 -7.836425 0.202211 17 | C -0.279437 -2.527328 -2.462049 18 | C -0.635825 -1.188988 -2.564657 19 | H -0.940018 -3.285933 -2.871070 20 | H 0.774742 -2.787902 -2.405056 21 | C 0.198418 -0.125813 -2.105213 22 | H 1.264867 -0.297056 -2.256263 23 | Cl -0.095011 0.144077 2.232543 24 | Cl -2.230330 0.205439 -0.168376 25 | H -1.669803 -0.955600 -2.808640 26 | H -0.133172 0.848121 -2.461929 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O -1.761697 0.093906 -0.147927 4 | C -2.508255 0.872254 -0.898075 5 | C -3.966830 0.616851 -0.888129 6 | H -2.222830 1.924249 -0.958224 7 | C -4.493100 -0.622854 -0.490326 8 | C -4.831248 1.650413 -1.283190 9 | C -5.873189 -0.818182 -0.481954 10 | H -3.818946 -1.416014 -0.182916 11 | C -6.211448 1.450239 -1.272729 12 | H -4.418560 2.608575 -1.590970 13 | C -6.734665 0.214847 -0.873882 14 | H -6.280142 -1.775173 -0.167388 15 | H -6.877630 2.254749 -1.571274 16 | H -7.809770 0.057755 -0.865266 17 | C -2.130235 0.310106 -2.822240 18 | C -0.790161 0.665633 -2.783944 19 | H -2.826768 0.918293 -3.390653 20 | H -2.407619 -0.730262 -2.672408 21 | C 0.214359 -0.098425 -2.117945 22 | H 0.101158 -1.174252 -2.249856 23 | Cl -0.197736 0.236739 2.222278 24 | Cl -0.010225 -2.238430 0.177168 25 | H -0.530629 1.658966 -3.143962 26 | H 1.230995 0.239973 -2.317236 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide/readme: -------------------------------------------------------------------------------- 1 | TS structures for the allylation of benzaldehyde catalyzed by 2,2'-bipyriding-N,N'-dioxide 2 | 3 | see B. J. Rooks, M. R. Haas, D. Sepulveda, T. Lu, and S. E. Wheeler, "Prospects for the Computational Design of Bipyridine N,N′-Dioxide Catalysts for Asymmetric Propargylations", ACS Catal. 5, 272 (2015) and references cited therein. 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.232600 -0.004245 -1.779187 4 | C -0.416322 -0.658900 -2.711947 5 | C 0.146040 -0.587109 -4.078725 6 | H -1.505932 -0.674547 -2.647877 7 | C 1.472917 -0.184856 -4.305256 8 | C -0.683469 -0.903899 -5.166791 9 | C 1.958157 -0.096803 -5.609002 10 | H 2.106126 0.064250 -3.459762 11 | C -0.193701 -0.814227 -6.469524 12 | H -1.710535 -1.212957 -4.987136 13 | C 1.128608 -0.412748 -6.692842 14 | H 2.983083 0.219170 -5.783766 15 | H -0.840368 -1.053915 -7.308826 16 | H 1.510995 -0.343479 -7.707537 17 | C -0.109026 -2.662310 -2.344277 18 | C -0.647435 -2.606075 -1.069262 19 | H -0.681931 -3.109048 -3.150752 20 | H 0.971338 -2.644469 -2.467517 21 | C 0.059516 -2.080067 0.059595 22 | H 1.130364 -2.289782 0.054876 23 | Cl -2.234822 0.141722 -0.142501 24 | Cl -0.026570 0.145276 2.252676 25 | H -1.716248 -2.781131 -0.961488 26 | H -0.412965 -2.304403 1.015041 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.039000 -1.767861 0.038359 4 | C -0.688023 -2.602390 0.758649 5 | C -0.610224 -4.034013 0.377927 6 | H -0.737866 -2.410514 1.833121 7 | C -0.233425 -4.431733 -0.914795 8 | C -0.925843 -5.002611 1.343754 9 | C -0.165842 -5.788064 -1.230546 10 | H 0.008158 -3.675811 -1.655551 11 | C -0.855817 -6.358822 1.023929 12 | H -1.219688 -4.688206 2.342540 13 | C -0.477649 -6.753672 -0.264379 14 | H 0.130553 -6.095501 -2.229679 15 | H -1.093416 -7.105545 1.776450 16 | H -0.424415 -7.809676 -0.514889 17 | C -2.619502 -2.274624 0.306829 18 | C -2.625080 -0.937354 0.686746 19 | H -3.110741 -3.006742 0.940632 20 | H -2.556731 -2.519511 -0.750859 21 | C -2.077230 0.102125 -0.127273 22 | H -2.247875 -0.030582 -1.195673 23 | Cl -0.092409 0.199918 2.288872 24 | Cl 0.210585 -0.094075 -2.283235 25 | H -2.861934 -0.705717 1.723164 26 | H -2.302510 1.108790 0.225390 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.056842 -0.002939 -1.805016 4 | C 0.934990 -0.545673 -2.613587 5 | C 0.630237 -0.506209 -4.058141 6 | H 1.991295 -0.449672 -2.354601 7 | C -0.677461 -0.303433 -4.530209 8 | C 1.689064 -0.646772 -4.970159 9 | C -0.916119 -0.236475 -5.901732 10 | H -1.490225 -0.193514 -3.819144 11 | C 1.445646 -0.577231 -6.341544 12 | H 2.699625 -0.803328 -4.599816 13 | C 0.142354 -0.373898 -6.809734 14 | H -1.926995 -0.076667 -6.266405 15 | H 2.268126 -0.680440 -7.043684 16 | H -0.048718 -0.321811 -7.878049 17 | C 0.798864 -2.599650 -2.313388 18 | C 1.046880 -2.527570 -0.953164 19 | H 1.569964 -2.964434 -2.984528 20 | H -0.227603 -2.680143 -2.662058 21 | C 0.070170 -2.083400 -0.003132 22 | H -0.956296 -2.342641 -0.265881 23 | Cl -2.228254 0.143992 -0.114536 24 | Cl -0.014337 0.132973 2.251388 25 | H 2.077370 -2.626776 -0.616056 26 | H 0.316392 -2.323105 1.030578 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 47 2 | F:19-25;2-15 C:25 L:26-47 K:1,2 3 | O 0.205872 0.016851 -1.787569 4 | C -0.363342 -0.778729 -2.668396 5 | C -0.115051 -0.508227 -4.103805 6 | H -0.427000 -1.836342 -2.407359 7 | C 0.473445 0.686053 -4.546360 8 | C -0.459432 -1.498575 -5.039808 9 | C 0.706487 0.890044 -5.906150 10 | H 0.765097 1.435648 -3.822177 11 | C -0.226196 -1.292346 -6.398455 12 | H -0.907600 -2.428305 -4.697478 13 | C 0.353065 -0.094750 -6.835975 14 | H 1.170033 1.814049 -6.241278 15 | H -0.491718 -2.063686 -7.115794 16 | H 0.535240 0.066092 -7.894966 17 | C -2.362447 -0.359166 -2.610676 18 | C -2.503760 -0.688427 -1.270562 19 | H -2.749566 -1.032646 -3.368488 20 | H -2.272100 0.686583 -2.894727 21 | C -2.077851 0.159920 -0.201361 22 | H -2.213683 1.226639 -0.386333 23 | Cl -0.157534 0.257219 2.248285 24 | Cl 0.021324 -2.233313 0.173433 25 | H -2.760847 -1.717656 -1.026942 26 | H -2.443780 -0.151493 0.775569 27 | Si 0.000000 0.000000 0.000000 28 | O 1.875060 -0.000000 -0.000000 29 | O 0.127042 1.935326 0.000000 30 | C 2.817969 2.049798 0.619379 31 | C 2.271038 2.663665 -0.601204 32 | C 0.367843 3.179714 -1.933160 33 | C 3.066888 0.109858 1.979324 34 | C 3.874707 0.803808 2.865352 35 | C 3.631307 2.766862 1.493847 36 | C 4.162917 2.147586 2.624105 37 | C 3.072210 3.414061 -1.459448 38 | C 2.514881 4.053656 -2.564657 39 | C 1.143652 3.935594 -2.796220 40 | H 3.821661 3.812340 1.282298 41 | H 4.789455 2.709846 3.307733 42 | H 4.133194 3.477679 -1.248968 43 | H 3.141878 4.634085 -3.232229 44 | H 0.664677 4.416615 -3.641100 45 | H -0.699165 3.036219 -2.031467 46 | N 2.569844 0.733328 0.886082 47 | N 0.930979 2.567290 -0.863705 48 | H 2.795357 -0.932383 2.073428 49 | H 4.265805 0.283692 3.731801 50 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/Structures: -------------------------------------------------------------------------------- 1 | R/ts2.xyz 2 | S/ts1.xyz 3 | S/ts2.xyz 4 | S/ts3.xyz 5 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/NN-dioxide_example/readme: -------------------------------------------------------------------------------- 1 | This is an abridged set of TS structures for the allylation of benzaldehyde catalyzed by 2,2'-bipyriding-N,N'-dioxide for example purposes only! 2 | 3 | see B. J. Rooks, M. R. Haas, D. Sepulveda, T. Lu, and S. E. Wheeler, "Prospects for the Computational Design of Bipyridine N,N′-Dioxide Catalysts for Asymmetric Propargylations", ACS Catal. 5, 272 (2015) and references cited therein. 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Allylation/Templates: -------------------------------------------------------------------------------- 1 | NN-dioxide 2 | NN-dioxide_example 3 | -------------------------------------------------------------------------------- /TS_geoms/Dearomatization/Templates: -------------------------------------------------------------------------------- 1 | thiourea 2 | -------------------------------------------------------------------------------- /TS_geoms/Dearomatization/thiourea/Structures: -------------------------------------------------------------------------------- 1 | R/int2/min1.xyz 2 | R/int2/min2.xyz 3 | R/int2/min3.xyz 4 | R/int2/min4.xyz 5 | R/int2/min5.xyz 6 | R/int3/min1.xyz 7 | R/int3/min2.xyz 8 | R/int3/min3.xyz 9 | R/int3/min4.xyz 10 | R/int3/min5.xyz 11 | R/TS1/ts1.xyz 12 | R/TS1/ts2.xyz 13 | R/TS1/ts3.xyz 14 | R/TS1/ts4.xyz 15 | R/TS1/ts5.xyz 16 | R/TS2/ts1.xyz 17 | S/int2/min1.xyz 18 | S/int2/min2.xyz 19 | S/int2/min3.xyz 20 | S/int2/min4.xyz 21 | S/int2/min5.xyz 22 | S/int3/min1.xyz 23 | S/int3/min2.xyz 24 | S/int3/min3.xyz 25 | S/int3/min4.xyz 26 | S/int3/min5.xyz 27 | S/TS1/ts1.xyz 28 | S/TS1/ts2.xyz 29 | S/TS1/ts3.xyz 30 | S/TS1/ts4.xyz 31 | S/TS1/ts5.xyz 32 | S/TS2/ts1.xyz 33 | S/TS2/ts2.xyz 34 | -------------------------------------------------------------------------------- /TS_geoms/Dearomatization/thiourea/readme: -------------------------------------------------------------------------------- 1 | TS structures for the dearomatization of beta-naphthols catalyzed by Nakajima's bifunctional thiourea catalyst 2 | 3 | Included are TS structures for the two key steps (TS2 and TS3) and the surrounding energy minima (int 2 and int3). 4 | 5 | See https://doi.org/10.1002/anie.201507998 for experimental data 6 | -------------------------------------------------------------------------------- /TS_geoms/Enamide_Hydrogenation/BIBOP/Structures: -------------------------------------------------------------------------------- 1 | TS1/R/tsa1.xyz 2 | TS1/R/tsb1.xyz 3 | TS1/S/tsa1.xyz 4 | TS1/S/tsb1.xyz 5 | TS2/R/tsa1.xyz 6 | TS2/R/tsa2.xyz 7 | TS2/R/tsb1.xyz 8 | TS2/R/tsb2.xyz 9 | TS2/S/tsa1.xyz 10 | TS2/S/tsa2.xyz 11 | TS2/S/tsb1.xyz 12 | TS2/S/tsb2.xyz 13 | -------------------------------------------------------------------------------- /TS_geoms/Enamide_Hydrogenation/BIBOP/readme: -------------------------------------------------------------------------------- 1 | Rh-catalyzed asymmetric hydrogenation of β-aryl-N-acetyl enamides using BIBOP ligand. 2 | 3 | Geometries from Y. Guan and S. E. Wheeler, "Automated Quantum Mechanical Predictions of Enantioselectivity in a Rh-Catalyzed Asymmetric Hydrogenation", Angew. Chem. Int. Ed. 56, 9101 (2017). 4 | 5 | TS structures are for the two H-transfer steps, and are named as in Scheme 2 from the reference above, with 'a' replacing α and 'b' replacing β. 6 | For example, TS1β1 from Scheme 2 is TS1/tsb1.xyz below. 7 | TS1β2 and TS1α2 are omitted from the library because they tend to be very high in energy. 8 | 9 | For experiments, see G. Liu, X. Liu, Z. Cai, G. Jiao, G. Xu, W. Tang, Angew. Chem. Int. Ed. 2013, 52, 4235-4238. 10 | 11 | Note: Assumes C2-symmetric ligand! 12 | -------------------------------------------------------------------------------- /TS_geoms/Enamide_Hydrogenation/Templates: -------------------------------------------------------------------------------- 1 | BIBOP 2 | -------------------------------------------------------------------------------- /TS_geoms/Heck_Allenylation/2-t-BuPyrOx/Structures: -------------------------------------------------------------------------------- 1 | R/ts1/Cf1.xyz 2 | R/ts1/Cf2.xyz 3 | R/ts2/Cf1.xyz 4 | R/ts2/Cf2.xyz 5 | R/ts3/Cf1.xyz 6 | R/ts3/Cf2.xyz 7 | R/ts4/Cf1.xyz 8 | R/ts4/Cf2.xyz 9 | S/ts1/Cf1.xyz 10 | S/ts1/Cf2.xyz 11 | S/ts2/Cf1.xyz 12 | S/ts2/Cf2.xyz 13 | S/ts3/Cf1.xyz 14 | S/ts3/Cf2.xyz 15 | S/ts4/Cf1.xyz 16 | S/ts4/Cf2.xyz 17 | -------------------------------------------------------------------------------- /TS_geoms/Heck_Allenylation/2-t-BuPyrOx/readme: -------------------------------------------------------------------------------- 1 | Enantioselective Pd catalyzed addition of 2-methylbut-2-ene to 2-methylcyclohex-2-en-1-one using the chiral ligand ligand 2-t-Bu-PyrOx. 2 | 3 | TS structures computed at the M06/6-31+G(d)/LANDL2DZ level of theory by Wiest et al., as well as additional conformations arising from ring puckering. 4 | 5 | See Zhang, C.; Tutkowski, B.; DeLuca, R. J.; Joyce, L. A.; Wiest, O.; Sigman, M. S., Palladium-Catalyzed Enantioselective Heck Alkenylation of Trisubstituted Allylic Alkenols: A Redox-Relay Strategy to Construct Vicinal Stereocenters. Chem. Sci. 2017, 8, 2277-2282. 6 | -------------------------------------------------------------------------------- /TS_geoms/Heck_Allenylation/Templates: -------------------------------------------------------------------------------- 1 | 2-t-BuPyrOx 2 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/CH3/Structures: -------------------------------------------------------------------------------- 1 | ts2.xyz 2 | ts3.xyz 3 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/CH3/readme: -------------------------------------------------------------------------------- 1 | See 10.1021/acscentsci.8b00264 2 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/CH3/ts2.xyz: -------------------------------------------------------------------------------- 1 | 54 2 | F:2-9;2-22;9-29; 3 | C 3.286806 1.022601 0.109372 4 | H 0.211469 1.485828 -0.605153 5 | C 3.277106 0.911847 -1.302638 6 | C 4.473889 1.013699 -2.024457 7 | C 5.651186 1.209329 -1.327311 8 | C 5.645508 1.303022 0.072414 9 | H 4.509428 1.291071 1.893830 10 | C 4.474159 1.209846 0.813103 11 | C 1.100787 0.680752 -0.605758 12 | C 1.926459 0.715983 -1.710628 13 | H 4.468579 0.940090 -3.108949 14 | H 6.592335 1.292853 -1.863030 15 | H 6.584749 1.457359 0.596903 16 | H 1.575084 0.679506 -2.736728 17 | N 1.962755 0.877609 0.537237 18 | C 1.388948 0.854153 1.774483 19 | O 0.230565 0.411815 1.879920 20 | C 2.127511 1.341764 2.968704 21 | H 2.878168 0.601458 3.272164 22 | H 2.639018 2.287207 2.765507 23 | H 1.419197 1.467610 3.788765 24 | O -0.725916 2.617582 -0.324348 25 | O -2.031649 0.848780 0.118650 26 | C -1.823412 2.111205 -0.027871 27 | C -3.026436 2.981697 0.190338 28 | H -2.805910 4.014020 -0.083451 29 | H -3.871893 2.604924 -0.391517 30 | H -3.314009 2.935987 1.245611 31 | Ir -0.544389 -0.626504 0.051389 32 | C -2.006539 -2.199399 -0.398268 33 | C 0.058841 -2.638450 0.606146 34 | C 0.293284 -2.456968 -0.789558 35 | C -0.979493 -2.122996 -1.417184 36 | C -1.371592 -2.470913 0.856599 37 | C 1.598642 -2.615660 -1.483691 38 | C 1.077376 -2.961052 1.640331 39 | C -2.025208 -2.596182 2.185987 40 | C -3.449419 -1.929005 -0.617245 41 | C -1.209038 -1.916429 -2.872104 42 | H -0.342332 -1.451612 -3.352548 43 | H -2.073760 -1.270666 -3.050844 44 | H -1.395391 -2.874406 -3.373859 45 | H -3.937287 -1.581140 0.297038 46 | H -3.957089 -2.841761 -0.952339 47 | H -3.595405 -1.159256 -1.380904 48 | H -2.996107 -2.093816 2.204395 49 | H -1.407953 -2.150017 2.973053 50 | H -2.183925 -3.651335 2.441629 51 | H 0.836903 -2.484558 2.596505 52 | H 2.075976 -2.630274 1.334802 53 | H 1.123273 -4.043644 1.812244 54 | H 2.433765 -2.277974 -0.860304 55 | H 1.631955 -2.050572 -2.419711 56 | H 1.766518 -3.671916 -1.727227 57 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/CH3/ts3.xyz: -------------------------------------------------------------------------------- 1 | 54 2 | F:7-8;7-22;8-29; 3 | C 1.990176 -1.489337 -0.320332 4 | H 3.378666 -2.905106 2.315399 5 | C 3.252758 -1.837433 -0.824522 6 | C 3.540711 -1.572660 -2.165062 7 | C 2.558334 -0.995072 -2.965697 8 | C 1.304612 -0.683536 -2.439946 9 | H -0.146335 -1.445913 -0.944778 10 | C 0.968739 -0.906807 -1.088382 11 | C 3.190633 -2.508955 1.327664 12 | C 3.990750 -2.470339 0.241964 13 | H 4.508239 -1.840003 -2.583145 14 | H 2.762636 -0.814157 -4.017778 15 | H 0.534719 -0.285035 -3.100014 16 | H 4.999014 -2.859591 0.187389 17 | N 1.950686 -1.898152 1.024562 18 | C 0.927913 -1.673749 1.908903 19 | O -0.022250 -0.926278 1.644902 20 | C 0.997703 -2.343182 3.241761 21 | H 1.182865 -3.417088 3.143118 22 | H 1.808588 -1.913039 3.842344 23 | H 0.053322 -2.179762 3.761628 24 | O -1.306994 -2.222813 -0.850379 25 | O -2.056463 -0.202272 -0.254274 26 | C -2.234639 -1.430792 -0.578501 27 | C -3.658670 -1.895592 -0.618001 28 | H -4.252629 -1.220997 -1.240864 29 | H -3.718881 -2.915095 -1.000325 30 | H -4.078210 -1.855233 0.392148 31 | Ir -0.157813 0.648654 0.056127 32 | C 1.361840 2.200454 -0.192356 33 | C -0.480716 2.450867 1.239021 34 | C -0.934782 2.678472 -0.102437 35 | C 0.183294 2.480992 -1.001209 36 | C 0.945624 2.156938 1.173929 37 | C -2.325101 2.988844 -0.520112 38 | C -1.292831 2.519238 2.482623 39 | C 1.807768 1.865361 2.349822 40 | C 2.750655 2.041819 -0.699364 41 | C 0.165676 2.717167 -2.469786 42 | H -0.762688 2.355897 -2.923996 43 | H 1.002717 2.218269 -2.966694 44 | H 0.244204 3.791186 -2.680887 45 | H 3.371680 1.469109 -0.003247 46 | H 3.217774 3.025531 -0.831407 47 | H 2.773574 1.526145 -1.664638 48 | H 2.664804 1.240237 2.076453 49 | H 1.244762 1.354299 3.138055 50 | H 2.198586 2.797266 2.776912 51 | H -0.999782 1.736558 3.190691 52 | H -2.357496 2.387446 2.270273 53 | H -1.164614 3.488086 2.981328 54 | H -3.056640 2.576365 0.179933 55 | H -2.543540 2.573454 -1.508294 56 | H -2.469727 4.075115 -0.568945 57 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/Ph/Structures: -------------------------------------------------------------------------------- 1 | ts2.xyz 2 | ts3.xyz 3 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/Ph/readme: -------------------------------------------------------------------------------- 1 | See 10.1021/acscentsci.8b00264 2 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/Ph/ts2.xyz: -------------------------------------------------------------------------------- 1 | 61 2 | F:9-36;2-9;2-22; 3 | C 3.304303 1.008751 0.197102 4 | H 0.243253 1.495401 -0.573928 5 | C 3.317273 0.902301 -1.215798 6 | C 4.526783 0.993401 -1.917878 7 | C 5.693923 1.174631 -1.200878 8 | C 5.665823 1.266481 0.198972 9 | H 4.498373 1.265051 2.001892 10 | C 4.481603 1.184491 0.920572 11 | C 1.129043 0.683401 -0.555438 12 | C 1.972653 0.717611 -1.646628 13 | H 4.538363 0.921621 -3.002368 14 | H 6.645033 1.249171 -1.720178 15 | H 6.598273 1.410421 0.738352 16 | H 1.638183 0.685321 -2.678358 17 | N 1.972203 0.872361 0.601512 18 | C 1.375383 0.847611 1.828522 19 | O 0.212513 0.412621 1.910052 20 | C 2.097523 1.324941 3.036852 21 | H 2.847943 0.584831 3.341512 22 | H 2.608653 2.273961 2.848982 23 | H 1.378813 1.441251 3.849122 24 | O -0.720157 2.616731 -0.374248 25 | O -2.017027 0.841611 0.038552 26 | C -1.832157 2.100171 -0.151288 27 | C -3.101078 2.948022 -0.216074 28 | C -3.557696 3.430634 -1.447053 29 | C -3.806504 3.241850 0.955576 30 | C -5.425167 4.500901 -0.334733 31 | C -4.968548 4.018290 0.896246 32 | C -4.719740 4.207073 -1.506383 33 | H -3.009373 3.202243 -2.357771 34 | H -5.074667 4.582205 -2.463217 35 | H -6.328416 5.104423 -0.380850 36 | H -5.516872 4.246680 1.806963 37 | H -3.451578 2.866719 1.912409 38 | Ir -0.526327 -0.625969 0.063712 39 | C -2.018427 -2.198889 -0.282508 40 | C 0.127213 -2.637659 0.544442 41 | C 0.243033 -2.441459 -0.865228 42 | C -1.075597 -2.096349 -1.381228 43 | C -1.280937 -2.486049 0.908832 44 | C 1.491783 -2.593009 -1.656668 45 | C 1.232313 -2.981469 1.479432 46 | C -1.811297 -2.611069 2.291772 47 | C -3.470957 -1.910819 -0.388248 48 | C -1.439947 -1.840539 -2.800578 49 | H -0.590807 -1.449029 -3.369458 50 | H -2.249817 -1.106439 -2.868448 51 | H -1.776647 -2.762269 -3.291618 52 | H 2.367063 -2.231409 -1.105748 53 | H 1.443583 -2.055349 -2.607958 54 | H 1.655853 -3.653209 -1.886448 55 | H 1.014123 -2.639349 2.496462 56 | H 2.175563 -2.521889 1.162272 57 | H 1.386613 -4.066829 1.521672 58 | H -2.828057 -2.217809 2.371212 59 | H -1.186977 -2.056029 3.000572 60 | H -1.826747 -3.661949 2.606262 61 | H -3.927597 -1.774289 0.595572 62 | H -3.986777 -2.733949 -0.897298 63 | H -3.643217 -0.991979 -0.960158 64 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/Ph/ts3.xyz: -------------------------------------------------------------------------------- 1 | 61 2 | F:8-36;7-8;7-22; 3 | C 1.987378 -1.489822 -0.342763 4 | H 3.387278 -2.921952 2.279317 5 | C 3.242998 -1.847902 -0.857603 6 | C 3.526568 -1.576652 -2.197983 7 | C 2.545748 -0.983192 -2.988323 8 | C 1.297468 -0.665632 -2.453063 9 | H -0.162302 -1.410632 -0.969013 10 | C 0.965448 -0.895982 -1.101943 11 | C 3.192558 -2.523302 1.293897 12 | C 3.983718 -2.490022 0.201587 13 | H 4.489498 -1.849832 -2.622803 14 | H 2.745818 -0.794852 -4.039983 15 | H 0.527128 -0.259202 -3.107783 16 | H 4.988118 -2.887852 0.137727 17 | N 1.956678 -1.899012 1.003027 18 | C 0.944588 -1.669662 1.897687 19 | O 0.005588 -0.901352 1.652027 20 | C 1.010948 -2.357562 3.221297 21 | H 1.209208 -3.427732 3.110757 22 | H 1.810538 -1.924792 3.835007 23 | H 0.060158 -2.210792 3.734797 24 | O -1.341172 -2.173292 -0.891543 25 | O -2.043972 -0.185332 -0.160833 26 | C -2.250022 -1.397842 -0.519653 27 | C -3.681642 -1.924787 -0.442181 28 | C -4.589224 -1.637147 -1.467014 29 | C -4.085101 -2.694988 0.653600 30 | C -6.303722 -2.889910 -0.300287 31 | C -5.396141 -3.177550 0.724547 32 | C -5.900264 -2.119709 -1.396067 33 | H -4.275618 -1.038473 -2.318758 34 | H -6.605721 -1.896127 -2.192665 35 | H -7.322786 -3.265003 -0.245140 36 | H -5.709746 -3.776224 1.576291 37 | H -3.379643 -2.918569 1.450197 38 | Ir -0.139292 0.664048 0.059887 39 | C 1.385038 2.215768 -0.166293 40 | C -0.502162 2.475238 1.207147 41 | C -0.915452 2.682948 -0.154003 42 | C 0.231878 2.484128 -1.013743 43 | C 0.926338 2.188868 1.188067 44 | C -2.296372 2.975518 -0.615433 45 | C -1.364852 2.542698 2.416787 46 | C 1.757648 1.892018 2.384337 47 | C 2.789868 2.055968 -0.626983 48 | C 0.261488 2.697508 -2.485373 49 | H -0.664992 2.357258 -2.959083 50 | H 1.095028 2.164808 -2.952783 51 | H 0.378678 3.765298 -2.709533 52 | H -3.044892 2.542078 0.053987 53 | H -2.475622 2.568528 -1.615153 54 | H -2.458142 4.059598 -0.656363 55 | H -1.036222 1.828738 3.179417 56 | H -2.404442 2.302478 2.173477 57 | H -1.343212 3.544708 2.862787 58 | H 2.624538 1.274398 2.123517 59 | H 1.179328 1.366458 3.151397 60 | H 2.132438 2.821138 2.831137 61 | H 3.379398 1.458488 0.075967 62 | H 3.272888 3.036788 -0.717113 63 | H 2.843168 1.565858 -1.604193 64 | -------------------------------------------------------------------------------- /TS_geoms/Indole_CH_functionalization/Templates: -------------------------------------------------------------------------------- 1 | CH3 2 | Ph 3 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.249166 2.042312 0.028781 4 | C -1.199019 3.355268 -0.185011 5 | C -2.505904 3.995306 -0.494775 6 | H -0.363140 3.697155 -0.801288 7 | C -3.719118 3.425215 -0.078085 8 | C -2.509911 5.203162 -1.209062 9 | C -4.923812 4.057174 -0.384804 10 | H -3.706476 2.492519 0.477162 11 | C -3.717493 5.831867 -1.514928 12 | H -1.567588 5.641459 -1.529153 13 | C -4.926329 5.260973 -1.101445 14 | H -5.862813 3.612790 -0.066112 15 | H -3.716516 6.762073 -2.076250 16 | H -5.867177 5.750436 -1.338095 17 | C -0.698133 4.350995 1.401110 18 | C 0.140787 3.406835 1.937640 19 | H -1.632748 4.533827 1.932092 20 | H -0.257011 5.237797 0.946061 21 | C 0.667569 2.266732 2.077299 22 | H 1.335510 1.831392 2.806343 23 | Cl -1.402948 0.067085 2.124653 24 | Cl 1.573285 1.824737 -0.848427 25 | Si 0.029866 0.977130 0.603136 26 | O -0.414142 -0.224332 -0.729891 27 | O 1.268891 -0.284839 1.278174 28 | C 0.317735 -2.402074 -0.242522 29 | C 1.713498 -1.958838 -0.306708 30 | C 3.417270 -0.480255 0.458590 31 | C -1.998965 -1.865473 -0.399942 32 | C -2.381565 -3.195155 -0.206739 33 | C -0.022022 -3.740703 -0.048889 34 | C -1.352027 -4.137896 -0.031368 35 | C 2.664030 -2.631489 -1.073469 36 | C 3.991708 -2.226180 -1.072158 37 | C 4.399756 -1.127301 -0.294436 38 | H 0.776211 -4.458758 0.096812 39 | H -1.594943 -5.184801 0.109857 40 | H 2.339119 -3.472756 -1.673888 41 | H 4.717934 -2.769582 -1.666005 42 | H 3.603981 0.382607 1.081417 43 | N -0.699229 -1.509909 -0.430425 44 | N 2.136432 -0.902749 0.451955 45 | H -2.691645 -1.047175 -0.533767 46 | C 5.794274 -0.649492 -0.261272 47 | C 6.324974 -0.051494 0.897396 48 | C 6.616334 -0.788264 -1.395229 49 | C 7.646405 0.392218 0.920592 50 | H 5.713859 0.040966 1.790560 51 | C 7.935386 -0.337448 -1.370223 52 | H 6.214680 -1.224747 -2.304914 53 | C 8.454936 0.251914 -0.212555 54 | H 8.046860 0.841144 1.825001 55 | H 8.555468 -0.440231 -2.256101 56 | H 9.483771 0.600234 -0.193511 57 | C -3.809606 -3.561970 -0.184879 58 | C -4.753511 -2.837458 -0.937339 59 | C -4.248728 -4.648491 0.595077 60 | C -6.101238 -3.192777 -0.910389 61 | H -4.431459 -2.013069 -1.566660 62 | C -5.598313 -4.996760 0.624311 63 | H -3.538480 -5.203647 1.200648 64 | C -6.528177 -4.271524 -0.128581 65 | H -6.816707 -2.631575 -1.504458 66 | H -5.925129 -5.829701 1.240135 67 | H -7.579232 -4.545351 -0.106086 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.018561 1.318646 0.060963 4 | C -1.998371 2.159191 0.349478 5 | C -3.042586 1.608410 1.252035 6 | H -2.373899 2.755638 -0.486009 7 | C -2.753532 0.574343 2.156831 8 | C -4.349115 2.110675 1.159782 9 | C -3.767235 0.043678 2.951607 10 | H -1.741344 0.188375 2.219214 11 | C -5.362873 1.573005 1.954806 12 | H -4.570850 2.906923 0.453400 13 | C -5.073277 0.540388 2.852200 14 | H -3.544207 -0.762208 3.645495 15 | H -6.376475 1.954191 1.869340 16 | H -5.862857 0.119252 3.468362 17 | C -1.341871 3.696906 1.388475 18 | C -0.094183 3.720818 0.825325 19 | H -1.412938 3.383360 2.430037 20 | H -2.062471 4.457924 1.089599 21 | C 0.887452 3.312635 0.137272 22 | H 1.891514 3.688929 0.002350 23 | Cl -0.639301 2.616400 -2.548764 24 | Cl 2.407786 1.714320 -2.013076 25 | Si 0.454561 1.571579 -0.901417 26 | O 1.311401 0.645715 0.540654 27 | O 0.206845 -0.089179 -1.714935 28 | C 1.653114 -1.622483 0.022642 29 | C 0.205909 -1.806666 -0.127327 30 | C -1.809047 -1.100867 -1.185001 31 | C 3.472449 -0.152572 0.467536 32 | C 4.407123 -1.186570 0.368947 33 | C 2.551373 -2.682362 -0.079629 34 | C 3.913894 -2.474466 0.092616 35 | C -0.511958 -2.781250 0.564113 36 | C -1.886679 -2.891970 0.398454 37 | C -2.573125 -2.031368 -0.478770 38 | H 2.162122 -3.667854 -0.307769 39 | H 4.597107 -3.313063 0.020793 40 | H 0.020999 -3.426316 1.252676 41 | H -2.433823 -3.645878 0.953267 42 | H -2.216611 -0.378758 -1.877895 43 | N 2.151573 -0.381354 0.317433 44 | N -0.477668 -1.013455 -1.001967 45 | H 3.728409 0.878072 0.665212 46 | C -4.038143 -2.051245 -0.637669 47 | C -4.641334 -1.686580 -1.856148 48 | C -4.856122 -2.406522 0.450187 49 | C -6.029582 -1.681647 -1.981472 50 | H -4.025590 -1.429753 -2.713503 51 | C -6.244052 -2.392856 0.323339 52 | H -4.406352 -2.656556 1.405777 53 | C -6.834816 -2.031829 -0.891945 54 | H -6.482755 -1.408542 -2.930067 55 | H -6.864400 -2.652973 1.176187 56 | H -7.916760 -2.021712 -0.989672 57 | C 5.844154 -0.906266 0.548918 58 | C 6.277703 0.128051 1.400058 59 | C 6.805824 -1.675446 -0.132673 60 | C 7.638326 0.382764 1.566363 61 | H 5.552557 0.717094 1.954177 62 | C 8.165453 -1.414002 0.031714 63 | H 6.489176 -2.459996 -0.813424 64 | C 8.586114 -0.386009 0.882334 65 | H 7.958567 1.177074 2.234468 66 | H 8.896121 -2.008009 -0.509745 67 | H 9.645917 -0.184710 1.010756 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O 1.064943 1.266207 0.123237 4 | C 2.362767 1.468784 0.240895 5 | C 3.006407 2.309839 -0.797935 6 | H 2.949783 0.589090 0.524365 7 | C 2.277296 3.274885 -1.511016 8 | C 4.371957 2.119571 -1.064889 9 | C 2.916351 4.039481 -2.486110 10 | H 1.222580 3.410874 -1.292740 11 | C 5.004853 2.883883 -2.044737 12 | H 4.930244 1.367282 -0.511455 13 | C 4.278116 3.847445 -2.754187 14 | H 2.354411 4.786144 -3.040463 15 | H 6.058975 2.728969 -2.256745 16 | H 4.770471 4.445846 -3.515908 17 | C 2.911912 2.467271 1.875940 18 | C 1.831184 2.091881 2.618187 19 | H 2.980480 3.515778 1.586373 20 | H 3.867384 1.972593 2.042559 21 | C 0.661477 1.672389 2.861732 22 | H 0.091977 1.630073 3.779723 23 | Cl -2.241435 0.862613 2.422644 24 | Cl -0.918839 3.297044 0.738155 25 | Si -0.381201 1.161761 1.164815 26 | O -1.218456 0.648967 -0.411998 27 | O -0.071413 -0.687795 1.540917 28 | C -1.627451 -1.657102 -0.508989 29 | C -0.184974 -1.915731 -0.452786 30 | C 1.856277 -1.691679 0.749411 31 | C -3.406880 -0.073021 -0.472786 32 | C -4.374292 -1.070404 -0.622136 33 | C -2.558839 -2.680895 -0.669751 34 | C -3.917165 -2.396551 -0.728560 35 | C 0.470263 -2.714070 -1.389025 36 | C 1.828176 -2.978508 -1.267160 37 | C 2.556439 -2.465209 -0.178381 38 | H -2.200203 -3.701329 -0.734871 39 | H -4.626230 -3.204806 -0.866938 40 | H -0.101007 -3.108118 -2.221167 41 | H 2.323617 -3.596580 -2.007130 42 | H 2.303917 -1.256992 1.632109 43 | N -2.093318 -0.374955 -0.436501 44 | N 0.544502 -1.421744 0.593174 45 | H -3.629593 0.979902 -0.378644 46 | C 4.003371 -2.690454 -0.007727 47 | C 4.577653 -2.774650 1.274578 48 | C 4.833498 -2.805185 -1.138247 49 | C 5.950411 -2.970821 1.420057 50 | H 3.947834 -2.715572 2.157829 51 | C 6.206709 -2.994392 -0.988293 52 | H 4.407614 -2.718002 -2.133462 53 | C 6.768711 -3.078510 0.290162 54 | H 6.380421 -3.046857 2.414550 55 | H 6.838375 -3.069535 -1.868686 56 | H 7.838495 -3.228046 0.405580 57 | C -5.805430 -0.716945 -0.659569 58 | C -6.231850 0.519711 -1.180156 59 | C -6.768318 -1.619330 -0.169771 60 | C -7.587856 0.841816 -1.212733 61 | H -5.506912 1.219890 -1.585083 62 | C -8.122863 -1.290999 -0.198837 63 | H -6.454889 -2.565827 0.260599 64 | C -8.536924 -0.061088 -0.721644 65 | H -7.903772 1.794879 -1.626970 66 | H -8.854299 -1.991728 0.193407 67 | H -9.593000 0.192647 -0.745016 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.193428 2.176972 0.561557 4 | C -1.630980 2.525910 -0.644751 5 | C -2.693383 3.568310 -0.664073 6 | H -1.796490 1.702066 -1.345102 7 | C -2.867902 4.462560 0.403410 8 | C -3.529447 3.649990 -1.788264 9 | C -3.877755 5.422850 0.344577 10 | H -2.219547 4.391616 1.270908 11 | C -4.539195 4.611453 -1.842799 12 | H -3.390919 2.955352 -2.613802 13 | C -4.713558 5.501027 -0.776758 14 | H -4.016692 6.110248 1.174501 15 | H -5.189740 4.665257 -2.711287 16 | H -5.499349 6.250449 -0.817328 17 | C -0.255405 3.403875 -1.682773 18 | C 0.799663 2.678874 -1.187638 19 | H -0.309033 4.448123 -1.373130 20 | H -0.590240 3.218161 -2.702923 21 | C 1.400115 1.922611 -0.371590 22 | H 2.453384 1.739759 -0.220298 23 | Cl -1.308240 -0.046359 2.357208 24 | Cl 0.947054 2.273256 2.569070 25 | Si 0.068849 1.006227 0.965614 26 | O -0.396241 -0.075338 -0.527941 27 | O 1.354000 -0.351110 1.377301 28 | C 0.296644 -2.296086 -0.322245 29 | C 1.692596 -1.858245 -0.399309 30 | C 3.456628 -0.499073 0.448227 31 | C -2.013353 -1.713825 -0.316351 32 | C -2.410228 -3.051726 -0.249807 33 | C -0.056566 -3.643676 -0.261847 34 | C -1.391573 -4.022451 -0.226860 35 | C 2.602592 -2.460224 -1.269147 36 | C 3.934621 -2.073752 -1.286604 37 | C 4.394701 -1.068743 -0.414679 38 | H 0.734160 -4.383935 -0.230467 39 | H -1.647090 -5.075284 -0.189131 40 | H 2.239429 -3.233180 -1.936114 41 | H 4.625257 -2.561344 -1.965106 42 | H 3.691031 0.270095 1.171716 43 | N -0.709337 -1.373848 -0.367783 44 | N 2.160404 -0.885493 0.443666 45 | H -2.698697 -0.878793 -0.323096 46 | C 5.797332 -0.614784 -0.393530 47 | C 6.387564 -0.142505 0.794167 48 | C 6.565278 -0.644436 -1.572920 49 | C 7.713808 0.286966 0.799808 50 | H 5.820801 -0.137497 1.720744 51 | C 7.889257 -0.207991 -1.564269 52 | H 6.117760 -0.982829 -2.502839 53 | C 8.467612 0.257686 -0.378499 54 | H 8.160647 0.638129 1.725381 55 | H 8.466948 -0.225170 -2.483888 56 | H 9.500089 0.595438 -0.372352 57 | C -3.842520 -3.397601 -0.195609 58 | C -4.807302 -2.578566 -0.812465 59 | C -4.265262 -4.556284 0.482746 60 | C -6.159361 -2.912355 -0.753837 61 | H -4.498776 -1.693341 -1.360742 62 | C -5.618978 -4.883630 0.544578 63 | H -3.537511 -5.185484 0.986125 64 | C -6.569452 -4.064341 -0.074098 65 | H -6.891912 -2.276640 -1.242664 66 | H -5.932687 -5.773762 1.082208 67 | H -7.623820 -4.321589 -0.025898 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.136542 2.109279 -0.062870 4 | C -2.061499 2.807976 0.585976 5 | C -3.070356 3.484514 -0.273760 6 | H -1.694069 3.406886 1.423522 7 | C -3.353179 3.031006 -1.571750 8 | C -3.752925 4.597286 0.241143 9 | C -4.306505 3.692039 -2.345846 10 | H -2.814316 2.176117 -1.967939 11 | C -4.704887 5.257067 -0.537136 12 | H -3.527597 4.949990 1.244854 13 | C -4.985471 4.803736 -1.830941 14 | H -4.518109 3.345214 -3.353684 15 | H -5.222913 6.124583 -0.137997 16 | H -5.726117 5.317105 -2.438059 17 | C -3.227981 1.672035 1.644108 18 | C -2.279241 0.740172 1.980418 19 | H -4.027693 1.350088 0.976556 20 | H -3.539675 2.383812 2.408008 21 | C -1.157629 0.162362 1.937335 22 | H -0.751223 -0.698174 2.448178 23 | Cl 1.610449 2.007375 -0.846568 24 | Cl 0.764066 2.516498 2.248683 25 | Si 0.174727 1.133197 0.598153 26 | O 1.410093 -0.132356 1.283715 27 | O -0.200691 -0.155567 -0.760667 28 | C 1.884809 -1.863552 -0.229584 29 | C 0.491328 -2.309642 -0.156512 30 | C -1.815624 -1.766281 -0.400994 31 | C 3.547231 -0.290523 0.432452 32 | C 4.540998 -0.945745 -0.299379 33 | C 2.848256 -2.553460 -0.963085 34 | C 4.162292 -2.106184 -0.999568 35 | C 0.137381 -3.632602 0.105561 36 | C -1.196569 -4.018120 0.119699 37 | C -2.213175 -3.078469 -0.135950 38 | H 2.543665 -3.435695 -1.513603 39 | H 4.900458 -2.662300 -1.566126 40 | H 0.926539 -4.347234 0.307434 41 | H -1.452339 -5.052912 0.317304 42 | H -2.499634 -0.956020 -0.606321 43 | N 2.282519 -0.757101 0.467716 44 | N -0.512136 -1.416872 -0.416015 45 | H 3.710256 0.609052 1.008136 46 | C -3.645567 -3.428917 -0.123955 47 | C -4.562253 -2.751721 -0.950495 48 | C -4.116141 -4.449530 0.723274 49 | C -5.914639 -3.089702 -0.930010 50 | H -4.214751 -1.981169 -1.632517 51 | C -5.470322 -4.780534 0.745328 52 | H -3.426898 -4.964883 1.385574 53 | C -6.373034 -4.103286 -0.081422 54 | H -6.608939 -2.567524 -1.581960 55 | H -5.821738 -5.562492 1.412264 56 | H -7.427460 -4.364134 -0.065188 57 | C 5.917653 -0.417353 -0.320966 58 | C 6.439890 0.286649 0.780792 59 | C 6.731008 -0.611899 -1.453254 60 | C 7.744207 0.777955 0.750832 61 | H 5.837011 0.427177 1.673125 62 | C 8.032791 -0.113722 -1.481723 63 | H 6.335161 -1.128423 -2.322588 64 | C 8.544071 0.580456 -0.379857 65 | H 8.137653 1.309731 1.612339 66 | H 8.645368 -0.260813 -2.366577 67 | H 9.559347 0.966349 -0.402560 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.201471 2.060428 -0.040024 4 | C -2.039649 2.851812 0.625726 5 | C -2.847644 3.771053 -0.220950 6 | H -2.593833 2.369455 1.436090 7 | C -2.405296 4.177473 -1.489633 8 | C -4.071574 4.243624 0.276883 9 | C -3.189136 5.041235 -2.253832 10 | H -1.457126 3.808133 -1.867432 11 | C -4.854016 5.106276 -0.492002 12 | H -4.410441 3.928105 1.260928 13 | C -4.413072 5.508286 -1.757753 14 | H -2.847855 5.350865 -3.237895 15 | H -5.805379 5.462096 -0.106449 16 | H -5.020977 6.181146 -2.356449 17 | C -1.120566 4.136879 1.743055 18 | C -0.071546 3.326293 2.097394 19 | H -1.893701 4.336948 2.484822 20 | H -0.891321 4.980956 1.091795 21 | C 0.694826 2.323357 2.029226 22 | H 1.617770 2.054890 2.522165 23 | Cl -1.385624 0.049983 2.129737 24 | Cl 1.558351 1.858839 -0.835618 25 | Si 0.033127 0.983597 0.609030 26 | O -0.376583 -0.228960 -0.730834 27 | O 1.288921 -0.260093 1.288657 28 | C 0.364313 -2.396085 -0.226039 29 | C 1.755167 -1.937989 -0.287915 30 | C 3.437120 -0.427346 0.460873 31 | C -1.955315 -1.879629 -0.407860 32 | C -2.328148 -3.211663 -0.212617 33 | C 0.034509 -3.736681 -0.029235 34 | C -1.292220 -4.144885 -0.022789 35 | C 2.713894 -2.601648 -1.052220 36 | C 4.034852 -2.174630 -1.059196 37 | C 4.427225 -1.062844 -0.292038 38 | H 0.837528 -4.447319 0.126153 39 | H -1.527801 -5.193259 0.119946 40 | H 2.400279 -3.451763 -1.646176 41 | H 4.767701 -2.710328 -1.651917 42 | H 3.613575 0.440570 1.079027 43 | N -0.658214 -1.513221 -0.427123 44 | N 2.163415 -0.870199 0.462406 45 | H -2.653349 -1.067622 -0.551735 46 | C 5.813207 -0.560180 -0.269149 47 | C 6.339452 0.054818 0.882631 48 | C 6.631140 -0.691141 -1.406979 49 | C 7.652829 0.522313 0.895392 50 | H 5.731826 0.142141 1.778731 51 | C 7.941957 -0.216437 -1.392477 52 | H 6.231820 -1.139919 -2.311714 53 | C 8.457354 0.389411 -0.241498 54 | H 8.050209 0.984258 1.794586 55 | H 8.558607 -0.313292 -2.281417 56 | H 9.479753 0.756523 -0.230618 57 | C -3.753002 -3.591452 -0.204068 58 | C -4.695663 -2.879018 -0.969559 59 | C -4.190146 -4.679083 0.575462 60 | C -6.040093 -3.247428 -0.955948 61 | H -4.374874 -2.054058 -1.598815 62 | C -5.536506 -5.040493 0.591231 63 | H -3.481250 -5.225219 1.190733 64 | C -6.465059 -4.327374 -0.174719 65 | H -6.754388 -2.695644 -1.560166 66 | H -5.861869 -5.874407 1.206515 67 | H -7.513525 -4.611594 -0.162917 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.096176 1.419517 -0.130271 4 | C -1.333240 1.520483 1.167942 5 | C -2.754977 1.359861 1.561968 6 | H -0.616505 1.026601 1.830105 7 | C -3.796686 1.571423 0.643844 8 | C -3.048657 0.934322 2.866853 9 | C -5.116190 1.342429 1.027267 10 | H -3.561190 1.895243 -0.364829 11 | C -4.372240 0.707772 3.246628 12 | H -2.239366 0.767795 3.574218 13 | C -5.406891 0.910604 2.327027 14 | H -5.918969 1.486619 0.310213 15 | H -4.595709 0.367514 4.253920 16 | H -6.436673 0.724843 2.619101 17 | C -0.924145 3.342736 1.815706 18 | C 0.110294 3.560210 0.945980 19 | H -0.700297 3.140056 2.862406 20 | H -1.843426 3.902438 1.642097 21 | C 0.844155 3.367015 -0.069433 22 | H 1.608620 3.969490 -0.539961 23 | Cl -0.614430 2.557411 -2.692802 24 | Cl 2.422055 1.654609 -2.090112 25 | Si 0.452457 1.568637 -1.004967 26 | O 1.300565 0.688880 0.479236 27 | O 0.192407 -0.122436 -1.755987 28 | C 1.601766 -1.605331 0.049008 29 | C 0.152162 -1.769764 -0.095898 30 | C -1.846590 -1.066733 -1.185269 31 | C 3.443297 -0.147546 0.441826 32 | C 4.362327 -1.197679 0.374939 33 | C 2.484213 -2.681001 -0.019484 34 | C 3.850193 -2.486798 0.141701 35 | C -0.586403 -2.698409 0.635391 36 | C -1.962792 -2.788121 0.471231 37 | C -2.631952 -1.949412 -0.440334 38 | H 2.080015 -3.667602 -0.214477 39 | H 4.521659 -3.336612 0.094270 40 | H -0.068432 -3.325159 1.351906 41 | H -2.524024 -3.507913 1.056179 42 | H -2.237195 -0.362869 -1.905472 43 | N 2.118854 -0.362511 0.300639 44 | N -0.513403 -1.000667 -1.005376 45 | H 3.714222 0.885556 0.603217 46 | C -4.097374 -1.940435 -0.595853 47 | C -4.696190 -1.567582 -1.814165 48 | C -4.921052 -2.270295 0.495499 49 | C -6.083977 -1.527643 -1.934904 50 | H -4.079012 -1.329999 -2.675811 51 | C -6.308437 -2.226155 0.372114 52 | H -4.476822 -2.524250 1.452762 53 | C -6.894302 -1.854789 -0.842097 54 | H -6.532979 -1.246053 -2.882976 55 | H -6.931911 -2.467928 1.227959 56 | H -7.975954 -1.818399 -0.936602 57 | C 5.803509 -0.930894 0.540650 58 | C 6.254140 0.121192 1.360506 59 | C 6.751525 -1.730510 -0.124680 60 | C 7.618669 0.363475 1.512561 61 | H 5.539014 0.734131 1.901674 62 | C 8.115111 -1.481147 0.024882 63 | H 6.421047 -2.529309 -0.781828 64 | C 8.552990 -0.435426 0.844658 65 | H 7.952436 1.171835 2.156745 66 | H 8.835487 -2.098269 -0.504352 67 | H 9.615872 -0.243569 0.961573 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O 0.981124 1.434074 -0.105617 4 | C 1.854939 2.419030 -0.285742 5 | C 3.037053 2.116408 -1.136375 6 | H 1.416943 3.404472 -0.459996 7 | C 3.409430 0.803760 -1.459445 8 | C 3.799254 3.191866 -1.622901 9 | C 4.535624 0.569333 -2.248304 10 | H 2.805591 -0.021950 -1.106428 11 | C 4.922059 2.955898 -2.414551 12 | H 3.507403 4.210812 -1.380486 13 | C 5.297155 1.642686 -2.723667 14 | H 4.819308 -0.450310 -2.491852 15 | H 5.503272 3.792702 -2.791498 16 | H 6.174654 1.458143 -3.337273 17 | C 2.755782 2.903832 1.378623 18 | C 1.676828 2.679411 2.192773 19 | H 3.037000 3.933283 1.160013 20 | H 3.594657 2.212094 1.462910 21 | C 0.528372 2.259030 2.514767 22 | H 0.002977 2.204947 3.457011 23 | Cl -2.362600 1.328546 2.182701 24 | Cl -1.151299 3.474184 0.109723 25 | Si -0.510645 1.483149 0.882544 26 | O -1.299635 0.640646 -0.576430 27 | O -0.126600 -0.247936 1.578307 28 | C -1.667180 -1.648784 -0.215555 29 | C -0.222177 -1.869525 -0.105510 30 | C 1.829731 -1.316063 0.969690 31 | C -3.473902 -0.125002 -0.521468 32 | C -4.422401 -1.150371 -0.476294 33 | C -2.580398 -2.700755 -0.171007 34 | C -3.941761 -2.461017 -0.300481 35 | C 0.441262 -2.854391 -0.835528 36 | C 1.803296 -3.061989 -0.666725 37 | C 2.535929 -2.280489 0.246161 38 | H -2.203048 -3.705470 -0.021692 39 | H -4.635734 -3.293489 -0.274125 40 | H -0.128690 -3.442652 -1.545044 41 | H 2.301208 -3.834567 -1.241277 42 | H 2.278490 -0.648173 1.691154 43 | N -2.156087 -0.387115 -0.410102 44 | N 0.505032 -1.139597 0.793095 45 | H -3.714471 0.921425 -0.642534 46 | C 3.993489 -2.414984 0.420911 47 | C 4.608810 -2.110869 1.649765 48 | C 4.796016 -2.824150 -0.660363 49 | C 5.992033 -2.211723 1.790488 50 | H 4.003993 -1.820165 2.503825 51 | C 6.179462 -2.918030 -0.517842 52 | H 4.340781 -3.038246 -1.622631 53 | C 6.781653 -2.611639 0.706916 54 | H 6.453012 -1.983692 2.747164 55 | H 6.787725 -3.221411 -1.365007 56 | H 7.859889 -2.684672 0.816959 57 | C -5.858548 -0.841259 -0.604636 58 | C -6.297259 0.256650 -1.369013 59 | C -6.814389 -1.647744 0.041539 60 | C -7.658008 0.536450 -1.486036 61 | H -5.577228 0.876605 -1.895172 62 | C -8.173795 -1.361003 -0.072917 63 | H -6.492423 -2.482568 0.656750 64 | C -8.599889 -0.269892 -0.837935 65 | H -7.983048 1.380345 -2.087612 66 | H -8.899805 -1.984638 0.440762 67 | H -9.659708 -0.048667 -0.927785 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.277363 2.058696 0.342682 4 | C -1.240995 3.377112 0.162761 5 | C -2.515433 3.984923 -0.313020 6 | H -0.733074 3.940854 0.950311 7 | C -3.486254 3.225491 -0.983681 8 | C -2.732242 5.352628 -0.087511 9 | C -4.666054 3.831480 -1.415373 10 | H -3.312826 2.167266 -1.152010 11 | C -3.914102 5.955418 -0.520183 12 | H -1.977656 5.937485 0.433062 13 | C -4.882323 5.196242 -1.186818 14 | H -5.420343 3.240525 -1.927922 15 | H -4.081452 7.012748 -0.334798 16 | H -5.803098 5.664635 -1.523728 17 | C -0.061867 3.889297 -1.266867 18 | C 0.858754 2.888165 -1.079436 19 | H 0.205700 4.900661 -0.961031 20 | H -0.660996 3.839412 -2.176597 21 | C 1.323889 1.813073 -0.608840 22 | H 2.224827 1.271220 -0.853570 23 | Cl -1.338837 -0.031147 2.269862 24 | Cl 0.914409 2.311099 2.398568 25 | Si 0.027390 0.983959 0.840608 26 | O -0.429440 -0.143897 -0.608861 27 | O 1.321749 -0.341019 1.313343 28 | C 0.281691 -2.358115 -0.312461 29 | C 1.679173 -1.923921 -0.390305 30 | C 3.436441 -0.531432 0.423111 31 | C -2.029921 -1.787003 -0.359252 32 | C -2.423336 -3.122484 -0.242425 33 | C -0.067747 -3.703957 -0.202054 34 | C -1.401449 -4.086994 -0.167192 35 | C 2.600436 -2.564750 -1.219975 36 | C 3.934042 -2.184097 -1.232739 37 | C 4.385170 -1.143001 -0.398938 38 | H 0.724971 -4.439377 -0.131735 39 | H -1.653207 -5.138520 -0.090013 40 | H 2.245348 -3.364954 -1.858409 41 | H 4.632865 -2.703541 -1.878362 42 | H 3.658581 0.276348 1.107294 43 | N -0.727166 -1.442949 -0.406090 44 | N 2.138744 -0.917414 0.416649 45 | H -2.716706 -0.954569 -0.414217 46 | C 5.789441 -0.694541 -0.376620 47 | C 6.362602 -0.171252 0.797946 48 | C 6.577169 -0.783866 -1.539891 49 | C 7.691615 0.249432 0.806971 50 | H 5.779656 -0.119972 1.712887 51 | C 7.903918 -0.356062 -1.528229 52 | H 6.143815 -1.163050 -2.460695 53 | C 8.465324 0.160201 -0.355292 54 | H 8.125073 0.640238 1.722967 55 | H 8.497294 -0.419896 -2.435728 56 | H 9.500134 0.490679 -0.346701 57 | C -3.854954 -3.471774 -0.191867 58 | C -4.814819 -2.682386 -0.853442 59 | C -4.282235 -4.603481 0.528054 60 | C -6.166402 -3.018578 -0.797535 61 | H -4.502523 -1.819323 -1.433933 62 | C -5.635590 -4.932952 0.586964 63 | H -3.558728 -5.209377 1.065219 64 | C -6.581176 -4.143155 -0.076046 65 | H -6.894891 -2.406131 -1.320950 66 | H -5.952917 -5.801599 1.156673 67 | H -7.635238 -4.402057 -0.029972 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | F:19-23;2-15 C:23 L:24-65; K:1,2 3 | O -1.011250 2.316879 0.151506 4 | C -2.252541 2.067819 -0.240533 5 | C -3.085246 3.254776 -0.568226 6 | H -2.365380 1.236440 -0.942117 7 | C -2.771932 4.532131 -0.078852 8 | C -4.214432 3.074190 -1.382088 9 | C -3.580704 5.618491 -0.412410 10 | H -1.895294 4.664126 0.547202 11 | C -5.020315 4.163408 -1.713438 12 | H -4.454156 2.081886 -1.757787 13 | C -4.705242 5.437527 -1.227365 14 | H -3.333553 6.608722 -0.039774 15 | H -5.888574 4.021156 -2.350751 16 | H -5.331688 6.287102 -1.485152 17 | C -3.321653 1.291242 1.201708 18 | C -2.303745 0.600745 1.808881 19 | H -4.074542 0.734620 0.643289 20 | H -3.711766 2.156523 1.737421 21 | C -1.105002 0.284062 2.048590 22 | H -0.626888 -0.311100 2.812751 23 | Cl 1.667175 1.994393 -0.795880 24 | Cl 0.929963 2.472741 2.336079 25 | Si 0.225614 1.168114 0.674200 26 | O 1.393377 -0.187305 1.288744 27 | O -0.300815 -0.065075 -0.693001 28 | C 1.818572 -1.826566 -0.330521 29 | C 0.421372 -2.258209 -0.248742 30 | C -1.889042 -1.707248 -0.359361 31 | C 3.530542 -0.356755 0.434563 32 | C 4.500887 -0.987082 -0.348531 33 | C 2.756838 -2.486854 -1.122191 34 | C 4.082786 -2.075922 -1.135926 35 | C 0.074677 -3.597173 -0.066470 36 | C -1.256523 -3.987539 -0.022327 37 | C -2.279757 -3.032799 -0.165513 38 | H 2.424380 -3.319553 -1.730338 39 | H 4.800982 -2.607475 -1.749910 40 | H 0.871789 -4.321632 0.052190 41 | H -1.505447 -5.033916 0.112832 42 | H -2.588183 -0.895919 -0.489994 43 | N 2.251922 -0.785162 0.439532 44 | N -0.589017 -1.349012 -0.406893 45 | H 3.723809 0.493579 1.072669 46 | C -3.711891 -3.378122 -0.106402 47 | C -4.662503 -2.645846 -0.842327 48 | C -4.147727 -4.445316 0.700823 49 | C -6.015430 -2.974256 -0.771974 50 | H -4.341297 -1.840148 -1.496142 51 | C -5.502528 -4.766805 0.773357 52 | H -3.429851 -5.005250 1.293108 53 | C -6.439712 -4.033567 0.037599 54 | H -6.737096 -2.409139 -1.354699 55 | H -5.827315 -5.585368 1.409106 56 | H -7.494569 -4.286941 0.093619 57 | C 5.893963 -0.504882 -0.333322 58 | C 6.441865 0.082709 0.822747 59 | C 6.697119 -0.627827 -1.482670 60 | C 7.761757 0.531267 0.828297 61 | H 5.845637 0.164213 1.726899 62 | C 8.014583 -0.172023 -1.475105 63 | H 6.281656 -1.054769 -2.390661 64 | C 8.551411 0.406577 -0.319865 65 | H 8.175360 0.972736 1.730409 66 | H 8.619652 -0.261843 -2.372679 67 | H 9.578874 0.759402 -0.314583 68 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/2a/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by (S)-5,5'-diphenyl-2,2'-bipyridine-N,N'-dioxide (Cat 2a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O 1.795083 -1.340271 0.030568 4 | C 2.233980 -2.580660 -0.166937 5 | C 3.677988 -2.697764 -0.503231 6 | H 1.573561 -3.222551 -0.755895 7 | C 4.604556 -1.716918 -0.116062 8 | C 4.110327 -3.825323 -1.218047 9 | C 5.949861 -1.862686 -0.452982 10 | H 4.261680 -0.849846 0.439746 11 | C 5.457174 -3.966802 -1.554512 12 | H 3.387868 -4.581781 -1.515627 13 | C 6.379163 -2.986417 -1.171139 14 | H 6.666255 -1.101000 -0.157403 15 | H 5.786517 -4.836251 -2.116568 16 | H 7.428308 -3.095995 -1.432044 17 | C 2.171399 -3.658086 1.447165 18 | C 1.030638 -3.102730 1.968737 19 | H 2.112781 -4.655501 1.011810 20 | H 3.103447 -3.448088 1.972778 21 | C 0.105430 -2.250050 2.090759 22 | H -0.682761 -2.097076 2.813891 23 | Cl 1.215382 0.558349 2.124822 24 | Cl -0.910302 -2.192051 -0.829719 25 | Si 0.212353 -0.822491 0.608816 26 | O 0.173349 0.450691 -0.729812 27 | O -1.403121 -0.108502 1.286987 28 | C -1.273699 2.227375 -0.211719 29 | C -2.421203 1.314405 -0.281550 30 | C -3.466063 -0.700241 0.431847 31 | C 1.076943 2.549099 -0.403823 32 | C 0.974125 3.923152 -0.187586 33 | C -1.423432 3.593415 -0.000046 34 | C -0.313152 4.435890 0.014073 35 | C -3.546095 1.604309 -1.044893 36 | C -4.630446 0.729464 -1.074837 37 | C -4.606989 -0.458044 -0.333202 38 | H -2.420425 3.982669 0.169683 39 | H -0.460386 5.494445 0.190518 40 | H -3.549455 2.514651 -1.632588 41 | H -5.487264 0.977916 -1.689169 42 | C -5.727510 -1.497222 -0.327387 43 | H -3.333661 -1.571101 1.057015 44 | N -0.009688 1.753914 -0.420925 45 | N -2.429749 0.161427 0.453767 46 | H 2.009194 2.032346 -0.580760 47 | C 2.252587 4.759802 -0.182838 48 | C 2.944525 4.624037 -1.560033 49 | C 1.959180 6.245484 0.083569 50 | C 3.195038 4.227340 0.923179 51 | H 2.291622 4.990237 -2.360370 52 | H 3.864358 5.218978 -1.556851 53 | H 3.211306 3.583272 -1.773597 54 | H 2.905147 6.795844 0.082613 55 | H 1.314987 6.671218 -0.694337 56 | H 1.478996 6.389090 1.058288 57 | H 3.465918 3.180095 0.751049 58 | H 4.113841 4.824140 0.924840 59 | H 2.721298 4.306560 1.907750 60 | C -5.164908 -2.830273 -0.877453 61 | C -6.225349 -1.704094 1.122516 62 | C -6.914255 -1.059457 -1.201390 63 | H -4.330648 -3.195851 -0.269333 64 | H -5.959836 -3.584126 -0.863854 65 | H -4.814836 -2.705409 -1.908123 66 | H -6.614800 -0.936111 -2.248433 67 | H -7.688088 -1.832211 -1.156368 68 | H -7.348019 -0.118467 -0.844045 69 | H -5.425028 -2.066053 1.776837 70 | H -6.620828 -0.768888 1.534716 71 | H -7.025669 -2.452107 1.118762 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O 1.046052 -1.221265 0.011319 4 | C 2.087852 -2.005492 0.238157 5 | C 3.104966 -1.435799 1.161653 6 | H 2.487996 -2.526689 -0.635684 7 | C 2.751147 -0.491724 2.138790 8 | C 4.436437 -1.862681 1.052437 9 | C 3.723234 0.015016 2.999013 10 | H 1.720066 -0.160349 2.209775 11 | C 5.408976 -1.346064 1.910806 12 | H 4.707643 -2.590324 0.291322 13 | C 5.052919 -0.411996 2.889123 14 | H 3.449414 0.749114 3.751707 15 | H 6.441358 -1.670417 1.815775 16 | H 5.809172 -0.011908 3.558708 17 | C 1.583123 -3.627781 1.211530 18 | C 0.297031 -3.698985 0.744235 19 | H 2.314851 -4.335608 0.822737 20 | H 1.712508 -3.372065 2.263118 21 | C -0.752916 -3.318193 0.151215 22 | H -1.746987 -3.732883 0.069697 23 | Cl 0.598269 -2.510488 -2.592695 24 | Cl -2.465990 -1.778706 -1.882148 25 | Si -0.460419 -1.535859 -0.877331 26 | O -1.277788 -0.673706 0.619076 27 | O -0.356166 0.130902 -1.688725 28 | C -1.748515 1.583943 0.156868 29 | C -0.324283 1.839195 -0.095162 30 | C 1.635957 1.262599 -1.324444 31 | C -3.474564 0.030485 0.670409 32 | C -4.461582 1.016681 0.635924 33 | C -2.694869 2.600415 0.131260 34 | C -4.040428 2.324706 0.368892 35 | C 0.387309 2.861145 0.530957 36 | C 1.729441 3.061504 0.233366 37 | C 2.391458 2.249952 -0.703945 38 | H -2.365519 3.606513 -0.100724 39 | H -4.756546 3.136289 0.331668 40 | H -0.122361 3.473111 1.265922 41 | H 2.273078 3.849134 0.742589 42 | C 3.870428 2.451706 -1.023849 43 | H 2.009894 0.572380 -2.066038 44 | N -2.174910 0.316633 0.453766 45 | N 0.330482 1.087236 -1.020013 46 | H -3.668992 -1.010895 0.882141 47 | C -5.913613 0.608516 0.882754 48 | C -6.024030 -0.046707 2.279946 49 | C -6.863801 1.815628 0.821011 50 | C -6.332005 -0.413829 -0.201291 51 | H -5.727756 0.659017 3.064356 52 | H -7.063712 -0.346332 2.451509 53 | H -5.394405 -0.939854 2.355469 54 | H -7.885864 1.467957 1.001386 55 | H -6.615518 2.560763 1.585563 56 | H -6.834073 2.295809 -0.163769 57 | H -5.698664 -1.306822 -0.177525 58 | H -7.367855 -0.721180 -0.019670 59 | H -6.267080 0.032462 -1.199685 60 | C 4.684059 2.337952 0.285825 61 | C 4.397974 1.404322 -2.018955 62 | C 4.050444 3.864489 -1.626620 63 | H 4.573575 1.343618 0.727674 64 | H 5.742503 2.507504 0.059173 65 | H 4.369404 3.085243 1.022188 66 | H 3.710343 4.639249 -0.930779 67 | H 5.113368 4.029999 -1.834324 68 | H 3.489403 3.962041 -2.562935 69 | H 4.286796 0.389316 -1.619409 70 | H 3.879803 1.466922 -2.982848 71 | H 5.462562 1.588638 -2.193179 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O -1.169590 -1.077380 0.099864 4 | C -2.477667 -1.146975 0.249652 5 | C -3.224723 -1.917084 -0.775903 6 | H -2.958611 -0.210921 0.550568 7 | C -2.593636 -2.918646 -1.530582 8 | C -4.583238 -1.629248 -0.985830 9 | C -3.320756 -3.620312 -2.491358 10 | H -1.544123 -3.132567 -1.354645 11 | C -5.304514 -2.330836 -1.951645 12 | H -5.068096 -0.854193 -0.397263 13 | C -4.674525 -3.329394 -2.703786 14 | H -2.833698 -4.394753 -3.077512 15 | H -6.352929 -2.100578 -2.118846 16 | H -5.236478 -3.878376 -3.454492 17 | C -3.087077 -2.098291 1.891510 18 | C -1.948564 -1.862721 2.604622 19 | H -3.974912 -1.501669 2.094925 20 | H -3.284313 -3.127133 1.590818 21 | C -0.731907 -1.582574 2.815346 22 | H -0.131171 -1.625530 3.713114 23 | Cl 2.226709 -1.062662 2.302696 24 | Cl 0.619684 -3.313455 0.618805 25 | Si 0.304961 -1.140371 1.094534 26 | O 1.132465 -0.675119 -0.498646 27 | O 0.189774 0.718194 1.527061 28 | C 1.859770 1.550293 -0.508567 29 | C 0.465481 2.002301 -0.416268 30 | C -1.582360 2.016281 0.792452 31 | C 3.400345 -0.260397 -0.611861 32 | C 4.496381 0.594436 -0.732443 33 | C 2.920005 2.438967 -0.638791 34 | C 4.228034 1.968865 -0.748305 35 | C -0.068752 2.937351 -1.294911 36 | C -1.372225 3.401298 -1.133653 37 | C -2.161973 2.948249 -0.068943 38 | H 2.707887 3.501839 -0.632312 39 | H 5.036365 2.684307 -0.837468 40 | H 0.549424 3.287483 -2.113383 41 | H -1.763424 4.121538 -1.841620 42 | C -3.591150 3.418857 0.205155 43 | H -2.076219 1.616966 1.667301 44 | N 2.143763 0.214984 -0.512382 45 | N -0.325259 1.560609 0.608988 46 | H 3.470921 -1.338451 -0.600280 47 | C 5.893366 -0.017168 -0.831869 48 | C 5.954826 -0.928745 -2.080816 49 | C 6.981345 1.063005 -0.947668 50 | C 6.159435 -0.861575 0.437872 51 | H 5.763872 -0.351055 -2.992191 52 | H 6.954219 -1.372155 -2.148548 53 | H 5.223328 -1.741732 -2.020682 54 | H 7.957667 0.572404 -1.011321 55 | H 6.845325 1.673127 -1.848104 56 | H 6.985572 1.721353 -0.071284 57 | H 5.432119 -1.673517 0.542836 58 | H 7.159472 -1.303375 0.366794 59 | H 6.113810 -0.235984 1.336154 60 | C -4.079919 4.405197 -0.868391 61 | C -4.536884 2.195366 0.222445 62 | C -3.628840 4.118368 1.584857 63 | H -4.080767 3.944704 -1.863029 64 | H -5.104380 4.706330 -0.628652 65 | H -3.456798 5.306111 -0.896102 66 | H -2.964136 4.989101 1.596662 67 | H -4.651982 4.454558 1.785926 68 | H -3.327834 3.436807 2.387987 69 | H -4.503388 1.664784 -0.735334 70 | H -4.275248 1.497726 1.025943 71 | H -5.561978 2.538110 0.398655 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O 1.711399 -1.611538 0.544140 4 | C 2.256878 -1.779775 -0.657250 5 | C 3.583087 -2.454787 -0.669281 6 | H 2.180179 -0.924418 -1.334444 7 | C 3.986885 -3.300111 0.375715 8 | C 4.435537 -2.238237 -1.762872 9 | C 5.237229 -3.915717 0.325173 10 | H 3.323192 -3.460025 1.219589 11 | C 5.686574 -2.855126 -1.808964 12 | H 4.119622 -1.580582 -2.569644 13 | C 6.088235 -3.697011 -0.765885 14 | H 5.551507 -4.565332 1.137470 15 | H 6.347092 -2.677794 -2.653165 16 | H 7.061637 -4.178677 -0.800693 17 | C 1.229867 -3.003218 -1.748228 18 | C -0.004646 -2.657917 -1.257061 19 | H 1.500532 -2.691606 -2.756815 20 | H 1.600917 -3.988960 -1.465793 21 | C -0.820104 -2.148146 -0.436903 22 | H -1.879455 -2.303717 -0.301178 23 | Cl 1.117632 0.518399 2.360007 24 | Cl -0.326915 -2.388211 2.509567 25 | Si 0.147293 -0.885460 0.935238 26 | O 0.281918 0.302203 -0.542475 27 | O -1.489233 0.011856 1.340366 28 | C -1.079563 2.190369 -0.343880 29 | C -2.266216 1.333248 -0.445926 30 | C -3.526021 -0.503624 0.390887 31 | C 1.292228 2.367415 -0.282859 32 | C 1.251372 3.759085 -0.196183 33 | C -1.168335 3.575359 -0.267137 34 | C -0.015784 4.355789 -0.195059 35 | C -3.304671 1.612400 -1.328723 36 | C -4.448629 0.818491 -1.360438 37 | C -4.581757 -0.270810 -0.488705 38 | H -2.152023 4.029505 -0.243064 39 | H -0.115469 5.432134 -0.126839 40 | H -3.193403 2.454866 -2.001550 41 | H -5.232753 1.055227 -2.069349 42 | C -5.787873 -1.208331 -0.448393 43 | H -3.522780 -1.291231 1.131744 44 | N 0.166291 1.631798 -0.366902 45 | N -2.414027 0.264170 0.396443 46 | H 2.205066 1.790305 -0.296835 47 | C 2.569243 4.526115 -0.094932 48 | C 3.442457 4.202105 -1.330597 49 | C 2.340031 6.045131 -0.033628 50 | C 3.305325 4.075986 1.190117 51 | H 2.937534 4.508659 -2.253665 52 | H 4.388218 4.749122 -1.249829 53 | H 3.672383 3.132825 -1.393645 54 | H 3.311582 6.544385 0.035219 55 | H 1.830706 6.408660 -0.933622 56 | H 1.748163 6.325315 0.845250 57 | H 3.516893 3.001408 1.177200 58 | H 4.256870 4.614196 1.260537 59 | H 2.705849 4.301644 2.078845 60 | C -6.852793 -0.808118 -1.482595 61 | C -5.306720 -2.647461 -0.755067 62 | C -6.416560 -1.163457 0.964535 63 | H -6.454518 -0.849327 -2.502938 64 | H -7.690315 -1.509151 -1.413894 65 | H -7.234748 0.201364 -1.292072 66 | H -6.758302 -0.150459 1.204467 67 | H -7.277335 -1.840432 0.992462 68 | H -5.705105 -1.484875 1.732987 69 | H -4.837958 -2.698151 -1.744213 70 | H -4.588843 -2.999213 -0.005864 71 | H -6.169389 -3.322250 -0.740930 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O 1.533529 -1.678661 -0.076901 4 | C 2.602246 -2.126097 0.572522 5 | C 3.755262 -2.510303 -0.286203 6 | H 2.395692 -2.809550 1.400734 7 | C 3.930253 -1.966401 -1.568331 8 | C 4.688375 -3.430218 0.215602 9 | C 5.028170 -2.346168 -2.339665 10 | H 3.200150 -1.261385 -1.953545 11 | C 5.784490 -3.809599 -0.560298 12 | H 4.546582 -3.853947 1.207022 13 | C 5.958172 -3.265490 -1.837650 14 | H 5.158807 -1.929681 -3.334745 15 | H 6.498715 -4.530323 -0.172091 16 | H 6.811708 -3.559966 -2.442192 17 | C 3.437305 -0.741310 1.650317 18 | C 2.282184 -0.081381 1.985569 19 | H 3.915995 -1.356722 2.411644 20 | H 4.132789 -0.221710 0.990233 21 | C 1.052627 0.198302 1.933223 22 | H 0.434947 0.923574 2.441802 23 | Cl -1.151135 -2.275577 -0.871784 24 | Cl -0.208359 -2.568145 2.222662 25 | Si 0.013609 -1.070558 0.579967 26 | O -1.502344 -0.163998 1.269127 27 | O 0.054034 0.272779 -0.770904 28 | C -2.374302 1.421083 -0.229277 29 | C -1.127185 2.189809 -0.139368 30 | C 1.242653 2.223823 -0.399366 31 | C -3.600601 -0.526016 0.377051 32 | C -4.711015 -0.138932 -0.373949 33 | C -3.466485 1.858958 -0.968691 34 | C -4.625741 1.088054 -1.043143 35 | C -1.099181 3.553256 0.148205 36 | C 0.108061 4.239671 0.170279 37 | C 1.317942 3.580174 -0.106141 38 | H -3.386068 2.795734 -1.507877 39 | H -5.455981 1.446114 -1.639348 40 | H -2.033372 4.054561 0.372430 41 | H 0.112345 5.296670 0.410748 42 | C 2.649016 4.326871 -0.073019 43 | H 2.089325 1.599085 -0.641206 44 | N -2.492240 0.237493 0.444708 45 | N 0.056132 1.569565 -0.412187 46 | H -3.549581 -1.436842 0.955710 47 | C -5.918903 -1.073003 -0.428589 48 | C -6.440299 -1.319469 1.007008 49 | C -7.058177 -0.483475 -1.276618 50 | C -5.470759 -2.416061 -1.054008 51 | H -6.760809 -0.379731 1.470844 52 | H -7.298535 -1.998516 0.960730 53 | H -5.675193 -1.780996 1.640366 54 | H -7.894858 -1.189128 -1.278860 55 | H -7.413346 0.468262 -0.864565 56 | H -6.743310 -0.324407 -2.314405 57 | H -4.681136 -2.891205 -0.462186 58 | H -6.329989 -3.094745 -1.092178 59 | H -5.097067 -2.261997 -2.072301 60 | C 2.845669 4.913465 1.345203 61 | C 3.841743 3.412324 -0.400906 62 | C 2.596997 5.475848 -1.107038 63 | H 2.875991 4.114604 2.094980 64 | H 3.795065 5.459189 1.375645 65 | H 2.041095 5.609415 1.605182 66 | H 1.782049 6.174077 -0.888064 67 | H 3.542050 6.028654 -1.072552 68 | H 2.458558 5.079809 -2.119340 69 | H 3.935593 2.600673 0.329768 70 | H 3.751875 2.979252 -1.403952 71 | H 4.760704 4.005607 -0.367428 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O 1.761687 -1.376636 -0.053449 4 | C 2.833450 -1.801034 0.609904 5 | C 3.929645 -2.346676 -0.234837 6 | H 3.165090 -1.154656 1.427497 7 | C 3.681225 -2.872594 -1.512301 8 | C 5.237118 -2.336897 0.275125 9 | C 4.737268 -3.373377 -2.273198 10 | H 2.667162 -2.877678 -1.899285 11 | C 6.291147 -2.837965 -0.489770 12 | H 5.423933 -1.929355 1.265959 13 | C 6.042463 -3.358753 -1.764673 14 | H 4.545039 -3.774752 -3.264488 15 | H 7.303117 -2.819781 -0.094884 16 | H 6.862323 -3.749826 -2.361035 17 | C 2.458286 -3.347942 1.718792 18 | C 1.187718 -2.979445 2.080792 19 | H 3.256152 -3.250420 2.454802 20 | H 2.552529 -4.212477 1.060831 21 | C 0.106663 -2.326321 2.021968 22 | H -0.844376 -2.413169 2.527325 23 | Cl 1.189342 0.558459 2.117969 24 | Cl -0.879106 -2.224786 -0.839810 25 | Si 0.213175 -0.839508 0.599200 26 | O 0.129564 0.434878 -0.741934 27 | O -1.411948 -0.158993 1.286996 28 | C -1.321826 2.194485 -0.191619 29 | C -2.459522 1.269352 -0.258281 30 | C -3.466423 -0.774231 0.425301 31 | C 1.022146 2.540371 -0.421264 32 | C 0.909329 3.912003 -0.195894 33 | C -1.481535 3.557720 0.030744 34 | C -0.379419 4.410851 0.031076 35 | C -3.594361 1.554621 -1.008492 36 | C -4.665194 0.663504 -1.046273 37 | C -4.616321 -0.537301 -0.327999 38 | H -2.479498 3.936293 0.218142 39 | H -0.533826 5.466950 0.215841 40 | H -3.615796 2.474322 -1.581058 41 | H -5.530609 0.909404 -1.649370 42 | C -5.721513 -1.592981 -0.329998 43 | H -3.318267 -1.653949 1.033925 44 | N -0.056750 1.734392 -0.423608 45 | N -2.445210 0.104771 0.458580 46 | H 1.956506 2.033850 -0.616294 47 | C 2.179339 4.761247 -0.209487 48 | C 2.848865 4.637516 -1.598860 49 | C 1.876553 6.243081 0.068115 50 | C 3.145589 4.234146 0.878414 51 | H 2.179078 5.001360 -2.386178 52 | H 3.763352 5.240536 -1.608692 53 | H 3.120811 3.600041 -1.821899 54 | H 2.817096 6.802471 0.051980 55 | H 1.214043 6.665826 -0.695893 56 | H 1.413222 6.378470 1.052118 57 | H 3.423276 3.189985 0.698462 58 | H 4.058752 4.839349 0.866021 59 | H 2.687896 4.306410 1.871127 60 | C -5.141538 -2.915524 -0.887024 61 | C -6.216334 -1.814101 1.118942 62 | C -6.914134 -1.166665 -1.201717 63 | H -4.303807 -3.275024 -0.280200 64 | H -5.927064 -3.679221 -0.878749 65 | H -4.791618 -2.780457 -1.916367 66 | H -6.615333 -1.029061 -2.247180 67 | H -7.675440 -1.952146 -1.164306 68 | H -7.363600 -0.236041 -0.836699 69 | H -5.410185 -2.166509 1.771380 70 | H -6.625804 -0.886742 1.535160 71 | H -7.005403 -2.574009 1.111881 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 69 2 | F:19-23;2-15 C:23 L:24-69; K:1,2 3 | O -1.128162 -1.315924 0.216195 4 | C -1.440900 -1.438375 -1.064910 5 | C -2.890500 -1.352920 -1.375910 6 | H -0.786876 -0.921091 -1.772846 7 | C -3.864793 -1.704181 -0.427859 8 | C -3.281428 -0.908329 -2.647838 9 | C -5.216299 -1.604059 -0.752910 10 | H -3.554005 -2.048362 0.553539 11 | C -4.636143 -0.806591 -2.968163 12 | H -2.524040 -0.634028 -3.378376 13 | C -5.605165 -1.157278 -2.022388 14 | H -5.969273 -1.869250 -0.016175 15 | H -4.935010 -0.450738 -3.950035 16 | H -6.659891 -1.077427 -2.270224 17 | C -1.027152 -3.249523 -1.739988 18 | C 0.011985 -3.493861 -0.882611 19 | H -0.808438 -3.043510 -2.787535 20 | H -1.947567 -3.806804 -1.566447 21 | C 0.762645 -3.320786 0.121721 22 | H 1.515644 -3.934402 0.594967 23 | Cl -0.531798 -2.376116 2.788403 24 | Cl 2.494104 -1.606340 1.989318 25 | Si 0.464950 -1.476786 1.009811 26 | O 1.249462 -0.678045 -0.549330 27 | O 0.312999 0.237406 1.717159 28 | C 1.730244 1.596219 -0.189961 29 | C 0.305040 1.862827 0.036043 30 | C -1.683907 1.320450 1.233084 31 | C 3.444092 0.014123 -0.655927 32 | C 4.438067 0.993422 -0.653639 33 | C 2.683603 2.606451 -0.198651 34 | C 4.026953 2.312360 -0.426224 35 | C -0.394854 2.853432 -0.649965 36 | C -1.745829 3.054998 -0.398938 37 | C -2.428833 2.273452 0.548298 38 | H 2.361849 3.622175 -0.000583 39 | H 4.749914 3.118704 -0.412955 40 | H 0.130706 3.437624 -1.396215 41 | H -2.279993 3.816645 -0.955583 42 | C -3.923096 2.459357 0.795562 43 | H -2.075590 0.661227 1.993089 44 | N 2.147432 0.317365 -0.443443 45 | N -0.367350 1.144214 0.976152 46 | H 3.629779 -1.035421 -0.831148 47 | C 5.886908 0.565635 -0.884751 48 | C 5.995247 -0.131156 -2.261779 49 | C 6.847561 1.765467 -0.855385 50 | C 6.293709 -0.429229 0.229036 51 | H 5.705624 0.553213 -3.067290 52 | H 7.033267 -0.442572 -2.421916 53 | H 5.360309 -1.022351 -2.312257 54 | H 7.867168 1.403102 -1.019709 55 | H 6.609725 2.488880 -1.643813 56 | H 6.817793 2.275863 0.114114 57 | H 5.651341 -1.316045 0.230489 58 | H 7.326544 -0.751726 0.057016 59 | H 6.232476 0.045554 1.214351 60 | C -4.667515 2.225798 -0.540481 61 | C -4.468657 1.474855 1.843514 62 | C -4.167650 3.906174 1.283405 63 | H -4.500124 1.207723 -0.904930 64 | H -5.741531 2.367079 -0.376544 65 | H -4.342458 2.935565 -1.308905 66 | H -3.818616 4.639882 0.548709 67 | H -5.242779 4.054326 1.432708 68 | H -3.653580 4.088001 2.233995 69 | H -4.331374 0.436937 1.521053 70 | H -3.983374 1.613755 2.816613 71 | H -5.541084 1.653290 1.968783 72 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/3a/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by (S)-5,5'-di(t-Bu)-2,2'-bipyridine-N,N'-dioxide (Cat 3a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.752566 -0.843250 -0.006013 4 | C 2.427089 -1.956945 -0.277760 5 | C 3.890202 -1.772586 -0.472810 6 | H 1.948073 -2.633082 -0.991185 7 | C 4.571758 -0.685543 0.097621 8 | C 4.593194 -2.715393 -1.238157 9 | C 5.942981 -0.540797 -0.109719 10 | H 4.021090 0.035084 0.693948 11 | C 5.965586 -2.566647 -1.443514 12 | H 4.060937 -3.556406 -1.676263 13 | C 6.642563 -1.479880 -0.878862 14 | H 6.469146 0.303304 0.327851 15 | H 6.505079 -3.293589 -2.044150 16 | H 7.711213 -1.363786 -1.037836 17 | C 2.428270 -3.204746 1.209143 18 | C 1.184537 -2.892950 1.697410 19 | H 2.558838 -4.149132 0.680985 20 | H 3.279591 -2.908541 1.822635 21 | C 0.129713 -2.210427 1.836888 22 | H -0.687882 -2.241314 2.542435 23 | Cl 0.700043 0.719184 2.177973 24 | Cl -0.695204 -2.048372 -1.149611 25 | Si 0.067119 -0.662014 0.478681 26 | O -0.117441 0.690385 -0.762042 27 | O -1.687656 -0.293907 1.089161 28 | C -1.796125 2.179259 -0.162195 29 | C -2.800672 1.123397 -0.388404 30 | C -3.657196 -1.071956 0.083214 31 | C 0.495917 2.898110 -0.281251 32 | C 0.096454 4.225293 0.074641 33 | C -2.202947 3.480608 0.182205 34 | C -1.270403 4.487443 0.311776 35 | C -3.908831 1.395263 -1.210358 36 | C -4.884381 0.441712 -1.402425 37 | C -4.785750 -0.809543 -0.757922 38 | H -3.257088 3.658792 0.354946 39 | H -1.580476 5.488600 0.593873 40 | H -3.959543 2.361294 -1.697586 41 | H -5.732620 0.646214 -2.047984 42 | C -5.769203 -1.822498 -0.904062 43 | C -3.532532 -2.300295 0.760493 44 | N -0.486055 1.925485 -0.367742 45 | N -2.697312 -0.079336 0.224230 46 | C 1.844575 2.585569 -0.541402 47 | C 1.098879 5.225030 0.171431 48 | C 2.416967 4.912941 -0.082440 49 | C 2.784903 3.591737 -0.440981 50 | H 2.121776 1.571941 -0.797850 51 | H 0.801588 6.232962 0.444499 52 | H 3.181472 5.680091 -0.009005 53 | H 3.827991 3.362093 -0.636224 54 | C -5.636361 -3.021965 -0.239636 55 | C -4.515736 -3.255563 0.595186 56 | H -2.671111 -2.484390 1.385376 57 | H -6.623268 -1.626793 -1.545093 58 | H -6.391087 -3.793972 -0.352210 59 | H -4.422538 -4.205610 1.112208 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -0.993125 -0.952511 -0.011363 4 | C -1.994476 -1.787854 -0.228972 5 | C -3.081487 -1.257629 -1.091318 6 | H -2.331967 -2.359480 0.639616 7 | C -2.868487 -0.172704 -1.956331 8 | C -4.354541 -1.841600 -1.003890 9 | C -3.925844 0.329124 -2.713816 10 | H -1.881469 0.272952 -2.021291 11 | C -5.409870 -1.337119 -1.763962 12 | H -4.516096 -2.680841 -0.331611 13 | C -5.197374 -0.250552 -2.620169 14 | H -3.761678 1.174842 -3.376090 15 | H -6.396087 -1.785885 -1.685741 16 | H -6.019581 0.144300 -3.210682 17 | C -1.414368 -3.356582 -1.258644 18 | C -0.154144 -3.410569 -0.725709 19 | H -2.152618 -4.083204 -0.920146 20 | H -1.503669 -3.069055 -2.306342 21 | C 0.854511 -3.018079 -0.068479 22 | H 1.837166 -3.441768 0.082000 23 | Cl -0.519643 -2.175433 2.631992 24 | Cl 2.500612 -1.351902 1.936334 25 | Si 0.514809 -1.207788 0.889816 26 | O 1.315008 -0.376768 -0.640743 27 | O 0.344765 0.488276 1.637461 28 | C 1.924848 1.815678 -0.155714 29 | C 0.501547 2.151677 0.025757 30 | C -1.599717 1.709425 1.100605 31 | C 3.578399 0.202674 -0.809168 32 | C 4.593236 1.206795 -0.706325 33 | C 2.907708 2.816296 -0.066854 34 | C 4.228201 2.515165 -0.321231 35 | C -0.068303 3.214829 -0.696282 36 | C -1.407505 3.508218 -0.553670 37 | C -2.205755 2.758689 0.337270 38 | H 2.597874 3.813630 0.220649 39 | H 4.993715 3.279795 -0.235486 40 | H 0.562848 3.761620 -1.386127 41 | H -1.858900 4.308083 -1.132251 42 | C -3.593907 2.998566 0.507318 43 | C -2.350862 0.953832 2.020045 44 | N 2.272867 0.554668 -0.501435 45 | N -0.253993 1.449396 0.895776 46 | C 3.891664 -1.104678 -1.228763 47 | C 5.931571 0.844308 -1.009237 48 | C 6.230939 -0.439910 -1.408997 49 | C 5.205083 -1.410824 -1.524520 50 | H 3.105014 -1.841344 -1.313186 51 | H 6.705155 1.601185 -0.922889 52 | H 7.255454 -0.712828 -1.641968 53 | H 5.454827 -2.416459 -1.848701 54 | C -4.327139 2.239921 1.393319 55 | C -3.698990 1.222039 2.152433 56 | H -1.872044 0.167416 2.587951 57 | H -4.058672 3.787561 -0.075807 58 | H -5.390105 2.422003 1.516480 59 | H -4.287921 0.635946 2.851250 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.134907 -0.640649 0.068251 4 | C -2.455497 -0.682383 0.124584 5 | C -3.148702 -1.623114 -0.792395 6 | H -2.928447 0.301878 0.187688 7 | C -2.493243 -2.735452 -1.342052 8 | C -4.491966 -1.370373 -1.117307 9 | C -3.180225 -3.583693 -2.210594 10 | H -1.455781 -2.919725 -1.085004 11 | C -5.173955 -2.219873 -1.987389 12 | H -4.995275 -0.504628 -0.692244 13 | C -4.519295 -3.330758 -2.533405 14 | H -2.671464 -4.443035 -2.638878 15 | H -6.210528 -2.017303 -2.241931 16 | H -5.049985 -3.994559 -3.210546 17 | C -3.198911 -1.255270 1.868176 18 | C -2.068939 -1.040652 2.604479 19 | H -4.015783 -0.539194 1.948215 20 | H -3.510693 -2.289844 1.728194 21 | C -0.842323 -0.844796 2.840311 22 | H -0.271673 -0.805314 3.756931 23 | Cl 2.162825 -0.642493 2.391726 24 | Cl 0.422781 -2.961661 0.957066 25 | Si 0.294583 -0.722207 1.115705 26 | O 1.206413 -0.550120 -0.490103 27 | O 0.362202 1.173534 1.298017 28 | C 2.087292 1.581307 -0.782823 29 | C 0.722223 2.139608 -0.782561 30 | C -1.342661 2.505521 0.385496 31 | C 3.531817 -0.335810 -0.659571 32 | C 4.665481 0.509809 -0.885094 33 | C 3.189026 2.420029 -1.022296 34 | C 4.463484 1.895421 -1.061157 35 | C 0.287129 2.954604 -1.843269 36 | C -0.971985 3.513550 -1.817117 37 | C -1.814451 3.307490 -0.701713 38 | H 3.007248 3.479980 -1.150945 39 | H 5.318858 2.542250 -1.229317 40 | H 0.957038 3.105237 -2.681053 41 | H -1.322589 4.119507 -2.646477 42 | C -3.111894 3.874073 -0.603758 43 | C -2.122746 2.320086 1.543927 44 | N 2.279051 0.255228 -0.605305 45 | N -0.090258 1.921667 0.274727 46 | C 3.680287 -1.728052 -0.509014 47 | C 5.951854 -0.087985 -0.931484 48 | C 6.090608 -1.449830 -0.775140 49 | C 4.950683 -2.266406 -0.568328 50 | H 2.809580 -2.346881 -0.335951 51 | H 6.814021 0.551032 -1.095646 52 | H 7.075684 -1.904447 -0.811970 53 | H 5.076131 -3.338090 -0.448200 54 | C -3.878723 3.669741 0.523676 55 | C -3.375793 2.899542 1.600786 56 | H -1.737321 1.723044 2.359053 57 | H -3.478224 4.475030 -1.430415 58 | H -4.869343 4.107696 0.594528 59 | H -3.983577 2.760500 2.489548 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.729595 -1.119779 0.470061 4 | C 2.361046 -1.141799 -0.698692 5 | C 3.788039 -1.556053 -0.652557 6 | H 2.158257 -0.298412 -1.365230 7 | C 4.292200 -2.351167 0.388105 8 | C 4.638062 -1.132726 -1.686022 9 | C 5.639335 -2.711413 0.392725 10 | H 3.629181 -2.670726 1.185686 11 | C 5.985721 -1.493526 -1.676293 12 | H 4.240723 -0.516390 -2.489301 13 | C 6.487630 -2.285898 -0.637826 14 | H 6.031169 -3.322218 1.201324 15 | H 6.642669 -1.156709 -2.473313 16 | H 7.536679 -2.568888 -0.629194 17 | C 1.645759 -2.490235 -1.904975 18 | C 0.343687 -2.339339 -1.506830 19 | H 1.953897 -2.093752 -2.871993 20 | H 2.143791 -3.414688 -1.611769 21 | C -0.602653 -1.985680 -0.744930 22 | H -1.635894 -2.300687 -0.726385 23 | Cl 0.613661 0.658836 2.420088 24 | Cl -0.261076 -2.442220 2.188917 25 | Si 0.029585 -0.719541 0.788139 26 | O 0.075477 0.619881 -0.561901 27 | O -1.761343 -0.145347 1.118513 28 | C -1.617652 2.190098 -0.359064 29 | C -2.615566 1.141438 -0.630219 30 | C -3.660253 -0.932007 -0.005336 31 | C 0.679613 2.845136 -0.104803 32 | C 0.270170 4.209257 0.044002 33 | C -2.032990 3.526078 -0.215947 34 | C -1.104652 4.523437 -0.013694 35 | C -3.595625 1.351288 -1.618634 36 | C -4.591031 0.422015 -1.823514 37 | C -4.653598 -0.735019 -1.017055 38 | H -3.094323 3.738892 -0.252076 39 | H -1.422905 5.554279 0.105057 40 | H -3.531585 2.252637 -2.215625 41 | H -5.336292 0.575594 -2.597375 42 | C -5.672712 -1.711421 -1.158910 43 | C -3.703348 -2.053759 0.845977 44 | N -0.302180 1.885391 -0.306642 45 | N -2.650589 0.016904 0.123686 46 | C 2.041646 2.492698 -0.054305 47 | C 1.270002 5.196895 0.241475 48 | C 2.600611 4.841895 0.283665 49 | C 2.981823 3.485470 0.136734 50 | H 2.333729 1.457321 -0.135391 51 | H 0.959581 6.230722 0.357451 52 | H 3.362723 5.599824 0.434851 53 | H 4.032308 3.215862 0.184668 54 | C -5.702964 -2.812174 -0.329483 55 | C -4.718240 -2.976753 0.674659 56 | H -2.947179 -2.180296 1.610120 57 | H -6.425054 -1.566466 -1.928120 58 | H -6.486069 -3.555713 -0.439565 59 | H -4.758342 -3.843620 1.326959 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.557956 -1.202251 -0.167185 4 | C 2.614429 -1.596457 0.536177 5 | C 3.882035 -1.728821 -0.232157 6 | H 2.426320 -2.399760 1.253176 7 | C 4.052870 -1.124591 -1.487357 8 | C 4.927430 -2.481959 0.325599 9 | C 5.259113 -1.272199 -2.172495 10 | H 3.235116 -0.565144 -1.929371 11 | C 6.131213 -2.629114 -0.362877 12 | H 4.790805 -2.957463 1.294047 13 | C 6.301329 -2.020200 -1.611895 14 | H 5.384404 -0.810688 -3.148153 15 | H 6.933147 -3.220474 0.069970 16 | H 7.238642 -2.134667 -2.149435 17 | C 3.149065 -0.273596 1.862360 18 | C 1.890566 0.199864 2.130618 19 | H 3.619645 -0.923311 2.599433 20 | H 3.837223 0.405307 1.358379 21 | C 0.647271 0.340330 1.970370 22 | H -0.102826 0.928434 2.478042 23 | Cl -0.948586 -2.043566 -1.275604 24 | Cl -0.226849 -2.585240 1.842634 25 | Si -0.087398 -0.883485 0.396066 26 | O -1.756147 -0.255489 1.047675 27 | O -0.139275 0.587810 -0.804365 28 | C -2.720228 1.342158 -0.344772 29 | C -1.589275 2.249815 -0.083500 30 | C 0.776615 2.657374 -0.195779 31 | C -3.803323 -0.770425 0.032129 32 | C -4.903103 -0.346433 -0.781733 33 | C -3.800058 1.776019 -1.133333 34 | C -4.873804 0.941415 -1.358556 35 | C -1.813193 3.571108 0.344145 36 | C -0.751089 4.431245 0.525069 37 | C 0.566402 3.998243 0.255434 38 | H -3.748832 2.764625 -1.572670 39 | H -5.701922 1.266644 -1.980583 40 | H -2.832345 3.879292 0.543869 41 | H -0.918504 5.445757 0.872832 42 | C 1.699871 4.839110 0.406138 43 | C 2.066075 2.184616 -0.505385 44 | N -2.743987 0.107468 0.207453 45 | N -0.327556 1.829472 -0.328238 46 | C -3.800413 -2.037112 0.647731 47 | C -5.987293 -1.242957 -0.968028 48 | C -5.974441 -2.482995 -0.367450 49 | C -4.879346 -2.874409 0.442507 50 | H -2.955812 -2.339171 1.252400 51 | H -6.819862 -0.926041 -1.588386 52 | H -6.805588 -3.166324 -0.511390 53 | H -4.882962 -3.854980 0.908505 54 | C 2.960547 4.367731 0.108358 55 | C 3.139118 3.039719 -0.354114 56 | H 2.189850 1.166566 -0.847370 57 | H 1.548169 5.855828 0.755055 58 | H 3.824111 5.015427 0.222472 59 | H 4.137412 2.684591 -0.591968 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.713233 -0.906142 -0.090689 4 | C 2.799177 -1.192849 0.623506 5 | C 4.030600 -1.452868 -0.168824 6 | H 2.952056 -0.572911 1.511453 7 | C 3.968359 -1.893036 -1.500178 8 | C 5.276635 -1.256727 0.446600 9 | C 5.147091 -2.123951 -2.208895 10 | H 3.000116 -2.043145 -1.967235 11 | C 6.453533 -1.487598 -0.266398 12 | H 5.317764 -0.917116 1.478920 13 | C 6.390126 -1.923662 -1.594717 14 | H 5.099341 -2.459732 -3.241152 15 | H 7.416313 -1.326499 0.210446 16 | H 7.305965 -2.105586 -2.150528 17 | C 2.639354 -2.870126 1.573163 18 | C 1.303258 -2.758393 1.863022 19 | H 3.356859 -2.696215 2.374991 20 | H 2.931050 -3.648259 0.867008 21 | C 0.131136 -2.290410 1.780234 22 | H -0.800269 -2.576558 2.245502 23 | Cl 0.663913 0.688972 2.183450 24 | Cl -0.695142 -2.088792 -1.141463 25 | Si 0.053081 -0.696839 0.477008 26 | O -0.155230 0.653039 -0.768618 27 | O -1.712224 -0.346842 1.086089 28 | C -1.800127 2.155580 -0.126421 29 | C -2.815541 1.112801 -0.362142 30 | C -3.687410 -1.085942 0.053896 31 | C 0.496143 2.851251 -0.282782 32 | C 0.118198 4.177496 0.098545 33 | C -2.186830 3.456215 0.242801 34 | C -1.240808 4.450885 0.367820 35 | C -3.920531 1.412802 -1.178640 36 | C -4.899835 0.470232 -1.400495 37 | C -4.809768 -0.797059 -0.787733 38 | H -3.235767 3.643532 0.436378 39 | H -1.533831 5.451359 0.670099 40 | H -3.963577 2.391690 -1.640236 41 | H -5.743715 0.695389 -2.044907 42 | C -5.799290 -1.799293 -0.964141 43 | C -3.582380 -2.328872 0.706386 44 | N -0.497584 1.890314 -0.359743 45 | N -2.718704 -0.105009 0.222317 46 | C 1.835286 2.527722 -0.575118 47 | C 1.133451 5.164794 0.187986 48 | C 2.442734 4.841914 -0.096515 49 | C 2.788814 3.522131 -0.480787 50 | H 2.093416 1.515327 -0.855575 51 | H 0.853233 6.172324 0.479811 52 | H 3.216959 5.599771 -0.028837 53 | H 3.824874 3.284887 -0.702402 54 | C -5.681528 -3.014362 -0.326027 55 | C -4.570747 -3.273324 0.513865 56 | H -2.732357 -2.531895 1.338584 57 | H -6.647166 -1.581981 -1.606387 58 | H -6.441044 -3.777859 -0.461905 59 | H -4.489273 -4.233516 1.013740 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.054027 -1.053575 0.244798 4 | C -1.328973 -1.328198 -1.021523 5 | C -2.765648 -1.248583 -1.388723 6 | H -0.645125 -0.907528 -1.764059 7 | C -3.773495 -1.300458 -0.413344 8 | C -3.108036 -1.088488 -2.740704 9 | C -5.110202 -1.182357 -0.790877 10 | H -3.499171 -1.414382 0.629691 11 | C -4.446948 -0.973003 -3.114615 12 | H -2.323954 -1.047403 -3.493260 13 | C -5.450471 -1.020624 -2.139764 14 | H -5.888909 -1.211998 -0.033764 15 | H -4.707867 -0.842646 -4.161107 16 | H -6.493688 -0.929126 -2.429702 17 | C -0.916008 -3.205224 -1.446563 18 | C 0.127646 -3.334495 -0.568062 19 | H -0.700035 -3.138613 -2.512549 20 | H -1.833305 -3.739815 -1.199042 21 | C 0.873600 -3.029533 0.408072 22 | H 1.633167 -3.567761 0.956476 23 | Cl -0.511464 -1.879352 2.923775 24 | Cl 2.497890 -1.075044 2.146479 25 | Si 0.510962 -1.106494 1.092652 26 | O 1.309420 -0.460101 -0.524657 27 | O 0.301558 0.666064 1.624306 28 | C 1.814657 1.803401 -0.351258 29 | C 0.378426 2.099999 -0.201867 30 | C -1.686229 1.756028 0.976652 31 | C 3.540858 0.186216 -0.771960 32 | C 4.508582 1.239302 -0.827886 33 | C 2.751833 2.848388 -0.415885 34 | C 4.084064 2.572127 -0.635826 35 | C -0.240246 3.028062 -1.057595 36 | C -1.585912 3.296939 -0.928280 37 | C -2.339997 2.667026 0.085055 38 | H 2.399130 3.862243 -0.272182 39 | H 4.813707 3.375020 -0.668848 40 | H 0.360711 3.492038 -1.830123 41 | H -2.074813 3.990939 -1.604690 42 | C -3.727006 2.905712 0.264684 43 | C -2.390469 1.135172 2.024970 44 | N 2.220025 0.523458 -0.515943 45 | N -0.338806 1.501362 0.773048 46 | C 3.912423 -1.155018 -0.989058 47 | C 5.861071 0.896532 -1.088038 48 | C 6.217774 -0.418486 -1.293862 49 | C 5.238152 -1.441622 -1.247929 50 | H 3.162199 -1.932700 -0.943973 51 | H 6.599037 1.692058 -1.125305 52 | H 7.252818 -0.676687 -1.494810 53 | H 5.534342 -2.472743 -1.414634 54 | C -4.412708 2.281902 1.283936 55 | C -3.737788 1.403186 2.166296 56 | H -1.877583 0.450376 2.686583 57 | H -4.227144 3.589592 -0.414146 58 | H -5.474197 2.465074 1.417832 59 | H -4.289890 0.923449 2.968578 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -0.975645 -0.993611 -0.132589 4 | C -1.940716 -1.890796 -0.302249 5 | C -3.116148 -1.455969 -1.103881 6 | H -1.599466 -2.905382 -0.520176 7 | C -3.373579 -0.105056 -1.377583 8 | C -3.984971 -2.441528 -1.601575 9 | C -4.488689 0.255526 -2.133334 10 | H -2.692609 0.651905 -1.012211 11 | C -5.098704 -2.079042 -2.357943 12 | H -3.782632 -3.490448 -1.397850 13 | C -5.356386 -0.728182 -2.621486 14 | H -4.678521 1.304280 -2.344706 15 | H -5.762833 -2.846926 -2.744446 16 | H -6.224612 -0.445150 -3.210239 17 | C -2.817255 -2.343124 1.380280 18 | C -1.701966 -2.223076 2.166995 19 | H -3.185126 -3.342373 1.150507 20 | H -3.596745 -1.592401 1.511474 21 | C -0.517993 -1.893147 2.462994 22 | H 0.041514 -1.900171 3.386642 23 | Cl 2.415178 -1.191474 2.050225 24 | Cl 0.959003 -3.229955 0.011820 25 | Si 0.534813 -1.179051 0.799755 26 | O 1.339869 -0.410179 -0.689451 27 | O 0.324481 0.577805 1.504704 28 | C 1.982429 1.790964 -0.306162 29 | C 0.564952 2.170332 -0.167301 30 | C -1.539647 1.894817 0.952925 31 | C 3.626221 0.104653 -0.785215 32 | C 4.656923 1.096892 -0.715952 33 | C 2.982517 2.776719 -0.248659 34 | C 4.304506 2.434225 -0.435247 35 | C 0.042237 3.232020 -0.928100 36 | C -1.271281 3.616061 -0.772132 37 | C -2.092148 2.959221 0.171199 38 | H 2.684998 3.796488 -0.037605 39 | H 5.081921 3.189255 -0.372604 40 | H 0.692047 3.714380 -1.647952 41 | H -1.685188 4.419606 -1.372701 42 | C -3.454548 3.301927 0.370465 43 | C -2.315377 1.224131 1.917031 44 | N 2.319382 0.505706 -0.553751 45 | N -0.218612 1.536780 0.732711 46 | C 3.927454 -1.235800 -1.093422 47 | C 5.997628 0.692081 -0.945301 48 | C 6.285372 -0.622762 -1.239704 49 | C 5.245499 -1.582432 -1.316963 50 | H 3.133686 -1.969262 -1.139776 51 | H 6.781550 1.441009 -0.888381 52 | H 7.311577 -0.929310 -1.416749 53 | H 5.487190 -2.614338 -1.552549 54 | C -4.212949 2.626480 1.302111 55 | C -3.636647 1.591912 2.078918 56 | H -1.869916 0.432694 2.503831 57 | H -3.880267 4.101868 -0.227517 58 | H -5.256378 2.887719 1.447394 59 | H -4.244076 1.075772 2.815989 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.788634 -0.838233 0.284676 4 | C 2.452588 -1.971877 0.068028 5 | C 3.882710 -1.811941 -0.314234 6 | H 2.262644 -2.766228 0.793853 7 | C 4.341733 -0.675969 -0.998160 8 | C 4.780471 -2.839270 0.011314 9 | C 5.689396 -0.564115 -1.336884 10 | H 3.640885 0.108893 -1.262183 11 | C 6.129849 -2.724249 -0.327923 12 | H 4.420845 -3.719460 0.538892 13 | C 6.586342 -1.587192 -1.002790 14 | H 6.042989 0.318866 -1.862307 15 | H 6.823456 -3.517464 -0.063378 16 | H 7.636310 -1.497045 -1.267520 17 | C 1.794617 -2.928628 -1.474084 18 | C 0.484410 -2.539351 -1.353427 19 | H 2.054926 -3.952815 -1.206869 20 | H 2.350076 -2.529786 -2.323194 21 | C -0.495443 -1.883081 -0.901979 22 | H -1.528170 -1.858828 -1.214018 23 | Cl 0.602549 0.769332 2.331344 24 | Cl -0.062885 -2.390111 2.103970 25 | Si 0.079459 -0.643332 0.704613 26 | O -0.028855 0.687145 -0.628504 27 | O -1.745263 -0.235046 1.096283 28 | C -1.767068 2.189290 -0.269340 29 | C -2.741332 1.115344 -0.527529 30 | C -3.623383 -1.065610 -0.022948 31 | C 0.519183 2.921952 -0.186626 32 | C 0.080125 4.264504 0.042782 33 | C -2.213154 3.504411 -0.043360 34 | C -1.304802 4.527604 0.118888 35 | C -3.789082 1.339069 -1.440593 36 | C -4.744105 0.371895 -1.660970 37 | C -4.686623 -0.850681 -0.957359 38 | H -3.280056 3.680224 0.014767 39 | H -1.646416 5.540580 0.306156 40 | H -3.808018 2.282343 -1.972343 41 | H -5.543634 0.542119 -2.374921 42 | C -5.646333 -1.880527 -1.132558 43 | C -3.532862 -2.263120 0.713042 44 | N -0.442341 1.934091 -0.329937 45 | N -2.675409 -0.058965 0.144429 46 | C 1.889218 2.608140 -0.271489 47 | C 1.063277 5.278221 0.183417 48 | C 2.402292 4.964141 0.095081 49 | C 2.811322 3.625997 -0.131756 50 | H 2.190902 1.580667 -0.417834 51 | H 0.734634 6.298086 0.358853 52 | H 3.151708 5.742061 0.202570 53 | H 3.870224 3.392931 -0.188680 54 | C -5.549269 -3.052077 -0.412599 55 | C -4.491455 -3.238323 0.510277 56 | H -2.718744 -2.405123 1.412206 57 | H -6.454049 -1.721852 -1.840437 58 | H -6.286420 -3.837128 -0.548805 59 | H -4.428422 -4.165286 1.071858 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.752101 -0.925071 -0.426032 4 | C 2.942618 -0.346357 -0.407778 5 | C 4.108516 -1.270954 -0.420604 6 | H 3.052680 0.508549 -1.080342 7 | C 3.994106 -2.589901 0.045102 8 | C 5.339700 -0.800901 -0.904116 9 | C 5.106725 -3.430409 0.019278 10 | H 3.035457 -2.942098 0.413324 11 | C 6.448851 -1.646603 -0.930579 12 | H 5.423492 0.222235 -1.264005 13 | C 6.334410 -2.962098 -0.466324 14 | H 5.017851 -4.453553 0.374151 15 | H 7.398068 -1.283729 -1.314880 16 | H 7.197733 -3.621688 -0.486715 17 | C 3.324581 0.694377 1.215468 18 | C 2.036738 0.799709 1.664624 19 | H 3.802301 1.577947 0.793339 20 | H 3.989228 0.051963 1.791834 21 | C 0.805042 0.538878 1.749288 22 | H 0.043724 0.812449 2.465781 23 | Cl -0.656758 -1.958819 -1.411256 24 | Cl 0.368178 -2.452303 1.670066 25 | Si 0.142057 -0.724693 0.229997 26 | O -1.554030 -0.407892 1.017367 27 | O -0.218799 0.805189 -0.909116 28 | C -2.901531 0.976565 -0.260317 29 | C -1.956587 2.079375 -0.012761 30 | C 0.223510 3.029707 -0.302769 31 | C -3.541509 -1.301383 0.145806 32 | C -4.753326 -1.084914 -0.586573 33 | C -4.090856 1.209296 -0.971281 34 | C -5.000612 0.187862 -1.145192 35 | C -2.423796 3.282287 0.546709 36 | C -1.563490 4.340370 0.741088 37 | C -0.223530 4.243817 0.307698 38 | H -4.258145 2.196502 -1.384751 39 | H -5.913757 0.355703 -1.707591 40 | H -3.464699 3.336571 0.840977 41 | H -1.911040 5.255743 1.209281 42 | C 0.697386 5.317918 0.423567 43 | C 1.516378 2.932763 -0.847020 44 | N -2.654661 -0.242199 0.261695 45 | N -0.659015 1.958816 -0.377769 46 | C -3.263463 -2.544654 0.744575 47 | C -5.666133 -2.164579 -0.709341 48 | C -5.385984 -3.380242 -0.123967 49 | C -4.184363 -3.564449 0.604777 50 | H -2.337472 -2.683523 1.287418 51 | H -6.583964 -2.006220 -1.267285 52 | H -6.087164 -4.203702 -0.217238 53 | H -3.978553 -4.528395 1.060034 54 | C 1.975668 5.198271 -0.077388 55 | C 2.375136 4.007922 -0.733095 56 | H 1.798829 2.035780 -1.376321 57 | H 0.364222 6.235412 0.898848 58 | H 2.674527 6.024322 0.008193 59 | H 3.370196 3.940336 -1.162258 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/4a/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by (S)-[2,2'-biquinoline] 1,1'-dioxide (Cat 4a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.376799 -0.489174 -0.009557 4 | C 3.299618 -1.426321 -0.205251 5 | C 4.637044 -0.923939 -0.620344 6 | H 2.958422 -2.317392 -0.739095 7 | C 5.082051 0.358531 -0.262754 8 | C 5.467827 -1.766949 -1.373965 9 | C 6.344490 0.791937 -0.665441 10 | H 4.435383 1.002906 0.324523 11 | C 6.730020 -1.328315 -1.777676 12 | H 5.118529 -2.759206 -1.649728 13 | C 7.171114 -0.049256 -1.421904 14 | H 6.687277 1.785867 -0.390827 15 | H 7.366054 -1.980772 -2.369348 16 | H 8.154413 0.292629 -1.733408 17 | C 3.784554 -2.352812 1.438425 18 | C 2.554363 -2.281594 2.040574 19 | H 4.110837 -3.311522 1.035504 20 | H 4.580948 -1.751946 1.878106 21 | C 1.368547 -1.882431 2.216549 22 | H 0.637667 -2.018888 3.000151 23 | Cl 1.143870 1.128766 2.034181 24 | Cl 0.275690 -2.487448 -0.616328 25 | Si 0.756797 -0.658436 0.668081 26 | O 0.103701 0.368789 -0.717088 27 | O -0.960522 -0.665254 1.450964 28 | C -1.990943 1.323122 -0.170778 29 | C -2.584395 -0.020835 -0.138370 30 | C -2.564115 -2.203704 0.833827 31 | C -0.043600 2.660679 -0.534109 32 | C -0.774966 3.845909 -0.353162 33 | C -2.749444 2.455240 0.015648 34 | C -2.177889 3.747144 -0.067158 35 | C -3.716570 -0.334509 -0.853068 36 | C -4.324052 -1.608491 -0.748226 37 | C -3.723633 -2.570433 0.131672 38 | H -3.802628 2.341413 0.246657 39 | C -2.924536 4.932609 0.129460 40 | H -4.135200 0.415424 -1.514713 41 | C -5.484791 -1.969425 -1.472030 42 | C -4.292212 -3.862355 0.268561 43 | H -2.042972 -2.864587 1.513679 44 | N -0.638544 1.470293 -0.452215 45 | N -2.038305 -0.985365 0.700244 46 | H 1.015175 2.640068 -0.756569 47 | C -0.153378 5.117682 -0.437714 48 | C -2.296424 6.160595 0.043526 49 | C -0.909825 6.254471 -0.239972 50 | H 0.908734 5.179878 -0.653343 51 | H -3.985720 4.862173 0.348366 52 | H -2.869614 7.070258 0.196051 53 | H -0.442586 7.232553 -0.299939 54 | C -6.020464 -3.234569 -1.322209 55 | C -5.424509 -4.182664 -0.451745 56 | H -3.828290 -4.582373 0.935603 57 | H -5.941994 -1.245074 -2.139246 58 | H -6.911001 -3.511372 -1.878646 59 | H -5.866287 -5.169622 -0.355376 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.202711 -1.260641 -0.071042 4 | C -2.346238 -1.867627 -0.331041 5 | C -3.401584 -0.990830 -0.901260 6 | H -2.688188 -2.582620 0.421661 7 | C -3.075689 0.198795 -1.573023 8 | C -4.747431 -1.341579 -0.716360 9 | C -4.088600 1.036593 -2.034735 10 | H -2.032700 0.460797 -1.716484 11 | C -5.759443 -0.500151 -1.181397 12 | H -4.997595 -2.262394 -0.194842 13 | C -5.431825 0.690613 -1.839114 14 | H -3.833680 1.962299 -2.542982 15 | H -6.800418 -0.769292 -1.026202 16 | H -6.219711 1.347528 -2.197356 17 | C -2.139858 -3.217133 -1.760480 18 | C -0.857779 -3.559537 -1.427211 19 | H -2.948182 -3.897184 -1.493779 20 | H -2.287950 -2.671116 -2.692187 21 | C 0.264763 -3.471313 -0.846973 22 | H 1.184578 -4.028478 -0.954590 23 | Cl -0.682264 -3.110871 2.150828 24 | Cl 2.369422 -2.617462 1.234244 25 | Si 0.334754 -1.928702 0.537784 26 | O 1.113015 -0.890479 -0.850254 27 | O 0.535610 -0.461413 1.669009 28 | C 1.959106 1.151090 -0.006551 29 | C 0.593730 1.518518 0.395668 30 | C -1.309441 0.936582 1.719382 31 | C 3.377226 -0.490569 -1.005232 32 | C 4.501145 0.340905 -0.864292 33 | C 3.025048 2.003832 0.148725 34 | C 4.326884 1.636280 -0.271372 35 | C -0.028190 2.669577 -0.025646 36 | C -1.343820 2.985102 0.393217 37 | C -1.998929 2.085278 1.300512 38 | H 2.855915 2.965102 0.621609 39 | C 5.452207 2.480010 -0.120561 40 | H 0.493815 3.320172 -0.718692 41 | C -2.045490 4.122754 -0.069601 42 | C -3.329907 2.338144 1.718497 43 | H -1.729093 0.194332 2.386017 44 | N 2.170830 -0.087987 -0.604740 45 | N -0.081541 0.679893 1.271261 46 | H 3.416358 -1.476143 -1.449158 47 | C 5.786685 -0.079117 -1.290832 48 | C 6.695477 2.048092 -0.542999 49 | C 6.864037 0.767532 -1.128535 50 | H 5.906708 -1.061350 -1.737619 51 | H 5.325113 3.460035 0.329154 52 | H 7.559135 2.695796 -0.425106 53 | H 7.852412 0.453407 -1.449641 54 | C -3.344510 4.344172 0.346476 55 | C -3.988958 3.450748 1.239777 56 | H -3.816376 1.644302 2.396925 57 | H -1.555010 4.804946 -0.757144 58 | H -3.885046 5.213203 -0.016652 59 | H -5.012343 3.646505 1.544296 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.437686 -0.899473 -0.067907 4 | C 2.713187 -0.677455 -0.313728 5 | C 3.672081 -0.977083 0.778777 6 | H 2.924308 0.253713 -0.851502 7 | C 3.356225 -1.890288 1.797227 8 | C 4.915649 -0.324802 0.781045 9 | C 4.281069 -2.140835 2.810473 10 | H 2.392686 -2.389425 1.780990 11 | C 5.835437 -0.576085 1.798423 12 | H 5.155660 0.380394 -0.011540 13 | C 5.520115 -1.487285 2.813627 14 | H 4.037417 -2.845748 3.600635 15 | H 6.793727 -0.064318 1.802144 16 | H 6.236929 -1.686255 3.605668 17 | C 3.499163 -1.798464 -1.766845 18 | C 2.313415 -2.059024 -2.388705 19 | H 4.169048 -1.053320 -2.193210 20 | H 3.995576 -2.630375 -1.267804 21 | C 1.060790 -2.172256 -2.529202 22 | H 0.458967 -2.589549 -3.324126 23 | Cl -1.903637 -2.342987 -1.847485 24 | Cl 0.334441 -3.587920 0.137944 25 | Si -0.000900 -1.596722 -0.855501 26 | O -0.866278 -0.993685 0.665477 27 | O -0.436302 0.046456 -1.715575 28 | C -2.130735 0.952977 0.243266 29 | C -0.886519 1.671223 -0.068221 30 | C 1.003204 1.845815 -1.518798 31 | C -3.155927 -1.111141 0.876581 32 | C -4.428116 -0.516183 0.899099 33 | C -3.352776 1.582311 0.256270 34 | C -4.537832 0.879522 0.582594 35 | C -0.543925 2.852951 0.544992 36 | C 0.608340 3.576910 0.155618 37 | C 1.399382 3.055038 -0.922803 38 | H -3.399125 2.632303 -0.010357 39 | C -5.814326 1.488826 0.597195 40 | H -1.172355 3.223134 1.347512 41 | C 1.005087 4.783835 0.778063 42 | C 2.558229 3.748756 -1.355326 43 | H 1.527491 1.392420 -2.350576 44 | N -2.073117 -0.395436 0.572032 45 | N -0.073633 1.187180 -1.088561 46 | H -2.976709 -2.152064 1.110644 47 | C -5.587192 -1.266843 1.220808 48 | C -6.929883 0.736553 0.913672 49 | C -6.817587 -0.642434 1.225327 50 | H -5.491248 -2.322291 1.456072 51 | H -5.902302 2.543897 0.356488 52 | H -7.909681 1.204720 0.923438 53 | H -7.711135 -1.209196 1.467945 54 | C 2.140916 5.439226 0.342464 55 | C 2.918651 4.922066 -0.725286 56 | H 3.147107 3.345648 -2.173450 57 | H 0.409685 5.179716 1.595118 58 | H 2.446460 6.364252 0.822120 59 | H 3.806091 5.458307 -1.046925 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.434154 -0.750059 0.507576 4 | C 2.919965 -0.738579 -0.730300 5 | C 4.405268 -0.774125 -0.833980 6 | H 2.436765 -0.041548 -1.421263 7 | C 5.202622 -1.279608 0.204279 8 | C 5.007183 -0.298098 -2.008918 9 | C 6.590381 -1.299738 0.065978 10 | H 4.730246 -1.643039 1.111372 11 | C 6.396056 -0.319262 -2.143189 12 | H 4.385759 0.093345 -2.811393 13 | C 7.189976 -0.822553 -1.106520 14 | H 7.206895 -1.685443 0.873321 15 | H 6.858139 0.057844 -3.051336 16 | H 8.271518 -0.840138 -1.209971 17 | C 2.461437 -2.345402 -1.699858 18 | C 1.238330 -2.547925 -1.109651 19 | H 2.495897 -2.006630 -2.735065 20 | H 3.246414 -3.053463 -1.432582 21 | C 0.340383 -2.401817 -0.232855 22 | H -0.527124 -2.999945 -0.000005 23 | Cl 1.093156 1.005080 2.325802 24 | Cl 1.104856 -2.225887 2.663267 25 | Si 0.738781 -0.759476 1.016355 26 | O 0.237081 0.272608 -0.493037 27 | O -1.083244 -0.653774 1.558077 28 | C -1.816033 1.377231 -0.192212 29 | C -2.489207 0.071318 -0.204982 30 | C -2.742061 -2.070976 0.825120 31 | C 0.244088 2.577573 -0.346213 32 | C -0.422202 3.810363 -0.253528 33 | C -2.515279 2.557969 -0.098778 34 | C -1.852273 3.808245 -0.127183 35 | C -3.571941 -0.180600 -1.016101 36 | C -4.285652 -1.399945 -0.941285 37 | C -3.853951 -2.372678 0.023045 38 | H -3.592287 2.517017 0.018171 39 | C -2.534930 5.042931 -0.023432 40 | H -3.871754 0.581424 -1.727181 41 | C -5.399178 -1.693998 -1.763153 42 | C -4.542882 -3.606399 0.147597 43 | H -2.359142 -2.736766 1.589248 44 | N -0.435493 1.430488 -0.327668 45 | N -2.089878 -0.910923 0.698344 46 | H 1.317118 2.485512 -0.445393 47 | C 0.289050 5.036767 -0.272580 48 | C -1.820087 6.225598 -0.045932 49 | C -0.407066 6.223618 -0.169875 50 | H 1.370905 5.025122 -0.363029 51 | H -3.616175 5.045065 0.075669 52 | H -2.344068 7.173252 0.035228 53 | H 0.128476 7.167843 -0.180981 54 | C -6.052213 -2.904060 -1.625155 55 | C -5.624771 -3.861318 -0.669213 56 | H -4.209478 -4.333404 0.881669 57 | H -5.729004 -0.961557 -2.493676 58 | H -6.907109 -3.129250 -2.255695 59 | H -6.157510 -4.803213 -0.582662 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.158500 -1.169348 -0.084756 4 | C 3.346828 -1.214862 0.507294 5 | C 4.518450 -1.208728 -0.411798 6 | H 3.426564 -1.911652 1.346193 7 | C 4.429005 -0.697674 -1.715824 8 | C 5.739775 -1.717486 0.056073 9 | C 5.552243 -0.703974 -2.542799 10 | H 3.479678 -0.312783 -2.074804 11 | C 6.861041 -1.723063 -0.774503 12 | H 5.804731 -2.114321 1.066503 13 | C 6.770006 -1.213521 -2.074594 14 | H 5.479233 -0.315714 -3.555101 15 | H 7.801750 -2.127029 -0.410844 16 | H 7.642430 -1.217707 -2.722350 17 | C 3.719113 0.387157 1.534016 18 | C 2.424727 0.658389 1.901032 19 | H 4.389936 -0.019216 2.290865 20 | H 4.194927 1.082965 0.842770 21 | C 1.170366 0.524640 1.900943 22 | H 0.367157 1.027602 2.418460 23 | Cl -0.192192 -2.686721 -0.692807 24 | Cl 0.949717 -2.495121 2.342823 25 | Si 0.554425 -1.083142 0.647132 26 | O -1.132612 -0.717189 1.416802 27 | O 0.071121 0.123560 -0.739341 28 | C -2.589893 0.352730 -0.106638 29 | C -1.708038 1.526926 -0.094017 30 | C 0.490764 2.379455 -0.483631 31 | C -3.006164 -1.855745 0.706653 32 | C -4.221939 -1.925351 0.007062 33 | C -3.773177 0.334906 -0.806714 34 | C -4.627535 -0.793260 -0.776927 35 | C -2.172849 2.796933 0.154937 36 | C -1.313799 3.919956 0.090616 37 | C 0.065501 3.695900 -0.240430 38 | H -4.036745 1.201066 -1.403735 39 | C -5.847470 -0.852948 -1.490310 40 | H -3.217452 2.924476 0.416500 41 | C -1.754747 5.240908 0.341030 42 | C 0.965969 4.789355 -0.313323 43 | H 1.506514 2.118653 -0.750154 44 | N -2.246595 -0.760781 0.651106 45 | N -0.365691 1.357671 -0.416614 46 | H -2.628382 -2.655827 1.329316 47 | C -5.039231 -3.083183 0.061542 48 | C -6.627055 -1.992222 -1.421784 49 | C -6.223553 -3.108751 -0.645726 50 | H -4.720403 -3.933978 0.655799 51 | H -6.155903 0.000118 -2.086943 52 | H -7.563171 -2.037768 -1.970299 53 | H -6.855005 -3.991161 -0.612064 54 | C -0.858627 6.289933 0.262754 55 | C 0.503216 6.064953 -0.064196 56 | H 2.006759 4.609126 -0.564540 57 | H -2.796963 5.414307 0.591210 58 | H -1.198281 7.303546 0.453621 59 | H 1.185107 6.907967 -0.118038 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.345258 -0.596284 -0.078798 4 | C 3.528023 -0.484937 0.516300 5 | C 4.710751 -0.605723 -0.377833 6 | H 3.602111 0.306287 1.267772 7 | C 4.636233 -1.272125 -1.610930 8 | C 5.926978 -0.043298 0.040468 9 | C 5.769603 -1.364306 -2.418618 10 | H 3.692066 -1.704032 -1.927310 11 | C 7.058220 -0.137469 -0.770498 12 | H 5.980615 0.471447 0.997125 13 | C 6.981753 -0.800310 -2.000899 14 | H 5.709797 -1.875529 -3.375609 15 | H 7.995462 0.306049 -0.446107 16 | H 7.862388 -0.875605 -2.633038 17 | C 3.888447 -1.952202 1.739923 18 | C 2.601314 -2.100087 2.189020 19 | H 4.615997 -1.473562 2.394678 20 | H 4.293226 -2.757075 1.125526 21 | C 1.346129 -1.949511 2.184575 22 | H 0.544408 -2.367689 2.775304 23 | Cl 1.135854 1.120323 2.011778 24 | Cl 0.269950 -2.523798 -0.592198 25 | Si 0.746242 -0.682470 0.667099 26 | O 0.078504 0.320652 -0.735289 27 | O -0.969801 -0.680702 1.452523 28 | C -1.986184 1.318998 -0.168936 29 | C -2.598653 -0.015770 -0.125093 30 | C -2.587895 -2.204662 0.831632 31 | C -0.024831 2.620055 -0.584881 32 | C -0.732853 3.818694 -0.399423 33 | C -2.722422 2.464880 0.022305 34 | C -2.130737 3.746053 -0.081908 35 | C -3.742165 -0.313464 -0.828322 36 | C -4.361440 -1.581726 -0.724675 37 | C -3.758432 -2.555827 0.139462 38 | H -3.772985 2.370660 0.272974 39 | C -2.852528 4.945658 0.122307 40 | H -4.159800 0.444211 -1.481590 41 | C -5.535034 -1.925675 -1.435822 42 | C -4.337522 -3.843309 0.274015 43 | H -2.069651 -2.877030 1.501920 44 | N -0.636853 1.440473 -0.476110 45 | N -2.053291 -0.989406 0.703545 46 | H 1.028489 2.581034 -0.829492 47 | C -0.091695 5.079018 -0.506759 48 | C -2.205383 6.161932 0.014270 49 | C -0.823852 6.229977 -0.300053 50 | H 0.966413 5.120912 -0.745787 51 | H -3.909820 4.895198 0.364638 52 | H -2.759330 7.082373 0.173109 53 | H -0.341268 7.199412 -0.376635 54 | C -6.080918 -3.186769 -1.288508 55 | C -5.482474 -4.147150 -0.433386 56 | H -3.871926 -4.572908 0.929379 57 | H -5.993668 -1.191627 -2.091382 58 | H -6.981407 -3.450806 -1.835068 59 | H -5.932455 -5.130544 -0.338570 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 1.235391 -1.438550 -0.072324 4 | C 1.646069 -1.175001 1.157124 5 | C 3.061976 -0.747604 1.275391 6 | H 0.948414 -0.620796 1.790366 7 | C 4.012853 -1.074559 0.295744 8 | C 3.432877 0.042261 2.374180 9 | C 5.318219 -0.600310 0.411792 10 | H 3.716600 -1.683463 -0.552389 11 | C 4.740450 0.516276 2.486085 12 | H 2.691072 0.294257 3.128438 13 | C 5.684663 0.196217 1.504502 14 | H 6.051802 -0.846852 -0.350769 15 | H 5.021254 1.136927 3.332334 16 | H 6.702508 0.567000 1.588974 17 | C 1.618775 -2.812054 2.273639 18 | C 0.550200 -3.388453 1.641021 19 | H 1.478576 -2.384769 3.266398 20 | H 2.596722 -3.261555 2.101130 21 | C -0.314460 -3.561538 0.731134 22 | H -1.004984 -4.365664 0.519432 23 | Cl 0.589964 -3.188966 -2.217819 24 | Cl -2.442630 -2.603433 -1.287584 25 | Si -0.382866 -1.983550 -0.607420 26 | O -1.141379 -0.935982 0.791590 27 | O -0.535760 -0.499921 -1.727856 28 | C -1.855521 1.169067 -0.021880 29 | C -0.473834 1.462449 -0.426159 30 | C 1.375897 0.807540 -1.790670 31 | C -3.374178 -0.406280 0.936017 32 | C -4.444926 0.494909 0.812274 33 | C -2.867173 2.088876 -0.156081 34 | C -4.189323 1.793262 0.256213 35 | C 0.212033 2.573652 0.003266 36 | C 1.531568 2.834778 -0.438700 37 | C 2.124978 1.919216 -1.372813 38 | H -2.638067 3.047574 -0.607802 39 | C -5.258667 2.710690 0.131232 40 | H -0.267558 3.238175 0.713494 41 | C 2.290661 3.938044 0.017137 42 | C 3.454128 2.122608 -1.822460 43 | H 1.748231 0.052599 -2.471176 44 | N -2.143255 -0.066755 0.549846 45 | N 0.144186 0.603776 -1.324631 46 | H -3.473629 -1.396753 1.358998 47 | C -5.755037 0.144028 1.226646 48 | C -6.526805 2.346092 0.543063 49 | C -6.776367 1.061720 1.090191 50 | H -5.937186 -0.841711 1.643763 51 | H -5.069370 3.693441 -0.289950 52 | H -7.347672 3.050441 0.446330 53 | H -7.782968 0.801611 1.402813 54 | C 3.585802 4.112143 -0.432342 55 | C 4.169659 3.203237 -1.351406 56 | H 3.894385 1.418411 -2.521049 57 | H 1.846210 4.633527 0.722679 58 | H 4.170202 4.955451 -0.076501 59 | H 5.191285 3.361522 -1.682394 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.258594 -1.279574 -0.176616 4 | C -2.377419 -1.954931 -0.396625 5 | C -3.502891 -1.187833 -0.993684 6 | H -2.248043 -2.961822 -0.800795 7 | C -3.482723 0.212111 -1.077014 8 | C -4.602651 -1.895501 -1.507232 9 | C -4.553328 0.896002 -1.652854 10 | H -2.620821 0.754296 -0.711577 11 | C -5.671207 -1.210723 -2.083956 12 | H -4.614428 -2.981543 -1.457316 13 | C -5.652212 0.187987 -2.152462 14 | H -4.525945 1.980298 -1.718319 15 | H -6.515970 -1.764894 -2.483202 16 | H -6.485424 0.721441 -2.601668 17 | C -3.203938 -2.550201 1.290169 18 | C -2.021422 -2.771547 1.943770 19 | H -3.774043 -3.409241 0.938834 20 | H -3.810265 -1.706995 1.622138 21 | C -0.773267 -2.726723 2.145067 22 | H -0.155262 -3.006488 2.985848 23 | Cl 2.220781 -2.459563 1.534006 24 | Cl 0.265064 -3.762380 -0.666953 25 | Si 0.264076 -1.882348 0.543674 26 | O 1.067680 -0.955331 -0.844386 27 | O 0.425419 -0.317848 1.612427 28 | C 2.011573 1.087950 -0.121471 29 | C 0.670112 1.573206 0.235158 30 | C -1.271209 1.249501 1.591623 31 | C 3.351821 -0.699030 -0.973825 32 | C 4.518761 0.076190 -0.873782 33 | C 3.124874 1.886881 -0.008220 34 | C 4.408337 1.418719 -0.379082 35 | C 0.174120 2.774266 -0.214731 36 | C -1.081405 3.260750 0.222697 37 | C -1.819229 2.471766 1.168508 38 | H 3.007291 2.887580 0.392488 39 | C 5.576295 2.209504 -0.272104 40 | H 0.761680 3.343521 -0.926516 41 | C -1.637223 4.477587 -0.238234 42 | C -3.084966 2.914170 1.631066 43 | H -1.757725 0.587628 2.295788 44 | N 2.166234 -0.199402 -0.624185 45 | N -0.088933 0.834766 1.136120 46 | H 3.338387 -1.714901 -1.346012 47 | C 5.783628 -0.443643 -1.248303 48 | C 6.798406 1.681283 -0.643608 49 | C 6.903575 0.353838 -1.131709 50 | H 5.853256 -1.461779 -1.618706 51 | H 5.497073 3.225536 0.102502 52 | H 7.694784 2.288689 -0.560791 53 | H 7.876915 -0.035405 -1.413923 54 | C -2.872868 4.886884 0.225377 55 | C -3.597899 4.105059 1.160951 56 | H -3.637156 2.307122 2.342141 57 | H -1.084696 5.076010 -0.956051 58 | H -3.299614 5.819847 -0.130489 59 | H -4.567437 4.450343 1.506387 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.425997 -0.455588 0.280316 4 | C 3.364093 -1.385378 0.113274 5 | C 4.646577 -0.893374 -0.465139 6 | H 3.480279 -2.083049 0.947000 7 | C 4.701599 0.273292 -1.242894 8 | C 5.817081 -1.629238 -0.227131 9 | C 5.920717 0.701484 -1.768019 10 | H 3.791968 0.838069 -1.421488 11 | C 7.035357 -1.197746 -0.753872 12 | H 5.771145 -2.531124 0.378822 13 | C 7.088994 -0.032479 -1.526751 14 | H 5.963003 1.609123 -2.364108 15 | H 7.940726 -1.765718 -0.558645 16 | H 8.037130 0.304542 -1.936923 17 | C 2.874041 -2.693641 -1.203154 18 | C 1.525017 -2.682665 -0.945210 19 | H 3.454286 -3.553920 -0.869383 20 | H 3.191927 -2.284305 -2.162564 21 | C 0.444583 -2.268873 -0.440882 22 | H -0.572759 -2.588263 -0.606068 23 | Cl 1.042346 1.117434 2.208462 24 | Cl 1.267481 -2.112369 2.520672 25 | Si 0.779931 -0.655584 0.888612 26 | O 0.178920 0.352070 -0.587569 27 | O -1.030208 -0.690756 1.483575 28 | C -1.941491 1.317185 -0.206740 29 | C -2.536557 -0.026275 -0.217399 30 | C -2.617842 -2.199295 0.780131 31 | C 0.029387 2.648225 -0.425041 32 | C -0.709186 3.835096 -0.287361 33 | C -2.709360 2.449721 -0.065747 34 | C -2.128889 3.740057 -0.098383 35 | C -3.629305 -0.333013 -0.995414 36 | C -4.264692 -1.594517 -0.916025 37 | C -3.738255 -2.555498 0.012493 38 | H -3.776001 2.337959 0.093355 39 | C -2.882880 4.926785 0.059105 40 | H -3.999449 0.418454 -1.683922 41 | C -5.387805 -1.942417 -1.703053 42 | C -4.343905 -3.832511 0.135661 43 | H -2.153403 -2.856207 1.505164 44 | N -0.573178 1.459086 -0.391955 45 | N -2.048238 -0.995122 0.656070 46 | H 1.101524 2.625273 -0.569229 47 | C -0.078975 5.104993 -0.316357 48 | C -2.245970 6.152919 0.028641 49 | C -0.843026 6.243113 -0.159086 50 | H 0.995929 5.165126 -0.455744 51 | H -3.956603 4.858551 0.205521 52 | H -2.824524 7.063559 0.152199 53 | H -0.368865 7.219571 -0.175881 54 | C -5.959511 -3.192974 -1.566085 55 | C -5.438181 -4.139037 -0.646256 56 | H -3.939520 -4.550817 0.842103 57 | H -5.789682 -1.218867 -2.405857 58 | H -6.822178 -3.459467 -2.169370 59 | H -5.908483 -5.113615 -0.560051 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.217790 -1.314879 0.132639 4 | C 3.062192 -0.402583 -0.323002 5 | C 4.406850 -0.901242 -0.715109 6 | H 2.639017 0.332336 -1.013954 7 | C 4.924288 -2.100130 -0.200870 8 | C 5.165877 -0.141287 -1.618103 9 | C 6.188647 -2.534340 -0.597738 10 | H 4.329295 -2.684059 0.494093 11 | C 6.430351 -0.579282 -2.012674 12 | H 4.757985 0.785333 -2.015565 13 | C 6.944436 -1.776094 -1.501066 14 | H 6.586139 -3.466434 -0.205677 15 | H 7.010981 0.007169 -2.719234 16 | H 7.928750 -2.119440 -1.807569 17 | C 3.567159 0.873225 1.073015 18 | C 2.363211 0.873788 1.730105 19 | H 3.848299 1.745337 0.482628 20 | H 4.401181 0.392810 1.584825 21 | C 1.214932 0.446920 2.038370 22 | H 0.520377 0.681432 2.832035 23 | Cl -0.173025 -2.667967 -0.629001 24 | Cl 0.890344 -2.515076 2.444185 25 | Si 0.573513 -1.090012 0.748767 26 | O -1.120594 -0.680831 1.465027 27 | O 0.194464 0.163218 -0.637520 28 | C -2.537582 0.302243 -0.141409 29 | C -1.688390 1.499479 -0.109424 30 | C 0.487236 2.437922 -0.388115 31 | C -2.961262 -1.874027 0.749522 32 | C -4.141911 -1.992899 -0.001717 33 | C -3.683673 0.234678 -0.897859 34 | C -4.522191 -0.904907 -0.858076 35 | C -2.215437 2.754309 0.090489 36 | C -1.403072 3.911823 0.057595 37 | C -0.000933 3.739503 -0.193262 38 | H -3.931208 1.070374 -1.542924 39 | C -5.703728 -1.016552 -1.627684 40 | H -3.277682 2.842658 0.289143 41 | C -1.910327 5.216324 0.262864 42 | C 0.858541 4.866907 -0.236564 43 | H 1.524921 2.227295 -0.603032 44 | N -2.214764 -0.771191 0.676595 45 | N -0.322752 1.377849 -0.350248 46 | H -2.598280 -2.641639 1.420167 47 | C -4.945173 -3.159844 0.065408 48 | C -6.470316 -2.163561 -1.544995 49 | C -6.091155 -3.236918 -0.698941 50 | H -4.645279 -3.977753 0.713175 51 | H -5.993365 -0.196502 -2.277666 52 | H -7.376737 -2.249070 -2.136891 53 | H -6.711032 -4.127099 -0.656504 54 | C -1.053267 6.299476 0.217819 55 | C 0.332402 6.125692 -0.032129 56 | H 1.917773 4.725127 -0.428712 57 | H -2.971018 5.349760 0.452802 58 | H -1.442527 7.300866 0.375356 59 | H 0.981913 6.994992 -0.061666 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/5a/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by (S)-[3,3'-biisoquinoline]-2,2'-dioxide (Cat 5a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.645080 -0.008363 -0.013753 4 | C 3.748795 -0.743244 -0.127178 5 | C 4.925607 -0.037697 -0.700919 6 | H 3.598931 -1.760210 -0.499963 7 | C 5.071383 1.354521 -0.594525 8 | C 5.910814 -0.796240 -1.351222 9 | C 6.190849 1.978373 -1.144042 10 | H 4.305964 1.933372 -0.087031 11 | C 7.028790 -0.167895 -1.901622 12 | H 5.792392 -1.874132 -1.432200 13 | C 7.171633 1.220074 -1.796756 14 | H 6.301270 3.056484 -1.065219 15 | H 7.784373 -0.757767 -2.412972 16 | H 8.042500 1.710248 -2.223489 17 | C 4.473691 -1.265476 1.598751 18 | C 3.274565 -1.393272 2.253126 19 | H 5.112400 -0.436164 1.904010 20 | H 5.012068 -2.170938 1.319571 21 | C 2.031760 -1.255575 2.437639 22 | H 1.370439 -1.439568 3.271960 23 | Cl 1.127831 1.564439 1.865898 24 | Cl 1.023550 -2.481169 -0.212205 25 | Si 1.129121 -0.434028 0.777847 26 | O 0.211217 0.206652 -0.705037 27 | O -0.545212 -0.698585 1.656186 28 | C -1.962915 0.801937 -0.110255 29 | C -2.252646 -0.637049 0.071311 30 | C -1.804870 -2.622123 1.330152 31 | C -0.383016 2.445114 -0.843077 32 | C -1.305765 3.446427 -0.723447 33 | C -2.939170 1.810665 0.099245 34 | C -2.603377 3.170396 -0.231541 35 | C -3.273197 -1.305604 -0.653416 36 | C -3.574403 -2.670929 -0.313393 37 | C -2.820692 -3.293828 0.709146 38 | H -3.024543 -4.320188 0.993374 39 | H -1.158414 -3.030991 2.092901 40 | N -0.733090 1.156759 -0.532576 41 | N -1.541569 -1.318451 0.994120 42 | H 0.638505 2.567555 -1.172699 43 | H -1.022707 4.460008 -0.985018 44 | C -3.988253 -0.681354 -1.711064 45 | C -4.600955 -3.350819 -1.013473 46 | C -5.289994 -2.711879 -2.023049 47 | H -6.074242 -3.235927 -2.560872 48 | C -4.973848 -1.375996 -2.377518 49 | C -4.221514 1.525996 0.640427 50 | C -3.569678 4.188770 -0.044516 51 | C -4.812423 3.878507 0.466967 52 | H -5.550077 4.661678 0.613105 53 | C -5.133492 2.543050 0.818879 54 | H -3.309299 5.210996 -0.301803 55 | H -6.108929 2.320227 1.239942 56 | H -4.475515 0.511002 0.920787 57 | H -3.751262 0.335895 -1.998423 58 | H -5.512034 -0.896265 -3.189063 59 | H -4.825133 -4.379401 -0.747297 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.782322 -0.853477 0.043771 4 | C -3.098905 -0.914772 -0.076942 5 | C -3.761246 0.384972 -0.365687 6 | H -3.611416 -1.546750 0.653307 7 | C -3.068632 1.435613 -0.988810 8 | C -5.098978 0.561484 0.017802 9 | C -3.706382 2.655448 -1.207842 10 | H -2.036737 1.290006 -1.290526 11 | C -5.734901 1.784248 -0.203911 12 | H -5.632224 -0.253558 0.501161 13 | C -5.039729 2.832991 -0.816130 14 | H -3.165151 3.469968 -1.681552 15 | H -6.767714 1.920453 0.104191 16 | H -5.534152 3.785316 -0.987351 17 | C -3.642599 -1.962268 -1.641125 18 | C -2.585731 -2.832343 -1.602282 19 | H -3.671178 -1.251308 -2.467004 20 | H -4.618849 -2.314037 -1.308759 21 | C -1.460730 -3.288074 -1.243911 22 | H -0.865508 -4.123507 -1.583107 23 | Cl -1.787555 -3.126397 1.901897 24 | Cl 1.052136 -3.683336 0.476204 25 | Si -0.601170 -2.165288 0.269700 26 | O 0.350057 -1.257695 -1.135973 27 | O 0.345493 -1.118914 1.497040 28 | C 2.070657 0.022049 -0.220723 29 | C 1.034194 0.838210 0.448894 30 | C -0.699773 0.873468 2.099299 31 | C 2.531710 -1.773889 -1.731005 32 | C 3.876171 -1.533109 -1.669999 33 | C 3.457317 0.284576 -0.077948 34 | C 4.386931 -0.511614 -0.834421 35 | C 0.866928 2.227087 0.216287 36 | C -0.115621 2.938036 0.990739 37 | C -0.872557 2.220654 1.947915 38 | H -1.616060 2.728726 2.552009 39 | H -1.256968 0.238847 2.773432 40 | N 1.662948 -0.996635 -1.007161 41 | N 0.235610 0.220376 1.340030 42 | H 2.059937 -2.547048 -2.319521 43 | H 4.549409 -2.149288 -2.255722 44 | C 1.602855 2.923661 -0.779102 45 | C -0.310449 4.321305 0.761386 46 | C 0.427150 4.973690 -0.204685 47 | H 0.273109 6.033832 -0.381248 48 | C 1.381716 4.268770 -0.980525 49 | C 3.955968 1.284079 0.800561 50 | C 5.775492 -0.261230 -0.711709 51 | C 6.228496 0.727293 0.136949 52 | H 7.293739 0.914605 0.232300 53 | C 5.313767 1.495899 0.900238 54 | H 6.469471 -0.865017 -1.288626 55 | H 5.688937 2.256554 1.577821 56 | H 3.268829 1.870906 1.398210 57 | H 2.328105 2.393113 -1.384647 58 | H 1.941402 4.794687 -1.747745 59 | H -1.052929 4.850065 1.351161 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.851786 -0.322186 0.172793 4 | C -2.930929 0.257051 0.662624 5 | C -3.953723 0.716780 -0.309420 6 | H -2.740555 0.957658 1.483313 7 | C -4.031447 0.171852 -1.600887 8 | C -4.852137 1.722769 0.082980 9 | C -5.000929 0.636251 -2.489384 10 | H -3.332325 -0.605237 -1.891268 11 | C -5.816957 2.186332 -0.810299 12 | H -4.788681 2.140440 1.085272 13 | C -5.894464 1.641104 -2.097706 14 | H -5.060572 0.216430 -3.489787 15 | H -6.506074 2.969368 -0.506708 16 | H -6.647636 1.999709 -2.794051 17 | C -4.069854 -0.916327 1.815647 18 | C -3.067296 -1.775320 2.155592 19 | H -4.863020 -1.302102 1.175379 20 | H -4.382251 -0.154473 2.527304 21 | C -1.959711 -2.381747 2.062427 22 | H -1.545684 -3.215228 2.612128 23 | Cl 0.576435 -3.491706 0.800814 24 | Cl -2.078760 -2.993159 -0.984639 25 | Si -0.852406 -1.769905 0.440579 26 | O 0.123100 -1.084537 -0.995996 27 | O 0.318333 -0.817887 1.631223 28 | C 2.135804 -0.176871 -0.260199 29 | C 1.346006 0.877099 0.413259 30 | C -0.187991 1.387385 2.175156 31 | C 2.091832 -2.085233 -1.705058 32 | C 3.457523 -2.133299 -1.748147 33 | C 3.552988 -0.217326 -0.217201 34 | C 4.232759 -1.218639 -0.996456 35 | C 1.486507 2.255847 0.110167 36 | C 0.767927 3.211253 0.910915 37 | C -0.051224 2.730740 1.960921 38 | H -0.590831 3.424631 2.596294 39 | H -0.796850 0.935609 2.945452 40 | N 1.469479 -1.114365 -0.963134 41 | N 0.492247 0.494928 1.385300 42 | H 1.421815 -2.761030 -2.216366 43 | H 3.939744 -2.897063 -2.348271 44 | C 2.290616 2.718200 -0.965572 45 | C 0.898293 4.592227 0.627391 46 | C 1.695596 5.011890 -0.417390 47 | H 1.790993 6.071165 -0.635743 48 | C 2.386873 4.069319 -1.219356 49 | C 4.316469 0.675623 0.582484 50 | C 5.648027 -1.269134 -0.977202 51 | C 6.362483 -0.377609 -0.204576 52 | H 7.447235 -0.421539 -0.188151 53 | C 5.691576 0.591036 0.584042 54 | H 6.152723 -2.025145 -1.570883 55 | H 6.269375 1.270499 1.202837 56 | H 3.816960 1.412825 1.199759 57 | H 2.818077 2.006953 -1.589839 58 | H 2.996220 4.416439 -2.047981 59 | H 0.357588 5.306867 1.240410 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.771196 -0.047327 0.504366 4 | C 3.184687 -0.105739 -0.759113 5 | C 4.620123 0.224803 -0.976301 6 | H 2.505365 0.328931 -1.497793 7 | C 5.566866 0.101900 0.052353 8 | C 5.022885 0.659617 -2.248369 9 | C 6.902700 0.418919 -0.193299 10 | H 5.247550 -0.230463 1.035006 11 | C 6.360261 0.976620 -2.489846 12 | H 4.286282 0.755475 -3.042886 13 | C 7.302967 0.854537 -1.462992 14 | H 7.633517 0.329817 0.605823 15 | H 6.665933 1.320904 -3.473966 16 | H 8.344676 1.101052 -1.649549 17 | C 3.126289 -1.905920 -1.454329 18 | C 2.028262 -2.322952 -0.742817 19 | H 4.082186 -2.337861 -1.156403 20 | H 3.023917 -1.737032 -2.526147 21 | C 1.163247 -2.278537 0.177177 22 | H 0.499505 -3.034444 0.568854 23 | Cl 1.080049 1.552750 2.164718 24 | Cl 1.968687 -1.469147 2.944834 25 | Si 1.170148 -0.418975 1.150387 26 | O 0.336205 0.203165 -0.457724 27 | O -0.612158 -0.704885 1.814068 28 | C -1.874720 0.797844 -0.079561 29 | C -2.166270 -0.643589 0.071693 30 | C -1.843980 -2.620135 1.383781 31 | C -0.238548 2.448617 -0.649009 32 | C -1.172997 3.445730 -0.611610 33 | C -2.871457 1.800568 0.043560 34 | C -2.510851 3.163201 -0.247180 35 | C -3.115859 -1.319915 -0.739229 36 | C -3.442591 -2.685425 -0.425135 37 | C -2.791414 -3.299860 0.671281 38 | H -3.027295 -4.321627 0.948253 39 | H -1.287990 -3.013568 2.223596 40 | N -0.610900 1.155992 -0.381753 41 | N -1.535458 -1.320490 1.055933 42 | H 0.809280 2.581602 -0.874015 43 | H -0.868812 4.461876 -0.837362 44 | C -3.736447 -0.700887 -1.857155 45 | C -4.396432 -3.372030 -1.214145 46 | C -4.994977 -2.738179 -2.283456 47 | H -5.725101 -3.266733 -2.888701 48 | C -4.655521 -1.401061 -2.608495 49 | C -4.196604 1.509462 0.465149 50 | C -3.493599 4.177841 -0.144269 51 | C -4.776754 3.861522 0.250399 52 | H -5.526870 4.642053 0.333548 53 | C -5.123956 2.523496 0.565272 54 | H -3.214385 5.202540 -0.370038 55 | H -6.132445 2.296134 0.896506 56 | H -4.472729 0.493044 0.718212 57 | H -3.481297 0.318084 -2.121540 58 | H -5.121919 -0.923562 -3.464600 59 | H -4.639248 -4.400646 -0.965660 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -2.638545 -0.531406 0.040868 4 | C -3.790710 -0.119118 -0.477861 5 | C -4.890856 0.094894 0.501722 6 | H -4.090465 -0.618061 -1.403564 7 | C -4.631079 0.331968 1.860414 8 | C -6.215302 0.064304 0.038674 9 | C -5.690882 0.528035 2.745757 10 | H -3.604695 0.345401 2.213342 11 | C -7.272814 0.259951 0.927554 12 | H -6.412304 -0.122252 -1.014402 13 | C -7.012270 0.494667 2.282405 14 | H -5.488891 0.702518 3.799086 15 | H -8.296833 0.225302 0.566318 16 | H -7.835210 0.646326 2.975600 17 | C -3.658571 1.659180 -1.231667 18 | C -2.361985 1.553825 -1.668241 19 | H -3.850423 2.350523 -0.410331 20 | H -4.454899 1.612611 -1.974302 21 | C -1.218395 1.032323 -1.781270 22 | H -0.311867 1.335093 -2.283754 23 | Cl -0.841567 -2.733554 0.317827 24 | Cl -1.945250 -1.822435 -2.599111 25 | Si -1.108246 -0.832114 -0.781160 26 | O 0.613307 -0.889009 -1.608722 27 | O -0.230118 -0.006707 0.716777 28 | C 2.299765 -0.560709 -0.034197 29 | C 1.839469 0.839773 0.076790 30 | C 0.056030 2.298654 0.726866 31 | C 2.051903 -2.654497 -1.168201 32 | C 3.132236 -3.180804 -0.516788 33 | C 3.390038 -1.073713 0.714994 34 | C 3.826033 -2.420549 0.454445 35 | C 2.675588 1.953518 -0.196553 36 | C 2.160684 3.274432 0.051529 37 | C 0.835600 3.404637 0.532808 38 | H 0.419243 4.385679 0.734104 39 | H -0.969538 2.304828 1.066369 40 | N 1.663062 -1.364498 -0.910693 41 | N 0.571122 1.048026 0.489405 42 | H 1.446203 -3.170949 -1.898511 43 | H 3.437187 -4.197868 -0.737909 44 | C 3.986486 1.808667 -0.725323 45 | C 2.983557 4.398636 -0.201319 46 | C 4.259179 4.225289 -0.697028 47 | H 4.887408 5.089043 -0.892304 48 | C 4.756135 2.925593 -0.968031 49 | C 4.045357 -0.316260 1.722938 50 | C 4.921055 -2.947877 1.181015 51 | C 5.549442 -2.181381 2.140144 52 | H 6.386546 -2.589559 2.698273 53 | C 5.101989 -0.864677 2.416401 54 | H 5.245629 -3.963139 0.974639 55 | H 5.594701 -0.283426 3.189559 56 | H 3.707040 0.687560 1.949972 57 | H 4.375264 0.821069 -0.942879 58 | H 5.754947 2.809347 -1.376949 59 | H 2.589769 5.391070 -0.004535 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -2.638910 -0.155724 0.074947 4 | C -3.784980 0.302086 -0.420506 5 | C -4.935107 0.298396 0.522207 6 | H -3.702195 1.201348 -1.037032 7 | C -4.978965 -0.566969 1.626561 8 | C -5.998349 1.183128 0.284035 9 | C -6.074863 -0.535116 2.488520 10 | H -4.152920 -1.248615 1.803284 11 | C -7.092203 1.212708 1.149480 12 | H -5.960268 1.850628 -0.573944 13 | C -7.132875 0.351960 2.252255 14 | H -6.105727 -1.200902 3.346709 15 | H -7.908919 1.905450 0.966759 16 | H -7.984707 0.373031 2.926607 17 | C -4.494060 -0.835137 -1.826751 18 | C -3.285477 -1.183773 -2.373342 19 | H -5.115071 -0.112236 -2.355075 20 | H -5.050089 -1.621918 -1.315935 21 | C -2.028551 -1.311603 -2.426807 22 | H -1.357036 -1.799999 -3.117880 23 | Cl -1.151307 1.577154 -1.809147 24 | Cl -1.000640 -2.525959 0.143040 25 | Si -1.127312 -0.454192 -0.783239 26 | O -0.203974 0.139099 0.719835 27 | O 0.545229 -0.666246 -1.675210 28 | C 1.951910 0.796652 0.134227 29 | C 2.262934 -0.630040 -0.099206 30 | C 1.833416 -2.581719 -1.414565 31 | C 0.351115 2.382171 0.945083 32 | C 1.257094 3.402077 0.860987 33 | C 2.910512 1.828831 -0.040744 34 | C 2.555472 3.167836 0.349256 35 | C 3.299524 -1.305621 0.596087 36 | C 3.618553 -2.654760 0.210844 37 | C 2.864829 -3.256922 -0.823837 38 | H 3.081247 -4.270759 -1.141594 39 | H 1.188149 -2.977903 -2.184676 40 | N 0.718997 1.113594 0.577799 41 | N 1.554364 -1.292872 -1.037171 42 | H -0.668559 2.474667 1.289864 43 | H 0.960283 4.398904 1.167992 44 | C 4.012543 -0.705307 1.668807 45 | C 4.661135 -3.340662 0.880924 46 | C 5.348080 -2.723979 1.905562 47 | H 6.144377 -3.252757 2.420568 48 | C 5.013538 -1.405612 2.305714 49 | C 4.193554 1.588053 -0.601802 50 | C 3.504664 4.208349 0.201169 51 | C 4.748948 3.940021 -0.329948 52 | H 5.473682 4.740182 -0.445672 53 | C 5.088313 2.626354 -0.741347 54 | H 3.230533 5.214145 0.504597 55 | H 6.064384 2.437356 -1.177198 56 | H 4.462193 0.590231 -0.927055 57 | H 3.761477 0.297721 1.991762 58 | H 5.549499 -0.944133 3.129231 59 | H 4.898638 -4.356559 0.579690 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.787389 -1.113599 0.188942 4 | C -2.245997 -0.522017 -0.904772 5 | C -3.387829 0.404417 -0.704306 6 | H -1.490778 -0.159610 -1.607010 7 | C -4.263726 0.276820 0.385384 8 | C -3.562555 1.449748 -1.624087 9 | C -5.297947 1.196665 0.553319 10 | H -4.120559 -0.533199 1.093575 11 | C -4.596507 2.370264 -1.450442 12 | H -2.879778 1.546224 -2.465013 13 | C -5.466729 2.243981 -0.362211 14 | H -5.973712 1.100360 1.398647 15 | H -4.722072 3.184040 -2.159106 16 | H -6.273583 2.958913 -0.226212 17 | C -3.024589 -1.839730 -2.146131 18 | C -2.165463 -2.855209 -1.821416 19 | H -2.900524 -1.328334 -3.100198 20 | H -4.057128 -1.941467 -1.811761 21 | C -1.295440 -3.475551 -1.140642 22 | H -0.934390 -4.493933 -1.168473 23 | Cl -1.534724 -3.337851 1.952195 24 | Cl 1.314962 -3.683239 0.472716 25 | Si -0.444722 -2.291019 0.318630 26 | O 0.437410 -1.318016 -1.099056 27 | O 0.439732 -1.179140 1.541589 28 | C 2.006902 0.150356 -0.187275 29 | C 0.893810 0.846133 0.495094 30 | C -0.797076 0.688617 2.183435 31 | C 2.656382 -1.597110 -1.686390 32 | C 3.965528 -1.206875 -1.638609 33 | C 3.356744 0.568343 -0.060070 34 | C 4.363924 -0.123566 -0.820257 35 | C 0.567620 2.207388 0.267907 36 | C -0.471068 2.804913 1.065278 37 | C -1.120376 2.008931 2.039486 38 | H -1.902278 2.431374 2.660607 39 | H -1.271139 -0.006833 2.861261 40 | N 1.710043 -0.912065 -0.965625 41 | N 0.186586 0.142881 1.400796 42 | H 2.269966 -2.425671 -2.261343 43 | H 4.699037 -1.751078 -2.223427 44 | C 1.199658 2.979547 -0.743250 45 | C -0.823952 4.157810 0.841155 46 | C -0.184761 4.885988 -0.140863 47 | H -0.459851 5.922081 -0.313358 48 | C 0.824829 4.290906 -0.938948 49 | C 3.747998 1.626029 0.804703 50 | C 5.715672 0.285722 -0.716940 51 | C 6.061966 1.327866 0.117501 52 | H 7.099530 1.637522 0.197799 53 | C 5.073550 1.992905 0.886054 54 | H 6.467804 -0.240562 -1.296806 55 | H 5.366236 2.797938 1.552941 56 | H 3.005242 2.136375 1.405773 57 | H 1.965194 2.531454 -1.365437 58 | H 1.304574 4.875158 -1.717967 59 | H -1.607561 4.602621 1.446965 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -1.842457 -0.778056 -0.120870 4 | C -3.158040 -0.886891 -0.247910 5 | C -3.901387 0.374289 -0.511409 6 | H -3.503584 -1.745140 -0.828981 7 | C -3.288183 1.631074 -0.403542 8 | C -5.246557 0.292142 -0.908671 9 | C -4.014368 2.790495 -0.676917 10 | H -2.243145 1.689968 -0.130276 11 | C -5.970494 1.451686 -1.181078 12 | H -5.720226 -0.681456 -1.007208 13 | C -5.357527 2.705089 -1.059995 14 | H -3.529812 3.760153 -0.599542 15 | H -7.008985 1.380212 -1.491710 16 | H -5.921882 3.608792 -1.273105 17 | C -3.998722 -1.461749 1.430684 18 | C -2.972865 -2.282514 1.817579 19 | H -4.911380 -1.916370 1.047036 20 | H -4.152389 -0.547737 2.004870 21 | C -1.813189 -2.788165 1.797759 22 | H -1.304670 -3.479168 2.454356 23 | Cl 0.944046 -3.582280 0.727526 24 | Cl -1.561297 -3.479575 -1.288929 25 | Si -0.667976 -2.085777 0.205050 26 | O 0.328173 -1.250501 -1.134286 27 | O 0.247073 -0.983707 1.478644 28 | C 2.102483 -0.039710 -0.233675 29 | C 1.106356 0.870909 0.373632 30 | C -0.623642 1.101781 2.012649 31 | C 2.482969 -1.940087 -1.640605 32 | C 3.838103 -1.777312 -1.563341 33 | C 3.500876 0.142084 -0.071070 34 | C 4.393248 -0.745921 -0.769573 35 | C 1.063214 2.263705 0.105713 36 | C 0.161842 3.081831 0.873732 37 | C -0.655105 2.458445 1.847609 38 | H -1.338943 3.048220 2.448082 39 | H -1.240607 0.537295 2.697353 40 | N 1.654580 -1.072146 -0.977339 41 | N 0.243496 0.344326 1.267587 42 | H 1.973102 -2.713947 -2.195823 43 | H 4.482933 -2.463218 -2.101666 44 | C 1.857256 2.866913 -0.905389 45 | C 0.104951 4.474018 0.622727 46 | C 0.896917 5.033453 -0.358553 47 | H 0.848061 6.100634 -0.552345 48 | C 1.769760 4.224094 -1.128507 49 | C 4.046216 1.147044 0.773121 50 | C 5.792342 -0.574058 -0.631671 51 | C 6.291001 0.423628 0.179339 52 | H 7.364016 0.550701 0.285996 53 | C 5.412500 1.279525 0.890418 54 | H 6.457617 -1.244590 -1.167004 55 | H 5.822317 2.045255 1.541647 56 | H 3.387866 1.801766 1.330896 57 | H 2.519513 2.255656 -1.506784 58 | H 2.372065 4.678796 -1.908802 59 | H -0.575502 5.084648 1.208198 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O 2.684622 0.089802 0.290888 4 | C 3.805853 -0.611753 0.136989 5 | C 4.897567 0.097858 -0.587439 6 | H 4.132722 -1.168654 1.019759 7 | C 4.622607 1.123805 -1.504640 8 | C 6.224956 -0.286428 -0.346675 9 | C 5.670516 1.763807 -2.165682 10 | H 3.592578 1.414859 -1.686019 11 | C 7.271460 0.357587 -1.008906 12 | H 6.434308 -1.079709 0.367058 13 | C 6.995996 1.382306 -1.920766 14 | H 5.456560 2.562486 -2.870778 15 | H 8.298651 0.063978 -0.811235 16 | H 7.810158 1.884133 -2.436521 17 | C 3.567556 -2.135092 -1.010339 18 | C 2.269825 -2.403648 -0.651092 19 | H 4.350232 -2.796444 -0.639094 20 | H 3.730798 -1.773302 -2.025969 21 | C 1.149886 -2.197926 -0.106072 22 | H 0.234084 -2.767230 -0.151782 23 | Cl 1.042460 1.513188 2.123378 24 | Cl 2.021081 -1.521341 2.753858 25 | Si 1.162112 -0.410360 1.020581 26 | O 0.284500 0.254098 -0.532984 27 | O -0.594972 -0.770641 1.721381 28 | C -1.934501 0.789079 -0.078480 29 | C -2.200993 -0.661701 0.028440 30 | C -1.814571 -2.682934 1.256322 31 | C -0.339528 2.487301 -0.626141 32 | C -1.287834 3.466974 -0.527182 33 | C -2.944402 1.769940 0.104820 34 | C -2.611703 3.148317 -0.142086 35 | C -3.163378 -1.321808 -0.781177 36 | C -3.465324 -2.701803 -0.507305 37 | C -2.775196 -3.347701 0.546740 38 | H -2.989116 -4.382565 0.790975 39 | H -1.220537 -3.101606 2.057091 40 | N -0.685503 1.180148 -0.398575 41 | N -1.534559 -1.365882 0.969719 42 | H 0.701589 2.641077 -0.870817 43 | H -1.006109 4.496220 -0.720328 44 | C -3.819728 -0.672685 -1.861076 45 | C -4.430838 -3.372784 -1.295460 46 | C -5.064780 -2.709812 -2.326033 47 | H -5.803726 -3.226401 -2.930896 48 | C -4.749605 -1.358151 -2.612689 49 | C -4.255494 1.442221 0.543094 50 | C -3.606906 4.142650 0.021897 51 | C -4.875615 3.791416 0.433194 52 | H -5.635215 4.556197 0.563453 53 | C -5.195449 2.436845 0.703089 54 | H -3.347982 5.179280 -0.171388 55 | H -6.192852 2.180721 1.046672 56 | H -4.511679 0.412502 0.760669 57 | H -3.582467 0.357245 -2.098138 58 | H -5.242981 -0.857486 -3.439943 59 | H -4.653802 -4.412868 -1.078278 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | F:19-23;2-15 C:23 L:24-57; K:1,2 3 | O -2.735679 -0.623435 -0.173377 4 | C -3.239799 0.459978 0.401551 5 | C -4.661322 0.364058 0.828028 6 | H -2.586960 0.954062 1.126930 7 | C -5.543834 -0.557172 0.243121 8 | C -5.118023 1.227508 1.835714 9 | C -6.869699 -0.613999 0.671569 10 | H -5.182507 -1.225159 -0.532177 11 | C -6.445106 1.166767 2.262004 12 | H -4.430000 1.937179 2.289567 13 | C -7.323919 0.247408 1.678532 14 | H -7.550522 -1.332203 0.223055 15 | H -6.792048 1.830622 3.048907 16 | H -8.357758 0.198825 2.009425 17 | C -3.357504 1.950715 -0.852836 18 | C -2.238114 1.636884 -1.581089 19 | H -3.327638 2.810537 -0.182865 20 | H -4.316612 1.806156 -1.350547 21 | C -1.292036 0.907706 -1.991091 22 | H -0.586159 0.987049 -2.804942 23 | Cl -0.846483 -2.691322 0.352173 24 | Cl -1.901406 -1.965410 -2.637533 25 | Si -1.128250 -0.860130 -0.864835 26 | O 0.608758 -0.910702 -1.642229 27 | O -0.327417 0.099427 0.604821 28 | C 2.238289 -0.581659 -0.015613 29 | C 1.812929 0.833358 0.027068 30 | C 0.071652 2.386325 0.541251 31 | C 2.014834 -2.686825 -1.133170 32 | C 3.056222 -3.218046 -0.424921 33 | C 3.280413 -1.099944 0.795562 34 | C 3.708523 -2.456352 0.573833 35 | C 2.706179 1.903167 -0.247770 36 | C 2.239689 3.252802 -0.070945 37 | C 0.903539 3.452660 0.349337 38 | H 0.520047 4.454964 0.505647 39 | H -0.960515 2.456672 0.847054 40 | N 1.631139 -1.389766 -0.907128 41 | N 0.534957 1.105715 0.367477 42 | H 1.435845 -3.205011 -1.883718 43 | H 3.359256 -4.240999 -0.619723 44 | C 4.031965 1.686394 -0.710797 45 | C 3.118826 4.332798 -0.326020 46 | C 4.406374 4.089480 -0.757160 47 | H 5.078752 4.918701 -0.954950 48 | C 4.858287 2.761109 -0.958151 49 | C 3.894696 -0.338561 1.825896 50 | C 4.754930 -2.990813 1.364148 51 | C 5.342866 -2.221858 2.346669 52 | H 6.142049 -2.635640 2.954042 53 | C 4.903061 -0.894670 2.582307 54 | H 5.073958 -4.013319 1.187075 55 | H 5.362998 -0.311338 3.373847 56 | H 3.561300 0.673340 2.022687 57 | H 4.388718 0.677457 -0.877815 58 | H 5.867851 2.588176 -1.317670 59 | H 2.758092 5.346928 -0.183341 60 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/6a/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by (S)-[1,1'-biisoquinoline]-2,2'-dioxide (Cat 6a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/R/ts1.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.026720 -1.751639 0.159572 4 | C -0.696826 -2.650981 -0.505690 5 | C -0.573320 -4.049430 -0.014337 6 | H -0.688017 -2.546012 -1.593760 7 | C -0.220899 -4.330926 1.314916 8 | C -0.826899 -5.100872 -0.908425 9 | C -0.114885 -5.655081 1.738892 10 | H -0.029110 -3.511381 2.000451 11 | C -0.718485 -6.424839 -0.480413 12 | H -1.096893 -4.877868 -1.938049 13 | C -0.364500 -6.703902 0.844246 14 | H 0.162903 -5.872351 2.766667 15 | H -0.905954 -7.236215 -1.178148 16 | H -0.280979 -7.734509 1.178342 17 | C -2.602555 -2.378089 -0.291679 18 | C -2.570213 -1.007932 -0.221765 19 | H -2.971599 -2.841072 -1.206796 20 | H -2.870390 -2.908765 0.622444 21 | C -2.049521 0.136199 -0.089195 22 | H -2.449051 1.133730 0.023830 23 | Cl -0.153689 0.220551 2.258883 24 | Cl 0.128617 -0.071788 -2.275300 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/R/ts2.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.196370 -0.014148 -1.769285 4 | C -0.400760 -0.782229 -2.668815 5 | C 0.073806 -0.605905 -4.066379 6 | H -1.483043 -0.886936 -2.556305 7 | C 1.348135 -0.087339 -4.346443 8 | C -0.782046 -0.964494 -5.119132 9 | C 1.753977 0.079824 -5.669754 10 | H 2.006075 0.183894 -3.527136 11 | C -0.372214 -0.794862 -6.442274 12 | H -1.768315 -1.365704 -4.897614 13 | C 0.896595 -0.273747 -6.719702 14 | H 2.738466 0.486015 -5.885757 15 | H -1.040870 -1.065023 -7.254693 16 | H 1.216237 -0.142505 -7.749839 17 | C -0.000201 -2.676414 -2.398419 18 | C 0.070184 -2.607098 -1.032783 19 | H -0.883558 -3.123489 -2.853074 20 | H 0.930378 -2.858664 -2.936205 21 | C 0.138530 -2.060374 0.106823 22 | H 0.275302 -2.460231 1.101331 23 | Cl -2.227780 0.034490 -0.114763 24 | Cl -0.039053 0.124745 2.252212 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/R/ts3.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.208795 -0.056811 -1.764964 4 | C -0.518808 -0.087209 -2.866478 5 | C -0.159116 -1.099969 -3.890211 6 | H -0.759473 0.898981 -3.279868 7 | C 0.569526 -2.252479 -3.556641 8 | C -0.560037 -0.883313 -5.219049 9 | C 0.896173 -3.174354 -4.550896 10 | H 0.870850 -2.410637 -2.526548 11 | C -0.228056 -1.806109 -6.209720 12 | H -1.127953 0.009460 -5.471139 13 | C 0.498990 -2.955260 -5.875929 14 | H 1.462604 -4.065400 -4.294462 15 | H -0.532867 -1.631864 -7.237769 16 | H 0.756780 -3.676757 -6.646473 17 | C -2.440849 -0.543125 -2.595970 18 | C -2.483080 -0.182655 -1.281291 19 | H -2.862960 0.128021 -3.341983 20 | H -2.536264 -1.603999 -2.826427 21 | C -2.049598 0.092284 -0.124207 22 | H -2.558275 0.270876 0.812641 23 | Cl -0.152995 0.250408 2.248054 24 | Cl 0.000066 -2.230030 0.174297 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/R/ts4.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O -0.045136 -1.762403 0.070045 4 | C 0.817867 -2.629023 -0.455344 5 | C 0.478569 -4.064681 -0.257454 6 | H 1.875008 -2.391671 -0.306043 7 | C -0.842789 -4.485453 -0.041509 8 | C 1.515513 -5.008986 -0.300483 9 | C -1.117338 -5.840929 0.137698 10 | H -1.639241 -3.748822 -0.007304 11 | C 1.236763 -6.364412 -0.119410 12 | H 2.537833 -4.676984 -0.466001 13 | C -0.080777 -6.782542 0.097446 14 | H -2.139541 -6.165588 0.311615 15 | H 2.043750 -7.091416 -0.143601 16 | H -0.299595 -7.837526 0.238276 17 | C 0.851872 -2.532752 -2.382990 18 | C 0.596358 -1.187527 -2.484862 19 | H 1.853173 -2.896046 -2.614267 20 | H 0.047316 -3.198371 -2.696907 21 | C 0.214985 -0.050729 -2.085147 22 | H -0.065743 0.837615 -2.630166 23 | Cl -0.146559 0.139261 2.209960 24 | Cl -2.189015 0.207204 -0.309042 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/R/ts5.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O -1.738068 0.201510 -0.185523 4 | C -2.576239 -0.488843 -0.954251 5 | C -3.991997 -0.030305 -0.926794 6 | H -2.446986 -1.574719 -0.928363 7 | C -4.336182 1.277117 -0.549923 8 | C -4.996862 -0.937219 -1.297408 9 | C -5.675492 1.666429 -0.537879 10 | H -3.555793 1.971278 -0.254840 11 | C -6.335493 -0.544360 -1.283198 12 | H -4.727776 -1.950827 -1.584719 13 | C -6.677161 0.759253 -0.905774 14 | H -5.940877 2.676356 -0.237270 15 | H -7.110245 -1.253628 -1.560673 16 | H -7.719490 1.065957 -0.893558 17 | C -2.185534 -0.272961 -2.836285 18 | C -0.823128 -0.165582 -2.709428 19 | H -2.588457 -1.208545 -3.223440 20 | H -2.725167 0.616573 -3.163352 21 | C 0.276782 -0.046948 -2.102182 22 | H 1.303101 0.011307 -2.433253 23 | Cl -0.164377 0.172151 2.200241 24 | Cl 0.045255 -2.226355 0.017927 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/S/ts1.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.032881 -1.758193 0.061844 4 | C -0.788772 -2.575487 0.718603 5 | C -0.609693 -4.023404 0.425877 6 | H -0.935738 -2.336919 1.775856 7 | C -0.041654 -4.463845 -0.779848 8 | C -1.035723 -4.958982 1.381237 9 | C 0.107470 -5.829899 -1.017661 10 | H 0.282630 -3.733381 -1.514286 11 | C -0.883764 -6.324730 1.139962 12 | H -1.477751 -4.613038 2.312583 13 | C -0.313534 -6.762464 -0.060914 14 | H 0.552375 -6.169911 -1.948853 15 | H -1.206510 -7.045588 1.885949 16 | H -0.196077 -7.825946 -0.250530 17 | C -2.635931 -2.351183 0.200449 18 | C -2.588649 -0.994751 -0.002767 19 | H -2.774998 -2.976366 -0.682219 20 | H -3.131344 -2.721491 1.097800 21 | C -2.047835 0.135147 -0.172849 22 | H -2.430880 1.116120 -0.413406 23 | Cl -0.166098 0.221726 2.258195 24 | Cl 0.136454 -0.078685 -2.266565 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/S/ts2.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.076448 -0.019991 -1.783935 4 | C 0.936258 -0.655961 -2.568839 5 | C 0.686633 -0.523528 -4.026653 6 | H 1.989002 -0.589849 -2.280517 7 | C -0.585232 -0.205088 -4.529035 8 | C 1.762597 -0.703541 -4.909599 9 | C -0.770884 -0.060644 -5.903359 10 | H -1.411787 -0.065229 -3.839598 11 | C 1.572826 -0.556193 -6.283995 12 | H 2.746755 -0.948343 -4.516718 13 | C 0.305306 -0.235973 -6.783038 14 | H -1.754274 0.189727 -6.291611 15 | H 2.410012 -0.688747 -6.963511 16 | H 0.155933 -0.122582 -7.853270 17 | C 0.810894 -2.602355 -2.339371 18 | C 0.468124 -2.566911 -1.013810 19 | H 0.032870 -2.906631 -3.039599 20 | H 1.818832 -2.912080 -2.613993 21 | C 0.069201 -2.058657 0.075302 22 | H -0.252150 -2.491424 1.012036 23 | Cl -2.219490 0.035045 -0.098755 24 | Cl -0.005610 0.105247 2.250167 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/S/ts3.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.182735 -0.017718 -1.775880 4 | C -0.494398 -0.757736 -2.646820 5 | C -0.154045 -0.562574 -4.081615 6 | H -0.645401 -1.800366 -2.356780 7 | C 0.640787 0.508232 -4.516341 8 | C -0.628780 -1.496726 -5.017537 9 | C 0.945478 0.649409 -5.870451 10 | H 1.035335 1.207659 -3.790105 11 | C -0.322653 -1.354269 -6.369880 12 | H -1.234541 -2.334752 -4.681657 13 | C 0.460608 -0.276418 -6.801063 14 | H 1.568645 1.476815 -6.199075 15 | H -0.689843 -2.083275 -7.086670 16 | H 0.699217 -0.165096 -7.855179 17 | C -2.393703 -0.295094 -2.665996 18 | C -2.481348 -0.022754 -1.326322 19 | H -2.479553 0.546656 -3.353653 20 | H -2.821216 -1.226888 -3.034196 21 | C -2.065123 0.204706 -0.153591 22 | H -2.565579 0.504127 0.755816 23 | Cl -0.169598 0.251398 2.242196 24 | Cl -0.036730 -2.217695 0.182872 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/S/ts4.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O 0.054047 -1.756015 0.119796 4 | C -0.606220 -2.647411 -0.619199 5 | C -0.328724 -4.073355 -0.290522 6 | H -1.662151 -2.419312 -0.787285 7 | C 0.873175 -4.469694 0.315574 8 | C -1.300645 -5.033845 -0.608777 9 | C 1.091669 -5.815658 0.608519 10 | H 1.620558 -3.721246 0.559623 11 | C -1.079078 -6.379614 -0.312885 12 | H -2.231368 -4.721730 -1.076848 13 | C 0.118508 -6.772970 0.294253 14 | H 2.019309 -6.120772 1.085144 15 | H -1.839235 -7.118307 -0.551099 16 | H 0.292205 -7.820393 0.525411 17 | C -0.074147 -2.605792 -2.460687 18 | C 0.150982 -1.252754 -2.528100 19 | H 0.800963 -3.252335 -2.534211 20 | H -0.967178 -3.003862 -2.942240 21 | C 0.308395 -0.080342 -2.086111 22 | H 0.594912 0.825644 -2.597750 23 | Cl -0.159822 0.163027 2.208539 24 | Cl -2.192236 0.210748 -0.330784 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/S/ts5.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | F:19-23;2-15 C:23 L:24-45; K:1,2 3 | O -1.751514 0.092809 -0.165338 4 | C -2.480054 0.902337 -0.922624 5 | C -3.946884 0.656933 -0.900870 6 | H -2.198166 1.958944 -0.887487 7 | C -4.474067 -0.595774 -0.550036 8 | C -4.809602 1.705217 -1.256169 9 | C -5.854809 -0.790071 -0.548775 10 | H -3.800520 -1.400817 -0.274233 11 | C -6.190666 1.506441 -1.252772 12 | H -4.397261 2.675032 -1.525398 13 | C -6.715216 0.257546 -0.901545 14 | H -6.262559 -1.758023 -0.270792 15 | H -6.855806 2.322886 -1.519689 16 | H -7.790499 0.101363 -0.899227 17 | C -2.122986 0.632944 -2.819822 18 | C -0.795906 0.307253 -2.694256 19 | H -2.795080 -0.175918 -3.106629 20 | H -2.392443 1.603769 -3.236548 21 | C 0.254788 -0.042878 -2.086739 22 | H 1.225936 -0.386786 -2.412358 23 | Cl -0.173915 0.136186 2.206049 24 | Cl 0.032988 -2.222539 -0.029342 25 | Si 0.000000 0.000000 0.000000 26 | O 1.875060 -0.000000 -0.000000 27 | O 0.127042 1.935326 0.000000 28 | C 2.817969 2.049798 0.619379 29 | C 2.271038 2.663665 -0.601204 30 | C 0.367843 3.179714 -1.933160 31 | C 3.066888 0.109858 1.979324 32 | C 3.874707 0.803808 2.865352 33 | C 3.631307 2.766862 1.493847 34 | C 4.162917 2.147586 2.624105 35 | C 3.072210 3.414061 -1.459448 36 | C 2.514881 4.053656 -2.564657 37 | C 1.143652 3.935594 -2.796220 38 | H 3.821661 3.812340 1.282298 39 | H 4.789455 2.709846 3.307733 40 | H 4.133194 3.477679 -1.248968 41 | H 3.141878 4.634085 -3.232229 42 | H 0.664677 4.416615 -3.641100 43 | H -0.699165 3.036219 -2.031467 44 | N 2.569844 0.733328 0.886082 45 | N 0.930979 2.567290 -0.863705 46 | H 2.795357 -0.932383 2.073428 47 | H 4.265805 0.283692 3.731801 48 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | R/ts5.xyz 6 | S/ts1.xyz 7 | S/ts2.xyz 8 | S/ts3.xyz 9 | S/ts4.xyz 10 | S/ts5.xyz 11 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/NN-dioxide/readme: -------------------------------------------------------------------------------- 1 | TS structures for the propargylation of benzaldehyde catalyzed by 2,2'-bipyridine-N,N'-dioxide (Cat 1a from Ref below) 2 | 3 | See A. C. Doney, B. J. Rooks, T. Lu, and S. E. Wheeler, "Design of Organocatalysts for Asymmetric Propargylations through Computational Screening ", ACS Catal. 6, 7948 (2016). 4 | 5 | Note: Assumes ligand is C2-symmetric! 6 | -------------------------------------------------------------------------------- /TS_geoms/Propargylation/Templates: -------------------------------------------------------------------------------- 1 | NN-dioxide 2 | 2a 3 | 3a 4 | 4a 5 | 5a 6 | 6a 7 | -------------------------------------------------------------------------------- /TS_geoms/Reactions: -------------------------------------------------------------------------------- 1 | Allylation 2 | Propargylation 3 | Dearomatization 4 | Enamide_Hydrogenation 5 | Heck_Allenylation 6 | Indole_CH_functionalization 7 | -------------------------------------------------------------------------------- /TS_geoms/Vinyl_boronic_acid_addition/BINOL/Structures: -------------------------------------------------------------------------------- 1 | R/ts1.xyz 2 | R/ts2.xyz 3 | R/ts3.xyz 4 | R/ts4.xyz 5 | S/ts1.xyz 6 | S/ts2.xyz 7 | S/ts3.xyz 8 | S/ts4.xyz 9 | -------------------------------------------------------------------------------- /TS_geoms/Vinyl_boronic_acid_addition/BINOL/readme: -------------------------------------------------------------------------------- 1 | BINOL catalyzed addition of vinyl boronic acids to heterocycle-appended enones, from May et al [Org. Lett. 14, 6104 (2012)]. 2 | -------------------------------------------------------------------------------- /TS_geoms/Vinyl_boronic_acid_addition/Templates: -------------------------------------------------------------------------------- 1 | BINOL 2 | BINOL-Ph 3 | -------------------------------------------------------------------------------- /bin/Aaron: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | use strict; 4 | use lib $ENV{'QCHASM'}; 5 | use lib $ENV{'PERL_LIB'}; 6 | 7 | use Aaron::AaronInit qw(init_main $parent write_status); 8 | use Aaron::AaronDriver qw(make_directories get_status_run analyze_result); 9 | use Aaron::AaronOutput qw(init_log print_status terminate_AARON sleep_AARON open_log_thermo 10 | close_log_thermo); 11 | #initiate AARON, reading needed information from command line and input files 12 | init_main(); 13 | init_log(print_params=>1); 14 | #clean_up($parent); 15 | 16 | my $Aaron_running = 1; 17 | 18 | while ($Aaron_running) { 19 | open_log_thermo(); 20 | make_directories(); 21 | get_status_run(); 22 | $Aaron_running = print_status(); 23 | analyze_result(); 24 | write_status(); 25 | last unless $Aaron_running; 26 | close_log_thermo(); 27 | sleep_AARON(); 28 | } 29 | 30 | terminate_AARON(); 31 | -------------------------------------------------------------------------------- /images/Allylation_RTS2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QChASM/Aaron/65051268d1235906ed94d7dc661e80cd44733fb2/images/Allylation_RTS2.png -------------------------------------------------------------------------------- /images/COOH.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QChASM/Aaron/65051268d1235906ed94d7dc661e80cd44733fb2/images/COOH.png -------------------------------------------------------------------------------- /images/Et.png: 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| 23 | =item B<--restart> 24 | 25 | Restart AARON workflow. All failed and repeated conformers will be recoverd. 26 | You should know what you are doing when using this flag! 27 | 28 | =item B<--record> 29 | 30 | The overwritten failed .log file will be saved for further examination 31 | 32 | =item B<--sleep> 33 | 34 | Sleeping time interval between neighboring circles 35 | 36 | =item B<--short> 37 | 38 | Use short wall time for all computations 39 | 40 | =back 41 | 42 | =cut 43 | -------------------------------------------------------------------------------- /test/environment_setup/environment_setup.t: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | # Test environmental variables are set appropriately 4 | # and that necessry configuration files are found 5 | 6 | use strict; 7 | use warnings; 8 | 9 | use Test::More; 10 | 11 | ok( $ENV{QCHASM}, 12 | "QCHASM environmental variable should be set to QCHASM path." ); 13 | 14 | my $QCHASM = $ENV{QCHASM}; 15 | ok( -f "$QCHASM/Aaron/.aaronrc", 16 | "$QCHASM/Aaron/.aaronrc should exist for storing group-specific configuration details." 17 | ); 18 | 19 | if ( -f "$ENV{HOME}/.aaronrc" ) { 20 | pass("$ENV{HOME}/.aaronrc exists"); 21 | } else { 22 | diag( 23 | "WARNING: $ENV{HOME}/.aaronrc not found. " . 24 | "This is optional, but useful for storing user-specific configuration details." 25 | ); 26 | } 27 | 28 | done_testing(); 29 | -------------------------------------------------------------------------------- /test/test_full_install.t: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | # Move through testing directories in the appropriate order 4 | 5 | use strict; 6 | use warnings; 7 | 8 | use Test::More; 9 | use Data::Dumper; 10 | 11 | my @tests = ( 'environment_setup', 12 | 'job_setup' ); 13 | 14 | # run each test 15 | my @failed; 16 | foreach my $t (@tests) { 17 | eval { 18 | chdir($t); 19 | my $status = system "./$t.t 1>/dev/null 2>stderr.tmp"; 20 | push @failed, $t if ($status); 21 | ok( !$status, "$t" ); 22 | if ( $status && -f 'stderr.tmp' ) { 23 | open ERR, '<', 'stderr.tmp'; 24 | while ( my $e = ) { 25 | diag($e); 26 | } 27 | } 28 | system "rm stderr.tmp" if ( -f 'stderr.tmp' ); 29 | chdir('..'); 30 | 1; 31 | } or do { 32 | fail("Couldn't test: $t.t"); 33 | }; 34 | diag($@) if $@; 35 | } 36 | 37 | # Summary of failed tests 38 | diag("\nFailed tests for:") if @failed; 39 | foreach my $f (@failed) { 40 | diag(" $f"); 41 | } 42 | diag("\n"); 43 | done_testing(); 44 | --------------------------------------------------------------------------------