Procedure for manipulating analysing Dynamic NMR DNMR data

Procedure for manipulating / analysing Dynamic NMR (DNMR) data (example: DNMR data for the compound 1 -Silyl-1 -Silacyclohexane, C 5 H 10 Si. H (schsih 3) By use of the programs: 1) Mestre C 2) WINDNMR (http: //www. chem. wisc. edu/areas/reich/plt/windnmr. htm ) 3) IGOR (http: //www. raunvis. hi. is/~agust/hugbkenn. htm ) - and analysis examples

Procedure (example: DNMR data for the compound ): nuts files (necessary input files for WINDNMR) are created with Mestre C as (inside Mestre C): File->import spectra->. . schsih 3 -> FIF gogn-> Select for example sow 417 mr. 163 ->open->FT -> 256 K->Apply along t 1 -> Phase correction(if needed): select region of interest by using magnifying glass(+) and click and drag untill satisfactory-> press phase correction button->click mouse as said and hold and drag up or down and you will see the phase change; stop when it is good ->OK->File->Export file -> nuts->. . . appropriate file-> type name: schsih 3 -163. nts->save Now schsih 3 -163. nts should be ready for WINDNMR to read: Inside WINDNMR (has to be without some other experimental spectrum inside): File->open new spectrum->. . select appropriate file>select schsih 3 -163. nts->open-> select the spectrum area of interest by click, drag drop and choose “Expand spectrum”; You may need to do this several time untill you ar happy. NB!: Simulation er framkvæmd manually, þ. e. með því að breyta parametrum handvirkt og lágmarka error og/eða með því að fá besta sjónræna fit! Move date from WINDNMR to IGOR: After simulation has been performed inside WINDNMR: Export->Spectrum data to Clipboard (for spreadsheet)-> move to a table inside IGOR and simply paste => calculated and experimental spectra are copied to four columns as: 1 st column: x axis values for calc. ; 2 nd column: y axis values for calc. ; 3 rd column: x axis values for exp. ; 4 st column: y axis values for exp. ;

Analysis examples are shown below:

“Difference spectrum” = exp. – calc. exp. Tcorr = 100. calc. 120509: item 1, simulation group schsih 3 -105 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. Tcorr = 110. calc. 120509: item 1, simulation group schsih 3 -115 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 115. exp. calc. 120509: item 2, simulation group schsih 3 -124 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 122. exp. calc. 120509: item 1, simulation group schsih 3 -132 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 123. calc. exp. 120509: item 1, simulation group schsih 3 -133 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 128. exp. calc. 120509: item 1, simulation group schsih 3 -138 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 135. exp. calc. 120509: item 1, simulation group schsih 3 -145 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 138. exp. calc. 120509: item 1, simulation group schsih 3 -148 -32 K. sim, C 3, C 5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. Tcorr = 100. calc. 120509: item 2, simulation group schsih 3 -105 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. Tcorr = 110. calc. 120509: item 2, simulation group schsih 3 -115 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 115. calc. exp. 120509: item 3, simulation group schsih 3 -124 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. calc. Tcorr = 122. 120509: item 2, simulation group schsih 3 -132 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 123. calc. exp. 120509: item 2, simulation group schsih 3 -133 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 128. calc. exp. 120509: item 2, simulation group schsih 3 -138 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 135. exp. calc. 120509: item 2, simulation group schsih 3 -145 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 154. exp. calc. 120509: item -, simulation group schsih 3 -163. sim, C 2, C 6; see parameters above and/or in table;

Tcorr = 154. exp. calc. 120509: item -, simulation group schsih 3 -163. sim, C 2, C 6; see parameters above and/or in table;

Tcorr = 128. calc. exp. 120509: item 3, simulation group schsih 3 -138 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. calc. Tcorr = 123. 120509: item 3, simulation group schsih 3 -133 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. exp. calc. Tcorr = 122. 120509: item 3, simulation group schsih 3 -132 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 115. calc. exp. 120509: item 4, simulation group schsih 3 -124 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 110. exp. calc. 120509: item 3, simulation group schsih 3 -115 -32 K. sim, C 2, C 6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc. Tcorr = 100. calc. exp. 120509: item 3, simulation group schsih 3 -105 -32 K. sim, C 2, C 6; see parameters above and/or in table;

WINDNMR analysis for SCH-Si. H 3 , C 3, C 5: Tcorr kab + kba %a 100 0 54 110 7 58 115 39 57 122 400 54 (assumed) 123 400 54 (assumed) 128 1100 54 (assumed) 135 9500 54 (assumed) 138 13500 54 (assumed) Low field a b eq ax High field NB!: This data needs to be used to derive K, A and DG#

WINDNMR analysis for SCH-Si. H 3 , C 2, C 6: Tcorr kab + kba %a 100 15 56 115 39 56 122 400 56 (assumed) 123 400 56 (assumed) 128 1100 56 (assumed) 135 9500 56 (assumed) 154 ¥ (95000) 56 (assumed) Low field a b eq ax High field NB!: This data needs to be used to derive K, A and DG#

130509: Paper by Hans J. Reich , Birgir Ö. Guðmundsson et al. Including rate constant detemination by WINDNMR et c. : See: http: //www. chem. wisc. edu/areas/reich/papers/Reich-2001 -JACS-123, 8067 -Amine-chelated-aryllithium. pdf Good ref. for standard transition state theory, which relates DG# and kab is: http: //arxiv. org/ftp/arxiv/papers/0706. 1504. pdf (see also my notes, 130509; 1 -2) Main eq. : eq ; k = rate constant ax DG# eq 56% ax 44% DGeq, ax

DGeq, ax and Keq, ax : Keq, ax = 44/56 = 0. 786: DGeq, ax = A = -RT ln(Keq, ax); T = average T where K is determined in experiment, i. e. in the regin 100 – 115 K, = <T> = say 110 K DGeq, ax = A =Gax - Geq = -8. 315 (J K-1 mol-1)*110(T) ln(0. 786) = 0. 22 k. J mol-1 = 0. 053 kcal mol-1; (see below) More details (from excel): parameter value unit R 8. 315 T 110 K 0. 785714286 %a 56 %b 44 J K-1 mol-1 K - DGeq, ax 220. 5788753 J mol-1 DGeq, ax 0. 220578875 k. J mol-1 DGeq, ax 5. 27 E-02 kcal mol-1 conversion factor 2. 39 E-01 kcal/k. J Does this make sense? 1)

1) To be compared, for example, with A = Gax – Geq = +0. 4 kcal mol-1 derived for T = 113 for SCH-CF 3, See: http: //www 3. hi. is/~agust/ritsmidar/SCHCF 3 nmredabinitio-0207. pdf Determinaton of individual rate constants from the equilibrium constant (Keq, ax) and “the rate constant sum” (kab + kba = ksum) which is derived from the temperature dependend NMR data Comment / NB!: kab = keq, ax ; kba = kax, eq Keq, ax = keq, ax/kax, eq; keq, ax + kax, eq = ksum; => keq, ax = ksum /(1 + (Keq, ax)-1) kax, eq = ksum /(1 + Keq, ax)

Analysis for SCH-Si. H 3 , C 3, C 5: Keq, ax = 0. 786 T /K keq, ax + kax, eq = ksum keq, ax /s-1 kax, eq /s-1 DG#/ kcal mol-1 100 0 110 7 3 4 6. 0 115 39 17 22 5. 9 122 400 176 224 5. 7 123 400 176 224 5. 7 128 1100 484 616 5. 7 135 9500 4181 5319 5. 5 138 13500 5941 7559 5. 5 Does this make sense? ! : This can be compared with the value 5. 5 kcal mol-1 for SCH-CF 3, with coalescence point near 113 K. (http: //www 3. hi. is/~agust/ritsmidar/SCHCF 3 nmredabinitio-0207. pdf ) ERGO: yes it makes sense!

Analysis for SCH-Si. H 3 , C 2, C 6: Does this make sense? ! : Keq, ax = 0. 786 Tcorr keq, ax + kax, eq = ksum keq, ax /s-1 kax, eq /s-1 DG#/ kcal mol-1 100 15 7 8 5. 3 110 15 7 8 5. 8 115 39 17 22 5. 9 122 400 176 224 5. 7 123 400 176 224 5. 7 128 1100 484 616 5. 7 135 9500 4180 5319 5. 5 154 ¥ (95000) This can be compared with the value 5. 5 kcal mol-1 for SCH-CF 3, with coalescence point near 113 K. (http: //www 3. hi. is/~agust/ritsmidar/SCHCF 3 nmredabinitio-0207. pdf ) ERGO: yes it makes sense!

SCHSi. H 3, 130509 ak C 2, C 6, 13 C-NMR, 250 MHz Simulation: Calc. : solid fat line Exp. : solid thin line Average DG#eq, ax = 5. 7 kcal mol-1 Keq, ax = 0. 8 DGeq, ax = 0. 05 kcal mol-1 See also SCHSi. H 3 -simul. figs. -130509 ak. ppt

C 3, C 5 DG#/ kcal mol-1 ? Great uncertainty C 2, C 6 Average DG#eq, ax = 5. 7 kcal mol-1 T/k See also PC, AK, . . . /SCHSi. H 3 -DNMR-simul-figs-130509 ak. pxp

140509: WINDNMR analysis for SCH-Si. H 3 , C 4: Tcorr kab + kba %a 100 15 51 ? 1) 105 13 45 1) 110 24 46 ? ? 115 69 170 infinit Low field High field a b 46 (assumed) eq ax 53 (assumed) NB!: This data needs to be used to derive 1) K, A and DG# 1) Could it be that eq and ax are reversed here / for C 4?

140509: Tcorr(K) 164 115 110 105 100 SCH-Si. H 3 , C 4:

140509: C 3, C 5 data => Coefficient values ± one standard deviation a = 7. 9532 ± 0. 224 b = -0. 017993 ± 0. 00179 DG# T/K

140509: DG# = DH# – T DS# Coefficient values ± one standard deviation a = 7. 9532 ± 0. 224 = DH#eq, compl. kcal mol-1 b = -0. 017993 ± 0. 00179 = -DS# kcal mol-1 K-1 Þ DH#eq, compl. = + 8. 0 kcal mol-1 Þ DS#eq, compl. = +18 cal mol-1 K-1 Þ eq. complex involves increase in entropy i. e. : kcal mol-1 8 5 0 DH# complex DG# complex Eq.