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Procedure for manipulating / analysing Dynamic NMR (DNMR) data (example: DNMR data for the compound 1-Silyl-1-Silacyclohexane, C5H10SiHSiH (schsih3) By.

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Presentation on theme: "Procedure for manipulating / analysing Dynamic NMR (DNMR) data (example: DNMR data for the compound 1-Silyl-1-Silacyclohexane, C5H10SiHSiH (schsih3) By."— Presentation transcript:

1 Procedure for manipulating / analysing Dynamic NMR (DNMR) data (example: DNMR data for the compound 1-Silyl-1-Silacyclohexane, C5H10SiHSiH (schsih3) By use of the programs: 1) Mestre C 2) WINDNMR (http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm )http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm 3) IGOR (http://www.raunvis.hi.is/~agust/hugbkenn.htm )http://www.raunvis.hi.is/~agust/hugbkenn.htm - and analysis examples

2 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->....schsih3-> FIF gogn-> Select for example sow417mr.163->open->FT -> 256K->Apply along t1-> 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: schsih3-163.nts->save Now schsih3-163.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 schsih3-163.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: 1st column: x axis values for calc.; 2nd column: y axis values for calc.; 3rd column: x axis values for exp.; 4st column: y axis values for exp.;

3 Analysis examples are shown below:

4 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 100.

5 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 110.

6 120509: item 2, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 115.

7 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 122.

8 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 123.

9 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 128.

10 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 135.

11 120509: item 1, simulation group schsih K.sim, C3,C5; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 138.

12 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 100.

13 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 110.

14 item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = :

15 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 122.

16 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 123.

17 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 128.

18 120509: item 2, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 135.

19 120509: item -, simulation group schsih3-163.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 154.

20 120509: item -, simulation group schsih3-163.sim, C2,C6; see parameters above and/or in table; exp. calc. T corr = 154.

21 120509: item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; exp. calc. T corr = 128.

22 120509: item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 123.

23 120509: item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 122.

24 item 4, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = :

25 120509: item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 110.

26 120509: item 3, simulation group schsih K.sim, C2,C6; see parameters above and/or in table; “Difference spectrum” = exp. – calc. exp. calc. T corr = 100.

27 T corr k ab + k ba % a (assumed) (assumed) (assumed) (assumed) (assumed) WINDNMR analysis for SCH-SiH3, C3,C5: Low field High field a b eq ax NB!: This data needs to be used to derive K, A and  G #

28 T corr k ab + k ba % a (assumed) (assumed) (assumed) (assumed) 154  (95000) 56 (assumed) WINDNMR analysis for SCH-SiH3, C2,C6: Low field High field a b eq ax NB!: This data needs to be used to derive K, A and  G #

29 130509: Paper by Hans J. Reich, Birgir Ö. Guðmundsson et al. Including rate constant detemination by WINDNMR et c.: See: Good ref. for standard transition state theory, which relates  G # and k ab is: (see also my notes, ;1-2) Main eq.: ; k = rate constant eq ax 56%44%  G eq,ax G#G# eq ax

30 K eq,ax = 44/56 = 0.786:  G eq,ax = A = -RT ln(K eq,ax ); T = average T where K is determined in experiment, i.e. in the regin 100 – 115K, = = say 110K  G eq,ax = A =G ax - G eq = (J K -1 mol -1 )*110(T) ln(0.786) = 0.22 kJ mol -1 = kcal mol -1 ; (see below) parametervalueunit R8.315J K-1 mol-1 T110K K %a56 %b44 DGeq,ax J mol-1 DGeq,ax kJ mol-1  G eq,ax 5.27E-02kcal mol -1 conversion factor2.39E-01kcal/kJ Does this make sense? 1) More details (from excel):  G eq,ax and K eq,ax :

31 1)To be compared, for example, with A = G ax – G eq = +0.4 kcal mol -1 derived for T = 113 for SCH-CF3, See: Determinaton of individual rate constants from the equilibrium constant (K eq,ax ) and “the rate constant sum” (k ab + k ba = k sum ) which is derived from the temperature dependend NMR data Comment / NB!: k ab = k eq,ax ; k ba = k ax,eq K eq,ax = k eq,ax /k ax,eq ; k eq,ax + k ax,eq = k sum ; => k eq,ax = k sum /(1 + (K eq,ax ) -1 ) k ax,eq = k sum /(1 + K eq,ax )

32 T /Kk eq,ax + k ax,eq = k sum k eq,ax /s -1 k ax,eq /s -1  G # / kcal mol Analysis for SCH-SiH3, C3,C5: K eq,ax = Does this make sense?! : This can be compared with the value 5.5 kcal mol -1 for SCH-CF3, with coalescence point near 113K. ( ) ERGO: yes it makes sense!

33 T corr k eq,ax + k ax,eq = k sum k eq,ax /s -1 k ax,eq /s -1  G # / kcal mol  (95000) Analysis for SCH-SiH3, C2,C6: K eq,ax = Does this make sense?! : This can be compared with the value 5.5 kcal mol -1 for SCH-CF3, with coalescence point near 113K. ( ) ERGO: yes it makes sense!

34 SCHSiH3, ak C2,C6, 13 C-NMR, 250 MHz Simulation: Calc.: solid fat line Exp. : solid thin line Average  G # eq,ax = 5.7 kcal mol -1 K eq,ax = 0.8  G eq,ax = 0.05 kcal mol -1 See also SCHSiH3-simul.figs ak.ppt

35  G # / kcal mol -1 T/k C2,C6 C3,C5 See also PC,AK,...../SCHSiH3-DNMR-simul-figs ak.pxp Average  G # eq,ax = 5.7 kcal mol -1 ? Great uncertainty

36 T corr k ab + k ba % a (assumed) 170infinit53 (assumed) WINDNMR analysis for SCH-SiH3, C4: Low field High field a b eq ax NB!: This data needs to be used to derive K, A and  G # : ? ? ? 1) Could it be that eq and ax are reversed here / for C4? 1)

37 T corr (K) SCH-SiH3, C4: :

38 T/K G#G# Coefficient values ± one standard deviation a = ± b = ± C3,C5 data => :

39 Coefficient values ± one standard deviation a = ± =  H # eq,compl. kcal mol -1 b = ± = -  S # kcal mol -1 K -1  H # eq,compl. = kcal mol -1  S # eq,compl. = +18 cal mol -1 K -1  eq. complex involves increase in entropy  G # =  H # – T  S # : i.e.: Eq G#G# H#H# kcal mol -1 complex


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