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 )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->....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 saidand 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->saveNow 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.;

Analysis examples are shown below:

120509: item 1, simulation group schsih3-105-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 100 .

120509: item 1, simulation group schsih3-115-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 110 .

120509: item 2, simulation group schsih3-124-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 115 .

120509: item 1, simulation group schsih3-132-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.calc.

Tcorr = 122 .

120509: item 1, simulation group schsih3-133-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 123 .

120509: item 1, simulation group schsih3-138-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.calc.

Tcorr = 128 .

120509: item 1, simulation group schsih3-145-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 135 .

120509: item 1, simulation group schsih3-148-32K.sim, C3,C5; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 138 .

120509: item 2, simulation group schsih3-105-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 100 .

120509: item 2, simulation group schsih3-115-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 110 .

item 3, simulation group schsih3-124-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 115 .

120509:

120509: item 2, simulation group schsih3-132-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.calc.

Tcorr = 122 .

120509: item 2, simulation group schsih3-133-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 123 .

120509: item 2, simulation group schsih3-138-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 128 .

120509: item 2, simulation group schsih3-145-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 135 .

120509: item -, simulation group schsih3-163.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 154 .

120509: item -, simulation group schsih3-163.sim, C2,C6; see parameters above and/or in table;

exp. calc.

Tcorr = 154 .

120509: item 3, simulation group schsih3-138-32K.sim, C2,C6; see parameters above and/or in table;

exp.

calc.

Tcorr = 128 .

120509: item 3, simulation group schsih3-133-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.calc.

Tcorr = 123 .

120509: item 3, simulation group schsih3-132-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.calc.

Tcorr = 122 .

item 4, simulation group schsih3-124-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 115 .

120509:

120509: item 3, simulation group schsih3-115-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp. calc.

Tcorr = 110 .

120509: item 3, simulation group schsih3-105-32K.sim, C2,C6; see parameters above and/or in table;

“Difference spectrum” = exp. – calc.

exp.

calc.

Tcorr = 100 .

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)

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#

Tcorr kab + kba % a

100 15 56

110 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)

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#

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 G# and kab is:http://arxiv.org/ftp/arxiv/papers/0706/0706.1504.pdf (see also my notes, 130509;1-2)

Main eq.: ; k = rate constant

hTk

kRTG

B /ln#

eqax

56% 44%

Geq,ax

G#

eq ax

Keq,ax = 44/56 = 0.786: Geq,ax = A = -RT ln(Keq,ax);T = average T where K is determined in experiment,i.e. in the regin 100 – 115K, = <T> = say 110K

Geq,ax = A =Gax - Geq = -8.315 (J K-1 mol-1)*110(T) ln(0.786) = 0.22 kJ mol-1

= 0.053 kcal mol-1; (see below)

parameter value unit

R 8.315 J K-1 mol-1

T 110 K

K 0.785714286 -

%a 56

%b 44

DGeq,ax 220.5788753 J mol-1

DGeq,ax 0.220578875 kJ mol-1

Geq,ax 5.27E-02 kcal mol-1

conversion factor 2.39E-01 kcal/kJ

Does this make sense? 1)

More details (from excel):

Geq,ax and Keq,ax :

1) To be compared, for example, with A = Gax – Geq = +0.4 kcal mol-1 derived for T = 113 for SCH-CF3,See: http://www3.hi.is/~agust/ritsmidar/SCHCF3nmredabinitio-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)

T /K keq,ax + kax,eq

= ksum

keq,ax

/s-1

kax,eq

/s-1

G#/

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

Analysis for SCH-SiH3 , C3,C5:

Keq,ax = 0.786

Does this make sense?! :

This can be compared with the value5.5 kcal mol-1 forSCH-CF3, with coalescence pointnear 113K.(http://www3.hi.is/~agust/ritsmidar/SCHCF3nmredabinitio-0207.pdf )

ERGO: yes it makes sense!

Tcorr keq,ax + kax,eq

= ksum

keq,ax

/s-1

kax,eq

/s-1

G#/

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)

Analysis for SCH-SiH3 , C2,C6:

Keq,ax = 0.786 Does this make sense?! :

This can be compared with the value5.5 kcal mol-1 forSCH-CF3, with coalescence pointnear 113K.(http://www3.hi.is/~agust/ritsmidar/SCHCF3nmredabinitio-0207.pdf )

ERGO: yes it makes sense!

SCHSiH3, 130509ak

C2,C6,

13C-NMR,

250 MHz

Simulation:Calc.: solid fat lineExp. : solid thin line

Average G#eq,ax = 5.7 kcal mol-1

Keq,ax = 0.8Geq,ax = 0.05 kcal mol-1

3 2 1 0 -1 -2 -3See also SCHSiH3-simul.figs.-130509ak.ppt

7

6

5

4

3

2

1

0

130120110100

G#/kcal mol-1

T/k

C2,C6

C3,C5

See also PC,AK,...../SCHSiH3-DNMR-simul-figs-130509ak.pxp

AverageG#eq,ax = 5.7 kcal mol-1

?Great uncertainty

Tcorr kab + kba % a

100 15 51

105 13 45

110 24 46

115 69 46 (assumed)

170 infinit 53 (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#

140509:

??

?

1) Could it be that eq and ax are reversed here / for C4?

1)

1)

1)

-1.0-0.50.00.5

Tcorr(K)

164

115

110

105

100

SCH-SiH3 , C4:

140509:

6.0

5.9

5.8

5.7

5.6

5.5

135130125120115110

T/K

G#

Coefficient values ± one standard deviation a = 7.9532 ± 0.224 b = -0.017993 ± 0.00179

C3,C5 data =>

140509:

Coefficient values ± one standard deviation a = 7.9532 ± 0.224 = H#

eq,compl. kcal mol-1

b = -0.017993 ± 0.00179 = -S# kcal mol-1 K-1

H#eq,compl. = + 8.0 kcal mol-1

S#eq,compl. = +18 cal mol-1 K-1

eq. complex involves increase in entropy

G# = H# – T S#140509:

i.e.:

Eq.0

5

8

G#

H#

kcal mol-1

complex

complex