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1
Viologen based redox switchable anion binding receptors
R. Kannappan,[a] C. Bucher,*[a] E. Saint-Aman,* [a] J.-C. Moutet,[a]
A. Milet,[b] M. Oltean, [b] E. Métay,[c] S. Pellet-Rostaing,[c] M. Lemaire[c], Carole Chaix[d],
Département de chimie moléculaire, [a] laboratoire de chimie inorganique rédox, [b] laboratoire
de chimie théorique, UMR-5250, ICMG FR-2607, Institut de Chimie Moléculaire de Grenoble, FR
CNRS 2607, Université Joseph Fourier, BP 53, 38041 Grenoble Cédex 9, France.
[c] Institut de chimie et biochimie moléculaires et supramoléculaires (ICBMS-UMR5246),
Université Claude Bernard Lyon 1, Domaine Scientifique de la Doua, 43 Boulevard du 11
Novembre 1918, 69622 Villeurbanne Cedex, France.
[d] UMR des Sciences Analytiques (UMR5180), Université Claude Bernard, Bât. J. Raulin, 69622
Villeurbanne Cedex – France.
1. RMN 1H spectrum of 2·(PF6)4 (DMSO d6) .................................................................................................2
2. COSY 1H-1H map of 2·(PF6)4 (DMSO d6) ...................................................................................................3
3. COSY 1H-1H map of 2·(PF6)4 (DMSO d6) ...................................................................................................4
4. COSY 1H-1H map of 2·(PF6)4 (DMSO d6) ...............................................................................................5
5. NOESY 1H-1H map of 2·(PF6)4 (DMSO d6)................................................................................................6
6. NOESY 1H-1H map of 2·(PF6)4 (DMSO d6)................................................................................................7
7. NMR titration of of 1·(PF6)2 with TBA.Cl ...................................................................................................8
8. NMR titration of of 1·(PF6)2 with TBA.Br ..................................................................................................9
9. NMR titration of of 2·(PF6)4 with TBA.Cl ................................................................................................ 10
10. NMR titration of of 2·(PF6)4 with TBA.Cl _Shift of Hf, Hc, He, Hd ............................................. 10
11. NMR titration of of 2·(PF6)4 with TBA.Cl _ Shift of Hi, Hg, Ha, Hb ............................................ 11
12. Cyclic voltammograms of 2.(PF6)4 ...................................................................................................... 12
13. Cyclic voltammograms of 1.(PF6)2 ...................................................................................................... 13
14. Spectroelectrochemistry experiment carried out with 1.(PF6)2 .............................................. 14
15. Spectroelectrochemistry experiment carried out with 2.(PF6)4 .............................................. 14
16. RDE experiments carried out with 2.(PF6)4 and 1.(PF6)4 in presence of Fluoride.......... 15
17. UV-Visible changes observed with 2.(PF6)4 and 1.(PF6)4 in presence of Fluoride .......... 16
18. Computational Details............................................................................................................................... 17
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
2
1. RMN 1H spectrum of 2 ·(PF6)4 (DMSO d6)
3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
ppm
2.7552.7732.791
3.321
4.8084.8264.844
5.514
7.795
8.124
8.7948.8128.8578.8749.2759.2939.3779.395
2.021
4.027
4.000
1.901
1.897
4.0054.014
4.0074.022
Current Data Parameters
NAME CB8X80FX
EXPNO 1
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.02
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG zg30
TD 32768
SOLVENT DMSO
NS 70
DS 2
SWH 8223.685 Hz
FIDRES 0.250967 Hz
AQ 1.9923444 sec
RG 228
DW 60.800 usec
DE 6.00 usec
TE 298.0 K
D1 1.00000000 sec
TD0 1
======== CHANNEL f1 ========
NUC1 1H
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1324710 MHz
F2 - Processing parameters
SI 16384
SF 400.1300000 MHz
WDW EM
SSB 0
LB 0.30 Hz
GB 0
PC 1.00
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
3
2. COSY 1H-1H map of 2 ·(PF6)4 (DMSO d6)
ppm
23
45
67
89
10
ppm
2 3 4 5 6 7 8 9
10
Current Data Parameters
NAME CB8X80FX
EXPNO 3
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.06
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG cosygpqf
TD 2048
SOLVENT DMSO
NS 4
DS 8
SWH 3472.222 Hz
FIDRES 1.695421 Hz
AQ 0.2949620 sec
RG 228
DW 144.000 usec
DE 6.00 usec
TE 298.0 K
D0 0.00000300 sec
D1 1.35213399 sec
D13 0.00000400 sec
D16 0.00020000 sec
IN0 0.00028800 sec
======== CHANNEL f1 ========
NUC1 1H
P0 8.00 usec
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1322935 MHz
====== GRADIENT CHANNEL =====
GPNAM1 SINE.100
GPZ1 10.00 %
P16 1000.00 usec
F1 - Acquisition parameters
ND0 1
TD 200
SFO1 400.1323 MHz
FIDRES 17.361111 Hz
SW 8.678 ppm
FnMODE QF
F2 - Processing parameters
SI 1024
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
PC 1.40
F1 - Processing parameters
SI 1024
MC2 QF
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
4
3. COSY 1H-1H map of 2 ·(PF6)4 (DMSO d6)
ppm
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
ppm
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
Current Data Parameters
NAME CB8X80FX
EXPNO 3
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.06
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG cosygpqf
TD 2048
SOLVENT DMSO
NS 4
DS 8
SWH 3472.222 Hz
FIDRES 1.695421 Hz
AQ 0.2949620 sec
RG 228
DW 144.000 usec
DE 6.00 usec
TE 298.0 K
D0 0.00000300 sec
D1 1.35213399 sec
D13 0.00000400 sec
D16 0.00020000 sec
IN0 0.00028800 sec
======== CHANNEL f1 ========
NUC1 1H
P0 8.00 usec
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1322935 MHz
====== GRADIENT CHANNEL =====
GPNAM1 SINE.100
GPZ1 10.00 %
P16 1000.00 usec
F1 - Acquisition parameters
ND0 1
TD 200
SFO1 400.1323 MHz
FIDRES 17.361111 Hz
SW 8.678 ppm
FnMODE QF
F2 - Processing parameters
SI 1024
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
PC 1.40
F1 - Processing parameters
SI 1024
MC2 QF
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
5
4. COSY 1H-1H map of 2·(PF 6)4 (DMSO d6)
ppm
7.6
7.8
8.0
8.2
8.4
8.6
8.8
9.0
9.2
9.4
9.6
ppm
7.6
7.8
8.0
8.2
8.4
8.6
8.8
9.0
9.2
9.4
9.6
Current Data Parameters
NAME CB8X80FX
EXPNO 3
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.06
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG cosygpqf
TD 2048
SOLVENT DMSO
NS 4
DS 8
SWH 3472.222 Hz
FIDRES 1.695421 Hz
AQ 0.2949620 sec
RG 228
DW 144.000 usec
DE 6.00 usec
TE 298.0 K
D0 0.00000300 sec
D1 1.35213399 sec
D13 0.00000400 sec
D16 0.00020000 sec
IN0 0.00028800 sec
======== CHANNEL f1 ========
NUC1 1H
P0 8.00 usec
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1322935 MHz
====== GRADIENT CHANNEL =====
GPNAM1 SINE.100
GPZ1 10.00 %
P16 1000.00 usec
F1 - Acquisition parameters
ND0 1
TD 200
SFO1 400.1323 MHz
FIDRES 17.361111 Hz
SW 8.678 ppm
FnMODE QF
F2 - Processing parameters
SI 1024
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
PC 1.40
F1 - Processing parameters
SI 1024
MC2 QF
SF 400.1300000 MHz
WDW SINE
SSB 0
LB 0.00 Hz
GB 0
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
6
5. NOESY 1H-1H map of 2 ·(PF6)4 (DMSO d6)
Current Data Parameters
NAME CB8X80FX
EXPNO 4
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.32
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG noesyph
TD 2048
SOLVENT DMSO
NS 32
DS 16
SWH 3472.222 Hz
FIDRES 1.695421 Hz
AQ 0.2949620 sec
RG 228
DW 144.000 usec
DE 6.00 usec
TE 298.0 K
D0 0.00013381 sec
D1 1.86524200 sec
D8 0.60000002 sec
IN0 0.00028800 sec
======== CHANNEL f1 ========
NUC1 1H
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1322935 MHz
F1 - Acquisition parameters
ND0 1
TD 350
SFO1 400.1323 MHz
FIDRES 9.920635 Hz
SW 8.678 ppm
FnMODE States-TPPI
F2 - Processing parameters
SI 1024
SF 400.1300000 MHz
WDW QSINE
SSB 2
LB 0.00 Hz
GB 0
PC 1.00
F1 - Processing parameters
SI 1024
MC2 States-TPPI
SF 400.1300000 MHz
WDW QSINE
SSB 2
LB 0.00 Hz
GB 0
ppm
34
56
78
910
ppm
2.5
3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
7
6. NOESY 1H-1H map of 2 ·(PF6)4 (DMSO d6)
ppm
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
ppm
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
Current Data Parameters
NAME CB8X80FX
EXPNO 4
PROCNO 1
F2 - Acquisition Parameters
Date_ 20090126
Time 22.32
INSTRUM spect
PROBHD 5 mm PABBI 1H/
PULPROG noesyph
TD 2048
SOLVENT DMSO
NS 32
DS 16
SWH 3472.222 Hz
FIDRES 1.695421 Hz
AQ 0.2949620 sec
RG 228
DW 144.000 usec
DE 6.00 usec
TE 298.0 K
D0 0.00013381 sec
D1 1.86524200 sec
D8 0.60000002 sec
IN0 0.00028800 sec
======== CHANNEL f1 ========
NUC1 1H
P1 8.00 usec
PL1 -1.00 dB
PL1W 9.67656994 W
SFO1 400.1322935 MHz
F1 - Acquisition parameters
ND0 1
TD 350
SFO1 400.1323 MHz
FIDRES 9.920635 Hz
SW 8.678 ppm
FnMODE States-TPPI
F2 - Processing parameters
SI 1024
SF 400.1300000 MHz
WDW QSINE
SSB 2
LB 0.00 Hz
GB 0
PC 1.00
F1 - Processing parameters
SI 1024
MC2 States-TPPI
SF 400.1300000 MHz
WDW QSINE
SSB 2
LB 0.00 Hz
GB 0
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
8
7. NMR titration of of 1·(PF 6)2 with TBA.Cl (8 mM, 300 mHz, DMSO d6, 2% D2O) 1-determination of the binding constant from ∆δ(NHa) = f (CChloride) According to the equilibrium L + S = LS ∆δ=( ∆δmax /(2*L))*((L+S+(1/K))-(sqrt(((L+S+(1/K))^2)-4*L*S))) With L : total concentration in L
S : total concentration in S K : binding constant ∆δ = δobs-δ0
[ppm]9.5 9.0 8.5 8.0
CB8X121 2 1 d:\ Christobald
CB8X121 3 1 d:\ Christobald
CB8X121 4 1 d:\ Christobald
CB8X121 5 1 d:\ Christobald
CB8X121 6 1 d:\ Christobald
CB8X121 7 1 d:\ Christobald
1(PF6)2
+T
BA
.Cl
+2.75 eq.
+4 eq.
+6 eq.
+8 eq.
+1.5 eq.
+0.5 eq.
[ppm]9.5 9.0 8.5 8.0
CB8X121 2 1 d:\ Christobald
CB8X121 3 1 d:\ Christobald
CB8X121 4 1 d:\ Christobald
CB8X121 5 1 d:\ Christobald
CB8X121 6 1 d:\ Christobald
CB8X121 7 1 d:\ Christobald
1(PF6)2
+T
BA
.Cl
+2.75 eq.
+4 eq.
+6 eq.
+8 eq.
+1.5 eq.
+0.5 eq.
0,00 0,02 0,04 0,06 0,08 0,10 0,12-0,05
0,00
0,05
0,10
0,15
0,20
0,25
0,30
0,35
Data: Data1_H
Chi^2/DoF = 7.5638E-6R^2 = 0.99952 M 0.51442 ±0.01059L 0.00792 ±0K 18.76628 ±0.80358
NHa
∆δ (
ppm
)
TBACl (mol.l-1)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
9
8. NMR titration of of 1·(PF 6)2 with TBA.Br (8 mM, 300 mHz, DMSO d6, 2% D2O)
determination of the binding constant from ∆δ(NHa) = f (CChloride)
According to the equilibrium
L + S = LS
∆δ=( ∆δmax /(2*L))*((L+S+(1/K))-(sqrt(((L+S+(1/K))^2)-4*L*S)))
With L : total concentration in L
S : total concentration in S
K : binding constant
∆δ = δobs-δ0
0,00 0,05 0,10 0,15 0,20
0,00
0,02
0,04
0,06
0,08 NHa
Data: Data1_deltaModel: RMN1Weighting: y No weighting Chi^2/DoF = 1.0056E-6R^2 = 0.99767 M 0.13033 ±0L 0.00792 ±0K 8.12991 ±0.06304
∆δ (
ppm
)
TBABr (mol.l-1)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
10
9. NMR titration of of 2·(PF 6)4 with TBA.Cl (3.9 mM, 300 mHz, DMSO d6, 2% D2O)
CB8X113 2 1 d:\ Christobald
CB8X113 3 1 d:\ Christobald
CB8X113 4 1 d:\ Christobald
CB8X113 5 1 d:\ Christobald
CB8X113 6 1 d:\ Christobald
[ppm]9.5 9.0 8.5 8.0
2(PF6)4
+TB
A.C
l
+2.5 eq.
+5.5 eq.
+7.75 eq.
+10.2 eq.
+15.75 eq.
CB8X113 2 1 d:\ Christobald
CB8X113 3 1 d:\ Christobald
CB8X113 4 1 d:\ Christobald
CB8X113 5 1 d:\ Christobald
CB8X113 6 1 d:\ Christobald
[ppm]9.5 9.0 8.5 8.0
2(PF6)4
+TB
A.C
l
+2.5 eq.
+5.5 eq.
+7.75 eq.
+10.2 eq.
+15.75 eq.
10. NMR titration of of 2 ·(PF6)4 with TBA.Cl _Shift of Hf, Hc, He, Hd (3.9 mM, 300 mHz, DMSO d6, 2% D2O)
0 5 10 15 20
0,00
0,05
0,10
0,15
0,20
0,25
0,30
Hf Hc He Hd∆δ
(ppm
)
TBACl (molar equivalents)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
11
11. NMR titration of of 2 ·(PF6)4 with TBA.Cl _ Shift of Hi, Hg, Ha, Hb (3.9 mM, 300 mHz, DMSO d6, 2% D2O)
0 5 10 15 20
0,00
0,05
0,10
0,15
0,20
0,25
0,30
NHaNHbHg Hi
∆δ (
ppm
)
TBACl (molar equivalents)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
12
12. Cyclic voltammograms of 2.(PF 6)4 10A→ (10-3 M, 20mV/s, Pt Ø=2 mm, CD3CN 0.1 MTBAPF6)
10B→ (10-3 M, 20mV/s, Pt Ø=2 mm, DMF 0.1 MTBAPF6)
10C→ (10-3M + Ferrocene as int. ref., 100mV/s, Pt Ø=2 mm, DMF 0.1 MTBAPF6)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
13
13. Cyclic voltammograms of 1.(PF 6)2 11A→ (10-3 M, Pt Ø=2 mm, 20mV/s, CD3CN 0.1 MTBAPF6)
11B→ (10-3 M, CV Pt Ø=2 mm, 20mV/s, DMF 0.1 MTBAPF6)
11C→ (10-3M + Ferrocene as int. ref., 100mV/s, Pt Ø=2 mm, DMF 0.1 MTBAPF6)
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
14
14. Spectroelectrochemistry experiment carried out with 1.(PF 6)2 Evolution of the UV-vis abs. spectum during the 1e– reduction of 1.(PF6)2 at – 1.0 V
(E vs Ag/Ag+, 2.5 × 10−4 M, V= 25 mL DMF 0.1 M TBAP). Spectra were recorded at ca. 10 s intervals . Arrows indicate the directions of absorbance change
400 600 800 10000,0
0,1
0,2
0,3
0,4
0,5
0,6
0,7
Abs
Wavelength/nm
15. Spectroelectrochemistry experiment carried out with 2.(PF 6)4 Evolution of the UV-vis abs. spectum during the 2e– reduction of 2.(PF6)4 at – 1.0 V
(E vs Ag/Ag+, 2.5 × 10−4 M, V= 25 mL DMF 0.1 M TBAP). Spectra were recorded at ca. 10-s intervals .
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
15
16. RDE experiments carried out with 2.(PF 6)4 and 1.(PF 6)4 in presence of Fluoride Rotating disc measurements conducted in glove box on (left) 1.(PF6)4 and (right) 2.(PF6)4 in
DMF at 1 × 10 – 3 M in presence of increasing amounts of fluoride ( TBAF).
a: 12+
b: 12+ + 1 eq. F�
c: 12+ + 2 eq. F�
a
b
c
-0.2-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)
a: 12+
b: 12+ + 1 eq. F�
c: 12+ + 2 eq. F�
a
b
c
-0.2-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)
a : 24+
b : 24+ + 1 eq. F�
a
b
(Cur
rent
; A)
(Cur
rent
; A)
-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)-1.6
a: 12+
b: 12+ + 1 eq. F�
c: 12+ + 2 eq. F�
a
b
c
-0.2-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)
a: 12+
b: 12+ + 1 eq. F�
c: 12+ + 2 eq. F�
a
b
c
-0.2-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)
a : 24+
b : 24+ + 1 eq. F�
a
b
a : 24+
b : 24+ + 1 eq. F�
a
b
(Cur
rent
; A)
(Cur
rent
; A)
-0.4-0.6-0.8-1.0-1.2-1.4 (E, V)-1.6
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
16
17. UV-Visible changes observed with 2.(PF 6)4 and 1.(PF 6)4 in presence of Fluoride
15A→ Color changes observed before and after addition of 0.2 equiv. of F− or 2 equiv. of
representative anions or base in DMF solutions of the receptors (R) and 1.(PF6)4 or 2.(PF6)4
(1mM, Argon atm) (from the left to the right: R, R+F−, R+Cl−, R+Br−, R+I−, R+Di-isopropylamine)
1.(PF6)4 2.(PF6)4
15B→ Changes in the Absorption spectrum of 2.(PF6)4 and 1.(PF6)4 (1mM) in DMF under
argon atmosphere upon addition of various amounts of tetra-n-butylammonium salts of F– (0.2
equiv.) or Cl–, Br–, I– and Di-isopropylamine (2 equiv.).
400 600 800 10000,0
0,5
1,0
1,5
2,0
2,5
3,0
3,5
Free
2.0 eq. Cl-,Br- and I-
2.0 eq. base
0.2 eq.F-
Abs
Wavelength/nm400 600 800 1000
0,0
0,5
1,0
1,5
2,0
2,5
Free
2.0 eq. Cl-,Br- and I-
2.0 eq. base
0.2 eq.F-
Abs
Wavelength/nm
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010
17
18. Computational Details The quantum chemistry calculations were carried out with both the CP2KQuickStep program and
the Gaussian031 program. With this latter code, we used the BLYP, B3LYP2, B3LYP-CP3
(Corrected Potential) and MP24 functional with the 6-31+G(d,p)5 basis sets.
Solvent effects have been evaluated using the polarizable continuum model (PCM)6 in which the
cavity is created via a series of overlapping spheres.
The ab initio Born-Oppenheimer dynamics calculations were performed using the CP2K- QuickStep
program7 at the DFT level with the BLYP8 + D9 functional. QuickStep is an implementation of the
Gaussian Plane Waves (GPW) method based on the Kohn- Sham formulation of the density
functional theory (DFT). It is a hybrid method using a linear combination of Gaussian-type orbitals
to describe the Kohn-Sham orbitals, whereas an auxiliary plane waves basis set is employed to
expand the electronic charge density.
The basis set used was a double-ζ valence set of Gaussian orbitals10 in conjunction with the
Goedecker-Teter-Hutter11 pseudopotentials. The auxiliary PW basis set was defined by a cubic box
of 25 Å3 and by a density cutoff of 360 Ry.
Metadynamics12 has been used to overcome the problem of observing rare events in conventional
molecular dynamics and determining the energy barrier of our system. The method consist in a series
1 M. J. Frisch et all ; Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT, 2004.
2 Becke, A. D. J. Chem. Phys. 1993, 98, 5648
3 Gino A. DiLabio; Chem. Phys. Lett. , 2008,455, 348-353
4 C. Moller and M. S. Plesset, Phys. Rev. 1934, 46, 618
5 (a) M. J. Frisch, J. A. Pople, and J. S. Binkley, J. Chem. Phys. , 1984, 80, 3265 ; (b) T. Clark, J. Chandrasekhar, G. W.
Spitznagel, and P. v. R. Schleyer, J. Comp. Chem. , 1983, 4, 294
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of small repulsive Gaussian potentials, centered on the values of some collective variables, added
during the dynamics, preventing the system from revisiting the same points in configurational space
and creating a historydependent multidimensional biasing potential. A time step of 1 fs is used for
the dynamics, and the deposition rate of the hills is every τG=20 fs. The height (w) and with (δs) of
the Gaussians-shaped potential hills added are 0.6 kcal/mol and 1 Bohr respectively.
In the present study, we considered distances R1 and R2 as collective variables. The definition of R1
and R2 can be seen in the figure 1. Velocity rescaling algorithm was used to enforce the system to a
given temperature T, of 300 Kelvin. The Hydrogen atoms are changed to Deuterium in conjunction
with integration step of 1 fs. The duration of our simulation is approximately 5 ps of Metadynamics
and after 3 ps the system starts to opening. This is clearly emphasized by the variation of the
collective variable R1 showed in the figure 2.
The free energy surface F(S(R)) is then reconstructed on a 100 × 100 grid in the (1.052Å < R1 <
6.843Å) × (1.362Å < R2<16.560Å) region with an integration step of 0.111Å and 0.290Å
respectively see figure 3.
Fig.1 Collective variable R1 and R2, which represents the distances between the nitrogen atoms.
Fig.2 Time evolution of collective variable R1
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Fig. 3 Free energy surface reconstructions from Metadynamics run at T=300K with the bottom
representations of the Free Energy Surface depth.
Supplementary Material (ESI) for New Journal of ChemistryThis journal is © The Royal Society of Chemistry and The Centre National de la Recherche Scientifique, 2010