Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270113015084/lg3111sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270113015084/lg3111Isup2.hkl | |
Chemdraw file https://doi.org/10.1107/S0108270113015084/lg3111Isup3.cdx | |
Chemdraw file https://doi.org/10.1107/S0108270113015084/lg3111Isup4.cdx |
CCDC reference: 957033
Synthesis of (I). To a mixture of N,N'-bis(2-hydroxylethyl)ethylenediamine (0.74 g, 5 mmol) and triethylamine (1.21 g, 12 mmol) in dichloromethane (25 ml) in an ice bath was added dropwise a solution of tert-butyldimethylsilyl chloride in dichloromethane (25 ml) under a dinitrogen atomsphere. The resulting suspension was allowed to react for 48 h at room temperature. The solvent was then removed and the solid was washed thoroughly with n-hexane. Recrystallization from a solution in ethanol afforded colourless plate-like crystals of (I) (m.p. 452–454 K). ESI-MS: m/z 377.44 [100%, (M - H - 2Cl)+]. Spectroscopic analysis: 1H NMR (Frequency?, d6-DMSO, δ, p.p.m.): 3.88 (t, 4H, OCH2C), 3.68 (t, 4H, OCH2CH2N), 3.32 (s, 4H, N(CH2)2N), 0.88 [s, 18H, SiC(CH3)3], 0.09 [s, 12H, Si(CH3)2].
Synthesis of (II). To a mixture of N,N'-bis(2-hydroxylethyl)ethylenediamine (2.31 g, 15.6 mmol), triethylamine (3.04 g, 30.1 mmol) and 4-dimethylaminopyridine (0.24 g, 1.97 mmol) in dichloromethane (40 ml) in an ice bath was added dropwise a solution of tert-butyldimethylsilyl chloride (5.15 g, 34.3 mmol) in dichloromethane (40 ml) under a dinitrogen atomsphere. After reaction overnight at room temperature the solution was washed with water (50 ml) and saturated sodium bicarbonate (50 ml). The organic phase was dried with anhydrous magnesium sulfate. Removal of the dichloromethane afforded a light-yellow oily product, which was purified by column chromatography (chloroform/methanol = 10/1 v/v). ESI-MS: m/z 377.40 [100%, (M + H)+]. Spectroscopic analysis: 1H NMR (Frequency?, CDCl3, δ, p.p.m.): 3.65 (t, 4H, OCH2C), 2.66 (t, 4H, OCH2CH2N), 2.64 [s, 4H, N(CH2)2N], 2.40 (br, s, 2H, NH), 0.82 [s, 18H, SiC(CH3)3], 0.02 [s, 12H, Si(CH3)2].
Secondary H atoms attached to C atoms were positioned geometrically and allowed to ride on their parent atoms, with C—H = 0.99 Å and Uiso(H) = 1.2Ueq(C). N-bound H atoms were located in a difference Fourier map and treated in the riding-model approximation, with N—H = 0.90 Å and Uiso(H) = 1.5Ueq(N). For the methyl groups, Si—C—H and C—C—H angles (109.5°) were kept fixed while the torsion angle was allowed to refine, with the starting positions based on the circular Fourier synthesis averaged using the local threefold axis, and with C—H = 0.98 Å and Uiso(H) = 1.5Ueq(C).
Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 (Bruker, 2004); data reduction: APEX2 (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).
C18H46N2O2Si22+·2Cl− | Z = 1 |
Mr = 449.65 | F(000) = 246 |
Triclinic, P1 | Dx = 1.134 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.2088 (4) Å | Cell parameters from 7080 reflections |
b = 6.4128 (6) Å | θ = 6.5–54.8° |
c = 18.7953 (10) Å | µ = 0.35 mm−1 |
α = 88.989 (2)° | T = 150 K |
β = 87.640 (2)° | Plate, colourless |
γ = 61.736 (2)° | 0.35 × 0.24 × 0.16 mm |
V = 658.57 (8) Å3 |
Bruker APEXII CCD area-detector diffractometer | 2859 independent reflections |
Radiation source: fine-focus sealed tube | 2483 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.041 |
ϕ and ω scans | θmax = 27.0°, θmin = 3.3° |
Absorption correction: multi-scan SADABS (Sheldrick, 2005) | h = −7→6 |
Tmin = 0.887, Tmax = 0.946 | k = −8→8 |
7608 measured reflections | l = −23→23 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0552P)2 + 0.3038P] where P = (Fo2 + 2Fc2)/3 |
2859 reflections | (Δ/σ)max = 0.001 |
123 parameters | Δρmax = 0.69 e Å−3 |
0 restraints | Δρmin = −0.36 e Å−3 |
C18H46N2O2Si22+·2Cl− | γ = 61.736 (2)° |
Mr = 449.65 | V = 658.57 (8) Å3 |
Triclinic, P1 | Z = 1 |
a = 6.2088 (4) Å | Mo Kα radiation |
b = 6.4128 (6) Å | µ = 0.35 mm−1 |
c = 18.7953 (10) Å | T = 150 K |
α = 88.989 (2)° | 0.35 × 0.24 × 0.16 mm |
β = 87.640 (2)° |
Bruker APEXII CCD area-detector diffractometer | 2859 independent reflections |
Absorption correction: multi-scan SADABS (Sheldrick, 2005) | 2483 reflections with I > 2σ(I) |
Tmin = 0.887, Tmax = 0.946 | Rint = 0.041 |
7608 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.69 e Å−3 |
2859 reflections | Δρmin = −0.36 e Å−3 |
123 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
Cl1 | 0.79662 (8) | 0.84481 (8) | 0.55047 (2) | 0.03111 (15) | |
Si1 | 0.79366 (8) | 0.74565 (8) | 0.22119 (2) | 0.02190 (15) | |
O1 | 0.8381 (3) | 0.9500 (2) | 0.26035 (6) | 0.0296 (3) | |
N1 | 0.6726 (2) | 1.2484 (2) | 0.43581 (7) | 0.0201 (3) | |
H1D | 0.6347 | 1.1460 | 0.4594 | 0.024* | |
H1E | 0.8256 | 1.2143 | 0.4467 | 0.024* | |
C1 | 0.4999 (3) | 1.4930 (3) | 0.45974 (8) | 0.0226 (4) | |
H1A | 0.3331 | 1.5366 | 0.4446 | 0.027* | |
H1B | 0.5499 | 1.6057 | 0.4378 | 0.027* | |
C2 | 0.6667 (3) | 1.2147 (3) | 0.35779 (8) | 0.0237 (4) | |
H2A | 0.7075 | 1.3272 | 0.3314 | 0.028* | |
H2B | 0.4998 | 1.2487 | 0.3454 | 0.028* | |
C3 | 0.8472 (4) | 0.9641 (3) | 0.33584 (9) | 0.0290 (4) | |
H3A | 1.0143 | 0.9261 | 0.3494 | 0.035* | |
H3B | 0.8025 | 0.8503 | 0.3597 | 0.035* | |
C4 | 0.4906 (3) | 0.7762 (4) | 0.25201 (10) | 0.0323 (4) | |
H4A | 0.4769 | 0.7842 | 0.3041 | 0.048* | |
H4B | 0.4758 | 0.6392 | 0.2358 | 0.048* | |
H4C | 0.3597 | 0.9213 | 0.2323 | 0.048* | |
C5 | 1.0403 (3) | 0.4452 (3) | 0.24472 (10) | 0.0313 (4) | |
H5A | 1.0434 | 0.4272 | 0.2966 | 0.047* | |
H5B | 1.1987 | 0.4261 | 0.2264 | 0.047* | |
H5C | 1.0083 | 0.3245 | 0.2235 | 0.047* | |
C6 | 0.8039 (3) | 0.8067 (3) | 0.12290 (9) | 0.0265 (4) | |
C7 | 0.6039 (4) | 1.0575 (4) | 0.10578 (11) | 0.0411 (5) | |
H7A | 0.6139 | 1.0886 | 0.0548 | 0.062* | |
H7B | 0.6270 | 1.1730 | 0.1334 | 0.062* | |
H7C | 0.4429 | 1.0709 | 0.1181 | 0.062* | |
C8 | 1.0549 (4) | 0.7849 (4) | 0.10001 (10) | 0.0368 (5) | |
H8A | 1.0573 | 0.8189 | 0.0490 | 0.055* | |
H8B | 1.1836 | 0.6238 | 0.1094 | 0.055* | |
H8C | 1.0835 | 0.8982 | 0.1271 | 0.055* | |
C9 | 0.7630 (4) | 0.6268 (4) | 0.08066 (10) | 0.0382 (5) | |
H9A | 0.7653 | 0.6604 | 0.0296 | 0.057* | |
H9B | 0.6041 | 0.6385 | 0.0951 | 0.057* | |
H9C | 0.8932 | 0.4666 | 0.0902 | 0.057* |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cl1 | 0.0247 (2) | 0.0366 (3) | 0.0372 (3) | −0.0184 (2) | −0.00962 (18) | 0.0106 (2) |
Si1 | 0.0206 (2) | 0.0233 (3) | 0.0209 (2) | −0.0096 (2) | −0.00125 (18) | −0.00182 (18) |
O1 | 0.0409 (7) | 0.0328 (7) | 0.0198 (6) | −0.0212 (6) | 0.0019 (5) | −0.0061 (5) |
N1 | 0.0193 (6) | 0.0217 (7) | 0.0201 (7) | −0.0103 (6) | −0.0023 (5) | −0.0003 (5) |
C1 | 0.0245 (8) | 0.0205 (8) | 0.0212 (8) | −0.0092 (7) | −0.0021 (6) | −0.0018 (6) |
C2 | 0.0240 (8) | 0.0289 (9) | 0.0182 (8) | −0.0124 (7) | −0.0025 (6) | −0.0015 (6) |
C3 | 0.0349 (10) | 0.0294 (9) | 0.0205 (8) | −0.0129 (8) | −0.0023 (7) | −0.0053 (7) |
C4 | 0.0252 (9) | 0.0335 (10) | 0.0338 (10) | −0.0106 (8) | −0.0010 (7) | 0.0065 (8) |
C5 | 0.0248 (9) | 0.0298 (9) | 0.0336 (10) | −0.0082 (7) | −0.0033 (7) | 0.0015 (8) |
C6 | 0.0253 (8) | 0.0330 (9) | 0.0209 (8) | −0.0135 (7) | −0.0014 (7) | −0.0028 (7) |
C7 | 0.0420 (11) | 0.0404 (12) | 0.0301 (10) | −0.0107 (9) | −0.0047 (8) | 0.0079 (8) |
C8 | 0.0337 (10) | 0.0543 (13) | 0.0275 (9) | −0.0251 (10) | 0.0012 (8) | 0.0010 (9) |
C9 | 0.0378 (11) | 0.0500 (13) | 0.0301 (10) | −0.0233 (10) | −0.0001 (8) | −0.0120 (9) |
Si1—O1 | 1.6520 (14) | C4—H4B | 0.9800 |
Si1—C4 | 1.866 (2) | C4—H4C | 0.9800 |
Si1—C5 | 1.8667 (19) | C5—H5A | 0.9800 |
Si1—C6 | 1.8865 (18) | C5—H5B | 0.9800 |
O1—C3 | 1.429 (2) | C5—H5C | 0.9800 |
N1—C1 | 1.485 (2) | C6—C9 | 1.534 (3) |
N1—C2 | 1.490 (2) | C6—C7 | 1.535 (3) |
N1—H1D | 0.8999 | C6—C8 | 1.541 (3) |
N1—H1E | 0.9000 | C7—H7A | 0.9800 |
C1—C1i | 1.518 (3) | C7—H7B | 0.9800 |
C1—H1A | 0.9900 | C7—H7C | 0.9800 |
C1—H1B | 0.9900 | C8—H8A | 0.9800 |
C2—C3 | 1.513 (2) | C8—H8B | 0.9800 |
C2—H2A | 0.9900 | C8—H8C | 0.9800 |
C2—H2B | 0.9900 | C9—H9A | 0.9800 |
C3—H3A | 0.9900 | C9—H9B | 0.9800 |
C3—H3B | 0.9900 | C9—H9C | 0.9800 |
C4—H4A | 0.9800 | ||
O1—Si1—C4 | 109.19 (8) | Si1—C4—H4C | 109.5 |
O1—Si1—C5 | 109.75 (8) | H4A—C4—H4C | 109.5 |
C4—Si1—C5 | 109.46 (9) | H4B—C4—H4C | 109.5 |
O1—Si1—C6 | 104.78 (8) | Si1—C5—H5A | 109.5 |
C4—Si1—C6 | 111.92 (8) | Si1—C5—H5B | 109.5 |
C5—Si1—C6 | 111.62 (8) | H5A—C5—H5B | 109.5 |
C3—O1—Si1 | 122.76 (12) | Si1—C5—H5C | 109.5 |
C1—N1—C2 | 112.73 (12) | H5A—C5—H5C | 109.5 |
C1—N1—H1D | 109.1 | H5B—C5—H5C | 109.5 |
C2—N1—H1D | 108.9 | C9—C6—C7 | 109.11 (16) |
C1—N1—H1E | 109.2 | C9—C6—C8 | 108.86 (15) |
C2—N1—H1E | 108.9 | C7—C6—C8 | 108.83 (17) |
H1D—N1—H1E | 107.9 | C9—C6—Si1 | 109.51 (13) |
N1—C1—C1i | 109.48 (16) | C7—C6—Si1 | 110.24 (12) |
N1—C1—H1A | 109.8 | C8—C6—Si1 | 110.25 (12) |
C1i—C1—H1A | 109.8 | C6—C7—H7A | 109.5 |
N1—C1—H1B | 109.8 | C6—C7—H7B | 109.5 |
C1i—C1—H1B | 109.8 | H7A—C7—H7B | 109.5 |
H1A—C1—H1B | 108.2 | C6—C7—H7C | 109.5 |
N1—C2—C3 | 110.79 (13) | H7A—C7—H7C | 109.5 |
N1—C2—H2A | 109.5 | H7B—C7—H7C | 109.5 |
C3—C2—H2A | 109.5 | C6—C8—H8A | 109.5 |
N1—C2—H2B | 109.5 | C6—C8—H8B | 109.5 |
C3—C2—H2B | 109.5 | H8A—C8—H8B | 109.5 |
H2A—C2—H2B | 108.1 | C6—C8—H8C | 109.5 |
O1—C3—C2 | 107.19 (14) | H8A—C8—H8C | 109.5 |
O1—C3—H3A | 110.3 | H8B—C8—H8C | 109.5 |
C2—C3—H3A | 110.3 | C6—C9—H9A | 109.5 |
O1—C3—H3B | 110.3 | C6—C9—H9B | 109.5 |
C2—C3—H3B | 110.3 | H9A—C9—H9B | 109.5 |
H3A—C3—H3B | 108.5 | C6—C9—H9C | 109.5 |
Si1—C4—H4A | 109.5 | H9A—C9—H9C | 109.5 |
Si1—C4—H4B | 109.5 | H9B—C9—H9C | 109.5 |
H4A—C4—H4B | 109.5 | ||
C4—Si1—O1—C3 | 60.90 (15) | C4—Si1—C6—C9 | −61.47 (15) |
C5—Si1—O1—C3 | −59.08 (15) | C5—Si1—C6—C9 | 61.61 (15) |
C6—Si1—O1—C3 | −179.05 (13) | O1—Si1—C6—C7 | −59.61 (16) |
C2—N1—C1—C1i | 174.94 (17) | C4—Si1—C6—C7 | 58.59 (17) |
C1—N1—C2—C3 | 179.38 (15) | C5—Si1—C6—C7 | −178.34 (15) |
Si1—O1—C3—C2 | −127.31 (14) | O1—Si1—C6—C8 | 60.57 (15) |
N1—C2—C3—O1 | −177.39 (14) | C4—Si1—C6—C8 | 178.77 (14) |
O1—Si1—C6—C9 | −179.67 (12) | C5—Si1—C6—C8 | −58.15 (16) |
Symmetry code: (i) −x+1, −y+3, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1D···Cl1 | 0.90 | 2.42 | 3.1604 (14) | 140 |
N1—H1D···Cl1ii | 0.90 | 2.66 | 3.2391 (15) | 123 |
N1—H1E···Cl1iii | 0.90 | 2.19 | 3.0797 (14) | 168 |
Symmetry codes: (ii) −x+1, −y+2, −z+1; (iii) −x+2, −y+2, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C18H46N2O2Si22+·2Cl− |
Mr | 449.65 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 150 |
a, b, c (Å) | 6.2088 (4), 6.4128 (6), 18.7953 (10) |
α, β, γ (°) | 88.989 (2), 87.640 (2), 61.736 (2) |
V (Å3) | 658.57 (8) |
Z | 1 |
Radiation type | Mo Kα |
µ (mm−1) | 0.35 |
Crystal size (mm) | 0.35 × 0.24 × 0.16 |
Data collection | |
Diffractometer | Bruker APEXII CCD area-detector diffractometer |
Absorption correction | Multi-scan SADABS (Sheldrick, 2005) |
Tmin, Tmax | 0.887, 0.946 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7608, 2859, 2483 |
Rint | 0.041 |
(sin θ/λ)max (Å−1) | 0.639 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.115, 1.07 |
No. of reflections | 2859 |
No. of parameters | 123 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.69, −0.36 |
Computer programs: APEX2 (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 2012), PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1D···Cl1 | 0.90 | 2.42 | 3.1604 (14) | 140 |
N1—H1D···Cl1i | 0.90 | 2.66 | 3.2391 (15) | 123 |
N1—H1E···Cl1ii | 0.90 | 2.19 | 3.0797 (14) | 168 |
Symmetry codes: (i) −x+1, −y+2, −z+1; (ii) −x+2, −y+2, −z+1. |
There are a variety of hydroxyl-group protection methods in organic synthesis (Greene & Wuts, 1991; Kocienski, 2005). Silyl ethers are usually used as protecting groups for alcohols. The reagent tert-butyldimethylsilyl chloride in a basic environment can react readily with alcohols to form tert-butyldimethylsilyl ether. This method is highly specific in the presence of amino or imino groups, and the subsequent deprotection is easy to achieve with fluoride.
In our efforts to protect the two hydroxyl groups of N,N'-bis(2-hydroxylethyl)ethylenediamine with tert-butyldimethylsilyl chloride accompanied by triethylamine, which has not been reported in the literature before, we unexpectedly obtained the title compound, (I). Although the hydroxyl groups were transformed to silyl ether groups as expected, the two imine groups were unfortunately protonated, despite excess triethylamine being used. A similar protection process normally keeps the imino group intact. Although in a few references the silyl ethers which contain an imine group are declared as hydrochloride salts (Nemoto et al., 2012; Zhai et al., 2009; Shin et al., 2008; Diaz-Oltra et al., 2008; Breccia et al., 2003; Herdeis & Telser, 1999; Herdeis & Schiffer, 1999; Fahrni & Pfaltz, 1998; Pohlmann et al., 1997), the structures have not been clearly established. There is only one crystallographic analysis of such a compound, namely (1R,2S)-(-)-2-benzylamino-1- tert-butyldimethylsiloxy-1-phenylpropane hydrochloride, which was in fact not obtained directly in the silyl ether protection process (Gorter & Brussee, 1992).
The diffraction data for (I) are of high quality and the amino H atoms can be located clearly in the difference Fourier map. As shown in Fig. 1, the cation of (I) lies across an inversion centre. The six methylene groups and the two amino groups between the two silyl O atoms are aligned as a zigzag line. The two terminal tert-butyldimethylsiloxy groups are positioned as in other silyl ether compounds (Yao & Lu, 2011; Dutta et al., 2011; Johansson et al., 2004; White & Hansen, 2002; Robinson & Donahue, 1992; Habich et al., 1988). Each chloride anion is located in the vicinity of the amino groups, forming three kinds of N—H···Cl hydrogen bond with three nearby parallel silyl ether dications (Table 1 and Fig. 2). As shown in Fig. 2, the connection of these N—H···Cl hydrogen bonds leads to two patterns of circles, which can be encoded as R22(4) and R42(8) according to graph-set theory for hydrogen-bond patterns in organic compounds (Etter, 1990). One amino group [Which?] is involved in an R22(4) and a neighbouring R42(8) ring. The infinite expansion of alternately linked rings form a one-dimensional straight belt. The other amino group [Which?] participates in another belt, so each silyl ether fragment is involved in two parallel belts. Due to the large steric effect of the silyl groups, neighbouring parallel silyl ether dicationic rods are aligned in a staggered arrangement. Parallel belts linked by the silyl ether rods constitute a two-dimensional network (Fig. 2). No significant interactions are found between the two-dimensional layers.
The crystal structure analysis of (I) has solved a significant chemistry problem for us. Before obtaining crystals of (I) and analysing its structure, we believed that the synthetic procedure for (I) yielded the expected N,N'-bis[2-tert-butyldimethylsiloxyethyl]ethylenediamine, (II), because the ESI-MS and 1H NMR results for the solid product appeared to be in agreement with (II). But the fact that the product existed in the solid state and was quite soluble in water raised some suspicions, given the presence of the two large hydrophobic tert-butyldimethylsilyl groups. The chemical reactivity of the product was also not that expected for (II), for example it was unable to react with alkyl halides. The present X-ray diffraction analysis reveals that the product is in fact (I) and thus the questions raised were resolved. In order to keep the imine groups unprotonated while protecting the hydroxyl groups, we added 4-dimethylaminopyridine, which was found to be an efficient and selective catalyst for the silyation of alcohols by Chaudhary & Hernandez (1979). The desired compound, (II), was thus obtained successfully. It is oily, as are many other silyl ethers. In contrast, the melting point of (I) is quite high (452–454 K), due to the extensive hydrogen-bonding interactions. The absence of positive charges on the N atoms in (II) moves the corresponding chemical shifts for (II) upfield compared with those for (I) in the 1H NMR spectroscopic data.