Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801010716/tk6031sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536801010716/tk6031Isup2.hkl |
CCDC reference: 170929
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (C-C) = 0.007 Å
- R factor = 0.039
- wR factor = 0.125
- Data-to-parameter ratio = 7.8
checkCIF results
No syntax errors found ADDSYM reports no extra symmetry General Notes
REFLT_03 From the CIF: _diffrn_reflns_theta_max 25.00 From the CIF: _reflns_number_total 1286 Count of symmetry unique reflns 1235 Completeness (_total/calc) 104.13% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 51 Fraction of Friedel pairs measured 0.041 Are heavy atom types Z>Si present no ALERT: MoKa measured Friedel data cannot be used to determine absolute structure in a light-atom study EXCEPT under VERY special conditions. It is preferred that Friedel data is merged in such cases.
The title compound was prepared according to the method of Reid et al. (1998), by reacting 5-amino-1,1,3,3-tetramethylisoindolin-2-yloxyl in tetrahydrafuran containing 1.5 equivalents of sodium bicarbonate, with 10 equivalents of acetyl chloride. Extraction into diethyl ether and recrystallization from acetonitrile gave data quality crystals.
Data collection: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1999a); cell refinement: MSC/AFC Diffractometer Control Software; data reduction: TEXSAN for Windows (Molecular Structure Corporation, 1999b); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); software used to prepare material for publication: TEXSAN for Windows (Molecular Structure Corporation, 1999b) and PLATON for Windows (Spek, 1999).
Fig. 1. The molecular conformation and atom-naming scheme with the atoms shown as 30% probability ellipsoids (Spek, 1999). |
C14H19N2O2 | F(000) = 532 |
Mr = 247.32 | Dx = 1.167 Mg m−3 |
Monoclinic, Cc | Melting point: 467–471 K K |
Hall symbol: C -2yc | Mo Kα radiation, λ = 0.71069 Å |
a = 14.325 (4) Å | Cell parameters from 25 reflections |
b = 8.536 (8) Å | θ = 10.4–16.3° |
c = 11.513 (4) Å | µ = 0.08 mm−1 |
β = 91.56 (2)° | T = 295 K |
V = 1407 (1) Å3 | Block, yellow |
Z = 4 | 0.38 × 0.28 × 0.15 mm |
Rigaku AFC-7R diffractometer | Rint = 0.020 |
Radiation source: Rigaku rotating anode | θmax = 25.0°, θmin = 2.8° |
Graphite monochromator | h = 0→16 |
ω–2θ scans | k = 0→10 |
1384 measured reflections | l = −13→13 |
1286 independent reflections | 3 standard reflections every 150 reflections |
716 reflections with I > 2σ(I) | intensity decay: 2.6% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.039 | H-atom parameters constrained |
wR(F2) = 0.125 | w = 1/[σ2(Fo2) + (0.0598P)2 + 0.1927P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max = 0.007 |
1286 reflections | Δρmax = 0.20 e Å−3 |
164 parameters | Δρmin = −0.16 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0023 (2) |
C14H19N2O2 | V = 1407 (1) Å3 |
Mr = 247.32 | Z = 4 |
Monoclinic, Cc | Mo Kα radiation |
a = 14.325 (4) Å | µ = 0.08 mm−1 |
b = 8.536 (8) Å | T = 295 K |
c = 11.513 (4) Å | 0.38 × 0.28 × 0.15 mm |
β = 91.56 (2)° |
Rigaku AFC-7R diffractometer | Rint = 0.020 |
1384 measured reflections | 3 standard reflections every 150 reflections |
1286 independent reflections | intensity decay: 2.6% |
716 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.039 | 0 restraints |
wR(F2) = 0.125 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.20 e Å−3 |
1286 reflections | Δρmin = −0.16 e Å−3 |
164 parameters |
Experimental. The scan width was (1.78 + 0.35tanθ)° with an ω scan speed of 16° per minute (up to 5 scans to achieve I/σ(I) > 15). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1. |
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. The absolute configuration could not be determined with any certainty, using the method of Flack (1983). The lower-than-desirable reflection-to-parameter ratio (7.84) could not be improved upon since all hydrogen atoms were constrained and no chance of data re-collection is possible. It is noted that the space group is non-centrosymmetric. |
x | y | z | Uiso*/Ueq | ||
O8 | 1.0616 (3) | 0.6239 (5) | 0.8706 (4) | 0.0831 (16) | |
O31 | 0.7736 (3) | 1.2419 (4) | 0.5737 (4) | 0.0715 (13) | |
N8 | 0.9920 (3) | 0.6661 (5) | 0.8060 (4) | 0.0560 (13) | |
N31 | 0.7083 (3) | 1.0132 (4) | 0.5138 (3) | 0.0456 (12) | |
C1 | 0.8856 (3) | 0.8167 (6) | 0.7049 (4) | 0.0391 (13) | |
C2 | 0.8374 (4) | 0.9389 (6) | 0.6520 (4) | 0.0443 (14) | |
C3 | 0.7596 (4) | 0.9011 (6) | 0.5801 (4) | 0.0435 (13) | |
C4 | 0.7326 (3) | 0.7449 (6) | 0.5685 (4) | 0.0435 (14) | |
C5 | 0.7817 (3) | 0.6249 (6) | 0.6225 (4) | 0.0461 (14) | |
C6 | 0.8601 (3) | 0.6634 (6) | 0.6907 (4) | 0.0387 (13) | |
C7 | 0.9263 (4) | 0.5504 (5) | 0.7516 (5) | 0.0436 (12) | |
C9 | 0.9731 (4) | 0.8346 (6) | 0.7814 (4) | 0.0452 (14) | |
C31 | 0.7188 (4) | 1.1701 (6) | 0.5101 (5) | 0.0494 (13) | |
C32 | 0.6599 (4) | 1.2509 (7) | 0.4193 (5) | 0.0620 (15) | |
C71 | 0.9793 (4) | 0.4484 (7) | 0.6681 (5) | 0.0621 (17) | |
C72 | 0.8809 (5) | 0.4528 (7) | 0.8452 (5) | 0.0666 (17) | |
C91 | 0.9564 (4) | 0.9208 (7) | 0.8951 (5) | 0.0617 (16) | |
C92 | 1.0550 (4) | 0.9052 (7) | 0.7178 (5) | 0.0687 (18) | |
H2 | 0.8545 | 1.0449 | 0.6645 | 0.050* | |
H4 | 0.6782 | 0.7212 | 0.5218 | 0.054* | |
H5 | 0.7626 | 0.5183 | 0.6116 | 0.050* | |
H31 | 0.6635 | 0.9583 | 0.4625 | 0.086* | |
H321 | 0.6977 | 1.3021 | 0.3649 | 0.070* | |
H322 | 0.6201 | 1.3267 | 0.4546 | 0.070* | |
H323 | 0.6209 | 1.1760 | 0.3794 | 0.070* | |
H711 | 0.9382 | 0.3706 | 0.6356 | 0.072* | |
H712 | 1.0292 | 0.3979 | 0.7090 | 0.072* | |
H713 | 1.0028 | 0.5107 | 0.6077 | 0.072* | |
H721 | 0.9271 | 0.4035 | 0.8923 | 0.075* | |
H722 | 0.8420 | 0.3731 | 0.8090 | 0.075* | |
H723 | 0.8426 | 0.5174 | 0.8910 | 0.075* | |
H911 | 0.9504 | 1.0305 | 0.8794 | 0.074* | |
H912 | 1.0070 | 0.9037 | 0.9473 | 0.074* | |
H913 | 0.9001 | 0.8840 | 0.9270 | 0.074* | |
H921 | 1.0578 | 0.8588 | 0.6423 | 0.082* | |
H922 | 1.1109 | 0.8869 | 0.7598 | 0.082* | |
H923 | 1.0452 | 1.0154 | 0.7085 | 0.082* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O8 | 0.072 (3) | 0.077 (3) | 0.097 (3) | 0.014 (3) | −0.055 (3) | 0.009 (3) |
O31 | 0.069 (2) | 0.041 (2) | 0.102 (3) | −0.001 (2) | −0.040 (2) | −0.012 (2) |
N8 | 0.056 (3) | 0.055 (3) | 0.056 (3) | 0.004 (3) | −0.030 (2) | 0.002 (3) |
N31 | 0.045 (3) | 0.036 (2) | 0.054 (3) | −0.001 (2) | −0.022 (2) | 0.003 (2) |
C1 | 0.031 (3) | 0.042 (3) | 0.044 (3) | −0.003 (2) | −0.010 (2) | −0.002 (2) |
C2 | 0.049 (3) | 0.030 (3) | 0.053 (3) | −0.010 (3) | −0.016 (3) | 0.001 (2) |
C3 | 0.035 (3) | 0.048 (3) | 0.046 (3) | −0.003 (3) | −0.009 (2) | 0.001 (3) |
C4 | 0.039 (2) | 0.041 (3) | 0.050 (4) | 0.001 (2) | −0.017 (3) | −0.001 (2) |
C5 | 0.043 (3) | 0.045 (3) | 0.049 (3) | −0.003 (3) | −0.010 (3) | −0.002 (3) |
C6 | 0.034 (3) | 0.045 (4) | 0.036 (3) | 0.000 (3) | −0.010 (2) | −0.003 (3) |
C7 | 0.041 (3) | 0.045 (3) | 0.044 (3) | 0.003 (3) | −0.012 (2) | 0.003 (3) |
C9 | 0.033 (3) | 0.060 (3) | 0.042 (3) | −0.001 (3) | −0.011 (2) | 0.000 (3) |
C31 | 0.040 (3) | 0.044 (3) | 0.063 (4) | 0.009 (3) | −0.008 (3) | −0.002 (3) |
C32 | 0.063 (3) | 0.052 (3) | 0.070 (4) | 0.006 (3) | −0.014 (3) | 0.010 (3) |
C71 | 0.054 (3) | 0.068 (4) | 0.064 (4) | 0.019 (3) | −0.015 (3) | −0.012 (3) |
C72 | 0.074 (4) | 0.057 (4) | 0.068 (4) | 0.000 (3) | −0.011 (3) | 0.016 (3) |
C91 | 0.064 (4) | 0.066 (4) | 0.054 (3) | −0.003 (3) | −0.022 (3) | −0.014 (3) |
C92 | 0.044 (3) | 0.087 (4) | 0.074 (4) | −0.013 (3) | −0.016 (3) | 0.013 (3) |
O8—N8 | 1.279 (5) | C7—C72 | 1.521 (8) |
O31—C31 | 1.224 (6) | C9—C92 | 1.523 (8) |
N8—C9 | 1.490 (7) | C9—C91 | 1.527 (7) |
N8—C7 | 1.491 (7) | C31—C32 | 1.494 (7) |
N31—C31 | 1.348 (6) | C32—H321 | 0.95 |
N31—C3 | 1.417 (6) | C32—H322 | 0.96 |
N31—H31 | 0.98 | C32—H323 | 0.96 |
C1—C6 | 1.367 (7) | C71—H711 | 0.96 |
C1—C2 | 1.383 (7) | C71—H712 | 0.95 |
C1—C9 | 1.520 (5) | C71—H713 | 0.95 |
C2—C3 | 1.407 (7) | C72—H721 | 0.94 |
C2—H2 | 0.95 | C72—H722 | 0.97 |
C3—C4 | 1.394 (7) | C72—H723 | 0.95 |
C4—C5 | 1.381 (7) | C91—H911 | 0.96 |
C4—H4 | 0.96 | C91—H912 | 0.94 |
C5—C6 | 1.392 (6) | C91—H913 | 0.95 |
C5—H5 | 0.96 | C92—H921 | 0.96 |
C6—C7 | 1.511 (7) | C92—H922 | 0.94 |
C7—C71 | 1.516 (8) | C92—H923 | 0.96 |
O8—N8—C9 | 121.1 (5) | C92—C9—C91 | 111.2 (5) |
O8—N8—C7 | 122.1 (4) | O31—C31—N31 | 123.2 (5) |
C9—N8—C7 | 116.7 (4) | O31—C31—C32 | 121.9 (5) |
C31—N31—C3 | 129.2 (4) | N31—C31—C32 | 114.9 (5) |
C31—N31—H31 | 122 | C31—C32—H321 | 111 |
C3—N31—H31 | 109 | C31—C32—H322 | 110 |
C6—C1—C2 | 122.7 (4) | H321—C32—H322 | 109 |
C6—C1—C9 | 112.3 (5) | C31—C32—H323 | 110 |
C2—C1—C9 | 125.0 (5) | H321—C32—H323 | 109 |
C1—C2—C3 | 117.7 (4) | H322—C32—H323 | 108 |
C1—C2—H2 | 122 | C7—C71—H711 | 110 |
C3—C2—H2 | 120 | C7—C71—H712 | 109 |
C4—C3—C2 | 119.3 (4) | H711—C71—H712 | 109 |
C4—C3—N31 | 117.1 (4) | C7—C71—H713 | 110 |
C2—C3—N31 | 123.6 (4) | H711—C71—H713 | 109 |
C5—C4—C3 | 121.9 (5) | H712—C71—H713 | 110 |
C5—C4—H4 | 120 | C7—C72—H721 | 110 |
C3—C4—H4 | 118 | C7—C72—H722 | 110 |
C4—C5—C6 | 118.2 (5) | H721—C72—H722 | 109 |
C4—C5—H5 | 120 | C7—C72—H723 | 110 |
C6—C5—H5 | 121 | H721—C72—H723 | 110 |
C1—C6—C5 | 120.1 (4) | H722—C72—H723 | 108 |
C1—C6—C7 | 113.2 (4) | C9—C91—H911 | 109 |
C5—C6—C7 | 126.7 (5) | C9—C91—H912 | 110 |
N8—C7—C6 | 98.8 (3) | H911—C91—H912 | 110 |
N8—C7—C71 | 109.0 (5) | C9—C91—H913 | 109 |
C6—C7—C71 | 113.0 (4) | H911—C91—H913 | 109 |
N8—C7—C72 | 110.0 (4) | H912—C91—H913 | 110 |
C6—C7—C72 | 113.8 (5) | C9—C92—H921 | 109 |
C71—C7—C72 | 111.4 (4) | C9—C92—H922 | 110 |
N8—C9—C1 | 99.0 (5) | H921—C92—H922 | 110 |
N8—C9—C92 | 109.6 (5) | C9—C92—H923 | 109 |
C1—C9—C92 | 113.3 (4) | H921—C92—H923 | 108 |
N8—C9—C91 | 109.5 (4) | H922—C92—H923 | 110 |
C1—C9—C91 | 113.5 (4) | ||
C6—C1—C2—C3 | −0.6 (8) | C1—C6—C7—N8 | 1.7 (6) |
C9—C1—C2—C3 | 177.6 (5) | C5—C6—C7—N8 | 179.7 (5) |
C1—C2—C3—C4 | 2.3 (8) | C1—C6—C7—C71 | −113.3 (5) |
C1—C2—C3—N31 | −175.0 (5) | C5—C6—C7—C71 | 64.7 (7) |
C31—N31—C3—C4 | 178.9 (5) | C1—C6—C7—C72 | 118.3 (5) |
C31—N31—C3—C2 | −3.7 (8) | C5—C6—C7—C72 | −63.7 (7) |
C2—C3—C4—C5 | −2.2 (8) | O8—N8—C9—C1 | −179.4 (5) |
N31—C3—C4—C5 | 175.3 (5) | C7—N8—C9—C1 | 0.7 (6) |
C3—C4—C5—C6 | 0.3 (7) | O8—N8—C9—C92 | 61.8 (7) |
C2—C1—C6—C5 | −1.2 (7) | C7—N8—C9—C92 | −118.0 (5) |
C9—C1—C6—C5 | −179.6 (5) | O8—N8—C9—C91 | −60.5 (7) |
C2—C1—C6—C7 | 176.9 (5) | C7—N8—C9—C91 | 119.7 (5) |
C9—C1—C6—C7 | −1.5 (6) | C6—C1—C9—N8 | 0.5 (5) |
C4—C5—C6—C1 | 1.3 (7) | C2—C1—C9—N8 | −177.8 (5) |
C4—C5—C6—C7 | −176.5 (5) | C6—C1—C9—C92 | 116.5 (6) |
O8—N8—C7—C6 | 178.7 (5) | C2—C1—C9—C92 | −61.9 (7) |
C9—N8—C7—C6 | −1.5 (7) | C6—C1—C9—C91 | −115.4 (5) |
O8—N8—C7—C71 | −63.2 (7) | C2—C1—C9—C91 | 66.2 (7) |
C9—N8—C7—C71 | 116.7 (5) | C3—N31—C31—O31 | −5.5 (9) |
O8—N8—C7—C72 | 59.2 (7) | C3—N31—C31—C32 | 172.9 (5) |
C9—N8—C7—C72 | −120.9 (5) |
Experimental details
Crystal data | |
Chemical formula | C14H19N2O2 |
Mr | 247.32 |
Crystal system, space group | Monoclinic, Cc |
Temperature (K) | 295 |
a, b, c (Å) | 14.325 (4), 8.536 (8), 11.513 (4) |
β (°) | 91.56 (2) |
V (Å3) | 1407 (1) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.38 × 0.28 × 0.15 |
Data collection | |
Diffractometer | Rigaku AFC-7R diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1384, 1286, 716 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.039, 0.125, 1.03 |
No. of reflections | 1286 |
No. of parameters | 164 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.20, −0.16 |
Computer programs: MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1999a), MSC/AFC Diffractometer Control Software, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), TEXSAN for Windows (Molecular Structure Corporation, 1999b) and PLATON for Windows (Spek, 1999).
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Nitroxides are often utilized as reporter molecules and, as such, are commonly referred to as spin labels or spin probes depending upon whether they are covalently linked (labels), or not (probes), to the system being studied. Precise knowledge of the bonding structure of spin labels is essential to obtain information on complex systems such as enzymes and other macromolecules (Farrens et al., 1996; Steinhoff et al., 1997; Rink et al., 1997; Mchaourab et al., 1997). Another crucial issue in the utilization of stable nitroxide probes in biological systems is the partitioning behaviour which governs membrane transfer. Charged nitroxides generally do not cross cell membranes, although there are exceptions (Kocherginsky & Swartz, 1995) and amphiphilic nitroxides may orient themselves with the non-polar portion of the molecule embedded in the lipid bilayer. Lipophilic nitroxides have also been associated with enhanced cytotoxicity, albeit in high concentrations (>1 mM). We have synthesized (Reid et al., 1998) amino substituted isoindoline nitroxides as potential new EPR spin labels/probes and in order to contrast the toxicity and partitioning preferences, have now synthesized the novel 5-acetamido-1,1,3,3-tetramethylisoindolin-2-yloxyl, (I). reported here.
Single-crystal X-ray analysis of the structure of this amide (Fig. 1) provides insight into the bonding characteristics resulting when this type of EPR label is bound to an amino acid sequence. This reveals a basic tetramethylisoindoline core which is relatively inflexible and therefore similar to the previously reported compounds of the same type (Micallef et al., 1999). The N8—O8 bond distance [1.279 (5) Å] compares closely with these examples. The amide side chain adopts a conformation such that it is almost coplanar with the parent aromatic ring system [torsion angles C4–C3–N31–C31 172.9 (5)° and C3–N31–C31–O31 - 5.5 (9)°]. This is stabilized by the presence of an intramolecular hydrogen bond between the amide-O and a ring-H atom [O31···H2—O2 2.880 (7) Å]. A single head-to-tail hydrogen bond between the amide group and the nitroxide O atom [N31—H31···O8i 2.884 (7) Å and N—H···O, 171 (3)°] [symmetry code: (i) -1/2 + x, 3/2 - y, -1/2 + z] links the molecules into an infinite poymericchain.