An isoindoline EPR label: 5-acet­amido-1,1,3,3-tetra­methyl­isoindolin-2-yl­oxyl

The crystal structure of the isoindoline nitro­xide amide 5-acet­amido-1,1,3,3-tetra­methyl­isoindolin-2-yl­oxyl, C₁₄H₁₉N₂O₂, which has utility as an EPR label, shows a characteristically stable tetra­methyl-substituted nitro­xide ring system which is essentially coplanar with the amide side-chain substituent. A single intermolecular hydrogen bond between the amide H atom and the nitro­xide O atom links the mol­ecules head-to-tail into an infinite polymeric chain.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](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.

---

S1. Comment

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.

S2. Experimental

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.

Computing details

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).

Figures

Fig. 1. The molecular conformation and atom-naming scheme with the atoms shown as 30% probability ellipsoids (Spek, 1999).

5-acetamido-1,1,3,3-tetramethylisoindolin-2-yloxyl

Crystal data

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) Å^3	Block, yellow
Z = 4	0.38 × 0.28 × 0.15 mm

Data collection

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

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.039	H-atom parameters constrained
wR(F^2) = 0.125	w = 1/[σ^2(Fo^2) + (0.0598P)^2 + 0.1927P] where P = (Fo^2 + 2Fc^2)/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+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0023 (2)

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	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*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

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)