Charge-density analysis of 1-nitroindoline: refinement quality using free R factors and restraints

Nitramines and related N-nitro compounds have attracted significant attention owing to their use in rocket fuel and as explosives. The charge density of 1-nitroindoline was determined experimentally and from theoretical calculations. Electron-density refinements were performed using the multipolar atom formalism. In order to design the ideal restraint strategy for the charge-density parameters, R-free analyses were performed involving a series of comprehensive refinements. Different weights were applied to the charge-density restraints, namely the similarity between chemically equivalent atoms and local symmetry. Additionally, isotropic thermal motion and an anisotropic model calculated by rigid-body analysis were tested on H atoms. The restraint weights which resulted in the lowest values of the averaged R-free factors and the anisotropic H-atom model were considered to yield the best charge density and were used in the final refinement. The derived experimental charge density along with intra- and intermolecular interactions was analysed and compared with theoretical calculations, notably with respect to the symmetry of multipole parameters. A comparison of different refinements suggests that the appropriate weighting scheme applied to charge-density restraints can reduce the observed artefacts. The topological bond orders of the molecule were calculated.

Computing details

Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: MoPro (J. Appl. Cryst. 2005, 38, 38-54); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: MoPro (Guillot et al., 2001; Jelsch et al., 2005).

Figures

(I)

Crystal data

C8H8N2O2	Z = 2
Mr = 164.15	F(000) = 172
Triclinic, P1	Dx = 1.502 Mg m^−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.7913 (3) Å	Cell parameters from 29060 reflections
b = 8.2458 (6) Å	θ = 2.8–70.8°
c = 8.9223 (10) Å	µ = 0.11 mm^−1
α = 116.823 (8)°	T = 90 K
β = 104.589 (9)°	Irregular, colourless
γ = 91.602 (5)°	0.9 × 0.7 × 0.6 mm
V = 362.99 (5) Å^3

Data collection

Oxford Diffraction Xcalibur System diffractometer	8768 independent reflections
Radiation source: Enhance (Mo) X-ray Source	7946 reflections with > 2.0σ(I)
Graphite monochromator	Rint = 0.037
Detector resolution: 10.4508 pixels mm^-1	θmax = 70.2°, θmin = 2.8°
ω–scan	h = −14→13
Absorption correction: empirical (using intensity measurements) CrysAlis RED (Oxford Diffraction, 2007)	k = −21→18
Tmin = 0.923, Tmax = 0.946	l = 0→23
29060 measured reflections

Refinement

Refinement on F	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.021	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.024	Only H-atom coordinates refined
S = 0.96	w = 1/[1.1712*σ^2(Fo^2) + 0.0007*Yo^2]
8768 reflections	(Δ/^σ)max < 0.001
385 parameters	Δ^ρmax = 0.23 e Å−3
203 restraints	Δ^ρmin =^−0.20 e Å−3

Special details

Refinement. Refinement of F² against reflections. The threshold expression of F² > σ(F²) is used for calculating R-factors(gt) 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.

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

	x	y	z	Uiso*/Ueq
O1	0.78192 (5)	1.08684 (3)	0.27352 (4)	0.01910 (10)
O2	1.11924 (5)	1.13974 (3)	0.48239 (3)	0.01850 (10)
N1	1.06725 (3)	0.90148 (2)	0.22094 (2)	0.01330 (10)
N2	0.98503 (3)	1.05034 (2)	0.33008 (2)	0.01380 (10)
C1	0.96755 (3)	0.79791 (2)	0.03622 (2)	0.01080 (10)
C2	1.12758 (3)	0.67051 (2)	−0.02713 (2)	0.01090 (10)
C3	1.07498 (3)	0.54989 (2)	−0.20611 (2)	0.01410 (10)
C4	0.86148 (3)	0.55753 (3)	−0.32114 (2)	0.01590 (10)
C5	0.70391 (3)	0.68537 (3)	−0.25621 (2)	0.01550 (10)
C6	0.75379 (3)	0.80809 (2)	−0.07582 (2)	0.01380 (10)
C8	1.34213 (3)	0.68715 (2)	0.12131 (2)	0.01280 (10)
C7	1.30992 (3)	0.85638 (3)	0.28538 (2)	0.01400 (10)
H3	1.1918 (8)	0.4520 (6)	−0.2576 (6)	0.03042
H4	0.8181 (9)	0.4646 (6)	−0.4610 (3)	0.03331
H5	0.5412 (6)	0.6893 (7)	−0.3457 (5)	0.03402
H6	0.6344 (7)	0.9046 (6)	−0.0270 (6)	0.03051
H8A	1.5142 (4)	0.7031 (8)	0.0973 (5)	0.03048
H8B	1.3436 (9)	0.5621 (4)	0.1343 (6)	0.02969
H7A	1.3134 (10)	0.8371 (8)	0.3989 (5)	0.03012
H7B	1.4406 (8)	0.9817 (5)	0.3418 (7)	0.02993

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0190 (3)	0.0165 (3)	0.0213 (3)	0.00739 (7)	0.01020 (10)	0.00620 (10)
O2	0.0255 (3)	0.0134 (3)	0.0122 (3)	0.00055 (7)	0.00720 (10)	0.00170 (10)
N1	0.0137 (3)	0.0131 (3)	0.0100 (3)	0.00341 (6)	0.00351 (9)	0.00270 (10)
N2	0.0172 (3)	0.0108 (3)	0.0128 (3)	0.00218 (6)	0.00735 (9)	0.00340 (10)
C1	0.0105 (3)	0.0107 (3)	0.0103 (3)	0.00193 (6)	0.00295 (9)	0.00430 (10)
C2	0.0106 (3)	0.0111 (3)	0.0096 (3)	0.00177 (6)	0.00296 (9)	0.00370 (10)
C3	0.0142 (3)	0.0144 (3)	0.0103 (3)	0.00216 (6)	0.00391 (9)	0.00290 (10)
C4	0.0158 (3)	0.0181 (3)	0.0100 (3)	−0.00010 (6)	0.00194 (9)	0.00460 (10)
C5	0.0136 (3)	0.0185 (3)	0.0131 (3)	0.00078 (6)	0.00061 (9)	0.00820 (10)
C6	0.0120 (3)	0.0149 (3)	0.0143 (3)	0.00341 (6)	0.00274 (9)	0.00720 (10)
C8	0.0107 (3)	0.0141 (3)	0.0126 (3)	0.00271 (6)	0.00289 (9)	0.00570 (10)
C7	0.0133 (3)	0.0143 (3)	0.0107 (3)	0.00097 (6)	0.00142 (9)	0.00390 (10)
H3	0.0308	0.0294	0.0269	0.0126	0.0136	0.0068
H4	0.0385	0.0348	0.0145	0.0016	0.0039	0.0039
H5	0.0254	0.0435	0.0280	0.0066	−0.0032	0.0184
H6	0.0261	0.0321	0.0331	0.0151	0.0102	0.0140
H8A	0.0189	0.0391	0.0314	0.0040	0.0095	0.0140
H8B	0.0351	0.0235	0.0306	0.0065	0.0061	0.0147
H7A	0.0357	0.0364	0.0229	0.0078	0.0086	0.0178
H7B	0.0252	0.0241	0.0322	−0.0036	0.0044	0.0091

Geometric parameters (Å, º)

O1—N2	1.2596 (4)	C4—C5	1.4312 (3)
O2—N2	1.2354 (3)	C4—H4	1.084 (2)
N1—N2	1.3672 (3)	C5—C6	1.4062 (3)
N1—C1	1.4149 (3)	C5—H5	1.083 (5)
N1—C7	1.5030 (3)	C6—H6	1.082 (5)
C1—C2	1.4368 (3)	C8—C7	1.5600 (3)
C1—C6	1.4132 (3)	C8—H8A	1.087 (5)
C2—C8	1.5213 (3)	C8—H8B	1.089 (5)
C2—C3	1.3917 (3)	C7—H7A	1.089 (5)
C3—C4	1.4176 (3)	C7—H7B	1.090 (5)
C3—H3	1.083 (5)
O1—N2—O2	124.25 (3)	C2—C8—H8B	112.3 (2)
O1—N2—N1	119.87 (2)	C2—C3—C4	118.05 (2)
O2—N2—N1	115.87 (2)	C2—C3—H3	121.7 (3)
N1—C1—C2	107.230 (10)	C3—C2—C8	127.870 (10)
N1—C1—C6	129.82 (2)	C3—C4—C5	121.31 (2)
N1—C7—C8	104.920 (10)	C3—C4—H4	118.9 (3)
N1—C7—H7A	108.7 (3)	C4—C3—H3	120.3 (3)
N1—C7—H7B	106.5 (3)	C4—C5—C6	121.46 (2)
N2—N1—C1	126.03 (2)	C4—C5—H5	120.4 (3)
N2—N1—C7	120.72 (2)	C5—C6—H6	121.3 (3)
C1—N1—C7	112.150 (10)	C5—C4—H4	119.7 (3)
C1—C2—C8	112.100 (10)	C6—C5—H5	118.1 (3)
C1—C2—C3	120.03 (2)	C8—C7—H7A	116.7 (3)
C1—C6—C5	116.19 (2)	C8—C7—H7B	116.5 (3)
C1—C6—H6	122.5 (3)	C7—C8—H8A	113.8 (3)
C2—C1—C6	122.95 (2)	C7—C8—H8B	113.1 (3)
C2—C8—C7	102.910 (10)	H8A—C8—H8B	102.6 (4)
C2—C8—H8A	112.5 (2)	H7A—C7—H7B	103.0 (4)
O1—N2—N1—C1	12.48 (2)	C2—C1—C6—C5	−0.120 (10)
O1—N2—N1—C7	179.51 (2)	C2—C1—C6—H6	−179.90 (10)
O2—N2—N1—C1	−168.60 (2)	C2—C8—C7—H7A	128.2 (3)
O2—N2—N1—C7	−1.57 (2)	C2—C8—C7—H7B	−109.6 (3)
N1—C1—C2—C8	0.820 (10)	C2—C3—C4—C5	0.11 (2)
N1—C1—C2—C3	−179.830 (10)	C2—C3—C4—H4	179.90 (10)
N1—C1—C6—C5	179.690 (10)	C3—C2—C1—C6	0.000 (15)
N1—C1—C6—H6	−0.1 (2)	C3—C2—C8—C7	175.140 (10)
N1—C7—C8—C2	7.810 (10)	C3—C2—C8—H8A	52.3 (2)
N1—C7—C8—H8A	129.8 (3)	C3—C2—C8—H8B	−62.9 (2)
N1—C7—C8—H8B	−113.6 (3)	C3—C4—C5—C6	−0.22 (2)
N2—N1—C1—C2	172.710 (10)	C3—C4—C5—H5	−179.80 (10)
N2—N1—C1—C6	−7.12 (2)	C4—C3—C2—C8	179.230 (10)
N2—N1—C7—C8	−176.820 (10)	C4—C5—C6—H6	−180.00 (10)
N2—N1—C7—H7A	57.7 (3)	C5—C4—C3—H3	179.80 (10)
N2—N1—C7—H7B	−52.8 (3)	C6—C1—N1—C7	−175.100 (10)
C1—N1—C7—C8	−8.120 (10)	C6—C1—C2—C8	−179.340 (10)
C1—N1—C7—H7A	−133.6 (3)	C6—C5—C4—H4	180.00 (10)
C1—N1—C7—H7B	115.9 (3)	C8—C2—C3—H3	−0.5 (2)
C1—C2—C8—C7	−5.570 (10)	H3—C3—C4—H4	−0.4 (3)
C1—C2—C8—H8A	−128.4 (3)	H4—C4—C5—H5	0.4 (3)
C1—C2—C8—H8B	116.4 (3)	H5—C5—C6—H6	−0.4 (3)
C1—C2—C3—C4	0.000 (14)	H8A—C8—C7—H7A	−109.8 (4)
C1—C2—C3—H3	−179.70 (10)	H8A—C8—C7—H7B	12.4 (4)
C1—C6—C5—C4	0.22 (2)	H8B—C8—C7—H7A	6.8 (4)
C1—C6—C5—H5	179.80 (10)	H8B—C8—C7—H7B	129.0 (4)
C2—C1—N1—C7	4.740 (10)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O2^i	1.083 (5)	2.499 (4)	3.3395 (3)	133.6 (3)
C6—H6···O1	1.082 (5)	2.306 (4)	2.8779 (3)	111.1 (2)
C7—H7B···O1^ii	1.090 (5)	2.453 (4)	3.3363 (3)	137.2 (4)
C5—H5···O1	1.083 (5)	2.656 (4)	3.4361 (3)	128.5 (3)

Symmetry codes: (i) x, y−1, z−1; (ii) x+1, y, z.