A top–down approach to crystal engineering of a racemic Δ2-isoxazoline

Lombardo, G.M.; Rescifina, A.; Chiacchio, U.; Bacchi, A.; Punzo, F.

doi:10.1107/S2052520613030862

A top–down approach to crystal engineering of a racemic Δ²-isoxazoline

G. M. Lombardo, A. Rescifina, U. Chiacchio, A. Bacchi and F. Punzo

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C₁₃H₁₂N₂O₇, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top–down approach to be a useful tool for crystal engineering.

Keywords: crystal morphology; density functional theory; Wulff plot; periodic bond chain theory.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2052520613030862/bi5027sup1.cif Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2052520613030862/bi5027Isup2.hkl Contains datablock I
	Portable Document Format (PDF) file https://doi.org/10.1107/S2052520613030862/bi5027sup3.pdf Details of the morphology prediction

CCDC reference: 958815

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: SHELXTL (Bruker, 2008); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2008) and WinGX (Farrugia, 1999).

Figures top

Dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate top

Crystal data top

C₁₃H₁₂N₂O₇	F(000) = 640
M_r = 308.25	D_x = 1.494 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54178 Å
a = 7.2032 (2) Å	Cell parameters from 4957 reflections
b = 6.9183 (3) Å	θ = 3.2–69.8°
c = 27.515 (2) Å	µ = 1.07 mm⁻¹
β = 92.134 (4)°	T = 293 K
V = 1370.23 (12) Å³	Prism, colorless
Z = 4	0.90 × 0.45 × 0.25 mm

Data collection top

Bruker APEX-II CCD diffractometer	2596 independent reflections
Radiation source: fine-focus sealed tube	2490 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.016
φ and ω scans	θ_max = 69.8°, θ_min = 3.2°
Absorption correction: multi-scan SADABS (Bruker, 2008)	h = −8→8
T_min = 0.98, T_max = 0.99	k = −8→1
4957 measured reflections	l = −32→33

Refinement top

Refinement on F²	Hydrogen site location: difference Fourier map
Least-squares matrix: full	All H-atom parameters refined
R[F² > 2σ(F²)] = 0.040	w = 1/[σ²(F_o²) + (0.0613P)² + 0.4588P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.114	(Δ/σ)_max < 0.001
S = 1.05	Δρ_max = 0.30 e Å⁻³
2596 reflections	Δρ_min = −0.24 e Å⁻³
248 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
3 restraints	Extinction coefficient: 0.0090 (7)

Crystal data top

C₁₃H₁₂N₂O₇	V = 1370.23 (12) Å³
M_r = 308.25	Z = 4
Monoclinic, P2₁/c	Cu Kα radiation
a = 7.2032 (2) Å	µ = 1.07 mm⁻¹
b = 6.9183 (3) Å	T = 293 K
c = 27.515 (2) Å	0.90 × 0.45 × 0.25 mm
β = 92.134 (4)°

Data collection top

Bruker APEX-II CCD diffractometer	2596 independent reflections
Absorption correction: multi-scan SADABS (Bruker, 2008)	2490 reflections with I > 2σ(I)
T_min = 0.98, T_max = 0.99	R_int = 0.016
4957 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.040	3 restraints
wR(F²) = 0.114	All H-atom parameters refined
S = 1.05	Δρ_max = 0.30 e Å⁻³
2596 reflections	Δρ_min = −0.24 e Å⁻³
248 parameters

Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.1514 (2)	0.1930 (2)	−0.06205 (5)	0.0538 (4)
N2	0.40842 (18)	0.84188 (19)	0.09400 (5)	0.0430 (3)
O1	0.1488 (3)	0.0178 (2)	−0.05648 (6)	0.0821 (5)
O2	0.1104 (2)	0.2730 (2)	−0.10048 (5)	0.0743 (4)
O3	0.43675 (16)	0.93415 (17)	0.13944 (4)	0.0495 (3)
O4	0.59575 (17)	0.42401 (19)	0.14255 (4)	0.0543 (3)
O5	0.5048 (2)	0.4656 (3)	0.21773 (5)	0.0876 (6)
O6	0.11028 (19)	1.07368 (18)	0.17241 (5)	0.0600 (4)
O7	0.05328 (16)	0.79192 (17)	0.20942 (4)	0.0510 (3)
C1	0.2054 (2)	0.3150 (2)	−0.02012 (5)	0.0417 (4)
C2	0.2380 (2)	0.5091 (2)	−0.02755 (5)	0.0439 (4)
C3	0.2866 (2)	0.6236 (2)	0.01190 (5)	0.0403 (3)
C4	0.29951 (19)	0.5448 (2)	0.05864 (5)	0.0349 (3)
C5	0.2636 (2)	0.3482 (2)	0.06492 (6)	0.0432 (4)
C6	0.2183 (2)	0.2323 (2)	0.02550 (6)	0.0470 (4)
C7	0.34806 (18)	0.6699 (2)	0.10043 (5)	0.0347 (3)
C8	0.3312 (2)	0.6186 (2)	0.15339 (5)	0.0355 (3)
C9	0.3426 (2)	0.8226 (2)	0.17495 (5)	0.0403 (4)
C10	0.4867 (2)	0.4927 (2)	0.17506 (5)	0.0409 (4)
C11	0.1549 (2)	0.9142 (2)	0.18422 (5)	0.0412 (4)
C12	0.7500 (3)	0.3034 (4)	0.15973 (8)	0.0684 (6)
C13	−0.1297 (3)	0.8578 (3)	0.22185 (8)	0.0596 (5)
H8	0.220 (3)	0.553 (2)	0.1599 (6)	0.039 (4)*
H5	0.268 (3)	0.293 (3)	0.0972 (7)	0.055 (5)*
H2	0.230 (3)	0.561 (3)	−0.0582 (8)	0.055 (5)*
H6	0.192 (3)	0.099 (3)	0.0300 (7)	0.055 (5)*
H3	0.314 (3)	0.758 (3)	0.0075 (7)	0.052 (5)*
H121	0.791 (5)	0.229 (5)	0.1359 (10)	0.121 (11)*
H122	0.704 (4)	0.222 (4)	0.1839 (11)	0.104 (10)*
H133	−0.180 (3)	0.757 (4)	0.2416 (10)	0.081 (7)*
H131	−0.201 (3)	0.881 (4)	0.1921 (10)	0.075 (7)*
H132	−0.126 (4)	0.983 (4)	0.2392 (10)	0.088 (8)*
H123	0.836 (4)	0.381 (4)	0.1734 (11)	0.106 (11)*
H9	0.414 (3)	0.827 (3)	0.2054 (7)	0.051 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0537 (8)	0.0654 (10)	0.0423 (8)	−0.0091 (7)	0.0009 (6)	−0.0122 (7)
N2	0.0487 (7)	0.0416 (7)	0.0386 (7)	−0.0011 (5)	0.0016 (5)	−0.0008 (5)
O1	0.1212 (14)	0.0595 (9)	0.0653 (9)	−0.0237 (9)	−0.0023 (9)	−0.0174 (7)
O2	0.0896 (10)	0.0886 (11)	0.0433 (7)	−0.0087 (8)	−0.0142 (6)	−0.0109 (7)
O3	0.0560 (7)	0.0461 (6)	0.0467 (6)	−0.0109 (5)	0.0037 (5)	−0.0090 (5)
O4	0.0573 (7)	0.0662 (8)	0.0391 (6)	0.0304 (6)	−0.0012 (5)	0.0069 (5)
O5	0.1002 (12)	0.1259 (14)	0.0368 (7)	0.0538 (11)	0.0029 (7)	0.0226 (8)
O6	0.0652 (8)	0.0451 (7)	0.0698 (8)	0.0140 (6)	0.0044 (6)	0.0049 (6)
O7	0.0523 (6)	0.0531 (7)	0.0482 (6)	0.0166 (5)	0.0102 (5)	0.0071 (5)
C1	0.0382 (7)	0.0502 (9)	0.0367 (8)	0.0000 (6)	−0.0006 (6)	−0.0078 (6)
C2	0.0487 (8)	0.0529 (9)	0.0300 (7)	0.0051 (7)	−0.0006 (6)	0.0033 (6)
C3	0.0483 (8)	0.0373 (8)	0.0353 (7)	0.0053 (6)	−0.0001 (6)	0.0037 (6)
C4	0.0346 (6)	0.0384 (7)	0.0315 (7)	0.0064 (5)	−0.0006 (5)	0.0020 (5)
C5	0.0532 (9)	0.0413 (8)	0.0347 (7)	−0.0001 (7)	−0.0032 (6)	0.0050 (6)
C6	0.0552 (9)	0.0397 (8)	0.0458 (9)	−0.0042 (7)	−0.0014 (7)	−0.0001 (7)
C7	0.0346 (6)	0.0359 (7)	0.0333 (7)	0.0064 (5)	−0.0008 (5)	0.0028 (5)
C8	0.0375 (7)	0.0390 (7)	0.0301 (7)	0.0038 (6)	0.0001 (5)	−0.0008 (5)
C9	0.0440 (8)	0.0432 (8)	0.0332 (7)	0.0026 (6)	−0.0042 (6)	−0.0046 (6)
C10	0.0470 (8)	0.0420 (8)	0.0336 (7)	0.0049 (6)	−0.0021 (6)	0.0053 (6)
C11	0.0498 (8)	0.0418 (8)	0.0317 (7)	0.0066 (6)	−0.0035 (6)	−0.0047 (6)
C12	0.0682 (13)	0.0737 (14)	0.0624 (12)	0.0381 (12)	−0.0096 (10)	0.0067 (11)
C13	0.0536 (10)	0.0612 (12)	0.0648 (12)	0.0152 (9)	0.0158 (9)	0.0046 (10)

Geometric parameters (Å, º) top

N1—O2	1.220 (2)	C4—C5	1.396 (2)
N1—O1	1.222 (2)	C4—C7	1.471 (2)
N1—C1	1.470 (2)	C5—C6	1.378 (2)
N2—C7	1.2811 (19)	C5—H5	0.97 (2)
N2—O3	1.4117 (17)	C6—H6	0.95 (2)
O3—C9	1.4353 (19)	C7—C8	1.5090 (19)
O4—C10	1.3018 (19)	C8—C10	1.5232 (19)
O4—C12	1.454 (2)	C8—C9	1.532 (2)
O5—C10	1.1912 (19)	C8—H8	0.947 (18)
O6—C11	1.1912 (19)	C9—C11	1.523 (2)
O7—C11	1.330 (2)	C9—H9	0.97 (2)
O7—C13	1.448 (2)	C12—H121	0.89 (3)
C1—C6	1.380 (2)	C12—H122	0.94 (3)
C1—C2	1.380 (2)	C12—H123	0.89 (3)
C2—C3	1.378 (2)	C13—H133	0.96 (3)
C2—H2	0.92 (2)	C13—H131	0.96 (3)
C3—C4	1.397 (2)	C13—H132	0.99 (3)
C3—H3	0.96 (2)

O2—N1—O1	123.65 (16)	C7—C8—C9	98.74 (11)
O2—N1—C1	117.92 (16)	C10—C8—C9	110.33 (12)
O1—N1—C1	118.43 (15)	C7—C8—H8	113.3 (10)
C7—N2—O3	109.64 (12)	C10—C8—H8	105.5 (10)
N2—O3—C9	107.65 (11)	C9—C8—H8	113.8 (10)
C10—O4—C12	117.33 (14)	O3—C9—C11	109.59 (12)
C11—O7—C13	116.52 (14)	O3—C9—C8	104.57 (11)
C6—C1—C2	122.18 (14)	C11—C9—C8	114.41 (12)
C6—C1—N1	118.86 (15)	O3—C9—H9	108.8 (11)
C2—C1—N1	118.95 (14)	C11—C9—H9	106.7 (11)
C3—C2—C1	118.81 (14)	C8—C9—H9	112.7 (11)
C3—C2—H2	120.4 (12)	O5—C10—O4	124.97 (15)
C1—C2—H2	120.8 (12)	O5—C10—C8	121.85 (14)
C2—C3—C4	120.48 (15)	O4—C10—C8	113.16 (12)
C2—C3—H3	120.4 (11)	O6—C11—O7	125.66 (15)
C4—C3—H3	119.1 (11)	O6—C11—C9	124.89 (15)
C5—C4—C3	119.20 (14)	O7—C11—C9	109.38 (12)
C5—C4—C7	121.09 (13)	O4—C12—H121	111 (2)
C3—C4—C7	119.71 (13)	O4—C12—H122	106.7 (19)
C6—C5—C4	120.60 (14)	H121—C12—H122	108 (2)
C6—C5—H5	119.5 (12)	O4—C12—H123	108 (2)
C4—C5—H5	119.9 (12)	H121—C12—H123	115 (3)
C5—C6—C1	118.72 (15)	H122—C12—H123	108 (2)
C5—C6—H6	120.2 (12)	O7—C13—H133	105.6 (15)
C1—C6—H6	121.0 (12)	O7—C13—H131	108.1 (15)
N2—C7—C4	120.70 (13)	H133—C13—H131	114 (2)
N2—C7—C8	113.07 (13)	O7—C13—H132	112.5 (17)
C4—C7—C8	126.22 (13)	H133—C13—H132	111 (2)
C7—C8—C10	115.36 (12)	H131—C13—H132	106 (2)

Experimental details

Crystal data
Chemical formula	C₁₃H₁₂N₂O₇
M_r	308.25
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	7.2032 (2), 6.9183 (3), 27.515 (2)
β (°)	92.134 (4)
V (Å³)	1370.23 (12)
Z	4
Radiation type	Cu Kα
µ (mm⁻¹)	1.07
Crystal size (mm)	0.90 × 0.45 × 0.25

Data collection
Diffractometer	Bruker APEX-II CCD diffractometer
Absorption correction	Multi-scan SADABS (Bruker, 2008)
T_min, T_max	0.98, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	4957, 2596, 2490
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.609

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.114, 1.05
No. of reflections	2596
No. of parameters	248
No. of restraints	3
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.30, −0.24

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SIR97 (Altomare et al., 1999), SHELXTL (Bruker, 2008), SHELXL2013 (Sheldrick, 2008) and WinGX (Farrugia, 1999).

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A top–down approach to crystal engineering of a racemic Δ²-isoxazoline

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