π–π-Stacking and nitro–π-stacking interactions of 1-(4-nitro­phenyl)-4-phenyl-2,4-bis­(phenyl­ethynyl)­buta­diene

The first observed side product, C₃₂H₂₁NO₂, in the Sonogashira coupling reaction is reported. The molecular packing shows a high degree of π-stacking interactions in the solid state.

Key indicators

• Single-crystal synchrotron study
• T = 173 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.059
• wR factor = 0.156
• Data-to-parameter ratio = 10.9

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level A:



DIFF_020  Alert A _diffrn_standards_interval_count and
          _diffrn_standards_interval_time are missing. Number of measurements
          between standards or time (min) between standards.

Author response: _diffrn_standards_number given as 0 which is appropriate for area detectors. Frames from the first run were recollected at the end.

 Alert Level B:



THETM_01  Alert B The value of sine(theta_max)/wavelength is less than 0.575
          Calculated sin(theta_max)/wavelength =    0.5556

Author response: Data collection is restricted by the physical experimental setup constraints. Additionally, processing data beyond the diffracting ability of the sample is meaningless. The following statement appears in the _publ_section_exptl_prep section: Due to the weakly diffracting nature of the sample and the small crystal size, it was necessary to collect data using synchrotron radiation rather than a lab source.

 Alert Level C:



PLAT_371  Alert C Long   C(sp2)-C(sp1) Bond  C(2)   -   C(5)   =       1.44 Ang.

PLAT_371  Alert C Long   C(sp2)-C(sp1) Bond  C(4)   -   C(7)   =       1.44 Ang.

PLAT_371  Alert C Long   C(sp2)-C(sp1) Bond  C(6)   -   C(21)  =       1.44 Ang.

PLAT_371  Alert C Long   C(sp2)-C(sp1) Bond  C(8)   -   C(31)  =       1.43 Ang.

General Notes



ABSMU_01  Radiation type not identified. Calculation of
          _exptl_absorpt_correction_mu not performed.


 1 Alert Level A = Potentially serious problem

 1 Alert Level B = Potential problem

 4 Alert Level C = Please check

---

S1. Comment

In this paper, we report the X-ray structure and stacking of 1-(4-nitrophenyl)-4-phenyl-2,4-bis(phenylethynyl)butadiene, (IV). This compound was isolated as a side product during the Sonogashira (Shonogashira et al., 1975) coupling reaction of β,β-dibromo-p-nitrostyrene, (I), and phenylacetylene to afford Y-enyne (II) (Kaafarani & Neckers, 2001; Kaafarani et al., 2001; Kaafarani, Wex, Krause Bauer & Neckers, 2002; Kaafarani, Wex, Strehmel & Neckers, 2002). Diyne, formed by reductive elimination, is a classical side product in the course of the Sonogahsira coupling reaction [in this case, 1,4-diphenylbutadiyne (III)] (Nicholaou & Sorensen, 1996). It appears to us that compound (IV) is formed after the addition of another phenylacetylene to Y-enyne (II). To the best of our knowledge, this is the first report of such a side product in the Sonogashira coupling reaction.

The molecular structure of (IV) is shown in Fig. 1. Nitro substitution was reported to induce π–π-stacking interactions (Garden et al., 2002). The nitro-substitution-induced π–π-stacking and nitro–π-stacking interactions in (IV) are shown in Fig. 2. The distance between the centroids of the phenyl rings alternates between 4.96 and 5.35 Å. The distance between the centers of the acetylene triple bonds is 3.28 Å. The strong electron-withdrawing NO₂ group interacts with the π-system of the phenyl ring of a neighboring molecule. The distance between the N atom and the center of the phenyl rings varies between 3.58 and 5.08 Å for the alternating layers (Fig. 2). The molecular packing of (IV) is shown in Fig. 3.

The scanning electron micrograph (SEM) of (IV) shows its crystal habit in the form of complex, cactus-like needles with a diameter of several micrometers (Fig. 4). Interestingly, these tubes seem hollow; however, a shadow effect induced by the restricted lateral placement of the detector in the SEM can not be excluded and further analysis will be required to confirm this observation.

S2. Experimental

Single crystals were obtained from methanol–methylene chloride solutions. Due to the weakly diffracting nature of the sample and the small crystal size, it was necessary to collect data using synchrotron radiation rather than a laboratory source. A suitable crystal was mounted on the tip of a glass fiber with paratone-N and immediately transferred to the goniostat bathed in a cold stream. Intensity data were collected at 173 K using a Proteum300 detector at Beamline 11.3.1 at the Advanced Light Source (Lawrence Berkeley National Laboratory). The detector was set at a distance of 6.6 cm from the crystal. A series of 1 s data frames measured at 0.2° increments of ω were collected to calculate a unit cell and to measure a hemisphere of intensity data. Data were corrected for absorption using SADABS (6, 1 harmonics) and a high resolution limit of 0.85 Å applied, based on examination of the final merged listing from SAINT. A high |I-<I>| error was also applied (10 s.u.) to remove outliers from the data set.

S3. Refinement

All H atoms were included in calculated geometries (C—H = 0.95 Å) riding on the atoms to which they are bonded. The isotropic displacement parameters for the H atoms were set as 1.2U_eq of the adjacent atom.

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SMART; data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXTL (Bruker, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL and DIAMOND (Crystal Impact, 1997); software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The structure of (IV) at 173 K, showing the atomic labelling and 50% probability ellipsoids.
	Fig. 2. π–π-Stacking and nitro–π interactions of (IV).
	Fig. 3. The molecular packing of (IV), viewed (a) in the bc plane and (b) in the ab plane.
	Fig. 4. An SEM micrograph of (IV).

2,4-bis(phenylethynyl)-4-phenyl-1-(4-nitrophenyl)butadiene

Crystal data

C32H21NO2	F(000) = 944
Mr = 451.50	Dx = 1.253 Mg m^−3
Monoclinic, P21/c	Synchrotron radiation, λ = 0.88500 Å
a = 13.583 (3) Å	Cell parameters from 4292 reflections
b = 7.6515 (14) Å	θ = 6.9–29.0°
c = 23.399 (5) Å	µ = 0.08 mm^−1
β = 100.093 (11)°	T = 173 K
V = 2394.2 (9) Å^3	Needle, orange
Z = 4	0.07 × 0.06 × 0.05 mm

Data collection

Proteum 300 detector diffractometer	3438 independent reflections
Radiation source: Beamline 11.3.1 ALS at LBL	2579 reflections with I > 2σ(I)
Channel cut SiIII monochromator	Rint = 0.095
ω scans	θmax = 29.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	h = −15→15
Tmin = 0.995, Tmax = 0.996	k = −7→8
19213 measured reflections	l = −25→25

Refinement

Refinement on F^2	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)] = 0.059	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.156	H-atom parameters constrained
S = 1.07	w = 1/[σ^2(Fo^2) + 0.5111P] where P = (Fo^2 + 2Fc^2)/3
3438 reflections	(Δ/σ)max < 0.001
316 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.24 e Å^−3

Special details

Experimental. Single crystals were obtained from methanol-methylene chloride solutions. Due to the weakly diffracting nature of the sample and the small crystal size, it was necessary to collect data using synchrotron radiation rather than a lab source. A suitable crystal was mounted on the tip of a glass fiber with paratone-N and immediately transferred to the goniostat bathed in a cold stream. Intensity data was collected at 173 K using a Proteum300 detector at Beamline 11.3.1 at the Advanced Light Source (Lawrence Berkeley National Laboratory). The detector was set at a distance of 6.6-cm from the crystal. A series of 1 − s data frames measured at 0.2° increments of ω were collected to calculate a unit cell and to measure a hemisphere of intensity data. Data was corrected for absorption using SADABS (6, 1 harmonics) and a high resolution limit of 0.85 Å applied, based on examination of the final merged listing from SAINT. A high |I-<I>| error was also applied (10 su) to remove outliers from the dataset. No formal measure of the extent of decay is printed out by this program.

The final unit cell is obtained from the refinement of the XYZ weighted centroids of reflections above 20 σ(I).

Note that the absorption correction parameters Tmin and Tmax also reflect beam corrections, etc. As a result, the numerical values for Tmin and Tmax may differ from expected values based solely absorption effects and crystal size.

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 out to 0.85 Å. 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.

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

	x	y	z	Uiso*/Ueq
O1	0.02775 (16)	0.9713 (3)	0.13521 (12)	0.0680 (8)
O2	−0.05727 (15)	0.8194 (3)	0.18773 (11)	0.0639 (7)
N1	0.02171 (19)	0.8735 (3)	0.17582 (13)	0.0453 (7)
C1	0.38061 (18)	0.6603 (3)	0.32111 (12)	0.0304 (6)
H1	0.3725	0.6362	0.3598	0.037*
C2	0.47420 (17)	0.6394 (3)	0.30964 (11)	0.0253 (6)
C3	0.49742 (17)	0.6450 (3)	0.25153 (11)	0.0253 (6)
H3	0.4447	0.6119	0.2212	0.030*
C4	0.58388 (17)	0.6910 (3)	0.23476 (11)	0.0232 (6)
C5	0.55104 (19)	0.5937 (3)	0.35773 (12)	0.0322 (7)
C6	0.6116 (2)	0.5504 (3)	0.39859 (12)	0.0342 (7)
C7	0.66254 (18)	0.7693 (3)	0.27574 (11)	0.0254 (6)
C8	0.72854 (18)	0.8400 (3)	0.30769 (11)	0.0262 (6)
C11	0.29091 (18)	0.7152 (3)	0.28175 (11)	0.0262 (6)
C12	0.29205 (18)	0.8179 (3)	0.23300 (12)	0.0289 (6)
H12	0.3544	0.8525	0.2235	0.035*
C13	0.20470 (19)	0.8709 (3)	0.19798 (12)	0.0316 (7)
H13	0.2062	0.9412	0.1647	0.038*
C14	0.11478 (18)	0.8188 (3)	0.21268 (12)	0.0322 (7)
C15	0.11026 (19)	0.7179 (3)	0.26037 (13)	0.0370 (7)
H15	0.0476	0.6833	0.2694	0.044*
C16	0.19769 (19)	0.6675 (3)	0.29493 (12)	0.0348 (7)
H16	0.1952	0.5989	0.3285	0.042*
C21	0.68427 (18)	0.4998 (3)	0.44801 (11)	0.0291 (6)
C22	0.6596 (2)	0.3797 (3)	0.48760 (13)	0.0403 (7)
H22	0.5942	0.3315	0.4824	0.048*
C23	0.7305 (2)	0.3304 (3)	0.53474 (12)	0.0428 (8)
H23	0.7137	0.2473	0.5616	0.051*
C24	0.8246 (2)	0.4003 (3)	0.54289 (12)	0.0389 (7)
H24	0.8727	0.3662	0.5755	0.047*
C25	0.8495 (2)	0.5194 (3)	0.50418 (12)	0.0364 (7)
H25	0.9148	0.5683	0.5101	0.044*
C26	0.78007 (19)	0.5686 (3)	0.45645 (12)	0.0335 (7)
H26	0.7981	0.6499	0.4294	0.040*
C31	0.81010 (18)	0.9151 (3)	0.34704 (11)	0.0247 (6)
C32	0.7951 (2)	1.0115 (3)	0.39437 (12)	0.0396 (7)
H32	0.7291	1.0308	0.4013	0.048*
C33	0.8757 (3)	1.0803 (4)	0.43174 (14)	0.0557 (9)
H33	0.8652	1.1466	0.4645	0.067*
C34	0.9715 (3)	1.0527 (4)	0.42150 (15)	0.0556 (10)
H34	1.0268	1.1006	0.4472	0.067*
C35	0.9872 (2)	0.9574 (4)	0.37489 (14)	0.0456 (8)
H35	1.0533	0.9382	0.3683	0.055*
C36	0.90747 (19)	0.8890 (3)	0.33745 (12)	0.0328 (7)
H36	0.9187	0.8234	0.3047	0.039*
C41	0.60290 (18)	0.6674 (3)	0.17517 (11)	0.0262 (6)
C42	0.6912 (2)	0.7229 (3)	0.15912 (14)	0.0442 (8)
H42	0.7403	0.7774	0.1874	0.053*
C43	0.7102 (3)	0.7023 (4)	0.10406 (16)	0.0577 (9)
H43	0.7713	0.7435	0.0946	0.069*
C44	0.6417 (3)	0.6226 (4)	0.06259 (14)	0.0528 (9)
H44	0.6538	0.6104	0.0240	0.063*
C45	0.5545 (2)	0.5600 (4)	0.07773 (14)	0.0584 (9)
H45	0.5070	0.5019	0.0494	0.070*
C46	0.5354 (2)	0.5805 (4)	0.13287 (13)	0.0456 (8)
H46	0.4753	0.5348	0.1425	0.055*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0564 (15)	0.0513 (12)	0.083 (2)	0.0100 (11)	−0.0259 (13)	0.0134 (13)
O2	0.0229 (12)	0.0813 (15)	0.0836 (19)	0.0082 (11)	−0.0016 (11)	−0.0222 (13)
N1	0.0337 (16)	0.0364 (13)	0.0584 (19)	0.0103 (12)	−0.0120 (13)	−0.0161 (13)
C1	0.0300 (16)	0.0351 (13)	0.0251 (16)	−0.0014 (12)	0.0019 (12)	−0.0020 (12)
C2	0.0222 (14)	0.0266 (12)	0.0248 (16)	−0.0013 (10)	−0.0026 (11)	−0.0020 (11)
C3	0.0211 (14)	0.0261 (12)	0.0260 (15)	0.0003 (10)	−0.0036 (11)	0.0015 (11)
C4	0.0232 (15)	0.0169 (11)	0.0275 (16)	0.0009 (10)	−0.0011 (11)	0.0025 (10)
C5	0.0277 (15)	0.0374 (14)	0.0311 (17)	−0.0013 (12)	0.0036 (13)	−0.0008 (13)
C6	0.0313 (16)	0.0412 (15)	0.0293 (17)	0.0024 (12)	0.0028 (14)	0.0022 (13)
C7	0.0223 (14)	0.0178 (11)	0.0364 (17)	0.0010 (11)	0.0059 (12)	0.0030 (11)
C8	0.0252 (15)	0.0210 (11)	0.0324 (17)	−0.0025 (11)	0.0055 (12)	0.0023 (11)
C11	0.0227 (14)	0.0252 (12)	0.0304 (16)	−0.0007 (10)	0.0035 (11)	−0.0055 (12)
C12	0.0202 (14)	0.0238 (12)	0.0418 (18)	−0.0043 (10)	0.0034 (12)	−0.0023 (12)
C13	0.0324 (16)	0.0222 (12)	0.0376 (18)	−0.0001 (11)	−0.0010 (13)	−0.0011 (11)
C14	0.0213 (15)	0.0257 (12)	0.0460 (19)	0.0049 (11)	−0.0041 (12)	−0.0125 (13)
C15	0.0209 (15)	0.0399 (15)	0.052 (2)	0.0010 (12)	0.0104 (13)	−0.0086 (14)
C16	0.0311 (16)	0.0399 (14)	0.0354 (17)	0.0003 (12)	0.0115 (13)	−0.0008 (13)
C21	0.0309 (15)	0.0329 (13)	0.0217 (15)	0.0017 (12)	−0.0003 (11)	−0.0025 (12)
C22	0.0381 (17)	0.0481 (16)	0.0335 (18)	−0.0099 (13)	0.0030 (13)	0.0020 (14)
C23	0.060 (2)	0.0428 (15)	0.0252 (17)	−0.0025 (15)	0.0053 (14)	0.0072 (13)
C24	0.0455 (19)	0.0398 (15)	0.0260 (17)	0.0042 (14)	−0.0084 (13)	−0.0035 (13)
C25	0.0315 (16)	0.0377 (14)	0.0368 (18)	−0.0009 (12)	−0.0024 (13)	−0.0059 (13)
C26	0.0363 (16)	0.0320 (13)	0.0311 (17)	−0.0027 (12)	0.0026 (12)	0.0050 (12)
C31	0.0301 (15)	0.0159 (10)	0.0260 (16)	−0.0014 (10)	−0.0006 (11)	0.0040 (11)
C32	0.0485 (18)	0.0324 (13)	0.0373 (19)	−0.0004 (13)	0.0058 (14)	−0.0035 (13)
C33	0.087 (3)	0.0383 (15)	0.037 (2)	−0.0080 (17)	−0.0037 (18)	−0.0118 (14)
C34	0.064 (2)	0.0416 (17)	0.048 (2)	−0.0186 (16)	−0.0258 (18)	0.0075 (16)
C35	0.0334 (17)	0.0461 (16)	0.051 (2)	−0.0066 (13)	−0.0113 (15)	0.0056 (16)
C36	0.0294 (16)	0.0311 (13)	0.0359 (17)	−0.0020 (11)	0.0001 (12)	0.0003 (12)
C41	0.0262 (14)	0.0207 (11)	0.0312 (17)	0.0010 (11)	0.0036 (11)	0.0047 (11)
C42	0.0440 (18)	0.0455 (16)	0.046 (2)	−0.0193 (14)	0.0157 (15)	−0.0096 (14)
C43	0.069 (2)	0.0522 (18)	0.061 (3)	−0.0232 (17)	0.0359 (19)	−0.0114 (17)
C44	0.076 (2)	0.0515 (18)	0.036 (2)	0.0057 (17)	0.0239 (18)	0.0065 (15)
C45	0.055 (2)	0.087 (2)	0.032 (2)	−0.0006 (18)	0.0016 (16)	−0.0109 (17)
C46	0.0319 (17)	0.0696 (19)	0.0344 (19)	−0.0056 (14)	0.0031 (14)	−0.0047 (15)

Geometric parameters (Å, º)

O1—N1	1.224 (3)	C23—C24	1.368 (4)
O2—N1	1.227 (3)	C23—H23	0.9500
N1—C14	1.461 (3)	C24—C25	1.368 (4)
C1—C2	1.354 (3)	C24—H24	0.9500
C1—C11	1.454 (3)	C25—C26	1.382 (4)
C1—H1	0.9500	C25—H25	0.9500
C2—C5	1.437 (4)	C26—H26	0.9500
C2—C3	1.449 (4)	C31—C32	1.376 (4)
C3—C4	1.348 (3)	C31—C36	1.394 (4)
C3—H3	0.9500	C32—C33	1.380 (4)
C4—C7	1.436 (3)	C32—H32	0.9500
C4—C41	1.473 (4)	C33—C34	1.380 (5)
C5—C6	1.193 (3)	C33—H33	0.9500
C6—C21	1.436 (4)	C34—C35	1.360 (5)
C7—C8	1.192 (3)	C34—H34	0.9500
C8—C31	1.431 (3)	C35—C36	1.371 (4)
C11—C12	1.388 (4)	C35—H35	0.9500
C11—C16	1.403 (4)	C36—H36	0.9500
C12—C13	1.379 (3)	C41—C42	1.385 (4)
C12—H12	0.9500	C41—C46	1.394 (4)
C13—C14	1.384 (4)	C42—C43	1.367 (4)
C13—H13	0.9500	C42—H42	0.9500
C14—C15	1.367 (4)	C43—C44	1.364 (4)
C15—C16	1.370 (4)	C43—H43	0.9500
C15—H15	0.9500	C44—C45	1.380 (4)
C16—H16	0.9500	C44—H44	0.9500
C21—C26	1.386 (4)	C45—C46	1.369 (4)
C21—C22	1.387 (4)	C45—H45	0.9500
C22—C23	1.384 (4)	C46—H46	0.9500
C22—H22	0.9500
O1—N1—O2	124.3 (3)	C23—C24—C25	120.1 (3)
O1—N1—C14	117.7 (3)	C23—C24—H24	119.9
O2—N1—C14	118.0 (3)	C25—C24—H24	119.9
C2—C1—C11	128.3 (3)	C24—C25—C26	120.2 (3)
C2—C1—H1	115.8	C24—C25—H25	119.9
C11—C1—H1	115.8	C26—C25—H25	119.9
C1—C2—C5	116.8 (2)	C25—C26—C21	120.2 (2)
C1—C2—C3	123.3 (2)	C25—C26—H26	119.9
C5—C2—C3	119.6 (2)	C21—C26—H26	119.9
C4—C3—C2	128.6 (2)	C32—C31—C36	119.0 (2)
C4—C3—H3	115.7	C32—C31—C8	121.8 (2)
C2—C3—H3	115.7	C36—C31—C8	119.2 (2)
C3—C4—C7	119.9 (2)	C31—C32—C33	120.1 (3)
C3—C4—C41	123.3 (2)	C31—C32—H32	119.9
C7—C4—C41	116.7 (2)	C33—C32—H32	119.9
C6—C5—C2	176.8 (3)	C34—C33—C32	119.9 (3)
C5—C6—C21	179.5 (3)	C34—C33—H33	120.0
C8—C7—C4	176.8 (3)	C32—C33—H33	120.0
C7—C8—C31	176.7 (2)	C35—C34—C33	120.4 (3)
C12—C11—C16	117.9 (2)	C35—C34—H34	119.8
C12—C11—C1	123.7 (2)	C33—C34—H34	119.8
C16—C11—C1	118.3 (2)	C34—C35—C36	120.0 (3)
C13—C12—C11	121.5 (2)	C34—C35—H35	120.0
C13—C12—H12	119.3	C36—C35—H35	120.0
C11—C12—H12	119.3	C35—C36—C31	120.5 (3)
C12—C13—C14	118.2 (3)	C35—C36—H36	119.7
C12—C13—H13	120.9	C31—C36—H36	119.7
C14—C13—H13	120.9	C42—C41—C46	116.6 (3)
C15—C14—C13	122.2 (2)	C42—C41—C4	121.5 (2)
C15—C14—N1	119.0 (3)	C46—C41—C4	121.8 (2)
C13—C14—N1	118.7 (3)	C43—C42—C41	122.4 (3)
C14—C15—C16	118.8 (3)	C43—C42—H42	118.8
C14—C15—H15	120.6	C41—C42—H42	118.8
C16—C15—H15	120.6	C44—C43—C42	120.3 (3)
C15—C16—C11	121.3 (3)	C44—C43—H43	119.9
C15—C16—H16	119.4	C42—C43—H43	119.9
C11—C16—H16	119.4	C43—C44—C45	118.8 (3)
C26—C21—C22	119.2 (2)	C43—C44—H44	120.6
C26—C21—C6	120.6 (2)	C45—C44—H44	120.6
C22—C21—C6	120.3 (2)	C46—C45—C44	121.0 (3)
C23—C22—C21	119.8 (3)	C46—C45—H45	119.5
C23—C22—H22	120.1	C44—C45—H45	119.5
C21—C22—H22	120.1	C45—C46—C41	120.9 (3)
C24—C23—C22	120.5 (3)	C45—C46—H46	119.5
C24—C23—H23	119.8	C41—C46—H46	119.5
C22—C23—H23	119.8