(Z,Z)-3,6-Bis[(3,4,5-trimethoxy­phen­yl)methyl­ene]piperazine-2,5-dione

The title compound, C₂₄H₂₆N₂O₈, is a derivative of neihumicin, a cytotoxic antibiotic from Micromonospora neihuensis. The compound crystallizes as discrete mol­ecules with crystallographic inversion symmetry. Inter­molecular N—H...O hydrogen bonds yield polymeric chains along the c axis. The trimethoxy­phenyl­methyl­ene side chain is found to be in a Z configuration about the C=C double bond.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.052
• wR factor = 0.189
• Data-to-parameter ratio = 13.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5
PLAT601_ALERT_2_C Structure Contains Solvent Accessible VOIDS of .      31.00 A   3  

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); cell refinement: MSC/AFC7 Diffractometer Control Software (Molecular Structure Corporation, 1999); data reduction: TEXSAN for Windows (Molecular Structure Corporation, 2001); program(s) used to solve structure: TEXSAN for Windows; program(s) used to refine structure: TEXSAN for Windows and SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: TEXSAN for Windows and PLATON (Spek, 2003).

3,6-(Z,Z)-Bis[(3,4,5-trimethyoxyphenyl)methylene]piperazine-2,5-dione

Crystal data

C24H26N2O8	F(000) = 992
Mr = 470.47	Dx = 1.331 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: -C 2yc	Cell parameters from 25 reflections
a = 35.204 (3) Å	θ = 18.5–19.9°
b = 5.282 (6) Å	µ = 0.10 mm^−1
c = 12.738 (4) Å	T = 295 K
β = 97.503 (15)°	Plate, yellow
V = 2348 (3) Å^3	0.50 × 0.20 × 0.05 mm
Z = 4

Data collection

Rigaku AFC-7R diffractometer	Rint = 0.037
Radiation source: Rigaku rotating anode	θmax = 25.0°, θmin = 2.3°
Graphite monochromator	h = 0→41
ω–2θ scans	k = 0→6
2106 measured reflections	l = −15→15
2070 independent reflections	3 standard reflections every 150 reflections
1094 reflections with I > 2σ(I)	intensity decay: 0.3%

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)] = 0.052	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.189	H-atom parameters constrained
S = 1.03	w = 1/[σ^2(Fo^2) + (0.0815P)^2 + 4.1485P] where P = (Fo^2 + 2Fc^2)/3
2070 reflections	(Δ/σ)max = 0.001
154 parameters	Δρmax = 0.23 e Å^−3
0 restraints	Δρmin = −0.23 e Å^−3

Special details

Experimental. The scan width was (1.68 + 0.35tanθ)° with an ω scan speed of 16° per minute (up to 4 scans to achieve I/σ(I) > 10). Stationary background counts were recorded at each end of the scan, and the scan time:background time ratio was 2:1.

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

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 > 2σ(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	0.53698 (7)	0.0575 (8)	0.69482 (18)	0.0693 (12)
O2	0.36291 (7)	0.3712 (5)	0.76440 (19)	0.0476 (9)
O3	0.30077 (7)	0.0919 (6)	0.7169 (2)	0.0522 (10)
O4	0.29522 (7)	−0.2530 (6)	0.5583 (2)	0.0556 (10)
N1	0.48120 (8)	0.0309 (7)	0.5871 (2)	0.0469 (12)
C1	0.51982 (10)	0.0344 (9)	0.6049 (3)	0.0435 (13)
C2	0.45894 (10)	−0.0070 (8)	0.4879 (2)	0.0395 (13)
C3	0.42094 (10)	−0.0229 (8)	0.4709 (2)	0.0384 (13)
C4	0.39136 (9)	0.0048 (7)	0.5411 (2)	0.0343 (10)
C5	0.39360 (9)	0.1813 (7)	0.6232 (3)	0.0353 (11)
C6	0.36389 (10)	0.2043 (7)	0.6830 (3)	0.0356 (11)
C7	0.33085 (10)	0.0520 (7)	0.6613 (3)	0.0374 (11)
C8	0.32854 (10)	−0.1199 (8)	0.5775 (3)	0.0402 (14)
C9	0.35875 (10)	−0.1416 (8)	0.5181 (3)	0.0377 (11)
C10	0.39351 (13)	0.5489 (9)	0.7836 (3)	0.0569 (16)
C11	0.29179 (13)	−0.1128 (10)	0.7822 (3)	0.0607 (17)
C12	0.29279 (12)	−0.4492 (9)	0.4805 (4)	0.0574 (17)
H1	0.46850	0.05470	0.64330	0.0560*
H3	0.41110	−0.05910	0.39950	0.0460*
H5	0.41560	0.28550	0.63790	0.0420*
H9	0.35700	−0.25830	0.46090	0.0450*
H10A	0.41680	0.46130	0.80480	0.0680*
H10B	0.39550	0.64170	0.72070	0.0680*
H10C	0.38850	0.66220	0.83820	0.0680*
H11A	0.29580	−0.26860	0.74810	0.0730*
H11B	0.26570	−0.10090	0.79380	0.0730*
H11C	0.30780	−0.10530	0.84820	0.0730*
H12A	0.31240	−0.57050	0.49980	0.0690*
H12B	0.26850	−0.52910	0.47630	0.0690*
H12C	0.29590	−0.37840	0.41360	0.0690*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0385 (15)	0.148 (3)	0.0210 (13)	−0.0108 (18)	0.0028 (10)	−0.0094 (17)
O2	0.0571 (17)	0.0465 (17)	0.0404 (15)	−0.0041 (14)	0.0113 (12)	−0.0121 (13)
O3	0.0484 (16)	0.0506 (18)	0.0634 (18)	0.0054 (13)	0.0287 (13)	0.0042 (15)
O4	0.0383 (15)	0.069 (2)	0.0607 (18)	−0.0147 (14)	0.0107 (13)	−0.0196 (17)
N1	0.0289 (16)	0.092 (3)	0.0205 (14)	−0.0032 (17)	0.0061 (11)	−0.0026 (17)
C1	0.0281 (18)	0.077 (3)	0.0249 (17)	−0.0044 (19)	0.0018 (13)	−0.0045 (19)
C2	0.035 (2)	0.061 (3)	0.0218 (16)	−0.0040 (19)	0.0013 (13)	0.0016 (18)
C3	0.0330 (19)	0.057 (3)	0.0252 (16)	0.0003 (18)	0.0038 (13)	0.0008 (17)
C4	0.0299 (18)	0.047 (2)	0.0249 (16)	0.0023 (17)	0.0000 (13)	0.0047 (17)
C5	0.0319 (19)	0.045 (2)	0.0283 (17)	0.0007 (16)	0.0008 (14)	0.0034 (17)
C6	0.040 (2)	0.036 (2)	0.0304 (18)	0.0058 (17)	0.0029 (15)	0.0037 (17)
C7	0.0341 (19)	0.042 (2)	0.0376 (19)	0.0071 (17)	0.0109 (15)	0.0065 (18)
C8	0.032 (2)	0.048 (3)	0.040 (2)	−0.0014 (17)	0.0021 (15)	0.0018 (19)
C9	0.0313 (19)	0.051 (2)	0.0304 (18)	0.0013 (18)	0.0022 (14)	−0.0047 (18)
C10	0.068 (3)	0.050 (3)	0.051 (2)	−0.006 (2)	0.001 (2)	−0.011 (2)
C11	0.067 (3)	0.066 (3)	0.053 (3)	−0.009 (2)	0.023 (2)	0.001 (2)
C12	0.050 (3)	0.053 (3)	0.066 (3)	−0.007 (2)	−0.004 (2)	−0.012 (2)

Geometric parameters (Å, º)

O1—C1	1.229 (5)	C6—C7	1.412 (5)
O2—C6	1.365 (5)	C7—C8	1.396 (6)
O2—C10	1.426 (6)	C8—C9	1.388 (5)
O3—C7	1.365 (5)	C3—H3	0.9500
O3—C11	1.425 (6)	C5—H5	0.9500
O4—C8	1.362 (5)	C9—H9	0.9500
O4—C12	1.429 (6)	C10—H10A	0.9500
N1—C1	1.349 (5)	C10—H10B	0.9500
N1—C2	1.412 (4)	C10—H10C	0.9500
N1—H1	0.9000	C11—H11A	0.9500
C1—C2^i	1.486 (5)	C11—H11B	0.9500
C2—C3	1.330 (5)	C11—H11C	0.9500
C3—C4	1.466 (5)	C12—H12A	0.9500
C4—C9	1.383 (5)	C12—H12B	0.9500
C4—C5	1.396 (5)	C12—H12C	0.9500
C5—C6	1.377 (5)
O1···O1^ii	3.116 (5)	C12···H9	2.5200
O1···N1^ii	2.934 (5)	H1···C4	2.8700
O1···C5^ii	3.208 (6)	H1···C5	2.7000
O2···O3	2.642 (5)	H1···H5	2.2200
O3···O2	2.642 (5)	H1···O1^ii	2.1000
O3···O4	2.708 (5)	H3···H9	2.3900
O4···C11	2.964 (6)	H3···O1^i	2.3100
O4···O3	2.708 (5)	H3···O2^xii	2.7900
O4···C12^iii	3.253 (6)	H3···C10^xii	3.0000
O1···H10A^ii	2.6800	H3···C10^vi	3.1000
O1···H1^ii	2.1000	H3···H10A^xii	2.4600
O1···H5^ii	2.8000	H3···H10C^vi	2.3400
O1···H3^i	2.3100	H5···N1	2.8200
O2···H3^iv	2.7900	H5···C2	3.0200
O2···H9^iv	2.6100	H5···C10	2.5200
O3···H11B^v	2.8400	H5···H1	2.2200
O4···H11A	2.4200	H5···H10A	2.3200
O4···H12B^iii	2.6800	H5···H10B	2.3100
N1···C5	3.275 (6)	H5···O1^ii	2.8000
N1···O1^ii	2.934 (5)	H9···C12	2.5200
N1···N1^i	2.748 (5)	H9···H3	2.3900
N1···H5	2.8200	H9···H12A	2.3700
C3···C10^vi	3.506 (7)	H9···H12C	2.2500
C5···O1^ii	3.208 (6)	H9···O2^xii	2.6100
C5···N1	3.275 (6)	H10A···C5	2.7800
C10···C3^vii	3.506 (7)	H10A···H5	2.3200
C11···C12^viii	3.422 (8)	H10A···O1^ii	2.6800
C11···O4	2.964 (6)	H10A···H3^iv	2.4600
C12···O4^iii	3.253 (6)	H10B···C4^xi	2.9700
C12···C11^ix	3.422 (8)	H10B···C5	2.7300
C2···H5	3.0200	H10B···C8^xi	3.0600
C3···H10C^vi	2.7000	H10B···C9^xi	2.9600
C4···H10B^x	2.9700	H10B···H5	2.3100
C4···H1	2.8700	H10C···C3^vii	2.7000
C5···H10A	2.7800	H10C···H3^vii	2.3400
C5···H1	2.7000	H11A···O4	2.4200
C5···H10B	2.7300	H11A···C8	2.7100
C6···H12A^xi	3.0100	H11B···O3^xiii	2.8400
C7···H12A^xi	2.8800	H11C···C9^iv	2.9300
C8···H12A^xi	3.0900	H11C···C12^viii	2.9800
C8···H10B^x	3.0600	H11C···H12A^viii	2.5700
C8···H11A	2.7100	H12A···C6^x	3.0100
C9···H10B^x	2.9600	H12A···C7^x	2.8800
C9···H11C^xii	2.9300	H12A···C8^x	3.0900
C9···H12A	2.7800	H12A···C9	2.7800
C9···H12C	2.7300	H12A···H9	2.3700
C10···H5	2.5200	H12A···H11C^ix	2.5700
C10···H3^vii	3.1000	H12B···O4^iii	2.6800
C10···H3^iv	3.0000	H12C···C9	2.7300
C11···H12C^iv	3.0800	H12C···H9	2.2500
C12···H11C^ix	2.9800	H12C···C11^xii	3.0800
C6—O2—C10	117.5 (3)	C4—C9—C8	120.8 (4)
C7—O3—C11	115.6 (3)	C2—C3—H3	114.00
C8—O4—C12	118.1 (3)	C4—C3—H3	114.00
C1—N1—C2	125.6 (3)	C4—C5—H5	120.00
C2—N1—H1	117.00	C6—C5—H5	120.00
C1—N1—H1	117.00	C4—C9—H9	120.00
O1—C1—C2^i	120.9 (3)	C8—C9—H9	120.00
N1—C1—C2^i	117.8 (3)	O2—C10—H10A	109.00
O1—C1—N1	121.3 (3)	O2—C10—H10B	109.00
C1^i—C2—C3	117.7 (3)	O2—C10—H10C	109.00
N1—C2—C3	125.7 (3)	H10A—C10—H10B	110.00
N1—C2—C1^i	116.6 (3)	H10A—C10—H10C	110.00
C2—C3—C4	132.4 (3)	H10B—C10—H10C	109.00
C5—C4—C9	119.8 (3)	O3—C11—H11A	109.00
C3—C4—C9	116.8 (3)	O3—C11—H11B	109.00
C3—C4—C5	123.3 (3)	O3—C11—H11C	110.00
C4—C5—C6	120.1 (3)	H11A—C11—H11B	109.00
C5—C6—C7	120.5 (3)	H11A—C11—H11C	110.00
O2—C6—C5	125.0 (3)	H11B—C11—H11C	109.00
O2—C6—C7	114.5 (3)	O4—C12—H12A	110.00
C6—C7—C8	119.0 (3)	O4—C12—H12B	109.00
O3—C7—C6	119.1 (3)	O4—C12—H12C	109.00
O3—C7—C8	121.7 (3)	H12A—C12—H12B	109.00
O4—C8—C7	115.9 (3)	H12A—C12—H12C	109.00
O4—C8—C9	124.2 (4)	H12B—C12—H12C	109.00
C7—C8—C9	119.9 (3)
C10—O2—C6—C5	5.3 (5)	C2—C3—C4—C9	−147.4 (5)
C10—O2—C6—C7	−173.7 (3)	C3—C4—C5—C6	177.1 (3)
C11—O3—C7—C6	−116.2 (4)	C3—C4—C9—C8	−177.2 (4)
C11—O3—C7—C8	69.4 (5)	C5—C4—C9—C8	−1.7 (6)
C12—O4—C8—C7	−173.9 (4)	C9—C4—C5—C6	1.9 (5)
C12—O4—C8—C9	7.9 (6)	C4—C5—C6—C7	−0.6 (6)
C2—N1—C1—O1	−176.7 (4)	C4—C5—C6—O2	−179.5 (3)
C2—N1—C1—C2^i	2.7 (7)	O2—C6—C7—C8	178.2 (3)
C1—N1—C2—C3	176.5 (4)	O2—C6—C7—O3	3.7 (5)
C1—N1—C2—C1^i	−2.7 (6)	C5—C6—C7—C8	−0.8 (6)
O1—C1—C2^i—N1^i	177.0 (4)	C5—C6—C7—O3	−175.3 (3)
O1—C1—C2^i—C3^i	−3.8 (7)	O3—C7—C8—O4	−3.0 (5)
N1—C1—C2^i—N1^i	−2.5 (6)	C6—C7—C8—C9	1.0 (6)
N1—C1—C2^i—C3^i	176.8 (4)	O3—C7—C8—C9	175.3 (4)
N1—C2—C3—C4	3.7 (8)	C6—C7—C8—O4	−177.4 (3)
C1^i—C2—C3—C4	−177.1 (4)	C7—C8—C9—C4	0.2 (6)
C2—C3—C4—C5	37.3 (7)	O4—C8—C9—C4	178.5 (4)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, y, −z+3/2; (iii) −x+1/2, −y−1/2, −z+1; (iv) x, −y, z+1/2; (v) −x+1/2, y+1/2, −z+3/2; (vi) x, −y+1, z−1/2; (vii) x, −y+1, z+1/2; (viii) x, −y−1, z+1/2; (ix) x, −y−1, z−1/2; (x) x, y−1, z; (xi) x, y+1, z; (xii) x, −y, z−1/2; (xiii) −x+1/2, y−1/2, −z+3/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^ii	0.90	2.10	2.934 (5)	154
C3—H3···O1^i	0.95	2.31	2.739 (5)	106
C11—H11A···O4	0.95	2.42	2.964 (6)	116

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, y, −z+3/2.