The title compound, C
24H
26N
2O
8, 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.
Supporting information
CCDC reference: 271825
Key indicators
- Single-crystal X-ray study
- T = 295 K
- Mean (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
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
top
Crystal data top
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) Å3 | 0.50 × 0.20 × 0.05 mm |
Z = 4 | |
Data collection top
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 top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.052 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.189 | H-atom parameters constrained |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0815P)2 + 4.1485P] where P = (Fo2 + 2Fc2)/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 top
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 (Å2) top | 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 (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
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) top
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—C2i | 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···O1ii | 3.116 (5) | C12···H9 | 2.5200 |
O1···N1ii | 2.934 (5) | H1···C4 | 2.8700 |
O1···C5ii | 3.208 (6) | H1···C5 | 2.7000 |
O2···O3 | 2.642 (5) | H1···H5 | 2.2200 |
O3···O2 | 2.642 (5) | H1···O1ii | 2.1000 |
O3···O4 | 2.708 (5) | H3···H9 | 2.3900 |
O4···C11 | 2.964 (6) | H3···O1i | 2.3100 |
O4···O3 | 2.708 (5) | H3···O2xii | 2.7900 |
O4···C12iii | 3.253 (6) | H3···C10xii | 3.0000 |
O1···H10Aii | 2.6800 | H3···C10vi | 3.1000 |
O1···H1ii | 2.1000 | H3···H10Axii | 2.4600 |
O1···H5ii | 2.8000 | H3···H10Cvi | 2.3400 |
O1···H3i | 2.3100 | H5···N1 | 2.8200 |
O2···H3iv | 2.7900 | H5···C2 | 3.0200 |
O2···H9iv | 2.6100 | H5···C10 | 2.5200 |
O3···H11Bv | 2.8400 | H5···H1 | 2.2200 |
O4···H11A | 2.4200 | H5···H10A | 2.3200 |
O4···H12Biii | 2.6800 | H5···H10B | 2.3100 |
N1···C5 | 3.275 (6) | H5···O1ii | 2.8000 |
N1···O1ii | 2.934 (5) | H9···C12 | 2.5200 |
N1···N1i | 2.748 (5) | H9···H3 | 2.3900 |
N1···H5 | 2.8200 | H9···H12A | 2.3700 |
C3···C10vi | 3.506 (7) | H9···H12C | 2.2500 |
C5···O1ii | 3.208 (6) | H9···O2xii | 2.6100 |
C5···N1 | 3.275 (6) | H10A···C5 | 2.7800 |
C10···C3vii | 3.506 (7) | H10A···H5 | 2.3200 |
C11···C12viii | 3.422 (8) | H10A···O1ii | 2.6800 |
C11···O4 | 2.964 (6) | H10A···H3iv | 2.4600 |
C12···O4iii | 3.253 (6) | H10B···C4xi | 2.9700 |
C12···C11ix | 3.422 (8) | H10B···C5 | 2.7300 |
C2···H5 | 3.0200 | H10B···C8xi | 3.0600 |
C3···H10Cvi | 2.7000 | H10B···C9xi | 2.9600 |
C4···H10Bx | 2.9700 | H10B···H5 | 2.3100 |
C4···H1 | 2.8700 | H10C···C3vii | 2.7000 |
C5···H10A | 2.7800 | H10C···H3vii | 2.3400 |
C5···H1 | 2.7000 | H11A···O4 | 2.4200 |
C5···H10B | 2.7300 | H11A···C8 | 2.7100 |
C6···H12Axi | 3.0100 | H11B···O3xiii | 2.8400 |
C7···H12Axi | 2.8800 | H11C···C9iv | 2.9300 |
C8···H12Axi | 3.0900 | H11C···C12viii | 2.9800 |
C8···H10Bx | 3.0600 | H11C···H12Aviii | 2.5700 |
C8···H11A | 2.7100 | H12A···C6x | 3.0100 |
C9···H10Bx | 2.9600 | H12A···C7x | 2.8800 |
C9···H11Cxii | 2.9300 | H12A···C8x | 3.0900 |
C9···H12A | 2.7800 | H12A···C9 | 2.7800 |
C9···H12C | 2.7300 | H12A···H9 | 2.3700 |
C10···H5 | 2.5200 | H12A···H11Cix | 2.5700 |
C10···H3vii | 3.1000 | H12B···O4iii | 2.6800 |
C10···H3iv | 3.0000 | H12C···C9 | 2.7300 |
C11···H12Civ | 3.0800 | H12C···H9 | 2.2500 |
C12···H11Cix | 2.9800 | H12C···C11xii | 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—C2i | 120.9 (3) | C8—C9—H9 | 120.00 |
N1—C1—C2i | 117.8 (3) | O2—C10—H10A | 109.00 |
O1—C1—N1 | 121.3 (3) | O2—C10—H10B | 109.00 |
C1i—C2—C3 | 117.7 (3) | O2—C10—H10C | 109.00 |
N1—C2—C3 | 125.7 (3) | H10A—C10—H10B | 110.00 |
N1—C2—C1i | 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—C2i | 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—C1i | −2.7 (6) | C5—C6—C7—C8 | −0.8 (6) |
O1—C1—C2i—N1i | 177.0 (4) | C5—C6—C7—O3 | −175.3 (3) |
O1—C1—C2i—C3i | −3.8 (7) | O3—C7—C8—O4 | −3.0 (5) |
N1—C1—C2i—N1i | −2.5 (6) | C6—C7—C8—C9 | 1.0 (6) |
N1—C1—C2i—C3i | 176.8 (4) | O3—C7—C8—C9 | 175.3 (4) |
N1—C2—C3—C4 | 3.7 (8) | C6—C7—C8—O4 | −177.4 (3) |
C1i—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) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1ii | 0.90 | 2.10 | 2.934 (5) | 154 |
C3—H3···O1i | 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. |