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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2017 Jan 1;73(Pt 1):56–58. doi: 10.1107/S2056989016019769

Crystal structure of 4-(4b,8a-di­hydro-9H-pyrido[3,4-b]indol-1-yl)-7-methyl-2H-chromen-2-one

S Samundeeswari a, Manohar V Kulkarni a,*, G N Anil Kumar b
PMCID: PMC5209772  PMID: 28083136

In the title compound, the dihedral angle between the mean planes of the coumarin and β-carboline ring systems is 63.8 (2)°. In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming chains along the [010] direction.

Keywords: crystal structure, coumarins, β-carboline, norharman, hydrogen bonding, π-π inter­actions

Abstract

The title compound, C21H14N2O2, was prepared by Pictet–Spengler cyclization of tryptamine and 4-formyl coumarin. In the mol­ecule, the dihedral angle between the mean planes of the coumarin and β-carboline ring systems is 63.8 (2)°. In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming chains along the b-axis direction. Within the chains, there are a number of offset π–π inter­actions present [shortest inter­centroid distance = 3.457 (2) Å].

Chemical context  

Naturally occurring coumarins (Murry, 2002) and their deriv­atives have a vast number of applications in different areas. They are precursor reagents for synthetic anti-coagulants (Bairagi et al., 2012), the most notable being warfarin (Holbrook et al., 2005). Coumarin dyes are also widely used in blue–green organic dyes (Schafer, 1990; Duarte & Hillman, 1990; Duarte, 2003) and in OLED emitters (Duarte et al., 2005). Norharman is a β-carboline alkaloid which has the basic structural unit for a wide range of naturally occurring compounds, and is found in plants, animals and humans (Fekkes et al., 1992). They are used widely as neurotoxins to Parkinson’s disease (Kuhn et al., 1996) and as mediators in the mutagenesis of DNA in the presence of another mol­ecule (Mori et al., 1996). Given the ongoing research into the biological functions of norharman and the many related β-carboline derivatives, a single-crystal X-ray structure of norharman would be of use in theoretical modelling and related structural work. Norharman exhibits a one-dimensional herringbone motif (Thatcher & Douthwaite, 2011). Due to their extensive natural occurrence and common biological origin, there are no reports on compounds which contain these two systems in a single mol­ecule. It was hence thought of considerable biological inter­est to synthesize new mol­ecules which contain both β-carboline and coumarin ring systems.graphic file with name e-73-00056-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound is shown in Fig. 1. The coumarin (r.m.s. deviation = 0.019 Å) and β-carboline (r.m.s. deviation = 0.034 Å) ring systems exhibit an s-trans arrangement across the bridging C7—C6 bond; their mean planes are inclined to one another by 63.8 (2)°.

Figure 1.

Figure 1

The mol­ecular structure of the title compound, with the atom labelling and displacement ellipsoids drawn at the 50% probability level.

Supra­molecular features  

In the crystal, mol­ecules are linked via N—H⋯N hydrogen bonds, forming chains along [010]; see Table 1 and Fig. 2. Within the chains there are a number of offset π–π inter­actions present; the shortest inter­centroid distance of 3.457 (2) Å, involves rings N2/C18–C20/C22 of the β-carboline ring system and O1/C1–C3/C8/C9 of the coumarin system.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H2⋯N1i 0.86 2.47 2.994 (3) 120

Symmetry code: (i) Inline graphic.

Figure 2.

Figure 2

A view along the a axis of the crystal packing of the title compound. The N—H⋯N hydrogen bonds are shown as dashed lines (see Table 1), and the shortest offset π–π inter­actions by a double-headed arrow. For clarity, only H atom H2 (grey ball) has been included.

Database survey  

A search of the Cambridge Structural Database (CSD, Version 5.37, last update May 2016; Groom et al., 2016) using 4,7-dimethyl-2H-chromen-2-one as the main skeleton revealed the presence of 66 structures. However, only six of these structures contain the 7-methyl-4-phenyl-2H-chromen-2-one nucleus (refcodes: BUFQUQ, FINNEX, GUFTUY, IFUMED, LENYIO, DUVVIB). There were no structures reported for a search of 7-methyl-4-(pyridin-2-yl)-2H-chromen-2-one skeleton.

Synthesis and crystallization  

Acetic acid (10 ml) was added drop wise, at 273 K, to a mixture of tryptamine (1 eq) and 4-formyl coumarin (1 eq). The reaction mixture was stirred at room temperature for ca 12 h. After completion of the reaction, the solid that separated was filtered, washed several times with water and dried (yield >70%) to give the inter­mediate. This inter­mediate compound (1 eq) was taken in 10 ml of dry chloro­form and 2,3-di­chloro-5,6-di­cyano-1,4-benzo­quinone (2 eq) was added at inter­vals of 5 min in cold conditions, 273 K. Stirring was continued for ca 10 h. The reaction mixture was then quenched using aqueous sodium bicarbonate and extracted with chloro­form. The organic layer was washed 2–3 times with sodium bicarbonate, water and brine solution, dried using sodium sulfate, and concentrated to afford the crude title product. It was purified by flash chromatography using 230–400 mesh silica-gels (35% ethyl acetate in hexane mixture; yield 75%). The solid obtained was recrystallized from dichloromethane, giving colourless block-like crystals of the title compound on slow evaporation of the solvent

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were positioned geometrically, with N—H = 0.86 Å and C—H = 0.93–0.96 Å, and constrained to ride on their parent atoms with U iso(H) = 1.5U eq(C-meth­yl) and 1.2U eq(C,N) for other H atoms.

Table 2. Experimental details.

Crystal data
Chemical formula C21H14N2O2
M r 326.34
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 10.6784 (8), 8.0954 (6), 17.9032 (14)
β (°) 98.105 (5)
V3) 1532.2 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.20 × 0.15 × 0.10
 
Data collection
Diffractometer Bruker SMART CCD area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2012)
T min, T max 0.941, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections 11601, 2848, 1446
R int 0.059
(sin θ/λ)max−1) 0.606
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.060, 0.166, 0.94
No. of reflections 2848
No. of parameters 227
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.21, −0.27

Computer programs: SMART and SAINT (Bruker, 2012), SHELXS97 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), ORTEP-3 for Windows and WinGX (Farrugia, 2012), Mercury (Macrae et al., 2008) and PLATON (Spek, 2009).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016019769/su5339sup1.cif

e-73-00056-sup1.cif (24.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016019769/su5339Isup2.hkl

e-73-00056-Isup2.hkl (156.5KB, hkl)

Supporting information file. DOI: 10.1107/S2056989016019769/su5339Isup3.cml

CCDC reference: 1522101

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

SS acknowledges Karnatak University for the data collection and support.

supplementary crystallographic information

Crystal data

C21H14N2O2 F(000) = 680
Mr = 326.34 Dx = 1.415 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc Cell parameters from 1990 reflections
a = 10.6784 (8) Å θ = 3.3–26.4°
b = 8.0954 (6) Å µ = 0.09 mm1
c = 17.9032 (14) Å T = 296 K
β = 98.105 (5)° Block, colourless
V = 1532.2 (2) Å3 0.20 × 0.15 × 0.10 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer 2848 independent reflections
Radiation source: fine-focus sealed tube 1446 reflections with I > 2σ(I)
Graphite monochromator Rint = 0.059
ω and φ scans θmax = 25.5°, θmin = 1.9°
Absorption correction: multi-scan (SADABS; Bruker, 2012) h = −12→11
Tmin = 0.941, Tmax = 0.971 k = −9→9
11601 measured reflections l = −21→21

Refinement

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)] = 0.060 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.166 H-atom parameters constrained
S = 0.94 w = 1/[σ2(Fo2) + (0.0799P)2] where P = (Fo2 + 2Fc2)/3
2848 reflections (Δ/σ)max < 0.001
227 parameters Δρmax = 0.21 e Å3
0 restraints Δρmin = −0.27 e Å3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

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

x y z Uiso*/Ueq
O1 0.85044 (16) 0.1787 (2) 0.24656 (10) 0.0445 (6)
O2 0.87191 (18) 0.3169 (3) 0.35363 (12) 0.0602 (7)
N1 0.3818 (2) 0.2835 (3) 0.17822 (12) 0.0413 (7)
N2 0.4360 (2) 0.0447 (3) 0.35591 (12) 0.0407 (7)
H2 0.5149 0.0259 0.3707 0.049*
C1 0.7990 (3) 0.2565 (4) 0.30347 (17) 0.0429 (8)
C2 0.6635 (2) 0.2570 (3) 0.29733 (15) 0.0427 (8)
H2A 0.6264 0.3055 0.3359 0.051*
C3 0.5878 (2) 0.1912 (3) 0.23877 (15) 0.0341 (7)
C4 0.5774 (3) 0.0283 (4) 0.11849 (15) 0.0401 (8)
H4 0.4895 0.0273 0.1126 0.048*
C5 0.6389 (3) −0.0500 (4) 0.06608 (15) 0.0459 (8)
H5 0.5921 −0.1047 0.0258 0.055*
C6 0.7705 (3) −0.0486 (4) 0.07241 (15) 0.0427 (8)
C7 0.8384 (3) 0.0291 (4) 0.13369 (15) 0.0431 (8)
H7 0.9263 0.0302 0.1395 0.052*
C8 0.6443 (2) 0.1088 (3) 0.18005 (15) 0.0353 (7)
C9 0.7754 (2) 0.1051 (4) 0.18637 (15) 0.0370 (7)
C10 0.8380 (3) −0.1277 (4) 0.01293 (17) 0.0635 (10)
H10A 0.924 −0.1509 0.0339 0.095*
H10B 0.8369 −0.0537 −0.0291 0.095*
H10C 0.7961 −0.2287 −0.0038 0.095*
C11 0.4475 (2) 0.2009 (4) 0.23601 (15) 0.0356 (7)
C12 0.2541 (3) 0.2974 (4) 0.17666 (16) 0.0464 (8)
H12 0.2093 0.3581 0.1376 0.056*
C13 0.1874 (3) 0.2280 (4) 0.22862 (17) 0.0449 (8)
H13 0.1 0.2388 0.2242 0.054*
C14 0.1087 (3) 0.0115 (4) 0.37782 (19) 0.0542 (9)
H14 0.0321 0.0482 0.3519 0.065*
C15 0.1115 (3) −0.0820 (4) 0.44170 (19) 0.0595 (10)
H15 0.0361 −0.1107 0.4587 0.071*
C16 0.2255 (3) −0.1345 (4) 0.48153 (18) 0.0589 (9)
H16 0.2248 −0.1961 0.5253 0.071*
C17 0.3403 (3) −0.0978 (4) 0.45785 (16) 0.0489 (9)
H17 0.4166 −0.1329 0.4847 0.059*
C18 0.2223 (3) 0.0506 (4) 0.35234 (15) 0.0411 (8)
C19 0.3358 (3) −0.0063 (4) 0.39225 (15) 0.0403 (7)
C20 0.2544 (2) 0.1410 (3) 0.28810 (16) 0.0370 (7)
C22 0.3865 (2) 0.1313 (3) 0.29183 (15) 0.0342 (7)

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0319 (11) 0.0588 (15) 0.0433 (12) −0.0005 (10) 0.0069 (9) −0.0029 (11)
O2 0.0450 (13) 0.0760 (18) 0.0575 (14) −0.0050 (12) −0.0001 (11) −0.0134 (13)
N1 0.0356 (14) 0.0428 (17) 0.0454 (15) 0.0022 (12) 0.0056 (11) 0.0007 (13)
N2 0.0321 (13) 0.0503 (18) 0.0406 (14) 0.0004 (12) 0.0083 (11) 0.0003 (13)
C1 0.0423 (18) 0.044 (2) 0.0434 (18) −0.0038 (16) 0.0090 (15) −0.0018 (16)
C2 0.0376 (17) 0.049 (2) 0.0419 (18) 0.0018 (15) 0.0083 (14) −0.0027 (16)
C3 0.0332 (15) 0.0306 (19) 0.0397 (16) 0.0001 (13) 0.0086 (13) 0.0041 (14)
C4 0.0372 (16) 0.043 (2) 0.0409 (17) −0.0026 (15) 0.0071 (13) 0.0029 (15)
C5 0.048 (2) 0.048 (2) 0.0419 (18) −0.0040 (16) 0.0066 (15) 0.0008 (16)
C6 0.055 (2) 0.037 (2) 0.0376 (17) 0.0076 (16) 0.0135 (15) 0.0056 (15)
C7 0.0359 (16) 0.049 (2) 0.0468 (18) 0.0071 (15) 0.0150 (14) 0.0058 (16)
C8 0.0385 (17) 0.0310 (19) 0.0373 (16) −0.0013 (14) 0.0086 (13) 0.0032 (14)
C9 0.0311 (16) 0.041 (2) 0.0393 (17) −0.0008 (14) 0.0060 (13) 0.0051 (15)
C10 0.070 (2) 0.071 (3) 0.054 (2) 0.0156 (19) 0.0223 (17) −0.0037 (19)
C11 0.0333 (16) 0.036 (2) 0.0382 (16) −0.0008 (14) 0.0086 (13) −0.0025 (14)
C12 0.0383 (18) 0.050 (2) 0.0500 (19) 0.0041 (16) 0.0011 (15) −0.0005 (16)
C13 0.0320 (16) 0.045 (2) 0.058 (2) 0.0013 (15) 0.0074 (15) −0.0065 (17)
C14 0.0461 (19) 0.048 (2) 0.074 (2) 0.0008 (17) 0.0276 (17) −0.0005 (19)
C15 0.064 (2) 0.051 (2) 0.073 (2) −0.0048 (19) 0.0414 (19) −0.001 (2)
C16 0.078 (2) 0.049 (2) 0.056 (2) −0.006 (2) 0.0313 (19) 0.0005 (18)
C17 0.059 (2) 0.041 (2) 0.0487 (19) 0.0011 (17) 0.0127 (16) 0.0001 (16)
C18 0.0375 (17) 0.037 (2) 0.0509 (19) −0.0006 (15) 0.0157 (14) −0.0048 (16)
C19 0.0418 (17) 0.0379 (19) 0.0440 (18) −0.0030 (15) 0.0157 (14) −0.0038 (15)
C20 0.0310 (16) 0.036 (2) 0.0445 (17) 0.0027 (14) 0.0093 (13) −0.0075 (15)
C22 0.0324 (16) 0.033 (2) 0.0372 (17) 0.0017 (13) 0.0059 (13) −0.0078 (14)

Geometric parameters (Å, º)

O1—C1 1.377 (3) C8—C9 1.389 (3)
O1—C9 1.383 (3) C10—H10A 0.96
O2—C1 1.206 (3) C10—H10B 0.96
N1—C11 1.344 (3) C10—H10C 0.96
N1—C12 1.365 (3) C11—C22 1.388 (3)
N2—C22 1.384 (3) C12—C13 1.369 (4)
N2—C19 1.391 (3) C12—H12 0.93
N2—H2 0.86 C13—C20 1.388 (4)
C1—C2 1.435 (4) C13—H13 0.93
C2—C3 1.341 (3) C14—C15 1.368 (4)
C2—H2A 0.93 C14—C18 1.392 (4)
C3—C8 1.447 (3) C14—H14 0.93
C3—C11 1.494 (3) C15—C16 1.388 (4)
C4—C5 1.374 (4) C15—H15 0.93
C4—C8 1.388 (3) C16—C17 1.385 (4)
C4—H4 0.93 C16—H16 0.93
C5—C6 1.394 (4) C17—C19 1.384 (4)
C5—H5 0.93 C17—H17 0.93
C6—C7 1.379 (4) C18—C19 1.396 (4)
C6—C10 1.510 (4) C18—C20 1.445 (4)
C7—C9 1.378 (4) C20—C22 1.405 (3)
C7—H7 0.93
C1—O1—C9 121.7 (2) H10A—C10—H10C 109.5
C11—N1—C12 117.9 (2) H10B—C10—H10C 109.5
C22—N2—C19 108.0 (2) N1—C11—C22 120.6 (2)
C22—N2—H2 126 N1—C11—C3 117.7 (2)
C19—N2—H2 126 C22—C11—C3 121.7 (2)
O2—C1—O1 117.0 (3) C13—C12—N1 124.5 (3)
O2—C1—C2 126.4 (3) C13—C12—H12 117.8
O1—C1—C2 116.6 (3) N1—C12—H12 117.8
C3—C2—C1 123.3 (3) C12—C13—C20 117.9 (3)
C3—C2—H2A 118.4 C12—C13—H13 121
C1—C2—H2A 118.4 C20—C13—H13 121
C2—C3—C8 119.0 (2) C15—C14—C18 118.8 (3)
C2—C3—C11 119.7 (3) C15—C14—H14 120.6
C8—C3—C11 121.3 (2) C18—C14—H14 120.6
C5—C4—C8 121.1 (3) C14—C15—C16 120.9 (3)
C5—C4—H4 119.4 C14—C15—H15 119.6
C8—C4—H4 119.4 C16—C15—H15 119.6
C4—C5—C6 121.0 (3) C17—C16—C15 121.8 (3)
C4—C5—H5 119.5 C17—C16—H16 119.1
C6—C5—H5 119.5 C15—C16—H16 119.1
C7—C6—C5 118.6 (3) C16—C17—C19 116.6 (3)
C7—C6—C10 120.3 (3) C16—C17—H17 121.7
C5—C6—C10 121.0 (3) C19—C17—H17 121.7
C6—C7—C9 119.7 (3) C14—C18—C19 119.5 (3)
C6—C7—H7 120.1 C14—C18—C20 133.8 (3)
C9—C7—H7 120.1 C19—C18—C20 106.7 (2)
C9—C8—C4 117.0 (3) C17—C19—N2 128.3 (3)
C9—C8—C3 118.0 (2) C17—C19—C18 122.3 (3)
C4—C8—C3 124.9 (2) N2—C19—C18 109.4 (2)
C7—C9—O1 116.1 (2) C13—C20—C22 118.0 (3)
C7—C9—C8 122.5 (3) C13—C20—C18 135.5 (3)
O1—C9—C8 121.4 (2) C22—C20—C18 106.4 (2)
C6—C10—H10A 109.5 C11—C22—N2 129.7 (2)
C6—C10—H10B 109.5 C11—C22—C20 120.9 (3)
H10A—C10—H10B 109.5 N2—C22—C20 109.4 (2)
C6—C10—H10C 109.5
C9—O1—C1—O2 179.9 (2) C11—N1—C12—C13 −2.4 (4)
C9—O1—C1—C2 0.2 (4) N1—C12—C13—C20 1.7 (4)
O2—C1—C2—C3 178.1 (3) C18—C14—C15—C16 1.3 (5)
O1—C1—C2—C3 −2.2 (4) C14—C15—C16—C17 −1.2 (5)
C1—C2—C3—C8 2.8 (4) C15—C16—C17—C19 −0.2 (4)
C1—C2—C3—C11 −178.5 (3) C15—C14—C18—C19 0.1 (4)
C8—C4—C5—C6 −1.1 (4) C15—C14—C18—C20 178.5 (3)
C4—C5—C6—C7 1.8 (4) C16—C17—C19—N2 −179.0 (3)
C4—C5—C6—C10 −177.1 (3) C16—C17—C19—C18 1.6 (4)
C5—C6—C7—C9 −0.9 (4) C22—N2—C19—C17 179.2 (3)
C10—C6—C7—C9 178.0 (3) C22—N2—C19—C18 −1.3 (3)
C5—C4—C8—C9 −0.5 (4) C14—C18—C19—C17 −1.6 (4)
C5—C4—C8—C3 −178.6 (3) C20—C18—C19—C17 179.7 (3)
C2—C3—C8—C9 −1.4 (4) C14—C18—C19—N2 178.9 (3)
C11—C3—C8—C9 179.8 (2) C20—C18—C19—N2 0.1 (3)
C2—C3—C8—C4 176.6 (3) C12—C13—C20—C22 0.7 (4)
C11—C3—C8—C4 −2.2 (4) C12—C13—C20—C18 −179.2 (3)
C6—C7—C9—O1 179.3 (2) C14—C18—C20—C13 2.6 (6)
C6—C7—C9—C8 −0.8 (4) C19—C18—C20—C13 −178.9 (3)
C1—O1—C9—C7 −179.1 (2) C14—C18—C20—C22 −177.4 (3)
C1—O1—C9—C8 1.0 (4) C19—C18—C20—C22 1.1 (3)
C4—C8—C9—C7 1.5 (4) N1—C11—C22—N2 −178.8 (2)
C3—C8—C9—C7 179.7 (2) C3—C11—C22—N2 −0.5 (4)
C4—C8—C9—O1 −178.6 (2) N1—C11—C22—C20 2.0 (4)
C3—C8—C9—O1 −0.4 (4) C3—C11—C22—C20 −179.7 (2)
C12—N1—C11—C22 0.4 (4) C19—N2—C22—C11 −177.3 (3)
C12—N1—C11—C3 −177.9 (2) C19—N2—C22—C20 2.0 (3)
C2—C3—C11—N1 118.4 (3) C13—C20—C22—C11 −2.5 (4)
C8—C3—C11—N1 −62.9 (3) C18—C20—C22—C11 177.4 (2)
C2—C3—C11—C22 −60.0 (4) C13—C20—C22—N2 178.1 (2)
C8—C3—C11—C22 118.8 (3) C18—C20—C22—N2 −1.9 (3)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
N2—H2···N1i 0.86 2.47 2.994 (3) 120

Symmetry code: (i) −x+1, y−1/2, −z+1/2.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016019769/su5339sup1.cif

e-73-00056-sup1.cif (24.9KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016019769/su5339Isup2.hkl

e-73-00056-Isup2.hkl (156.5KB, hkl)

Supporting information file. DOI: 10.1107/S2056989016019769/su5339Isup3.cml

CCDC reference: 1522101

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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