research communications
H-pyrido[3,4-b]indol-1-yl)-7-methyl-2H-chromen-2-one
of 4-(4b,8a-dihydro-9aDepartment of Chemistry, Karnatak University, Dharwad, India, and bDepartment of Physics, M. S. Ramaiah Institute of Technology, Bangalore, India
*Correspondence e-mail: anilgn@msrit.edu
The title compound, C21H14N2O2, was prepared by Pictet–Spengler 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].
Keywords: crystal structure; coumarins; β-carboline; norharman; hydrogen bonding; π-π interactions.
CCDC reference: 1522101
1. Chemical context
Naturally occurring ) 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.
(Murry, 20022. 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)°.
3. 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.
4. 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.
5. 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 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
6. Refinement
Crystal data, data collection and structure . 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 Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C,N) for other H atoms.
details are summarized in Table 2Supporting information
CCDC reference: 1522101
https://doi.org/10.1107/S2056989016019769/su5339sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016019769/su5339Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989016019769/su5339Isup3.cml
Data collection: SMART (Bruker, 2012); cell
SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 2012) and PLATON (Spek, 2009).C21H14N2O2 | F(000) = 680 |
Mr = 326.34 | Dx = 1.415 Mg m−3 |
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 mm−1 |
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 |
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 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 Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
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. |
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) |
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) |
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) |
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. |
Acknowledgements
SS acknowledges Karnatak University for the data collection and support.
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