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ISSN: 2056-9890

Crystal structure of 7-hy­dr­oxy-8-[(4-methyl­piperazin-1-yl)meth­yl]-2H-chromen-2-one

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aDivision of Natural Sciences, Osaka Kyoiku University, Kashiwara, Osaka 582-8582, Japan, and bOsaka Municipal Technical Research Institute, Osaka 536-8553, Japan
*Correspondence e-mail: kubono@cc.osaka-kyoiku.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 14 October 2016; accepted 26 October 2016; online 4 November 2016)

In the title compound, C15H18N2O3, the coumarin ring is essentially planar, with an r.m.s. deviation of 0.012 Å. An intra­molecular O—H⋯N hydrogen bond forms an S(6) ring motif. The piperazine ring adopts a chair conformation. In the crystal, a C—H⋯O hydrogen bond generates a C(4) chain motif running along the c axis. The chain structure is stabilized by a C—H⋯π inter­action. The chains are linked by ππ inter­actions [centroid–centroid distance of 3.5745 (11) Å], forming a sheet structure parallel to the bc plane.

1. Chemical context

Coumarin (2H-chromen-2-one) derivatives have wide applications in diverse areas such as pharmaceuticals (Neyts et al., 2009[Neyts, J., De Clercq, E., Singha, R., Chang, Y. H., Das, A. R., Chakraborty, S. K., Hong, S. C., Tsay, S.-C., Hsu, M.-H. & Hwu, J. R. (2009). J. Med. Chem. 52, 1486-1490.]), dyes (Hara et al., 2003[Hara, K., Kurashige, M., Dan-oh, Y., Kasada, C., Shinpo, A., Suga, S., Sayama, K. & Arakawa, H. (2003). New J. Chem. 27, 783-785.]) and liquid crystal (Schadt et al., 1996[Schadt, M., Seiberle, H. & Schuster, A. (1996). Nature, 381, 212-215.]). Since piperazine is a heterocyclic and aliphatic di­amine, having a flexible structure and a high solubility not only in organic solvents but also in water, its derivatives form complexes with various metal ions in chair and boat conformations. For example, the piperazine ring in a dinuclear zinc(II) complex with a piperazine-based Schiff base adopts a chair form, whereas that in a mononuclear cobalt(III) complex with the same ligand is in a boat form (Cretu et al., 2015[Cretu, C., Tudose, R., Cseh, L., Linert, W., Halevas, E., Hatzidimitriou, A., Costisor, O. & Salifoglou, A. (2015). Polyhedron, 85, 48-59.]). Moreover, the piperazine ring has recently been utilized as a proton-recognition site in pH-sensitive fluorescent probes (Lee et al., 2014[Lee, M. H., Park, N., Yi, C., Han, J. H., Hong, J. H., Kim, K. P., Kang, D. H., Sessler, J. L., Kang, C. & Kim, J. S. (2014). J. Am. Chem. Soc. 136, 14136-14142.]) and a linker bridging two chromophores in fluorescent ion-sensors (Srivastava et al., 2014[Srivastava, P., Razi, S. S., Ali, R., Gupta, R. C., Yadav, S. S., Narayan, G. & Misra, A. (2014). Anal. Chem. 86, 8693-8699.]; Jiang et al., 2011[Jiang, J., Jiang, H., Tang, X., Yang, L., Dou, W., Liu, W., Fang, R. & Liu, W. (2011). Dalton Trans. 40, 6367-6370.]). We are attempting to develop water-soluble chemosensors based on coumarin, and report here the mol­ecular and crystal structure of the title compound.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound is shown in Fig. 1[link]. The coumarin ring is almost planar with a maximum deviation of 0.023 (2) Å for atom C6. There is an intra­molecular O—H⋯N hydrogen bond involving the hy­droxy group (O1—H1) and a piperazine N atom (N4), generating an S(6) ring motif (Fig. 1[link] and Table 1[link]). The piperazine ring adopts a chair conformation with puckering parameters: Q = 0.582 (2) Å, θ = 1.9 (2)° and φ = 22 (7)°. The C16—N4—C15—C14 and C19—N4—C15—C14 torsion angles are −78.8 (2) and 158.52 (16)°, respectively. The bond lengths and angles of the title compound are normal and agree with those values in other Mannich bases of 7-hy­droxy­coumarin (Leong & Vittal, 2010[Leong, W. L. & Vittal, J. J. (2010). New J. Chem. 34, 2145-2152.]; Kobayashi et al., 2014[Kobayashi, H., Katano, K., Hashimoto, T. & Hayashita, T. (2014). Anal. Sci. 30, 1045-1050.]).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the O3/C9–C13 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H1⋯N4 1.02 (3) 1.66 (3) 2.607 (2) 153 (3)
C11—H11⋯O2i 0.93 2.59 3.239 (2) 128
C15—H15BCg1ii 0.97 2.99 3.802 (2) 142
Symmetry codes: (i) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (ii) [x, -y-{\script{1\over 2}}, z-{\script{3\over 2}}].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The intra­molecular O—H⋯N hydrogen bond is shown as a dashed line.

3. Supra­molecular features

In the crystal, mol­ecules are linked by a C—H⋯O hydrogen bond (C11—H11⋯O2i; symmetry code in Table 1[link]), forming a C(4) chain motif running parallel to the c axis. A C—H⋯π inter­action (C15—H15BCg1ii; Cg1 is the centroid of the O3/C9–C13 ring; symmetry code in Table 1[link]) is also observed in the chain (Fig. 2[link]). The chains are linked through slipped parallel ππ inter­actions [Cg1⋯Cg1iii = 3.5745 (11) Å, inter-planar distance = 3.404 Å and slippage = 1.090 Å; symmetry code: (iii) −x, −y, −z + 1], forming a supra­molecular sheet parallel to the bc plane.

[Figure 2]
Figure 2
A view along the a axis of the crystal packing of the title compound. The hydrogen bonds and C—H⋯π inter­actions are shown as dashed lines. H atoms not involved in these inter­actions have been omitted for clarity.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.37; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) gave 1700 and 85 structures containing coumarin and 7-hy­droxy­coumarin, respectively. Of these structures, the compounds that resemble the title compound are N-(7-hy­droxy-4-methyl-8-coumarin­yl)-L-alanine (Leong & Vittal, 2010[Leong, W. L. & Vittal, J. J. (2010). New J. Chem. 34, 2145-2152.]) and 8-{[bis­(pyridin-2-ylmeth­yl)amino]­meth­yl}-7-hy­droxy-2H-chromen-2-one (Kobayashi et al., 2014[Kobayashi, H., Katano, K., Hashimoto, T. & Hayashita, T. (2014). Anal. Sci. 30, 1045-1050.]). A search for the fragment methyl­piperazine gave 666 hits, but none contained coumarin.

5. Synthesis and crystallization

The title compound was prepared by modification of the reported procedure (Mazzei et al., 2008[Mazzei, M., Nieddu, E., Miele, M., Balbi, A., Ferrone, M., Fermeglia, M., Mazzei, M. T., Pricl, S., La Colla, P., Marongiu, F., Ibba, C. & Loddo, R. (2008). Bioorg. Med. Chem. 16, 2591-2605.]). 1-Methyl­piperazine (0.64 g, 6.4 mmol) and formaldehyde (37% aqueous solution 0.64 mL, 0.64 mmol) in 50 ml of aceto­nitrile was stirred for 30 min at 333 K. To the product obtained was added 7-hy­droxy­coumarin (1.04 g, 0.64 mmol), and the mixture was heated for 3 h at 338 K. After the completion of the reaction, as indicated by TLC, the solvent was removed under vacuum. The residue was suspended in water and extracted with chloro­form, and the extract was washed with a saturated sodium chloride aqueous solution. The organic phase was separated, dried with anhydrous sodium sulfate, and the solvent was removed under vacuum to yield a yellow product. The product was recrystallized from aceto­nitrile solution to obtained colorless crystals of the title compound (yield: 76%). MS (m/z): [M + H]+, 275.1. Analysis calculated for C15H18N2O3: C 65.68, H 6.61, N 10.21%; found: C 65.40, H 6.45, N 10.06%.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The hy­droxy H atom was located in a difference Fourier map and freely refined. The C-bound H atoms were positioned geometrically and refined using a riding model: C—H = 0.93–0.97 Å with Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C15H18N2O3
Mr 274.31
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 15.3519 (6), 9.4005 (4), 9.9702 (4)
β (°) 106.954 (1)
V3) 1376.32 (10)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.20 × 0.10 × 0.10
 
Data collection
Diffractometer Rigaku R-AXIS RAPID
Absorption correction Multi-scan (ABSCOR; Higashi, 1995[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.])
Tmin, Tmax 0.823, 0.991
No. of measured, independent and observed [F2 > 2.0σ(F2)] reflections 13237, 3136, 1566
Rint 0.037
(sin θ/λ)max−1) 0.648
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.162, 1.05
No. of reflections 3136
No. of parameters 186
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.19, −0.18
Computer programs: RAPID-AUTO (Rigaku, 2006[Rigaku (2006). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]), SIR92 (Altomare et al., 1993[Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343-350.]), SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), PLATON (Spek, 2015[Spek, A. L. (2015). Acta Cryst. C71, 9-18.]), CrystalStructure (Rigaku, 2016[Rigaku (2016). CrystalStructure. Rigaku Corporation, Tokyo, Japan.]).

Supporting information


Computing details top

Data collection: RAPID-AUTO (Rigaku, 2006); cell refinement: RAPID-AUTO (Rigaku, 2006); data reduction: RAPID-AUTO (Rigaku, 2006); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2015); software used to prepare material for publication: CrystalStructure (Rigaku, 2016).

7-Hydroxy-8-[(4-methylpiperazin-1-yl)methyl]-2H-chromen-2-one top
Crystal data top
C15H18N2O3F(000) = 584.00
Mr = 274.31Dx = 1.324 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71075 Å
a = 15.3519 (6) ÅCell parameters from 6828 reflections
b = 9.4005 (4) Åθ = 3.0–27.4°
c = 9.9702 (4) ŵ = 0.09 mm1
β = 106.954 (1)°T = 296 K
V = 1376.32 (10) Å3Block, colorless
Z = 40.20 × 0.10 × 0.10 mm
Data collection top
Rigaku R-AXIS RAPID
diffractometer
1566 reflections with F2 > 2.0σ(F2)
Detector resolution: 10.000 pixels mm-1Rint = 0.037
ω scansθmax = 27.4°, θmin = 3.0°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 1919
Tmin = 0.823, Tmax = 0.991k = 1212
13237 measured reflectionsl = 1211
3136 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.162H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.0829P)2 + 0.0112P]
where P = (Fo2 + 2Fc2)/3
3136 reflections(Δ/σ)max < 0.001
186 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.18 e Å3
Primary atom site location: structure-invariant direct methods
Special details top

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.

Refinement. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F2. R-factor (gt) are based on F. The threshold expression of F2 > 2.0 sigma(F2) is used only for calculating R-factor (gt).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.30930 (10)0.15085 (16)0.50405 (16)0.0643 (4)
O20.04527 (10)0.32032 (16)0.48480 (15)0.0652 (5)
O30.06794 (9)0.17001 (13)0.49705 (13)0.0516 (4)
N40.26991 (10)0.05030 (17)0.31592 (15)0.0490 (4)
N50.41058 (11)0.13494 (18)0.19673 (17)0.0570 (5)
C60.24973 (13)0.0902 (2)0.5650 (2)0.0506 (5)
C70.25092 (14)0.1386 (2)0.6984 (2)0.0552 (5)
H70.29310.20720.74320.066*
C80.19055 (13)0.0858 (2)0.7631 (2)0.0535 (5)
H80.19170.11940.85130.064*
C90.12716 (12)0.0182 (2)0.69801 (18)0.0471 (5)
C100.06032 (14)0.0772 (2)0.7567 (2)0.0525 (5)
H100.05750.04560.84380.063*
C110.00197 (14)0.1765 (2)0.6887 (2)0.0530 (5)
H110.04070.21280.72940.064*
C120.00365 (13)0.2289 (2)0.5539 (2)0.0507 (5)
C130.12898 (12)0.0672 (2)0.56609 (19)0.0455 (5)
C140.18880 (12)0.0155 (2)0.49655 (18)0.0484 (5)
C150.18271 (13)0.0648 (2)0.3490 (2)0.0588 (6)
H15A0.13650.00940.28220.071*
H15B0.16390.16370.33870.071*
C160.33329 (15)0.1654 (2)0.3767 (2)0.0638 (6)
H16A0.34300.16900.47720.077*
H16B0.30770.25570.33700.077*
C170.42259 (15)0.1407 (3)0.3465 (2)0.0698 (7)
H17A0.46450.21690.38760.084*
H17B0.44900.05200.38930.084*
C180.34652 (13)0.0235 (2)0.1345 (2)0.0565 (5)
H18A0.37160.06780.17190.068*
H18B0.33700.02220.03400.068*
C190.25631 (13)0.0457 (2)0.16373 (19)0.0558 (5)
H19A0.22910.13410.12140.067*
H19B0.21520.03140.12270.067*
C200.49746 (16)0.1123 (3)0.1694 (3)0.0822 (8)
H20A0.53790.18940.20850.099*
H20B0.48830.10820.07000.099*
H20C0.52360.02450.21150.099*
H10.3043 (18)0.092 (3)0.417 (3)0.107 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0681 (10)0.0675 (10)0.0633 (10)0.0177 (7)0.0287 (8)0.0060 (7)
O20.0673 (10)0.0717 (10)0.0621 (10)0.0164 (8)0.0276 (8)0.0063 (8)
O30.0511 (8)0.0612 (9)0.0469 (8)0.0076 (6)0.0210 (6)0.0021 (6)
N40.0470 (9)0.0617 (10)0.0418 (9)0.0007 (8)0.0184 (7)0.0019 (7)
N50.0529 (10)0.0658 (11)0.0559 (10)0.0037 (8)0.0217 (8)0.0024 (8)
C60.0502 (11)0.0537 (12)0.0499 (11)0.0005 (9)0.0179 (9)0.0016 (9)
C70.0526 (11)0.0600 (13)0.0510 (12)0.0015 (10)0.0119 (10)0.0065 (10)
C80.0566 (12)0.0598 (12)0.0434 (10)0.0070 (10)0.0137 (9)0.0040 (9)
C90.0488 (10)0.0532 (11)0.0408 (10)0.0086 (9)0.0155 (9)0.0037 (8)
C100.0577 (12)0.0604 (12)0.0420 (10)0.0081 (10)0.0186 (9)0.0039 (9)
C110.0557 (12)0.0601 (13)0.0489 (11)0.0047 (10)0.0242 (10)0.0075 (10)
C120.0495 (11)0.0562 (12)0.0496 (11)0.0030 (10)0.0197 (10)0.0065 (9)
C130.0437 (10)0.0484 (11)0.0441 (11)0.0007 (8)0.0126 (9)0.0013 (8)
C140.0460 (10)0.0572 (12)0.0437 (10)0.0004 (9)0.0159 (9)0.0001 (9)
C150.0518 (12)0.0777 (15)0.0508 (12)0.0094 (10)0.0210 (10)0.0095 (10)
C160.0708 (14)0.0702 (15)0.0533 (12)0.0131 (11)0.0226 (11)0.0149 (10)
C170.0592 (13)0.0911 (18)0.0593 (14)0.0175 (12)0.0176 (11)0.0095 (12)
C180.0616 (12)0.0662 (13)0.0461 (11)0.0004 (11)0.0227 (10)0.0011 (9)
C190.0546 (12)0.0709 (14)0.0426 (11)0.0024 (10)0.0153 (9)0.0028 (9)
C200.0641 (15)0.105 (2)0.0864 (18)0.0046 (14)0.0366 (14)0.0032 (15)
Geometric parameters (Å, º) top
O1—C61.361 (2)C10—H100.9300
O1—H11.02 (3)C11—C121.438 (3)
O2—C121.215 (2)C11—H110.9300
O3—C131.382 (2)C13—C141.390 (2)
O3—C121.389 (2)C14—C151.519 (2)
N4—C161.463 (2)C15—H15A0.9700
N4—C191.471 (2)C15—H15B0.9700
N4—C151.475 (2)C16—C171.505 (3)
N5—C181.447 (2)C16—H16A0.9700
N5—C171.451 (3)C16—H16B0.9700
N5—C201.453 (3)C17—H17A0.9700
C6—C141.399 (3)C17—H17B0.9700
C6—C71.401 (3)C18—C191.511 (2)
C7—C81.368 (3)C18—H18A0.9700
C7—H70.9300C18—H18B0.9700
C8—C91.399 (3)C19—H19A0.9700
C8—H80.9300C19—H19B0.9700
C9—C131.401 (2)C20—H20A0.9600
C9—C101.433 (3)C20—H20B0.9600
C10—C111.334 (3)C20—H20C0.9600
C6—O1—H1105.1 (15)N4—C15—H15A109.1
C13—O3—C12122.33 (15)C14—C15—H15A109.1
C16—N4—C19109.05 (15)N4—C15—H15B109.1
C16—N4—C15112.12 (15)C14—C15—H15B109.1
C19—N4—C15111.59 (15)H15A—C15—H15B107.8
C18—N5—C17109.58 (15)N4—C16—C17109.76 (16)
C18—N5—C20111.11 (17)N4—C16—H16A109.7
C17—N5—C20110.52 (18)C17—C16—H16A109.7
O1—C6—C14121.37 (17)N4—C16—H16B109.7
O1—C6—C7117.59 (18)C17—C16—H16B109.7
C14—C6—C7121.03 (18)H16A—C16—H16B108.2
C8—C7—C6120.47 (19)N5—C17—C16111.21 (18)
C8—C7—H7119.8N5—C17—H17A109.4
C6—C7—H7119.8C16—C17—H17A109.4
C7—C8—C9120.69 (18)N5—C17—H17B109.4
C7—C8—H8119.7C16—C17—H17B109.4
C9—C8—H8119.7H17A—C17—H17B108.0
C8—C9—C13117.62 (17)N5—C18—C19111.37 (16)
C8—C9—C10124.42 (17)N5—C18—H18A109.4
C13—C9—C10117.96 (18)C19—C18—H18A109.4
C11—C10—C9121.20 (18)N5—C18—H18B109.4
C11—C10—H10119.4C19—C18—H18B109.4
C9—C10—H10119.4H18A—C18—H18B108.0
C10—C11—C12121.47 (18)N4—C19—C18109.93 (15)
C10—C11—H11119.3N4—C19—H19A109.7
C12—C11—H11119.3C18—C19—H19A109.7
O2—C12—O3116.46 (17)N4—C19—H19B109.7
O2—C12—C11126.57 (18)C18—C19—H19B109.7
O3—C12—C11116.97 (18)H19A—C19—H19B108.2
O3—C13—C14116.53 (16)N5—C20—H20A109.5
O3—C13—C9120.07 (16)N5—C20—H20B109.5
C14—C13—C9123.38 (18)H20A—C20—H20B109.5
C13—C14—C6116.77 (16)N5—C20—H20C109.5
C13—C14—C15120.91 (17)H20A—C20—H20C109.5
C6—C14—C15122.18 (16)H20B—C20—H20C109.5
N4—C15—C14112.61 (16)
O1—C6—C7—C8177.60 (18)O3—C13—C14—C153.3 (3)
C14—C6—C7—C81.8 (3)C9—C13—C14—C15175.31 (17)
C6—C7—C8—C90.6 (3)O1—C6—C14—C13178.06 (17)
C7—C8—C9—C131.0 (3)C7—C6—C14—C131.3 (3)
C7—C8—C9—C10178.61 (19)O1—C6—C14—C152.5 (3)
C8—C9—C10—C11179.86 (19)C7—C6—C14—C15176.87 (18)
C13—C9—C10—C110.6 (3)C16—N4—C15—C1478.8 (2)
C9—C10—C11—C120.1 (3)C19—N4—C15—C14158.52 (16)
C13—O3—C12—O2178.67 (16)C13—C14—C15—N4155.52 (18)
C13—O3—C12—C110.9 (3)C6—C14—C15—N429.1 (3)
C10—C11—C12—O2178.7 (2)C19—N4—C16—C1759.0 (2)
C10—C11—C12—O30.8 (3)C15—N4—C16—C17176.87 (17)
C12—O3—C13—C14179.00 (16)C18—N5—C17—C1657.7 (2)
C12—O3—C13—C90.3 (3)C20—N5—C17—C16179.51 (18)
C8—C9—C13—O3179.94 (16)N4—C16—C17—N559.5 (2)
C10—C9—C13—O30.4 (3)C17—N5—C18—C1957.0 (2)
C8—C9—C13—C141.5 (3)C20—N5—C18—C19179.46 (18)
C10—C9—C13—C14178.15 (17)C16—N4—C19—C1858.4 (2)
O3—C13—C14—C6178.98 (16)C15—N4—C19—C18177.23 (16)
C9—C13—C14—C60.3 (3)N5—C18—C19—N458.1 (2)
Hydrogen-bond geometry (Å, º) top
Cg1 is the centroid of the O3/C9–C13 ring.
D—H···AD—HH···AD···AD—H···A
O1—H1···N41.02 (3)1.66 (3)2.607 (2)153 (3)
C11—H11···O2i0.932.593.239 (2)128
C15—H15B···Cg1ii0.972.993.802 (2)142
Symmetry codes: (i) x, y+1/2, z+1/2; (ii) x, y1/2, z3/2.
 

Acknowledgements

This study was supported financially in part by JSPS KAKENHI grant No. JP15K05539.

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