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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2016 Nov 4;72(Pt 12):1751–1753. doi: 10.1107/S2056989016017217

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

Koji Kubono a,*, Ryuma Kise a, Yukiyasu Kashiwagi b, Keita Tani a, Kunihiko Yokoi a
PMCID: PMC5137600  PMID: 27980822

There is an intra­molecular O—H⋯N hydrogen bond forming an S(6) ring motif in the title compound. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds with a C(4) chain motif, and also by C—H⋯π inter­actions. The chains are linked by π–π inter­actions, forming a sheet parallel to the bc plane.

Keywords: crystal structure, coumarin, piperazine, hydrogen bonding, π–π inter­actions

Abstract

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 π–π inter­actions [centroid–centroid distance of 3.5745 (11) Å], forming a sheet structure parallel to the bc plane.

Chemical context  

Coumarin (2H-chromen-2-one) derivatives have wide applications in diverse areas such as pharmaceuticals (Neyts et al., 2009), dyes (Hara et al., 2003) and liquid crystal (Schadt et al., 1996). 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). Moreover, the piperazine ring has recently been utilized as a proton-recognition site in pH-sensitive fluorescent probes (Lee et al., 2014) and a linker bridging two chromophores in fluorescent ion-sensors (Srivastava et al., 2014; Jiang et al., 2011). We are attempting to develop water-soluble chemosensors based on coumarin, and report here the mol­ecular and crystal structure of the title compound.graphic file with name e-72-01751-scheme1.jpg

Structural commentary  

The mol­ecular structure of the title compound is shown in Fig. 1. 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 and Table 1). 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; Kobayashi et al., 2014).

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.

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) Inline graphic; (ii) Inline graphic.

Supra­molecular features  

In the crystal, mol­ecules are linked by a C—H⋯O hydrogen bond (C11—H11⋯O2i; symmetry code in Table 1), 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) is also observed in the chain (Fig. 2). The chains are linked through slipped parallel π–π 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.

Database survey  

A search of the Cambridge Structural Database (CSD, Version 5.37; Groom et al., 2016) 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) and 8-{[bis­(pyridin-2-ylmeth­yl)amino]­meth­yl}-7-hy­droxy-2H-chromen-2-one (Kobayashi et al., 2014). A search for the fragment methyl­piperazine gave 666 hits, but none contained coumarin.

Synthesis and crystallization  

The title compound was prepared by modification of the reported procedure (Mazzei et al., 2008). 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%.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2. 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 U iso(H) = 1.2U eq(C).

Table 2. Experimental details.

Crystal data
Chemical formula C15H18N2O3
M r 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)
T min, T max 0.823, 0.991
No. of measured, independent and observed [F 2 > 2.0σ(F 2)] reflections 13237, 3136, 1566
R int 0.037
(sin θ/λ)max−1) 0.648
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), 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), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2015), CrystalStructure (Rigaku, 2016).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016017217/is5461sup1.cif

e-72-01751-sup1.cif (409.8KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016017217/is5461Isup2.hkl

e-72-01751-Isup2.hkl (250.6KB, hkl)

Supporting information file. DOI: 10.1107/S2056989016017217/is5461Isup3.cml

CCDC reference: 1511659

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

Acknowledgments

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

supplementary crystallographic information

Crystal data

C15H18N2O3 F(000) = 584.00
Mr = 274.31 Dx = 1.324 Mg m3
Monoclinic, P21/c Mo Kα radiation, λ = 0.71075 Å
a = 15.3519 (6) Å Cell parameters from 6828 reflections
b = 9.4005 (4) Å θ = 3.0–27.4°
c = 9.9702 (4) Å µ = 0.09 mm1
β = 106.954 (1)° T = 296 K
V = 1376.32 (10) Å3 Block, colorless
Z = 4 0.20 × 0.10 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID diffractometer 1566 reflections with F2 > 2.0σ(F2)
Detector resolution: 10.000 pixels mm-1 Rint = 0.037
ω scans θmax = 27.4°, θmin = 3.0°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) h = −19→19
Tmin = 0.823, Tmax = 0.991 k = −12→12
13237 measured reflections l = −12→11
3136 independent reflections

Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.162 H 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 parameters Δρmax = 0.19 e Å3
0 restraints Δρmin = −0.18 e Å3
Primary atom site location: structure-invariant direct methods

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.
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)

x y z Uiso*/Ueq
O1 0.30930 (10) −0.15085 (16) 0.50405 (16) 0.0643 (4)
O2 −0.04527 (10) 0.32032 (16) 0.48480 (15) 0.0652 (5)
O3 0.06794 (9) 0.17001 (13) 0.49705 (13) 0.0516 (4)
N4 0.26991 (10) 0.05030 (17) 0.31592 (15) 0.0490 (4)
N5 0.41058 (11) 0.13494 (18) 0.19673 (17) 0.0570 (5)
C6 0.24973 (13) −0.0902 (2) 0.5650 (2) 0.0506 (5)
C7 0.25092 (14) −0.1386 (2) 0.6984 (2) 0.0552 (5)
H7 0.2931 −0.2072 0.7432 0.066*
C8 0.19055 (13) −0.0858 (2) 0.7631 (2) 0.0535 (5)
H8 0.1917 −0.1194 0.8513 0.064*
C9 0.12716 (12) 0.0182 (2) 0.69801 (18) 0.0471 (5)
C10 0.06032 (14) 0.0772 (2) 0.7567 (2) 0.0525 (5)
H10 0.0575 0.0456 0.8438 0.063*
C11 0.00197 (14) 0.1765 (2) 0.6887 (2) 0.0530 (5)
H11 −0.0407 0.2128 0.7294 0.064*
C12 0.00365 (13) 0.2289 (2) 0.5539 (2) 0.0507 (5)
C13 0.12898 (12) 0.0672 (2) 0.56609 (19) 0.0455 (5)
C14 0.18880 (12) 0.0155 (2) 0.49655 (18) 0.0484 (5)
C15 0.18271 (13) 0.0648 (2) 0.3490 (2) 0.0588 (6)
H15A 0.1365 0.0094 0.2822 0.071*
H15B 0.1639 0.1637 0.3387 0.071*
C16 0.33329 (15) 0.1654 (2) 0.3767 (2) 0.0638 (6)
H16A 0.3430 0.1690 0.4772 0.077*
H16B 0.3077 0.2557 0.3370 0.077*
C17 0.42259 (15) 0.1407 (3) 0.3465 (2) 0.0698 (7)
H17A 0.4645 0.2169 0.3876 0.084*
H17B 0.4490 0.0520 0.3893 0.084*
C18 0.34652 (13) 0.0235 (2) 0.1345 (2) 0.0565 (5)
H18A 0.3716 −0.0678 0.1719 0.068*
H18B 0.3370 0.0222 0.0340 0.068*
C19 0.25631 (13) 0.0457 (2) 0.16373 (19) 0.0558 (5)
H19A 0.2291 0.1341 0.1214 0.067*
H19B 0.2152 −0.0314 0.1227 0.067*
C20 0.49746 (16) 0.1123 (3) 0.1694 (3) 0.0822 (8)
H20A 0.5379 0.1894 0.2085 0.099*
H20B 0.4883 0.1082 0.0700 0.099*
H20C 0.5236 0.0245 0.2115 0.099*
H1 0.3043 (18) −0.092 (3) 0.417 (3) 0.107 (9)*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0681 (10) 0.0675 (10) 0.0633 (10) 0.0177 (7) 0.0287 (8) 0.0060 (7)
O2 0.0673 (10) 0.0717 (10) 0.0621 (10) 0.0164 (8) 0.0276 (8) 0.0063 (8)
O3 0.0511 (8) 0.0612 (9) 0.0469 (8) 0.0076 (6) 0.0210 (6) 0.0021 (6)
N4 0.0470 (9) 0.0617 (10) 0.0418 (9) −0.0007 (8) 0.0184 (7) −0.0019 (7)
N5 0.0529 (10) 0.0658 (11) 0.0559 (10) −0.0037 (8) 0.0217 (8) 0.0024 (8)
C6 0.0502 (11) 0.0537 (12) 0.0499 (11) −0.0005 (9) 0.0179 (9) −0.0016 (9)
C7 0.0526 (11) 0.0600 (13) 0.0510 (12) 0.0015 (10) 0.0119 (10) 0.0065 (10)
C8 0.0566 (12) 0.0598 (12) 0.0434 (10) −0.0070 (10) 0.0137 (9) 0.0040 (9)
C9 0.0488 (10) 0.0532 (11) 0.0408 (10) −0.0086 (9) 0.0155 (9) −0.0037 (8)
C10 0.0577 (12) 0.0604 (12) 0.0420 (10) −0.0081 (10) 0.0186 (9) −0.0039 (9)
C11 0.0557 (12) 0.0601 (13) 0.0489 (11) −0.0047 (10) 0.0242 (10) −0.0075 (10)
C12 0.0495 (11) 0.0562 (12) 0.0496 (11) −0.0030 (10) 0.0197 (10) −0.0065 (9)
C13 0.0437 (10) 0.0484 (11) 0.0441 (11) −0.0007 (8) 0.0126 (9) −0.0013 (8)
C14 0.0460 (10) 0.0572 (12) 0.0437 (10) 0.0004 (9) 0.0159 (9) −0.0001 (9)
C15 0.0518 (12) 0.0777 (15) 0.0508 (12) 0.0094 (10) 0.0210 (10) 0.0095 (10)
C16 0.0708 (14) 0.0702 (15) 0.0533 (12) −0.0131 (11) 0.0226 (11) −0.0149 (10)
C17 0.0592 (13) 0.0911 (18) 0.0593 (14) −0.0175 (12) 0.0176 (11) −0.0095 (12)
C18 0.0616 (12) 0.0662 (13) 0.0461 (11) 0.0004 (11) 0.0227 (10) −0.0011 (9)
C19 0.0546 (12) 0.0709 (14) 0.0426 (11) −0.0024 (10) 0.0153 (9) −0.0028 (9)
C20 0.0641 (15) 0.105 (2) 0.0864 (18) −0.0046 (14) 0.0366 (14) 0.0032 (15)

Geometric parameters (Å, º)

O1—C6 1.361 (2) C10—H10 0.9300
O1—H1 1.02 (3) C11—C12 1.438 (3)
O2—C12 1.215 (2) C11—H11 0.9300
O3—C13 1.382 (2) C13—C14 1.390 (2)
O3—C12 1.389 (2) C14—C15 1.519 (2)
N4—C16 1.463 (2) C15—H15A 0.9700
N4—C19 1.471 (2) C15—H15B 0.9700
N4—C15 1.475 (2) C16—C17 1.505 (3)
N5—C18 1.447 (2) C16—H16A 0.9700
N5—C17 1.451 (3) C16—H16B 0.9700
N5—C20 1.453 (3) C17—H17A 0.9700
C6—C14 1.399 (3) C17—H17B 0.9700
C6—C7 1.401 (3) C18—C19 1.511 (2)
C7—C8 1.368 (3) C18—H18A 0.9700
C7—H7 0.9300 C18—H18B 0.9700
C8—C9 1.399 (3) C19—H19A 0.9700
C8—H8 0.9300 C19—H19B 0.9700
C9—C13 1.401 (2) C20—H20A 0.9600
C9—C10 1.433 (3) C20—H20B 0.9600
C10—C11 1.334 (3) C20—H20C 0.9600
C6—O1—H1 105.1 (15) N4—C15—H15A 109.1
C13—O3—C12 122.33 (15) C14—C15—H15A 109.1
C16—N4—C19 109.05 (15) N4—C15—H15B 109.1
C16—N4—C15 112.12 (15) C14—C15—H15B 109.1
C19—N4—C15 111.59 (15) H15A—C15—H15B 107.8
C18—N5—C17 109.58 (15) N4—C16—C17 109.76 (16)
C18—N5—C20 111.11 (17) N4—C16—H16A 109.7
C17—N5—C20 110.52 (18) C17—C16—H16A 109.7
O1—C6—C14 121.37 (17) N4—C16—H16B 109.7
O1—C6—C7 117.59 (18) C17—C16—H16B 109.7
C14—C6—C7 121.03 (18) H16A—C16—H16B 108.2
C8—C7—C6 120.47 (19) N5—C17—C16 111.21 (18)
C8—C7—H7 119.8 N5—C17—H17A 109.4
C6—C7—H7 119.8 C16—C17—H17A 109.4
C7—C8—C9 120.69 (18) N5—C17—H17B 109.4
C7—C8—H8 119.7 C16—C17—H17B 109.4
C9—C8—H8 119.7 H17A—C17—H17B 108.0
C8—C9—C13 117.62 (17) N5—C18—C19 111.37 (16)
C8—C9—C10 124.42 (17) N5—C18—H18A 109.4
C13—C9—C10 117.96 (18) C19—C18—H18A 109.4
C11—C10—C9 121.20 (18) N5—C18—H18B 109.4
C11—C10—H10 119.4 C19—C18—H18B 109.4
C9—C10—H10 119.4 H18A—C18—H18B 108.0
C10—C11—C12 121.47 (18) N4—C19—C18 109.93 (15)
C10—C11—H11 119.3 N4—C19—H19A 109.7
C12—C11—H11 119.3 C18—C19—H19A 109.7
O2—C12—O3 116.46 (17) N4—C19—H19B 109.7
O2—C12—C11 126.57 (18) C18—C19—H19B 109.7
O3—C12—C11 116.97 (18) H19A—C19—H19B 108.2
O3—C13—C14 116.53 (16) N5—C20—H20A 109.5
O3—C13—C9 120.07 (16) N5—C20—H20B 109.5
C14—C13—C9 123.38 (18) H20A—C20—H20B 109.5
C13—C14—C6 116.77 (16) N5—C20—H20C 109.5
C13—C14—C15 120.91 (17) H20A—C20—H20C 109.5
C6—C14—C15 122.18 (16) H20B—C20—H20C 109.5
N4—C15—C14 112.61 (16)
O1—C6—C7—C8 −177.60 (18) O3—C13—C14—C15 −3.3 (3)
C14—C6—C7—C8 1.8 (3) C9—C13—C14—C15 175.31 (17)
C6—C7—C8—C9 −0.6 (3) O1—C6—C14—C13 178.06 (17)
C7—C8—C9—C13 −1.0 (3) C7—C6—C14—C13 −1.3 (3)
C7—C8—C9—C10 178.61 (19) O1—C6—C14—C15 2.5 (3)
C8—C9—C10—C11 179.86 (19) C7—C6—C14—C15 −176.87 (18)
C13—C9—C10—C11 −0.6 (3) C16—N4—C15—C14 −78.8 (2)
C9—C10—C11—C12 −0.1 (3) C19—N4—C15—C14 158.52 (16)
C13—O3—C12—O2 178.67 (16) C13—C14—C15—N4 155.52 (18)
C13—O3—C12—C11 −0.9 (3) C6—C14—C15—N4 −29.1 (3)
C10—C11—C12—O2 −178.7 (2) C19—N4—C16—C17 −59.0 (2)
C10—C11—C12—O3 0.8 (3) C15—N4—C16—C17 176.87 (17)
C12—O3—C13—C14 179.00 (16) C18—N5—C17—C16 −57.7 (2)
C12—O3—C13—C9 0.3 (3) C20—N5—C17—C16 179.51 (18)
C8—C9—C13—O3 −179.94 (16) N4—C16—C17—N5 59.5 (2)
C10—C9—C13—O3 0.4 (3) C17—N5—C18—C19 57.0 (2)
C8—C9—C13—C14 1.5 (3) C20—N5—C18—C19 179.46 (18)
C10—C9—C13—C14 −178.15 (17) C16—N4—C19—C18 58.4 (2)
O3—C13—C14—C6 −178.98 (16) C15—N4—C19—C18 −177.23 (16)
C9—C13—C14—C6 −0.3 (3) N5—C18—C19—N4 −58.1 (2)

Hydrogen-bond geometry (Å, º)

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

D—H···A D—H H···A D···A 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—H15B···Cg1ii 0.97 2.99 3.802 (2) 142

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

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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/S2056989016017217/is5461sup1.cif

e-72-01751-sup1.cif (409.8KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016017217/is5461Isup2.hkl

e-72-01751-Isup2.hkl (250.6KB, hkl)

Supporting information file. DOI: 10.1107/S2056989016017217/is5461Isup3.cml

CCDC reference: 1511659

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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