Crystal structure of 3-(hy­droxy­meth­yl)chromone

Abstract

In the title compound, C₁₀H₈O₃ (systematic name 3-hy­droxy­methyl-4H-chromen-4-one), the fused-ring system is slightly puckered [dihedral angle between the rings = 3.84 (11)°]. The hy­droxy O atom deviates from the heterocyclic ring by 1.422 (1) Å. In the crystal, inversion dimers linked by pairs of O—H⋯O hydrogen bonds generate R ₂ ²(12) loops. The dimers are linked by aromatic π–π stacking [shortest centroid–centroid distance = 3.580 (3) Å], and C—H⋯O hydrogen bonds, generating a three-dimensional network.

Related literature  

For the biological activities of related compounds, see: Sun et al. (2009 ▸); Helguera et al. (2013 ▸); Venkateswararao et al. (2014 ▸). For the synthesis of the title compound, see: Araya-Maturana et al. (2003 ▸).

Experimental  

Crystal data  

• C₁₀H₈O₃

• M _r = 176.17

• Triclinic,

• a = 6.756 (4) Å

• b = 7.988 (6) Å

• c = 7.991 (6) Å

• α = 94.48 (6)°

• β = 108.27 (5)°

• γ = 103.31 (5)°

• V = 393.2 (5) ų

• Z = 2

• Mo Kα radiation

• μ = 0.11 mm⁻¹

• T = 100 K

• 0.32 × 0.32 × 0.16 mm

Data collection  

• Rigaku AFC-7R diffractometer

• 2219 measured reflections

• 1805 independent reflections

• 1537 reflections with F ² > 2.0σ(F ²)

• R _int = 0.089

• 3 standard reflections every 150 reflections intensity decay: 0.1%

Refinement  

• R[F ² > 2σ(F ²)] = 0.065

• wR(F ²) = 0.202

• S = 1.06

• 1805 reflections

• 119 parameters

• H-atom parameters constrained

• Δρ_max = 0.42 e Å⁻³

• Δρ_min = −0.49 e Å⁻³

Data collection: WinAFC Diffractometer Control Software (Rigaku, 1999 ▸); cell refinement: WinAFC Diffractometer Control Software; data reduction: WinAFC Diffractometer Control Software; program(s) used to solve structure: SIR2008 (Burla et al., 2007 ▸); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▸); molecular graphics: CrystalStructure (Rigaku, 2010 ▸); software used to prepare material for publication: CrystalStructure.

Supplementary Material

CCDC reference: 1406927

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

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
O3H8O2i	0.84	1.94	2.757(3)	165
C1H1O2ii	0.95	2.58	3.283(4)	131

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

S1. Comment

Many derivatives of the title compound (3-hydroxymethylchromone) are reported as retinoic acid receptor binders (Sun et al. (2009)), human monoamine oxidase inhibitors (Helguera et al. (2013)) and anti-proliferative agents (Venkateswararao et al. (2014)).

The mean deviation of the least-square planes for the non-hydrogen atoms except hydroxy O3 atom is 0.0479 Å, and the largest deviation is 0.146 (2) Å for C10. These mean that these atoms are essentially coplanar (Fig.1). The dihedral angle of C3–C2–C10–O3 is 70.6 (2). In the crystal, the pyran rings are stacked [centroid–centroid distance between the pyran rings of the 4H-chromene units = 3.894 (3) Å], and C–H···O hydrogen bonds are formed to give dimers running along the c direction, as shown in Fig.2.

S2. Experimental

The title compound was synthesized from 3-formylchromone according to the literature method (Araya-Maturana et al. 2003). Colourless blocks were obtained by slow evaporation of an ethyl acetate solution of the title compound at room temperature.

S3. Refinement

All hydrogen atoms were placed in geometrical positions [C–H 0.95 Å and O–H 0.84 Å], and refined using a riding model with U_iso(H) = 1.2U_eq of the parent atoms.

Figures

Fig. 1.

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

Fig. 2.

A view of the packing of the title compound. O—H···O hydrogen bonds are represented as dashed lines.

Crystal data

C10H8O3	Z = 2
Mr = 176.17	F(000) = 184.00
Triclinic, P1	Dx = 1.488 Mg m−3
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71069 Å
a = 6.756 (4) Å	Cell parameters from 25 reflections
b = 7.988 (6) Å	θ = 15.5–17.3°
c = 7.991 (6) Å	µ = 0.11 mm−1
α = 94.48 (6)°	T = 100 K
β = 108.27 (5)°	Block, colorless
γ = 103.31 (5)°	0.32 × 0.32 × 0.16 mm
V = 393.2 (5) Å3

Data collection

Rigaku AFC-7R diffractometer	θmax = 27.5°
ω–2θ scans	h = −4→8
2219 measured reflections	k = −10→10
1805 independent reflections	l = −10→9
1537 reflections with F2 > 2.0σ(F2)	3 standard reflections every 150 reflections
Rint = 0.089	intensity decay: 0.1%

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.065	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.202	H-atom parameters constrained
S = 1.06	w = 1/[σ2(Fo2) + (0.1399P)2 + 0.1723P] where P = (Fo2 + 2Fc2)/3
1805 reflections	(Δ/σ)max < 0.001
119 parameters	Δρmax = 0.42 e Å−3
0 restraints	Δρmin = −0.49 e Å−3
Primary atom site location: structure-invariant direct methods

Special details

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 σ(F2) is used only for calculating R-factor (gt).

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

	x	y	z	Uiso*/Ueq
O1	0.72779 (19)	1.01991 (17)	0.70911 (18)	0.0179 (4)
O2	1.19522 (19)	0.80874 (17)	0.63213 (18)	0.0190 (4)
O3	0.7925 (2)	0.48525 (17)	0.56522 (17)	0.0195 (4)
C1	0.6785 (3)	0.8666 (3)	0.6006 (3)	0.0167 (4)
C2	0.8224 (3)	0.7871 (3)	0.5707 (3)	0.0146 (4)
C3	1.0527 (3)	0.8696 (3)	0.6575 (3)	0.0133 (4)
C4	1.3221 (3)	1.1214 (3)	0.8824 (3)	0.0168 (4)
C5	1.3681 (3)	1.2688 (3)	1.0053 (3)	0.0209 (5)
C6	1.1985 (3)	1.3325 (3)	1.0269 (3)	0.0218 (5)
C7	0.9868 (3)	1.2504 (3)	0.9255 (3)	0.0200 (5)
C8	1.1070 (3)	1.0325 (3)	0.7810 (3)	0.0147 (4)
C9	0.9416 (3)	1.0995 (3)	0.8033 (3)	0.0153 (4)
C10	0.7477 (3)	0.6132 (3)	0.4539 (3)	0.0165 (4)
H1	0.5294	0.8101	0.5403	0.0201*
H2	1.4369	1.0798	0.8665	0.0202*
H3	1.5139	1.3272	1.0751	0.0251*
H4	1.2306	1.4333	1.1123	0.0262*
H5	0.8729	1.2955	0.9382	0.0240*
H6A	0.5905	0.5855	0.3870	0.0198*
H7B	0.8247	0.6145	0.3669	0.0198*
H8	0.8200	0.4052	0.5093	0.0234*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0130 (6)	0.0202 (7)	0.0240 (7)	0.0070 (5)	0.0090 (5)	0.0043 (5)
O2	0.0112 (6)	0.0225 (7)	0.0252 (7)	0.0067 (5)	0.0075 (5)	0.0032 (6)
O3	0.0195 (7)	0.0188 (7)	0.0236 (7)	0.0069 (5)	0.0104 (6)	0.0052 (5)
C1	0.0110 (8)	0.0212 (9)	0.0193 (9)	0.0041 (7)	0.0061 (7)	0.0073 (7)
C2	0.0108 (8)	0.0202 (9)	0.0144 (8)	0.0046 (7)	0.0050 (6)	0.0067 (7)
C3	0.0115 (8)	0.0168 (9)	0.0129 (8)	0.0043 (6)	0.0052 (6)	0.0053 (6)
C4	0.0158 (8)	0.0179 (9)	0.0168 (8)	0.0054 (7)	0.0044 (7)	0.0050 (7)
C5	0.0205 (9)	0.0212 (10)	0.0174 (9)	0.0040 (7)	0.0021 (7)	0.0055 (7)
C6	0.0302 (10)	0.0184 (9)	0.0171 (9)	0.0071 (8)	0.0077 (8)	0.0042 (7)
C7	0.0264 (9)	0.0198 (9)	0.0212 (9)	0.0113 (8)	0.0136 (8)	0.0068 (7)
C8	0.0144 (8)	0.0179 (9)	0.0140 (8)	0.0055 (7)	0.0061 (7)	0.0071 (7)
C9	0.0149 (8)	0.0191 (9)	0.0144 (8)	0.0055 (7)	0.0068 (7)	0.0069 (7)
C10	0.0101 (8)	0.0204 (9)	0.0178 (9)	0.0026 (7)	0.0039 (6)	0.0038 (7)

Geometric parameters (Å, º)

O1—C1	1.352 (3)	C6—C7	1.375 (3)
O1—C9	1.371 (2)	C7—C9	1.400 (3)
O2—C3	1.236 (3)	C8—C9	1.396 (3)
O3—C10	1.429 (3)	O3—H8	0.840
C1—C2	1.346 (3)	C1—H1	0.950
C2—C3	1.455 (3)	C4—H2	0.950
C2—C10	1.495 (3)	C5—H3	0.950
C3—C8	1.468 (3)	C6—H4	0.950
C4—C5	1.381 (3)	C7—H5	0.950
C4—C8	1.404 (3)	C10—H6A	0.990
C5—C6	1.407 (4)	C10—H7B	0.990
C1—O1—C9	117.98 (17)	O3—C10—C2	108.17 (15)
O1—C1—C2	125.63 (15)	C10—O3—H8	109.472
C1—C2—C3	119.38 (17)	O1—C1—H1	117.186
C1—C2—C10	120.66 (15)	C2—C1—H1	117.188
C3—C2—C10	119.93 (18)	C5—C4—H2	119.761
O2—C3—C2	123.48 (17)	C8—C4—H2	119.765
O2—C3—C8	121.37 (15)	C4—C5—H3	120.061
C2—C3—C8	115.15 (18)	C6—C5—H3	120.064
C5—C4—C8	120.5 (2)	C5—C6—H4	119.658
C4—C5—C6	119.88 (16)	C7—C6—H4	119.653
C5—C6—C7	120.69 (19)	C6—C7—H5	120.506
C6—C7—C9	119.0 (3)	C9—C7—H5	120.503
C3—C8—C4	121.64 (19)	O3—C10—H6A	110.064
C3—C8—C9	119.77 (15)	O3—C10—H7B	110.063
C4—C8—C9	118.56 (17)	C2—C10—H6A	110.069
O1—C9—C7	116.70 (19)	C2—C10—H7B	110.064
O1—C9—C8	121.91 (17)	H6A—C10—H7B	108.407
C7—C9—C8	121.38 (16)
C1—O1—C9—C7	−174.88 (15)	C5—C4—C8—C3	−176.20 (17)
C1—O1—C9—C8	4.2 (3)	C5—C4—C8—C9	1.9 (3)
C9—O1—C1—C2	−2.8 (3)	C8—C4—C5—C6	−1.2 (3)
C9—O1—C1—H1	177.2	C8—C4—C5—H3	178.8
H8—O3—C10—C2	−148.1	H2—C4—C5—C6	178.8
H8—O3—C10—H6A	91.6	H2—C4—C5—H3	−1.2
H8—O3—C10—H7B	−27.8	H2—C4—C8—C3	3.8
O1—C1—C2—C3	−1.0 (3)	H2—C4—C8—C9	−178.1
O1—C1—C2—C10	177.18 (16)	C4—C5—C6—C7	−0.7 (3)
H1—C1—C2—C3	179.0	C4—C5—C6—H4	179.3
H1—C1—C2—C10	−2.8	H3—C5—C6—C7	179.3
C1—C2—C3—O2	−177.19 (17)	H3—C5—C6—H4	−0.7
C1—C2—C3—C8	3.3 (3)	C5—C6—C7—C9	1.6 (3)
C1—C2—C10—O3	−107.56 (19)	C5—C6—C7—H5	−178.4
C1—C2—C10—H6A	12.7	H4—C6—C7—C9	−178.4
C1—C2—C10—H7B	132.2	H4—C6—C7—H5	1.6
C3—C2—C10—O3	70.6 (2)	C6—C7—C9—O1	178.25 (17)
C3—C2—C10—H6A	−169.1	C6—C7—C9—C8	−0.8 (3)
C3—C2—C10—H7B	−49.7	H5—C7—C9—O1	−1.8
C10—C2—C3—O2	4.6 (3)	H5—C7—C9—C8	179.2
C10—C2—C3—C8	−174.93 (15)	C3—C8—C9—O1	−1.8 (3)
O2—C3—C8—C4	−3.4 (3)	C3—C8—C9—C7	177.23 (16)
O2—C3—C8—C9	178.52 (16)	C4—C8—C9—O1	−179.96 (16)
C2—C3—C8—C4	176.19 (15)	C4—C8—C9—C7	−0.9 (3)
C2—C3—C8—C9	−1.9 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H8···O2i	0.84	1.94	2.757 (3)	165
C1—H1···O2ii	0.95	2.58	3.283 (4)	131

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