Crystal structure of 3-(hy­droxy­meth­yl)chromone

Ishikawa, Y.

doi:10.1107/S2056989015011627

organic compounds

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Volume 71| Part 7| July 2015| Page o495

doi:10.1107/S2056989015011627

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Crystal structure of 3-(hydroxymethyl)chromone

Yoshinobu Ishikawa ^a ^*

^aSchool of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
^*Correspondence e-mail: ishi206@u-shizuoka-ken.ac.jp

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 11 June 2015; accepted 16 June 2015; online 20 June 2015)

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 R₂²(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.

Keywords: crystal structure; chromone; hydrogen bonding; π–π stacking.

CCDC reference: 1406927

1. 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 ).

2. Experimental

2.1. Crystal data

C₁₀H₈O₃
M_r = 176.17
Triclinic, $[P \overline 1]$
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) Å³
Z = 2
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 100 K
0.32 × 0.32 × 0.16 mm

2.2. Data collection

Rigaku AFC-7R diffractometer
2219 measured reflections
1805 independent reflections
1537 reflections with F² > 2.0σ(F²)
R_int = 0.089
3 standard reflections every 150 reflections intensity decay: 0.1%

2.3. Refinement

R[F² > 2σ(F²)] = 0.065
wR(F²) = 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

Table 1
Hydrogen-bond geometry (Å, °)

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.

Data collection: WinAFC Diffractometer Control Software (Rigaku, 1999 $[Rigaku (1999). WinAFC Diffractometer Control Software. Rigaku Corporation, Tokyo, Japan.]$ ); 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.

Supporting information

CCDC reference: 1406927

Crystal structure: contains datablocks General, I. DOI: 10.1107/S2056989015011627/hb7444sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S2056989015011627/hb7444Isup2.hkl

Supporting information file. DOI: 10.1107/S2056989015011627/hb7444Isup3.cml

checkCIF report

Comment top

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.

Related literature top

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 top

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.

Computing details top

Data collection: WinAFC Diffractometer Control Software (Rigaku, 1999); cell refinement: WinAFC Diffractometer Control Software (Rigaku, 1999); data reduction: WinAFC Diffractometer Control Software (Rigaku, 1999); 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 (Rigaku, 2010).

Figures top

	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.

3-(Hydroxymethyl)-4H-chromen-4-one top

Crystal data top

C₁₀H₈O₃	Z = 2
M_r = 176.17	F(000) = 184.00
Triclinic, P1	D_x = 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 top

Rigaku AFC-7R diffractometer	θ_max = 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
R_int = 0.089	intensity decay: 0.1%

Refinement top

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(F_o²) + (0.1399P)² + 0.1723P] where P = (F_o² + 2F_c²)/3
1805 reflections	(Δ/σ)_max < 0.001
119 parameters	Δρ_max = 0.42 e Å⁻³
0 restraints	Δρ_min = −0.49 e Å⁻³
Primary atom site location: structure-invariant direct methods

Crystal data top

C₁₀H₈O₃	γ = 103.31 (5)°
M_r = 176.17	V = 393.2 (5) Å³
Triclinic, P1	Z = 2
a = 6.756 (4) Å	Mo Kα radiation
b = 7.988 (6) Å	µ = 0.11 mm⁻¹
c = 7.991 (6) Å	T = 100 K
α = 94.48 (6)°	0.32 × 0.32 × 0.16 mm
β = 108.27 (5)°

Data collection top

Rigaku AFC-7R diffractometer	R_int = 0.089
2219 measured reflections	3 standard reflections every 150 reflections
1805 independent reflections	intensity decay: 0.1%
1537 reflections with F² > 2.0σ(F²)

Refinement top

R[F² > 2σ(F²)] = 0.065	0 restraints
wR(F²) = 0.202	H-atom parameters constrained
S = 1.06	Δρ_max = 0.42 e Å⁻³
1805 reflections	Δρ_min = −0.49 e Å⁻³
119 parameters

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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) top

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) top

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.

Hydrogen-bond geometry (Å, º) top

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.

Acknowledgements

The University of Shizuoka is acknowledged for instrumental support.

References

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