(S)-2-(1H-Imidazol-1-yl)-3-phenyl­propanol

In the title compound, C₁₂H₁₄N₂O, the middle C atom in the propanol chain is a chiral center and possesses an S absolute configuration, according to the synthesis. In the crystal structure, inter­molecular O—H...N hydrogen bonds link the mol­ecules into a chain along the b axis.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.005 Å
• R factor = 0.037
• wR factor = 0.091
• Data-to-parameter ratio = 8.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT147_ALERT_1_C su on Symmetry Constrained Cell Angle(s) .......          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ...          5

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           25.43
           From the CIF: _reflns_number_total               1146
           Count of symmetry unique reflns         1147
           Completeness (_total/calc)             99.91%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C8     ...          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   5 ALERT level G = General alerts; check

   4 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Imidazoles are an important group in biological systems, and their derivatives have attracted widespread interest due to their application as precursors for imidazolium-based ionic liquids (Baudequin et al., 2003), N-heterocyclic carbenes (Nair et al., 2004) and molecular sensors (Sambrook et al., 2005). We have focused our interest on the synthesis and applications of imidazole derivatives (Lan et al., 2004; Wang et al., 2007) and have reported several chiral cyclophanes and chiral molecular tweezers containing imidazole residues as receptors for the enantioselective recognition of amino acids or their derivatives (You et al., 2001). Here, we report the crystal structure of the title compound, (I), which is a basic unit in the construction of chiral receptors and could be applied in the preparation of chair heterocyclic carbenes and ionic liquids.

In the structure of (I), the hydroxyl group and the imidazol-1-yl nitrogen atom are hydrogen bonded via an intermolecular O—H···N hydrogen bond as illustrated in Table 1 to result in the formation of a helical chain.

Related literature

For related literature, see: Bao et al. (2003); Baudequin et al. (2003); Lan et al. (2004); Matsuoka et al. (2006); Nair et al. (2004); Sambrook et al. (2005); Wang et al. (2007); You et al. (2001).

S2. Experimental

Since enantiopure amines are easily available and the chiral carbon has little risk of the racemization, they are usually applied for the preparation of chiral imidazole derivatives by cyclocondensation of ring fragments (Matsuoka et al., 2006). The methyl 2-(1H-imidazol-1-yl)-3-phenylpropanoate was easily prepared according to a literature procedure (Bao et al., 2003). Thereafter, NaBH₄ (1.52 g, 40 mmol) was added to methyl 2-(1H-imidazol-1-yl)-3-phenylpropanoate (2.16 g, 10.0 mmol) in ethanol (150 ml) at 273 K over 30 min. The mixture was stirred at 333 K for another 20 h and then evaporated under vacuum. The residue was diluted with 20 ml saturated K₂CO₃ and extracted with 50 ml e thyl acetate. The organic layer was dried over anhydrous Na₂SO₄ and concentrated under reduced pressure. The resulting residue was purified by column chromatography on silica gel eluting with CH₂Cl₂/CH₃OH (20/1, V/V), and then recrystallized from CH₂Cl₂ to give colorless crystals. Yield: 86%, mp 359–361 K, ¹H NMR (300 MHz, CDCl₃): δ 2.94–3.17 (dd, J=13.8 Hz, 7.7 Hz, 2H), 3.78–3.88 (m, 2H), 4.13–4.29 (m, 1H.), 6.88 (m, 2H), 7.02 (m, 2H), 7.28 (s, 1H), 7.03–7.26 (m, 5H). ¹³C NMR (75 MHz, CDCl₃): δ 38.41, 62.26, 64.21, 117.61, 126.99, 128.59, 128.76, 128.90, 136.47, 137.10 p.p.m..

S3. Refinement

All H atoms were positioned geometrically and refined in the riding model approximation with C—H = 0.93, 0.97 Å and O—H = 0.82 Å. Since there is no atom heavier than oxygen it was not possible to determine the absolute structure exactly. However, the chiral carbon does not directly participate in the cyclocondensation in this reaction (Matsuoka et al., 2006). Herein, the desired product (S)-2-(1H-imidazol-1-yl)-3-phenylpropanol was obtained starting from (S)-2-amino-3-phenylpropanoic acid, whose absolute configuration (S) is consistent with the starting material.

Computing details

Data collection: DIFRAC (Gabe & White, 1993); cell refinement: DIFRAC (Gabe & White, 1993); data reduction: NRCVAX (Gabe et al., 1989); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPIII (Burnett & Johnson, 1996); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2003).

Figures

Fig. 1. The molecular structure of (I), showing 30% probability displacement ellipsoids and the atomic numbering.

(S)-2-(1H-Imidazol-1-yl)-3-phenylpropanol

Crystal data

C12H14N2O	F(000) = 216
Mr = 202.25	Dx = 1.186 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 26 reflections
a = 8.021 (4) Å	θ = 4.6–7.8°
b = 6.069 (3) Å	µ = 0.08 mm^−1
c = 11.629 (5) Å	T = 293 K
β = 90.13 (5)°	Block, colorless
V = 566.1 (5) Å^3	0.40 × 0.33 × 0.23 mm
Z = 2

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.055
Radiation source: fine-focus sealed tube	θmax = 25.4°, θmin = 1.8°
Graphite monochromator	h = −9→0
ω/2θ scans	k = −7→7
1909 measured reflections	l = −13→14
1146 independent reflections	3 standard reflections every 200 reflections
826 reflections with I > 2σ(I)	intensity decay: 1.2%

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.036	H-atom parameters constrained
wR(F^2) = 0.090	w = 1/[σ^2(Fo^2) + (0.0335P)^2 + 0.0435P] where P = (Fo^2 + 2Fc^2)/3
S = 1.05	(Δ/σ)max < 0.001
1146 reflections	Δρmax = 0.13 e Å^−3
142 parameters	Δρmin = −0.12 e Å^−3
1 restraint	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.045 (8)

Special details

Experimental. In the crystal structure, there is not any heavy atom than silicon, so we can't get the absolute structure exactly. However, the chiral carbon does not directly participate in the cyclocondensation in this reaction (Matsuoka et al., Tetrahedron. 2006, 62, 8199–8206). From starting material (S)-2-amino-3-phenylpropanoic acid, it give (S)-2-(1H-imidazol-1-yl)-3-phenylpropanol as product, whose absolute configuration (S) is consistent with the absolute structure characterized by X-ray structure analysis.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	Uiso*/Ueq
O1	0.6488 (3)	0.9519 (5)	−0.06637 (15)	0.0601 (7)
H1	0.7178	1.0460	−0.0835	0.086 (15)*
N1	0.8556 (3)	0.8538 (4)	0.13967 (17)	0.0418 (6)
N2	1.1263 (3)	0.7863 (6)	0.1257 (2)	0.0651 (9)
C1	0.7787 (4)	0.7337 (7)	0.4142 (2)	0.0628 (10)
H1B	0.8315	0.8693	0.4069	0.073 (4)*
C2	0.8278 (4)	0.5915 (8)	0.5001 (3)	0.0747 (12)
H2	0.9137	0.6313	0.5497	0.073 (4)*
C3	0.7501 (5)	0.3908 (7)	0.5128 (3)	0.0725 (12)
H3	0.7824	0.2955	0.5714	0.073 (4)*
C4	0.6247 (5)	0.3324 (7)	0.4383 (2)	0.0680 (10)
H4	0.5716	0.1970	0.4464	0.073 (4)*
C5	0.5773 (4)	0.4746 (6)	0.3512 (2)	0.0565 (9)
H5	0.4935	0.4324	0.3003	0.073 (4)*
C6	0.6522 (3)	0.6781 (6)	0.3385 (2)	0.0456 (8)
C7	0.5912 (3)	0.8393 (6)	0.2488 (2)	0.0498 (8)
H7A	0.6073	0.9875	0.2780	0.046 (4)*
H7B	0.4723	0.8176	0.2383	0.046 (4)*
C8	0.6752 (3)	0.8225 (6)	0.1318 (2)	0.0431 (7)
H8	0.6550	0.6738	0.1021	0.040 (7)*
C9	0.5963 (3)	0.9848 (6)	0.0484 (2)	0.0517 (8)
H9A	0.4760	0.9703	0.0520	0.046 (4)*
H9B	0.6248	1.1335	0.0719	0.046 (4)*
C10	0.9385 (4)	1.0364 (6)	0.1796 (2)	0.0514 (9)
H1A	0.8907	1.1653	0.2075	0.073 (4)*
C11	1.1038 (4)	0.9919 (7)	0.1705 (2)	0.0607 (10)
H11	1.1892	1.0874	0.1917	0.073 (4)*
C12	0.9738 (4)	0.7106 (6)	0.1088 (2)	0.0542 (8)
H12	0.9510	0.5720	0.0785	0.073 (4)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0642 (15)	0.0700 (16)	0.0462 (11)	−0.0137 (15)	−0.0054 (9)	0.0087 (11)
N1	0.0410 (12)	0.0430 (15)	0.0414 (11)	0.0035 (14)	−0.0051 (9)	−0.0040 (11)
N2	0.0411 (16)	0.088 (3)	0.0659 (16)	0.0082 (17)	−0.0038 (12)	−0.0079 (17)
C1	0.057 (2)	0.066 (3)	0.0656 (19)	−0.009 (2)	−0.0107 (15)	0.0151 (19)
C2	0.065 (2)	0.093 (3)	0.066 (2)	−0.001 (2)	−0.0198 (18)	0.017 (2)
C3	0.085 (3)	0.075 (3)	0.058 (2)	0.016 (3)	0.0044 (18)	0.0208 (19)
C4	0.101 (3)	0.050 (2)	0.0522 (17)	0.001 (2)	0.0205 (18)	0.0072 (19)
C5	0.074 (2)	0.050 (2)	0.0459 (15)	−0.004 (2)	0.0051 (14)	−0.0072 (16)
C6	0.0442 (16)	0.050 (2)	0.0429 (15)	−0.0001 (17)	0.0058 (12)	0.0041 (14)
C7	0.0440 (16)	0.056 (2)	0.0496 (15)	0.0050 (18)	−0.0027 (12)	−0.0008 (16)
C8	0.0419 (15)	0.0454 (19)	0.0419 (13)	0.0001 (16)	−0.0061 (11)	−0.0023 (14)
C9	0.0467 (17)	0.056 (2)	0.0527 (15)	0.0023 (19)	−0.0078 (12)	0.0072 (16)
C10	0.0512 (19)	0.051 (2)	0.0519 (16)	−0.0015 (18)	−0.0039 (14)	−0.0075 (15)
C11	0.0465 (19)	0.081 (3)	0.0544 (16)	−0.007 (2)	−0.0072 (13)	−0.002 (2)
C12	0.056 (2)	0.060 (2)	0.0471 (15)	0.012 (2)	−0.0004 (13)	−0.0109 (16)

Geometric parameters (Å, º)

O1—C9	1.415 (3)	C4—H4	0.9300
O1—H1	0.8200	C5—C6	1.382 (5)
N1—C12	1.336 (4)	C5—H5	0.9300
N1—C10	1.372 (4)	C6—C7	1.511 (4)
N1—C8	1.462 (3)	C7—C8	1.522 (3)
N2—C12	1.321 (4)	C7—H7A	0.9700
N2—C11	1.364 (5)	C7—H7B	0.9700
C1—C2	1.377 (5)	C8—C9	1.519 (4)
C1—C6	1.383 (4)	C8—H8	0.9800
C1—H1B	0.9300	C9—H9A	0.9700
C2—C3	1.376 (6)	C9—H9B	0.9700
C2—H2	0.9300	C10—C11	1.358 (4)
C3—C4	1.373 (5)	C10—H1A	0.9300
C3—H3	0.9300	C11—H11	0.9300
C4—C5	1.384 (5)	C12—H12	0.9300
C9—O1—H1	109.5	C8—C7—H7A	108.4
C12—N1—C10	105.8 (2)	C6—C7—H7B	108.4
C12—N1—C8	127.0 (3)	C8—C7—H7B	108.4
C10—N1—C8	127.2 (3)	H7A—C7—H7B	107.5
C12—N2—C11	104.6 (3)	N1—C8—C9	111.5 (2)
C2—C1—C6	121.1 (4)	N1—C8—C7	112.0 (2)
C2—C1—H1B	119.4	C9—C8—C7	110.0 (2)
C6—C1—H1B	119.4	N1—C8—H8	107.7
C3—C2—C1	120.3 (3)	C9—C8—H8	107.7
C3—C2—H2	119.9	C7—C8—H8	107.7
C1—C2—H2	119.9	O1—C9—C8	112.7 (3)
C4—C3—C2	119.5 (3)	O1—C9—H9A	109.0
C4—C3—H3	120.3	C8—C9—H9A	109.0
C2—C3—H3	120.3	O1—C9—H9B	109.0
C3—C4—C5	120.1 (4)	C8—C9—H9B	109.0
C3—C4—H4	120.0	H9A—C9—H9B	107.8
C5—C4—H4	120.0	C11—C10—N1	106.6 (3)
C6—C5—C4	121.1 (3)	C11—C10—H1A	126.7
C6—C5—H5	119.4	N1—C10—H1A	126.7
C4—C5—H5	119.4	C10—C11—N2	110.0 (3)
C5—C6—C1	117.9 (3)	C10—C11—H11	125.0
C5—C6—C7	120.8 (3)	N2—C11—H11	125.0
C1—C6—C7	121.2 (3)	N2—C12—N1	113.0 (3)
C6—C7—C8	115.5 (3)	N2—C12—H12	123.5
C6—C7—H7A	108.4	N1—C12—H12	123.5

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N2^i	0.82	1.98	2.802 (4)	177

Symmetry code: (i) −x+2, y+1/2, −z.