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Logo of actae2this articlesearchopen accesssubmitActa Crystallographica Section E: Crystallographic CommunicationsActa Crystallographica Section E: Crystallographic Communications
 
Acta Crystallogr E Crystallogr Commun. 2017 July 1; 73(Pt 8): 1172–1174.
Published online 2017 July 13. doi:  10.1107/S2056989017010027
PMCID: PMC5598842

Crystal structure of 2-chloro-5-(3-hy­droxy-3-methyl­but-1-yn-1-yl)pyrimidine

Abstract

In the title compound, C9H9ClN2O, the ethynyl­pyrimidine moiety displays an almost planar geometry. In the crystal, mol­ecules are linked by O—H(...)N and C—Hpyrimidine(...)O hydrogen bonds, forming a three-dimensional supra­molecular architecture.

Keywords: crystal structure, 5-ethynyl­pyrimidine derivative, O—H(...)N hydrogen bonding, C—H(...)O contact

Chemical context  

The title compound, featuring a blocked acetyl­enic group and a chloro-substituted pyrimidine ring, is an inter­esting synthetic inter­mediate for the preparation of application-oriented solid materials including both porous coordination polymers (MacGillivray, 2010  ) and metal-organic frameworks (Noro & Kitagawa, 2010  ). Deprotection of the acetyl­enic functional group and transformation of the chloro substituent, e.g. into thiol or amino groups, should result in mol­ecular building blocks for the formation of corresponding aggregate structures (Hübscher et al., 2015  ; Günthel et al., 2015  ; Hübscher et al., 2017  ). Aside from this experimental preparative relevance, substituted 3-hy­droxy­alkynes are also of considerable inter­est due to their structural capacity in supra­molecular inter­actions, giving rise to particular modes of aggregation and behavior in the solid state (Toda et al., 1983  , 1985  ; Bourne et al., 1994  ). In combination with heterocyclic nitro­gen donors and chlorine substitution, as in the present title compound, a structural study involving competition aspects with regard to hydrogen bonding (Wang & Zheng, 2015  ) and potential halogen (Mukherjee et al., 2014  ) or π-electron assisted (Tiekink & Zukerman-Schpector, 2012  ) inter­actions should be a promising field of inquiry for crystal engineering (Desiraju et al., 2012  ) being subject to the contacts emanating from a variety of functional groups. Thus, in this respect, the title compound could serve as a worthwhile test substance.

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Structural commentary  

A perspective view of the mol­ecular structure of the title compound is depicted in Fig. 1  . The ethynyl­pyrimidine moiety of the mol­ecule is almost planar with the largest atomic distances from the mean plane being 0.015 (1) Å for atom C1 and 0.013 (1) Å for atom C4. The OH group adopts a staggered arrangement with respect to the ethynyl unit and the methyl group C9, the C6—C7—O1–H1 torsion angle being 57.0°.

Figure 1
Perspective view of the mol­ecular structure of the title compound including the atom-numbering scheme. Displacement parameters are drawn at the 50% probability level.

Supra­molecular features  

An O—H(...)πC[equivalent]C hydrogen-bond type inter­molecular inter­action mode typical of 3-hy­droxy­alkyne structure units (Desiraju & Steiner, 1999  ) is not present here, apparently in favor of a stronger O—H(...)N hydrogen bond involving the hy­droxy group and a pyrimidine nitro­gen atom (N2). Aside from this, C—Hpyrimidine(...)O hydrogen bonds are found to yield a three-dimensional supra­molecular architecture (Table 1  , Fig. 2  ). No other types of directed inter­molecular contacts, including those involving the Cl atom or π–arene stacking, are observed. Hence, this shows that in the presence of a strong donor center such as a nitro­gen atom, competing with the acetyl­enic moiety, the common O—H(...)πC[equivalent]C hydrogen bonding is suppressed, which could be a useful finding in relation to aspects of crystal engineering.

Figure 2
Packing excerpt of the title compound. Hydrogen bonds are shown as dashed lines.
Table 1
Hydrogen-bond geometry (Å, °)

Database survey  

The title compound represents the first example of a 5-(3-hy­droxy-3-methyl­but-1-yn-1-yl)pyrimidine. A search in the Cambridge Structural Database (CSD, Version 5.38, update February 2017; Groom et al., 2016  ) for compounds containing the 4-ethynyl­pyrimidine fragment excluding metal complexes and co-crystals revealed nine hits. Of particular inter­est is the crystal structure of 5,5′-ethyne-1,2-diylbis(2-chloro­pyrimidine) (refcode: PUMHIQ; Hübscher et al., 2015  ). In this case, the absence of a strongly coordinating donor/acceptor substituent results in poor mol­ecular association, which is restricted to πpyrimidine(...)πethyne stacking inter­actions.

Synthesis and crystallization  

The title compound was prepared from 2-hy­droxy-5-iodo­pyrimidine (Pérez-Palado et al., 2007  ) and 2-methyl-3-butyn-2-ol (MEBYNOL) via a Shonogashira–Hagihara cross-coupling reaction (Sonogashira et al., 1975  ) as follows. 2-Chloro-5-iodo­pyrimidine (2.0 g, 8.4 mmol) and MEBYNOL (0.7 g, 8.7 mmol) were dissolved in a degassed mixture of dry diiso­propyl­amine and THF (60 ml each). To this solution, the catalyst being composed of tri­phenyl­phosphine (2 mol%), copper(I) and iodide (3 mol-%) and trans-di­chloro­bis­(tri­phenyl­phosphine)palladium(II) (2 mol%) was added. The mixture was stirred at room temperature away from light for 12 h, then filtered over Celite and evaporated. Crystallization from n-hexane gave colourless crystals of the title compound on slow evaporation of the solvent (yield 1.1 g, 70%; m.p. 455 K). 1H NMR (CDCl3): δH 8.64 (2H, s, pyr-H), 2.67 (1H, s, OH), 1.64 (6H, s, Me). 13C NMR (CDCl3): δC 161.1 (pyrC-4), 159.4 (pyrC-2), 117.8 (pyrC-5), 102.4 (pyr-C[equivalent]C), 74.1 (pyr-C[equivalent]C), 65.5 (Cquat.), 31.1 (CH3). IR (KBr) νmax. 2240 (C[equivalent]C). GC–MS: calculated for C9H9N2OCl (196.04), found 196 [M]+. Analysis calculated for C9H9N2OCl: C, 54.97; H, 4.61; N, 14.25; found: C, 54.81; H, 4.56; N, 14.05%. Colourless crystals suitable for X-ray diffraction were obtained by slow evaporation of solvent from a chloro­form solution.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2  . H atoms were included in calculated positions (C—H = 0.95, 0.98 Å; O—H = 0.84 Å) and allowed to ride on their parent atoms with U iso(H) = 1.5U eq(C,O) for methyl and hy­droxy H atoms and 1.2U eq(C) for aryl H atoms.

Table 2
Experimental details

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017010027/zq2237sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017010027/zq2237Isup2.hkl

CCDC reference: 1560599

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

supplementary crystallographic information

Crystal data

C9H9ClN2OF(000) = 408
Mr = 196.63Dx = 1.363 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.5555 (3) ÅCell parameters from 5586 reflections
b = 13.0278 (7) Åθ = 2.6–29.2°
c = 9.7397 (5) ŵ = 0.36 mm1
β = 91.767 (2)°T = 153 K
V = 958.24 (8) Å3Block, colourless
Z = 40.60 × 0.60 × 0.20 mm

Data collection

Bruker X8 APEX2 CCD detector diffractometer1795 reflections with I > 2σ(I)
[var phi] and ω scansRint = 0.021
Absorption correction: multi-scan (SADABS; Bruker, 2008)θmax = 26.5°, θmin = 2.6°
Tmin = 0.814, Tmax = 0.932h = −9→9
8464 measured reflectionsk = −15→16
1988 independent reflectionsl = −10→12

Refinement

Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.027H-atom parameters constrained
wR(F2) = 0.074w = 1/[σ2(Fo2) + (0.0363P)2 + 0.3033P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
1988 reflectionsΔρmax = 0.22 e Å3
121 parametersΔρmin = −0.26 e Å3

Special details

Experimental. The melting point was measured using a microscope heating stage (Thermovar, Reichert–Jung). The NMR spectra were obtained on a Bruker Avance 500.1 (1H) and 125.8 MHz (13C) with TMS as internal standard (δ in ppm). The IR spectrum was determined on a Nicolet FT–IR 510 spectrometer as KBr pellet (wavenumber is given in cm-1). The mass spectrum was recorded on a Hewlett–Packard 5890 Series II/MS 5989A. Elemental analysis was carried out with a Hanau vario MICRO cube.
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/Ueq
Cl10.23192 (4)0.39748 (3)0.09166 (3)0.03135 (12)
O10.40922 (11)−0.02601 (6)0.82873 (9)0.0229 (2)
H10.48360.02170.83680.034*
N10.33701 (13)0.23553 (8)0.22655 (10)0.0237 (2)
N20.14057 (13)0.34952 (8)0.33846 (10)0.0227 (2)
C10.23671 (15)0.31831 (9)0.23470 (12)0.0205 (2)
C20.14420 (15)0.28822 (9)0.44881 (12)0.0219 (3)
H20.07680.30660.52580.026*
C30.24367 (15)0.19835 (9)0.45432 (12)0.0196 (2)
C40.34057 (16)0.17568 (9)0.33843 (12)0.0228 (3)
H40.41170.11550.33890.027*
C50.24486 (15)0.13360 (10)0.57316 (12)0.0222 (3)
C60.24267 (15)0.08049 (9)0.67312 (12)0.0221 (3)
C70.23766 (15)0.01625 (9)0.79857 (12)0.0205 (2)
C80.11447 (17)−0.07507 (11)0.77342 (14)0.0292 (3)
H8A0.1610−0.11820.70040.044*
H8B−0.0037−0.05030.74570.044*
H8C0.1070−0.11540.85800.044*
C90.17864 (17)0.08197 (11)0.91878 (13)0.0281 (3)
H9A0.18250.04081.00300.042*
H9B0.05740.10620.90030.042*
H9C0.25810.14100.93000.042*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.03714 (19)0.0336 (2)0.02359 (18)0.00504 (13)0.00606 (13)0.01072 (12)
O10.0209 (4)0.0193 (4)0.0288 (5)0.0002 (3)0.0028 (3)0.0023 (3)
N10.0271 (5)0.0234 (5)0.0209 (5)0.0017 (4)0.0062 (4)−0.0002 (4)
N20.0255 (5)0.0229 (5)0.0197 (5)0.0039 (4)0.0020 (4)0.0003 (4)
C10.0221 (5)0.0213 (6)0.0180 (6)−0.0013 (4)0.0010 (4)0.0017 (4)
C20.0238 (6)0.0246 (6)0.0174 (6)0.0019 (5)0.0031 (4)−0.0024 (5)
C30.0211 (5)0.0200 (6)0.0176 (6)−0.0021 (4)0.0003 (4)−0.0005 (4)
C40.0265 (6)0.0194 (6)0.0228 (6)0.0024 (5)0.0043 (5)−0.0004 (5)
C50.0228 (6)0.0224 (6)0.0215 (6)0.0003 (5)0.0033 (5)−0.0015 (5)
C60.0231 (6)0.0222 (6)0.0213 (6)0.0007 (5)0.0041 (5)−0.0007 (5)
C70.0202 (5)0.0224 (6)0.0189 (6)−0.0001 (4)0.0032 (4)0.0023 (5)
C80.0298 (6)0.0314 (7)0.0264 (6)−0.0090 (5)0.0016 (5)0.0032 (5)
C90.0287 (6)0.0330 (7)0.0230 (6)0.0040 (5)0.0075 (5)0.0000 (5)

Geometric parameters (Å, º)

Cl1—C11.7329 (12)C4—H40.9500
O1—C71.4304 (14)C5—C61.1950 (18)
O1—H10.8400C6—C71.4824 (16)
N1—C11.3219 (16)C7—C81.5257 (17)
N1—C41.3396 (16)C7—C91.5280 (17)
N2—C11.3265 (16)C8—H8A0.9800
N2—C21.3386 (15)C8—H8B0.9800
C2—C31.3914 (17)C8—H8C0.9800
C2—H20.9500C9—H9A0.9800
C3—C41.3958 (17)C9—H9B0.9800
C3—C51.4320 (16)C9—H9C0.9800
C7—O1—H1109.5O1—C7—C8106.10 (10)
C1—N1—C4115.04 (10)C6—C7—C8109.81 (10)
C1—N2—C2115.51 (10)O1—C7—C9110.02 (9)
N1—C1—N2128.63 (11)C6—C7—C9109.31 (10)
N1—C1—Cl1115.79 (9)C8—C7—C9111.65 (10)
N2—C1—Cl1115.58 (9)C7—C8—H8A109.5
N2—C2—C3122.05 (11)C7—C8—H8B109.5
N2—C2—H2119.0H8A—C8—H8B109.5
C3—C2—H2119.0C7—C8—H8C109.5
C2—C3—C4116.30 (11)H8A—C8—H8C109.5
C2—C3—C5121.11 (11)H8B—C8—H8C109.5
C4—C3—C5122.59 (11)C7—C9—H9A109.5
N1—C4—C3122.47 (11)C7—C9—H9B109.5
N1—C4—H4118.8H9A—C9—H9B109.5
C3—C4—H4118.8C7—C9—H9C109.5
C6—C5—C3178.65 (13)H9A—C9—H9C109.5
C5—C6—C7178.79 (13)H9B—C9—H9C109.5
O1—C7—C6109.91 (9)
C4—N1—C1—N20.20 (19)N2—C2—C3—C40.30 (17)
C4—N1—C1—Cl1179.40 (9)N2—C2—C3—C5−179.66 (11)
C2—N2—C1—N1−0.89 (19)C1—N1—C4—C30.82 (17)
C2—N2—C1—Cl1179.91 (8)C2—C3—C4—N1−1.05 (18)
C1—N2—C2—C30.58 (17)C5—C3—C4—N1178.91 (11)

Hydrogen-bond geometry (Å, º)

D—H···AD—HH···AD···AD—H···A
C8—H8A···Cl1i0.982.993.7911 (14)140
C4—H4···O1ii0.952.453.1963 (15)136
C2—H2···O1iii0.952.603.2816 (14)129
O1—H1···N2iv0.842.052.8881 (13)172

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

Funding Statement

This work was funded by Deutsche Forschungsgemeinschaft grant . European Regional Development Fund grant . Ministry of Science and Art of Saxony grant .

This paper was supported by the following grant(s):

Deutsche Forschungsgemeinschaft .
European Regional Development Fund .
Ministry of Science and Art of Saxony .

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