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

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aInstitut für Organische Chemie, TU Bergakademie Freiberg, Leipziger Strasse 29, D-09596 Freiberg/Sachsen, Germany
*Correspondence e-mail: edwin.weber@chemie.tu-freiberg.de

Edited by O. Blacque, University of Zürich, Switzerland (Received 30 June 2017; accepted 6 July 2017; online 13 July 2017)

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.

1. 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[MacGillivray, L. R. (2010). In Metal-Organic Frameworks. Hoboken: Wiley.]) and metal-organic frameworks (Noro & Kitagawa, 2010[Noro, S.-I. & Kitagawa, S. (2010). The Supramolecular Chemistry of Organic Hybrid Materials, edited by K. Rurack & R. Martinez-Mánez, pp. 235-269. Chichester: Wiley.]). 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[Hübscher, J., Seichter, W., Gruber, T., Kortus, J. & Weber, E. (2015). J. Heterocycl. Chem. 52, 1062-1074.]; Günthel et al., 2015[Günthel, M., Hübscher, J., Dittrich, R., Weber, E., Joseph, I. & Mertens, F. (2015). J. Polym. Sci. Part B Polym. Phys. 53, 335-344.]; Hübscher et al., 2017[Hübscher, J., Seichter, W. & Weber, E. (2017). CrystEngComm, 19, 3026-3036.]). 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[Toda, F., Tanaka, K., Ueda, H. & Oshima, T. (1983). J. Chem. Soc. Chem. Commun. pp. 743-744.], 1985[Toda, F., Tanaka, K., Ueda, H. & Ōshima, T. (1985). Isr. J. Chem. 25, 338-345.]; Bourne et al., 1994[Bourne, S. A., Caira, M. R., Nassimbeni, L. R., Sakamoto, M., Tanaka, K. & Toda, F. (1994). J. Chem. Soc. Perkin Trans. 2, pp. 1899-1900.]). 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[Wang, L.-C. & Zheng, Q.-Y. (2015). In Hydrogen Bonded Supramolecular Structures. Lecture Notes in Supramolecular Chemistry, edited by Z.-T. Li & L. Z. Wu, Vol. 87, pp. 69-113. Berlin, Heidelberg: Springer.]) and potential halogen (Mukherjee et al., 2014[Mukherjee, A., Tothadi, S. & Desiraju, G. R. (2014). Acc. Chem. Res. 47, 2514-2524.]) or π-electron assisted (Tiekink & Zukerman-Schpector, 2012[Tiekink, E. R. T. & Zukerman-Schpector, J. (2012). In The Importance of Pi-Interactions in Crystal Engineering. Frontiers in Crystal Engineering. Chichester: Wiley.]) inter­actions should be a promising field of inquiry for crystal engineering (Desiraju et al., 2012[Desiraju, G. R. , Vittal, G. G. & Ramonau, A. (2012). In Crystal Engineering. London: Imperial College Press.]) 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.

[Scheme 1]

2. Structural commentary

A perspective view of the mol­ecular structure of the title compound is depicted in Fig. 1[link]. 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]
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.

3. Supra­molecular features

An O—H⋯πC≡C hydrogen-bond type inter­molecular inter­action mode typical of 3-hy­droxy­alkyne structure units (Desiraju & Steiner, 1999[Desiraju, G. R. & Steiner, T. (1999). The Weak Hydrogen Bond. IUCr Monographs on Crystallography, Vol. 9, ch. 3, p. 164. Oxford University Press.]) 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[link], Fig. 2[link]). 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≡C hydrogen bonding is suppressed, which could be a useful finding in relation to aspects of crystal engineering.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C8—H8A⋯Cl1i 0.98 2.99 3.7911 (14) 140
C4—H4⋯O1ii 0.95 2.45 3.1963 (15) 136
C2—H2⋯O1iii 0.95 2.60 3.2816 (14) 129
O1—H1⋯N2iv 0.84 2.05 2.8881 (13) 172
Symmetry codes: (i) [-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) -x+1, -y, -z+1; (iii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iv) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
Packing excerpt of the title compound. Hydrogen bonds are shown as dashed lines.

4. 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[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) 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[Hübscher, J., Seichter, W., Gruber, T., Kortus, J. & Weber, E. (2015). J. Heterocycl. Chem. 52, 1062-1074.]). In this case, the absence of a strongly coordinating donor/acceptor substituent results in poor mol­ecular association, which is restricted to πpyrimidineπethyne stacking inter­actions.

5. Synthesis and crystallization

The title compound was prepared from 2-hy­droxy-5-iodo­pyrimidine (Pérez-Palado et al., 2007[Pérez-Balado, C., Ormerod, D., Aelterman, W. & Mertens, N. (2007). Org. Process Res. Dev. 11, 237-240.]) and 2-methyl-3-butyn-2-ol (MEBYNOL) via a Shonogashira–Hagihara cross-coupling reaction (Sonogashira et al., 1975[Sonogashira, K., Tohda, Y. & Hagihara, N. (1975). Tetrahedron Lett. 16, 4467-4470.]) 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≡C), 74.1 (pyr-C≡C), 65.5 (Cquat.), 31.1 (CH3). IR (KBr) νmax. 2240 (C≡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.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. 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 Uiso(H) = 1.5Ueq(C,O) for methyl and hy­droxy H atoms and 1.2Ueq(C) for aryl H atoms.

Table 2
Experimental details

Crystal data
Chemical formula C9H9ClN2O
Mr 196.63
Crystal system, space group Monoclinic, P21/n
Temperature (K) 153
a, b, c (Å) 7.5555 (3), 13.0278 (7), 9.7397 (5)
β (°) 91.767 (2)
V3) 958.24 (8)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.36
Crystal size (mm) 0.60 × 0.60 × 0.20
 
Data collection
Diffractometer Bruker X8 APEX2 CCD detector
Absorption correction Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.814, 0.932
No. of measured, independent and observed [I > 2σ(I)] reflections 8464, 1988, 1795
Rint 0.021
(sin θ/λ)max−1) 0.628
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.074, 1.07
No. of reflections 1988
No. of parameters 121
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.22, −0.26
Computer programs: APEX2 and SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2015 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]).

Supporting information


Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2015 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

2-Chloro-5-(3-hydroxy-3-methylbut-1-yn-1-yl)pyrimidine top
Crystal data top
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 top
Bruker X8 APEX2 CCD detector
diffractometer
1795 reflections with I > 2σ(I)
φ and ω scansRint = 0.021
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
θmax = 26.5°, θmin = 2.6°
Tmin = 0.814, Tmax = 0.932h = 99
8464 measured reflectionsk = 1516
1988 independent reflectionsl = 1012
Refinement top
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) = 0.074 w = 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 top

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) top
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)
H8A0.16100.11820.70040.044*
H8B0.00370.05030.74570.044*
H8C0.10700.11540.85800.044*
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) top
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) top
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—C5179.66 (11)
C2—N2—C1—N10.89 (19)C1—N1—C4—C30.82 (17)
C2—N2—C1—Cl1179.91 (8)C2—C3—C4—N11.05 (18)
C1—N2—C2—C30.58 (17)C5—C3—C4—N1178.91 (11)
Hydrogen-bond geometry (Å, º) top
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, y1/2, 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 information

This work was supported by the Deutsche Forschungsgemeinschaft (DFG) under the program SPP 1362/1 and by the European Union (European Regional Development Fund) including the Ministry of Science and Art of Saxony (Cluster of Excellence "Structure Design of Novel High-Performance Materials via Atomic Design and Defect Engineering, ADDE").

References

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