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Crystal structure of 4-(pyrazin-2-yl)morpholine

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aInstitut für Biochemie, Ernst-Moritz-Arndt Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany, and bDepartment of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400 019, India
*Correspondence e-mail: carola.schulzke@uni-greifswald.de

Edited by P. Dastidar, Indian Association for the Cultivation of Science, India (Received 23 December 2017; accepted 5 January 2018; online 12 January 2018)

The mol­ecular structure of the title compound, C8H11N3O, is nearly planar despite the chair conformation of the morpholine moiety. In the crystal, the mol­ecules form sheets parallel to the b axis, which are supported by non-classical hydrogen-bonding inter­actions between C—H functionalities and the O atom of morpholine and the 4-N atom of pyrazine, respectively. The title compound crystallizes in the monoclinic space group P21/c with four mol­ecules in the unit cell.

1. Chemical context

The potential applications of aryl and heteroaryl amines in chemistry, materials science and pharmaceutical industries encourages research into the formation of C—N bonds (Rappoport, 2007[Rappoport, Z. (2007). Editor. The Chemistry of Anilines. Weinheim: Wiley-VCH.]; Lawrence, 2004[Lawrence, S. A. (2004). Editor. Amines: Synthesis, Properties, Application. Cambridge University Press.], Weissermel & Arpe 1997[Weissermel, K. & Arpe, H. J. (1997). Editors. Industrial Organic Chemistry. Weinheim: Wiley-VCH.]). N-Hetero­aryl­morpholine moieties are prevalent in biologically active mol­ecules such as medicines for the treatment of schizophrenia or type-2 diabetes mellitus (Bartolomé-Nebreda et al., 2014[Bartolomé-Nebreda, J. M., Delgado, F., Martín-Martín, M. L., Martínez-Viturro, C. M., Pastor, J., Tong, H. M., Iturrino, L., Macdonald, G. J., Sanderson, W., Megens, A., Langlois, X., Somers, M., Vanhoof, G. & Conde-Ceide, S. (2014). J. Med. Chem. 57, 4196-4212.]). In this context we are engaged in the synthesis of a library of heterocyclic amine derivatives. In course of these investigations, pure crystalline 4-(pyrazin-2-yl)morpholine was isolated with the crystals being obtained upon purification by column chromatography.

[Scheme 1]

2. Structural commentary

4-(Pyrazin-2-yl)morpholine (Fig. 1[link]) crystallizes in the monoclinic space group P21/c with four mol­ecules in the unit cell. There are reports in the literature of the mol­ecular structures of compounds in which the morpholine nitro­gen atom is coupled to the carbon atom of a non-annelated N-heterocyclic pyridine (Dahlgren et al., 2012[Dahlgren, M. K., Garcia, A. B., Hare, A. A., Tirado-Rives, J., Leng, L., Bucala, R. & Jorgensen, W. L. (2012). J. Med. Chem. 55, 10148-10159.]; Horton et al., 2012[Horton, P. N., Mohamed, S. K., Soliman, A. M., Abdel-Raheem, E. M. M. & Akkurt, M. (2012). Acta Cryst. E68, o885-o886.]; Huth et al., 2007[Huth, S. L., Hursthouse, M. B. & Withnell, J. (2007). University of Southampton, Crystal Structure Report Archive, 355.]; Klauschenz et al., 1994[Klauschenz, E., Hagen, V., Wiesner, B., Hagen, A., Reck, G. & Krause, E. G. (1994). Eur. J. Med. Chem. 29, 175-184.]; Li et al., 2014[Li, Q., Zhang, S.-Y., He, G., Ai, Z., Nack, W. A. & Chen, G. (2014). Org. Lett. 16, 1764-1767.], Reck et al., 1992[Reck, G., Hagen, V. & Bannier, G. (1992). Pharmazie, 47, 852-856.]) or pyrimidine (Cheprakova et al., 2014[Cheprakova, E. M., Verbitskiy, E. V., Ezhikova, M. A., Kodess, M. I., Pervova, M. G., Slepukhin, P. A., Toporova, M. S., Kravchenko, M. A., Medvinskiy, I. D., Rusinov, G. L. & Charushin, V. N. (2014). Russ. Chem. Bull. 63, 1350-1358.]; García et al., 2009[García, A., Insuasty, B., Cobo, J. & Glidewell, C. (2009). Acta Cryst. C65, o598-o600.]; Gorbunov et al., 2013[Gorbunov, E. B., Novikova, R. K., Plekhanov, P. V., Slepukhin, P. A., Rusinov, G. L., Rusinov, V. L., Charushin, V. N. & Chupakhin, O. N. (2013). Chem. Heterocycl. Compd, 49, 766-775.]; Hansen & Geffken, 2012[Hansen, F. K. & Geffken, D. (2012). J. Heterocycl. Chem. 49, 321-328.]; Vinogradova et al., 2016[Vinogradova, K. A., Krivopalov, V. P., Nikolaenkova, E. B., Pervukhina, N. V., Naumov, D. Y., Boguslavsky, E. G. & Bushuev, M. B. (2016). Dalton Trans. 45, 515-524.]). For pyrazine as the heterocycle, however, (to the best of our knowledge and after conducting a database search, see §4[link]) the present work constitutes the first structural report even though the title compound itself has been known since 1969 (Abe et al., 1969[Abe, Y., Shigeta, Y., Uchimaru, F. & Okada, S. (1969). Daiichi Seiyaku Co., Ltd. . JP44012739B.]).

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling and 50% probability displacement ellipsoids.

The orientation of the morpholine ring, in its typical chair conformation, relative to the aromatic plane can be either more or less in plane (e.g. Vinogradova et al., 2016[Vinogradova, K. A., Krivopalov, V. P., Nikolaenkova, E. B., Pervukhina, N. V., Naumov, D. Y., Boguslavsky, E. G. & Bushuev, M. B. (2016). Dalton Trans. 45, 515-524.]), tilted around the N—C bond (e.g. Li et al., 2014[Li, Q., Zhang, S.-Y., He, G., Ai, Z., Nack, W. A. & Chen, G. (2014). Org. Lett. 16, 1764-1767.]), bent away from the aromatic plane (e.g. Hansen & Geffken, 2012[Hansen, F. K. & Geffken, D. (2012). J. Heterocycl. Chem. 49, 321-328.]) or a combination of the latter two (e.g. Reck et al., 1992[Reck, G., Hagen, V. & Bannier, G. (1992). Pharmazie, 47, 852-856.]), depending on the other substituents on the heterocycle. In the present case, a morpholine ring is as much aligned with the N1/N2/C1–C4 plane as its conformation allows, with the carbon C8 showing the largest distance from the plane of 0.414 (1) Å. This distance is shorter than for any of the pyridine or pyrimidine derivatives without morpholine disorder from the reports mentioned above. The largest deviation from the plane of the pyrizine atoms was found to be 0.013 (1) Å for C1 and C4.

The quality of the crystallographic data allowed the hydrogen atoms to be located and refined entirely freely without any constraints or restraints. The information content of the metrical parameters involving the hydrogen atoms, including non-classical hydrogen-bonding inter­actions, is therefore comparably high. The C—H distances for the aromatic atoms are 0.999 (15) Å for C2, 0.976 (16) Å for C3 and 0.962 (16) Å for C4. The methyl­ene protons are in a distance range from their parent carbon atoms of 0.978 (14) to 1.016 (14) Å with a tendency for the longer C—H bond to be for the hydrogen atom in the axial position [only C7 is an exception with distances of 1.003 (14) Å for the axial and 1.005 (14) Å for the equatorial position]. All C—C, C—N and C—O bond lengths are within the commonly observed ranges.

3. Supra­molecular features

In the crystal, the mol­ecules form sheets parallel to the b axis supported by non-classical hydrogen-bonding inter­actions (Fig. 2[link], Table 1[link]). In each mol­ecule, the pyrazine ring is tilted slightly out of the general orientation of the sheets and the direction of the rotation alternates between adjacent rows (protruding along the b axis) as well as between adjacent layers with an angle of 17.95° between the two variants of torsion.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C6—H6A⋯O1i 0.988 (14) 2.561 (14) 3.4841 (16) 155.5 (10)
C3—H3⋯N2ii 0.976 (16) 2.670 (16) 3.5723 (19) 153.9 (13)
C2—H2⋯N2iii 0.999 (15) 2.743 (15) 3.6840 (19) 157.2 (11)
C4—H4⋯N1iv 0.962 (16) 2.787 (16) 3.6775 (18) 154.3 (11)
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (iii) x, y+1, z; (iv) x, y-1, z.
[Figure 2]
Figure 2
The crystal packing (Mercury; Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) viewed (top) along the c axis and (bottom) along the b axis showing the layered arrangement and the non-classical hydrogen-bonding inter­actions (Table 1[link]) between the mol­ecules of a sheet.

Within the sheets, each mol­ecule forms hydrogen-bonding interactions to six surrounding mol­ecules. These are donor inter­actions involving C2 [C2—H2⋯N2(x, y + 1, z)], C3 [C3—H3⋯N2(−x + 2, y + [{1\over 2}], −z + [{3\over 2}]], C4 [C4—H4⋯N1(x, y − 1, z)] and C6 [C6—H6A⋯O1(−x + 1, y + [{1\over 2}], −z + [{1\over 2}])] and acceptor inter­actions involving N1 [N1⋯H4—C4(x, y + 1, z)], N2 [N2⋯H2—C2(x, y − 1, z), N2⋯H3—C3(−x + 2, y + [{1\over 2}], −z + [{3\over 2}]] and O1 [O1⋯H6A—C6(1 − x, [{1\over 2}] + y, [{1\over 2}] − z)].

No ππ inter­actions are apparent between the sheets, with the closest distance between aromatic ring centroids being 4.2470 (11) Å while two sheets are 3.564 Å apart.

4. Synthesis and crystallization

The synthesis was carried out under an inert gas atmosphere (N2) applying the typical Schlenk line procedures. To an oven-dried Schlenk tube (25 mL) were added Pd(OAc)2 (1 mol%, 0.0024 g) and PTABS (phosphatriazene adamantyl butane saltone; 2 mol%, 0.00586 g) and a nitro­gen atmosphere was generated. To this were added 3 mL of dry DMF followed by the addition of 2-chloro­pyrazine (0.086 mL, 1mmol), 1.5 equivalents of tri­ethyl­amine (0.3 mL, 1.5 mmol) and 1.1 equivalent of morpholine (0.1 mL, 1.1 mmol). The suspension was stirred at room temperature for 4 h and progress of the reaction was monitored by TLC. After completion of the reaction, the crude product was purified and isolated by column chromatography in an EtOAc:hexane (1:3) solvent system. The final sharp colourless needles (0.124 mg, 0.83 mmol, 83%) were obtained directly after the column purification step by crystallizing from the eluent. The mounted crystal was a block cut from a large needle. The compound has a low melting point of only 318 K and the crystals were stored in the fridge until they were measured.

1H NMR (300 MHz, chloro­form-d) δ ppm 3.51–3.63 (m, 4 H), 3.79–3.90 (m, 4 H), 7.90 (d, J = 2.64 Hz, 1 H), 8.14 (d, J = 7.6Hz, 1 H), 9.61 (d, J = 7.8 Hz, 1 H). 13C NMR (75 MHz, chloro­form-d) δ ppm 45.18 (s, 1C) 66.93 (s, 1C) 77.42 (s, 1C) 77.84 (s, 1C) 131.33 (s, 1C) 133.98 (s, 1C) 142.16 (s, 1C) 155.48 (s, 1C). ESI–MS (m/z) = 166.17 (M + H)+, 167.22 (M + 2H)2+ (cf. Graham et al., 2011[Graham, T. H., Liu, W. & Shen, D.-M. (2011). Org. Lett. 13, 6232-6235.]).

5. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All hydrogen atoms were located and refined freely without any constraints or restraints.

Table 2
Experimental details

Crystal data
Chemical formula C8H11N3O
Mr 165.20
Crystal system, space group Monoclinic, P21/c
Temperature (K) 170
a, b, c (Å) 17.069 (3), 5.9278 (12), 7.8053 (16)
β (°) 90.54 (3)
V3) 789.7 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.10
Crystal size (mm) 0.38 × 0.31 × 0.26
 
Data collection
Diffractometer Stoe IPDS2T
No. of measured, independent and observed [I > 2σ(I)] reflections 6583, 1666, 1285
Rint 0.044
(sin θ/λ)max−1) 0.634
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.081, 1.01
No. of reflections 1666
No. of parameters 153
H-atom treatment All H-atom parameters refined
Δρmax, Δρmin (e Å−3) 0.19, −0.18
Computer programs: X-AREA (Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA. Stoe & Cie, Darmstadt, Germany.]), SHELXT2016 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2016 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), XP in SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) and CIFTAB (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Computing details top

Data collection: X-AREA (Stoe & Cie, 2010); cell refinement: X-AREA (Stoe & Cie, 2010); data reduction: X-AREA (Stoe & Cie, 2010); program(s) used to solve structure: SHELXT2016 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006); software used to prepare material for publication: CIFTAB (Sheldrick, 2008).

4-(Pyrazin-2-yl)morpholine top
Crystal data top
C8H11N3OF(000) = 352
Mr = 165.20Dx = 1.389 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 17.069 (3) ÅCell parameters from 7070 reflections
b = 5.9278 (12) Åθ = 5.2–53.6°
c = 7.8053 (16) ŵ = 0.10 mm1
β = 90.54 (3)°T = 170 K
V = 789.7 (3) Å3Block, colourless
Z = 40.38 × 0.31 × 0.26 mm
Data collection top
Stoe IPDS2T
diffractometer
1285 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.044
Detector resolution: 6.67 pixels mm-1θmax = 26.8°, θmin = 3.6°
ω scansh = 2121
6583 measured reflectionsk = 77
1666 independent reflectionsl = 99
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032All H-atom parameters refined
wR(F2) = 0.081 w = 1/[σ2(Fo2) + (0.0391P)2 + 0.1242P]
where P = (Fo2 + 2Fc2)/3
S = 1.01(Δ/σ)max < 0.001
1666 reflectionsΔρmax = 0.19 e Å3
153 parametersΔρmin = 0.18 e Å3
Special details top

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
O10.56805 (5)0.49320 (14)0.28629 (10)0.0288 (2)
N10.80725 (6)0.78798 (17)0.57424 (13)0.0273 (2)
N20.91130 (6)0.4299 (2)0.62453 (16)0.0389 (3)
N30.71160 (5)0.53996 (16)0.47126 (12)0.0225 (2)
C10.78753 (7)0.57747 (19)0.53119 (14)0.0227 (3)
C20.87897 (7)0.8160 (2)0.64356 (18)0.0327 (3)
C30.93002 (8)0.6409 (2)0.66999 (19)0.0370 (3)
C40.84119 (7)0.4000 (2)0.55398 (17)0.0318 (3)
C50.66501 (6)0.73760 (19)0.42267 (15)0.0226 (3)
C60.57955 (7)0.6729 (2)0.40626 (15)0.0255 (3)
C70.61043 (7)0.3001 (2)0.34360 (16)0.0271 (3)
C80.69742 (7)0.3467 (2)0.35819 (15)0.0258 (3)
H6B0.5600 (7)0.621 (2)0.5203 (17)0.028 (3)*
H5B0.6834 (7)0.804 (2)0.3125 (16)0.023 (3)*
H5A0.6694 (7)0.853 (2)0.5118 (17)0.027 (3)*
H8B0.7235 (8)0.210 (3)0.4052 (17)0.031 (4)*
H7B0.5899 (7)0.248 (2)0.4570 (17)0.029 (3)*
H6A0.5487 (8)0.802 (2)0.3624 (16)0.028 (3)*
H40.8289 (8)0.248 (3)0.5193 (18)0.038 (4)*
H7A0.6002 (8)0.177 (2)0.2579 (17)0.028 (3)*
H8A0.7193 (8)0.380 (2)0.2402 (17)0.034 (4)*
H20.8931 (8)0.975 (3)0.6735 (17)0.035 (4)*
H30.9810 (9)0.670 (3)0.723 (2)0.049 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0287 (5)0.0263 (5)0.0310 (4)0.0026 (4)0.0104 (3)0.0010 (3)
N10.0217 (5)0.0252 (5)0.0348 (6)0.0007 (4)0.0041 (4)0.0036 (4)
N20.0255 (6)0.0337 (6)0.0571 (7)0.0040 (5)0.0100 (5)0.0021 (5)
N30.0200 (5)0.0191 (5)0.0283 (5)0.0005 (4)0.0037 (4)0.0012 (4)
C10.0199 (5)0.0240 (6)0.0242 (5)0.0006 (4)0.0009 (4)0.0009 (4)
C20.0251 (6)0.0303 (7)0.0427 (7)0.0023 (5)0.0065 (5)0.0042 (6)
C30.0219 (6)0.0382 (8)0.0507 (8)0.0016 (6)0.0094 (6)0.0013 (6)
C40.0259 (6)0.0247 (6)0.0448 (7)0.0013 (5)0.0057 (5)0.0011 (5)
C50.0215 (6)0.0212 (5)0.0251 (6)0.0003 (5)0.0023 (4)0.0003 (5)
C60.0222 (6)0.0245 (6)0.0297 (6)0.0005 (5)0.0039 (5)0.0006 (5)
C70.0300 (6)0.0228 (6)0.0282 (6)0.0044 (5)0.0054 (5)0.0005 (5)
C80.0286 (6)0.0209 (6)0.0279 (6)0.0001 (5)0.0024 (5)0.0023 (5)
Geometric parameters (Å, º) top
O1—C71.4238 (15)C3—H30.976 (16)
O1—C61.4307 (14)C4—H40.962 (16)
N1—C11.3345 (15)C5—C61.5126 (16)
N1—C21.3441 (16)C5—H5B0.999 (13)
N2—C41.3244 (16)C5—H5A0.978 (14)
N2—C31.3381 (18)C6—H6B1.002 (13)
N3—C11.3917 (15)C6—H6A0.988 (14)
N3—C51.4639 (15)C7—C81.5135 (17)
N3—C81.4648 (14)C7—H7B1.003 (14)
C1—C41.4051 (17)C7—H7A1.005 (14)
C2—C31.3693 (19)C8—H8B0.995 (15)
C2—H20.999 (15)C8—H8A1.016 (14)
C7—O1—C6109.07 (9)N3—C5—H5A109.7 (8)
C1—N1—C2116.31 (10)C6—C5—H5A107.7 (8)
C4—N2—C3116.61 (11)H5B—C5—H5A108.3 (10)
C1—N3—C5117.46 (9)O1—C6—C5111.74 (10)
C1—N3—C8118.39 (9)O1—C6—H6B108.0 (7)
C5—N3—C8112.55 (9)C5—C6—H6B109.3 (7)
N1—C1—N3117.76 (10)O1—C6—H6A106.3 (7)
N1—C1—C4120.38 (11)C5—C6—H6A110.1 (8)
N3—C1—C4121.79 (11)H6B—C6—H6A111.4 (10)
N1—C2—C3122.88 (12)O1—C7—C8111.85 (10)
N1—C2—H2115.3 (8)O1—C7—H7B110.0 (8)
C3—C2—H2121.9 (8)C8—C7—H7B109.9 (7)
N2—C3—C2121.23 (12)O1—C7—H7A106.9 (7)
N2—C3—H3119.1 (10)C8—C7—H7A110.3 (8)
C2—C3—H3119.7 (10)H7B—C7—H7A107.8 (11)
N2—C4—C1122.53 (12)N3—C8—C7110.14 (10)
N2—C4—H4115.9 (9)N3—C8—H8B110.2 (8)
C1—C4—H4121.6 (9)C7—C8—H8B108.3 (8)
N3—C5—C6109.88 (10)N3—C8—H8A109.6 (8)
N3—C5—H5B111.4 (7)C7—C8—H8A109.6 (8)
C6—C5—H5B109.7 (7)H8B—C8—H8A108.9 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C6—H6A···O1i0.988 (14)2.561 (14)3.4841 (16)155.5 (10)
C3—H3···N2ii0.976 (16)2.670 (16)3.5723 (19)153.9 (13)
C2—H2···N2iii0.999 (15)2.743 (15)3.6840 (19)157.2 (11)
C4—H4···N1iv0.962 (16)2.787 (16)3.6775 (18)154.3 (11)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+2, y+1/2, z+3/2; (iii) x, y+1, z; (iv) x, y1, z.
 

Funding information

ARK and CS acknowledges `The Alexander von Humboldt Foundation' for the research cooperation programme and the equipment grant to ARK. CS gratefully acknowledges funding from the ERC for the project MocoModels.

References

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