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ISSN: 2056-9890

4-Morpholine­carboxamidine

aFakultät Chemie/Organische Chemie, Hochschule Aalen, Beethovenstrasse 1, D-73430 Aalen, Germany
*Correspondence e-mail: Ioannis.Tiritiris@htw-aalen.de

(Received 5 October 2012; accepted 8 October 2012; online 13 October 2012)

In the crystal structure of the title compound, C5H11N3O, the C=N and C—N bond lengths in the CN3 unit are 1.2971 (14), 1.3595 (14) (NH2) and 1.3902 (13) Å, indicating double- and single-bond character, respectively. The N—C—N angles are 115.49 (9)°, 119.68 (10)° and 124.83 (10)°, showing a deviation of the CN3 plane from an ideal trigonal–planar geometry. The morpholine ring is in a chair conformation. In the crystal, the mol­ecules are linked by N—H⋯N and N—H⋯O hydrogen bonds, generating a three-dimensional network.

Related literature

For the synthesis of carboxamides by amidination of secondary amines with 4-benzyl-3,5-dimethyl-1H-pyrazole-1-carboxamidine hydro­chloride, see: Dräger et al. (2002[Dräger, G., Solodenko, W., Messinger, J., Schön, U. & Kirschning, A. (2002). Tetrahedron Lett. 43, 1401-1403.]). For the crystal structure of 4,4′-carbonyl-dimorpholine, see: Zhou et al. (2003[Zhou, W. Q., Zhu, L. M., Cao, Zh. B., Zhang, Y., Lu, W. D. & Lu, L. D. (2003). J. Mol. Struct. 565, 405-411.]).

[Scheme 1]

Experimental

Crystal data
  • C5H11N3O

  • Mr = 129.17

  • Tetragonal, I 41 /a

  • a = 16.5910 (6) Å

  • c = 9.7939 (3) Å

  • V = 2695.9 (2) Å3

  • Z = 16

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 100 K

  • 0.17 × 0.15 × 0.13 mm

Data collection
  • Bruker–Nonius KappaCCD diffractometer

  • 2889 measured reflections

  • 1628 independent reflections

  • 1341 reflections with I > 2σ(I)

  • Rint = 0.022

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.091

  • S = 1.06

  • 1628 reflections

  • 94 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.27 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N2—H21⋯N1i 0.90 (2) 2.03 (2) 2.930 (1) 174 (1)
N2—H22⋯O1ii 0.88 (2) 2.13 (2) 3.007 (1) 174 (1)
Symmetry codes: (i) [y-{\script{1\over 4}}, -x-{\script{1\over 4}}, z-{\script{1\over 4}}]; (ii) [-y+{\script{1\over 4}}, x-{\script{1\over 4}}, z-{\script{1\over 4}}].

Data collection: COLLECT (Hooft, 2004[Hooft, R. W. W. (2004). COLLECT. Nonius BV, Delft, The Netherlands.]); cell refinement: SCALEPACK (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

4-Morpholine-carboxamidine is a guanidine derivative, bearing one morpholine moiety. It can be synthesized in a two-step synthesis by reacting first O-methylisourea sulfate with two equivalents of morpholine, giving the salt 4-morpholine-carboxamidinium sulfate (I). After deprotonation of (I) with a strong base, the carboxamidine can be isolated in good yield. Similar compounds have also been synthesized by amidination of secondary amines with 4-benzyl-3,5-dimethyl-1H-pyrazole-1-carboxamidine hydrochloride (Dräger et al., 2002). In order to study the CO2 absorption ability of carboxamides, the title compound was prepared. Since its crystal structure was not known so far, it was decided to carry out an appropriate investigation. According to the structure analysis, the C1–N1 bond in the title compound is 1.2971 (14) Å, indicating double bond character. The bond lengths C1–N2 = 1.3595 (14) Å and C1–N3 = 1.3902 (13) Å are elongated and characteristic for a C–N amine single bond (Fig. 1). The N–C1–N angles are: 115.49 (9)° (N2–C1–N3), 119.68 (10)° (N1–C1–N3) and 124.83 (10)° (N1–C1–N2), showing a deviation of the CN3 plane from an ideal trigonal-planar geometry. The structural parameters of the morpholine ring in the here presented title compound agree very well with the data obtained from the X-ray analysis of the urea 4,4'-carbonyl-di-morpholine (Zhou et al., 2003). In both crystal structures the morpholine rings adopt a chair conformation. Strong N—H···N and N—H···O hydrogen bonds between nitrogen atoms and oxygen atoms of neighboring molecules have been determined [d(H···N) = 2.03 (2) Å and d(H···O) = 2.13 (2) Å] (Tab. 1). Every carboxamidine molecule is sourrounded by four neighboring molecules (Fig. 2), generating a three-dimensional network (Fig. 3). In contrast, the imine hydrogen atom H11 is not involved in the hydrogen bonding system.

Related literature top

For the synthesis of carboxamides by amidination of secondary amines with 4-benzyl-3,5-dimethyl-1H-pyrazole-1-carboxamidine hydrochloride, see: Dräger et al. (2002). For the crystal structure of 4,4'-carbonyl-dimorpholine, see: Zhou et al. (2003).

Experimental top

4-Morpholine-carboxamidinium sulfate (I) was prepared by heating one equivalent O-methylisourea sulfate with two equivalents of morpholine under reflux. The methanol formed in the reaction was distilled off and (I) precipitated in nearly quantitative yield. To a solution of 15.0 g (42 mmol) (I) in 50 ml water, a solution of 3.4 g (85 mmol) sodium hydroxide dissolved in 25 ml water was added dropwise under ice cooling. After warming to room temperature the aqueous phase was extracted with diethyl ether. The organic phase was finally dried over sodium sulfate. After evaporation of the solvent, the title compound precipitated in form of a colorless solid. Yield: 5.1 g (94%). On slow evaporation of an acetonitrile solution at room temperature, colorless single crystals suitable for X-ray analysis were obtained. 1H NMR (500 MHz, CD3CN/TMS): δ = 3.35–3.39 [m, 4 H, –CH2–], 3.74–3.78 [m, 4 H, –CH2–], 5.50 [s, 1 H, –NH], 6.35 [s, 2 H, –NH2]. 13C NMR (125 MHz, CD3CN/TMS): δ = 45.0 (–CH2–), 65.9 (–CH2–), 160.8 (CN).

Refinement top

The N-bound H atoms were located in a difference Fourier map and were refined freely [N—H = 0.88 (2)–0.92 (2) Å]. The hydrogen atoms of the methylene groups were placed in calculated positions with d(C—H) = 0.99 Å. They were included in the refinement in the riding model approximation, with U(H) set to 1.2 Ueq(C).

Computing details top

Data collection: COLLECT (Hooft, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with displacement ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. N–H···N and N–H···O hydrogen bonds between neighboring molecules, ab-view. The hydrogen bonds are indicated by dashed lines.
[Figure 3] Fig. 3. N–H···N and N–H···O hydrogen bonds generating a three-dimensional network, ab-view. The hydrogen bonds are indicated by dashed lines.
4-Morpholinecarboxamidine top
Crystal data top
C5H11N3ODx = 1.273 Mg m3
Mr = 129.17Melting point: 433 K
Tetragonal, I41/aMo Kα radiation, λ = 0.71073 Å
Hall symbol: -I 4adCell parameters from 5017 reflections
a = 16.5910 (6) Åθ = 0.4–28.3°
c = 9.7939 (3) ŵ = 0.09 mm1
V = 2695.9 (2) Å3T = 100 K
Z = 16Polyhedral, colorless
F(000) = 11200.17 × 0.15 × 0.13 mm
Data collection top
Bruker–Nonius KappaCCD
diffractometer
1341 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.022
Graphite monochromatorθmax = 28.1°, θmin = 2.5°
ϕ scans, and ω scansh = 2121
2889 measured reflectionsk = 2121
1628 independent reflectionsl = 1212
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: difference Fourier map
wR(F2) = 0.091H atoms treated by a mixture of independent and constrained refinement
S = 1.06 w = 1/[σ2(Fo2) + (0.0306P)2 + 2.2674P]
where P = (Fo2 + 2Fc2)/3
1628 reflections(Δ/σ)max < 0.001
94 parametersΔρmax = 0.27 e Å3
0 restraintsΔρmin = 0.19 e Å3
Crystal data top
C5H11N3OZ = 16
Mr = 129.17Mo Kα radiation
Tetragonal, I41/aµ = 0.09 mm1
a = 16.5910 (6) ÅT = 100 K
c = 9.7939 (3) Å0.17 × 0.15 × 0.13 mm
V = 2695.9 (2) Å3
Data collection top
Bruker–Nonius KappaCCD
diffractometer
1341 reflections with I > 2σ(I)
2889 measured reflectionsRint = 0.022
1628 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.091H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.27 e Å3
1628 reflectionsΔρmin = 0.19 e Å3
94 parameters
Special details top

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 (Å2) top
xyzUiso*/Ueq
N10.14446 (6)0.03950 (6)0.30140 (11)0.0159 (2)
H110.1813 (9)0.0047 (9)0.2645 (15)0.019 (4)*
N20.06037 (6)0.03560 (6)0.15536 (11)0.0157 (2)
H210.1050 (9)0.0608 (9)0.1248 (16)0.022 (4)*
H220.0127 (10)0.0587 (9)0.1491 (16)0.025 (4)*
N30.00555 (5)0.05719 (5)0.30717 (10)0.0125 (2)
C10.07396 (6)0.02009 (6)0.25455 (11)0.0114 (2)
C20.06247 (7)0.07582 (7)0.21681 (12)0.0158 (3)
H2A0.05070.12520.16360.019*
H2B0.07110.03090.15190.019*
C30.13724 (7)0.08832 (7)0.30179 (13)0.0190 (3)
H3A0.15020.03790.35130.023*
H3B0.18320.10130.24130.023*
O10.12587 (5)0.15229 (5)0.39777 (9)0.0192 (2)
C40.06078 (7)0.13290 (8)0.48713 (12)0.0199 (3)
H4A0.05350.17720.55370.024*
H4B0.07420.08340.53870.024*
C50.01736 (7)0.11994 (7)0.40977 (12)0.0170 (3)
H5A0.06050.10360.47400.020*
H5B0.03400.17080.36490.020*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0111 (4)0.0149 (5)0.0217 (5)0.0013 (4)0.0005 (4)0.0051 (4)
N20.0106 (5)0.0143 (5)0.0222 (5)0.0007 (4)0.0018 (4)0.0082 (4)
N30.0106 (4)0.0134 (4)0.0137 (5)0.0020 (3)0.0023 (4)0.0056 (4)
C10.0129 (5)0.0088 (5)0.0126 (5)0.0004 (4)0.0008 (4)0.0002 (4)
C20.0142 (5)0.0172 (5)0.0160 (6)0.0041 (4)0.0038 (4)0.0043 (4)
C30.0141 (5)0.0197 (6)0.0232 (6)0.0035 (4)0.0029 (5)0.0050 (5)
O10.0168 (4)0.0196 (4)0.0213 (4)0.0088 (3)0.0012 (3)0.0052 (3)
C40.0185 (6)0.0260 (6)0.0153 (6)0.0064 (5)0.0011 (5)0.0064 (5)
C50.0145 (5)0.0179 (6)0.0185 (6)0.0014 (4)0.0019 (4)0.0088 (5)
Geometric parameters (Å, º) top
N1—C11.2971 (14)C2—H2B0.9900
N1—H110.916 (15)C3—O11.4302 (14)
N2—C11.3595 (14)C3—H3A0.9900
N2—H210.901 (16)C3—H3B0.9900
N2—H220.881 (16)O1—C41.4268 (14)
N3—C11.3902 (13)C4—C51.5169 (16)
N3—C51.4602 (14)C4—H4A0.9900
N3—C21.4671 (14)C4—H4B0.9900
C2—C31.5081 (16)C5—H5A0.9900
C2—H2A0.9900C5—H5B0.9900
C1—N1—H11107.8 (9)C2—C3—H3A109.5
C1—N2—H21114.6 (10)O1—C3—H3B109.5
C1—N2—H22119.6 (10)C2—C3—H3B109.5
H21—N2—H22120.8 (14)H3A—C3—H3B108.1
C1—N3—C5117.47 (9)C4—O1—C3109.61 (9)
C1—N3—C2119.85 (9)O1—C4—C5111.87 (9)
C5—N3—C2111.60 (9)O1—C4—H4A109.2
N1—C1—N2124.83 (10)C5—C4—H4A109.2
N1—C1—N3119.68 (10)O1—C4—H4B109.2
N2—C1—N3115.49 (9)C5—C4—H4B109.2
N3—C2—C3109.19 (9)H4A—C4—H4B107.9
N3—C2—H2A109.8N3—C5—C4109.27 (9)
C3—C2—H2A109.8N3—C5—H5A109.8
N3—C2—H2B109.8C4—C5—H5A109.8
C3—C2—H2B109.8N3—C5—H5B109.8
H2A—C2—H2B108.3C4—C5—H5B109.8
O1—C3—C2110.87 (9)H5A—C5—H5B108.3
O1—C3—H3A109.5
C5—N3—C1—N12.87 (16)N3—C2—C3—O158.69 (12)
C2—N3—C1—N1143.83 (11)C2—C3—O1—C460.42 (12)
C5—N3—C1—N2177.42 (10)C3—O1—C4—C559.34 (13)
C2—N3—C1—N236.46 (14)C1—N3—C5—C4161.31 (10)
C1—N3—C2—C3160.75 (10)C2—N3—C5—C454.67 (12)
C5—N3—C2—C356.20 (12)O1—C4—C5—N356.31 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···N1i0.90 (2)2.03 (2)2.930 (1)174 (1)
N2—H22···O1ii0.88 (2)2.13 (2)3.007 (1)174 (1)
Symmetry codes: (i) y1/4, x1/4, z1/4; (ii) y+1/4, x1/4, z1/4.

Experimental details

Crystal data
Chemical formulaC5H11N3O
Mr129.17
Crystal system, space groupTetragonal, I41/a
Temperature (K)100
a, c (Å)16.5910 (6), 9.7939 (3)
V3)2695.9 (2)
Z16
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.17 × 0.15 × 0.13
Data collection
DiffractometerBruker–Nonius KappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2889, 1628, 1341
Rint0.022
(sin θ/λ)max1)0.662
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.091, 1.06
No. of reflections1628
No. of parameters94
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.27, 0.19

Computer programs: COLLECT (Hooft, 2004), SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg & Putz, 2005).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N2—H21···N1i0.90 (2)2.03 (2)2.930 (1)174 (1)
N2—H22···O1ii0.88 (2)2.13 (2)3.007 (1)174 (1)
Symmetry codes: (i) y1/4, x1/4, z1/4; (ii) y+1/4, x1/4, z1/4.
 

Acknowledgements

The author thanks Dr F. Lissner (Institut für Anorganische Chemie, Universität Stuttgart) for the data collection.

References

First citationBrandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.
First citationDräger, G., Solodenko, W., Messinger, J., Schön, U. & Kirschning, A. (2002). Tetrahedron Lett. 43, 1401–1403.
First citationHooft, R. W. W. (2004). COLLECT. Nonius BV, Delft, The Netherlands.
First citationOtwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationZhou, W. Q., Zhu, L. M., Cao, Zh. B., Zhang, Y., Lu, W. D. & Lu, L. D. (2003). J. Mol. Struct. 565, 405–411.  Web of Science CSD CrossRef

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