organic compounds
4-Morpholinecarboxamidine
aFakultät Chemie/Organische Chemie, Hochschule Aalen, Beethovenstrasse 1, D-73430 Aalen, Germany
*Correspondence e-mail: Ioannis.Tiritiris@htw-aalen.de
In the 5H11N3O, 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.
of the title compound, CRelated literature
For the synthesis of H-pyrazole-1-carboxamidine hydrochloride, see: Dräger et al. (2002). For the of 4,4′-carbonyl-dimorpholine, see: Zhou et al. (2003).
by amidination of secondary with 4-benzyl-3,5-dimethyl-1Experimental
Crystal data
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Data collection
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Refinement
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Data collection: COLLECT (Hooft, 2004); cell SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK; 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.
Supporting information
10.1107/S1600536812042201/zl2510sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812042201/zl2510Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812042201/zl2510Isup3.cml
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 (C═N).
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
in the riding model approximation, with U(H) set to 1.2 Ueq(C).Data collection: COLLECT (Hooft, 2004); cell
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).C5H11N3O | Dx = 1.273 Mg m−3 |
Mr = 129.17 | Melting point: 433 K |
Tetragonal, I41/a | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -I 4ad | Cell parameters from 5017 reflections |
a = 16.5910 (6) Å | θ = 0.4–28.3° |
c = 9.7939 (3) Å | µ = 0.09 mm−1 |
V = 2695.9 (2) Å3 | T = 100 K |
Z = 16 | Polyhedral, colorless |
F(000) = 1120 | 0.17 × 0.15 × 0.13 mm |
Bruker–Nonius KappaCCD diffractometer | 1341 reflections with I > 2σ(I) |
Radiation source: sealed tube | Rint = 0.022 |
Graphite monochromator | θmax = 28.1°, θmin = 2.5° |
ϕ scans, and ω scans | h = −21→21 |
2889 measured reflections | k = −21→21 |
1628 independent reflections | l = −12→12 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.037 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.091 | H 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 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
C5H11N3O | Z = 16 |
Mr = 129.17 | Mo Kα radiation |
Tetragonal, I41/a | µ = 0.09 mm−1 |
a = 16.5910 (6) Å | T = 100 K |
c = 9.7939 (3) Å | 0.17 × 0.15 × 0.13 mm |
V = 2695.9 (2) Å3 |
Bruker–Nonius KappaCCD diffractometer | 1341 reflections with I > 2σ(I) |
2889 measured reflections | Rint = 0.022 |
1628 independent reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.091 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.27 e Å−3 |
1628 reflections | Δρmin = −0.19 e Å−3 |
94 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
N1 | −0.14446 (6) | 0.03950 (6) | 0.30140 (11) | 0.0159 (2) | |
H11 | −0.1813 (9) | 0.0047 (9) | 0.2645 (15) | 0.019 (4)* | |
N2 | −0.06037 (6) | −0.03560 (6) | 0.15536 (11) | 0.0157 (2) | |
H21 | −0.1050 (9) | −0.0608 (9) | 0.1248 (16) | 0.022 (4)* | |
H22 | −0.0127 (10) | −0.0587 (9) | 0.1491 (16) | 0.025 (4)* | |
N3 | −0.00555 (5) | 0.05719 (5) | 0.30717 (10) | 0.0125 (2) | |
C1 | −0.07396 (6) | 0.02009 (6) | 0.25455 (11) | 0.0114 (2) | |
C2 | 0.06247 (7) | 0.07582 (7) | 0.21681 (12) | 0.0158 (3) | |
H2A | 0.0507 | 0.1252 | 0.1636 | 0.019* | |
H2B | 0.0711 | 0.0309 | 0.1519 | 0.019* | |
C3 | 0.13724 (7) | 0.08832 (7) | 0.30179 (13) | 0.0190 (3) | |
H3A | 0.1502 | 0.0379 | 0.3513 | 0.023* | |
H3B | 0.1832 | 0.1013 | 0.2413 | 0.023* | |
O1 | 0.12587 (5) | 0.15229 (5) | 0.39777 (9) | 0.0192 (2) | |
C4 | 0.06078 (7) | 0.13290 (8) | 0.48713 (12) | 0.0199 (3) | |
H4A | 0.0535 | 0.1772 | 0.5537 | 0.024* | |
H4B | 0.0742 | 0.0834 | 0.5387 | 0.024* | |
C5 | −0.01736 (7) | 0.11994 (7) | 0.40977 (12) | 0.0170 (3) | |
H5A | −0.0605 | 0.1036 | 0.4740 | 0.020* | |
H5B | −0.0340 | 0.1708 | 0.3649 | 0.020* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0111 (4) | 0.0149 (5) | 0.0217 (5) | −0.0013 (4) | 0.0005 (4) | −0.0051 (4) |
N2 | 0.0106 (5) | 0.0143 (5) | 0.0222 (5) | 0.0007 (4) | −0.0018 (4) | −0.0082 (4) |
N3 | 0.0106 (4) | 0.0134 (4) | 0.0137 (5) | −0.0020 (3) | 0.0023 (4) | −0.0056 (4) |
C1 | 0.0129 (5) | 0.0088 (5) | 0.0126 (5) | −0.0004 (4) | −0.0008 (4) | −0.0002 (4) |
C2 | 0.0142 (5) | 0.0172 (5) | 0.0160 (6) | −0.0041 (4) | 0.0038 (4) | −0.0043 (4) |
C3 | 0.0141 (5) | 0.0197 (6) | 0.0232 (6) | −0.0035 (4) | 0.0029 (5) | −0.0050 (5) |
O1 | 0.0168 (4) | 0.0196 (4) | 0.0213 (4) | −0.0088 (3) | 0.0012 (3) | −0.0052 (3) |
C4 | 0.0185 (6) | 0.0260 (6) | 0.0153 (6) | −0.0064 (5) | 0.0011 (5) | −0.0064 (5) |
C5 | 0.0145 (5) | 0.0179 (6) | 0.0185 (6) | −0.0014 (4) | 0.0019 (4) | −0.0088 (5) |
N1—C1 | 1.2971 (14) | C2—H2B | 0.9900 |
N1—H11 | 0.916 (15) | C3—O1 | 1.4302 (14) |
N2—C1 | 1.3595 (14) | C3—H3A | 0.9900 |
N2—H21 | 0.901 (16) | C3—H3B | 0.9900 |
N2—H22 | 0.881 (16) | O1—C4 | 1.4268 (14) |
N3—C1 | 1.3902 (13) | C4—C5 | 1.5169 (16) |
N3—C5 | 1.4602 (14) | C4—H4A | 0.9900 |
N3—C2 | 1.4671 (14) | C4—H4B | 0.9900 |
C2—C3 | 1.5081 (16) | C5—H5A | 0.9900 |
C2—H2A | 0.9900 | C5—H5B | 0.9900 |
C1—N1—H11 | 107.8 (9) | C2—C3—H3A | 109.5 |
C1—N2—H21 | 114.6 (10) | O1—C3—H3B | 109.5 |
C1—N2—H22 | 119.6 (10) | C2—C3—H3B | 109.5 |
H21—N2—H22 | 120.8 (14) | H3A—C3—H3B | 108.1 |
C1—N3—C5 | 117.47 (9) | C4—O1—C3 | 109.61 (9) |
C1—N3—C2 | 119.85 (9) | O1—C4—C5 | 111.87 (9) |
C5—N3—C2 | 111.60 (9) | O1—C4—H4A | 109.2 |
N1—C1—N2 | 124.83 (10) | C5—C4—H4A | 109.2 |
N1—C1—N3 | 119.68 (10) | O1—C4—H4B | 109.2 |
N2—C1—N3 | 115.49 (9) | C5—C4—H4B | 109.2 |
N3—C2—C3 | 109.19 (9) | H4A—C4—H4B | 107.9 |
N3—C2—H2A | 109.8 | N3—C5—C4 | 109.27 (9) |
C3—C2—H2A | 109.8 | N3—C5—H5A | 109.8 |
N3—C2—H2B | 109.8 | C4—C5—H5A | 109.8 |
C3—C2—H2B | 109.8 | N3—C5—H5B | 109.8 |
H2A—C2—H2B | 108.3 | C4—C5—H5B | 109.8 |
O1—C3—C2 | 110.87 (9) | H5A—C5—H5B | 108.3 |
O1—C3—H3A | 109.5 | ||
C5—N3—C1—N1 | −2.87 (16) | N3—C2—C3—O1 | −58.69 (12) |
C2—N3—C1—N1 | −143.83 (11) | C2—C3—O1—C4 | 60.42 (12) |
C5—N3—C1—N2 | 177.42 (10) | C3—O1—C4—C5 | −59.34 (13) |
C2—N3—C1—N2 | 36.46 (14) | C1—N3—C5—C4 | 161.31 (10) |
C1—N3—C2—C3 | −160.75 (10) | C2—N3—C5—C4 | −54.67 (12) |
C5—N3—C2—C3 | 56.20 (12) | O1—C4—C5—N3 | 56.31 (13) |
D—H···A | D—H | H···A | D···A | 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−1/4, −x−1/4, z−1/4; (ii) −y+1/4, x−1/4, z−1/4. |
Experimental details
Crystal data | |
Chemical formula | C5H11N3O |
Mr | 129.17 |
Crystal system, space group | Tetragonal, I41/a |
Temperature (K) | 100 |
a, c (Å) | 16.5910 (6), 9.7939 (3) |
V (Å3) | 2695.9 (2) |
Z | 16 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.17 × 0.15 × 0.13 |
Data collection | |
Diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2889, 1628, 1341 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.662 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.091, 1.06 |
No. of reflections | 1628 |
No. of parameters | 94 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.27, −0.19 |
Computer programs: COLLECT (Hooft, 2004), SCALEPACK (Otwinowski & Minor, 1997), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg & Putz, 2005).
D—H···A | D—H | H···A | D···A | 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−1/4, −x−1/4, z−1/4; (ii) −y+1/4, x−1/4, z−1/4. |
Acknowledgements
The author thanks Dr F. Lissner (Institut für Anorganische Chemie, Universität Stuttgart) for the data collection.
References
Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Dräger, G., Solodenko, W., Messinger, J., Schön, U. & Kirschning, A. (2002). Tetrahedron Lett. 43, 1401–1403. Google Scholar
Hooft, R. W. W. (2004). COLLECT. Nonius BV, Delft, The Netherlands. Google Scholar
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. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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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.