2-Imi­niumyl-1,3-diazepane-4-carboxyl­ate

Yang, F.

doi:10.1107/S1600536810049676

organic compounds

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ISSN: 2056-9890

Volume 67| Part 1| January 2011| Page o10

https://doi.org/10.1107/S1600536810049676

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2-Iminiumyl-1,3-diazepane-4-carboxylate

Feng Yang ^a ^*

^aSchool of Chemistry and Chemical Engneering, Guangxi Normal University, Guilin 541004, People's Republic of China
^*Correspondence e-mail: jxyangfeng@gmail.com

(Received 20 October 2010; accepted 28 November 2010; online 4 December 2010)

The title compound, C₆H₁₁N₃O₂, is a cyclized derivative of L-arginine and the molecule is a zwitterion with the positive and negative charge residing in the guanidinium and carboxylate groups, respectively. The conformation of 1,3-diazepane ring is close to a twisted chair. One intramolecular and three intermolecular N—H⋯O hydrogen bonds stabilize the molecular conformation and the crystal structure, respectively.

Related literature

For related structures, see: Karapetyan (2008a ,b ).

Experimental

Crystal data

C₆H₁₁N₃O₂
M_r = 157.18
Orthorhombic, P 2₁ 2₁ 2₁
a = 6.1740 (3) Å
b = 8.7979 (5) Å
c = 14.2036 (7) Å
V = 771.51 (7) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 293 K
0.23 × 0.15 × 0.10 mm

Data collection

Siemens SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.773, T_max = 1.000
3426 measured reflections
834 independent reflections
694 reflections with I > 2σ(I)
R_int = 0.026

Refinement

R[F² > 2σ(F²)] = 0.042
wR(F²) = 0.116
S = 1.08
834 reflections
100 parameters
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1ⁱ	0.86	2.17	2.918 (3)	146
N3—H3A⋯O2ⁱ	0.86	2.06	2.870 (4)	157
N3—H3B⋯O2ⁱⁱ	0.86	1.95	2.788 (4)	163
N2—H2A⋯O1	0.86	2.19	2.601 (3)	109
Symmetry codes: (i) $[-x+{\script{3\over 2}}, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: SMART (Siemens, 1996 ); cell refinement: SMART and SAINT (Siemens, 1994 ); data reduction: XPREP (Siemens, 1994); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536810049676/bx2320sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810049676/bx2320Isup2.hkl

checkCIF report

Comment top

The title compound (I) was hydrothermally synthesized from L-Arginine via an unusual annulation reaction. We report here a new annulation product derived from the linear arginine molecule. The title compound is the cyclic form of L-Arginine and this molecule is a zwitterion with the positive and negative charge residing in the guanidinium and carboxylate groups respectively.The conformation of 1,3-diazepane ring is close to twisted chair.One intramolecular and three intermolecular N—H···O hydrogen bonds stabilize the molecular conformation and the crystal structure respectively (Fig. 2). The C—N distances in the guanidinium group are obviously shorter than that of the normal C—N single bond, indicating delocalized bond of the guanidinium group.

Related literature top

For related structures, see: Karapetyan (2008a,b).

Experimental top

A mixture of Cu(ClO₄)₂^.6H₂O (0.186 g, 0.5 mmol), L-Arginine (0.087 g, 0.5 mmol) and water (10 ml) was sealed in a 15 ml teflon-lined stainless steel reactor and heated to 423 K for 60 h. Colorless crystals of (I) suitable for X-ray analysis were obtained.

Structure description top

For related structures, see: Karapetyan (2008a,b).

Computing details top

Data collection: SMART (Siemens, 1996); cell refinement: SMART and SAINT (Siemens, 1994); data reduction: XPREP (Siemens, 1994); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. A view of (I) with 50% probability displacement ellipsoids; H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. The hydrogen bonding interactions between the molecules. The H- atoms not involved in hydrogen bond are omitted for charity

2-iminiumyl-1,3-diazepane-4-carboxylate top

Crystal data top

C₆H₁₁N₃O₂	F(000) = 336
M_r = 157.18	D_x = 1.353 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1112 reflections
a = 6.1740 (3) Å	θ = 2.7–20.9°
b = 8.7979 (5) Å	µ = 0.10 mm⁻¹
c = 14.2036 (7) Å	T = 293 K
V = 771.51 (7) Å³	Prism, colorless
Z = 4	0.23 × 0.15 × 0.10 mm

Data collection top

Siemens SMART CCD area-detector diffractometer	834 independent reflections
Radiation source: fine-focus sealed tube	694 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
phi and ω scans	θ_max = 25.1°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −7→5
T_min = 0.773, T_max = 1.000	k = −9→10
3426 measured reflections	l = −16→13

Refinement top

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.116	H-atom parameters constrained
S = 1.08	w = 1/[σ²(F_o²) + (0.0573P)² + 0.2708P] where P = (F_o² + 2F_c²)/3
834 reflections	(Δ/σ)_max = 0.002
100 parameters	Δρ_max = 0.25 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₆H₁₁N₃O₂	V = 771.51 (7) Å³
M_r = 157.18	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.1740 (3) Å	µ = 0.10 mm⁻¹
b = 8.7979 (5) Å	T = 293 K
c = 14.2036 (7) Å	0.23 × 0.15 × 0.10 mm

Data collection top

Siemens SMART CCD area-detector diffractometer	834 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	694 reflections with I > 2σ(I)
T_min = 0.773, T_max = 1.000	R_int = 0.026
3426 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.042	0 restraints
wR(F²) = 0.116	H-atom parameters constrained
S = 1.08	Δρ_max = 0.25 e Å⁻³
834 reflections	Δρ_min = −0.23 e Å⁻³
100 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

	x	y	z	U_iso*/U_eq
O1	0.9643 (4)	0.4869 (3)	0.67888 (15)	0.0471 (7)
O2	0.8529 (4)	0.2509 (2)	0.64723 (15)	0.0463 (7)
N1	0.5689 (4)	0.4568 (3)	0.97693 (19)	0.0413 (8)
H1A	0.5874	0.4365	1.0356	0.050*
N2	0.7752 (5)	0.5024 (3)	0.84226 (17)	0.0383 (7)
H2A	0.8317	0.5757	0.8105	0.046*
N3	0.8387 (5)	0.6355 (3)	0.9771 (2)	0.0492 (8)
H3A	0.8106	0.6559	1.0350	0.059*
H3B	0.9404	0.6835	0.9483	0.059*
C1	0.7420 (6)	0.3583 (4)	0.7926 (2)	0.0352 (8)
H1B	0.8059	0.2765	0.8303	0.042*
C2	0.5046 (7)	0.3203 (4)	0.7748 (2)	0.0486 (10)
H2B	0.4346	0.4071	0.7457	0.058*
H2C	0.4962	0.2359	0.7310	0.058*
C3	0.3829 (7)	0.2787 (4)	0.8645 (3)	0.0558 (11)
H3C	0.2381	0.2455	0.8479	0.067*
H3D	0.4560	0.1940	0.8946	0.067*
C4	0.3667 (6)	0.4072 (4)	0.9331 (3)	0.0510 (10)
H4A	0.3033	0.4936	0.9008	0.061*
H4B	0.2671	0.3775	0.9826	0.061*
C5	0.7260 (5)	0.5309 (4)	0.9325 (2)	0.0348 (8)
C6	0.8659 (6)	0.3684 (4)	0.6983 (2)	0.0372 (8)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0583 (16)	0.0522 (14)	0.0306 (12)	−0.0038 (14)	0.0092 (11)	0.0005 (11)
O2	0.0625 (17)	0.0467 (13)	0.0299 (11)	0.0092 (13)	0.0014 (13)	−0.0071 (10)
N1	0.0450 (18)	0.0527 (17)	0.0261 (13)	−0.0089 (15)	0.0052 (13)	0.0025 (13)
N2	0.0500 (18)	0.0391 (14)	0.0257 (13)	−0.0051 (14)	0.0053 (12)	−0.0024 (12)
N3	0.057 (2)	0.0567 (18)	0.0343 (14)	−0.0191 (17)	0.0114 (15)	−0.0135 (14)
C1	0.043 (2)	0.0356 (15)	0.0264 (16)	0.0019 (16)	−0.0015 (15)	−0.0009 (14)
C2	0.051 (2)	0.057 (2)	0.038 (2)	−0.008 (2)	0.0000 (19)	−0.0098 (17)
C3	0.049 (2)	0.061 (2)	0.057 (2)	−0.017 (2)	0.005 (2)	−0.005 (2)
C4	0.042 (2)	0.063 (2)	0.047 (2)	−0.0080 (19)	0.009 (2)	−0.0011 (18)
C5	0.0395 (19)	0.0370 (16)	0.0279 (15)	0.0017 (17)	0.0017 (15)	0.0010 (14)
C6	0.040 (2)	0.046 (2)	0.0256 (16)	0.0110 (18)	−0.0035 (16)	0.0018 (15)

Geometric parameters (Å, º) top

O1—C6	1.238 (4)	C1—C2	1.524 (6)
O2—C6	1.265 (4)	C1—C6	1.545 (4)
N1—C5	1.329 (4)	C1—H1B	0.9800
N1—C4	1.462 (4)	C2—C3	1.523 (5)
N1—H1A	0.8600	C2—H2B	0.9700
N2—C5	1.340 (4)	C2—H2C	0.9700
N2—C1	1.465 (4)	C3—C4	1.496 (5)
N2—H2A	0.8600	C3—H3C	0.9700
N3—C5	1.317 (4)	C3—H3D	0.9700
N3—H3A	0.8600	C4—H4A	0.9700
N3—H3B	0.8600	C4—H4B	0.9700

C5—N1—C4	124.6 (3)	H2B—C2—H2C	107.8
C5—N1—H1A	117.7	C4—C3—C2	113.3 (3)
C4—N1—H1A	117.7	C4—C3—H3C	108.9
C5—N2—C1	126.1 (3)	C2—C3—H3C	108.9
C5—N2—H2A	116.9	C4—C3—H3D	108.9
C1—N2—H2A	116.9	C2—C3—H3D	108.9
C5—N3—H3A	120.0	H3C—C3—H3D	107.7
C5—N3—H3B	120.0	N1—C4—C3	116.5 (3)
H3A—N3—H3B	120.0	N1—C4—H4A	108.2
N2—C1—C2	113.9 (3)	C3—C4—H4A	108.2
N2—C1—C6	107.3 (3)	N1—C4—H4B	108.2
C2—C1—C6	110.2 (3)	C3—C4—H4B	108.2
N2—C1—H1B	108.4	H4A—C4—H4B	107.3
C2—C1—H1B	108.4	N3—C5—N1	120.0 (3)
C6—C1—H1B	108.4	N3—C5—N2	118.1 (3)
C3—C2—C1	112.8 (3)	N1—C5—N2	121.9 (3)
C3—C2—H2B	109.0	O1—C6—O2	126.2 (3)
C1—C2—H2B	109.0	O1—C6—C1	119.0 (3)
C3—C2—H2C	109.0	O2—C6—C1	114.8 (3)
C1—C2—H2C	109.0

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86	2.17	2.918 (3)	146
N3—H3A···O2ⁱ	0.86	2.06	2.870 (4)	157
N3—H3B···O2ⁱⁱ	0.86	1.95	2.788 (4)	163
N2—H2A···O1	0.86	2.19	2.601 (3)	109

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

Experimental details

Crystal data
Chemical formula	C₆H₁₁N₃O₂
M_r	157.18
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	6.1740 (3), 8.7979 (5), 14.2036 (7)
V (Å³)	771.51 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.23 × 0.15 × 0.10

Data collection
Diffractometer	Siemens SMART CCD area-detector
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.773, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	3426, 834, 694
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.598

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.116, 1.08
No. of reflections	834
No. of parameters	100
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.23

Computer programs: SMART (Siemens, 1996), SMART and SAINT (Siemens, 1994), XPREP (Siemens, 1994), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1ⁱ	0.86	2.17	2.918 (3)	146
N3—H3A···O2ⁱ	0.86	2.06	2.870 (4)	157
N3—H3B···O2ⁱⁱ	0.86	1.95	2.788 (4)	163
N2—H2A···O1	0.86	2.19	2.601 (3)	109

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

Acknowledgements

This study was supported by the National Science Foundation of China (C050102).

References

Karapetyan, H. A. (2008a). Acta Cryst. E64, o1222. Web of Science CSD CrossRef IUCr Journals Google Scholar
Karapetyan, H. A. (2008b). Acta Cryst. E64, o943. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Siemens (1994). SAINT. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Google Scholar
Siemens (1996). SMART. Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA. Google Scholar