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

Abstract

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,

• a = 6.1740 (3) Å

• b = 8.7979 (5) Å

• c = 14.2036 (7) Å

• V = 771.51 (7) ų

• 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[F ² > 2σ(F ²)] = 0.042

• wR(F ²) = 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

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.

Supplementary Material

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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) ; (ii) .

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

All H atoms were placed at calculated positions, and refined with isotropic displacement parameters, using a riding model [C—H = 0.97 Å and U_iso(H) = 1.2U_eq(C), C—H = 0.98 Å and U_iso(H) = 1.5U_eq(C), N—H = 0.86 Å and U_iso(H) = 1.2U_eq(N)].

Figures

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

Crystal data

C6H11N3O2	F(000) = 336
Mr = 157.18	Dx = 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

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

Refinement

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(Fo2) + (0.0573P)2 + 0.2708P] where P = (Fo2 + 2Fc2)/3
834 reflections	(Δ/σ)max = 0.002
100 parameters	Δρmax = 0.25 e Å−3
0 restraints	Δρmin = −0.23 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
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 (Ų)

	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, °)

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, °)

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.