3-Diazo-N-[(2S)-1-hy­droxy­propan-2-yl]-2-oxopropanamide

Chen, X.; Hu, W.; Li, X.; Xu, H.

doi:10.1107/S1600536811014413

organic compounds

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Volume 67| Part 5| May 2011| Page o1192

doi:10.1107/S1600536811014413

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3-Diazo-N-[(2S)-1-hydroxypropan-2-yl]-2-oxopropanamide

Xiao-na Chen,^a Wen-hao Hu,^b Xiao-liu Li ^a ^* and Hua-dong Xu ^b ^*

^aCollege of Chemistry and Environment Science, Hebei University, 180 East Wu Si Road, Baoding 071002, People's Republic of China, and ^bInstitute of Drug Discovery and Development, and Department of Chemistry, East China Normal University, Shanghai 200062, People's Republic of China
^*Correspondence e-mail: lixl@hbu.edu.cn, huadongxu@gmail.com

(Received 15 April 2011; accepted 17 April 2011; online 22 April 2011)

In the title compound, C₆H₉N₃O₃, the 3-diazo-2-oxopropanamide section of the molecule is nearly planar, with a maximum deviation of 0.025 (1) Å from the mean plane of its constituent atoms. The diazo C=N=N angle is 178.0 (3)°. In the crystal, pairs of intermolecular O—H⋯O and N—H⋯O hydrogen bonds link the molecules into infinite double chains along the [100] direction. The double chains are additionally stabilized by weak C—H⋯O contacts with C⋯O distances of 3.039 (3) Å. Neighboring double chains in turn interact with each other through π–π stacking interactions [centroid–centroid distance of the 3-diazo-2-oxopropanamide units = 3.66 (6) Å] to form infinite stacks along the b axis. Molecules from neighboring stacks interdigitate with each other in the c-axis direction, thus leading to an interwoven three-dimensional network held together by O—H⋯O, N—H⋯O and C—H⋯O interactions and π–π stacking.

Related literature

For general background to diazo compounds, see: Doyle & Forbes (1998 ); Doyle (1986 ); Zhang & Wang (2008 ). For the synthetic procedure, see: Pedone & Brocchini (2006 ).

Experimental

Crystal data

C₆H₉N₃O₃
M_r = 171.16
Orthorhombic, P 2₁ 2₁ 2₁
a = 5.3136 (3) Å
b = 6.7551 (3) Å
c = 23.3958 (11) Å
V = 839.77 (7) Å³
Z = 4
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 296 K
0.46 × 0.38 × 0.32 mm

Data collection

Bruker SMART CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ) T_min = 0.951, T_max = 0.965
9692 measured reflections
903 independent reflections
826 reflections with I > 2σ(I)
R_int = 0.027

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.123
S = 1.17
903 reflections
109 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.14 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1C⋯O1ⁱ	0.82	1.99	2.811 (4)	179
N1—H1D⋯O2ⁱⁱ	0.86	2.35	3.1024 (18)	146
C6—H6A⋯O3ⁱⁱⁱ	0.93	2.18	3.039 (3)	153
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z]$ ; (ii) x+1, y, z; (iii) x-1, y, z.

Data collection: SMART (Bruker, 2007 ); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811014413/zl2366sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811014413/zl2366Isup2.hkl

checkCIF report

Comment top

Diazo refers to a type of organic compounds that have two linked nitrogen atoms as a terminal functional group. The simplest example of a diazo compound is diazomethane. The electronic structure of diazo compounds involves a positive charge on the central nitrogen and negative charge distributed between the terminal nitrogen and the carbon. The diazo compounds have wide applications in organic synthesis, such as C—H or C—N bonds insertion, 1,3-dipolar cyclization and transition metal complexes catalyzed transformations (Doyle & Forbes, 1998; Zhang & Wang, 2008; Doyle, 1986). To investigate the relationship between structure and reactivity, the title compound was synthesized and its structure was determined by X-ray diffraction. In this article, we present the synthesis and crystal structure of this new diazo compound.

As shown in figure 1, the 3-diazo-2-oxopropanamide section of the molecule is nearly planar with a maximum deviation of 0.025 (1) Å from the mean plane of its constituting atoms. The diazo unit is almost linear with an C5–N2–N3 angle of 178.0 (3)°. The N2—N3, C4—O2 and C5—O3 bond length of 1.113 (3), 1.215 (3) and 1.213 (3) Å, respectively, indicate the presence of a typical N═N and C═O bonds. Whereas the C1–O1 [1.396 (3) Å] and C2–N1 [1.468 (2) Å] bond lengths correspond to typical single bonds.

In the crystal structure, it is noteworthy that pairs of intermolecular O—H···O and N—H···O hydrogen bonds link the molecules into infinite double chains along the [1 0 0] direction. The double chains are further stabilized by weak C—H···O contacts with the C···O distances of 3.039 (3) Å (Fig. 2). Neighboring double chains are in turn interacting with each other through π–π stacking interactions [centroid to centroid distances of the 3-diazo-2-oxopropanamide units are 3.66 (6)Å] to form infinite stacks along b. Molecules from neighboring stacks interdigitate with each other in the c-direction, thus leading to an interwoven three dimensional network held together by O—H···O, N—H···O and C—H···O interactions and π–π stacking.

Related literature top

For general background to diazo compounds, see: Doyle & Forbes (1998); Doyle (1986); Zhang & Wang (2008). For the synthetic procedure, see: Pedone & Brocchini (2006).

Experimental top

To a dried flame-dried 20 ml three-necked round bottomed flask filled with nitrogen and equipped with a refluxing condenser was added diazo ethyl pyruvate (0.5 g, 3.5 mmol), (S)-2-aminopropan-1-ol (0.345 g, 4.6 mmol) in 10 ml anhydrous ethanol. This suspension was stirred at room temperature and the reaction was monitored by TLC. When the diazo ethyl pyruvate was consumed, the yellow brown reaction mixture was concentrated to dryness. The crude product was purified by column chromatography on silica gel with petroleum ether/ethyl acetate (1/1) as eluent to give the product in yield of 63% (0.377 g, 2.2 mmol). Single crystals suitable for X-ray diffraction study were obtained by recrystallization of the crude from a diethyl ether solution. ¹H NMR (CDCl₃, 400 MHz), δ (p.p.m.): 6.36 (s, 1H), 4.05 (br, 1H), 3.69 (m, 1H), 3.61 (m, 1H), 2.25 (br, 1H), 1.61 (s, 1H), 1.24 (d, J = 6.8 Hz, 3H); ¹³C NMR (125 MHz, CDCl₃), δ (p.p.m.): 181.64, 159.86, 65.38, 54.99, 47.65, 16.42; IR (KBr pellet, ν, cm^-1): 3327, 3083, 2110, 1733, 1666, 1536, 1381, 788, 706.

Computing details top

Data collection: SMART (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound, with displacement ellipsoids at the 30% probability level.
	Fig. 2. Part of infinite double chains structure of the title compound, linked via hydrogen bonds (dashed lines) extending in the [1 0 0] direction. H atoms have been omitted for clarity, except for those involved in hydrogen-bonding interactions.
	Fig. 3. The π–π stacking interactions in the structure of the title compound.

3-Diazo-N-[(2S)-1-hydroxypropan-2-yl]-2-oxopropanamide top

Crystal data top

C₆H₉N₃O₃	F(000) = 360
M_r = 171.16	D_x = 1.354 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 4465 reflections
a = 5.3136 (3) Å	θ = 1.7–25°
b = 6.7551 (3) Å	µ = 0.11 mm⁻¹
c = 23.3958 (11) Å	T = 296 K
V = 839.77 (7) Å³	Block, colourless
Z = 4	0.46 × 0.38 × 0.32 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	903 independent reflections
Radiation source: sealed tube	826 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.027
ϕ and ω scans	θ_max = 25.0°, θ_min = 1.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −6→6
T_min = 0.951, T_max = 0.965	k = −7→8
9692 measured reflections	l = −27→27

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.123	H-atom parameters constrained
S = 1.17	w = 1/[σ²(F_o²) + (0.0698P)² + 0.1238P] where P = (F_o² + 2F_c²)/3
903 reflections	(Δ/σ)_max < 0.001
109 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.14 e Å⁻³

Crystal data top

C₆H₉N₃O₃	V = 839.77 (7) Å³
M_r = 171.16	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 5.3136 (3) Å	µ = 0.11 mm⁻¹
b = 6.7551 (3) Å	T = 296 K
c = 23.3958 (11) Å	0.46 × 0.38 × 0.32 mm

Data collection top

Bruker SMART CCD area-detector diffractometer	903 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	826 reflections with I > 2σ(I)
T_min = 0.951, T_max = 0.965	R_int = 0.027
9692 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.123	H-atom parameters constrained
S = 1.17	Δρ_max = 0.21 e Å⁻³
903 reflections	Δρ_min = −0.14 e Å⁻³
109 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 > 2σ(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	0.4929 (5)	0.2784 (4)	0.01785 (8)	0.0988 (9)
H1C	0.6387	0.2627	0.0073	0.148*
O2	−0.0639 (3)	0.5086 (4)	0.16571 (7)	0.0626 (6)
O3	0.4091 (3)	0.5355 (5)	0.26799 (8)	0.0855 (9)
N1	0.3555 (4)	0.5279 (4)	0.15304 (8)	0.0617 (7)
H1D	0.4963	0.5452	0.1705	0.074*
N2	0.0058 (4)	0.5073 (3)	0.33780 (8)	0.0539 (5)
N3	0.0377 (5)	0.5040 (5)	0.38481 (9)	0.0801 (8)
C1	0.4894 (7)	0.3193 (5)	0.07632 (11)	0.0653 (8)
H1A	0.6612	0.3245	0.0903	0.078*
H1B	0.4045	0.2121	0.0960	0.078*
C2	0.3606 (5)	0.5101 (5)	0.09052 (9)	0.0592 (7)
H2A	0.1870	0.5038	0.0765	0.071*
C3	0.4882 (9)	0.6869 (6)	0.06378 (14)	0.0911 (11)
H3A	0.3976	0.8050	0.0736	0.137*
H3B	0.4904	0.6717	0.0230	0.137*
H3C	0.6577	0.6963	0.0777	0.137*
C4	0.1495 (4)	0.5190 (4)	0.18416 (9)	0.0454 (6)
C5	0.1975 (4)	0.5223 (5)	0.24897 (9)	0.0500 (6)
C6	−0.0232 (4)	0.5110 (4)	0.28220 (8)	0.0487 (6)
H6A	−0.1818	0.5063	0.2655	0.058*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0713 (13)	0.162 (2)	0.0635 (12)	0.0092 (19)	0.0014 (12)	−0.0457 (14)
O2	0.0318 (8)	0.1035 (15)	0.0526 (9)	−0.0011 (11)	−0.0073 (7)	−0.0031 (11)
O3	0.0278 (8)	0.175 (3)	0.0533 (10)	−0.0017 (14)	−0.0039 (7)	−0.0179 (14)
N1	0.0315 (9)	0.1099 (19)	0.0437 (10)	−0.0016 (15)	−0.0021 (8)	−0.0148 (12)
N2	0.0382 (10)	0.0707 (13)	0.0528 (11)	−0.0018 (13)	0.0038 (9)	−0.0049 (10)
N3	0.0732 (16)	0.115 (2)	0.0524 (13)	0.000 (2)	−0.0004 (12)	−0.0025 (14)
C1	0.0535 (15)	0.0875 (18)	0.0549 (14)	−0.0038 (18)	0.0029 (15)	−0.0151 (14)
C2	0.0379 (11)	0.098 (2)	0.0413 (12)	0.0055 (18)	−0.0016 (9)	−0.0081 (13)
C3	0.105 (3)	0.097 (2)	0.0711 (19)	0.008 (3)	0.006 (2)	0.0113 (17)
C4	0.0316 (10)	0.0561 (14)	0.0484 (12)	0.0012 (13)	−0.0022 (9)	−0.0071 (11)
C5	0.0297 (11)	0.0698 (16)	0.0504 (13)	0.0019 (14)	−0.0029 (9)	−0.0091 (12)
C6	0.0322 (10)	0.0680 (14)	0.0460 (11)	−0.0005 (15)	−0.0020 (9)	−0.0014 (12)

Geometric parameters (Å, º) top

O1—C1	1.396 (3)	C1—H1A	0.9700
O1—H1C	0.8200	C1—H1B	0.9700
O2—C4	1.215 (3)	C2—C3	1.509 (5)
O3—C5	1.213 (3)	C2—H2A	0.9800
N1—C4	1.316 (3)	C3—H3A	0.9600
N1—C2	1.468 (2)	C3—H3B	0.9600
N1—H1D	0.8600	C3—H3C	0.9600
N2—N3	1.113 (3)	C4—C5	1.538 (3)
N2—C6	1.310 (3)	C5—C6	1.409 (3)
C1—C2	1.497 (4)	C6—H6A	0.9300

C1—O1—H1C	109.5	C3—C2—H2A	108.6
C4—N1—C2	124.25 (19)	C2—C3—H3A	109.5
C4—N1—H1D	117.9	C2—C3—H3B	109.5
C2—N1—H1D	117.9	H3A—C3—H3B	109.5
N3—N2—C6	178.0 (3)	C2—C3—H3C	109.5
O1—C1—C2	113.2 (3)	H3A—C3—H3C	109.5
O1—C1—H1A	108.9	H3B—C3—H3C	109.5
C2—C1—H1A	108.9	O2—C4—N1	125.6 (2)
O1—C1—H1B	108.9	O2—C4—C5	120.4 (2)
C2—C1—H1B	108.9	N1—C4—C5	114.01 (18)
H1A—C1—H1B	107.7	O3—C5—C6	125.0 (2)
N1—C2—C1	107.5 (2)	O3—C5—C4	121.1 (2)
N1—C2—C3	110.9 (3)	C6—C5—C4	113.92 (18)
C1—C2—C3	112.6 (2)	N2—C6—C5	116.8 (2)
N1—C2—H2A	108.6	N2—C6—H6A	121.6
C1—C2—H2A	108.6	C5—C6—H6A	121.6

C4—N1—C2—C1	−112.0 (3)	O2—C4—C5—O3	−178.9 (4)
C4—N1—C2—C3	124.6 (3)	N1—C4—C5—O3	1.3 (5)
O1—C1—C2—N1	176.3 (3)	O2—C4—C5—C6	0.4 (5)
O1—C1—C2—C3	−61.3 (3)	N1—C4—C5—C6	−179.5 (3)
C2—N1—C4—O2	−5.2 (5)	O3—C5—C6—N2	−2.7 (5)
C2—N1—C4—C5	174.6 (3)	C4—C5—C6—N2	178.1 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1C···O1ⁱ	0.82	1.99	2.811 (4)	179
N1—H1D···O2ⁱⁱ	0.86	2.35	3.1024 (18)	146
C6—H6A···O3ⁱⁱⁱ	0.93	2.18	3.039 (3)	153

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

Experimental details

Crystal data
Chemical formula	C₆H₉N₃O₃
M_r	171.16
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	5.3136 (3), 6.7551 (3), 23.3958 (11)
V (Å³)	839.77 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.11
Crystal size (mm)	0.46 × 0.38 × 0.32

Data collection
Diffractometer	Bruker SMART CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.951, 0.965
No. of measured, independent and observed [I > 2σ(I)] reflections	9692, 903, 826
R_int	0.027
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.123, 1.17
No. of reflections	903
No. of parameters	109
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.14

Computer programs: SMART (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1C···O1ⁱ	0.82	1.99	2.811 (4)	179.2
N1—H1D···O2ⁱⁱ	0.86	2.35	3.1024 (18)	145.8
C6—H6A···O3ⁱⁱⁱ	0.93	2.18	3.039 (3)	153

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

Acknowledgements

The authors would like to thank Hebei University and East China Normal University for financial support. This work was also supported by the National Natural Science Foundation of China (grant No. 21002032).

References

Bruker (2007). SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Doyle, M. P. (1986). Chem. Rev. 86, 919–939. CrossRef CAS Google Scholar
Doyle, M. P. & Forbes, D. C. (1998). Chem. Rev. 98, 911–935. CrossRef PubMed CAS Google Scholar
Pedone, E. & Brocchini, S. (2006). React. Funct. Polym. 66, 167–176. CrossRef CAS 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
Zhang, Z. H. & Wang, J. B. (2008). Tetrahedron, 64, 6577–6605. CrossRef CAS Google Scholar