Methyl (E)-2-acetyl-3-amino-2-pentenoate

The structure of the title compound, C₈H₁₃NO₃, refined in space group Pna2₁, which was chosen over Pnam as the space group because of the lack of mirror or inversion symmetry. An N—H...O intermolecular hydrogen bond is observed.

Key indicators

• Single-crystal X-ray study
• T = 294 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.048
• wR factor = 0.087
• Data-to-parameter ratio = 18.0

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



STRVAL_01
         From the CIF: _refine_ls_abs_structure_Flack   -0.500
         From the CIF: _refine_ls_abs_structure_Flack_su    1.600
           Alert C Flack parameter is too small

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           27.55
         From the CIF: _reflns_number_total               2037
         Count of symmetry unique reflns         1134
         Completeness (_total/calc)            179.63%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured       903
         Fraction of Friedel pairs measured     0.796
         Are heavy atom types Z>Si present           no
          ALERT: MoKa measured Friedel data cannot be used to
                 determine absolute structure in a light-atom
                 study EXCEPT under VERY special conditions.
                 It is preferred that Friedel data is merged in such cases.


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

---

S1. Comment

The title compound, (I), is one of the by-products obtained during the synthesis of methyl 3-acetamido-2-pentenoate from the reaction of methyl 3-aminopent-2-enoate reflux with acetic anhydride in THF for 24 h (Hackler et al., 1985; Lubell et al., 1991; Yasutake et al., 2001). The structure determination of (I) was conducted in order to obtain more sterochemical imformation.

In the crystal structure of (I) (Fig. 1), the N1—C1—C2—C5, C1—C2—C5—O3 and C1—C2—C5—C6 torsion angles are −2.0 (4), −1.1 (4) and 179.4 (3)°, respectively. This show that atoms N1/C1/C2/C5/O3 are almost in the same plane and the C1═C2 and C5═O3 double bond form a conjugated system (Table 1). The molecules in the crystal structure are interconnected by N—H···O hydrogen bonding (Table 2). As shown in the packing diagram (Fig. 2), the hydrogen bond links the molecules along the c axis.

S2. Experimental

The title compound, (I), was synthesized according the literature (Zhu et al., 1999). A crystal suitable for X-ray analysis was grown slowly from mixed solution in ethyl acetate and hexane (1:5) at room temperature.

S3. Refinement

H atoms were included in the riding-model approximation, with U_iso values equal to U_eq of the atom to which they were bound.

Computing details

Data collection: SMART (Siemens, 1995); cell refinement: SMART; data reduction: SHELXTL (Siemens, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. The molecular structure of (I), showing ellipsoids at the 50% probability level (Siemens, 1995).
	Fig. 2. Packing diagram for (I). The hydrogen bonds are indicated by dashed lines.

(I)

Crystal data

C8H13NO3	Dx = 1.238 Mg m^−3
Mr = 171.19	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna21	Cell parameters from 1585 reflections
a = 23.998 (7) Å	θ = 1–27.5°
b = 4.2785 (13) Å	µ = 0.10 mm^−1
c = 8.944 (3) Å	T = 294 K
V = 918.3 (5) Å^3	Needle, colorless
Z = 4	0.50 × 0.40 × 0.38 mm
F(000) = 368

Data collection

Siemens SMART CCD area-detector diffractometer	2037 independent reflections
Radiation source: fine-focus sealed tube	903 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.069
ϕ and ω scans	θmax = 27.6°, θmin = 3.4°
Absorption correction: empirical (using intensity measurements) (SADABS; Sheldrick, 1996)	h = −27→31
Tmin = 0.954, Tmax = 0.965	k = −5→5
5793 measured reflections	l = −11→10

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.048	w = 1/[σ^2(Fo^2) + (0.015P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.088	(Δ/σ)max < 0.001
S = 1.03	Δρmax = 0.15 e Å^−3
2037 reflections	Δρmin = −0.14 e Å^−3
113 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0098 (18)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983)
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.5 (16)

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	0.44379 (8)	0.1383 (5)	0.2634 (2)	0.0754 (8)
O2	0.45293 (7)	0.3468 (6)	0.4878 (2)	0.0698 (7)
O3	0.29467 (8)	0.0214 (6)	0.5840 (2)	0.0787 (8)
N1	0.27088 (9)	0.2708 (7)	0.3271 (3)	0.0679 (8)
H1A	0.2578	0.1805	0.4055	0.081*
H1B	0.2485	0.3391	0.2594	0.081*
C1	0.32485 (12)	0.3042 (7)	0.3106 (3)	0.0447 (7)
C2	0.36303 (12)	0.1983 (7)	0.4164 (3)	0.0405 (7)
C3	0.42254 (11)	0.2214 (8)	0.3776 (4)	0.0489 (8)
C4	0.51181 (11)	0.3632 (9)	0.4619 (5)	0.0940 (13)
H4A	0.5281	0.1611	0.4781	0.141*
H4B	0.5282	0.5114	0.5295	0.141*
H4C	0.5186	0.4280	0.3608	0.141*
C5	0.34507 (13)	0.0534 (7)	0.5535 (3)	0.0519 (8)
C6	0.38585 (12)	−0.0638 (7)	0.6674 (4)	0.0655 (9)
H6A	0.4012	0.1100	0.7213	0.098*
H6B	0.4153	−0.1753	0.6179	0.098*
H6C	0.3672	−0.2011	0.7359	0.098*
C7	0.34162 (11)	0.4897 (8)	0.1762 (3)	0.0498 (7)
H7A	0.3784	0.5769	0.1928	0.060*
H7B	0.3158	0.6624	0.1636	0.060*
C8	0.34246 (13)	0.2961 (8)	0.0336 (3)	0.0672 (10)
H8A	0.3699	0.1340	0.0424	0.101*
H8B	0.3515	0.4282	−0.0497	0.101*
H8C	0.3065	0.2040	0.0180	0.101*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0569 (13)	0.118 (2)	0.0511 (15)	−0.0050 (12)	0.0160 (13)	−0.0220 (15)
O2	0.0460 (12)	0.105 (2)	0.0586 (16)	−0.0033 (12)	0.0041 (13)	−0.0246 (14)
O3	0.0556 (13)	0.126 (2)	0.0547 (15)	0.0022 (15)	0.0120 (11)	0.0308 (15)
N1	0.0440 (15)	0.114 (2)	0.0456 (19)	−0.0007 (16)	−0.0024 (13)	0.0214 (18)
C1	0.0500 (18)	0.052 (2)	0.0325 (17)	−0.0022 (15)	0.0016 (15)	−0.0011 (17)
C2	0.0437 (16)	0.050 (2)	0.0279 (16)	0.0013 (14)	0.0019 (14)	0.0012 (17)
C3	0.0469 (17)	0.058 (2)	0.0413 (19)	0.0021 (18)	−0.0046 (18)	−0.0036 (16)
C4	0.045 (2)	0.136 (4)	0.101 (3)	−0.007 (2)	−0.0074 (19)	−0.027 (3)
C5	0.0592 (19)	0.058 (2)	0.039 (2)	0.0067 (17)	0.0050 (16)	−0.0019 (18)
C6	0.078 (2)	0.077 (2)	0.0412 (18)	0.0095 (19)	−0.0014 (18)	0.013 (2)
C7	0.0565 (17)	0.0484 (17)	0.045 (2)	−0.0012 (15)	0.0023 (16)	0.0079 (19)
C8	0.091 (2)	0.070 (2)	0.040 (2)	−0.001 (2)	0.0037 (17)	0.0063 (18)

Geometric parameters (Å, º)

O1—C3	1.196 (4)	C4—H4B	0.9600
O2—C3	1.339 (3)	C4—H4C	0.9600
O2—C4	1.433 (3)	C5—C6	1.499 (4)
O3—C5	1.247 (3)	C6—H6A	0.9600
N1—C1	1.311 (3)	C6—H6B	0.9600
N1—H1A	0.8600	C6—H6C	0.9600
N1—H1B	0.8600	C7—C8	1.521 (4)
C1—C2	1.393 (4)	C7—H7A	0.9700
C1—C7	1.496 (4)	C7—H7B	0.9700
C2—C5	1.440 (4)	C8—H8A	0.9600
C2—C3	1.473 (3)	C8—H8B	0.9600
C4—H4A	0.9600	C8—H8C	0.9600
C3—O2—C4	115.9 (3)	O3—C5—C6	116.6 (3)
C1—N1—H1A	120.0	C2—C5—C6	121.8 (3)
C1—N1—H1B	120.0	C5—C6—H6A	109.5
H1A—N1—H1B	120.0	C5—C6—H6B	109.5
N1—C1—C2	122.5 (3)	H6A—C6—H6B	109.5
N1—C1—C7	114.4 (3)	C5—C6—H6C	109.5
C2—C1—C7	122.8 (2)	H6A—C6—H6C	109.5
C1—C2—C5	121.4 (3)	H6B—C6—H6C	109.5
C1—C2—C3	117.1 (2)	C1—C7—C8	112.9 (2)
C5—C2—C3	121.3 (3)	C1—C7—H7A	109.0
O1—C3—O2	121.1 (3)	C8—C7—H7A	109.0
O1—C3—C2	126.5 (3)	C1—C7—H7B	109.0
O2—C3—C2	112.4 (3)	C8—C7—H7B	109.0
O2—C4—H4A	109.5	H7A—C7—H7B	107.8
O2—C4—H4B	109.5	C7—C8—H8A	109.5
H4A—C4—H4B	109.5	C7—C8—H8B	109.5
O2—C4—H4C	109.5	H8A—C8—H8B	109.5
H4A—C4—H4C	109.5	C7—C8—H8C	109.5
H4B—C4—H4C	109.5	H8A—C8—H8C	109.5
O3—C5—C2	121.6 (3)	H8B—C8—H8C	109.5
N1—C1—C2—C5	−2.0 (4)	C1—C2—C3—O2	132.4 (3)
C7—C1—C2—C5	172.4 (3)	C5—C2—C3—O2	−51.7 (4)
N1—C1—C2—C3	173.9 (3)	C1—C2—C5—O3	−1.1 (4)
C7—C1—C2—C3	−11.7 (4)	C3—C2—C5—O3	−176.9 (3)
C4—O2—C3—O1	−2.2 (5)	C1—C2—C5—C6	179.4 (3)
C4—O2—C3—C2	177.0 (3)	C3—C2—C5—C6	3.7 (5)
C1—C2—C3—O1	−48.5 (5)	N1—C1—C7—C8	−82.2 (3)
C5—C2—C3—O1	127.5 (4)	C2—C1—C7—C8	102.9 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O3	0.86	1.95	2.597 (3)	131
N1—H1B···O3^i	0.86	2.04	2.890 (3)	172

Symmetry code: (i) −x+1/2, y+1/2, z−1/2.