tert-Butyl 4-carbamoyl-3-methoxy­imino-4-methyl­piperidine-1-carboxyl­ate

The title compound, C₁₃H₂₃N₃O₄, was prepared starting from ethyl N-benzyl-3-oxopiperidine-4-carboxyl­ate through a nine-step reaction, including hydrogenation, Boc (tert-butoxy­carbon­yl) protection, methyl­ation, oximation, hydrolysis, esterification and ammonolysis. In the crystal structure, mol­ecules are linked by inter­molecular N—H...O hydrogen bonds to form a porous three-dimensional network with solvent-free hydro­phobic channels extending along the c axis.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.039
• wR factor = 0.113
• Data-to-parameter ratio = 15.3

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT601_ALERT_2_B Structure Contains Solvent Accessible VOIDS of .     105.00 A   3 

Alert level C
            Value of measurement temperature given =   293.000
            Value of melting point given =     0.000
PLAT242_ALERT_2_C Check Low       Ueq as Compared to Neighbors for         C7

Alert level G
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT793_ALERT_4_G The Model has Chirality at C3      (Verify) ....          R

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   3 ALERT level G = General alerts; check

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

Quinolones, a class of synthetic antibacterial compounds based on a 4-quinolone skeleton, have been the landmark discovery in the treatment of bacterial infections in both community and hospital setting (Ray et al., 2005; Ball et al., 1998; Bryskier, 1997). The most intensive structural variations have been carried out on the basic group at the C-7 position, partially due to the ease of their introduction through a nucleophilic aromatic substitution reaction on the corresponding halide. Piperazine, aminopyrolidine and their derivatives have been the most successfully employed side chains, as evidenced by the compounds currently on the market (De Sarro & De Sarro, 2001; Anderson & Osheroff, 2001; Dang et al., 2007). Recently, as part of an ongoing study aimed to find potent and broad-spectrum antibacterial agents displaying strong Gram-positive activity, we have focused our attention on the synthesis of C-7 substituted quinolones (Wang et al., 2008). We report here the crystal structure of the title compound, which is a key intermediate of 3-methoxyimino-4-amino-4-methylpiperidine.

In the molecule of the title compound (Fig. 1), the N1—C6 (1.352 (2) Å) and N3—C12 (1.323 (2) Å) bond lengths are significantly shorter than the normal C—N single bond (1.47 Å), indicating some conjugation with the C6═O2 and C12═O4 carbonyl groups, respectively. The six-membered piperidine ring adopts a boat conformation, with N1 and C3 displaced by 0.533 (2) and 0.632 (2) Å, respectively, from the mean-plane through C1, C2, C4 and C5. In the crystal structure, molecules are linked by intermolecular N—H···O hydrogen bonds (Table 1) to form a porous three-dimensional network with solvent-free hydrophobic channels extending along the c axis (Fig. 2).

Related literature

For the synthesis and properties of quinolone derivatives, see: Ray et al. (2005); Ball et al. (1998); Bryskier (1997); De Sarro & De Sarro (2001); Anderson & Osheroff (2001); Dang et al. (2007); Wang et al. (2008).

S2. Experimental

To a solution of ethyl N-Boc-3-methoxyimino-4-methylpiperidine-4-carboxylate (12.71 g, 40.5 mmol) in ethanol (50 ml) was added dropwise a solution of sodium hydroxide (2.75 g, 68.85 mmol) in water (5 ml) at room temperature. After stirring for 4.5 h, ethanol was removed under reduced pressure. After addition of water (20 ml), acetic acid (5 ml, 86.5 mmol) and triethylamine (17 ml, 122 mmol), the mixture was stirred for 10 min and extracted with CH₂Cl₂ (3 × 40 ml). The combined organic extracts were washed with saturated brine (3 × 20 ml) and dried over anhydrous sodium sulfate. The reaction mixture was then cooled to 259-261 K, and isobutyl chloroformate (13.1 ml, 101.8 mmol) was added. After 0.5 h, the reaction mixture was washed with 1 N HCl (4 × 20 ml) and saturated brine (4 × 40 ml), and dried over anhydrous sodium sulfate. The resulting yellow residue was purified by column chromatography, with petroleum ether/diethyl ether (3:1 v/v) as eluent to afford the title compound (4.92 g, 42.6%; mp: 140–142 °C). Single crystals suitable for X-ray analysis were obtained by slow evaporation of an ethanol/ethyl acetoacetate solution (1:1 v/v). ¹H NMR (CDCl₃, δ): 1.37-1.46 (12H, m, CH₃), 1.50-1.57 (1H, m, C₅), 2.43-2.49 (1H, m, C₅), 3.38-3.53 (2H, m, C₆), 3.89 (3H, s, OCH₃), 4.17-4.45 (2H, m, C₂), 5.57 (1H, br, CONH), 6.00 (1H, br, CONH). MS (ESI, m/z): 286 (M+1)⁺.

S3. Refinement

All H atoms were placed at calculated positions, with C—H = 0.95–0.98 Å, N—H = 0.86 Å, and included in the final cycles of refinement using a riding model, with U_iso(H) = 1.2 U_eq(C, N) or 1.5 U_eq(C) for methyl H atoms. The crystal structure contains voids of about 105 ų connected to form channels along the c axis, which may accommodate solvent molecules. However, significant residual densities in the void could not be observed in the difference Fourier map.

Computing details

Data collection: SMART (Bruker, 1998); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT (Bruker, 1999); 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

	Fig. 1. The molecular structure of the title compound, showing 40% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 2. Crystal packing of the title compound viewed along the c axis.

tert-Butyl 4-carbamoyl-3-methoxyimino-4-methylpiperidine-1-carboxylate

Crystal data

C13H23N3O4	Dx = 1.206 Mg m^−3
Mr = 285.34	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I41/a	Cell parameters from 3595 reflections
Hall symbol: -I 4ad	θ = 2.5–22.6°
a = 22.813 (2) Å	µ = 0.09 mm^−1
c = 12.0742 (16) Å	T = 293 K
V = 6283.8 (11) Å^3	Block, colorless
Z = 16	0.48 × 0.46 × 0.45 mm
F(000) = 2464

Data collection

Bruker SMART APEX CCD diffractometer	2763 independent reflections
Radiation source: fine-focus sealed tube	1794 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.049
ϕ and ω scans	θmax = 25.0°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −27→27
Tmin = 0.957, Tmax = 0.963	k = −27→18
16003 measured reflections	l = −14→14

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.113	H-atom parameters constrained
S = 1.01	w = 1/[σ^2(Fo^2) + (0.0607P)^2] where P = (Fo^2 + 2Fc^2)/3
2763 reflections	(Δ/σ)max < 0.001
181 parameters	Δρmax = 0.19 e Å^−3
0 restraints	Δρmin = −0.12 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
N1	0.38925 (6)	0.53733 (7)	0.27764 (13)	0.0504 (4)
N2	0.29390 (6)	0.58484 (6)	0.05570 (12)	0.0430 (4)
N3	0.41951 (6)	0.51996 (6)	−0.00791 (13)	0.0484 (4)
H3A	0.4432	0.4941	−0.0342	0.058*
H3B	0.3830	0.5189	−0.0253	0.058*
O1	0.46173 (5)	0.48101 (5)	0.33671 (11)	0.0554 (4)
O2	0.37946 (6)	0.43856 (6)	0.26866 (13)	0.0694 (4)
O3	0.24359 (5)	0.55589 (5)	0.09853 (10)	0.0501 (4)
O4	0.49117 (5)	0.56448 (5)	0.08658 (12)	0.0570 (4)
C1	0.33172 (8)	0.54686 (10)	0.23109 (17)	0.0558 (5)
H1A	0.3080	0.5692	0.2828	0.067*
H1B	0.3126	0.5094	0.2189	0.067*
C2	0.33613 (7)	0.57937 (7)	0.12372 (14)	0.0400 (4)
C3	0.39477 (7)	0.60751 (7)	0.09840 (14)	0.0405 (4)
C4	0.41585 (8)	0.63467 (8)	0.20750 (15)	0.0502 (5)
H4A	0.4531	0.6541	0.1949	0.060*
H4B	0.3879	0.6642	0.2309	0.060*
C5	0.42325 (9)	0.58985 (8)	0.30031 (16)	0.0558 (5)
H5A	0.4643	0.5796	0.3074	0.067*
H5B	0.4105	0.6069	0.3698	0.067*
C6	0.40799 (8)	0.48163 (10)	0.29224 (16)	0.0503 (5)
C7	0.49544 (8)	0.42673 (9)	0.34839 (16)	0.0544 (5)
C8	0.50169 (11)	0.39737 (11)	0.2370 (2)	0.0890 (8)
H8A	0.4643	0.3824	0.2138	0.134*
H8B	0.5292	0.3657	0.2426	0.134*
H8C	0.5155	0.4254	0.1837	0.134*
C9	0.55329 (9)	0.44949 (10)	0.3911 (2)	0.0709 (6)
H9A	0.5703	0.4754	0.3372	0.106*
H9B	0.5794	0.4172	0.4041	0.106*
H9C	0.5471	0.4704	0.4590	0.106*
C10	0.46678 (10)	0.38805 (11)	0.4341 (2)	0.0861 (8)
H10A	0.4619	0.4096	0.5017	0.129*
H10B	0.4910	0.3544	0.4475	0.129*
H10C	0.4291	0.3755	0.4076	0.129*
C11	0.19775 (8)	0.55590 (9)	0.01807 (17)	0.0588 (6)
H11A	0.1818	0.5947	0.0115	0.088*
H11B	0.1674	0.5293	0.0408	0.088*
H11C	0.2132	0.5437	−0.0522	0.088*
C12	0.43929 (8)	0.56124 (7)	0.05932 (14)	0.0401 (4)
C13	0.39064 (9)	0.65416 (8)	0.00759 (16)	0.0529 (5)
H13A	0.3761	0.6366	−0.0593	0.079*
H13B	0.4288	0.6705	−0.0057	0.079*
H13C	0.3644	0.6847	0.0308	0.079*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0401 (9)	0.0565 (10)	0.0546 (10)	0.0059 (8)	−0.0052 (7)	0.0066 (8)
N2	0.0373 (9)	0.0459 (9)	0.0457 (9)	0.0019 (7)	0.0041 (7)	−0.0026 (7)
N3	0.0342 (8)	0.0456 (9)	0.0655 (11)	0.0027 (7)	0.0014 (7)	−0.0195 (8)
O1	0.0444 (8)	0.0558 (8)	0.0661 (9)	0.0102 (6)	−0.0121 (6)	0.0019 (7)
O2	0.0574 (9)	0.0617 (10)	0.0890 (11)	−0.0071 (7)	−0.0152 (8)	0.0097 (8)
O3	0.0346 (7)	0.0627 (8)	0.0529 (8)	−0.0010 (6)	0.0000 (6)	0.0073 (6)
O4	0.0338 (7)	0.0607 (9)	0.0766 (10)	0.0034 (6)	−0.0029 (6)	−0.0254 (7)
C1	0.0360 (11)	0.0753 (14)	0.0560 (13)	0.0088 (9)	0.0019 (9)	0.0136 (10)
C2	0.0345 (10)	0.0412 (10)	0.0442 (10)	0.0093 (8)	0.0030 (8)	−0.0041 (8)
C3	0.0398 (10)	0.0369 (10)	0.0447 (10)	0.0042 (8)	0.0025 (8)	−0.0042 (8)
C4	0.0525 (12)	0.0423 (11)	0.0559 (12)	0.0054 (9)	−0.0005 (9)	−0.0119 (9)
C5	0.0593 (13)	0.0571 (13)	0.0509 (12)	0.0100 (10)	−0.0094 (10)	−0.0106 (10)
C6	0.0433 (12)	0.0622 (14)	0.0453 (12)	0.0027 (10)	−0.0009 (9)	0.0055 (10)
C7	0.0512 (12)	0.0570 (13)	0.0549 (13)	0.0139 (9)	0.0011 (10)	0.0058 (10)
C8	0.0959 (19)	0.0966 (19)	0.0744 (17)	0.0334 (15)	−0.0017 (14)	−0.0162 (14)
C9	0.0470 (13)	0.0821 (16)	0.0837 (17)	0.0128 (11)	−0.0020 (11)	0.0093 (13)
C10	0.0726 (16)	0.0894 (18)	0.0962 (19)	0.0002 (13)	−0.0024 (14)	0.0364 (15)
C11	0.0409 (11)	0.0714 (14)	0.0641 (13)	−0.0025 (9)	−0.0097 (10)	0.0085 (11)
C12	0.0345 (10)	0.0393 (10)	0.0467 (11)	−0.0006 (8)	0.0024 (8)	−0.0035 (8)
C13	0.0551 (12)	0.0464 (11)	0.0571 (12)	0.0021 (9)	0.0057 (9)	0.0021 (9)

Geometric parameters (Å, º)

N1—C6	1.352 (2)	C4—H4B	0.9700
N1—C1	1.444 (2)	C5—H5A	0.9700
N1—C5	1.453 (2)	C5—H5B	0.9700
N2—C2	1.272 (2)	C7—C10	1.509 (3)
N2—O3	1.4217 (17)	C7—C9	1.509 (3)
N3—C12	1.323 (2)	C7—C8	1.509 (3)
N3—H3A	0.8600	C8—H8A	0.9600
N3—H3B	0.8600	C8—H8B	0.9600
O1—C6	1.339 (2)	C8—H8C	0.9600
O1—C7	1.465 (2)	C9—H9A	0.9600
O2—C6	1.213 (2)	C9—H9B	0.9600
O3—C11	1.427 (2)	C9—H9C	0.9600
O4—C12	1.2308 (19)	C10—H10A	0.9600
C1—C2	1.497 (2)	C10—H10B	0.9600
C1—H1A	0.9700	C10—H10C	0.9600
C1—H1B	0.9700	C11—H11A	0.9600
C2—C3	1.515 (2)	C11—H11B	0.9600
C3—C13	1.531 (2)	C11—H11C	0.9600
C3—C4	1.533 (2)	C13—H13A	0.9600
C3—C12	1.539 (2)	C13—H13B	0.9600
C4—C5	1.526 (3)	C13—H13C	0.9600
C4—H4A	0.9700
C6—N1—C1	118.66 (17)	O1—C7—C10	109.46 (16)
C6—N1—C5	125.56 (16)	O1—C7—C9	101.60 (15)
C1—N1—C5	115.73 (16)	C10—C7—C9	110.25 (18)
C2—N2—O3	109.33 (14)	O1—C7—C8	109.82 (17)
C12—N3—H3A	120.0	C10—C7—C8	113.1 (2)
C12—N3—H3B	120.0	C9—C7—C8	111.98 (17)
H3A—N3—H3B	120.0	C7—C8—H8A	109.5
C6—O1—C7	121.90 (15)	C7—C8—H8B	109.5
N2—O3—C11	110.11 (13)	H8A—C8—H8B	109.5
N1—C1—C2	110.52 (15)	C7—C8—H8C	109.5
N1—C1—H1A	109.5	H8A—C8—H8C	109.5
C2—C1—H1A	109.5	H8B—C8—H8C	109.5
N1—C1—H1B	109.5	C7—C9—H9A	109.5
C2—C1—H1B	109.5	C7—C9—H9B	109.5
H1A—C1—H1B	108.1	H9A—C9—H9B	109.5
N2—C2—C1	123.83 (16)	C7—C9—H9C	109.5
N2—C2—C3	119.79 (16)	H9A—C9—H9C	109.5
C1—C2—C3	116.37 (15)	H9B—C9—H9C	109.5
C2—C3—C13	112.63 (14)	C7—C10—H10A	109.5
C2—C3—C4	105.95 (14)	C7—C10—H10B	109.5
C13—C3—C4	110.71 (14)	H10A—C10—H10B	109.5
C2—C3—C12	110.73 (13)	C7—C10—H10C	109.5
C13—C3—C12	107.33 (14)	H10A—C10—H10C	109.5
C4—C3—C12	109.49 (14)	H10B—C10—H10C	109.5
C5—C4—C3	113.25 (14)	O3—C11—H11A	109.5
C5—C4—H4A	108.9	O3—C11—H11B	109.5
C3—C4—H4A	108.9	H11A—C11—H11B	109.5
C5—C4—H4B	108.9	O3—C11—H11C	109.5
C3—C4—H4B	108.9	H11A—C11—H11C	109.5
H4A—C4—H4B	107.7	H11B—C11—H11C	109.5
N1—C5—C4	110.80 (15)	O4—C12—N3	122.35 (15)
N1—C5—H5A	109.5	O4—C12—C3	120.75 (15)
C4—C5—H5A	109.5	N3—C12—C3	116.84 (15)
N1—C5—H5B	109.5	C3—C13—H13A	109.5
C4—C5—H5B	109.5	C3—C13—H13B	109.5
H5A—C5—H5B	108.1	H13A—C13—H13B	109.5
O2—C6—O1	125.26 (19)	C3—C13—H13C	109.5
O2—C6—N1	124.14 (18)	H13A—C13—H13C	109.5
O1—C6—N1	110.60 (17)	H13B—C13—H13C	109.5
C2—N2—O3—C11	−173.54 (15)	C1—N1—C5—C4	−40.4 (2)
C6—N1—C1—C2	−118.26 (19)	C3—C4—C5—N1	−20.9 (2)
C5—N1—C1—C2	59.1 (2)	C7—O1—C6—O2	8.3 (3)
O3—N2—C2—C1	0.3 (2)	C7—O1—C6—N1	−172.16 (15)
O3—N2—C2—C3	−178.79 (13)	C1—N1—C6—O2	0.0 (3)
N1—C1—C2—N2	167.35 (16)	C5—N1—C6—O2	−177.08 (19)
N1—C1—C2—C3	−13.5 (2)	C1—N1—C6—O1	−179.54 (15)
N2—C2—C3—C13	16.4 (2)	C5—N1—C6—O1	3.4 (3)
C1—C2—C3—C13	−162.72 (16)	C6—O1—C7—C10	−68.6 (2)
N2—C2—C3—C4	137.60 (16)	C6—O1—C7—C9	174.80 (16)
C1—C2—C3—C4	−41.54 (19)	C6—O1—C7—C8	56.1 (2)
N2—C2—C3—C12	−103.77 (18)	C2—C3—C12—O4	−142.74 (17)
C1—C2—C3—C12	77.10 (19)	C13—C3—C12—O4	93.96 (19)
C2—C3—C4—C5	59.91 (19)	C4—C3—C12—O4	−26.3 (2)
C13—C3—C4—C5	−177.69 (15)	C2—C3—C12—N3	40.0 (2)
C12—C3—C4—C5	−59.54 (19)	C13—C3—C12—N3	−83.25 (19)
C6—N1—C5—C4	136.72 (18)	C4—C3—C12—N3	156.51 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···O4^i	0.86	2.11	2.9607 (18)	173
N3—H3B···O3^ii	0.86	2.34	3.1334 (19)	153

Symmetry codes: (i) −x+1, −y+1, −z; (ii) y−1/4, −x+3/4, z−1/4.