Synthesis and crystal structure of (2S,4aR,8aR)-6-oxo-2,4a,6,8a-tetra­hydro­pyrano[3,2-b]pyran-2-carboxamide

(2S,4aR,8aR)-6-Oxo-2,4a,6,8a-tetra­hydro­pyrano[3,2-b]pyran-2-carboxamide, a potentially effective anti­bacterial agent, was prepared by a chemoselective hydration of the corresponding nitrile using a heterogeneous catalytic method based on copper(II) supported on mol­ecular sieves, in the presence of acetaldoxime. It belongs to a new class of pyran­opyrans that possess anti­bacterial and phytotoxic activity.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.032
• wR factor = 0.080
• Data-to-parameter ratio = 18.2

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Datablock: I


Alert level G
PLAT032_ALERT_4_G Std. Uncertainty on Flack Parameter Value High .      0.300 Report
PLAT791_ALERT_4_G Model has Chirality at C4A         (Sohnke SpGr)          R Verify
PLAT791_ALERT_4_G Model has Chirality at C6          (Sohnke SpGr)          S Verify
PLAT791_ALERT_4_G Model has Chirality at C8A         (Sohnke SpGr)          R Verify
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          7 Info

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   5 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 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
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Computing details

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2015); data reduction: SAINT (Bruker, 2015); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

(2S,4aR,8aR)-6-Oxo-2,4a,6,8a-tetrahydropyrano[3,2-b]pyran-2-carboxamide

Crystal data

C9H9NO4	Dx = 1.558 Mg m^−3
Mr = 195.17	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 8408 reflections
a = 4.9279 (1) Å	θ = 2.3–30.2°
b = 10.6350 (3) Å	µ = 0.12 mm^−1
c = 15.8788 (4) Å	T = 100 K
V = 832.18 (4) Å^3	Prism, colourless
Z = 4	0.4 × 0.3 × 0.18 mm
F(000) = 408

Data collection

Bruker SMART APEXII area detector diffractometer	2461 independent reflections
Radiation source: sealed tube	2366 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.031
Detector resolution: 8 pixels mm^-1	θmax = 30.2°, θmin = 2.3°
ω and φ scans	h = −5→6
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	k = −15→14
Tmin = 0.654, Tmax = 0.746	l = −22→22
14252 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.032	w = 1/[σ^2(Fo^2) + (0.0446P)^2 + 0.205P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.080	(Δ/σ)max < 0.001
S = 1.04	Δρmax = 0.35 e Å^−3
2461 reflections	Δρmin = −0.20 e Å^−3
135 parameters	Absolute structure: Flack x determined using 928 quotients [(I^+)-(I^-)]/[(I^+)+(I^-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: −0.1 (3)
Primary atom site location: structure-invariant direct methods

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. 1. Fixed Uiso At 1.2 times of: All C(H) groups 2.a Ternary CH refined with riding coordinates: C4A(H4A), C6(H6), C8A(H8A) 2.b Aromatic/amide H refined with riding coordinates: C3(H3), C4(H4), C7(H7), C8(H8) 3. N1(H1A) and N1(H1B) located from the difference map with refined Uiso

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.7129 (2)	0.30730 (10)	0.31022 (7)	0.0145 (2)
C2	0.5987 (3)	0.22091 (15)	0.36070 (9)	0.0141 (3)
O2	0.7069 (3)	0.11890 (11)	0.36663 (8)	0.0198 (3)
C3	0.3563 (3)	0.25659 (15)	0.40997 (9)	0.0155 (3)
H3	0.2482	0.1928	0.4350	0.019*
C4	0.2869 (3)	0.37655 (14)	0.41980 (10)	0.0154 (3)
H4	0.1413	0.3982	0.4562	0.019*
C4A	0.4377 (3)	0.47756 (14)	0.37369 (9)	0.0121 (3)
H4A	0.3071	0.5453	0.3574	0.015*
O5	0.6340 (2)	0.52880 (10)	0.43085 (6)	0.0118 (2)
C6	0.7796 (3)	0.63226 (13)	0.39613 (9)	0.0107 (3)
H6	0.9519	0.6405	0.4289	0.013*
C7	0.8579 (3)	0.61248 (14)	0.30510 (9)	0.0126 (3)
H7	0.9754	0.6718	0.2792	0.015*
C8	0.7700 (3)	0.51613 (14)	0.25988 (9)	0.0140 (3)
H8	0.8362	0.5046	0.2042	0.017*
C8A	0.5687 (3)	0.42536 (14)	0.29495 (9)	0.0124 (3)
H8A	0.4244	0.4103	0.2518	0.015*
C9	0.6280 (3)	0.75809 (14)	0.40406 (8)	0.0112 (3)
O3	0.3793 (2)	0.76516 (11)	0.40436 (7)	0.0163 (2)
N1	0.7940 (3)	0.85729 (13)	0.40610 (9)	0.0151 (3)
H1A	0.735 (5)	0.933 (2)	0.4068 (15)	0.033 (6)*
H1B	0.967 (5)	0.845 (2)	0.4125 (13)	0.017 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0173 (5)	0.0092 (5)	0.0170 (5)	0.0032 (4)	0.0028 (4)	−0.0007 (4)
C2	0.0161 (7)	0.0111 (7)	0.0151 (6)	−0.0009 (5)	−0.0026 (5)	−0.0014 (5)
O2	0.0235 (6)	0.0102 (5)	0.0255 (6)	0.0034 (4)	0.0003 (5)	0.0013 (4)
C3	0.0137 (6)	0.0138 (7)	0.0189 (7)	−0.0026 (6)	0.0003 (5)	0.0016 (6)
C4	0.0121 (6)	0.0140 (7)	0.0202 (7)	−0.0014 (5)	0.0027 (5)	−0.0012 (5)
C4A	0.0104 (6)	0.0093 (6)	0.0166 (6)	0.0006 (5)	0.0004 (5)	−0.0011 (5)
O5	0.0140 (5)	0.0093 (5)	0.0121 (4)	−0.0021 (4)	0.0006 (4)	0.0006 (4)
C6	0.0103 (6)	0.0087 (6)	0.0130 (6)	−0.0001 (5)	−0.0001 (5)	0.0005 (5)
C7	0.0116 (6)	0.0119 (6)	0.0145 (6)	0.0021 (5)	0.0030 (5)	0.0029 (5)
C8	0.0170 (7)	0.0133 (7)	0.0117 (6)	0.0035 (6)	0.0023 (5)	0.0018 (5)
C8A	0.0153 (7)	0.0088 (6)	0.0130 (6)	0.0021 (5)	−0.0017 (5)	−0.0005 (5)
C9	0.0144 (6)	0.0096 (6)	0.0097 (5)	0.0009 (5)	0.0001 (5)	−0.0001 (5)
O3	0.0121 (5)	0.0128 (5)	0.0240 (5)	0.0019 (4)	0.0016 (4)	−0.0016 (4)
N1	0.0155 (6)	0.0082 (6)	0.0215 (6)	0.0000 (5)	−0.0023 (5)	0.0015 (5)

Geometric parameters (Å, º)

O1—C2	1.3428 (18)	C6—H6	1.0000
O1—C8A	1.4629 (18)	C6—C7	1.511 (2)
C2—O2	1.2126 (19)	C6—C9	1.538 (2)
C2—C3	1.478 (2)	C7—H7	0.9500
C3—H3	0.9500	C7—C8	1.324 (2)
C3—C4	1.330 (2)	C8—H8	0.9500
C4—H4	0.9500	C8—C8A	1.492 (2)
C4—C4A	1.497 (2)	C8A—H8A	1.0000
C4A—H4A	1.0000	C9—O3	1.2280 (19)
C4A—O5	1.4343 (18)	C9—N1	1.335 (2)
C4A—C8A	1.513 (2)	N1—H1A	0.86 (3)
O5—C6	1.4243 (17)	N1—H1B	0.87 (2)
C2—O1—C8A	118.85 (12)	C7—C6—C9	108.88 (11)
O1—C2—C3	118.63 (14)	C9—C6—H6	107.1
O2—C2—O1	118.31 (14)	C6—C7—H7	118.6
O2—C2—C3	122.97 (14)	C8—C7—C6	122.88 (13)
C2—C3—H3	119.5	C8—C7—H7	118.6
C4—C3—C2	121.08 (14)	C7—C8—H8	119.5
C4—C3—H3	119.5	C7—C8—C8A	121.06 (13)
C3—C4—H4	119.9	C8A—C8—H8	119.5
C3—C4—C4A	120.23 (14)	O1—C8A—C4A	112.66 (12)
C4A—C4—H4	119.9	O1—C8A—C8	107.10 (12)
C4—C4A—H4A	108.9	O1—C8A—H8A	108.7
C4—C4A—C8A	110.65 (12)	C4A—C8A—H8A	108.7
O5—C4A—C4	107.33 (12)	C8—C8A—C4A	110.78 (12)
O5—C4A—H4A	108.9	C8—C8A—H8A	108.7
O5—C4A—C8A	112.00 (12)	O3—C9—C6	122.57 (14)
C8A—C4A—H4A	108.9	O3—C9—N1	124.26 (15)
C6—O5—C4A	112.85 (11)	N1—C9—C6	113.09 (13)
O5—C6—H6	107.1	C9—N1—H1A	122.5 (17)
O5—C6—C7	113.04 (12)	C9—N1—H1B	118.8 (14)
O5—C6—C9	113.33 (12)	H1A—N1—H1B	118 (2)
C7—C6—H6	107.1
O1—C2—C3—C4	−15.0 (2)	O5—C4A—C8A—C8	−47.00 (16)
C2—O1—C8A—C4A	41.32 (17)	O5—C6—C7—C8	8.0 (2)
C2—O1—C8A—C8	163.37 (12)	O5—C6—C9—O3	−30.03 (19)
C2—C3—C4—C4A	6.2 (2)	O5—C6—C9—N1	153.21 (13)
O2—C2—C3—C4	161.46 (16)	C6—C7—C8—C8A	4.7 (2)
C3—C4—C4A—O5	−98.05 (16)	C7—C6—C9—O3	96.70 (16)
C3—C4—C4A—C8A	24.4 (2)	C7—C6—C9—N1	−80.06 (15)
C4—C4A—O5—C6	−176.04 (11)	C7—C8—C8A—O1	−108.78 (16)
C4—C4A—C8A—O1	−46.75 (16)	C7—C8—C8A—C4A	14.4 (2)
C4—C4A—C8A—C8	−166.70 (12)	C8A—O1—C2—O2	173.12 (13)
C4A—O5—C6—C7	−41.21 (16)	C8A—O1—C2—C3	−10.21 (19)
C4A—O5—C6—C9	83.29 (14)	C8A—C4A—O5—C6	62.33 (15)
O5—C4A—C8A—O1	72.95 (15)	C9—C6—C7—C8	−118.85 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O2^i	0.86 (3)	2.08 (3)	2.8840 (18)	156 (2)
N1—H1B···O3^ii	0.87 (2)	2.21 (2)	3.0462 (18)	163.1 (19)
C6—H6···O3^ii	1.00	2.52	3.2787 (19)	133

Symmetry codes: (i) x, y+1, z; (ii) x+1, y, z.