(Z)-2-Thio­phen-3-yl­methyl­ene-1-aza-bi­cyclo­[2.2.2]­octan-3-one

The crystal structure of C₁₂H₁₃NOS, which was obtained in a base-catalysed condensation reaction of thio­phene-3-carbox­aldehyde with 1-aza-bi­cyclo­[2.2.2]­octan-3-one, is presented. The title compound, which contains a double bond connecting an aza­bicyclic ring system to a thio­phen-3-yl­methyl­ene moiety, crystallizes from solution in methanol and has a thienyl ring-flip disorder.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.045
• wR factor = 0.122
• Data-to-parameter ratio = 17.1

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .......          ?
PLAT301_ALERT_3_C Main Residue  Disorder .........................      12.00 Perc.
PLAT779_ALERT_2_C Suspect or Irrelevant (Bond) Angle in CIF ......       7.70 Deg.
              C5'  -C2   -S1      1.555   1.555   1.555
PLAT779_ALERT_2_C Suspect or Irrelevant (Bond) Angle in CIF ......       8.10 Deg.
              C5   -C4   -S1'     1.555   1.555   1.555
PLAT790_ALERT_4_C Centre of Gravity not Within Unit Cell: Resd.  #          1
              C12 H13 N O S

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

   0 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
   1 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion

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Computing details

Data collection: COLLECT (Nonius, 1999); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO-SMN (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP in SHELXTL (Sheldrick, 1994); software used to prepare material for publication: SHELX97 (Sheldrick, 1997) and local procedures.

(Z)-2-Thiophen-3-ylmethylene-1-aza-bicyclo[2.2.2]octan-3-one

Crystal data

C12H13NOS	F(000) = 464
Mr = 219.29	Dx = 1.363 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71073 Å
a = 11.321 (1) Å	Cell parameters from 6483 reflections
b = 5.8790 (6) Å	θ = 1.0–27.5°
c = 16.100 (2) Å	µ = 0.27 mm^−1
β = 94.058 (10)°	T = 173 K
V = 1068.9 (2) Å^3	Rod, yellow
Z = 4	0.40 × 0.33 × 0.20 mm

Data collection

Nonius KappaCCD diffractometer	2452 independent reflections
Radiation source: fine-focus sealed tube	1802 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.042
Detector resolution: 18 pixels mm^-1	θmax = 27.5°, θmin = 2.1°
ω scans at fixed χ = 55°	h = −14→14
Absorption correction: multi-scan (SCALEPACK; Otwinowski & Minor, 1997)	k = −7→7
Tmin = 0.899, Tmax = 0.947	l = −20→20
7996 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.045	H-atom parameters constrained
wR(F^2) = 0.122	w = 1/[σ^2(Fo^2) + (0.0604P)^2 + 0.2115P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max = 0.002
2452 reflections	Δρmax = 0.24 e Å^−3
143 parameters	Δρmin = −0.25 e Å^−3
8 restraints	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.020 (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	Occ. (<1)
S1	−0.1702 (3)	−0.3427 (5)	0.29234 (16)	0.0389 (4)	0.50
C5'	−0.1557 (11)	−0.317 (2)	0.2840 (7)	0.0389 (4)	0.50
H5'	−0.2144	−0.4059	0.3082	0.047*	0.50
C2	−0.11178 (15)	−0.3704 (3)	0.20480 (11)	0.0374 (4)
H2	−0.1329	−0.4921	0.1678	0.045*
C3	−0.02826 (14)	−0.2065 (3)	0.18579 (10)	0.0296 (4)
C4	−0.01283 (15)	−0.0427 (3)	0.24936 (10)	0.0333 (4)
H4	0.0395	0.0838	0.2502	0.040*
C5	−0.0883 (8)	−0.0997 (15)	0.3110 (4)	0.0366 (3)	0.50
H5	−0.0940	−0.0106	0.3598	0.044*	0.50
S1'	−0.09402 (17)	−0.0817 (3)	0.33130 (8)	0.0366 (3)	0.50
C6	0.03386 (14)	−0.2198 (3)	0.11007 (10)	0.0294 (4)
H6	0.0006	−0.3209	0.0687	0.035*
C7	0.13123 (14)	−0.1097 (3)	0.09042 (10)	0.0272 (4)
N8	0.19491 (12)	0.0516 (2)	0.14457 (8)	0.0304 (4)
C9	0.21488 (18)	0.2604 (3)	0.09625 (12)	0.0415 (5)
H9A	0.2560	0.3744	0.1332	0.050*
H9B	0.1375	0.3252	0.0759	0.050*
C10	0.28946 (18)	0.2139 (3)	0.02131 (12)	0.0440 (5)
H10A	0.2472	0.2696	−0.0307	0.053*
H10B	0.3664	0.2940	0.0289	0.053*
C11	0.30970 (15)	−0.0440 (3)	0.01581 (10)	0.0351 (4)
H11	0.3527	−0.0837	−0.0344	0.042*
C12	0.37970 (16)	−0.1217 (3)	0.09611 (10)	0.0370 (4)
H12A	0.4594	−0.0515	0.1000	0.044*
H12B	0.3893	−0.2891	0.0958	0.044*
C13	0.31109 (15)	−0.0486 (3)	0.17110 (10)	0.0354 (4)
H13A	0.2991	−0.1826	0.2068	0.043*
H13B	0.3586	0.0642	0.2047	0.043*
C14	0.19134 (15)	−0.1599 (3)	0.01362 (10)	0.0323 (4)
O15	0.15168 (12)	−0.2842 (2)	−0.04277 (7)	0.0451 (4)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0353 (9)	0.0493 (8)	0.0325 (7)	−0.0044 (5)	0.0049 (5)	−0.0035 (6)
C5'	0.0353 (9)	0.0493 (8)	0.0325 (7)	−0.0044 (5)	0.0049 (5)	−0.0035 (6)
C2	0.0299 (9)	0.0437 (11)	0.0379 (10)	−0.0042 (8)	−0.0021 (8)	0.0008 (8)
C3	0.0242 (8)	0.0339 (9)	0.0303 (9)	0.0038 (7)	−0.0013 (6)	0.0009 (7)
C4	0.0305 (9)	0.0352 (10)	0.0342 (9)	0.0036 (8)	0.0018 (7)	−0.0056 (7)
C5	0.0321 (5)	0.0473 (6)	0.0305 (8)	0.0003 (4)	0.0040 (6)	−0.0064 (6)
S1'	0.0321 (5)	0.0473 (6)	0.0305 (8)	0.0003 (4)	0.0040 (6)	−0.0064 (6)
C6	0.0276 (9)	0.0309 (9)	0.0290 (9)	0.0010 (7)	−0.0033 (7)	−0.0044 (7)
C7	0.0287 (9)	0.0263 (9)	0.0265 (8)	0.0013 (7)	0.0002 (6)	−0.0018 (6)
N8	0.0339 (8)	0.0264 (7)	0.0308 (7)	−0.0042 (6)	0.0018 (6)	−0.0034 (6)
C9	0.0540 (11)	0.0256 (9)	0.0453 (11)	−0.0028 (9)	0.0060 (9)	−0.0007 (8)
C10	0.0592 (13)	0.0355 (10)	0.0376 (11)	−0.0087 (9)	0.0056 (9)	0.0080 (8)
C11	0.0392 (10)	0.0386 (10)	0.0283 (9)	−0.0043 (8)	0.0085 (7)	−0.0003 (7)
C12	0.0319 (9)	0.0394 (10)	0.0399 (10)	−0.0009 (8)	0.0035 (7)	−0.0008 (8)
C13	0.0354 (10)	0.0400 (10)	0.0303 (9)	−0.0059 (8)	−0.0017 (7)	0.0018 (8)
C14	0.0384 (10)	0.0310 (9)	0.0272 (9)	0.0007 (8)	0.0011 (7)	0.0002 (7)
O15	0.0531 (8)	0.0502 (8)	0.0320 (7)	−0.0098 (7)	0.0035 (6)	−0.0123 (6)

Geometric parameters (Å, º)

S1—C2	1.607 (3)	N8—C13	1.476 (2)
S1—C5	1.718 (8)	N8—C9	1.480 (2)
C5'—C2	1.436 (10)	C9—C10	1.545 (3)
C5'—S1'	1.705 (11)	C9—H9A	0.9900
C5'—H5'	0.9500	C9—H9B	0.9900
C2—C3	1.399 (2)	C10—C11	1.537 (3)
C2—H2	0.9500	C10—H10A	0.9900
C3—C4	1.407 (2)	C10—H10B	0.9900
C3—C6	1.452 (2)	C11—C14	1.501 (2)
C4—C5	1.395 (7)	C11—C12	1.537 (2)
C4—S1'	1.676 (2)	C11—H11	1.0000
C4—H4	0.9500	C12—C13	1.542 (2)
C5—H5	0.9500	C12—H12A	0.9900
C6—C7	1.335 (2)	C12—H12B	0.9900
C6—H6	0.9500	C13—H13A	0.9900
C7—N8	1.4456 (19)	C13—H13B	0.9900
C7—C14	1.483 (2)	C14—O15	1.2255 (19)
C2—S1—C5	89.3 (2)	N8—C9—H9A	109.2
C2—C5'—S1'	114.7 (7)	C10—C9—H9A	109.2
C2—C5'—H5'	122.7	N8—C9—H9B	109.2
S1'—C5'—H5'	122.7	C10—C9—H9B	109.2
C3—C2—C5'	109.0 (4)	H9A—C9—H9B	107.9
C3—C2—S1	116.65 (17)	C11—C10—C9	108.16 (14)
C5'—C2—S1	7.7 (5)	C11—C10—H10A	110.1
C3—C2—H2	121.7	C9—C10—H10A	110.1
C5'—C2—H2	129.3	C11—C10—H10B	110.1
S1—C2—H2	121.7	C9—C10—H10B	110.1
C2—C3—C4	111.30 (15)	H10A—C10—H10B	108.4
C2—C3—C6	121.44 (15)	C14—C11—C10	108.21 (15)
C4—C3—C6	127.22 (15)	C14—C11—C12	106.92 (14)
C5—C4—C3	107.6 (3)	C10—C11—C12	108.34 (15)
C5—C4—S1'	8.1 (4)	C14—C11—H11	111.1
C3—C4—S1'	115.59 (15)	C10—C11—H11	111.1
C5—C4—H4	126.2	C12—C11—H11	111.1
C3—C4—H4	126.2	C11—C12—C13	108.51 (14)
S1'—C4—H4	118.2	C11—C12—H12A	110.0
C4—C5—S1	115.2 (4)	C13—C12—H12A	110.0
C4—C5—H5	122.4	C11—C12—H12B	110.0
S1—C5—H5	122.4	C13—C12—H12B	110.0
C4—S1'—C5'	89.4 (4)	H12A—C12—H12B	108.4
C7—C6—C3	129.04 (15)	N8—C13—C12	111.86 (13)
C7—C6—H6	115.5	N8—C13—H13A	109.2
C3—C6—H6	115.5	C12—C13—H13A	109.2
C6—C7—N8	124.03 (15)	N8—C13—H13B	109.2
C6—C7—C14	122.43 (14)	C12—C13—H13B	109.2
N8—C7—C14	113.26 (13)	H13A—C13—H13B	107.9
C7—N8—C13	107.99 (12)	O15—C14—C7	124.81 (16)
C7—N8—C9	108.39 (13)	O15—C14—C11	124.58 (16)
C13—N8—C9	108.48 (14)	C7—C14—C11	110.58 (13)
N8—C9—C10	112.07 (14)
S1'—C5'—C2—C3	−1.1 (10)	C6—C7—N8—C13	112.28 (17)
S1'—C5'—C2—S1	173 (6)	C14—C7—N8—C13	−61.85 (17)
C5—S1—C2—C3	1.2 (4)	C6—C7—N8—C9	−130.39 (17)
C5—S1—C2—C5'	−5 (5)	C14—C7—N8—C9	55.48 (17)
C5'—C2—C3—C4	0.2 (6)	C7—N8—C9—C10	−60.80 (19)
S1—C2—C3—C4	−0.7 (2)	C13—N8—C9—C10	56.22 (19)
C5'—C2—C3—C6	178.3 (6)	N8—C9—C10—C11	5.4 (2)
S1—C2—C3—C6	177.40 (19)	C9—C10—C11—C14	53.67 (19)
C2—C3—C4—C5	−0.4 (4)	C9—C10—C11—C12	−61.91 (19)
C6—C3—C4—C5	−178.3 (4)	C14—C11—C12—C13	−60.59 (18)
C2—C3—C4—S1'	0.7 (2)	C10—C11—C12—C13	55.84 (18)
C6—C3—C4—S1'	−177.21 (15)	C7—N8—C13—C12	54.49 (18)
C3—C4—C5—S1	1.2 (7)	C9—N8—C13—C12	−62.79 (17)
S1'—C4—C5—S1	−172 (4)	C11—C12—C13—N8	5.7 (2)
C2—S1—C5—C4	−1.4 (6)	C6—C7—C14—O15	8.8 (3)
C5—C4—S1'—C5'	6 (3)	N8—C7—C14—O15	−176.96 (15)
C3—C4—S1'—C5'	−1.1 (5)	C6—C7—C14—C11	−169.17 (15)
C2—C5'—S1'—C4	1.3 (9)	N8—C7—C14—C11	5.06 (18)
C2—C3—C6—C7	−164.64 (16)	C10—C11—C14—O15	121.19 (18)
C4—C3—C6—C7	13.1 (3)	C12—C11—C14—O15	−122.30 (18)
C3—C6—C7—N8	−0.2 (3)	C10—C11—C14—C7	−60.82 (17)
C3—C6—C7—C14	173.45 (15)	C12—C11—C14—C7	55.69 (18)