Literature DB >> 21203274

rac-2-Hydroxy-2,8-dimethyl-4-morpho-linoethyl-1-thia-4-aza-spiro-[4.5]decan-3-one.

Mehmet Akkurt, Serife Pınar Yalçın, Nalan Terzioğlu Klip, Orhan Büyükgüngör.   

Abstract

The title compound, C(16)H(28)N(2)O(3)S, is dimerized by inversion symmetry-related inter-molecular O-H⋯N hydrogen bonding, forming an R(2) (2)(16) motif. The dimers are also linked through inter-molecular C-H⋯O hydrogen bonding. The compound is chiral with a stereogenic centre located in the thia-zole ring, but in the crystal structure it forms a racemate. The thia-zole ring has an envelope conformation, while the cyclo-hexane and morpholine rings adopt chair conformations.

Entities:  

Year:  2008        PMID： 21203274      PMCID： PMC2962193          DOI： 10.1107/S1600536808022447

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN： 1600-5368


Related literature

For general background, see: Andres et al. (2000 ▶); Çapan et al. (1999 ▶); Srivastava et al. (2005 ▶). For related literature and bond-length data, see: Akkurt et al. (2007 ▶); Akkurt, Yalçın, Güzeldemirci et al. (2008 ▶); Akkurt, Yalçın, Klip et al. (2008 ▶). For ring conformation puckering parameters, see: Cremer & Pople (1975 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C16H28N2O3S M = 328.47 Triclinic, a = 8.0753 (4) Å b = 10.2002 (5) Å c = 11.8734 (6) Å α = 82.467 (4)° β = 71.487 (4)° γ = 68.965 (4)° V = 865.44 (8) Å3 Z = 2 Mo Kα radiation μ = 0.20 mm−1 T = 296 K 0.73 × 0.45 × 0.29 mm

Data collection

Stoe IPDS-2 diffractometer Absorption correction: integration (X-RED32; Stoe & Cie, 2002 ▶) T min = 0.867, T max = 0.944 18220 measured reflections 3693 independent reflections 3319 reflections with I > 2σ(I) R int = 0.038

Refinement

R[F 2 > 2σ(F 2)] = 0.035 wR(F 2) = 0.093 S = 1.04 3693 reflections 199 parameters H-atom parameters constrained Δρmax = 0.31 e Å−3 Δρmin = −0.21 e Å−3 Data collection: X-AREA (Stoe & Cie, 2002 ▶); cell refinement: X-AREA; data reduction: X-RED32 (Stoe & Cie, 2002 ▶); program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶) and PLATON (Spek, 2003 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808022447/kp2184sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536808022447/kp2184Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C16H28N2O3SZ = 2
Mr = 328.47F000 = 356
Triclinic, P1Dx = 1.260 Mg m−3
Hall symbol: -P 1Mo Kα radiation λ = 0.71073 Å
a = 8.0753 (4) ÅCell parameters from 29023 reflections
b = 10.2002 (5) Åθ = 2.1–27.4º
c = 11.8734 (6) ŵ = 0.20 mm−1
α = 82.467 (4)ºT = 296 K
β = 71.487 (4)ºBlock, colourless
γ = 68.965 (4)º0.73 × 0.45 × 0.29 mm
V = 865.44 (8) Å3
Stoe IPDS-2 diffractometer3693 independent reflections
Monochromator: plane graphite3319 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm-1Rint = 0.038
T = 296 Kθmax = 26.9º
ω scansθmin = 2.1º
Absorption correction: integration(X-RED32; Stoe & Cie, 2002)h = −10→10
Tmin = 0.867, Tmax = 0.944k = −12→12
18220 measured reflectionsl = −15→15
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.093  w = 1/[σ2(Fo2) + (0.0478P)2 + 0.1524P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3693 reflectionsΔρmax = 0.31 e Å−3
199 parametersΔρmin = −0.21 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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.
xyzUiso*/Ueq
S10.33771 (4)0.24227 (4)0.79561 (3)0.0486 (1)
O10.45350 (15)0.25388 (12)0.45525 (9)0.0555 (3)
O21.23062 (15)0.29531 (12)0.15285 (9)0.0597 (3)
O30.11938 (12)0.32395 (10)0.65362 (9)0.0480 (3)
N10.59680 (14)0.23670 (11)0.59509 (9)0.0389 (3)
N20.90885 (14)0.39307 (11)0.34820 (9)0.0372 (3)
C10.28811 (17)0.22315 (13)0.65981 (12)0.0417 (4)
C20.45358 (17)0.24085 (13)0.55883 (11)0.0408 (3)
C30.58346 (16)0.22120 (13)0.72210 (10)0.0369 (3)
C40.7085 (2)0.07643 (14)0.75151 (12)0.0482 (4)
C50.7034 (2)0.06187 (17)0.88162 (14)0.0583 (5)
C60.7495 (2)0.17691 (19)0.92078 (13)0.0587 (5)
C70.6200 (2)0.31982 (17)0.89350 (13)0.0541 (5)
C80.62959 (19)0.33651 (14)0.76215 (12)0.0445 (4)
C90.7389 (3)0.1587 (3)1.05180 (17)0.0881 (8)
C100.76951 (17)0.23709 (13)0.50474 (11)0.0413 (3)
C110.75792 (17)0.38482 (13)0.45390 (11)0.0408 (3)
C120.90146 (19)0.34106 (16)0.24137 (11)0.0471 (4)
C131.0540 (2)0.36400 (19)0.13593 (12)0.0584 (5)
C141.2384 (2)0.34737 (18)0.25562 (13)0.0554 (5)
C151.09318 (17)0.32359 (15)0.36461 (11)0.0432 (4)
C160.2750 (2)0.08031 (15)0.65024 (15)0.0561 (5)
H30.122100.402600.658200.0720*
H4A0.668700.004700.733100.0580*
H4B0.835000.061400.702200.0580*
H5A0.580700.063900.930200.0700*
H5B0.79130−0.028500.894800.0700*
H60.876900.169600.874900.0700*
H7A0.653700.393200.915100.0650*
H7B0.493700.330500.941000.0650*
H8A0.543000.427300.748500.0530*
H8B0.753300.333700.715100.0530*
H9A0.822700.068001.065400.1320*
H9B0.614700.166301.098300.1320*
H9C0.772700.230401.074300.1320*
H10A0.795400.175700.440900.0500*
H10B0.871100.200600.539700.0500*
H11A0.641700.427500.434600.0490*
H11B0.754500.440500.515400.0490*
H12A0.781700.390700.228100.0570*
H12B0.917500.241800.251400.0570*
H13A1.050100.328800.065100.0700*
H13B1.033200.463900.123900.0700*
H14A1.219200.447100.244800.0670*
H14B1.360300.300500.266400.0670*
H15A1.115700.223600.378300.0520*
H15B1.099700.361200.433400.0520*
H16A0.171600.068400.713000.0840*
H16B0.387200.007900.656700.0840*
H16C0.257900.074300.574900.0840*
U11U22U33U12U13U23
S10.0372 (2)0.0676 (2)0.0380 (2)−0.0232 (2)−0.0003 (1)−0.0024 (1)
O10.0540 (6)0.0738 (7)0.0406 (5)−0.0258 (5)−0.0106 (4)−0.0033 (4)
O20.0495 (6)0.0739 (7)0.0429 (5)−0.0201 (5)0.0074 (4)−0.0128 (5)
O30.0364 (5)0.0458 (5)0.0612 (6)−0.0141 (4)−0.0110 (4)−0.0065 (4)
N10.0332 (5)0.0452 (6)0.0346 (5)−0.0165 (4)−0.0011 (4)−0.0009 (4)
N20.0344 (5)0.0407 (5)0.0322 (5)−0.0144 (4)−0.0012 (4)−0.0031 (4)
C10.0360 (6)0.0429 (6)0.0448 (7)−0.0163 (5)−0.0054 (5)−0.0035 (5)
C20.0389 (6)0.0406 (6)0.0407 (6)−0.0150 (5)−0.0059 (5)−0.0034 (5)
C30.0334 (5)0.0390 (6)0.0353 (6)−0.0152 (5)−0.0026 (4)−0.0006 (4)
C40.0480 (7)0.0408 (7)0.0478 (7)−0.0115 (6)−0.0081 (6)0.0007 (5)
C50.0593 (9)0.0556 (8)0.0498 (8)−0.0133 (7)−0.0140 (7)0.0106 (6)
C60.0453 (7)0.0845 (11)0.0437 (7)−0.0222 (7)−0.0098 (6)−0.0002 (7)
C70.0564 (8)0.0637 (9)0.0458 (7)−0.0296 (7)−0.0056 (6)−0.0099 (6)
C80.0460 (7)0.0430 (7)0.0447 (7)−0.0210 (5)−0.0064 (5)−0.0018 (5)
C90.0772 (13)0.1301 (19)0.0518 (10)−0.0263 (12)−0.0219 (9)−0.0022 (10)
C100.0330 (6)0.0421 (6)0.0391 (6)−0.0125 (5)0.0022 (5)−0.0012 (5)
C110.0355 (6)0.0396 (6)0.0387 (6)−0.0126 (5)0.0018 (5)−0.0038 (5)
C120.0457 (7)0.0579 (8)0.0387 (6)−0.0195 (6)−0.0102 (5)−0.0038 (5)
C130.0639 (9)0.0734 (10)0.0334 (7)−0.0260 (8)−0.0045 (6)−0.0019 (6)
C140.0409 (7)0.0703 (9)0.0520 (8)−0.0259 (7)0.0014 (6)−0.0080 (7)
C150.0355 (6)0.0517 (7)0.0395 (6)−0.0150 (5)−0.0048 (5)−0.0055 (5)
C160.0533 (8)0.0466 (8)0.0683 (9)−0.0239 (6)−0.0077 (7)−0.0058 (6)
S1—C11.8295 (14)C4—H4B0.9700
S1—C31.8410 (14)C5—H5A0.9700
O1—C21.2197 (16)C5—H5B0.9700
O2—C131.412 (2)C6—H60.9800
O2—C141.4204 (19)C7—H7A0.9700
O3—C11.3990 (17)C7—H7B0.9700
O3—H30.8200C8—H8A0.9700
N1—C31.4688 (15)C8—H8B0.9700
N1—C101.4659 (18)C9—H9A0.9600
N1—C21.3420 (19)C9—H9B0.9600
N2—C121.4633 (17)C9—H9C0.9600
N2—C151.4651 (19)C10—H10A0.9700
N2—C111.4636 (17)C10—H10B0.9700
C1—C21.535 (2)C11—H11A0.9700
C1—C161.520 (2)C11—H11B0.9700
C3—C81.524 (2)C12—H12A0.9700
C3—C41.5298 (19)C12—H12B0.9700
C4—C51.521 (2)C13—H13A0.9700
C5—C61.516 (2)C13—H13B0.9700
C6—C91.521 (2)C14—H14A0.9700
C6—C71.523 (2)C14—H14B0.9700
C7—C81.527 (2)C15—H15A0.9700
C10—C111.5297 (18)C15—H15B0.9700
C12—C131.513 (2)C16—H16A0.9600
C14—C151.506 (2)C16—H16B0.9600
C4—H4A0.9700C16—H16C0.9600
S1···N12.6146 (11)H5B···H9A2.4800
S1···H5A2.8900H6···H8B2.5600
S1···H7B2.8200H6···H16Av2.5100
O1···O32.8913 (15)H7A···H9C2.5400
O1···C113.187 (2)H7A···H14Avi2.5400
O1···C14i3.221 (2)H7B···S12.8200
O1···C15i3.230 (2)H7B···O2x2.8100
O2···N22.8364 (16)H7B···H5A2.5600
O3···C15ii3.3942 (17)H7B···H9B2.5300
O3···O12.8913 (15)H8A···H12Aii2.5600
O3···N2ii2.8104 (14)H8B···O3v2.7800
O1···H10A2.5400H8B···C102.7500
O1···H11A2.6600H8B···C113.0700
O1···H15Bi2.7500H8B···H62.5600
O1···H16C2.8000H8B···H10B2.3800
O1···H14Bi2.5200H8B···H11B2.4700
O1···H16Biii2.8200H8B···H14Avi2.4400
O2···H9Biv2.7900H9A···H5B2.4800
O2···H7Biv2.8100H9B···O2x2.7900
O3···H15Bi2.6400H9B···C14x3.0700
O3···H8Bi2.7800H9B···H5A2.5000
O3···H14Aii2.9100H9B···H7B2.5300
N1···S12.6146 (11)H9B···H14Bx2.4800
N2···O22.8364 (16)H9C···C12xi3.0000
N2···O3ii2.8104 (14)H9C···H7A2.5400
N2···H3ii2.0000H10A···O12.5400
C2···C11ii3.5847 (18)H10A···C122.8100
C8···C113.4925 (18)H10A···H12B2.2700
C11···C83.4925 (18)H10B···C42.8100
C11···C2ii3.5847 (18)H10B···C82.9100
C11···O13.187 (2)H10B···C152.7700
C14···O1v3.221 (2)H10B···H4B2.2500
C15···O1v3.230 (2)H10B···H8B2.3800
C15···O3ii3.3942 (17)H10B···H15A2.3300
C2···H11A2.8300H11A···O12.6600
C4···H10B2.8100H11A···C22.8300
C8···H14Avi2.8600H11A···H12A2.3700
C8···H10B2.9100H11A···C11ii3.0600
C8···H11B2.9700H11A···H11Aii2.4000
C10···H12B2.8600H11B···C82.9700
C10···H4B2.8300H11B···H8B2.4700
C10···H15A2.6800H11B···H15B2.5000
C10···H8B2.7500H12A···H11A2.3700
C11···H8B3.0700H12A···H8Aii2.5600
C11···H3ii2.7100H12B···C102.8600
C11···H11Aii3.0600H12B···H10A2.2700
C12···H3ii2.9300H12B···H15A2.4700
C12···H10A2.8100H13B···H14A2.3400
C12···H9Cvii3.0000H14A···H13B2.3400
C14···H9Biv3.0700H14A···O3ii2.9100
C14···H3ii3.0800H14A···C8vi2.8600
C15···H10B2.7700H14A···H3ii2.5900
C15···H3ii2.7400H14A···H7Avi2.5400
H3···N2ii2.0000H14A···H8Bvi2.4400
H3···C11ii2.7100H14B···O1v2.5200
H3···C12ii2.9300H14B···H9Biv2.4800
H3···C14ii3.0800H15A···C102.6800
H3···C15ii2.7400H15A···H10B2.3300
H3···H14Aii2.5900H15A···H12B2.4700
H4A···H15Aviii2.5800H15A···H4Aviii2.5800
H4B···C102.8300H15B···O1v2.7500
H4B···H10B2.2500H15B···O3v2.6400
H5A···S12.8900H15B···H11B2.5000
H5A···H7B2.5600H16A···H6i2.5100
H5A···H9B2.5000H16B···O1iii2.8200
H5A···H5Aix2.3300H16C···O12.8000
C1—S1—C394.96 (6)C6—C7—H7B109.00
C13—O2—C14109.74 (12)C8—C7—H7A109.00
C1—O3—H3109.00C8—C7—H7B109.00
C2—N1—C10118.36 (10)H7A—C7—H7B108.00
C3—N1—C10121.36 (11)C3—C8—H8A109.00
C2—N1—C3120.12 (11)C3—C8—H8B109.00
C11—N2—C15113.24 (10)C7—C8—H8A109.00
C12—N2—C15109.83 (11)C7—C8—H8B109.00
C11—N2—C12113.29 (11)H8A—C8—H8B108.00
S1—C1—C2104.53 (10)C6—C9—H9A109.00
S1—C1—C16113.45 (10)C6—C9—H9B109.00
S1—C1—O3110.65 (9)C6—C9—H9C109.00
O3—C1—C16107.00 (12)H9A—C9—H9B110.00
C2—C1—C16108.91 (11)H9A—C9—H9C109.00
O3—C1—C2112.40 (11)H9B—C9—H9C109.00
O1—C2—C1121.93 (14)N1—C10—H10A109.00
N1—C2—C1113.93 (11)N1—C10—H10B109.00
O1—C2—N1124.12 (13)C11—C10—H10A109.00
S1—C3—N1103.79 (9)C11—C10—H10B109.00
S1—C3—C8109.34 (9)H10A—C10—H10B108.00
N1—C3—C4111.50 (10)N2—C11—H11A108.00
S1—C3—C4110.49 (9)N2—C11—H11B108.00
C4—C3—C8110.34 (12)C10—C11—H11A108.00
N1—C3—C8111.20 (10)C10—C11—H11B108.00
C3—C4—C5111.95 (11)H11A—C11—H11B107.00
C4—C5—C6112.88 (13)N2—C12—H12A110.00
C5—C6—C7109.51 (14)N2—C12—H12B110.00
C7—C6—C9111.87 (16)C13—C12—H12A110.00
C5—C6—C9110.62 (16)C13—C12—H12B110.00
C6—C7—C8111.54 (12)H12A—C12—H12B108.00
C3—C8—C7111.69 (12)O2—C13—H13A109.00
N1—C10—C11111.71 (11)O2—C13—H13B109.00
N2—C11—C10115.84 (11)C12—C13—H13A109.00
N2—C12—C13109.15 (13)C12—C13—H13B109.00
O2—C13—C12111.53 (12)H13A—C13—H13B108.00
O2—C14—C15111.11 (14)O2—C14—H14A109.00
N2—C15—C14109.61 (11)O2—C14—H14B109.00
C3—C4—H4A109.00C15—C14—H14A109.00
C3—C4—H4B109.00C15—C14—H14B109.00
C5—C4—H4A109.00H14A—C14—H14B108.00
C5—C4—H4B109.00N2—C15—H15A110.00
H4A—C4—H4B108.00N2—C15—H15B110.00
C4—C5—H5A109.00C14—C15—H15A110.00
C4—C5—H5B109.00C14—C15—H15B110.00
C6—C5—H5A109.00H15A—C15—H15B108.00
C6—C5—H5B109.00C1—C16—H16A109.00
H5A—C5—H5B108.00C1—C16—H16B109.00
C5—C6—H6108.00C1—C16—H16C109.00
C7—C6—H6108.00H16A—C16—H16B109.00
C9—C6—H6108.00H16A—C16—H16C109.00
C6—C7—H7A109.00H16B—C16—H16C109.00
C3—S1—C1—O3−136.07 (10)C12—N2—C15—C1456.88 (15)
C3—S1—C1—C2−14.85 (9)C12—N2—C11—C1071.48 (15)
C3—S1—C1—C16103.66 (11)S1—C1—C2—N112.26 (13)
C1—S1—C3—N113.84 (9)O3—C1—C2—O1−49.39 (17)
C1—S1—C3—C4−105.81 (9)O3—C1—C2—N1132.32 (12)
C1—S1—C3—C8132.57 (9)C16—C1—C2—O169.00 (17)
C14—O2—C13—C12−59.69 (17)C16—C1—C2—N1−109.30 (13)
C13—O2—C14—C1559.60 (16)S1—C1—C2—O1−169.45 (11)
C2—N1—C10—C1179.30 (14)N1—C3—C8—C7−178.85 (12)
C3—N1—C2—O1179.78 (12)C8—C3—C4—C552.97 (16)
C10—N1—C2—O1−4.83 (19)S1—C3—C8—C767.13 (14)
C3—N1—C10—C11−105.38 (13)N1—C3—C4—C5177.06 (13)
C2—N1—C3—C8−126.75 (13)C4—C3—C8—C7−54.59 (16)
C10—N1—C3—C858.01 (15)S1—C3—C4—C5−68.06 (15)
C10—N1—C2—C1173.42 (10)C3—C4—C5—C6−54.55 (19)
C2—N1—C3—C4109.65 (14)C4—C5—C6—C755.23 (18)
C2—N1—C3—S1−9.30 (13)C4—C5—C6—C9178.97 (16)
C10—N1—C3—S1175.45 (9)C5—C6—C7—C8−56.25 (18)
C10—N1—C3—C4−65.59 (15)C9—C6—C7—C8−179.25 (16)
C3—N1—C2—C1−1.97 (16)C6—C7—C8—C357.30 (18)
C11—N2—C12—C13175.83 (12)N1—C10—C11—N2−169.01 (11)
C15—N2—C11—C10−54.44 (15)N2—C12—C13—O258.47 (17)
C15—N2—C12—C13−56.45 (15)O2—C14—C15—N2−58.52 (16)
C11—N2—C15—C14−175.38 (11)
D—H···AD—HH···AD···AD—H···A
O3—H3···N2ii0.822.002.8104 (14)169
C7—H7B···S10.972.823.2235 (18)106
C14—H14B···O1v0.972.523.221 (2)129
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯AD⋯AD—H⋯A
O3—H3⋯N2i0.822.002.8104 (14)169
C7—H7B⋯S10.972.823.2235 (18)106
C14—H14B⋯O1ii0.972.523.221 (2)129

Symmetry codes: (i) ; (ii) .

  4 in total

1.  N-(3-Oxo-1-thia-4-aza-spiro-[4.5]dec-4-yl)-6-phenyl-imidazo[2,1-b][1,3]thia-zole-3-acetamide hemihydrate.

Authors:  Mehmet Akkurt; Serife Pınar Yalçın; Nuray Ulusoy Güzeldemirci; Orhan Büyükgüngör
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-04-10

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  4-Thiazolidinones: novel inhibitors of the bacterial enzyme MurB.

Authors:  C J Andres; J J Bronson; S V D'Andrea; M S Deshpande; P J Falk; K A Grant-Young; W E Harte; H T Ho; P F Misco; J G Robertson; D Stock; Y Sun; A W Walsh
Journal:  Bioorg Med Chem Lett       Date:  2000-04-17       Impact factor: 2.823

4.  8-Methyl-4-morpholinoethyl-1-thia-4-aza-spiro-[4.5]decan-3-one.

Authors:  Mehmet Akkurt; Serife Pınar Yalçın; Nalan Terzioğlu Klip; Orhan Büyükgüngör
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-07-23
  4 in total
  1 in total

1.  8-Ethyl-2-hydr-oxy-2-methyl-4-morpholinoethyl-1-thia-4-aza-spiro-[4.5]decan-3-one.

Authors:  Mehmet Akkurt; Serife Pınar Yalçın; Nalan Terzioğlu Klip; Orhan Büyükgüngör
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2008-09-13
  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.