Literature DB >> 21583966

13-Hydr-oxy-4,16-dimethyl-4,16-diaza-penta-cyclo-[12.3.1.0.0.0]octa-deca-7(12),8,10-triene-6,18-dione.

J Suresh, K Gurunathan, R Suresh Kumar, S Perumal, P L Nilantha Lakshman.   

Abstract

In the title compound, C(18)H(20)N(2)O(3), the N-methyl-piperidone ring adopts a chair conformation. The pyrrolidine ring and the five-membered cyclo-pentane rings adopt envelope conformations. The five-membered ring of the ninhydrin system adopts an envelope conformation with the central C atom deviating by 0.217 (1)Å from the mean plane through the other atoms. The mol-ecular packing is characterized by inter-molecular C-H⋯O and intra-molecular C-H⋯O and O-H⋯N inter-actions.

Entities:  

Year:  2009        PMID: 21583966      PMCID: PMC2977829          DOI: 10.1107/S1600536809015293

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


Related literature

For the cytotoxic and anti­cancer properties of piperidinones, see: Dimmock et al. (1990 ▶, 2001 ▶). Piperidinone derivatives have attracted attention due to their predicted mode of inter­action with cellular thiols, having little or no affinity for the hydr­oxy and amino groups found in nucleic acids, see: Baluja et al. (1964 ▶); Mutus et al. (1989 ▶). Ninhydrin is used to monitor deprotection in solid phase peptide synthesis (Kaiser et al., 1970 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C18H20N2O3 M = 312.36 Monoclinic, a = 11.0862 (5) Å b = 11.6152 (5) Å c = 12.5670 (6) Å β = 102.851 (9)° V = 1577.70 (12) Å3 Z = 4 Mo Kα radiation μ = 0.09 mm−1 T = 293 K 0.18 × 0.13 × 0.11 mm

Data collection

Nonius MACH-3 diffractometer Absorption correction: ψ scan (North et al., 1968 ▶) T min = 0.984, T max = 0.990 3226 measured reflections 2764 independent reflections 1978 reflections with I > 2σ(I) R int = 0.046 2 standard reflections frequency: 60 min intensity decay: none

Refinement

R[F 2 > 2σ(F 2)] = 0.039 wR(F 2) = 0.120 S = 1.04 2764 reflections 211 parameters H-atom parameters constrained Δρmax = 0.16 e Å−3 Δρmin = −0.18 e Å−3 Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994 ▶); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1996 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶); software used to prepare material for publication: SHELXL97. Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809015293/at2770sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536809015293/at2770Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C18H20N2O3F(000) = 664
Mr = 312.36Dx = 1.315 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 25 reflections
a = 11.0862 (5) Åθ = 2–25°
b = 11.6152 (5) ŵ = 0.09 mm1
c = 12.5670 (6) ÅT = 293 K
β = 102.851 (9)°Needle, colourless
V = 1577.70 (12) Å30.18 × 0.13 × 0.11 mm
Z = 4
Nonius MACH-3 diffractometer1978 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.046
graphiteθmax = 25.0°, θmin = 2.2°
ω–2θ scansh = 0→13
Absorption correction: ψ scan (North et al., 1968)k = −1→13
Tmin = 0.984, Tmax = 0.990l = −14→14
3226 measured reflections2 standard reflections every 60 min
2764 independent reflections intensity decay: none
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.120H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0616P)2 + 0.2971P] where P = (Fo2 + 2Fc2)/3
2764 reflections(Δ/σ)max < 0.001
211 parametersΔρmax = 0.16 e Å3
0 restraintsΔρmin = −0.18 e Å3
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.
xyzUiso*/Ueq
C10.37990 (16)0.05350 (16)0.64487 (16)0.0558 (5)
C20.25684 (15)0.03912 (14)0.56351 (16)0.0496 (4)
C30.15940 (16)0.06258 (15)0.63055 (15)0.0517 (4)
H3A0.07720.04600.58740.062*
H3B0.17440.01430.69510.062*
C40.39217 (16)0.18110 (16)0.66421 (15)0.0537 (5)
H40.47500.20260.70510.064*
C50.29116 (17)0.21625 (17)0.72388 (14)0.0554 (5)
H5A0.30670.17960.79500.067*
H5B0.29350.29890.73490.067*
C60.36690 (14)0.22296 (15)0.54459 (15)0.0471 (4)
C70.26099 (14)0.14067 (15)0.48444 (13)0.0461 (4)
C80.14614 (15)0.21810 (16)0.45590 (13)0.0471 (4)
C90.18837 (16)0.33902 (15)0.47548 (14)0.0475 (4)
C100.31366 (16)0.34242 (15)0.52472 (14)0.0472 (4)
C110.37277 (19)0.44677 (16)0.54870 (16)0.0595 (5)
H110.45640.44980.58240.071*
C120.3053 (2)0.54695 (17)0.52175 (17)0.0680 (6)
H120.34450.61780.53630.082*
C130.1808 (2)0.54309 (18)0.47352 (17)0.0688 (6)
H130.13690.61140.45700.083*
C140.12088 (19)0.43966 (18)0.44954 (16)0.0602 (5)
H140.03700.43720.41670.072*
C150.24197 (18)−0.07110 (18)0.49582 (19)0.0671 (6)
H15A0.3119−0.12220.52030.080*
H15B0.1667−0.11130.50060.080*
C160.2361 (2)−0.0302 (2)0.3805 (2)0.0798 (7)
H16A0.2811−0.08240.34310.096*
H16B0.1509−0.02600.33970.096*
C170.2705 (2)0.1496 (2)0.28884 (17)0.0845 (7)
H17A0.18300.15630.26020.127*
H17B0.30750.11030.23690.127*
H17C0.30610.22490.30250.127*
C180.06767 (19)0.2233 (2)0.70672 (18)0.0693 (6)
H18A−0.00890.21230.65440.104*
H18B0.07870.30360.72400.104*
H18C0.06600.18080.77190.104*
N10.16914 (13)0.18280 (12)0.66132 (11)0.0479 (4)
N20.29314 (14)0.08429 (15)0.39070 (13)0.0603 (4)
O10.04209 (10)0.18577 (12)0.41422 (11)0.0618 (4)
O20.47670 (10)0.20956 (13)0.50608 (13)0.0650 (4)
H20.46730.15780.46060.098*
O30.45072 (13)−0.02185 (13)0.68415 (14)0.0810 (5)
U11U22U33U12U13U23
C10.0474 (10)0.0498 (11)0.0671 (12)0.0042 (8)0.0059 (9)0.0104 (9)
C20.0446 (9)0.0392 (9)0.0636 (11)−0.0012 (7)0.0093 (8)−0.0055 (8)
C30.0506 (10)0.0463 (10)0.0576 (11)−0.0046 (8)0.0110 (8)0.0019 (8)
C40.0431 (9)0.0535 (11)0.0569 (11)−0.0048 (8)−0.0055 (8)0.0016 (9)
C50.0653 (11)0.0536 (11)0.0430 (9)−0.0058 (9)0.0026 (8)0.0004 (8)
C60.0342 (8)0.0477 (10)0.0585 (10)−0.0011 (7)0.0082 (7)0.0006 (8)
C70.0390 (9)0.0495 (10)0.0493 (10)−0.0009 (7)0.0089 (7)−0.0065 (8)
C80.0395 (9)0.0594 (11)0.0416 (9)0.0023 (8)0.0073 (7)0.0001 (8)
C90.0505 (10)0.0509 (10)0.0434 (9)0.0056 (8)0.0150 (7)0.0053 (8)
C100.0504 (10)0.0472 (10)0.0463 (9)−0.0013 (8)0.0155 (8)0.0038 (8)
C110.0648 (12)0.0516 (12)0.0635 (12)−0.0107 (9)0.0171 (9)0.0023 (9)
C120.0982 (17)0.0463 (12)0.0655 (13)−0.0053 (11)0.0311 (12)0.0055 (10)
C130.0958 (17)0.0522 (13)0.0640 (13)0.0185 (11)0.0300 (12)0.0143 (10)
C140.0639 (12)0.0639 (13)0.0544 (11)0.0184 (10)0.0168 (9)0.0104 (9)
C150.0553 (11)0.0494 (11)0.0965 (16)−0.0015 (9)0.0170 (11)−0.0161 (11)
C160.0767 (15)0.0750 (16)0.0899 (17)−0.0090 (11)0.0229 (12)−0.0364 (13)
C170.0865 (16)0.117 (2)0.0548 (13)0.0058 (14)0.0251 (11)−0.0107 (13)
C180.0730 (13)0.0697 (14)0.0681 (13)0.0075 (11)0.0222 (10)−0.0097 (11)
N10.0508 (8)0.0466 (8)0.0461 (8)−0.0003 (6)0.0105 (6)−0.0013 (6)
N20.0567 (9)0.0692 (11)0.0584 (10)0.0002 (8)0.0201 (7)−0.0161 (8)
O10.0403 (7)0.0767 (10)0.0626 (8)−0.0001 (6)−0.0011 (6)−0.0024 (7)
O20.0405 (7)0.0683 (10)0.0891 (11)−0.0026 (6)0.0207 (6)−0.0079 (8)
O30.0642 (9)0.0617 (9)0.1068 (13)0.0116 (7)−0.0029 (8)0.0202 (8)
C1—O31.206 (2)C10—C111.379 (3)
C1—C41.503 (3)C11—C121.384 (3)
C1—C21.521 (2)C11—H110.9300
C2—C151.526 (3)C12—C131.379 (3)
C2—C31.535 (3)C12—H120.9300
C2—C71.549 (3)C13—C141.374 (3)
C3—N11.446 (2)C13—H130.9300
C3—H3A0.9700C14—H140.9300
C3—H3B0.9700C15—C161.513 (3)
C4—C51.535 (3)C15—H15A0.9700
C4—C61.545 (3)C15—H15B0.9700
C4—H40.9800C16—N21.466 (3)
C5—N11.458 (2)C16—H16A0.9700
C5—H5A0.9700C16—H16B0.9700
C5—H5B0.9700C17—N21.461 (3)
C6—O21.415 (2)C17—H17A0.9600
C6—C101.507 (2)C17—H17B0.9600
C6—C71.571 (2)C17—H17C0.9600
C7—N21.460 (2)C18—N11.448 (2)
C7—C81.535 (2)C18—H18A0.9600
C8—O11.2154 (19)C18—H18B0.9600
C8—C91.484 (3)C18—H18C0.9600
C9—C141.387 (3)O2—H20.8200
C9—C101.390 (2)
O3—C1—C4128.48 (17)C11—C10—C6128.58 (16)
O3—C1—C2126.90 (18)C9—C10—C6111.31 (14)
C4—C1—C2104.62 (14)C10—C11—C12118.75 (19)
C1—C2—C15115.87 (15)C10—C11—H11120.6
C1—C2—C3104.30 (15)C12—C11—H11120.6
C15—C2—C3116.94 (15)C13—C12—C11120.90 (19)
C1—C2—C7101.38 (13)C13—C12—H12119.6
C15—C2—C7107.23 (16)C11—C12—H12119.6
C3—C2—C7109.99 (14)C14—C13—C12120.86 (19)
N1—C3—C2107.36 (14)C14—C13—H13119.6
N1—C3—H3A110.2C12—C13—H13119.6
C2—C3—H3A110.2C13—C14—C9118.43 (19)
N1—C3—H3B110.2C13—C14—H14120.8
C2—C3—H3B110.2C9—C14—H14120.8
H3A—C3—H3B108.5C16—C15—C2104.31 (17)
C1—C4—C5106.95 (15)C16—C15—H15A110.9
C1—C4—C699.36 (15)C2—C15—H15A110.9
C5—C4—C6113.42 (14)C16—C15—H15B110.9
C1—C4—H4112.1C2—C15—H15B110.9
C5—C4—H4112.1H15A—C15—H15B108.9
C6—C4—H4112.1N2—C16—C15105.95 (17)
N1—C5—C4110.85 (14)N2—C16—H16A110.5
N1—C5—H5A109.5C15—C16—H16A110.5
C4—C5—H5A109.5N2—C16—H16B110.5
N1—C5—H5B109.5C15—C16—H16B110.5
C4—C5—H5B109.5H16A—C16—H16B108.7
H5A—C5—H5B108.1N2—C17—H17A109.5
O2—C6—C10112.31 (14)N2—C17—H17B109.5
O2—C6—C4108.33 (14)H17A—C17—H17B109.5
C10—C6—C4115.51 (15)N2—C17—H17C109.5
O2—C6—C7112.10 (14)H17A—C17—H17C109.5
C10—C6—C7104.91 (13)H17B—C17—H17C109.5
C4—C6—C7103.35 (13)N1—C18—H18A109.5
N2—C7—C8114.40 (14)N1—C18—H18B109.5
N2—C7—C2102.91 (14)H18A—C18—H18B109.5
C8—C7—C2117.03 (14)N1—C18—H18C109.5
N2—C7—C6111.76 (13)H18A—C18—H18C109.5
C8—C7—C6104.37 (14)H18B—C18—H18C109.5
C2—C7—C6106.28 (13)C3—N1—C18113.60 (15)
O1—C8—C9126.74 (16)C3—N1—C5113.99 (14)
O1—C8—C7125.32 (17)C18—N1—C5114.19 (15)
C9—C8—C7107.53 (13)C7—N2—C17116.69 (17)
C14—C9—C10120.94 (17)C7—N2—C16107.45 (16)
C14—C9—C8128.68 (16)C17—N2—C16114.03 (18)
C10—C9—C8110.36 (14)C6—O2—H2109.5
C11—C10—C9120.10 (17)
O3—C1—C2—C15−22.8 (3)C6—C7—C8—O1−175.36 (16)
C4—C1—C2—C15157.13 (17)N2—C7—C8—C9−110.88 (16)
O3—C1—C2—C3107.2 (2)C2—C7—C8—C9128.67 (15)
C4—C1—C2—C3−72.83 (18)C6—C7—C8—C911.57 (17)
O3—C1—C2—C7−138.5 (2)O1—C8—C9—C14−1.2 (3)
C4—C1—C2—C741.44 (18)C7—C8—C9—C14171.71 (17)
C1—C2—C3—N166.97 (17)O1—C8—C9—C10−179.96 (17)
C15—C2—C3—N1−163.63 (15)C7—C8—C9—C10−7.01 (19)
C7—C2—C3—N1−41.05 (18)C14—C9—C10—C110.1 (3)
O3—C1—C4—C5−112.9 (2)C8—C9—C10—C11178.94 (16)
C2—C1—C4—C567.20 (18)C14—C9—C10—C6−179.82 (16)
O3—C1—C4—C6129.0 (2)C8—C9—C10—C6−1.0 (2)
C2—C1—C4—C6−50.92 (17)O2—C6—C10—C11−49.6 (2)
C1—C4—C5—N1−56.50 (19)C4—C6—C10—C1175.3 (2)
C6—C4—C5—N152.0 (2)C7—C6—C10—C11−171.64 (18)
C1—C4—C6—O2−80.09 (16)O2—C6—C10—C9130.29 (15)
C5—C4—C6—O2166.74 (14)C4—C6—C10—C9−104.79 (17)
C1—C4—C6—C10152.95 (14)C7—C6—C10—C98.28 (18)
C5—C4—C6—C1039.8 (2)C9—C10—C11—C12−0.7 (3)
C1—C4—C6—C738.98 (16)C6—C10—C11—C12179.21 (17)
C5—C4—C6—C7−74.19 (17)C10—C11—C12—C131.1 (3)
C1—C2—C7—N2102.34 (15)C11—C12—C13—C14−0.9 (3)
C15—C2—C7—N2−19.57 (17)C12—C13—C14—C90.3 (3)
C3—C2—C7—N2−147.71 (14)C10—C9—C14—C130.1 (3)
C1—C2—C7—C8−131.31 (15)C8—C9—C14—C13−178.51 (17)
C15—C2—C7—C8106.79 (17)C1—C2—C15—C16−113.14 (18)
C3—C2—C7—C8−21.4 (2)C3—C2—C15—C16123.18 (18)
C1—C2—C7—C6−15.26 (17)C7—C2—C15—C16−0.81 (19)
C15—C2—C7—C6−137.16 (14)C2—C15—C16—N221.1 (2)
C3—C2—C7—C694.70 (15)C2—C3—N1—C18168.67 (15)
O2—C6—C7—N2−9.8 (2)C2—C3—N1—C5−58.18 (19)
C10—C6—C7—N2112.33 (16)C4—C5—N1—C353.1 (2)
C4—C6—C7—N2−126.26 (15)C4—C5—N1—C18−174.04 (16)
O2—C6—C7—C8−133.98 (15)C8—C7—N2—C1735.0 (2)
C10—C6—C7—C8−11.83 (17)C2—C7—N2—C17163.01 (16)
C4—C6—C7—C8109.58 (15)C6—C7—N2—C17−83.3 (2)
O2—C6—C7—C2101.72 (16)C8—C7—N2—C16−94.49 (19)
C10—C6—C7—C2−136.13 (14)C2—C7—N2—C1633.53 (18)
C4—C6—C7—C2−14.72 (16)C6—C7—N2—C16147.18 (16)
N2—C7—C8—O162.2 (2)C15—C16—N2—C7−35.3 (2)
C2—C7—C8—O1−58.3 (2)C15—C16—N2—C17−166.26 (17)
D—H···AD—HH···AD···AD—H···A
O2—H2···N20.822.122.655 (2)123
C15—H15A···O30.972.562.974 (3)106
C18—H18B···O3i0.962.393.288 (3)155
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O2—H2⋯N20.822.122.655 (2)123
C18—H18B⋯O3i0.962.393.288 (3)155

Symmetry code: (i) .

  6 in total

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Authors:  J R Dimmock; V K Arora; S L Wonko; N W Hamon; J W Quail; Z Jia; R C Warrington; W D Fang; J S Lee
Journal:  Drug Des Deliv       Date:  1990-09

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Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

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Authors:  E Kaiser; R L Colescott; C D Bossinger; P I Cook
Journal:  Anal Biochem       Date:  1970-04       Impact factor: 3.365

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Authors:  J R Dimmock; M P Padmanilayam; R N Puthucode; A J Nazarali; N L Motaganahalli; G A Zello; J W Quail; E O Oloo; H B Kraatz; J S Prisciak; T M Allen; C L Santos; J Balzarini; E De Clercq; E K Manavathu
Journal:  J Med Chem       Date:  2001-02-15       Impact factor: 7.446

5.  1-p-chlorophenyl-4,4-dimethyl-5-diethylamino-1-penten-3-one hydrobromide, a sulfhydryl-specific compound which reacts irreversibly with protein thiols but reversibly with small molecular weight thiols.

Authors:  B Mutus; J D Wagner; C J Talpas; J R Dimmock; O A Phillips; R S Reid
Journal:  Anal Biochem       Date:  1989-03       Impact factor: 3.365

6.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  6 in total

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