Literature DB >> 26594480

Crystal structure of 2-[(1R,2R,4aS,8aS)-2-hy-droxy-2,5,5,8a-tetra-methyl-deca-hydro-naphthalen-1-yl]-N-(o-tol-yl)acetamide.

Dang-Dang Li1, Xin-Wei Shi2, Qiang-Qiang Lu2, Sheng-Kun Li1.   

Abstract

The title compound, C23H35NO2, is an amide derivative of the lactone (+)-sclareolide, and was synthesized from natural sclareol. In the mol-ecular structure, the two six-membered rings (A and B) of the labdane skeleton are trans-fused, and adopt chair conformations. There is an intra-molecular N-H⋯O hydrogen bond present forming an S(7) ring motif. In the crystal, O-H⋯O hydrogen bonds link the mol-ecules into helical chains propagating along the b-axis direction. The chains are linked via C-H⋯π inter-actions, forming a three-dimensional structure.

Entities:  

Keywords:  C—H⋯π inter­actions; crystal structure; hydrogen bonding; sclareol; sclareolide

Year:  2015        PMID: 26594480      PMCID: PMC4647428          DOI: 10.1107/S2056989015017600

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


Related literature

For the chemistry and biological importance of sclareol and sclareolide, see: Barrero et al. (2004 ▸); Huang et al. (2001 ▸); Mohamad et al. (2005 ▸); Sy & Brown (1997 ▸). For the synthesis of coronarin and chinensines, see: Margaros & Vassilikogiannakis (2007 ▸). For related structures, see: Bernardinelli & Giersch (1985 ▸); Shi et al. (2015 ▸).

Experimental

Crystal data

C23H35NO2 M = 357.52 Monoclinic, a = 6.3001 (5) Å b = 13.2663 (10) Å c = 12.7082 (10) Å β = 96.983 (2)° V = 1054.26 (14) Å3 Z = 2 Mo Kα radiation μ = 0.07 mm−1 T = 296 K 0.22 × 0.20 × 0.18 mm

Data collection

Bruker SMART APEX CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2002 ▸) T min = 0.985, T max = 0.987 3714 measured reflections 3714 independent reflections 3121 reflections with I > 2σ(I) R int = 0.020

Refinement

R[F 2 > 2σ(F 2)] = 0.040 wR(F 2) = 0.095 S = 1.06 3714 reflections 242 parameters 1 restraint H-atom parameters constrained Δρmax = 0.11 e Å−3 Δρmin = −0.13 e Å−3

Data collection: SMART (Bruker, 2002 ▸); cell refinement: SAINT (Bruker, 2002 ▸); data reduction: SAINT; 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). Crystal structure: contains datablock(s) I, New_Global_Publ_Block. DOI: 10.1107/S2056989015017600/su5209sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015017600/su5209Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S2056989015017600/su5209Isup3.cdx Click here for additional data file. . DOI: 10.1107/S2056989015017600/su5209fig1.tif A view of the mol­ecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 30% probability level. The intra­molecular N—H⋯O hydrogen bonds is shown as a dashed line (see Table 1). Click here for additional data file. a . DOI: 10.1107/S2056989015017600/su5209fig2.tif Crystal packing of the title compound, viewed along the a axis. The hydrogen bonds are shown as dashed lines (see Table 1), and C-bound H atoms have been omitted for clarity. CCDC reference: 1426216 Additional supporting information: crystallographic information; 3D view; checkCIF report
C23H35NO2F(000) = 392
Mr = 357.52Dx = 1.126 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 2068 reflections
a = 6.3001 (5) Åθ = 3.1–23.4°
b = 13.2663 (10) ŵ = 0.07 mm1
c = 12.7082 (10) ÅT = 296 K
β = 96.983 (2)°Block, colorless
V = 1054.26 (14) Å30.22 × 0.20 × 0.18 mm
Z = 2
Bruker SMART APEX CCD diffractometer3714 independent reflections
Radiation source: fine-focus sealed tube3121 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
phi and ω scansθmax = 25.4°, θmin = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2002)h = −7→7
Tmin = 0.985, Tmax = 0.987k = −15→14
3714 measured reflectionsl = 0→15
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.095H-atom parameters constrained
S = 1.06w = 1/[σ2(Fo2) + (0.0452P)2 + 0.0489P] where P = (Fo2 + 2Fc2)/3
3714 reflections(Δ/σ)max < 0.001
242 parametersΔρmax = 0.11 e Å3
1 restraintΔρmin = −0.13 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
O10.4624 (2)0.38763 (11)0.90592 (12)0.0598 (4)
H1O0.53620.43620.92690.090*
O20.3383 (3)0.06216 (10)1.00512 (14)0.0661 (4)
N10.2698 (2)0.22934 (12)1.01913 (11)0.0413 (4)
H10.31340.28761.00120.050*
C10.0998 (3)0.23103 (14)1.08233 (13)0.0373 (4)
C20.0322 (3)0.32517 (14)1.11475 (15)0.0449 (5)
C3−0.1453 (4)0.32833 (19)1.16972 (18)0.0601 (6)
H3−0.19470.39061.19000.072*
C4−0.2502 (4)0.2428 (2)1.19504 (17)0.0647 (6)
H4−0.36920.24721.23150.078*
C5−0.1783 (4)0.1515 (2)1.16623 (18)0.0608 (6)
H5−0.24660.09311.18480.073*
C6−0.0049 (3)0.14439 (16)1.10965 (17)0.0503 (5)
H60.04190.08151.08980.060*
C70.3739 (3)0.15013 (14)0.98281 (15)0.0412 (4)
C80.5396 (3)0.17800 (15)0.91191 (16)0.0448 (5)
H8A0.60790.11670.89140.054*
H8B0.64850.21870.95230.054*
C90.4531 (3)0.23662 (13)0.80977 (13)0.0351 (4)
H90.29940.24390.81350.042*
C100.5404 (3)0.34563 (14)0.81224 (16)0.0461 (5)
C110.4370 (4)0.40191 (15)0.71547 (18)0.0601 (6)
H11A0.50340.46770.71310.072*
H11B0.28690.41230.72240.072*
C120.4552 (4)0.34729 (15)0.61180 (17)0.0584 (6)
H12A0.60460.34080.60160.070*
H12B0.38380.38620.55320.070*
C130.3536 (3)0.24265 (16)0.61310 (15)0.0458 (5)
H130.21130.25510.63420.055*
C140.4691 (3)0.17743 (14)0.70513 (14)0.0380 (4)
C150.7835 (4)0.35592 (19)0.82392 (19)0.0667 (7)
H15A0.82260.42440.84150.100*
H15B0.83490.33790.75840.100*
H15C0.84590.31200.87930.100*
C160.7032 (3)0.15146 (18)0.69257 (18)0.0558 (5)
H16A0.78180.14070.76120.084*
H16B0.76630.20610.65780.084*
H16C0.70730.09130.65080.084*
C170.3428 (3)0.07858 (15)0.71010 (17)0.0507 (5)
H17A0.41920.03470.76280.061*
H17B0.20470.09360.73290.061*
C180.3081 (5)0.02307 (19)0.6044 (2)0.0782 (8)
H18A0.44510.00160.58470.094*
H18B0.2220−0.03660.61160.094*
C190.1974 (4)0.0897 (2)0.5183 (2)0.0848 (9)
H19A0.05350.10320.53430.102*
H19B0.18580.05300.45180.102*
C200.3085 (4)0.1906 (2)0.50341 (17)0.0658 (6)
C210.5087 (5)0.1731 (3)0.4470 (2)0.0896 (9)
H21A0.60030.12480.48610.134*
H21B0.58430.23560.44310.134*
H21C0.46630.14820.37670.134*
C220.1549 (6)0.2562 (3)0.4303 (2)0.1163 (13)
H22A0.10830.21970.36640.174*
H22B0.22680.31670.41310.174*
H22C0.03330.27320.46550.174*
C230.1454 (4)0.42079 (16)1.0915 (2)0.0669 (7)
H23A0.07220.47741.11750.100*
H23B0.14670.42731.01640.100*
H23C0.28970.41881.12590.100*
U11U22U33U12U13U23
O10.0856 (11)0.0399 (8)0.0583 (9)−0.0191 (7)0.0266 (8)−0.0166 (7)
O20.0854 (11)0.0327 (8)0.0842 (11)0.0119 (8)0.0266 (9)0.0162 (8)
N10.0510 (9)0.0274 (8)0.0467 (9)−0.0027 (7)0.0110 (7)0.0035 (7)
C10.0414 (9)0.0384 (10)0.0314 (9)−0.0004 (9)0.0012 (7)0.0030 (8)
C20.0536 (12)0.0420 (11)0.0392 (11)0.0005 (9)0.0056 (9)−0.0023 (8)
C30.0650 (14)0.0676 (16)0.0497 (13)0.0086 (13)0.0145 (11)−0.0088 (11)
C40.0582 (13)0.092 (2)0.0467 (13)0.0002 (14)0.0160 (10)0.0072 (13)
C50.0603 (13)0.0724 (16)0.0495 (13)−0.0172 (12)0.0059 (11)0.0188 (12)
C60.0605 (13)0.0429 (11)0.0473 (12)−0.0045 (10)0.0051 (10)0.0092 (9)
C70.0497 (11)0.0344 (11)0.0379 (10)0.0053 (9)−0.0009 (8)0.0056 (8)
C80.0452 (11)0.0438 (11)0.0449 (11)0.0107 (9)0.0044 (8)−0.0001 (9)
C90.0365 (9)0.0314 (9)0.0383 (10)0.0025 (8)0.0075 (7)0.0001 (8)
C100.0594 (12)0.0352 (11)0.0459 (12)−0.0093 (9)0.0151 (9)−0.0071 (8)
C110.0855 (16)0.0337 (12)0.0642 (15)−0.0013 (11)0.0215 (12)0.0091 (10)
C120.0787 (15)0.0495 (13)0.0489 (13)0.0011 (11)0.0152 (11)0.0159 (10)
C130.0433 (10)0.0532 (12)0.0415 (11)0.0001 (9)0.0079 (8)0.0025 (9)
C140.0395 (10)0.0366 (10)0.0397 (10)−0.0017 (8)0.0116 (8)−0.0019 (7)
C150.0656 (14)0.0696 (16)0.0664 (15)−0.0320 (12)0.0143 (11)−0.0156 (12)
C160.0493 (12)0.0572 (13)0.0639 (14)0.0062 (10)0.0193 (10)−0.0053 (11)
C170.0610 (13)0.0417 (12)0.0520 (13)−0.0102 (10)0.0172 (10)−0.0090 (9)
C180.104 (2)0.0623 (17)0.0738 (19)−0.0359 (15)0.0339 (16)−0.0293 (13)
C190.0888 (19)0.111 (2)0.0561 (17)−0.0440 (17)0.0149 (14)−0.0369 (16)
C200.0702 (14)0.0887 (18)0.0385 (12)−0.0182 (13)0.0066 (11)−0.0055 (11)
C210.106 (2)0.117 (2)0.0529 (16)−0.0345 (18)0.0368 (15)−0.0212 (15)
C220.117 (3)0.166 (4)0.0575 (17)−0.009 (2)−0.0239 (17)0.0145 (19)
C230.0797 (16)0.0373 (12)0.0870 (18)−0.0010 (11)0.0236 (14)−0.0140 (11)
O1—C101.453 (2)C13—C201.551 (3)
O1—H1O0.8200C13—C141.562 (3)
O2—C71.228 (2)C13—H130.9800
N1—C71.349 (2)C14—C171.539 (3)
N1—C11.415 (2)C14—C161.541 (3)
N1—H10.8600C15—H15A0.9600
C1—C61.390 (3)C15—H15B0.9600
C1—C21.398 (3)C15—H15C0.9600
C2—C31.390 (3)C16—H16A0.9600
C2—C231.502 (3)C16—H16B0.9600
C3—C41.371 (3)C16—H16C0.9600
C3—H30.9300C17—C181.524 (3)
C4—C51.358 (4)C17—H17A0.9700
C4—H40.9300C17—H17B0.9700
C5—C61.382 (3)C18—C191.510 (4)
C5—H50.9300C18—H18A0.9700
C6—H60.9300C18—H18B0.9700
C7—C81.506 (3)C19—C201.533 (4)
C8—C91.554 (3)C19—H19A0.9700
C8—H8A0.9700C19—H19B0.9700
C8—H8B0.9700C20—C221.529 (4)
C9—C101.546 (3)C20—C211.542 (4)
C9—C141.558 (2)C21—H21A0.9600
C9—H90.9800C21—H21B0.9600
C10—C111.516 (3)C21—H21C0.9600
C10—C151.527 (3)C22—H22A0.9600
C11—C121.520 (3)C22—H22B0.9600
C11—H11A0.9700C22—H22C0.9600
C11—H11B0.9700C23—H23A0.9600
C12—C131.530 (3)C23—H23B0.9600
C12—H12A0.9700C23—H23C0.9600
C12—H12B0.9700
C10—O1—H1O109.5C17—C14—C16108.65 (16)
C7—N1—C1129.73 (16)C17—C14—C9107.87 (14)
C7—N1—H1115.1C16—C14—C9111.29 (15)
C1—N1—H1115.1C17—C14—C13107.85 (15)
C6—C1—C2119.63 (17)C16—C14—C13114.27 (15)
C6—C1—N1122.93 (18)C9—C14—C13106.69 (14)
C2—C1—N1117.40 (16)C10—C15—H15A109.5
C3—C2—C1117.90 (19)C10—C15—H15B109.5
C3—C2—C23120.25 (19)H15A—C15—H15B109.5
C1—C2—C23121.85 (18)C10—C15—H15C109.5
C4—C3—C2122.2 (2)H15A—C15—H15C109.5
C4—C3—H3118.9H15B—C15—H15C109.5
C2—C3—H3118.9C14—C16—H16A109.5
C5—C4—C3119.3 (2)C14—C16—H16B109.5
C5—C4—H4120.4H16A—C16—H16B109.5
C3—C4—H4120.4C14—C16—H16C109.5
C4—C5—C6120.8 (2)H16A—C16—H16C109.5
C4—C5—H5119.6H16B—C16—H16C109.5
C6—C5—H5119.6C18—C17—C14113.26 (17)
C5—C6—C1120.2 (2)C18—C17—H17A108.9
C5—C6—H6119.9C14—C17—H17A108.9
C1—C6—H6119.9C18—C17—H17B108.9
O2—C7—N1123.46 (17)C14—C17—H17B108.9
O2—C7—C8122.06 (17)H17A—C17—H17B107.7
N1—C7—C8114.48 (16)C19—C18—C17111.1 (2)
C7—C8—C9115.10 (15)C19—C18—H18A109.4
C7—C8—H8A108.5C17—C18—H18A109.4
C9—C8—H8A108.5C19—C18—H18B109.4
C7—C8—H8B108.5C17—C18—H18B109.4
C9—C8—H8B108.5H18A—C18—H18B108.0
H8A—C8—H8B107.5C18—C19—C20115.0 (2)
C10—C9—C8111.30 (15)C18—C19—H19A108.5
C10—C9—C14115.40 (14)C20—C19—H19A108.5
C8—C9—C14114.09 (15)C18—C19—H19B108.5
C10—C9—H9104.9C20—C19—H19B108.5
C8—C9—H9104.9H19A—C19—H19B107.5
C14—C9—H9104.9C22—C20—C19107.9 (2)
O1—C10—C11108.73 (17)C22—C20—C21107.2 (2)
O1—C10—C15108.72 (17)C19—C20—C21109.7 (2)
C11—C10—C15111.21 (18)C22—C20—C13109.0 (2)
O1—C10—C9102.74 (14)C19—C20—C13108.33 (18)
C11—C10—C9109.11 (16)C21—C20—C13114.47 (19)
C15—C10—C9115.82 (17)C20—C21—H21A109.5
C10—C11—C12113.45 (17)C20—C21—H21B109.5
C10—C11—H11A108.9H21A—C21—H21B109.5
C12—C11—H11A108.9C20—C21—H21C109.5
C10—C11—H11B108.9H21A—C21—H21C109.5
C12—C11—H11B108.9H21B—C21—H21C109.5
H11A—C11—H11B107.7C20—C22—H22A109.5
C11—C12—C13110.33 (17)C20—C22—H22B109.5
C11—C12—H12A109.6H22A—C22—H22B109.5
C13—C12—H12A109.6C20—C22—H22C109.5
C11—C12—H12B109.6H22A—C22—H22C109.5
C13—C12—H12B109.6H22B—C22—H22C109.5
H12A—C12—H12B108.1C2—C23—H23A109.5
C12—C13—C20115.19 (17)C2—C23—H23B109.5
C12—C13—C14110.69 (16)H23A—C23—H23B109.5
C20—C13—C14116.36 (18)C2—C23—H23C109.5
C12—C13—H13104.3H23A—C23—H23C109.5
C20—C13—H13104.3H23B—C23—H23C109.5
C14—C13—H13104.3
C7—N1—C1—C6−6.7 (3)C11—C12—C13—C20164.77 (19)
C7—N1—C1—C2175.54 (18)C11—C12—C13—C14−60.6 (2)
C6—C1—C2—C3−2.8 (3)C10—C9—C14—C17−170.84 (16)
N1—C1—C2—C3175.04 (18)C8—C9—C14—C1758.41 (19)
C6—C1—C2—C23177.3 (2)C10—C9—C14—C1670.1 (2)
N1—C1—C2—C23−4.9 (3)C8—C9—C14—C16−60.7 (2)
C1—C2—C3—C41.8 (3)C10—C9—C14—C13−55.19 (19)
C23—C2—C3—C4−178.3 (2)C8—C9—C14—C13174.06 (14)
C2—C3—C4—C50.4 (3)C12—C13—C14—C17173.35 (16)
C3—C4—C5—C6−1.7 (3)C20—C13—C14—C17−52.6 (2)
C4—C5—C6—C10.6 (3)C12—C13—C14—C16−65.7 (2)
C2—C1—C6—C51.7 (3)C20—C13—C14—C1668.3 (2)
N1—C1—C6—C5−176.07 (18)C12—C13—C14—C957.69 (19)
C1—N1—C7—O2−3.4 (3)C20—C13—C14—C9−168.28 (15)
C1—N1—C7—C8176.65 (17)C16—C14—C17—C18−70.6 (2)
O2—C7—C8—C9120.4 (2)C9—C14—C17—C18168.6 (2)
N1—C7—C8—C9−59.7 (2)C13—C14—C17—C1853.7 (2)
C7—C8—C9—C10113.33 (18)C14—C17—C18—C19−56.3 (3)
C7—C8—C9—C14−113.93 (17)C17—C18—C19—C2055.1 (3)
C8—C9—C10—O1−60.06 (18)C18—C19—C20—C22−168.8 (2)
C14—C9—C10—O1167.86 (14)C18—C19—C20—C2174.7 (3)
C8—C9—C10—C11−175.33 (16)C18—C19—C20—C13−51.0 (3)
C14—C9—C10—C1152.6 (2)C12—C13—C20—C22−60.1 (3)
C8—C9—C10—C1558.3 (2)C14—C13—C20—C22168.0 (2)
C14—C9—C10—C15−73.8 (2)C12—C13—C20—C19−177.2 (2)
O1—C10—C11—C12−163.68 (17)C14—C13—C20—C1950.8 (3)
C15—C10—C11—C1276.6 (2)C12—C13—C20—C2160.0 (3)
C9—C10—C11—C12−52.3 (2)C14—C13—C20—C21−72.0 (3)
C10—C11—C12—C1358.1 (3)
D—H···AD—HH···AD···AD—H···A
N1—H1···O10.862.092.894 (2)155
O1—H1O···O2i0.822.002.8054 (19)168
C8—H8B···Cgii0.972.793.632 (2)146
C22—H22A···Cgiii0.962.983.808 (3)145
Table 1

Hydrogen-bond geometry (, )

Cg is the centroid of benzene ring C1C6.

DHA DHHA D A DHA
N1H1O10.862.092.894(2)155
O1H1OO2i 0.822.002.8054(19)168
C8H8B Cg ii 0.972.793.632(2)146
C22H22A Cg iii 0.962.983.808(3)145

Symmetry codes: (i) ; (ii) ; (iii) .

  3 in total

1.  Antioxidative constituents of Etlingera elatior.

Authors:  Habsah Mohamad; Nordin H Lajis; Faridah Abas; Abdul Manaf Ali; Mohamad Aspollah Sukari; Hiroe Kikuzaki; Nobuji Nakatani
Journal:  J Nat Prod       Date:  2005-02       Impact factor: 4.050

2.  A short history of SHELX.

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

3.  Synthesis of chinensines A-E.

Authors:  Ioannis Margaros; Georgios Vassilikogiannakis
Journal:  J Org Chem       Date:  2007-05-27       Impact factor: 4.354

  3 in total

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