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Acta Cryst. (2008). E64, o384    [ doi:10.1107/S1600536807068171 ]

Dimethyl [1-(1-allyl-5-iodo-1H-indol-3-yl)-3-hydroxypropyl]phosphonate

Y.-C. Guo, X.-F. Wang and Y. Ding

Abstract top

In the title compound, C16H21INO4P, the molecular structure is stabilized by a weak intramolecular C-H...O hydrogen-bond interaction. The crystal packing is stabilized by strong intermolecular O-H ... O hydogen-bonding interactions to form a zigzag packing arrangement.

Comment top

Phosphorus has been recognized as an essential structural constituent of many biomolecules and a crucial element in many biological transformations (Horiguchi & Kandatsu,1959; Allen et al. 1989). With the advances in the development of chiral catalysts, asymmetric synthesis of some phosphorus compounds has been well documented in literatures (Carlone et al., 2007; Yang, et al., 2007; Ibrahem et al., 2007). As part of our ongoing project on enantioselective organocatalysis, a series of α-indolyl phosphonates have been highly enantioselectively synthesized via Friedel-Crafts alkylation of substituted indoles with (E)-dialkyl 3-oxoprop-1-enylphosphonate using MacMillan's imidazolidinone catalysts. The title compound (I) was synthesized and its crystal structure is presented here.

As seen in Fig. 1, the pyrrole plane (C1/C6—C8/N1) and the phenyl ring (C1—C6) are coplanar with each other with a dihedral angle between their mean planes of 2.2 (24)° in the molecule of the title compound (I), and the molecular structure is stablized by a week C12—H12 ··· O1 intramolecular hydrogen bonding interaction (Table 1).

The crystal packing (Fig. 2) is stabilized by strong intermolecular O—H ··· O hydogen bonds interaction (Table 1) to form a zigzag packing arrangement. Dipole–dipole and van der Waals interactions are also effective in the molecular packing in the crystal structure.

Related literature top

For asymmetric synthesis of phosphorus compounds, see: Carlone et al. (2007); Yang, et al. (2007); Ibrahem et al. (2007). For related structures, see: Sonar et al. (2006); Chen et al. (2007); Butcher et al. (2007). For related literature, see: Allen et al. (1989); Horiguchi & Kandatsu (1959).

Experimental top

The MacMillan's imidazolidinone catalysts (Fig 3) (0.02 mmol) and TFA (0.02 mmol) were stirred in 1 ml dichloromethane for 5 min at 195 K, then (E)-dialkyl 3-oxoprop-1-enylphosphonate 2 (0.1 mmol) was added and stirred for 15 min. And then 1-allyl-5-iodo-1H-indole 1 (0.11 mmol) was added. After the mixture was stirred for 48 h, the solvent (dichloromethane) was removed under reduced pressure at room temperature, and then the residue was added to a stirring solution of sodium borohydride (18.6 mg, 0.5 mmol, 5 equiv) in methanol (3.0 ml). After 15 min, the reaction was quenched with saturated aqueous NaHCO3 and extracted with CH2Cl2. The combined organic layer was washed with saturated solutions of NaHCO3 and NaCl and then dried over with Na2SO4. The combined organic layer was concentrated in vacuo and the product was purified by flash column chromatography on silica gel (ethyl acetate, Rf = 0.4), (14.3 mg, 48% yield). Compound 5 m: yellow solid; tr (minor) = 53.8 min, tr (major) = 59.5 min (Chiralcel AD—H, λ = 254 nm, 5% i-PrOH / hexanes, flow rate = 1.0 ml/min). 1H NMR (400 MHz, CDCl3) δ 2.10–2.18 (m, 1H), 2.28–2.35 (m, 1H), 2.59 (br, 1H), 3.49 (d, J = 10.8 Hz, 3H), 3.73 (d, J = 10.8 Hz, 3H), 3.50–3.75 (m, 3H), 4.67 (d, J = 5.2 Hz, 2H), 5.00 (d, J = 16.8 Hz, 1H), 5.19 (d, J = 10.4 Hz, 1H), 5.90–6.02 (m, 1H), 7.05–7.47 (m, 3H), 7.98 (s, 1H). 13C NMR (100 MHz, CDCl3) δ 29.9, 31.3, 33.3, 48.9, 52.67, 52.75, 53.4, 53.5, 59.7, 59.8, 83.0, 107.9, 111.8, 117.5, 127.9, 128.5, 129.5, 130.2, 132.8, 135.2.; MS (EI) m/z 449 (M+), 450 (M++1), 451 (M++2). Elemental Analysis calculated for C16H21INO4P: C 42.78, H 4.71, N 3.12%. Found: C 42.58, H 4.94, N 3.99%. [α]23D = -22.62 (C=2.35, CHCl3) (after recrystallization). Single crystals of (I) suitable for X-ray diffraction were obtained by slow evaporation of a CHCl3 solution.

Refinement top

All H atoms were positioned geometrically and treated as riding on their parent atoms, with C—H(methyl) = 0.96 Å, C—H(methylene) = 0.97 Å, C—H(methine) = 0.98 Å, C—H(aromatic) = 0.93 Å and O—H = 0.82 Å, and with Uiso(H) =1.5Ueq(Cmethyl,O) and 1.2Ueq(Caromatic,Cmethylene,Cmethineylene).

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Bruker, 2001); software used to prepare material for publication: SHELXTL (Bruker, 2001).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-labelling scheme and 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. The packing view of the title compound (I) along a axis, showing intermolecular hydrogen bonds as dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity..
[Figure 3] Fig. 3. The reaction scheme.
Dimethyl [1-(1-allyl-5-iodo-1H-indol-3-yl)-3-hydroxypropyl]phosphonate top
Crystal data top
C16H21INO4PF000 = 896
Mr = 449.21Dx = 1.646 Mg m−3
Orthorhombic, P212121Mo Kα radiation
λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 5073 reflections
a = 7.9983 (4) Åθ = 2.2–25.6º
b = 10.1295 (6) ŵ = 1.87 mm−1
c = 22.3722 (12) ÅT = 294 (2) K
V = 1812.57 (17) Å3Block, colourless
Z = 40.20 × 0.10 × 0.10 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		3314 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.051
T = 294(2) Kθmax = 26.0º
phi and ω scansθmin = 1.8º
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)		h = −7→9
Tmin = 0.706, Tmax = 0.835k = −11→12
10836 measured reflectionsl = −27→27
3564 independent reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.042  w = 1/[σ2(Fo2) + (0.0573P)2 + 0.6855P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.102(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.69 e Å−3
3564 reflectionsΔρmin = −0.30 e Å−3
211 parametersExtinction correction: none
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 1503 Freidel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.00 (1)
Crystal data top
C16H21INO4PV = 1812.57 (17) Å3
Mr = 449.21Z = 4
Orthorhombic, P212121Mo Kα
a = 7.9983 (4) ŵ = 1.87 mm−1
b = 10.1295 (6) ÅT = 294 (2) K
c = 22.3722 (12) Å0.20 × 0.10 × 0.10 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		3564 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1997)		3314 reflections with I > 2σ(I)
Tmin = 0.706, Tmax = 0.835Rint = 0.051
10836 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.042H-atom parameters constrained
wR(F2) = 0.102Δρmax = 0.69 e Å−3
S = 1.04Δρmin = −0.30 e Å−3
3564 reflectionsAbsolute structure: Flack (1983), 1503 Freidel pairs
211 parametersFlack parameter: 0.00 (1)
Special details top

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 (Å2) top
xyzUiso*/Ueq
I1−0.17244 (5)−0.23507 (4)1.053601 (16)0.06002 (15)
C1−0.1488 (6)0.1982 (4)0.96323 (18)0.0340 (9)
C2−0.2151 (6)0.1860 (5)1.0201 (2)0.0408 (11)
H2−0.25750.25871.04040.049*
C3−0.2158 (7)0.0611 (6)1.0455 (2)0.0460 (12)
H3−0.25800.04951.08380.055*
C4−0.1542 (7)−0.0467 (5)1.0142 (2)0.0414 (11)
C5−0.0842 (6)−0.0348 (5)0.95801 (19)0.0364 (10)
H5−0.0414−0.10810.93820.044*
C6−0.0794 (5)0.0896 (4)0.93175 (17)0.0299 (9)
C7−0.0233 (5)0.1394 (4)0.87529 (18)0.0303 (9)
C8−0.0615 (5)0.2707 (5)0.87450 (19)0.0365 (10)
H8−0.03950.32720.84270.044*
C9−0.1972 (10)0.4394 (5)0.9422 (2)0.0627 (17)
H9A−0.28180.43090.97310.075*
H9B−0.10500.48930.95910.075*
C10−0.2659 (14)0.5131 (9)0.8942 (4)0.105 (3)
H10−0.35740.47470.87530.126*
C11−0.2201 (13)0.6240 (7)0.8734 (3)0.089 (3)
H11A−0.12940.66790.89020.107*
H11B−0.27720.66130.84140.107*
C120.0602 (6)0.0611 (5)0.82594 (19)0.0324 (9)
H120.0481−0.03290.83550.039*
C13−0.0169 (6)0.0843 (5)0.76336 (19)0.0414 (11)
H13A−0.02100.17850.75550.050*
H13B0.05470.04430.73340.050*
C14−0.1891 (8)0.0284 (6)0.7576 (2)0.0541 (14)
H14A−0.26520.07770.78290.065*
H14B−0.22680.03740.71660.065*
C150.5194 (7)0.0595 (7)0.9005 (3)0.0577 (15)
H15A0.58800.00420.87570.087*
H15B0.53630.03670.94170.087*
H15C0.54940.15030.89430.087*
C160.3565 (9)−0.1289 (6)0.7724 (3)0.0686 (18)
H16A0.4059−0.16260.80840.103*
H16B0.4166−0.16200.73840.103*
H16C0.2419−0.15660.77010.103*
N1−0.1369 (5)0.3078 (4)0.92702 (16)0.0379 (9)
O1−0.1922 (9)−0.1050 (5)0.7740 (3)0.112 (2)
H1−0.2269−0.14920.74590.168*
O20.3445 (4)0.0404 (3)0.88494 (12)0.0386 (7)
O30.3641 (4)0.0129 (4)0.77276 (15)0.0494 (9)
O40.3217 (5)0.2376 (3)0.81376 (16)0.0521 (8)
P10.28050 (14)0.09837 (13)0.82350 (5)0.0338 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.0725 (3)0.0485 (2)0.0591 (2)−0.00777 (18)0.00460 (18)0.01635 (16)
C10.032 (2)0.034 (2)0.036 (2)0.0011 (18)−0.0051 (17)−0.0074 (16)
C20.037 (2)0.050 (3)0.036 (2)0.006 (2)0.0039 (19)−0.006 (2)
C30.047 (3)0.058 (3)0.032 (2)0.000 (2)0.008 (2)0.001 (2)
C40.041 (3)0.045 (3)0.038 (2)−0.003 (2)−0.003 (2)0.0070 (19)
C50.032 (2)0.037 (2)0.040 (3)−0.0025 (19)0.0006 (19)−0.0012 (19)
C60.024 (2)0.038 (2)0.028 (2)0.0039 (18)−0.0029 (16)−0.0024 (17)
C70.023 (2)0.038 (2)0.030 (2)0.0002 (18)−0.0002 (16)−0.0048 (17)
C80.037 (2)0.038 (2)0.035 (2)−0.003 (2)0.0003 (18)−0.0033 (19)
C90.104 (5)0.039 (3)0.045 (3)0.022 (3)0.005 (4)−0.002 (2)
C100.141 (8)0.083 (6)0.090 (6)0.057 (6)0.025 (5)0.008 (5)
C110.157 (8)0.053 (4)0.058 (4)0.043 (5)0.035 (4)0.010 (3)
C120.034 (2)0.032 (2)0.031 (2)0.0014 (19)0.0026 (18)−0.0003 (18)
C130.042 (3)0.054 (3)0.028 (2)0.002 (2)−0.0016 (19)−0.007 (2)
C140.056 (3)0.051 (3)0.055 (3)0.000 (3)−0.026 (3)−0.006 (2)
C150.038 (3)0.080 (4)0.056 (3)−0.006 (3)−0.013 (2)0.014 (3)
C160.060 (4)0.062 (4)0.083 (4)0.011 (3)0.004 (3)−0.029 (3)
N10.042 (2)0.035 (2)0.0367 (19)0.0083 (17)0.0030 (16)−0.0041 (15)
O10.153 (6)0.054 (3)0.129 (5)−0.034 (4)−0.088 (4)0.005 (3)
O20.0300 (16)0.0523 (19)0.0334 (15)−0.0042 (16)−0.0025 (14)0.0044 (13)
O30.035 (2)0.071 (3)0.0416 (18)0.0069 (17)0.0066 (15)−0.0039 (17)
O40.0469 (19)0.047 (2)0.062 (2)−0.007 (2)−0.0022 (16)0.0139 (16)
P10.0292 (6)0.0419 (7)0.0304 (5)0.0007 (5)0.0017 (4)0.0023 (5)
Geometric parameters (Å, °) top
I1—C42.107 (5)C11—H11B0.9300
C1—N11.378 (6)C12—C131.548 (6)
C1—C21.383 (6)C12—P11.803 (4)
C1—C61.419 (6)C12—H120.9800
C2—C31.387 (7)C13—C141.495 (8)
C2—H20.9300C13—H13A0.9700
C3—C41.387 (7)C13—H13B0.9700
C3—H30.9300C14—O11.400 (7)
C4—C51.382 (6)C14—H14A0.9700
C5—C61.391 (7)C14—H14B0.9700
C5—H50.9300C15—O21.455 (6)
C6—C71.432 (6)C15—H15A0.9600
C7—C81.365 (7)C15—H15B0.9600
C7—C121.514 (6)C15—H15C0.9600
C8—N11.374 (5)C16—O31.438 (7)
C8—H80.9300C16—H16A0.9600
C9—C101.419 (10)C16—H16B0.9600
C9—N11.458 (6)C16—H16C0.9600
C9—H9A0.9700O1—H10.8200
C9—H9B0.9700O2—P11.580 (3)
C10—C111.270 (12)O3—P11.576 (4)
C10—H100.9300O4—P11.464 (4)
C11—H11A0.9300
N1—C1—C2129.7 (4)C7—C12—H12107.8
N1—C1—C6107.8 (4)C13—C12—H12107.8
C2—C1—C6122.5 (4)P1—C12—H12107.8
C1—C2—C3117.3 (4)C14—C13—C12112.8 (4)
C1—C2—H2121.3C14—C13—H13A109.0
C3—C2—H2121.3C12—C13—H13A109.0
C4—C3—C2120.7 (4)C14—C13—H13B109.0
C4—C3—H3119.7C12—C13—H13B109.0
C2—C3—H3119.7H13A—C13—H13B107.8
C5—C4—C3122.2 (4)O1—C14—C13111.1 (5)
C5—C4—I1119.2 (4)O1—C14—H14A109.4
C3—C4—I1118.5 (3)C13—C14—H14A109.4
C4—C5—C6118.4 (4)O1—C14—H14B109.4
C4—C5—H5120.8C13—C14—H14B109.4
C6—C5—H5120.8H14A—C14—H14B108.0
C5—C6—C1118.8 (4)O2—C15—H15A109.5
C5—C6—C7134.4 (4)O2—C15—H15B109.5
C1—C6—C7106.7 (4)H15A—C15—H15B109.5
C8—C7—C6106.5 (4)O2—C15—H15C109.5
C8—C7—C12126.8 (4)H15A—C15—H15C109.5
C6—C7—C12126.7 (4)H15B—C15—H15C109.5
C7—C8—N1110.8 (4)O3—C16—H16A109.5
C7—C8—H8124.6O3—C16—H16B109.5
N1—C8—H8124.6H16A—C16—H16B109.5
C10—C9—N1115.6 (5)O3—C16—H16C109.5
C10—C9—H9A108.4H16A—C16—H16C109.5
N1—C9—H9A108.4H16B—C16—H16C109.5
C10—C9—H9B108.4C8—N1—C1108.2 (4)
N1—C9—H9B108.4C8—N1—C9126.6 (4)
H9A—C9—H9B107.4C1—N1—C9125.2 (4)
C11—C10—C9129.1 (11)C14—O1—H1109.5
C11—C10—H10115.5C15—O2—P1118.1 (3)
C9—C10—H10115.5C16—O3—P1122.4 (4)
C10—C11—H11A120.0O4—P1—O3109.0 (2)
C10—C11—H11B120.0O4—P1—O2114.5 (2)
H11A—C11—H11B120.0O3—P1—O2106.55 (19)
C7—C12—C13113.8 (4)O4—P1—C12115.2 (2)
C7—C12—P1110.1 (3)O3—P1—C12108.7 (2)
C13—C12—P1109.3 (3)O2—P1—C12102.26 (19)
N1—C1—C2—C3177.8 (5)C7—C12—C13—C14−69.1 (6)
C6—C1—C2—C3−1.6 (7)P1—C12—C13—C14167.4 (4)
C1—C2—C3—C4−0.9 (7)C12—C13—C14—O1−53.2 (7)
C2—C3—C4—C52.5 (8)C7—C8—N1—C1−0.1 (5)
C2—C3—C4—I1−176.4 (4)C7—C8—N1—C9−179.2 (5)
C3—C4—C5—C6−1.5 (7)C2—C1—N1—C8−179.9 (5)
I1—C4—C5—C6177.4 (3)C6—C1—N1—C8−0.5 (5)
C4—C5—C6—C1−1.0 (6)C2—C1—N1—C9−0.8 (8)
C4—C5—C6—C7−177.9 (5)C6—C1—N1—C9178.7 (5)
N1—C1—C6—C5−176.9 (4)C10—C9—N1—C835.3 (10)
C2—C1—C6—C52.6 (6)C10—C9—N1—C1−143.6 (7)
N1—C1—C6—C70.8 (5)C16—O3—P1—O4175.5 (4)
C2—C1—C6—C7−179.7 (4)C16—O3—P1—O251.4 (5)
C5—C6—C7—C8176.3 (5)C16—O3—P1—C12−58.1 (5)
C1—C6—C7—C8−0.8 (5)C15—O2—P1—O4−51.1 (5)
C5—C6—C7—C12−3.0 (8)C15—O2—P1—O369.5 (4)
C1—C6—C7—C12179.9 (4)C15—O2—P1—C12−176.4 (4)
C6—C7—C8—N10.6 (5)C7—C12—P1—O4−58.6 (4)
C12—C7—C8—N1179.9 (4)C13—C12—P1—O467.1 (4)
N1—C9—C10—C11−120.5 (9)C7—C12—P1—O3178.7 (3)
C8—C7—C12—C13−47.8 (6)C13—C12—P1—O3−55.6 (4)
C6—C7—C12—C13131.4 (5)C7—C12—P1—O266.3 (3)
C8—C7—C12—P175.3 (5)C13—C12—P1—O2−168.0 (3)
C6—C7—C12—P1−105.6 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C12—H12···O10.982.472.873 (7)104
O1—H1···O4i0.821.922.733 (6)174
Symmetry codes: (i) −x, y−1/2, −z+3/2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
C12—H12···O10.982.472.873 (7)104
O1—H1···O4i0.821.922.733 (6)174
Symmetry codes: (i) −x, y−1/2, −z+3/2.
Acknowledgements top

The authors acknowledge financial support from the Natural Science Foundation of Hubei Province of China (No. 2006ABA175) and the Natural Science Foundation of Central China Normal University, and are indebted to Dr Guangmin Yao of Shijiazhuang Pharmaceutical Group, Zhongqi (sjz) Pharmaceutical Technology Co. Ltd, and Professor Wenjing Xiao and Dr Xianggao Meng of Central China Normal University, for their advice and support.

references
References top

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