Literature DB >> 21579697

Redetermination and absolute configuration of atalaphylline.

Hoong-Kun Fun, Chin Sing Yeap, Suchada Chantrapromma.   

Abstract

THE TITLE ACRIDONE ALKALOID [SYSTEMATIC NAME: 1,3,5-trihydr-oxy-2,4-bis-(3-methyl-but-2-en-yl)acridin-9(10H)-one], C(23)H(25)NO(4), has previously been reported as crystallizing in the chiral ortho-rhom-bic space group P2(1)2(1)2(1) [Chantrapromma et al. (2010 ▶). Acta Cryst. E66, o81-o82] but the absolute configuration could not be determined from data collected with Mo radiation. The absolute configuration has now been determined by refinement of the Flack parameter with data collected using Cu radiation. All features of the mol-ecule and its crystal packing are similar to those previously described.

Entities:  

Year:  2010        PMID: 21579697      PMCID: PMC2979734          DOI: 10.1107/S160053680905449X

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


Related literature

For details of acridone alkaloids see: Basu & Basa (1972 ▶). For the previous structure determination, see: Chantrapromma et al. (2010 ▶). For hydrogen-bond motifs, see Bernstein et al. (1995 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see Cosier & Glazer, (1986 ▶).

Experimental

Crystal data

C23H25NO4 M = 379.44 Orthorhombic, a = 5.0838 (1) Å b = 15.0262 (3) Å c = 24.6412 (4) Å V = 1882.35 (6) Å3 Z = 4 Cu Kα radiation μ = 0.74 mm−1 T = 150 K 0.40 × 0.21 × 0.04 mm

Data collection

Bruker APEX Duo CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.755, T max = 0.970 11768 measured reflections 3145 independent reflections 3099 reflections with I > 2σ(I) R int = 0.017

Refinement

R[F 2 > 2σ(F 2)] = 0.025 wR(F 2) = 0.068 S = 1.06 3145 reflections 354 parameters All H-atom parameters refined Δρmax = 0.12 e Å−3 Δρmin = −0.10 e Å−3 Absolute structure: Flack (1983 ▶), 1280 Friedel pairs Flack parameter: 0.05 (13) Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053680905449X/sj2714sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S160053680905449X/sj2714Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C23H25NO4F(000) = 808
Mr = 379.44Dx = 1.339 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 3145 reflections
a = 5.0838 (1) Åθ = 6.1–64.9°
b = 15.0262 (3) ŵ = 0.74 mm1
c = 24.6412 (4) ÅT = 150 K
V = 1882.35 (6) Å3Plate, brown
Z = 40.40 × 0.21 × 0.04 mm
Bruker APEX Duo CCD area-detector diffractometer3145 independent reflections
Radiation source: sealed tube3099 reflections with I > 2σ(I)
graphiteRint = 0.017
φ and ω scansθmax = 64.9°, θmin = 6.1°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −5→5
Tmin = 0.755, Tmax = 0.970k = −17→17
11768 measured reflectionsl = −28→28
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullAll H-atom parameters refined
R[F2 > 2σ(F2)] = 0.025w = 1/[σ2(Fo2) + (0.0452P)2 + 0.1806P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.068(Δ/σ)max < 0.001
S = 1.06Δρmax = 0.12 e Å3
3145 reflectionsΔρmin = −0.10 e Å3
354 parametersExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0020 (7)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 1280 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.05 (13)
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 150.0 (1) K.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O10.33887 (19)0.33672 (5)0.16257 (4)0.0319 (2)
H1O10.469 (4)0.3351 (12)0.1882 (7)0.049 (5)*
O20.72372 (18)0.37879 (5)0.22397 (3)0.0312 (2)
O30.90459 (19)0.77102 (5)0.22853 (3)0.0318 (2)
H1O30.997 (4)0.8077 (12)0.2462 (7)0.044 (4)*
O4−0.06425 (19)0.56721 (6)0.06026 (4)0.0361 (2)
H1O4−0.139 (5)0.5215 (14)0.0460 (8)0.063 (6)*
N10.6200 (2)0.63969 (6)0.18325 (4)0.0264 (2)
H1N10.606 (4)0.6957 (12)0.1732 (6)0.038 (4)*
C10.1336 (2)0.44827 (8)0.11088 (5)0.0273 (3)
C20.3211 (2)0.42334 (8)0.14856 (5)0.0261 (3)
C30.4921 (2)0.48690 (7)0.17304 (4)0.0251 (3)
C40.6888 (2)0.46022 (8)0.21176 (5)0.0262 (3)
C50.8448 (3)0.52966 (8)0.23719 (5)0.0269 (3)
C61.0361 (3)0.50956 (8)0.27663 (5)0.0331 (3)
H6A1.074 (3)0.4477 (10)0.2852 (6)0.030 (3)*
C71.1787 (3)0.57660 (9)0.29998 (6)0.0381 (3)
H7A1.318 (4)0.5600 (11)0.3267 (7)0.045 (4)*
C81.1372 (3)0.66535 (9)0.28512 (5)0.0343 (3)
H8A1.240 (4)0.7140 (12)0.3021 (7)0.057 (5)*
C90.9535 (3)0.68681 (8)0.24628 (5)0.0281 (3)
C100.8034 (2)0.61840 (8)0.22173 (5)0.0259 (3)
C110.4625 (2)0.57783 (7)0.15855 (5)0.0255 (2)
C120.2744 (2)0.60509 (8)0.12029 (5)0.0274 (3)
C130.1178 (2)0.53936 (8)0.09727 (5)0.0277 (3)
C140.2289 (3)0.70240 (8)0.10748 (6)0.0319 (3)
H14A0.081 (4)0.7041 (11)0.0827 (7)0.049 (5)*
H14B0.184 (3)0.7325 (11)0.1402 (7)0.040 (4)*
C150.4574 (3)0.74968 (8)0.08153 (5)0.0313 (3)
H15A0.544 (3)0.7170 (10)0.0517 (6)0.041 (4)*
C160.5452 (3)0.83055 (8)0.09368 (5)0.0346 (3)
C170.7648 (4)0.87331 (12)0.06276 (8)0.0536 (4)
H17A0.917 (5)0.8886 (16)0.0890 (10)0.087 (7)*
H17B0.829 (4)0.8328 (14)0.0332 (8)0.065 (6)*
H17C0.715 (4)0.9270 (13)0.0451 (7)0.053 (5)*
C180.4364 (4)0.88686 (9)0.13869 (7)0.0469 (4)
H18A0.281 (5)0.8592 (14)0.1596 (9)0.071 (6)*
H18B0.563 (6)0.8967 (17)0.1648 (10)0.096 (8)*
H18C0.371 (4)0.9448 (14)0.1242 (8)0.063 (5)*
C19−0.0548 (3)0.38053 (8)0.08652 (5)0.0301 (3)
H19A−0.048 (3)0.3304 (11)0.1104 (6)0.039 (4)*
H19B−0.240 (4)0.4055 (10)0.0883 (6)0.042 (4)*
C200.0167 (3)0.35223 (7)0.02981 (5)0.0312 (3)
H20A0.179 (3)0.3171 (10)0.0264 (6)0.037 (4)*
C21−0.1104 (3)0.37003 (8)−0.01615 (5)0.0351 (3)
C22−0.0091 (4)0.33621 (11)−0.06969 (6)0.0509 (4)
H22A−0.149 (5)0.3035 (14)−0.0897 (8)0.069 (6)*
H22B0.043 (4)0.3915 (13)−0.0939 (8)0.061 (5)*
H22C0.179 (5)0.2984 (15)−0.0653 (9)0.080 (7)*
C23−0.3525 (3)0.42646 (13)−0.02079 (7)0.0520 (4)
H23A−0.490 (5)0.3962 (16)−0.0444 (9)0.083 (7)*
H23B−0.312 (6)0.4882 (19)−0.0386 (10)0.099 (8)*
H23C−0.438 (4)0.4365 (11)0.0152 (8)0.050 (5)*
U11U22U33U12U13U23
O10.0368 (5)0.0218 (4)0.0370 (5)−0.0033 (3)−0.0036 (4)−0.0006 (3)
O20.0342 (5)0.0199 (4)0.0395 (5)0.0001 (4)−0.0059 (4)0.0012 (3)
O30.0387 (5)0.0210 (4)0.0357 (4)−0.0020 (4)−0.0080 (4)−0.0015 (3)
O40.0340 (5)0.0337 (5)0.0406 (5)−0.0034 (4)−0.0116 (4)0.0020 (4)
N10.0280 (5)0.0194 (5)0.0318 (5)−0.0012 (4)−0.0023 (4)−0.0003 (4)
C10.0269 (6)0.0283 (6)0.0266 (5)−0.0036 (5)0.0034 (5)−0.0033 (4)
C20.0280 (6)0.0228 (5)0.0275 (5)−0.0009 (5)0.0051 (5)−0.0020 (4)
C30.0253 (6)0.0234 (5)0.0266 (5)−0.0007 (5)0.0032 (5)−0.0022 (4)
C40.0271 (6)0.0234 (5)0.0280 (5)0.0009 (4)0.0023 (5)−0.0008 (4)
C50.0286 (6)0.0229 (6)0.0290 (6)−0.0007 (5)0.0010 (5)−0.0014 (4)
C60.0396 (7)0.0238 (6)0.0358 (6)0.0027 (5)−0.0084 (6)0.0009 (5)
C70.0438 (8)0.0299 (6)0.0405 (7)−0.0008 (6)−0.0164 (6)−0.0005 (5)
C80.0402 (7)0.0271 (6)0.0356 (7)−0.0038 (5)−0.0096 (6)−0.0039 (5)
C90.0324 (7)0.0222 (5)0.0298 (6)−0.0015 (5)0.0004 (5)−0.0027 (4)
C100.0261 (6)0.0254 (6)0.0263 (6)0.0013 (5)0.0012 (5)−0.0011 (4)
C110.0245 (6)0.0234 (5)0.0285 (6)−0.0012 (5)0.0028 (5)−0.0016 (4)
C120.0254 (6)0.0261 (6)0.0306 (6)0.0000 (5)0.0001 (5)−0.0003 (5)
C130.0255 (6)0.0295 (6)0.0281 (5)−0.0004 (5)0.0012 (5)0.0012 (5)
C140.0286 (7)0.0269 (6)0.0403 (7)0.0007 (5)−0.0047 (6)0.0011 (5)
C150.0329 (7)0.0300 (6)0.0310 (6)0.0029 (6)−0.0039 (5)0.0032 (5)
C160.0325 (7)0.0297 (6)0.0414 (7)−0.0017 (5)−0.0116 (6)0.0106 (5)
C170.0408 (8)0.0440 (8)0.0759 (12)−0.0058 (7)−0.0023 (8)0.0237 (8)
C180.0621 (10)0.0288 (6)0.0497 (8)−0.0040 (7)−0.0127 (8)−0.0037 (6)
C190.0311 (7)0.0291 (6)0.0300 (6)−0.0058 (6)−0.0005 (5)−0.0009 (5)
C200.0338 (7)0.0245 (5)0.0353 (6)−0.0031 (5)0.0022 (5)−0.0027 (5)
C210.0413 (7)0.0318 (6)0.0323 (6)−0.0113 (6)−0.0007 (6)−0.0002 (5)
C220.0705 (11)0.0481 (8)0.0341 (7)−0.0124 (8)0.0028 (7)−0.0042 (6)
C230.0417 (8)0.0680 (11)0.0465 (9)0.0000 (8)−0.0128 (7)−0.0005 (8)
O1—C21.3497 (15)C12—C141.5137 (16)
O1—H1O10.92 (2)C14—C151.5045 (18)
O2—C41.2725 (14)C14—H14A0.97 (2)
O3—C91.3617 (14)C14—H14B0.954 (16)
O3—H1O30.845 (19)C15—C161.3285 (18)
O4—C131.3651 (15)C15—H15A0.986 (16)
O4—H1O40.86 (2)C16—C171.497 (2)
N1—C101.3679 (16)C16—C181.501 (2)
N1—C111.3695 (15)C17—H17A1.03 (3)
N1—H1N10.880 (17)C17—H17B1.00 (2)
C1—C21.3825 (18)C17—H17C0.95 (2)
C1—C131.4114 (17)C18—H18A1.03 (2)
C1—C191.5209 (16)C18—H18B0.92 (3)
C2—C31.4254 (16)C18—H18C1.00 (2)
C3—C111.4203 (16)C19—C201.5051 (17)
C3—C41.4393 (17)C19—H19A0.957 (16)
C4—C51.4525 (16)C19—H19B1.015 (19)
C5—C101.4026 (17)C20—C211.3311 (19)
C5—C61.4078 (18)C20—H20A0.982 (17)
C6—C71.3679 (19)C21—C231.499 (2)
C6—H6A0.973 (15)C21—C221.505 (2)
C7—C81.3990 (19)C22—H22A0.99 (2)
C7—H7A0.997 (18)C22—H22B1.06 (2)
C8—C91.3754 (18)C22—H22C1.12 (3)
C8—H8A0.99 (2)C23—H23A1.02 (3)
C9—C101.4159 (17)C23—H23B1.05 (3)
C11—C121.4041 (17)C23—H23C0.999 (19)
C12—C131.3895 (17)
C2—O1—H1O1104.5 (11)C12—C14—H14A106.0 (10)
C9—O3—H1O3109.9 (12)C15—C14—H14B108.8 (10)
C13—O4—H1O4109.2 (14)C12—C14—H14B108.6 (10)
C10—N1—C11123.22 (10)H14A—C14—H14B109.5 (14)
C10—N1—H1N1118.3 (11)C16—C15—C14126.55 (13)
C11—N1—H1N1118.5 (11)C16—C15—H15A118.3 (10)
C2—C1—C13117.48 (11)C14—C15—H15A115.1 (9)
C2—C1—C19121.19 (11)C15—C16—C17121.91 (15)
C13—C1—C19121.29 (11)C15—C16—C18123.95 (13)
O1—C2—C1118.64 (10)C17—C16—C18114.14 (14)
O1—C2—C3119.81 (11)C16—C17—H17A109.5 (14)
C1—C2—C3121.55 (11)C16—C17—H17B110.5 (12)
C11—C3—C2118.26 (10)H17A—C17—H17B110.4 (19)
C11—C3—C4120.55 (10)C16—C17—H17C113.6 (12)
C2—C3—C4121.18 (10)H17A—C17—H17C107.3 (17)
O2—C4—C3121.43 (11)H17B—C17—H17C105.5 (16)
O2—C4—C5120.84 (11)C16—C18—H18A115.1 (12)
C3—C4—C5117.72 (10)C16—C18—H18B110.4 (17)
C10—C5—C6119.67 (11)H18A—C18—H18B104.6 (18)
C10—C5—C4118.94 (11)C16—C18—H18C110.5 (11)
C6—C5—C4121.39 (11)H18A—C18—H18C105.9 (17)
C7—C6—C5119.90 (12)H18B—C18—H18C110 (2)
C7—C6—H6A120.5 (9)C20—C19—C1113.79 (10)
C5—C6—H6A119.5 (9)C20—C19—H19A109.9 (9)
C6—C7—C8120.79 (12)C1—C19—H19A105.1 (10)
C6—C7—H7A118.0 (10)C20—C19—H19B111.7 (9)
C8—C7—H7A121.2 (10)C1—C19—H19B108.6 (9)
C9—C8—C7120.54 (12)H19A—C19—H19B107.4 (14)
C9—C8—H8A118.7 (11)C21—C20—C19128.01 (13)
C7—C8—H8A120.8 (11)C21—C20—H20A116.2 (9)
O3—C9—C8124.42 (11)C19—C20—H20A115.8 (9)
O3—C9—C10116.04 (11)C20—C21—C23125.26 (13)
C8—C9—C10119.53 (11)C20—C21—C22120.79 (14)
N1—C10—C5120.86 (11)C23—C21—C22113.91 (14)
N1—C10—C9119.58 (11)C21—C22—H22A110.9 (12)
C5—C10—C9119.56 (11)C21—C22—H22B108.4 (10)
N1—C11—C12119.91 (10)H22A—C22—H22B106.7 (15)
N1—C11—C3118.64 (11)C21—C22—H22C112.3 (11)
C12—C11—C3121.44 (10)H22A—C22—H22C114.1 (16)
C13—C12—C11117.19 (11)H22B—C22—H22C103.9 (16)
C13—C12—C14120.93 (11)C21—C23—H23A110.8 (14)
C11—C12—C14121.73 (11)C21—C23—H23B111.8 (17)
O4—C13—C12116.30 (11)H23A—C23—H23B107 (2)
O4—C13—C1119.64 (11)C21—C23—H23C112.1 (11)
C12—C13—C1124.04 (11)H23A—C23—H23C106.0 (17)
C15—C14—C12115.26 (11)H23B—C23—H23C108.9 (17)
C15—C14—H14A108.6 (10)
C13—C1—C2—O1179.51 (10)O3—C9—C10—C5179.04 (11)
C19—C1—C2—O11.60 (17)C8—C9—C10—C5−0.24 (18)
C13—C1—C2—C30.19 (17)C10—N1—C11—C12178.53 (10)
C19—C1—C2—C3−177.72 (10)C10—N1—C11—C3−0.68 (17)
O1—C2—C3—C11−178.11 (10)C2—C3—C11—N1177.81 (10)
C1—C2—C3—C111.20 (17)C4—C3—C11—N1−1.72 (16)
O1—C2—C3—C41.42 (16)C2—C3—C11—C12−1.39 (16)
C1—C2—C3—C4−179.27 (11)C4—C3—C11—C12179.08 (11)
C11—C3—C4—O2−177.79 (11)N1—C11—C12—C13−179.03 (11)
C2—C3—C4—O22.69 (17)C3—C11—C12—C130.16 (17)
C11—C3—C4—C53.05 (16)N1—C11—C12—C14−3.44 (17)
C2—C3—C4—C5−176.47 (10)C3—C11—C12—C14175.74 (11)
O2—C4—C5—C10178.75 (11)C11—C12—C13—O4179.87 (10)
C3—C4—C5—C10−2.09 (16)C14—C12—C13—O44.25 (17)
O2—C4—C5—C6−1.00 (18)C11—C12—C13—C11.35 (18)
C3—C4—C5—C6178.17 (12)C14—C12—C13—C1−174.27 (11)
C10—C5—C6—C70.6 (2)C2—C1—C13—O4180.00 (10)
C4—C5—C6—C7−179.67 (12)C19—C1—C13—O4−2.10 (17)
C5—C6—C7—C8−0.1 (2)C2—C1—C13—C12−1.53 (18)
C6—C7—C8—C9−0.6 (2)C19—C1—C13—C12176.37 (11)
C7—C8—C9—O3−178.45 (13)C13—C12—C14—C15−119.77 (13)
C7—C8—C9—C100.8 (2)C11—C12—C14—C1564.81 (16)
C11—N1—C10—C51.65 (17)C12—C14—C15—C16−136.97 (13)
C11—N1—C10—C9−178.35 (11)C14—C15—C16—C17−176.18 (13)
C6—C5—C10—N1179.57 (11)C14—C15—C16—C183.8 (2)
C4—C5—C10—N1−0.18 (17)C2—C1—C19—C20−102.65 (13)
C6—C5—C10—C9−0.43 (18)C13—C1—C19—C2079.52 (15)
C4—C5—C10—C9179.82 (11)C1—C19—C20—C21−111.01 (15)
O3—C9—C10—N1−0.96 (16)C19—C20—C21—C232.4 (2)
C8—C9—C10—N1179.75 (11)C19—C20—C21—C22179.80 (13)
D—H···AD—HH···AD···AD—H···A
O1—H1O1···O20.915 (19)1.699 (19)2.5528 (13)154.1 (17)
O3—H1O3···O2i0.845 (19)1.923 (19)2.7501 (12)165.9 (19)
N1—H1N1···O30.880 (18)2.333 (18)2.6893 (13)104.3 (13)
C8—H8A···O2i0.991 (19)2.565 (18)3.2918 (16)130.1 (13)
C14—H14A···O40.969 (19)2.254 (17)2.7752 (16)112.6 (12)
C19—H19A···O10.957 (16)2.352 (15)2.8197 (17)109.6 (11)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O1⋯O20.915 (19)1.699 (19)2.5528 (13)154.1 (17)
O3—H1O3⋯O2i0.845 (19)1.923 (19)2.7501 (12)165.9 (19)
N1—H1N1⋯O30.880 (18)2.333 (18)2.6893 (13)104.3 (13)
C8—H8A⋯O2i0.991 (19)2.565 (18)3.2918 (16)130.1 (13)
C14—H14A⋯O40.969 (19)2.254 (17)2.7752 (16)112.6 (12)
C19—H19A⋯O10.957 (16)2.352 (15)2.8197 (17)109.6 (11)

Symmetry code: (i) .

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1.  A short history of SHELX.

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

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Authors:  Suchada Chantrapromma; Nawong Boonnak; Ibrahim Abdul Razak; Hoong-Kun Fun
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Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
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