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Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1370.
Published online 2009 May 23. doi:  10.1107/S1600536809018388
PMCID: PMC2969731

9-O-Butyl­berberrubinium bromide

Abstract

In the title compound, C23H24NO4 +·Br, the butyl chain is disordered between two conformations; the occupancies refined to 0.735 (7) and 0.265 (7). The dihedral angle between the naphthalene ring system and the phenyl ring is 11.6 (2)°. In the crystal structure, the cations are packed via π–π inter­actions into stacks propagating in the [010] direction. Weak inter­molecular C—H(...)O and C—H(...)Br hydrogen bonds contribute further to the crystal packing stability.

Related literature

For the bioactivity of berberine, see: Jiang et al. (1998 [triangle]); Kupeli et al.. (2002 [triangle]). For the bioactivity of 9-O-butyl-berberrubine bromide, see Ye & Li (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o1370-scheme1.jpg

Experimental

Crystal data

  • C23H24NO4 +·Br
  • M r = 458.34
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1370-efi1.jpg
  • a = 9.716 (4) Å
  • b = 7.623 (3) Å
  • c = 27.443 (11) Å
  • β = 92.983 (8)°
  • V = 2029.9 (14) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.06 mm−1
  • T = 295 K
  • 0.12 × 0.10 × 0.06 mm

Data collection

  • Bruker SMART CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker 2005 [triangle]) T min = 0.791, T max = 0.887
  • 10394 measured reflections
  • 3592 independent reflections
  • 1965 reflections with I > 2σ(I)
  • R int = 0.069

Refinement

  • R[F 2 > 2σ(F 2)] = 0.060
  • wR(F 2) = 0.161
  • S = 1.08
  • 3592 reflections
  • 276 parameters
  • H-atom parameters constrained
  • Δρmax = 0.58 e Å−3
  • Δρmin = −0.55 e Å−3

Data collection: SMART (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP in SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Centroid-to-centroid distances (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809018388/cv2550sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018388/cv2550Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the National Natural Science Foundation of China (grant No. 20673084), the Natural Science Foundation Project of CQ CSTC (grant No. 2008BB5257) and the Major Technologies R & D Program of CQ CSTC (grant No. 2008AA5021).

supplementary crystallographic information

Comment

Berberine is a main compound presented in the rhizome of Coptis chinensis Franch. Berberine and its derivatives are used for treating diarrhoea (Kupeli et al., 2002) and anti-inflammatory (Jiang et al., 1998). Herewith we report the crystal structure of the title compound (I), which exhibits an excellent antibacterial activity (Ye & Li, 2007).

In (I) (Fig. 1), the dihedral angles formed by the benzene rings C5–C10 and C15/C19/C20/C21/C22/C16 with the pyridine ring are 2.2 (3) and 12.8 (3)°, respectively. The six-membered heterocyclic ring (C13/C15/C16/C17/C18/N1) adopts screw-boat conformation. In the crystal structure, weak intermolecular C—H···O and C—H···Br hydrogen bonds (Table 2) link the molecules. The aromatic rings in the cations are involved in π–π interactions (Table 1). The cations are packed viaπ–π interactions into stacks propagated in direction [010].

Experimental

Berberrubine was obtained from berberine by pyrolysis at 180 °C for 1 h. Then dried berberrubine (10 mmol) was dissolved in DMF (200 ml) and incubated with n-butyl bromide (11 mmol) for 5 h at 100 °C to give the corresponding crude 9-O-butyl-berberrubine bromide. The product was purified by recrystallization from methanol at -18 °C. Crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution of the solid dissolved in methanol at room temperature for 15 d.

Refinement

All H atoms were placed in calculated positions,with C—H = 0.93–0.97 Å, and included in the final cycles of refinement using a riding model, with Uiso(H) = 1.2Ueq(C) for aryl and methylene H atoms or 1.5Ueq(C) for methyl H atoms.

Figures

Fig. 1.
View of the title compound showing the atom-labeling scheme and 30% probability displacement ellipsoids.

Crystal data

C23H24NO4+·BrF(000) = 944
Mr = 458.34Dx = 1.500 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1163 reflections
a = 9.716 (4) Åθ = 2.8–19.6°
b = 7.623 (3) ŵ = 2.06 mm1
c = 27.443 (11) ÅT = 295 K
β = 92.983 (8)°Block, yellow
V = 2029.9 (14) Å30.12 × 0.10 × 0.06 mm
Z = 4

Data collection

Bruker SMART CCD area-detector diffractometer3592 independent reflections
Radiation source: fine-focus sealed tube1965 reflections with I > 2σ(I)
graphiteRint = 0.069
[var phi] and ω scansθmax = 25.1°, θmin = 1.5°
Absorption correction: multi-scan (SADABS; Bruker 2005)h = −11→11
Tmin = 0.791, Tmax = 0.887k = −7→9
10394 measured reflectionsl = −32→32

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.060H-atom parameters constrained
wR(F2) = 0.161w = 1/[σ2(Fo2) + (0.0623P)2 + 1.1441P] where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max < 0.001
3592 reflectionsΔρmax = 0.58 e Å3
276 parametersΔρmin = −0.55 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0020 (7)

Special details

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)

xyzUiso*/UeqOcc. (<1)
Br10.19113 (6)0.34507 (10)0.58534 (2)0.0683 (3)
O10.4605 (4)0.4269 (6)0.31978 (15)0.0691 (13)
O20.8340 (4)−0.0249 (7)0.66220 (16)0.0802 (14)
O30.5968 (4)0.0055 (6)0.66073 (16)0.0708 (12)
O40.1935 (4)0.5291 (6)0.31514 (15)0.0741 (13)
N10.6413 (4)0.2391 (6)0.44906 (17)0.0469 (12)
C1'0.5253 (10)0.5997 (11)0.3125 (3)0.073 (2)0.735 (7)
H1'10.58140.63820.34070.088*0.735 (7)
H1'20.45890.68970.30270.088*0.735 (7)
C10.4509 (12)0.5865 (18)0.2933 (5)0.073 (2)0.265 (7)
H1A0.44970.68070.31700.088*0.265 (7)
H1B0.36170.58720.27570.088*0.265 (7)
C20.5550 (11)0.6342 (14)0.2577 (4)0.107 (3)0.735 (7)
H2A0.50420.67200.22820.128*0.735 (7)
H2B0.60330.73670.27080.128*0.735 (7)
C30.6599 (11)0.5126 (15)0.2427 (4)0.117 (3)0.735 (7)
H3A0.61960.39620.24100.140*0.735 (7)
H3B0.73350.51030.26790.140*0.735 (7)
C40.7234 (15)0.5492 (18)0.1943 (4)0.120 (4)0.735 (7)
H4A0.76200.44300.18220.180*0.735 (7)
H4B0.79480.63570.19900.180*0.735 (7)
H4C0.65370.59220.17130.180*0.735 (7)
C2'0.611 (3)0.540 (3)0.2709 (9)0.107 (3)0.265 (7)
H2'10.69050.47640.28430.128*0.265 (7)
H2'20.55620.45860.25060.128*0.265 (7)
C3'0.659 (3)0.687 (3)0.2392 (8)0.117 (3)0.265 (7)
H3'10.74350.73520.25430.140*0.265 (7)
H3'20.59040.77920.23820.140*0.265 (7)
C4'0.686 (5)0.633 (5)0.1874 (8)0.120 (4)0.265 (7)
H4'10.72400.73040.17050.180*0.265 (7)
H4'20.60090.59760.17090.180*0.265 (7)
H4'30.74980.53690.18800.180*0.265 (7)
C50.3838 (6)0.4217 (8)0.3608 (2)0.0544 (14)
C60.2479 (6)0.4712 (8)0.3590 (2)0.0570 (15)
C70.1715 (6)0.4554 (8)0.4011 (2)0.0592 (16)
H70.07920.48800.39950.071*
C80.2291 (6)0.3941 (8)0.4439 (2)0.0533 (15)
H80.17580.38350.47100.064*
C90.3696 (5)0.3464 (8)0.4475 (2)0.0482 (13)
C100.4459 (5)0.3590 (8)0.4044 (2)0.0479 (13)
C110.0506 (6)0.5753 (10)0.3118 (2)0.080 (2)
H11A−0.00390.47440.31900.121*
H11B0.02600.61570.27940.121*
H11C0.03390.66680.33480.121*
C120.4368 (5)0.2854 (7)0.4901 (2)0.0482 (14)
H120.38830.28090.51840.058*
C130.5723 (5)0.2312 (7)0.4923 (2)0.0460 (13)
C140.5833 (5)0.3019 (7)0.4082 (2)0.0488 (14)
H140.63560.30860.38080.059*
C150.6459 (5)0.1642 (7)0.5359 (2)0.0476 (13)
C160.7894 (5)0.1470 (8)0.5374 (2)0.0507 (14)
C170.8631 (6)0.2081 (8)0.4940 (2)0.0573 (16)
H17A0.87810.33370.49640.069*
H17B0.95240.15140.49380.069*
C180.7835 (5)0.1681 (8)0.4478 (2)0.0567 (15)
H18A0.77970.04210.44290.068*
H18B0.82920.21950.42060.068*
C190.5729 (6)0.1186 (7)0.5774 (2)0.0508 (14)
H190.47750.12840.57720.061*
C200.6445 (6)0.0617 (8)0.6165 (2)0.0532 (15)
C210.7863 (6)0.0423 (8)0.6182 (2)0.0597 (15)
C220.8615 (6)0.0853 (8)0.5790 (2)0.0580 (15)
H220.95690.07380.58030.070*
C230.7160 (7)−0.0309 (10)0.6915 (2)0.0759 (19)
H23A0.7082−0.14610.70610.091*
H23B0.72520.05540.71740.091*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Br10.0502 (4)0.0849 (6)0.0714 (5)−0.0009 (4)0.0186 (3)0.0016 (4)
O10.066 (3)0.088 (3)0.055 (3)0.020 (2)0.017 (2)−0.005 (2)
O20.069 (3)0.111 (4)0.060 (3)0.010 (3)−0.007 (3)0.011 (3)
O30.067 (3)0.088 (3)0.058 (3)0.000 (3)0.006 (2)0.010 (2)
O40.051 (3)0.116 (4)0.056 (3)0.018 (3)0.003 (2)−0.001 (3)
N10.039 (2)0.056 (3)0.047 (3)0.002 (2)0.010 (2)0.000 (2)
C1'0.077 (4)0.080 (4)0.064 (4)0.002 (4)0.020 (4)0.015 (4)
C10.077 (4)0.080 (4)0.064 (4)0.002 (4)0.020 (4)0.015 (4)
C20.117 (6)0.108 (6)0.098 (5)0.002 (5)0.034 (5)0.020 (5)
C30.133 (6)0.114 (6)0.107 (6)0.002 (6)0.039 (5)0.015 (5)
C40.140 (9)0.132 (10)0.092 (7)−0.003 (8)0.061 (6)0.002 (7)
C2'0.117 (6)0.108 (6)0.098 (5)0.002 (5)0.034 (5)0.020 (5)
C3'0.133 (6)0.114 (6)0.107 (6)0.002 (6)0.039 (5)0.015 (5)
C4'0.140 (9)0.132 (10)0.092 (7)−0.003 (8)0.061 (6)0.002 (7)
C50.052 (3)0.059 (3)0.054 (3)0.005 (3)0.016 (3)−0.002 (3)
C60.051 (3)0.071 (4)0.049 (3)0.004 (3)0.004 (3)−0.002 (3)
C70.044 (3)0.074 (4)0.060 (4)0.007 (3)0.005 (3)−0.005 (3)
C80.041 (3)0.066 (4)0.054 (3)0.003 (3)0.010 (3)−0.003 (3)
C90.044 (3)0.052 (3)0.049 (3)−0.001 (3)0.011 (3)−0.008 (3)
C100.043 (3)0.051 (3)0.050 (3)0.005 (3)0.008 (3)−0.002 (3)
C110.061 (4)0.114 (6)0.065 (5)0.016 (4)−0.003 (4)0.005 (4)
C120.044 (3)0.055 (3)0.047 (3)0.001 (3)0.012 (3)0.000 (3)
C130.040 (3)0.049 (3)0.049 (3)−0.004 (2)0.010 (3)−0.005 (3)
C140.043 (3)0.058 (3)0.047 (3)−0.001 (3)0.014 (3)−0.004 (3)
C150.043 (3)0.046 (3)0.055 (3)−0.003 (3)0.006 (3)0.001 (3)
C160.044 (3)0.053 (3)0.056 (3)0.001 (3)0.007 (3)−0.004 (3)
C170.041 (3)0.064 (4)0.068 (4)0.007 (3)0.011 (3)−0.001 (3)
C180.043 (3)0.066 (4)0.062 (4)0.011 (3)0.014 (3)−0.001 (3)
C190.041 (3)0.055 (3)0.057 (3)−0.005 (3)0.007 (3)−0.006 (3)
C200.048 (3)0.058 (4)0.053 (4)−0.003 (3)0.004 (3)−0.010 (3)
C210.053 (3)0.066 (4)0.059 (4)0.001 (3)−0.006 (3)0.001 (3)
C220.044 (3)0.068 (4)0.063 (4)0.003 (3)0.003 (3)−0.004 (3)
C230.074 (4)0.094 (5)0.060 (4)0.005 (4)0.005 (4)−0.001 (4)

Geometric parameters (Å, °)

O1—C51.382 (6)C4'—H4'30.9600
O1—C11.418 (12)C5—C61.372 (8)
O1—C1'1.477 (8)C5—C101.397 (8)
O2—C211.370 (7)C6—C71.412 (8)
O2—C231.434 (7)C7—C81.358 (8)
O3—C201.389 (7)C7—H70.9300
O3—C231.424 (7)C8—C91.412 (7)
O4—C61.361 (7)C8—H80.9300
O4—C111.430 (7)C9—C121.389 (7)
N1—C141.319 (7)C9—C101.431 (7)
N1—C131.393 (6)C10—C141.403 (7)
N1—C181.486 (6)C11—H11A0.9600
C1'—C2'1.517 (8)C11—H11B0.9600
C1'—H1'10.9700C11—H11C0.9600
C1'—H1'20.9700C12—C131.378 (7)
C1—C21.487 (7)C12—H120.9300
C1—H1A0.9700C13—C151.456 (8)
C1—H1B0.9700C14—H140.9300
C2—C31.454 (7)C15—C161.399 (7)
C2—H2A0.9700C15—C191.416 (7)
C2—H2B0.9700C16—C221.391 (8)
C3—C41.517 (7)C16—C171.497 (7)
C3—H3A0.9700C17—C181.483 (8)
C3—H3B0.9700C17—H17A0.9700
C4—H4A0.9600C17—H17B0.9700
C4—H4B0.9600C18—H18A0.9700
C4—H4C0.9600C18—H18B0.9700
C2'—C3'1.510 (8)C19—C201.321 (8)
C2'—H2'10.9700C19—H190.9300
C2'—H2'20.9700C20—C211.384 (8)
C3'—C4'1.516 (8)C21—C221.370 (8)
C3'—H3'10.9700C22—H220.9300
C3'—H3'20.9700C23—H23A0.9700
C4'—H4'10.9600C23—H23B0.9700
C4'—H4'20.9600
Cg1···Cg3i3.780 (4)Cg2···Cg3ii3.775 (4)
C5—O1—C1114.8 (6)C8—C7—H7119.0
C5—O1—C1'112.8 (5)C6—C7—H7119.0
C21—O2—C23105.2 (5)C7—C8—C9120.1 (5)
C20—O3—C23106.2 (5)C7—C8—H8119.9
C6—O4—C11117.9 (5)C9—C8—H8119.9
C14—N1—C13122.5 (5)C12—C9—C8123.7 (5)
C14—N1—C18117.9 (4)C12—C9—C10118.5 (5)
C13—N1—C18119.6 (5)C8—C9—C10117.8 (5)
O1—C1'—C2'95.0 (10)C5—C10—C14122.4 (5)
O1—C1'—H1'1112.7C5—C10—C9120.8 (5)
C2'—C1'—H1'1112.7C14—C10—C9116.7 (5)
O1—C1'—H1'2112.7O4—C11—H11A109.5
C2'—C1'—H1'2112.7O4—C11—H11B109.5
H1'1—C1'—H1'2110.2H11A—C11—H11B109.5
O1—C1—C2121.2 (9)O4—C11—H11C109.5
O1—C1—H1A107.0H11A—C11—H11C109.5
C2—C1—H1A107.0H11B—C11—H11C109.5
O1—C1—H1B107.0C13—C12—C9122.8 (5)
C2—C1—H1B107.0C13—C12—H12118.6
H1A—C1—H1B106.8C9—C12—H12118.6
C3—C2—C1122.8 (8)C12—C13—N1116.9 (5)
C3—C2—H2A106.6C12—C13—C15124.6 (5)
C1—C2—H2A106.6N1—C13—C15118.6 (5)
C3—C2—H2B106.6N1—C14—C10122.5 (5)
C1—C2—H2B106.6N1—C14—H14118.7
H2A—C2—H2B106.6C10—C14—H14118.7
C2—C3—C4117.0 (8)C16—C15—C19119.6 (5)
C2—C3—H3A108.0C16—C15—C13120.2 (5)
C4—C3—H3A108.0C19—C15—C13120.2 (5)
C2—C3—H3B108.0C22—C16—C15121.0 (5)
C4—C3—H3B108.0C22—C16—C17121.2 (5)
H3A—C3—H3B107.3C15—C16—C17117.7 (5)
C3—C4—H4A109.5C18—C17—C16111.6 (5)
C3—C4—H4B109.5C18—C17—H17A109.3
H4A—C4—H4B109.5C16—C17—H17A109.3
C3—C4—H4C109.5C18—C17—H17B109.3
H4A—C4—H4C109.5C16—C17—H17B109.3
H4B—C4—H4C109.5H17A—C17—H17B108.0
C3'—C2'—C1'114.1 (9)C17—C18—N1110.4 (5)
C3'—C2'—H2'1108.7C17—C18—H18A109.6
C1'—C2'—H2'1108.7N1—C18—H18A109.6
C3'—C2'—H2'2108.7C17—C18—H18B109.6
C1'—C2'—H2'2108.7N1—C18—H18B109.6
H2'1—C2'—H2'2107.6H18A—C18—H18B108.1
C2'—C3'—C4'114.3 (10)C20—C19—C15118.0 (5)
C2'—C3'—H3'1108.7C20—C19—H19121.0
C4'—C3'—H3'1108.7C15—C19—H19121.0
C2'—C3'—H3'2108.7C19—C20—C21123.0 (6)
C4'—C3'—H3'2108.7C19—C20—O3128.7 (5)
H3'1—C3'—H3'2107.6C21—C20—O3108.3 (6)
C3'—C4'—H4'1109.5O2—C21—C22127.7 (6)
C3'—C4'—H4'2109.5O2—C21—C20111.1 (6)
H4'1—C4'—H4'2109.5C22—C21—C20121.2 (6)
C3'—C4'—H4'3109.5C21—C22—C16117.3 (5)
H4'1—C4'—H4'3109.5C21—C22—H22121.3
H4'2—C4'—H4'3109.5C16—C22—H22121.3
C6—C5—O1121.4 (6)O3—C23—O2108.1 (5)
C6—C5—C10119.8 (5)O3—C23—H23A110.1
O1—C5—C10118.8 (5)O2—C23—H23A110.1
O4—C6—C5116.8 (5)O3—C23—H23B110.1
O4—C6—C7123.7 (5)O2—C23—H23B110.1
C5—C6—C7119.5 (6)H23A—C23—H23B108.4
C8—C7—C6121.9 (5)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C12—H12···Br10.932.773.658 (5)161
C2—H2A···O2iii0.972.643.404 (14)136

Symmetry codes: (iii) x−1/2, −y+1/2, z−1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CV2550).

References

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  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Ye, X. L. & Li, X. G. (2007). Chinese Patent No. 200710078505.X.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography