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Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kα room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree–Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768109046060/sn5088sup1.cif
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108768109046060/sn5088Isup2.hkl
Contains datablock I

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S0108768109046060/sn5088sup3.pdf
Tables of topological and atomic properties

CCDC reference: 760270

Computing details top

Data collection: STOE software; cell refinement: STOE software; data reduction: Stoe-routine REDUC; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: Volkov et al., (2006); molecular graphics: Volkov et al., (2006); software used to prepare material for publication: Volkov et al., (2006).

(I) top
Crystal data top
C14H16O9·H2OF(000) = 728
Mr = 346.28Dx = 1.544 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2AC 2ABCell parameters from 80 reflections
a = 7.488 (1) Åθ = 15–60°
b = 13.934 (1) ŵ = 1.16 mm1
c = 14.275 (1) ÅT = 293 K
V = 1489.4 (2) Å3Block, colourless
Z = 40.50 × 0.38 × 0.36 mm
Data collection top
Stoe four circle
diffractometer, microVAX controlled
Rint = 0.019
Radiation source: fine-focus sealed tubeθmax = 65.0°, θmin = 4.4°
No monochromatorh = 88
ω/2θ scansk = 016
5547 measured reflectionsl = 016
2531 independent reflections3 standard reflections every 90 min
2467 reflections with I > 2σ(I) intensity decay: none
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.013H-atom parameters not refined
wR(F2) = 0.026 w2 = 1/[s2(Fo2)]
S = 1.87(Δ/σ)max < 0.001
2436 reflectionsΔρmax = 0.09 e Å3
289 parametersΔρmin = 0.09 e Å3
0 restraintsAbsolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.02 (12)
Special details top

Experimental. Ni filter used

Refinement. The high Ueq(max)/Ueq(min) ratios for some H atoms are result of a free refinement of the H atoms against the room temperature low resolution data set. This could have been avoided by entering constraints in the hydrogen refinement (AFIX commands). This was, however, not wanted in this study.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.09469 (9)0.54517 (4)0.70334 (5)0.0490 (2)
O20.23566 (8)0.46031 (3)0.59799 (4)0.0338 (2)
O30.64579 (7)0.50208 (3)0.46534 (4)0.0269 (2)
O40.79144 (8)0.66321 (4)0.53086 (5)0.0412 (2)
O50.71597 (8)0.83840 (4)0.60482 (4)0.0343 (2)
O60.42365 (9)0.86746 (4)0.70709 (5)0.0423 (2)
O70.21037 (8)0.31955 (4)0.45427 (4)0.0307 (2)
O80.55706 (8)0.25544 (4)0.38785 (4)0.0318 (2)
O90.98285 (8)0.45312 (4)0.37933 (5)0.0388 (2)
C10.21936 (12)0.54087 (5)0.64921 (6)0.0320 (2)
C20.35520 (10)0.46117 (5)0.51925 (5)0.0245 (2)
C30.53599 (10)0.50105 (5)0.54696 (5)0.0242 (2)
C40.50983 (10)0.60015 (5)0.58644 (5)0.0254 (2)
C50.63557 (10)0.67356 (5)0.57752 (5)0.0273 (2)
C60.60151 (11)0.76362 (5)0.61761 (5)0.0273 (2)
C70.44611 (11)0.77859 (5)0.66980 (5)0.0295 (2)
C80.32216 (11)0.70561 (5)0.68053 (6)0.0314 (2)
C90.35432 (11)0.61731 (5)0.63747 (5)0.0273 (2)
C100.37522 (11)0.35857 (5)0.48535 (5)0.0245 (2)
C110.51737 (10)0.35269 (5)0.40842 (5)0.0244 (2)
C120.68882 (10)0.40654 (5)0.43547 (5)0.0253 (2)
C130.81504 (11)0.41451 (6)0.35266 (6)0.0315 (2)
C140.87567 (18)0.83156 (9)0.65681 (9)0.0598 (4)
O100.84509 (8)0.39232 (5)0.67789 (5)0.0376 (2)
H10.7881 (18)0.6062 (9)0.4996 (9)0.059 (4)*
H20.3157 (17)0.8738 (8)0.7450 (8)0.050 (3)*
H30.1425 (17)0.3669 (8)0.4237 (8)0.047 (3)*
H40.5978 (16)0.2282 (8)0.4424 (8)0.045 (3)*
H50.9904 (18)0.5114 (8)0.3584 (8)0.051 (3)*
H60.2968 (13)0.5063 (7)0.4644 (7)0.040 (2)*
H70.5954 (13)0.4554 (7)0.5991 (7)0.042 (3)*
H80.2041 (18)0.7148 (7)0.7206 (8)0.057 (3)*
H90.4150 (14)0.3155 (6)0.5435 (7)0.037 (2)*
H100.4626 (14)0.3849 (6)0.3461 (7)0.042 (3)*
H110.7543 (14)0.3682 (6)0.4933 (7)0.040 (3)*
H120.8402 (16)0.3459 (8)0.3259 (7)0.059 (3)*
H130.7535 (15)0.4592 (7)0.2988 (8)0.054 (3)*
H140.839 (3)0.8283 (12)0.7300 (14)0.120 (6)*
H150.952 (3)0.8935 (12)0.6544 (12)0.121 (6)*
H160.931 (4)0.7768 (16)0.6593 (16)0.188 (12)*
H170.9104 (17)0.3404 (8)0.6571 (8)0.053 (3)*
H180.9281 (18)0.4411 (9)0.6894 (9)0.062 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0455 (4)0.0399 (3)0.0616 (4)0.0171 (3)0.0312 (3)0.0201 (3)
O20.0324 (3)0.0260 (3)0.0429 (3)0.0089 (2)0.0126 (3)0.0065 (2)
O30.0251 (3)0.0217 (2)0.0339 (3)0.0007 (2)0.0043 (2)0.0016 (2)
O40.0311 (3)0.0394 (3)0.0530 (4)0.0118 (3)0.0144 (3)0.0136 (3)
O50.0353 (3)0.0269 (3)0.0407 (3)0.0089 (2)0.0001 (3)0.0023 (2)
O60.0442 (4)0.0211 (2)0.0616 (4)0.0030 (2)0.0160 (3)0.0075 (2)
O70.0281 (3)0.0235 (2)0.0405 (3)0.0050 (2)0.0009 (3)0.0015 (2)
O80.0340 (3)0.0246 (2)0.0367 (3)0.0020 (2)0.0017 (3)0.0063 (2)
O90.0256 (3)0.0332 (3)0.0575 (4)0.0017 (2)0.0004 (3)0.0072 (3)
C10.0291 (4)0.0275 (3)0.0395 (4)0.0063 (3)0.0122 (3)0.0061 (3)
C20.0228 (4)0.0204 (3)0.0303 (4)0.0011 (3)0.0018 (3)0.0016 (3)
C30.0233 (3)0.0212 (3)0.0282 (4)0.0009 (3)0.0001 (3)0.0013 (3)
C40.0233 (4)0.0218 (3)0.0310 (4)0.0021 (3)0.0027 (3)0.0032 (3)
C50.0245 (4)0.0251 (3)0.0324 (4)0.0047 (3)0.0026 (3)0.0035 (3)
C60.0280 (4)0.0224 (3)0.0314 (4)0.0034 (3)0.0006 (3)0.0003 (3)
C70.0297 (4)0.0218 (3)0.0370 (4)0.0009 (3)0.0028 (4)0.0022 (3)
C80.0300 (4)0.0231 (3)0.0412 (4)0.0014 (3)0.0083 (4)0.0053 (3)
C90.0249 (4)0.0219 (3)0.0352 (4)0.0031 (3)0.0046 (3)0.0041 (3)
C100.0262 (4)0.0189 (3)0.0283 (4)0.0002 (3)0.0006 (3)0.0013 (3)
C110.0247 (4)0.0222 (3)0.0262 (3)0.0006 (3)0.0018 (3)0.0004 (3)
C120.0228 (4)0.0236 (3)0.0294 (4)0.0024 (3)0.0009 (3)0.0015 (3)
C130.0286 (4)0.0305 (4)0.0353 (4)0.0023 (3)0.0046 (3)0.0031 (3)
C140.0552 (7)0.0556 (6)0.0686 (8)0.0278 (6)0.0256 (6)0.0158 (5)
O100.0294 (3)0.0348 (3)0.0485 (4)0.0007 (3)0.0037 (3)0.0017 (3)
Geometric parameters (Å, º) top
O1—C11.2133 (11)C3—C41.5042 (10)
O2—C11.3452 (9)C4—C91.3942 (11)
O2—C21.4369 (10)C4—C51.3961 (10)
O3—C31.4261 (9)C5—C61.4026 (10)
O3—C121.4345 (8)C6—C71.3974 (11)
O4—C51.3516 (10)C7—C81.3853 (11)
O5—C61.3615 (10)C8—C91.3963 (10)
O5—C141.4106 (15)C10—C111.5316 (11)
O6—C71.3583 (9)C11—C121.5363 (11)
O7—C101.4199 (10)C12—C131.5176 (11)
O8—C111.4180 (9)C2—H61.095 (10)
O9—C131.4189 (10)C3—H71.075 (10)
O4—H10.911 (13)C8—H81.061 (13)
O6—H20.977 (12)C10—H91.067 (10)
O7—H30.940 (12)C11—H101.078 (10)
O8—H40.918 (11)C12—H111.099 (10)
O9—H50.867 (11)C13—H131.091 (11)
O10—H180.936 (13)C13—H121.047 (11)
O10—H170.922 (12)C14—H160.87 (2)
C1—C91.4778 (11)C14—H141.08 (2)
C2—C31.5159 (11)C14—H151.036 (19)
C2—C101.5167 (10)
O1···O10i2.8568 (10)C14···H8ii3.086 (12)
O2···O72.8446 (8)H1···O31.865 (13)
O3···O92.8884 (9)H1···C32.483 (13)
O3···O42.6655 (8)H1···C123.022 (13)
O4···O32.6655 (8)H2···H82.393 (15)
O4···C143.0221 (15)H3···H5i2.494 (16)
O4···O52.7190 (9)H3···C13i2.735 (13)
O5···O62.6621 (10)H3···O22.893 (11)
O5···O42.7190 (9)H3···H62.334 (15)
O6···O52.6621 (10)H3···O9i1.809 (12)
O7···O22.8446 (8)H4···H92.332 (15)
O7···O82.9045 (9)H4···H112.389 (15)
O7···O9i2.7406 (9)H5···H3ii2.494 (16)
O8···O72.9045 (9)H6···O9i2.748 (10)
O9···O7ii2.7406 (9)H6···C92.947 (10)
O9···O32.8884 (9)H6···H32.334 (15)
O10···C33.3385 (11)H7···H92.501 (13)
O10···O1ii2.8568 (10)H7···H112.274 (14)
O1···H82.514 (10)H7···O102.352 (10)
O1···H18i1.923 (13)H8···H16i2.39 (3)
O2···H32.893 (11)H8···O12.514 (10)
O2···H18i2.660 (13)H8···C14i3.086 (12)
O3···H11.865 (13)H8···H22.393 (15)
O4···H162.64 (2)H9···H72.501 (13)
O8···H122.620 (12)H9···H42.332 (15)
O9···H6ii2.748 (10)H10···H132.505 (15)
O9···H3ii1.809 (12)H11···O102.742 (10)
O10···H112.742 (10)H11···H42.389 (15)
O10···H72.352 (10)H11···H72.274 (14)
C3···O103.3385 (11)H12···O82.620 (12)
C14···O43.0221 (15)H13···H102.505 (15)
C1···H18i2.649 (13)H16···C52.89 (3)
C3···H12.483 (13)H16···H8ii2.39 (3)
C5···H162.89 (3)H16···O42.64 (2)
C9···H62.947 (10)H18···O1ii1.923 (13)
C12···H13.022 (13)H18···O2ii2.660 (13)
C13···H3ii2.735 (13)H18···C1ii2.649 (13)
C1—O2—C2118.34 (6)O7—C10—C2112.01 (6)
C3—O3—C12111.28 (5)C10—C11—C12111.99 (6)
C6—O5—C14114.29 (7)O8—C11—C10110.20 (6)
C5—O4—H1108.1 (8)O8—C11—C12110.10 (6)
C7—O6—H2113.7 (7)O3—C12—C13107.67 (6)
C10—O7—H3110.3 (7)O3—C12—C11109.89 (6)
C11—O8—H4106.8 (7)C11—C12—C13111.12 (6)
C13—O9—H5108.7 (9)O9—C13—C12111.73 (7)
H17—O10—H18105.9 (11)C3—C2—H6109.4 (5)
O2—C1—C9118.54 (7)C10—C2—H6110.6 (5)
O1—C1—C9124.25 (7)O2—C2—H6108.4 (5)
O1—C1—O2117.20 (7)C2—C3—H7109.5 (5)
O2—C2—C3110.81 (6)C4—C3—H7109.7 (5)
C3—C2—C10109.91 (6)O3—C3—H7109.4 (5)
O2—C2—C10107.65 (6)C9—C8—H8119.2 (6)
C2—C3—C4108.54 (6)C7—C8—H8122.0 (6)
O3—C3—C2107.78 (6)O7—C10—H9105.7 (5)
O3—C3—C4111.84 (6)C2—C10—H9108.0 (5)
C5—C4—C9119.03 (7)C11—C10—H9109.5 (6)
C3—C4—C5123.41 (7)O8—C11—H10107.9 (5)
C3—C4—C9117.51 (6)C10—C11—H10107.8 (6)
O4—C5—C4123.31 (6)C12—C11—H10108.8 (5)
O4—C5—C6116.97 (7)C11—C12—H11108.9 (5)
C4—C5—C6119.71 (7)C13—C12—H11110.1 (5)
O5—C6—C5121.03 (7)O3—C12—H11109.2 (5)
C5—C6—C7120.17 (7)O9—C13—H12106.6 (7)
O5—C6—C7118.78 (6)C12—C13—H12109.2 (6)
O6—C7—C6116.62 (7)C12—C13—H13109.1 (6)
O6—C7—C8122.88 (7)O9—C13—H13110.3 (6)
C6—C7—C8120.48 (7)H12—C13—H13109.9 (8)
C7—C8—C9118.86 (7)O5—C14—H15113.2 (11)
C1—C9—C4120.45 (7)O5—C14—H16119.0 (17)
C1—C9—C8117.86 (7)O5—C14—H14107.2 (12)
C4—C9—C8121.68 (7)H14—C14—H1692.6 (18)
C2—C10—C11110.36 (6)H15—C14—H16118 (2)
O7—C10—C11111.08 (6)H14—C14—H15102.0 (14)
C2—O2—C1—O1166.15 (7)C3—C4—C9—C8176.94 (7)
C2—O2—C1—C914.80 (10)C5—C4—C9—C1179.31 (7)
C1—O2—C2—C349.41 (9)C3—C4—C9—C11.73 (11)
C1—O2—C2—C10169.62 (7)C3—C4—C5—O41.40 (11)
C12—O3—C3—C268.30 (7)C3—C4—C5—C6179.13 (7)
C12—O3—C3—C4172.47 (6)C5—C4—C9—C80.63 (11)
C3—O3—C12—C1162.48 (7)C4—C5—C6—O5175.60 (7)
C3—O3—C12—C13176.36 (6)O4—C5—C6—O53.90 (11)
C14—O5—C6—C574.25 (10)O4—C5—C6—C7177.66 (7)
C14—O5—C6—C7107.29 (9)C4—C5—C6—C72.84 (11)
O2—C1—C9—C8170.94 (7)O5—C6—C7—O62.15 (10)
O1—C1—C9—C810.09 (12)O5—C6—C7—C8176.85 (7)
O2—C1—C9—C410.34 (11)C5—C6—C7—C81.63 (11)
O1—C1—C9—C4168.64 (8)C5—C6—C7—O6179.37 (7)
O2—C2—C3—C457.25 (7)O6—C7—C8—C9178.24 (7)
C10—C2—C3—O362.59 (7)C6—C7—C8—C90.69 (12)
C10—C2—C3—C4176.11 (6)C7—C8—C9—C41.84 (12)
O2—C2—C3—O3178.55 (5)C7—C8—C9—C1179.45 (7)
O2—C2—C10—O762.06 (7)O7—C10—C11—C12172.26 (6)
O2—C2—C10—C11173.63 (6)C2—C10—C11—O8170.34 (6)
C3—C2—C10—O7177.16 (6)O7—C10—C11—O864.82 (8)
C3—C2—C10—C1152.85 (8)C2—C10—C11—C1247.42 (8)
O3—C3—C4—C9153.20 (6)O8—C11—C12—O3174.18 (6)
C2—C3—C4—C5148.11 (7)O8—C11—C12—C1366.75 (8)
O3—C3—C4—C529.34 (10)C10—C11—C12—C13170.27 (6)
C2—C3—C4—C934.43 (9)C10—C11—C12—O351.21 (8)
C9—C4—C5—O4178.82 (7)O3—C12—C13—O967.05 (8)
C9—C4—C5—C61.71 (11)C11—C12—C13—O9172.56 (6)
Symmetry codes: (i) x1, y, z; (ii) x+1, y, z.
 

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