Structure Determination of Monohydrated Trifolin (Kaempferol3-O-β-D-Galactopyranoside) from Laboratory PowderDiffraction Data

IVAN DA SILVA,1,2 JESUS G. DIAZ,3 JAVIER GONZALEZ-PLATAS4

1SpLine Spanish CRG Beamline at the ESRF. 6, Rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 09, France

2Instituto de Ciencia de Materiales de Madrid-ICMM/CSIC, Cantoblanco Madrid 28049, Spain

3Departamento de Quımica, Universidad de La Laguna. Instituto Universitario de Bio-Organica “Antonio Gonzalez”,38206 La Laguna, Tenerife, Spain

4Departamento de Fısica Fundamental II, Servicio de Difraccion de Rayos X, Universidad de La Laguna, 38206 La Laguna,Tenerife, Spain

Received 14 June 2010; revised 24 September 2010; accepted 24 September 2010

Published online 24 November 2010 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/jps.22379

ABSTRACT: The crystal structure of monohydrated trifolin (kaempferol 3-O-$-D-galactopyranoside) (an important biologically active compound, which was isolated from theaerial part of Consolida oliveriana) has been determined from conventional laboratory X-raypowder diffraction data. Variable counting time technique was used during measurement andcrystal structure was solved by means of Monte Carlo algorithm. The final structure wasachieved by Rietveld refinement using both constraints and restraints on interatomic bondlengths and angles. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J PharmSci 100:1588–1593, 2011Keywords: X-ray powder diffractometry; crystal structure; crystallography; ab initiocalculations; Monte Carlo

INTRODUCTION

The naturally originated compounds belonging tothe group of flavonoids, which are widely dis-tributed in the human diet,1 have generated par-ticular interest with regard to human health ef-fects, including antioxidant activities2,3 or protectionof cardiovascular diseases,4–6 and they have beena subject of intensive pharmacological studiesin recent years, as they are among the mostpromising anticancer agents.7–9 In this context,some flavonoid complexes have been previouslyinvestigated10 (kaempferol, quercetin, trifolin, hy-peroside, 2′-acetylhyperoside, 6′-acetylhyperoside, 7-glucotrifolin, biorobin, or robinin). Monohydrated tri-folin (C21H20O11·H2O) is a derivative of flavonoid and,recently, it has been shown that the acetyl derivatepresents cytotoxic properties.11 No suitable crystals

Correspondence to: Ivan da Silva (Tel: +33-476-88-2449; Fax:+33-476-88-2816; E-mail: dasilvag@esrf.fr)Journal of Pharmaceutical Sciences, Vol. 100, 1588–1593 (2011)© 2010 Wiley-Liss, Inc. and the American Pharmacists Association

for single-crystal diffraction were obtained, but thestructural information could be determined from pow-der diffraction data.

Here, we report the ab initio structural determina-tion of a monohydrated trifolin, using a Monte Carlo/parallel tempering method, in order to obtain a start-ing model, followed by Rietveld refinement using con-straints and restraints on bond lengths and angles.

EXPERIMENTAL

Monohydrated trifolin was isolated from Consolidaoliveriana. Details of extraction and isolation forthe compound have been published previously.10 Thesample was microcrystalline and attempts to growsingle crystals were unsuccessful.

Spectroscopic Study

The structural identity of the studied compound(see, Fig. 1) was determined spectroscopically (protonmagnetic resonance and 13C nuclear magnetic reso-nance, infrared and ultraviolet-visible spectroscopy,

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STRUCTURE DETERMINATION OF MONOHYDRATED TRIFOLIN 1589

Figure 1. Molecular structure of trifolin.

and mass spectrometry). The details of this study canbe found elsewhere.10

X-Ray Diffraction

The powder diffraction data were collected on aPANalytical X’Pert Pro diffractometer (PANalytical,Almelo, Netherlands) using Cu-K"1 radiation witha hybrid monochromator for parallel beam (Debye–Scherrer geometry-transmission mode). The samplewas introduced in a Hilgenberg glass capillary (di-ameter = 0.3 mm) and spinning rotation was activeto reduce the effect of possible preferential orienta-tions. The detector was a X’Celerator (PANalytical,Almelo. Netherlands), working in continuous modewith 2.149◦ active length; soller slits of 0.02 radianswere placed into the incident and diffracted beampath to reduce the asymmetry of peaks due to ax-ial divergence. The 22 range was 3.5◦–83◦, with astep width of 0.0169◦, and the total time of measure-ment was about 19 h. Variable counting time (VCT)procedure12 was used during data collection; it meansthat measurement time is increased toward higher22 angles and it allows to get substantial amountof peaks information present also at high 22 angles,which is otherwise lost in conventional (i.e., fixedcounting time) measurements. It is known that VCTprocedure, in general, improves results on structuredetermination and more stable refinement of atomscoordinates and thermal parameters, especially forthe organic compounds, are achieved.

RESULTS

Data Reduction and Indexing

Reflection positions were determined using the peaksearch algorithm implemented in the WinPLOTR

program13; the first 25 peaks, up to 29◦ in 22,were selected. Pattern indexing was performed withDicVOL06 program14 and a solution was obtained,which yielded a monoclinic cell with figures ofmerit15,16 of M(25) = 34.1, F(25) = 86.2 (0.0063, 46).

For space group determination, Expo2004program17 was used, where a statistical algo-rithm to determine the most probable space grouphave been implemented.18 In this case, the mostprobable extinction group was P 1 21 1, with aprobability factor of 0.776. There are two compatiblespace groups (P21 and P21/m) for this extinctiongroup, but taking into account the cell and moleculevolumes, they allowed us to choose only one (P21).

Structure Determination by Monte Carlo Methods

Structure solution, by means of Direct Methods, wasattempted with Expo2004 program, within P21 spacegroup, without success. Thus, to obtain a startingstructural model, Monte Carlo calculations were per-formed, using the parallel tempering algorithm im-plemented in the program FOX.19 A template of thetrifolin molecule was built with the software pack-age ChemBio Office (version 11.0), which was intro-duced in FOX, as well as a water oxygen. During thecalculations, the observed and calculated intensitieswere compared only in the 22range of 4◦–52◦ and themolecule could translate and rotate randomly; torsionangles between the benzopyran and phenyl rings andbetween both benzopyran and glucose moiety and theoxygen atom connecting the two groups could alsochange, as well as the torsion angle C-OH in theglucose moiety. After ca. 13 million trials, the agree-ment factors were Rwp = 0.0694 and GoF = 10.054.

Rietveld Refinement

The solution found by FOX program was introducedin FullProf program20 to perform a Rietveld refine-ment. Atomic coordinates of the 33 independent non-H atoms were fitted, but constraints on benzopy-ran and phenyl rings and restraints on the otherbond lengths and angles were introduced to limit thenumber of free parameters and ensure the conver-gence of the refinement process. The values for thesebond lengths and angles were taken from similarmolecules in The Cambridge Crystallographic DataCentre (CCDC) database and the mean-square devi-ations of assigned values were 0.01Å and 1◦, respec-tively. Three different isotropic temperature factorswere introduced: one for the water oxygen, other forthe OH oxygen, and one for the rest of atoms. In-tensities were corrected for absorption effects for acylindrical sample.

The peak function used was the Thompson—Cox–Hastings pseudo-Voigt,21 which can take into ac-count the experimental resolution and the broadening

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1590 SILVA, DIAZ, AND GONZALEZ-PLATAS

Figure 2. Comparison between the observed (red circles) and calculated (black continuousline, upper part) patterns of C21H20O11·H2O. The difference curve (blue continuous line, lowerpart) and the reflection positions (green vertical lines) are also represented in the lower part ofthe figure.

due to size and strain effects, typical in this type of or-ganic powder samples. The Finger’s treatment of theaxial divergence22 was taken into account to model

Table 1. Crystal Data and Structure Refinement forC21H20O11·H2O.

Crystal data

Formula C21H20O11·H2OFormula weight 466.39Cell setting, space group Monoclinic, P21Temperature (K) 298a, b, c (Å); $ (◦) 15.6461(3), 13.7636(2),

4.64731(8); 97.653(2)Volume (Å3) 991.87(3)Z, Dc (g·cm−3) 2, 1.56155Radiation type Cu K"1: (mm−1) 1.010Specimen form, color Cylinder, whiteRefinementRefinement method Rietveld refinementRF, RBRAGG 0.0525, 0.0331Goodness-of-fit 1.855Wavelength (Å) 1.54056Profile function Thompson–Cox–Hasting

pseudo-VoigtNo. of profile data steps 4671No. of contributing reflections 693No. of bond length restraints 25No. of bond angle restraints 41

the asymmetry of the peak profile, and 69 points werechosen regularly distributed on the experimental pat-tern, in the 22 range 4–83◦, to model the backgroundthrough a linear interpolation made between two suc-cessive points.

Hydrogen atoms for trifolin molecule were intro-duced in FullProf at their calculated positions withCALC-OH23 program, which combines geometric andforce-field calculations on the basis of hydrogen-bonding interactions, whereas H atoms’ positions forthe water molecule were obtained with CCDC Mer-cury program.24

On the final Rietveld fit, there are 85 adjustableparameters (scale factor, zero shift, atomic coor-dinates, temperature factors, cell parameters, andpeak shape), taking into account the introduced con-straints. The final Rietveld agreement factors wereRp = 0.036, Rwp = 0.047, and χ2 = 3.44. In Figure 2,the plot of the final fit is given. Crystallographicand refinement-related data are reported in Table 1,whereas atomic coordinates and displacement param-eters are reported in Table 2.

DISCUSSION

The Oak Ridge Thermal Ellipsoid Plot Program draw-ing of the molecule monohydrated trifolin is shown in

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Table 2. Atomic Coordinates and Isotropic DisplacementParameters (Å2) Obtained from Rietveld Refinement.

Atom x y z Uiso

O1w 0.2232(10) 0.83729 0.389(3) 0.092(9)O1 0.4065(6) 0.2176(11) 0.311(3) 0.041(1)O6 0.2577(8) 0.4151(13) 0.147(2) 0.041(1)O7 0.1151(5) 0.3993(10) 0.163(3) 0.041(1)C1’’ 0.1888(5) 0.4489(6) 0.287(3) 0.041(1)C2 0.3267(8) 0.2665(8) 0.243(3) 0.041(1)C2’’ 0.1661(6) 0.5552(6) 0.201(3) 0.041(1)C3 0.3220(12) 0.3605(7) 0.315(4) 0.041(1)C3’’ 0.0975(6) 0.6016(6) 0.366(3) 0.041(1)C4 0.3778(10) 0.4106(8) 0.572(4) 0.041(1)C4’’ 0.0184(8) 0.5455(6) 0.225(2) 0.041(1)C5’’ 0.0436(5) 0.4384(6) 0.279(3) 0.041(1)C6’’ −0.0310(9) 0.3715(6) 0.161(4) 0.041(1)H1’’ 0.1987(5) 0.4376(6) 0.497(3) 0.061(2)H2’’ 0.1493(6) 0.5611(6) −0.009(3) 0.061(2)H3’’ 0.1034(6) 0.6007(6) 0.578(3) 0.061(2)H4’’ −0.0334(8) 0.5588(6) 0.316(2) 0.061(2)H5’’ 0.0536(5) 0.4315(6) 0.491(3) 0.061(2)O2 0.36275 0.49713 0.62870 0.078(2)O3 0.4902(11) 0.4716(9) 1.045(3) 0.078(2)O4 0.6759(7) 0.1932(12) 1.036(4) 0.078(2)O5 0.1726(10) 0.0154(12) −0.663(3) 0.078(2)O8 0.2433(8) 0.6052(13) 0.292(4) 0.078(2)O9 0.0748(10) 0.6956(8) 0.256(4) 0.078(2)O10 0.0013(11) 0.5418(14) −0.0800(19) 0.078(2)O11 −0.0155(12) 0.2729(7) 0.251(4) 0.078(2)H3O 0.4465(11) 0.4931(9) 0.950(3) 0.116(4)H4O 0.6995(7) 0.2328(12) 1.152(4) 0.116(4)H5O 0.1277(10) 0.0374(12) −0.750(3) 0.116(4)H8O 0.2368(8) 0.6503(13) 0.403(4) 0.116(4)H9O 0.1121(10) 0.7331(8) 0.331(4) 0.116(4)H10O −0.0392(11) 0.5042(14) −0.1196(19) 0.116(4)H11O −0.0089(12) 0.2721(7) 0.429(4) 0.116(4)H1OWa 0.246(13) 0.819(15) 0.21(3) 0.138(12)H1OWb 0.178(10) 0.791(12) 0.43(5) 0.138(12)H6’’a −0.0432(9) 0.3726(6) −0.074(4) 0.061(2)H6’’b −0.0878(9) 0.3967(6) 0.249(4) 0.061(2)C5 0.51080 0.38080 0.92260 0.041(1)C6 0.58150 0.32771 1.04060 0.041(1)C7 0.59659 0.23601 0.93300 0.041(1)C8 0.54099 0.19892 0.70469 0.041(1)C9 0.47009 0.25241 0.58069 0.041(1)C10 0.45490 0.34350 0.69119 0.041(1)H6 0.61930 0.35340 1.19301 0.061(2)H8 0.55099 0.13752 0.63278 0.061(2)C1’ 0.29438 0.20570 −0.03210 0.041(1)C2’ 0.21220 0.22980 −0.16251 0.041(1)C3’ 0.16708 0.16790 −0.36252 0.041(1)C4’ 0.20349 0.08061 −0.43372 0.041(1)C5’ 0.28529 0.05601 −0.30471 0.041(1)C6’ 0.33109 0.11731 −0.10300 0.041(1)H2’ 0.18731 0.28799 −0.11510 0.061(2)H3’ 0.11210 0.18480 −0.44972 0.061(2)H5’ 0.30989 −0.00218 −0.35361 0.061(2)H6’ 0.38579 0.09991 −0.01520 0.061(2)

Figure 3. The trifolin molecule consists of a benzopy-ran moiety, almost coplanar [0.71(15)◦ as dihedralangle between planes of benzene and pyran rings],a planar phenyl ring rotated by 10.68(13)◦ from theplane of the benzopyran ring system and a galactopy-

Figure 3. Oak Ridge Thermal Ellipsoid Plot Programdrawing of the molecule trifolin in the asymmetric unit withlabeling scheme

Figure 4. Molecular packing viewed along c axis.

ranoside ring adopting the 4C1 chair conformationwith the benzopyran moiety positioned equatoriallyas substituent at C1’’. Bond distances and angles arecomparable with values reported for similarflavonoids.25 The lengthening of the double bondC4=O2 [1.238(12) Å] is due to strong intramolecularhydrogen bond between O2 and O3.

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Figure 5. Molecular stacking, showing the linking of the molecules by C−H · · · O and B–Binteractions.

The hydroxyl group, O3, has a gauche arrangementwith respect to H3-O3-C5-C10 torsion angle (1.74◦),giving rise to a short (1.831 Å) intramolecular con-tact between the H atom of the hydroxyl groupand carbonyl atom O2. The projection of the crys-tal structure down the c axis is shown in Figure 4.Weak intermolecular interactions play a decisiverole in determining the three-dimensional structurefor this compound, with the presence of short con-tacts of C−H · · · O type and B–B interactions with acentroid–centroid distance of 4.761 Å (see, Fig. 5). Fi-nal position and orientation of the water moleculeallows us to conclude that the water molecule plays astabilizing role in the molecular packing (see, Figs. 4and 5).

CONCLUSION

In this study, we have shown the structure determi-nation of monohydrated trifolin compound from con-ventional laboratory X-ray powder diffraction data,using a VCT procedure during measurement. Thisallowed us to determine the structure by means ofMonte Carlo methods and refine the model using theRietveld method. Recent advances on algorithms aim-ing to solve crystal structures using powder diffrac-tion data allow us to deal, in an easier way, new struc-tural studies on compounds in which only powdersamples can be obtained, as is the case of monohy-drated trifolin.

CCDC 775168 contains the supplementary crys-tallographic data for this paper. These data canbe obtained free of charge via www.ccdc.cam.ac.uk/data request/cif, or by emailing data request@ccdc.cam.ac.uk, or by contacting The Cambridge Crystal-lographic Data Centre, 12, Union Road, CambridgeCB2 1EZ, UK; Fax: +44-1223-336033.

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