research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

Crystal structure of a photobiologically active brominated angular pyran­ocoumarin: bromo-hy­dr­oxy-seselin

aBio-Organic Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India, bInstitute of Materials Science, Darmstadt University of Technology, Alarich-Weiss-Strasse 2, D-64287 Darmstadt, Germany, and cDepartment of Applied Chemistry & Chemical Engineering, University of Dhaka, Dhaka, Dhaka-1000, Bangladesh
*Correspondence e-mail: mustafizacce@du.ac.bd

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 13 February 2017; accepted 20 February 2017; online 28 February 2017)

The title compound, C14H13BrO3 [systematic name: rac-(9S,10R)-9-bromo-10-hy­droxy-8,8-dimethyl-9,10-di­hydro-2H,8H-pyrano[2,3-f]chromen-2-one], is a substituted pyran­ocoumarin, obtained by bromination of seselin [8,8-dimethyl-2H,8H-pyrano[2,3-f]chromen-2-one], which was isolated from the Indian herb Trachyspermum stictocarpum (Aajmod). The pyrano ring has a distorted half-chair conformation and its mean plane is inclined to the coumarin mean plane by 1.6 (2)°. In the crystal, mol­ecules are linked by pairs of O—H⋯O hydrogen bonds, forming inversion dimers with an R22(16) ring motif. The dimers stack along the a-axis direction and are linked by offset ππ inter­actions, forming columns [inter­centroid distance = 3.514 (4) Å].

1. Chemical context

The title compound, rac-(9S,10R)-9-bromo-10-hy­droxy-8,8-dimethyl-9,10-di­hydro-2H,8H-pyrano[2,3-f]chromen-2-one, is a substituted product of the angular pyran­ocoumarin seselin, with a bromine atom and a hy­droxy group at the asymmetric carbon atoms C3 and C4 in the pyrano ring (see Fig. 1[link]). This class of pyran­ocoumarins have absorption bands in the near UV region due to the presence of an extended conjugated enone system and exhibit photomutagenic (Appendino et al., 2004[Appendino, G., Bianchi, F., Bader, A., Campagnuolo, C., Fattorusso, E., Taglialatela-Scafati, O., Blanco-Molina, M., Macho, A., Fiebich, B. L., Bremner, P., Heinrich, M., Ballero, M. & Muñoz, E. (2004). J. Nat. Prod. 67, 532-536.]) and photocarcinogenic properties, binding with purin bases of DNA in living cells to yield photoadducts (Filomena et al., 2009[Conforti, F., Marrelli, M., Menichini, F., Bonesi, M., Statti, G., Provenzano, E. & Menichini, F. (2009). Curr. Drug Ther. 4, 38-58.]). Based on this property, these compounds are employed to treat numerous inflammatory skin diseases such as atopic dermatitis and pigment disorders such as vitiligo and psoriasis on exposure to ultraviolet (UV) radiation in photodynamic therapy (PDT). As a result of their strong ability to absorb UV radiation, this class of mol­ecules are also utilized as photoprotective agents to prevent the absorption of harmful UV radiation by the skin in the form of a variety of sun-screening lotions, widely used in dermatological applications in the cosmetic and pharmaceutical industries (Chen et al., 2007[Chen, Y., Fan, G., Zhang, Q., Wu, H. & Wu, Y. (2007). J. Pharm. Biomed. Anal. 43, 926-936.], 2009[Chen, D., Wang, J., Jiang, Y., Zhou, T., Fan, G. & Wu, Y. (2009). J. Pharm. Biomed. Anal. 50, 695-702.]). In addition, in vitro anti­proliferative activity and in vivo phototoxicity of the parent mol­ecule has been reported against numerous cancer cell lines, including HL60, A431 (Conconi et al., 1998[Conconi, M. T., Montesi, F. & Parnigotto, P. P. (1998). Basic Clin. Pharmacol. Toxicol. 82, 193-198.]). These classes of coumarins have been used successfully in combination with ultraviolet irradiation to treat psoriasis and vitiligo and have been found to inhibit proliferation in human hepatocellular carcinoma cell lines (March et al., 1993[March, K. L., Patton, B. L., Wilensky, R. L. & Hathaway, D. R. (1993). Circulation, 87, 184-191.]). Experimental results revealed that their phototoxicity is exerted via Diels–Alder reactions, binding to the double bond of a purin base of DNA in living cells with double bonds of the coumarin, to yield mono- and di-adducts (Conforti et al., 2009[Conforti, F., Marrelli, M., Menichini, F., Bonesi, M., Statti, G., Provenzano, E. & Menichini, F. (2009). Curr. Drug Ther. 4, 38-58.]). Recently, this type of mol­ecule has been combined with a porphyrin to obtain a scaffold-type macromolecule and employed to study of its inter­action (host–guest inter­action) with fullerenes, such as C60 and C70 in supra­molecular chemistry (Banerjee et al., 2014[Banerjee, S., Ghosh, B. K., Bauri, A. K. & Bhattacharya, S. (2014). J Spectrosc. Dyn. 4, 29-34.]; Ghosh et al., 2014[Ghosh, B. K., Bauri, A. K., Bhattacharya, S. & Banerjee, S. (2014). Spectrochim. Acta Part A, 125, 90-98.]). The mol­ecular tweezers containing a coumarin moiety showed better quantum yield and fluorescence absorption due to the presence of the extended conjugated enone of pyran­ocoumarin. As part of our studies in this area, we now describe the synthesis and structure of the title compound.

[Scheme 1]
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling and displacement ellipsoids drawn at the 50% probability level

2. Structural commentary

The title compound, Fig. 1[link], belongs to a class of naturally occurring pyran­ocoumarins, known as psoralenes. It is an angular isomer of the substituted pyran­ocoumarin seselin [8,8-dimethyl-2H,8H-pyrano[2,3-f]chromen-2-one], whose crystal structure has been reported (Kato, 1970[Kato, K. (1970). Acta Cryst. B26, 2022-2029.]; Bauri et al., 2006[Bauri, A. K., Foro, S., Lindner, H.-J. & Nayak, S. K. (2006). Acta Cryst. E62, o1340-o1341.]). It is composed of three different ring systems, viz. benzene, pyrone and pyrano, with (CH3)2, Br and OH substituents located at the C2, C3 and C4 positions, respectively, see Fig. 1[link]. The C5—C6—C10—C9 and O2—C6—C10—C11 torsion angles are almost the same, viz. 178.6 (6) and 178.3 (5)°, respectively, indicating that these rings are almost coplanar. The pyrano ring (O1/C1–C5) has a distorted half-chair conformation [puckering parameters: amplitude (Q) = 0.443 (7) Å, θ = 132.7 (9)°, φ = 91.7 (11)°], probably due to ring flexibility and the presence of the substituents. Its mean plane is inclined to the mean plane of the coumarin ring by 1.6 (2)°. There are two asymmetric centres at positions C3 and C4 in the mol­ecule (Fig. 1[link]). The present study of the title racemic compound revealed that the relative configuration of atoms C3 and C4 to be S and R, respectively.

3. Supra­molecular features

In the crystal, mol­ecules are linked by pairs of O—H⋯O hydrogen bonds, forming inversion dimers with an R22(16) ring motif (Table 1[link] and Fig. 2[link]). The dimers stack along the a-axis direction and are linked by offset ππ inter­actions, forming columns [Cg2⋯Cg2(−x + 1, −y, −z + 2) = 3.514 (4) Å, inter­planar distance = 3.422 (3) Å, slippage = 0.798 Å; Cg2 is the centroid of the O2/C6–C10 ring].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O3—H3O⋯O4i 0.81 (2) 1.95 (3) 2.734 (7) 162 (8)
Symmetry code: (i) -x, -y, -z+1.
[Figure 2]
Figure 2
A view along the a axis of the crystal packing of the title compound, with hydrogen bonds shown as dashed lines (see Table 1[link]).

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.38, last update November 2016; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) gave more than 25 hits for the pyran­ocoumarin structure. They include two reports of the crystal structure of seselin [CSD refcodes AMYROL (Kato, 1970[Kato, K. (1970). Acta Cryst. B26, 2022-2029.]) and AMYROL01 (Bauri et al., 2006[Bauri, A. K., Foro, S., Lindner, H.-J. & Nayak, S. K. (2006). Acta Cryst. E62, o1340-o1341.])], and a number of structures with various substituents at the C3 and C4 atoms; many of which are natural products.

5. Synthesis and crystallization

The compound seselin was isolated as a colourless crystalline solid from the methanol extract of T. stictocarpum (in local dialect known as Aajmod) by means of column chromatography over SiO2 gel, by gradient elution with a mixture of a binary solvent system of hexane and ethyl acetate. It was purified by reverse-phase high-pressure liquid chromatography followed by crystallization to yield a colourless solid. This compound was then brominated using NBS in aqueous tetra­hydro­furan (THF) in a 1:1 ratio at room temperature with continuous mechanical stirring over a period of 12 h. The reaction was quenched with ice-cold water and extracted with diethyl ether to yield the crude product. This was then purified by column chromatography over SiO2 with gradient solvent elution to yield the title compound. Colourless rod-like crystals were obtained after recrystallization three times from ethyl acetate:hexane (1:4) solution at room temperature.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The hydroxyl H atom was located in a difference Fourier map and refined with Uiso(H) = 1.2Ueq(O). The C-bound H atoms were included in calculated positions and treated as riding atoms: C—H = 0.93–0.98 Å with Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C14H13BrO4
Mr 325.15
Crystal system, space group Monoclinic, P21/n
Temperature (K) 299
a, b, c (Å) 6.9573 (6), 23.465 (2), 8.3435 (7)
β (°) 100.79 (1)
V3) 1338.0 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 3.08
Crystal size (mm) 0.44 × 0.20 × 0.16
 
Data collection
Diffractometer Oxford Diffraction Xcalibur Sapphire CCD detector
Absorption correction Multi-scan (CrysAlis RED; Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD & CrysAlis RED. Oxford Diffraction Ltd., Abingdon, England.])
Tmin, Tmax 0.344, 0.639
No. of measured, independent and observed [I > 2σ(I)] reflections 4521, 2392, 2063
Rint 0.022
(sin θ/λ)max−1) 0.602
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.063, 0.202, 1.12
No. of reflections 2392
No. of parameters 175
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 1.25, −1.02
Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2009[Oxford Diffraction (2009). CrysAlis CCD & CrysAlis RED. Oxford Diffraction Ltd., Abingdon, England.]), SHELXS97 and SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

rac-(9S,10R)-9-Bromo-10-hydroxy-8,8-dimethyl-9,10-dihydro-2H,8H-pyrano[2,3-f]chromen-2-one top
Crystal data top
C14H13BrO4F(000) = 656
Mr = 325.15Dx = 1.614 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3332 reflections
a = 6.9573 (6) Åθ = 2.5–27.4°
b = 23.465 (2) ŵ = 3.08 mm1
c = 8.3435 (7) ÅT = 299 K
β = 100.79 (1)°Rod, colourless
V = 1338.0 (2) Å30.44 × 0.20 × 0.16 mm
Z = 4
Data collection top
Oxford Diffraction Xcalibur Sapphire CCD detector
diffractometer
2392 independent reflections
Radiation source: fine-focus sealed tube2063 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
Rotation method data acquisition using ω scans.θmax = 25.4°, θmin = 2.6°
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2009)
h = 88
Tmin = 0.344, Tmax = 0.639k = 2028
4521 measured reflectionsl = 106
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.063Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.202H atoms treated by a mixture of independent and constrained refinement
S = 1.12 w = 1/[σ2(Fo2) + (0.0969P)2 + 6.1833P]
where P = (Fo2 + 2Fc2)/3
2392 reflections(Δ/σ)max = 0.005
175 parametersΔρmax = 1.25 e Å3
1 restraintΔρmin = 1.02 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2945 (9)0.1326 (3)0.9293 (8)0.0385 (14)
C20.2080 (10)0.2030 (3)0.7183 (8)0.0439 (15)
C30.2309 (9)0.1564 (3)0.5932 (8)0.0370 (14)
H30.15380.16730.48700.044*
C40.1631 (8)0.0972 (3)0.6392 (7)0.0337 (13)
H40.21930.06780.57870.040*
C50.2295 (8)0.0878 (3)0.8222 (7)0.0323 (13)
C60.2285 (8)0.0340 (3)0.8890 (8)0.0327 (13)
C70.1645 (9)0.0657 (3)0.8329 (8)0.0392 (15)
C80.2141 (10)0.0764 (3)1.0051 (9)0.0450 (16)
H80.20760.11351.04300.054*
C90.2692 (10)0.0345 (3)1.1120 (8)0.0415 (15)
H90.30070.04271.22290.050*
C100.2804 (9)0.0233 (3)1.0572 (8)0.0367 (14)
C110.3418 (10)0.0693 (3)1.1591 (8)0.0425 (15)
H110.37870.06351.27090.051*
C120.3486 (11)0.1233 (3)1.0959 (8)0.0462 (16)
H120.38970.15371.16530.055*
C130.0073 (12)0.2122 (3)0.7295 (10)0.0554 (19)
H13A0.01670.24180.80690.066*
H13B0.06020.17750.76410.066*
H13C0.07970.22300.62440.066*
C140.2986 (14)0.2596 (3)0.6815 (11)0.062 (2)
H14A0.43560.25430.68230.075*
H14B0.28190.28710.76290.075*
H14C0.23530.27300.57600.075*
O10.3137 (7)0.18705 (19)0.8778 (6)0.0473 (12)
O20.1716 (6)0.01003 (17)0.7824 (5)0.0366 (10)
O30.0446 (7)0.0926 (2)0.6070 (6)0.0455 (11)
H3O0.078 (11)0.089 (4)0.510 (3)0.055*
O40.1163 (8)0.1010 (2)0.7257 (6)0.0562 (14)
Br10.50492 (10)0.14733 (3)0.57070 (9)0.0528 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.038 (3)0.034 (3)0.041 (4)0.001 (3)0.000 (3)0.002 (3)
C20.057 (4)0.031 (3)0.041 (4)0.001 (3)0.000 (3)0.003 (3)
C30.039 (3)0.038 (3)0.028 (3)0.005 (2)0.009 (2)0.008 (3)
C40.033 (3)0.032 (3)0.034 (3)0.005 (2)0.000 (2)0.003 (3)
C50.030 (3)0.034 (3)0.030 (3)0.001 (2)0.001 (2)0.006 (3)
C60.028 (3)0.032 (3)0.036 (3)0.002 (2)0.001 (2)0.001 (3)
C70.038 (3)0.035 (3)0.043 (4)0.001 (3)0.004 (3)0.011 (3)
C80.044 (4)0.044 (4)0.047 (4)0.002 (3)0.008 (3)0.015 (3)
C90.044 (4)0.045 (4)0.034 (3)0.004 (3)0.004 (3)0.012 (3)
C100.034 (3)0.043 (4)0.032 (3)0.003 (3)0.003 (2)0.007 (3)
C110.048 (4)0.053 (4)0.024 (3)0.006 (3)0.000 (3)0.001 (3)
C120.055 (4)0.045 (4)0.034 (4)0.001 (3)0.003 (3)0.010 (3)
C130.068 (5)0.046 (4)0.051 (4)0.013 (4)0.007 (4)0.000 (3)
C140.087 (6)0.041 (4)0.056 (5)0.013 (4)0.006 (4)0.008 (4)
O10.063 (3)0.033 (2)0.041 (3)0.003 (2)0.005 (2)0.000 (2)
O20.043 (2)0.031 (2)0.032 (2)0.0022 (18)0.0017 (18)0.0054 (18)
O30.040 (2)0.052 (3)0.040 (3)0.008 (2)0.005 (2)0.006 (2)
O40.079 (4)0.033 (2)0.048 (3)0.008 (2)0.011 (3)0.000 (2)
Br10.0432 (4)0.0606 (5)0.0542 (5)0.0072 (3)0.0085 (3)0.0069 (4)
Geometric parameters (Å, º) top
C1—O11.362 (8)C7—O21.376 (7)
C1—C121.388 (10)C7—C81.435 (10)
C1—C51.399 (9)C8—C91.336 (10)
C2—O11.444 (8)C8—H80.9300
C2—C141.526 (9)C9—C101.438 (9)
C2—C131.533 (11)C9—H90.9300
C2—C31.540 (9)C10—C111.391 (9)
C3—C41.538 (8)C11—C121.375 (10)
C3—Br11.962 (7)C11—H110.9300
C3—H30.9800C12—H120.9300
C4—O31.424 (7)C13—H13A0.9600
C4—C51.526 (8)C13—H13B0.9600
C4—H40.9800C13—H13C0.9600
C5—C61.381 (8)C14—H14A0.9600
C6—O21.372 (7)C14—H14B0.9600
C6—C101.404 (9)C14—H14C0.9600
C7—O41.220 (8)O3—H3O0.81 (2)
O1—C1—C12116.1 (6)C9—C8—C7121.6 (6)
O1—C1—C5122.9 (6)C9—C8—H8119.2
C12—C1—C5121.0 (6)C7—C8—H8119.2
O1—C2—C14104.7 (6)C8—C9—C10120.6 (6)
O1—C2—C13108.3 (6)C8—C9—H9119.7
C14—C2—C13109.6 (6)C10—C9—H9119.7
O1—C2—C3109.9 (5)C11—C10—C6117.7 (6)
C14—C2—C3112.5 (6)C11—C10—C9124.5 (6)
C13—C2—C3111.5 (6)C6—C10—C9117.8 (6)
C4—C3—C2113.3 (5)C12—C11—C10120.5 (6)
C4—C3—Br1105.9 (4)C12—C11—H11119.7
C2—C3—Br1111.6 (4)C10—C11—H11119.7
C4—C3—H3108.6C11—C12—C1120.5 (6)
C2—C3—H3108.6C11—C12—H12119.7
Br1—C3—H3108.6C1—C12—H12119.7
O3—C4—C5106.5 (5)C2—C13—H13A109.5
O3—C4—C3111.7 (5)C2—C13—H13B109.5
C5—C4—C3109.4 (5)H13A—C13—H13B109.5
O3—C4—H4109.7C2—C13—H13C109.5
C5—C4—H4109.7H13A—C13—H13C109.5
C3—C4—H4109.7H13B—C13—H13C109.5
C6—C5—C1117.1 (5)C2—C14—H14A109.5
C6—C5—C4120.9 (5)C2—C14—H14B109.5
C1—C5—C4122.0 (5)H14A—C14—H14B109.5
O2—C6—C5116.7 (5)C2—C14—H14C109.5
O2—C6—C10120.2 (5)H14A—C14—H14C109.5
C5—C6—C10123.1 (6)H14B—C14—H14C109.5
O4—C7—O2116.1 (6)C1—O1—C2118.1 (5)
O4—C7—C8126.6 (6)C6—O2—C7122.5 (5)
O2—C7—C8117.3 (6)C4—O3—H3O107 (6)
O1—C2—C3—C456.8 (7)O2—C7—C8—C91.5 (10)
C14—C2—C3—C4173.0 (6)C7—C8—C9—C100.1 (10)
C13—C2—C3—C463.4 (7)O2—C6—C10—C11178.3 (5)
O1—C2—C3—Br162.7 (6)C5—C6—C10—C112.3 (9)
C14—C2—C3—Br153.5 (7)O2—C6—C10—C90.7 (9)
C13—C2—C3—Br1177.1 (5)C5—C6—C10—C9178.6 (6)
C2—C3—C4—O376.8 (6)C8—C9—C10—C11178.0 (7)
Br1—C3—C4—O3160.5 (4)C8—C9—C10—C61.0 (9)
C2—C3—C4—C540.8 (7)C6—C10—C11—C120.8 (10)
Br1—C3—C4—C581.9 (5)C9—C10—C11—C12179.8 (7)
O1—C1—C5—C6176.0 (6)C10—C11—C12—C10.1 (11)
C12—C1—C5—C62.3 (9)O1—C1—C12—C11177.4 (6)
O1—C1—C5—C43.7 (9)C5—C1—C12—C110.9 (11)
C12—C1—C5—C4178.1 (6)C12—C1—O1—C2161.8 (6)
O3—C4—C5—C674.4 (7)C5—C1—O1—C219.9 (9)
C3—C4—C5—C6164.7 (5)C14—C2—O1—C1166.3 (6)
O3—C4—C5—C1105.9 (6)C13—C2—O1—C176.9 (7)
C3—C4—C5—C114.9 (8)C3—C2—O1—C145.2 (8)
C1—C5—C6—O2177.6 (5)C5—C6—O2—C7179.9 (5)
C4—C5—C6—O22.1 (8)C10—C6—O2—C70.7 (8)
C1—C5—C6—C103.1 (9)O4—C7—O2—C6178.2 (6)
C4—C5—C6—C10177.3 (6)C8—C7—O2—C61.8 (8)
O4—C7—C8—C9178.5 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O3—H3O···O4i0.81 (2)1.95 (3)2.734 (7)162 (8)
Symmetry code: (i) x, y, z+1.
 

Acknowledgements

The authors thank Professor Dr. Hartmut, FG Strukturforschung, Material-und Geowissenschaften, Technische Universät Darmstadt, for his kind cooperation with the data collection, and for providing diffractometer time.

References

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