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ISSN: 2056-9890

Crystal structure of 5-(dibenzo­furan-4-yl)-2′-de­oxy­uridine

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aDepartment of Chemistry, Institute of Chemical Technology, Nathalal Parekh Road, Matunga, Mumbai 400 019, India, and bInstitut für Biochemie, Ernst-Moritz-Arndt Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
*Correspondence e-mail: carola.schulzke@uni-greifswald.de

Edited by P. Dastidar, Indian Association for the Cultivation of Science, India (Received 29 August 2017; accepted 13 September 2017; online 19 September 2017)

The mol­ecule of the title compound, C21H18N2O6, has a bent rather than a linear conformation supported by three intra­molecular C—H⋯O hydrogen bonds. The packing in the crystal lattice is largely determined by inter­actions between hydrogen atoms with oxygen atom lone pairs with one mol­ecule inter­acting with neigbouring mol­ecules via O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds. The title compound crystallizes in the chiral ortho­rhom­bic space group P212121. Its absolute structure could not be determined crystallographically and was assumed with reference to that of the reactant 5-iodo-2′-de­oxy­uridine.

1. Chemical context

As a result of their numerous applications, synthetically modified nucleoside analogues have attracted much attention in recent years. Many of these modified nucleosides show potential activity as drug candidates, biological probes etc (Huryn & Okabe, 1992[Huryn, D. M. & Okabe, M. (1992). Chem. Rev. 92, 1745-1768.]). Modern trends in this field of research consider palladium complexes to be active catalysts for the efficient modification of nucleosides because of their greater ability to perform such catalytic processes in aqueous media (Agrofoglio et al., 2003[Agrofoglio, L. A., Gillaizeau, I. & Saito, Y. (2003). Chem. Rev. 103, 1875-1916.]; Kapdi et al., 2014[Kapdi, A. R., Gayakhe, V., Sanghvi, Y. S., García, J., Lozano, P., da Silva, I., Pérez, J. & Serrano, J. S. (2014). RSC Adv. 4, 17567-17572.]). Base modification in purine and pyrimidine nucleosides, resulting in a new class of compounds with better fluorescence properties, enhancing their chances of being employed as biological probes for studying biological environments such as DNA damage, protein–DNA inter­actions and DNA probes is of great inter­est to chemical biologists as well as bio-organic chemists (Tanpure et al., 2013[Tanpure, A. A., Pawar, M. G. & Srivatsan, S. G. (2013). Isr. J. Chem. 53, 366-378.]). Structural elucidation of such compounds is an important task in order to understand the mechanistic pathways. Herein we present the synthesis and the crystal structure of the title compound, 5-(dibenzo­furan-4-yl)-2′-de­oxy­uridine.

[Scheme 1]

2. Structural commentary

The title compound crystallizes in the ortho­rhom­bic space group P212121 with four mol­ecules in the unit cell. The two aromatic π systems (pyrimidine and dibenzo­furan­yl), which are connected by a C—C bond [C7—C10 = 1.489 (6) Å] subtend a dihedral angle of 30.7 (2)° (Fig. 1[link]). All bond lengths or angles are comparable to those in related compounds. Fifty two entries can be found in the Cambridge Crystallographic Database (ConQuest Version 1.19; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for de­oxy­uridine with a substituent only in the C5 position of the base (i.e. C7 here) and neither substituents nor protecting groups anywhere else, nine of which are for compounds that had already been characterized (i.e. repeats, polymorphs, present/absent solvent). The bond lengths of the pyrimidine moiety observed for the title compound are very close to the average values found for related structures (see Table S1 in the Supporting information). As is typical for this class of compounds, the bond usually assigned to be a double bond within the six-membered ring (here C6=C7) is the shortest for the pyrimidine ring at 1.353 (6) Å and the bond between the second carbonyl carbon atom and the substituted carbon (here C7—C8) is the longest at 1.447 (6) Å. All four other ring atom-to-ring atom distances (N—C and C—C bonds) are shorter than 1.393 Å, indicating significant π-electron delocal­ization throughout the pyrimidine base. All this, however, is in accordance with the majority of previously reported structures.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling and 50% probability displacement ellipsoids. Atom C7 is in the C5 position of the pyrimidine base according to nucleoside/nucleotide nomenclature, atom C6 in C6.

The relative orientation between sugar and base moieties in the title compound is also comparable with compounds in the database. The hydrogen-bonding inter­action (or distance) between the C6-H function (here C6) and the ring oxygen atom of the sugar (here O3) and/or the –CH3–OH group (here O1) is useful for evaluation in this context. The C—H⋯O hydrogen-to-oxygen distances for the inter­action with the alcohol range from 2.29 to 5.98 Å (when the –CH3–OH moiety is pointing directly towards the C–H or completely turned away, respectively; Moore et al., 1989[Moore, S. A., Santarsiero, B. D., Lin, T., James, M. N. G., Tandon, M., Wiebe, L. I. & Knaus, E. E. (1989). Acta Cryst. C45, 647-650.]; Basnak et al., 1996[Basnak, I., Sun, M., Hamor, T. A., Spencer, N. & Walke, R. T. (1996). Nucleosides Nucleotides, 15, 1275-1285.]). The C—H⋯O hydrogen-to-oxygen distances for the inter­action with the furane ring oxygen atom (here O3) range from 2.26 to 3.43 Å (Greco & Tor, 2007[Greco, N. J. & Tor, Y. (2007). Tetrahedron, 63, 3515-3527.]; Basnak et al., 1996[Basnak, I., Sun, M., Hamor, T. A., Spencer, N. & Walke, R. T. (1996). Nucleosides Nucleotides, 15, 1275-1285.]) with the vast majority of orientations allowing at least weak hydrogen bonding between this oxygen and the C6–H hydrogen atom. No systematic dependency between these two groups of distances was found, i.e. a very short or long hydrogen bond with the ring oxygen atom does neither lead to particularly short nor long distances of the hydrogen atom to the methanoyl oxygen atom.

Only five of the related archived structures bear directly attached aromatic π-systems. In all five cases, the orientation of the sugar and the pyrimidine moieties are relatively similar in which the C6–H moiety points to some extent towards the methanoyl oxygen atom of the sugar, forming a weak intra­molecular hydrogen bond and resulting in comparable mol­ecular bends. The dihedral angles between the two aromatic systems do vary and range from 11.9° for a ferrocene substituent (Song et al., 2006[Song, H., Li, X., Long, Y., Schatte, G. & Kraatz, H.-B. (2006). Dalton Trans. pp. 4696-4701.]) to 37.2° for a para-biphenyl substituent (Gayakhe et al., 2016[Gayakhe, V., Ardhapure, A., Kapdi, A. R., Sanghvi, Y. S., Serrano, J. L., García, L., Pérez, J., García, J., Sánchez, G., Fischer, C. & Schulzke, C. (2016). J. Org. Chem. 81, 2713-2729.]), indicating that the extent of delocalization of the π-systems depends on the actual type of aromatic substituent but is not particularly strong in any case.

3. Supra­molecular Features

In the crystal, mol­ecules are linked by N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds (Fig. 2[link] and Table 1[link]). The mol­ecules form rows propagating along the a-axis direction, which are connected to adjacent rows in the c-axis direction by classical hydrogen bonds and in the b-axis direction only by weaker C—H⋯O contacts between two sugar moieties (C4—H4A⋯O3i, two-directional). In the c- and (by bifurcation) a-axis directions, both classical and non-classical hydrogen bonds are present (O2–H2O⋯O5ii; O1—H1O⋯O2iv; N2—H2N⋯O1iii; C13—H13⋯O4; C14—H14⋯O4ii). These interactions lead to the formation of slabs lying parallel to the ac plane.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C4—H4A⋯O3i 0.99 2.61 3.439 (6) 142
C6—H6⋯O6 0.95 2.34 2.915 (5) 119
C13—H13⋯O1 0.95 2.58 3.271 (6) 130
C21—H21⋯O5 0.95 2.33 2.876 (6) 116
C14—H14⋯O4ii 0.95 2.45 3.115 (6) 127
O2—H2O⋯O5ii 1.00 (5) 1.72 (5) 2.716 (5) 174 (5)
N2—H2N⋯O1iii 0.91 (5) 2.30 (5) 3.144 (5) 154 (5)
O1—H1O⋯O2iv 0.92 (6) 2.10 (6) 2.922 (5) 148 (6)
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1]; (ii) [-x+{\script{1\over 2}}, -y+1, z+{\script{1\over 2}}]; (iii) [-x+{\script{1\over 2}}, -y+1, z-{\script{1\over 2}}]; (iv) x+1, y, z.
[Figure 2]
Figure 2
The crystal packing (Mercury; Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) viewed along the a axis showing the classical hydrogen bonds which lead to a two-dimensional network parallel to (010).

4. Synthesis and crystallization

The title compound was synthesized according to our recently reported method (Bhilare et al., 2016[Bhilare, S., Gayakhe, V., Ardhapure, A. V., Sanghvi, Y. S., Schulzke, C., Borozdina, Y. & Kapdi, A. R. (2016). RSC Adv. 6, 83820-83830.]). This involves the cross-coupling reaction of 5-iodo-2′-deoxyuridine and 4-(dibenzofuranyl)boronic acid in the presence of Pd(OAc)2 and PTBS (phospha-triaza-adamantyl propane sulfonate) in water.

Synthesis of 5-(dibenzo­furan-4-yl)-2′-de­oxy­uridine: To a solution of palladium acetate (1.12 mg, 1.0 mol %) and PTABS ligand (2.93 mg, 2.0 mol %) in degassed water (1.0 ml) at ambient temperature under N2 were added 5-iodo-2′-de­oxy­uridine (0.5 mmol) and the solution stirred for 5 min at 353 K. After that, the reaction mixture was allowed to cool to room temperature and then 4-(dibenzo­furan­yl)boronic acid (0.75 mmol) was added along with tri­ethyl­amine (0.14 ml, 1.0 mmol) and degassed water (2.0 ml). The resulting solution was then stirred at 353 K for 3 h. The reaction progress was monitored by TLC. After the completion of reaction, the solvent was removed in vacuo and the resultant residue obtained was purified using column chromatography in CH2Cl2:MeOH solvent system (96:4) to afford the desired product as a white solid (162 mg, 82% yield).

UV–visible absorption and fluorescence emission in methanol (10 µM) λabs = 286 nm λfl = 392,427. 1H NMR (400 MHz, DMSO-d6) δ 11.62 (s, 1H), 8.41 (s, 1H), 8.12 (d, J = 7.4 Hz, 1H), 8.06 (d, J = 7.7 Hz, 1H), 7.67 (t, J = 7.8 Hz, 2H), 7.49 (t, J = 7.7 Hz, 1H), 7.38 (t, J = 7.6 Hz, 2H), 6.28 (t, J = 6.7 Hz, 1H), 5.29 (d, J = 3.8 Hz, 1H), 4.87 (t, J = 4.9 Hz, 1H), 4.27 (s, 1H), 3.81 (d, J = 2.9 Hz, 1H), 3.54 (s, 2H), 2.29–2.14 (m, 2H). 13C NMR (101 MHz, DMSO-d6) δ 161.7, 155.3, 152.9, 150.0, 140.1, 128.3, 127.6, 123.8, 123.6, 123.2, 122.8, 121.1, 120.3, 117.8, 111.7, 108.8, 87.6, 84.5, 70.5, 61.4, 39.9. ESI–MS (m/z) = 395 (M+ + H+). Analysis calculated for C21H18N2O6: C, 63.96; H, 4.60; N, 7.10. Found: C, 63.85; H, 4.64; N, 6.98.

5. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The two protons on oxygen (O1, O2) and the one on nitro­gen (N2) were located and refined with a constraint for the atom—H distance (SHELXL instruction: SADI 0.05 O1 H1O O2 H2O N2 H2N), as otherwise the N—H distance became rather short and the O—H distances rather long. The respective orientations, i.e. the directions the hydrogen atoms are pointing to (particularly important for the alcohol functions), were refined without any restraints or constraints. The C-bound H atoms were included in calculated positions and treated as riding: C—H = 0.95–1.00 Å with Uiso(H) = 1.2Ueq(C).

Table 2
Experimental details

Crystal data
Chemical formula C21H18N2O6
Mr 394.37
Crystal system, space group Orthorhombic, P212121
Temperature (K) 170
a, b, c (Å) 6.2899 (13), 15.167 (3), 17.938 (4)
V3) 1711.2 (6)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.46 × 0.09 × 0.09
 
Data collection
Diffractometer Stoe IPDS2T
Absorption correction Numerical face indexed (X-RED32 and X-SHAPE; Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA, X-RED32 and X-SHAPE. Stoe & Cie, Darmstadt, Germany.])
Tmin, Tmax 0.388, 0.875
No. of measured, independent and observed [I > 2σ(I)] reflections 14640, 3696, 2704
Rint 0.110
(sin θ/λ)max−1) 0.642
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.057, 0.143, 0.96
No. of reflections 3696
No. of parameters 274
No. of restraints 3
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.34, −0.37
Computer programs: X-AREA (Stoe & Cie, 2010[Stoe & Cie (2010). X-AREA, X-RED32 and X-SHAPE. Stoe & Cie, Darmstadt, Germany.]), SHELXT2014 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2013 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), XP in SHELXTL and CIFTAB (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Computing details top

Data collection: X-AREA (Stoe & Cie, 2010); cell refinement: X-AREA (Stoe & Cie, 2010); data reduction: X-AREA (Stoe & Cie, 2010); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2006); software used to prepare material for publication: CIFTAB (Sheldrick, 2008) and PLATON (Spek, 2009).

5-(Dibenzofuran-4-yl)-2'-deoxyuridine top
Crystal data top
C21H18N2O6Dx = 1.531 Mg m3
Mr = 394.37Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 14682 reflections
a = 6.2899 (13) Åθ = 6.5–54.3°
b = 15.167 (3) ŵ = 0.11 mm1
c = 17.938 (4) ÅT = 170 K
V = 1711.2 (6) Å3Needle, colourless
Z = 40.46 × 0.09 × 0.09 mm
F(000) = 824
Data collection top
Stoe IPDS2T
diffractometer
3696 independent reflections
Radiation source: fine-focus sealed tube2704 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm-1Rint = 0.110
ω scansθmax = 27.1°, θmin = 3.4°
Absorption correction: numerical
face indexed (X-Red32 and X-Shape; Stoe & Cie, 2010)
h = 78
Tmin = 0.388, Tmax = 0.875k = 1919
14640 measured reflectionsl = 2222
Refinement top
Refinement on F23 restraints
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.057H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.143 w = 1/[σ2(Fo2) + (0.0841P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.96(Δ/σ)max < 0.001
3696 reflectionsΔρmax = 0.34 e Å3
274 parametersΔρmin = 0.37 e Å3
Special details top

Experimental. The reaction was carried out in a Schlenk tube using Schlenk techniques under a nitrogen atmosphere. All other reagents and solvents were purchased commercially and used without any further purification. A UV–visible spectrum of the title compound (10 µM) was measured in methanol using a UV–visible spectrophotometer with a cell of 1 cm path length. A fluorescence spectrum of the same solution was obtained using a fluorescence spectrophotometer at 298 K using a 1 cm path-length cell. The reaction was monitored by thin layer chromatography using TLC silica gel 60 F254 precoated plates (Merck). Visualization was accomplished by irradiation with UV light. C, H, and N analyses was carried out locally. NMR data (1H, 13C) of the synthesized compound were recorded locally on 500 MHz spectrometers. Mass spectroscopic analysis was carried out with a mass spectrometer from Varian Inc, US: 10 Prostar Binary LC with 500 MS IT PDA detectors.

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.4367 (6)0.5659 (2)0.66750 (19)0.0316 (8)
O20.1365 (5)0.6212 (3)0.62349 (19)0.0355 (8)
O30.3555 (5)0.6634 (2)0.52801 (16)0.0251 (7)
O40.0678 (6)0.6179 (2)0.33056 (18)0.0342 (8)
O50.5541 (6)0.4112 (2)0.26958 (17)0.0319 (8)
O60.6845 (5)0.4177 (2)0.54844 (17)0.0271 (7)
N10.3167 (6)0.5825 (2)0.4169 (2)0.0244 (8)
N20.3171 (7)0.5149 (3)0.3022 (2)0.0278 (8)
C10.3630 (8)0.6543 (3)0.6624 (2)0.0268 (10)
H1A0.48690.69460.66120.032*
H1B0.27870.66850.70740.032*
C20.2282 (7)0.6702 (3)0.5941 (2)0.0238 (9)
H20.16720.73100.59700.029*
C30.0472 (7)0.6046 (3)0.5800 (2)0.0256 (9)
H30.09780.54280.58800.031*
C40.0039 (7)0.6206 (3)0.4983 (3)0.0264 (9)
H4A0.10460.66720.49150.032*
H4B0.04580.56600.47350.032*
C50.2197 (7)0.6500 (3)0.4670 (2)0.0253 (9)
H50.20200.70670.43910.030*
C60.4901 (7)0.5330 (3)0.4377 (2)0.0233 (9)
H60.54810.54090.48620.028*
C70.5806 (7)0.4735 (3)0.3914 (2)0.0239 (9)
C80.4944 (7)0.4627 (3)0.3171 (3)0.0262 (9)
C90.2231 (8)0.5755 (3)0.3485 (2)0.0282 (10)
C100.7714 (7)0.4220 (3)0.4143 (2)0.0250 (9)
C110.8132 (7)0.4001 (3)0.4874 (2)0.0256 (10)
C120.7864 (8)0.3833 (3)0.6103 (2)0.0271 (10)
C130.7096 (8)0.3830 (3)0.6814 (3)0.0296 (10)
H130.57670.40900.69350.036*
C140.8351 (8)0.3429 (3)0.7351 (3)0.0321 (10)
H140.78680.34120.78530.039*
C151.0316 (8)0.3047 (3)0.7172 (3)0.0310 (10)
H151.11390.27750.75520.037*
C161.1061 (8)0.3060 (3)0.6454 (3)0.0306 (10)
H161.23930.28020.63340.037*
C170.9829 (7)0.3460 (3)0.5904 (3)0.0262 (9)
C180.9993 (7)0.3562 (3)0.5105 (3)0.0250 (9)
C191.1478 (7)0.3293 (3)0.4577 (3)0.0280 (10)
H191.27410.29930.47200.034*
C201.1057 (7)0.3474 (3)0.3848 (3)0.0294 (10)
H201.20280.32780.34770.035*
C210.9242 (8)0.3939 (3)0.3626 (3)0.0281 (10)
H210.90410.40670.31120.034*
H2O0.097 (9)0.608 (4)0.676 (3)0.037 (15)*
H2N0.266 (9)0.506 (4)0.255 (3)0.034 (14)*
H1O0.567 (10)0.562 (5)0.644 (4)0.07 (2)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0278 (19)0.0285 (17)0.0385 (19)0.0033 (13)0.0009 (14)0.0040 (14)
O20.0208 (17)0.054 (2)0.0320 (19)0.0045 (15)0.0025 (13)0.0041 (16)
O30.0267 (17)0.0264 (15)0.0223 (16)0.0019 (12)0.0004 (12)0.0025 (12)
O40.0333 (19)0.0388 (18)0.0305 (17)0.0095 (15)0.0064 (14)0.0014 (15)
O50.0370 (19)0.0331 (17)0.0255 (16)0.0016 (14)0.0004 (14)0.0086 (14)
O60.0269 (17)0.0286 (16)0.0259 (15)0.0040 (13)0.0028 (13)0.0018 (12)
N10.024 (2)0.0249 (18)0.0243 (18)0.0037 (15)0.0004 (15)0.0000 (15)
N20.033 (2)0.0299 (19)0.0205 (19)0.0018 (16)0.0034 (16)0.0039 (15)
C10.029 (2)0.024 (2)0.028 (2)0.0031 (18)0.0007 (18)0.0005 (18)
C20.025 (2)0.021 (2)0.025 (2)0.0013 (16)0.0016 (18)0.0007 (17)
C30.022 (2)0.023 (2)0.031 (2)0.0002 (17)0.0024 (17)0.0028 (18)
C40.022 (2)0.026 (2)0.031 (2)0.0039 (17)0.0022 (19)0.0032 (18)
C50.032 (2)0.021 (2)0.023 (2)0.0024 (17)0.0011 (18)0.0010 (17)
C60.024 (2)0.023 (2)0.023 (2)0.0023 (16)0.0033 (16)0.0002 (16)
C70.024 (2)0.021 (2)0.026 (2)0.0018 (16)0.0020 (17)0.0012 (17)
C80.027 (2)0.024 (2)0.027 (2)0.0021 (17)0.0014 (18)0.0015 (17)
C90.032 (3)0.030 (2)0.023 (2)0.002 (2)0.0005 (18)0.0014 (18)
C100.026 (2)0.020 (2)0.029 (2)0.0015 (17)0.0010 (18)0.0024 (18)
C110.027 (3)0.020 (2)0.029 (2)0.0003 (17)0.0060 (18)0.0031 (16)
C120.029 (2)0.023 (2)0.030 (2)0.0016 (18)0.0041 (19)0.0003 (18)
C130.036 (3)0.023 (2)0.030 (2)0.0030 (19)0.001 (2)0.0011 (18)
C140.040 (3)0.027 (2)0.029 (2)0.004 (2)0.003 (2)0.0001 (19)
C150.030 (3)0.028 (2)0.036 (3)0.0010 (19)0.009 (2)0.0030 (19)
C160.030 (3)0.022 (2)0.040 (3)0.0015 (17)0.006 (2)0.004 (2)
C170.024 (2)0.023 (2)0.032 (2)0.0019 (17)0.0003 (19)0.0024 (18)
C180.025 (2)0.019 (2)0.031 (2)0.0012 (17)0.0012 (18)0.0005 (17)
C190.026 (2)0.017 (2)0.041 (3)0.0010 (16)0.004 (2)0.0001 (18)
C200.027 (2)0.029 (2)0.033 (3)0.0008 (18)0.0083 (19)0.0053 (19)
C210.033 (3)0.025 (2)0.026 (2)0.0032 (18)0.0028 (19)0.0045 (18)
Geometric parameters (Å, º) top
O1—C11.423 (6)C5—H51.0000
O1—H1O0.92 (6)C6—C71.353 (6)
O2—C31.417 (6)C6—H60.9500
O2—H2O1.00 (5)C7—C81.447 (6)
O3—C51.403 (5)C7—C101.489 (6)
O3—C21.435 (5)C10—C111.379 (6)
O4—C91.213 (6)C10—C211.402 (6)
O5—C81.216 (5)C11—C181.408 (6)
O6—C121.384 (5)C12—C131.364 (7)
O6—C111.387 (5)C12—C171.405 (6)
N1—C91.366 (6)C13—C141.386 (7)
N1—C61.375 (6)C13—H130.9500
N1—C51.492 (5)C14—C151.403 (7)
N2—C91.373 (6)C14—H140.9500
N2—C81.393 (6)C15—C161.370 (7)
N2—H2N0.91 (5)C15—H150.9500
C1—C21.508 (6)C16—C171.394 (6)
C1—H1A0.9900C16—H160.9500
C1—H1B0.9900C17—C181.445 (6)
C2—C31.533 (6)C18—C191.391 (6)
C2—H21.0000C19—C201.364 (7)
C3—C41.511 (6)C19—H190.9500
C3—H31.0000C20—C211.399 (7)
C4—C51.535 (7)C20—H200.9500
C4—H4A0.9900C21—H210.9500
C4—H4B0.9900
C1—O1—H1O109 (5)C6—C7—C10121.3 (4)
C3—O2—H2O106 (3)C8—C7—C10119.8 (4)
C5—O3—C2108.4 (3)O5—C8—N2118.5 (4)
C12—O6—C11106.8 (3)O5—C8—C7127.0 (4)
C9—N1—C6122.9 (4)N2—C8—C7114.4 (4)
C9—N1—C5114.7 (4)O4—C9—N1122.9 (4)
C6—N1—C5122.4 (4)O4—C9—N2122.8 (4)
C9—N2—C8127.5 (4)N1—C9—N2114.2 (4)
C9—N2—H2N121 (4)C11—C10—C21115.1 (4)
C8—N2—H2N112 (4)C11—C10—C7122.8 (4)
O1—C1—C2112.7 (4)C21—C10—C7122.0 (4)
O1—C1—H1A109.1C10—C11—O6126.3 (4)
C2—C1—H1A109.1C10—C11—C18123.5 (4)
O1—C1—H1B109.1O6—C11—C18110.2 (4)
C2—C1—H1B109.1C13—C12—O6125.9 (4)
H1A—C1—H1B107.8C13—C12—C17123.2 (4)
O3—C2—C1110.2 (4)O6—C12—C17110.8 (4)
O3—C2—C3103.3 (3)C12—C13—C14116.8 (5)
C1—C2—C3116.7 (4)C12—C13—H13121.6
O3—C2—H2108.8C14—C13—H13121.6
C1—C2—H2108.8C13—C14—C15121.5 (5)
C3—C2—H2108.8C13—C14—H14119.2
O2—C3—C4111.0 (4)C15—C14—H14119.2
O2—C3—C2113.5 (4)C16—C15—C14120.8 (5)
C4—C3—C2101.0 (4)C16—C15—H15119.6
O2—C3—H3110.4C14—C15—H15119.6
C4—C3—H3110.4C15—C16—C17118.8 (5)
C2—C3—H3110.4C15—C16—H16120.6
C3—C4—C5104.0 (4)C17—C16—H16120.6
C3—C4—H4A111.0C16—C17—C12118.9 (4)
C5—C4—H4A111.0C16—C17—C18135.2 (4)
C3—C4—H4B111.0C12—C17—C18105.8 (4)
C5—C4—H4B111.0C19—C18—C11119.8 (4)
H4A—C4—H4B109.0C19—C18—C17133.7 (4)
O3—C5—N1108.6 (3)C11—C18—C17106.4 (4)
O3—C5—C4107.2 (3)C20—C19—C18117.6 (4)
N1—C5—C4112.5 (4)C20—C19—H19121.2
O3—C5—H5109.5C18—C19—H19121.2
N1—C5—H5109.5C19—C20—C21122.2 (4)
C4—C5—H5109.5C19—C20—H20118.9
C7—C6—N1122.1 (4)C21—C20—H20118.9
C7—C6—H6118.9C20—C21—C10121.7 (4)
N1—C6—H6118.9C20—C21—H21119.2
C6—C7—C8118.8 (4)C10—C21—H21119.2
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C4—H4A···O3i0.992.613.439 (6)142
C6—H6···O60.952.342.915 (5)119
C13—H13···O10.952.583.271 (6)130
C21—H21···O50.952.332.876 (6)116
C13—H13···O4ii0.952.653.194 (6)117
C14—H14···O4ii0.952.453.115 (6)127
C1—H1B···O5ii0.992.663.401 (6)132
O2—H2O···O5ii1.00 (5)1.72 (5)2.716 (5)174 (5)
N2—H2N···O1iii0.91 (5)2.30 (5)3.144 (5)154 (5)
O1—H1O···O2iv0.92 (6)2.10 (6)2.922 (5)148 (6)
Symmetry codes: (i) x1/2, y+3/2, z+1; (ii) x+1/2, y+1, z+1/2; (iii) x+1/2, y+1, z1/2; (iv) x+1, y, z.
 

Acknowledgements

ARK and CS acknowledge 'The Alexander von Humboldt Foundation' for the research cooperation programme, which is also thanked for the equipment grant to ARK. We also thank the University Grants Commission India for a UGC–SAP fellowship for VG. YB and CS gratefully acknowledges funding from the ERC.

Funding information

Funding for this research was provided by: Alexander von Humboldt-Stiftung (grant No. 3.4 - IP - DEU/1131213 to A. R. Kapdi, C. Schulzke); University Grants Commission (scholarship to V. Gayakhe); FP7 Ideas: European Research Council (grant No. 281257 to C. Schulzke).

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