organic papers
Acta Cryst.(2004). E60, o1583±o1585 DOI: 10.1107/S1600536804020161 NourEddine Raouafiet al. C11H18N5OP
o1583
Acta Crystallographica Section E
Structure Reports Online
ISSN 1600-5368
2-Amino-1-[bis(
N
,
N
-dimethylamino)phosphor-amido]benzimidazole
NourEddine Raouafi,a* Matthias Freytag,bPeter G. Jonesb and Mohamed Lamine BenKhouda
aLaboratoire de Chimie Analytique et Electrochimie, Faculty of Science of Tunis El-Manar University, Tunis El-Manar 2092, Tunisia, andbInstitut fuÈr Anorganische und Analytische Chemie, Technische UniversitaÈt Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
Correspondence e-mail: [email protected]
Key indicators
Single-crystal X-ray study T= 133 K
Mean(C±C) = 0.002 AÊ Rfactor = 0.035 wRfactor = 0.102
Data-to-parameter ratio = 23.3
For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.
#2004 International Union of Crystallography Printed in Great Britain ± all rights reserved
The crystal structure of the title compound, C11H18N5OP, is
stabilized by an intermolecular NÐH N-type hydrogen bond and another CÐH O interaction that is intramol-ecular. The NÐH N hydrogen bonding leads to inversion-related dimers.
Comment
Phosphorylation of benzimidazole has been extensively studied by Matevosyan and co-workers (Matevosyan et al.
1981, 1990; Matevosyan & Zalvin, 1998). These substrates are known for their activities as growth regulators, stability inductors for plants and antifungal agents (Zalvinet al., 1999; Matevosyan & Zalvin, 1998; Andersonet al., 2001). They are also used as intermediates in the Wittig±Horner reaction for the preparation of substituted ole®ns (Maier & Rist, 1987). Direct phosphorylation of benzimidazole can be accomplished by the reaction the sodium salt of 2-aminobenzimidazole derivative with chlorophosphoramide (Raoua® et al., 2003). The structure determination of the title compound, (I), was undertaken as a part of our studies on phosphorylated benz-imidazole derivatives.
The X-ray structure of (I) (Fig. 1), shows that the ®ve-membered ring has an r.m.s. deviation of 0.004 AÊ, with the P atom lying 0.311 (2) AÊ outside this plane. The six-membered ring has an r.m.s deviation of 0.005 AÊ and makes an angle of 2.7 (9)with the ®ve-membered ring.
The PÐN4 [1.6317 (11) AÊ] and PÐN5 [1.6352 (10) AÊ] bonds are shorter than the PÐN1 bond [1.7124 (9) AÊ] (Table 1) which is close to standard non conjugated PÐN bond length (1.73 AÊ; Allen et al., 1987; Schulz et al., 1999; Cruickshank, 1964; Yamamoto & Akiba, 2000). The three CÐ N bond lengths of the cyclic guanidine function are not equal; the C1ÐN3 and C1ÐN2 bond lengths are 1.3199 (14) AÊ and 1.3396 (14) AÊ, respectively, while the C1ÐN1 bond length is
1.4140 (14) AÊ. These three bonds are shorter than a standard single CÐN bond (1.47 AÊ; Hamada et al., 1986) and longer than a pure non-conjugated C N bond (1.27 AÊ; HaÈfelinger, 1970). This could be explained by conjugation of only two bonds (C1ÐN2 and C1ÐN3). Unlike the non-cyclic guanidine (Bishopet al., 2003), the C1ÐN1 bond is not involved in this conjugation.
The packing reveals the presence of three intermolecular interactions (Table 2). The N3ÐH1 N2iii hydrogen bond
[symmetry code: (iii) ÿx, ÿy, ÿz] leads to inversion-related dimers (Fig. 2).
Experimental
The aminolysis of the product from the reaction ofN -benzimidazol-2-yl imidate sodium salt and tetrameth-benzimidazol-2-ylchlorophosphoramide gives the corresponding compound, (I), in 90% yield. Compound (I) was recrystallized twice from tetrahydrofuran (m.p. = 472±473 K). The spectroscopic characterization was obtained from the analysis of IR,
1H,13C and31P NMR spectra. IR (CHCl
3, cmÿ1):NH= 3489,NH=
3331,NH= 1633,PO= 1251. 1H NMR (CDCl3,, p.p.m.): 2.72 (d,
12H, NÐCH3,3JPH= 11 Hz), 6.93±7.31 (m, 6H, 4 CH = C, 2NÐH). 13C NMR: 36.09, 36.15, 111.20, 115.29, 119.33, 122.54, 132.68, 143.46,
157.07.31P NMR: 15.21.
Crystal data
C11H18N5OP
Mr= 267.27
Monoclinic,P21=n
a= 9.8997 (6) AÊ
b= 10.5514 (6) AÊ
c= 13.739 (1) AÊ
= 103.613 (3)
V= 1394.80 (15) AÊ3
Z= 4
Dx= 1.273 Mg mÿ3
MoKradiation Cell parameters from 5780
re¯ections
= 2±30
= 0.20 mmÿ1
T= 133 (2) K Prism, colourless 0.290.280.27 mm
Data collection
Bruker SMART 1000 CCD diffractometer
!and'scans
Absorption correction: none 28550 measured re¯ections 4081 independent re¯ections
3346 re¯ections with >2(I)
Rint= 0.036
max= 30.0
h=ÿ13!13
k=ÿ14!14
l=ÿ19!19
Re®nement
Re®nement onF2
R[F2> 2(F2)] = 0.035
wR(F2) = 0.102
S= 1.05 4081 re¯ections 175 parameters
H atoms treated by a mixture of independent and constrained re®nement
w= 1/[2(F
o2) + (0.057P)2
+ 0.3169P]
whereP= (Fo2+ 2Fc2)/3
(/)max< 0.001
max= 0.43 e AÊÿ3
min=ÿ0.24 e AÊÿ3
Table 1
Selected geometric parameters (AÊ,).
PÐN4 1.6317 (11) PÐN5 1.6352 (10) PÐN1 1.7124 (9)
N1ÐC1 1.4140 (14) N1ÐC2 1.4242 (14) N3ÐC1 1.3396 (14)
N4ÐPÐN1 111.39 (5) N5ÐPÐN1 101.86 (5) C1ÐN1ÐC2 104.65 (9)
N2ÐC1ÐN3 123.99 (10) N2ÐC1ÐN1 113.42 (10) N3ÐC1ÐN1 122.59 (10)
C2ÐN1ÐC1ÐN2 1.08 (13)
C2ÐN1ÐC1ÐN3 ÿ179.07 (11) PÐN1ÐC2ÐC7PÐN1ÐC2ÐC3 ÿ166.78 (8)16.60 (19)
Table 2
Hydrogen-bonding geometry (AÊ,).
DÐH A DÐH H A D A DÐH A
C6ÐH6 Oi 0.95 2.56 3.4982 (15) 169
C9ÐH9C Oii 0.98 2.62 3.5932 (18) 175
N3ÐH1 N2iii 0.925 (18) 2.024 (18) 2.9402 (14) 170.1 (15)
Symmetry codes: (i)1
2ÿx;yÿ12;21ÿz; (ii)32ÿx;yÿ12;12ÿz; (iii) 1ÿx;1ÿy;1ÿz.
Methyl H atoms were identi®ed in difference syntheses, idealized and then re®ned using rigid methyl groups [CÐH 0.98 AÊ,HÐCÐH 109.5;U
iso(H) = 1.2Ueq(C)] and allowed to rotate, but not to tip. H7
was included using a riding model, with CÐH = 0.95 AÊ andUiso(H) =
1.2Ueq(C). NÐH H atoms were freely re®ned.
Data collection:SMART(Bruker, 1998); cell re®nement:SAINT (Bruker, 1998); data reduction:SAINT; program(s) used to solve structure:SHELXS97 (Sheldrick, 1997); program(s) used to re®ne
organic papers
o1584
NourEddine Raouafiet al. C11H18N5OP Acta Cryst.(2004). E60, o1583±o1585Figure 1
ORTEX (McArdle, 1995) plot of the title compound. Displacement ellipsoids are drawn at the 40% probability level. H atoms are drawn as small spheres of arbitrary radius.
Figure 2
structure: SHELXL97 (Sheldrick, 1997); molecular graphics: XP (Siemens, 1994); software used to prepare material for publication: SHELXL97.
The authors thank SERT for ®nancial support (Lab-CH02). Professors Reinhard Schmutzler and Khaled Boujlel are acknowledged for their valuable help.
References
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987).J. Chem. Soc. Perkin Trans.2, pp. S1±19.
Anderson, R. J., Bendell, D. J., Hooper, M., Cairns, D., Mackay, S. P., Hiremath, S. P., Jivanagi, A. S., Badami, S., Biradar J. S. & Townson, S. (2001).J. Pharm. Pharmacol.53, 89±94.
Bishop, M. M., Lee, A. H. W., Lindoy, L. F. & Turner, P. (2003).Polyhedron,22, 735±743.
Bruker (1998).SMART(Version 5.0) andSAINT(Version 4.0). Bruker AXS Inc., Madison, Wisconsin, USA.
Cruickshank, D. W. J. (1964).Acta Cryst.17, 671±672. HaÈfelinger, G. (1970).Chem. Ber.103, 2902±2921.
Hamada, Y., Tsuboi, M., Yamanouchi, K. & Kuchitsu, K. (1986).J. Mol. Struct.
146, 253±262.
McArdle, P. (1995).J. Appl. Cryst.28, 65.
Maier, L. & Rist, G. (1987).Phosphorus Sulfur Silicon,32, 65±72.
Matevosyan, G. L., Matyushicheva, R. M., Vodovatova, S. N. & Zalvin, P. M. (1981).Russ. J. Gen. Chem.51, 636±638.
Matevosyan, G. L. & Zalvin, P. M. (1990).Chem. Heterocycl.Compd,26, 599± 616.
Matevosyan, G. L. & Zalvin, P. M. (1998).Russ. J. Gen. Chem.68, 1467±1476. Raoua®, N., Boujlel, K. & Benkhoud, M. L. (2003).Phosphorus Sulfur Silicon.
In the press.
Schulz, S., Bauer, T. & Nieger, M. (1999).Chem. Commun.pp. 879±880. Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of
GoÈttingen, Germany.
Siemens (1994).XP. Version 5.03. Siemens Analytical X-ray Instruments, Madison, Wisconsin, USA.
Spek, A. L. (2001).PLATON.University of Utrecht, The Netherlands. Yamamoto, Y. & Akiba, K. (2000).J. Organomet. Chem.611, 200±209. Zalvin, P. M., Matevosyan, G. L. & Ofengeim, D. L. (1999).Phosphorus Sulfur
Silicon,144±146, 629±632.
organic papers
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Acta Cryst. (2004). E60, o1583–o1585
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Acta Cryst. (2004). E60, o1583–o1585 [https://doi.org/10.1107/S1600536804020161]
2-Amino-1-[bis(
N
,
N
-dimethylamino)phosphoramido]benzimidazole
NourEddine Raouafi, Matthias Freytag, Peter G. Jones and Mohamed Lamine BenKhoud
1-(N,N,N′,N′-Tertramethylphosphoramido)-2-aminobenz[d]imidazole
Crystal data
C11H18N5OP Mr = 267.27
Monoclinic, P21/n a = 9.8997 (6) Å b = 10.5514 (6) Å c = 13.739 (1) Å β = 103.613 (3)° V = 1394.80 (15) Å3 Z = 4
F(000) = 568
Dx = 1.273 Mg m−3 Melting point: 199.50°C K Mo Kα radiation, λ = 0.71073 Å Cell parameters from 5780 reflections θ = 2–30°
µ = 0.20 mm−1 T = 133 K Prism, colourless 0.29 × 0.28 × 0.27 mm
Data collection
Bruker SMART 1000 CCD diffractometer
Radiation source: fine-focus sealed tube Graphite monochromator
Detector resolution: 8.192 pixels mm-1 ω & φ scans
28550 measured reflections
4081 independent reflections 3346 reflections with I > 2σ(I) Rint = 0.036
θmax = 30.0°, θmin = 2.3° h = −13→13
k = −14→14 l = −19→19
Refinement
Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.035 wR(F2) = 0.102 S = 1.05 4081 reflections 175 parameters 0 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ2(Fo2) + (0.057P)2 + 0.3169P] where P = (Fo2 + 2Fc2)/3
(Δ/σ)max < 0.001 Δρmax = 0.43 e Å−3 Δρmin = −0.24 e Å−3
Special details
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Acta Cryst. (2004). E60, o1583–o1585
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)
x y z Uiso*/Ueq
P 0.49345 (3) 0.20054 (3) 0.23693 (2) 0.01748 (9)
O 0.58500 (9) 0.30285 (8) 0.21649 (6) 0.02233 (18)
N1 0.41121 (10) 0.25522 (9) 0.32523 (7) 0.01761 (19)
N2 0.39248 (10) 0.36376 (9) 0.46544 (7) 0.0197 (2)
N3 0.55826 (11) 0.43631 (11) 0.38118 (8) 0.0249 (2)
H1 0.5768 (17) 0.5053 (17) 0.4239 (13) 0.038 (4)*
H2 0.5934 (17) 0.4266 (15) 0.3292 (12) 0.029 (4)*
N4 0.58220 (12) 0.07213 (11) 0.27469 (9) 0.0298 (2)
N5 0.36254 (10) 0.15227 (10) 0.14850 (7) 0.0230 (2)
C1 0.45762 (11) 0.35652 (10) 0.39212 (8) 0.0179 (2)
C3 0.29600 (12) 0.26529 (11) 0.44844 (8) 0.0187 (2)
C4 0.19830 (13) 0.23360 (12) 0.50263 (9) 0.0226 (2)
H4 0.1937 0.2787 0.5616 0.027*
C5 0.10789 (13) 0.13415 (12) 0.46790 (10) 0.0252 (3)
H5 0.0404 0.1110 0.5037 0.030*
C6 0.11435 (13) 0.06736 (12) 0.38114 (10) 0.0259 (3)
H6 0.0505 0.0004 0.3587 0.031*
C2 0.30385 (11) 0.19639 (10) 0.36226 (8) 0.0180 (2)
C7 0.21312 (13) 0.09732 (11) 0.32669 (9) 0.0236 (2)
H7 0.2179 0.0519 0.2679 0.028*
C8 0.5190 (2) −0.04732 (16) 0.29554 (18) 0.0572 (5)
H8A 0.5747 −0.1185 0.2809 0.069*
H8B 0.4245 −0.0534 0.2534 0.069*
H8C 0.5158 −0.0499 0.3662 0.069*
C9 0.73034 (16) 0.08340 (17) 0.32468 (13) 0.0447 (4)
H9A 0.7406 0.0890 0.3973 0.054*
H9B 0.7687 0.1599 0.3009 0.054*
H9C 0.7804 0.0088 0.3092 0.054*
C10 0.39383 (16) 0.07664 (15) 0.06603 (11) 0.0363 (3)
H10A 0.3147 0.0215 0.0377 0.044*
H10B 0.4766 0.0247 0.0918 0.044*
H10C 0.4110 0.1336 0.0139 0.044*
C11 0.24039 (14) 0.23365 (14) 0.11363 (10) 0.0294 (3)
H11A 0.2561 0.2897 0.0605 0.035*
H11B 0.2251 0.2847 0.1696 0.035*
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Acta Cryst. (2004). E60, o1583–o1585 Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
P 0.01790 (14) 0.01772 (15) 0.01805 (14) 0.00011 (10) 0.00672 (10) −0.00189 (10)
O 0.0237 (4) 0.0242 (4) 0.0220 (4) −0.0046 (3) 0.0112 (3) −0.0034 (3)
N1 0.0181 (4) 0.0190 (4) 0.0166 (4) −0.0038 (4) 0.0060 (3) −0.0041 (3)
N2 0.0204 (4) 0.0211 (5) 0.0186 (4) −0.0045 (4) 0.0070 (4) −0.0040 (4)
N3 0.0273 (5) 0.0277 (5) 0.0230 (5) −0.0113 (4) 0.0124 (4) −0.0092 (4)
N4 0.0270 (5) 0.0253 (5) 0.0393 (6) 0.0080 (4) 0.0119 (5) 0.0055 (5)
N5 0.0224 (5) 0.0265 (5) 0.0208 (5) −0.0017 (4) 0.0070 (4) −0.0095 (4)
C1 0.0182 (5) 0.0189 (5) 0.0161 (5) −0.0013 (4) 0.0029 (4) −0.0024 (4)
C3 0.0193 (5) 0.0193 (5) 0.0178 (5) −0.0009 (4) 0.0050 (4) −0.0016 (4)
C4 0.0252 (6) 0.0237 (5) 0.0213 (5) −0.0017 (4) 0.0104 (4) −0.0019 (4)
C5 0.0261 (6) 0.0241 (6) 0.0292 (6) −0.0042 (5) 0.0143 (5) 0.0008 (5)
C6 0.0257 (6) 0.0233 (6) 0.0307 (6) −0.0080 (5) 0.0104 (5) −0.0041 (5)
C2 0.0184 (5) 0.0188 (5) 0.0180 (5) −0.0018 (4) 0.0065 (4) −0.0011 (4)
C7 0.0262 (6) 0.0225 (5) 0.0238 (5) −0.0055 (5) 0.0095 (5) −0.0058 (5)
C8 0.0521 (10) 0.0317 (8) 0.0978 (15) 0.0139 (7) 0.0374 (10) 0.0261 (9)
C9 0.0352 (8) 0.0486 (9) 0.0445 (9) 0.0195 (7) −0.0023 (7) −0.0057 (7)
C10 0.0342 (7) 0.0438 (8) 0.0343 (7) −0.0090 (6) 0.0150 (6) −0.0238 (6)
C11 0.0283 (6) 0.0350 (7) 0.0223 (6) 0.0020 (5) 0.0005 (5) −0.0021 (5)
Geometric parameters (Å, º)
P—O 1.4784 (8) C5—C6 1.3991 (17)
P—N4 1.6317 (11) C6—C7 1.4000 (16)
P—N5 1.6352 (10) C2—C7 1.3899 (16)
P—N1 1.7124 (9) C7—H7 0.9500
N1—C1 1.4140 (14) C8—H8A 0.9800
N1—C2 1.4242 (14) C8—H8B 0.9800
N2—C1 1.3199 (14) C8—H8C 0.9800
N2—C3 1.3934 (14) C9—H9A 0.9800
N3—C1 1.3396 (14) C9—H9B 0.9800
N4—C8 1.4648 (19) C9—H9C 0.9800
N4—C9 1.4705 (19) C10—H10A 0.9800
N5—C11 1.4685 (17) C10—H10B 0.9800
N5—C10 1.4770 (15) C10—H10C 0.9800
C3—C4 1.3929 (15) C11—H11A 0.9800
C3—C2 1.4071 (15) C11—H11B 0.9800
C4—C5 1.3888 (17) C11—H11C 0.9800
O—P—N4 111.01 (6) C5—C4—H4 121.0
O—P—N5 120.02 (5) C3—C4—H4 121.0
N4—P—N5 104.53 (6) C4—C5—H5 119.4
O—P—N1 107.67 (5) C6—C5—H5 119.4
N4—P—N1 111.39 (5) C5—C6—H6 119.4
N5—P—N1 101.86 (5) C7—C6—H6 119.4
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Acta Cryst. (2004). E60, o1583–o1585
C1—N1—P 125.39 (8) C6—C7—H7 121.4
C2—N1—P 128.72 (8) N4—C8—H8A 109.5
C1—N2—C3 105.53 (9) N4—C8—H8B 109.5
C8—N4—C9 113.76 (13) H8A—C8—H8B 109.5
C8—N4—P 123.64 (10) N4—C8—H8C 109.5
C9—N4—P 118.98 (10) H8A—C8—H8C 109.5
C11—N5—C10 111.78 (11) H8B—C8—H8C 109.5
C11—N5—P 120.53 (8) N4—C9—H9A 109.5
C10—N5—P 117.75 (9) N4—C9—H9B 109.5
N2—C1—N3 123.99 (10) H9A—C9—H9B 109.5
N2—C1—N1 113.42 (10) N4—C9—H9C 109.5
N3—C1—N1 122.59 (10) H9A—C9—H9C 109.5
C4—C3—N2 128.63 (11) H9B—C9—H9C 109.5
C4—C3—C2 120.56 (11) N5—C10—H10A 109.5
N2—C3—C2 110.78 (9) N5—C10—H10B 109.5
C5—C4—C3 118.05 (11) H10A—C10—H10B 109.5
C4—C5—C6 121.22 (11) N5—C10—H10C 109.5
C5—C6—C7 121.28 (11) H10A—C10—H10C 109.5
C7—C2—C3 121.69 (10) H10B—C10—H10C 109.5
C7—C2—N1 132.61 (10) N5—C11—H11A 109.5
C3—C2—N1 105.61 (9) N5—C11—H11B 109.5
C2—C7—C6 117.18 (11) H11A—C11—H11B 109.5
C1—N3—H1 117.7 (10) N5—C11—H11C 109.5
C1—N3—H2 118.0 (11) H11A—C11—H11C 109.5
H1—N3—H2 123.7 (15) H11B—C11—H11C 109.5
O—P—N1—C1 −21.19 (11) P—N1—C1—N2 −167.09 (8)
N4—P—N1—C1 100.74 (10) C2—N1—C1—N3 −179.07 (11)
N5—P—N1—C1 −148.30 (10) P—N1—C1—N3 12.76 (16)
O—P—N1—C2 173.54 (9) C1—N2—C3—C4 −177.99 (12)
N4—P—N1—C2 −64.53 (11) C1—N2—C3—C2 0.22 (13)
N5—P—N1—C2 46.42 (11) N2—C3—C4—C5 176.82 (12)
O—P—N4—C8 −176.59 (14) C2—C3—C4—C5 −1.23 (18)
N5—P—N4—C8 −45.81 (15) C3—C4—C5—C6 0.05 (19)
N1—P—N4—C8 63.44 (15) C4—C5—C6—C7 0.7 (2)
O—P—N4—C9 26.22 (13) C4—C3—C2—C7 1.72 (18)
N5—P—N4—C9 157.00 (11) N2—C3—C2—C7 −176.65 (11)
N1—P—N4—C9 −93.76 (11) C4—C3—C2—N1 178.80 (11)
O—P—N5—C11 −70.53 (11) N2—C3—C2—N1 0.43 (13)
N4—P—N5—C11 164.19 (10) C1—N1—C2—C7 175.77 (13)
N1—P—N5—C11 48.13 (10) P—N1—C2—C7 −16.60 (19)
O—P—N5—C10 72.32 (12) C1—N1—C2—C3 −0.85 (12)
N4—P—N5—C10 −52.96 (11) P—N1—C2—C3 166.78 (8)
N1—P—N5—C10 −169.03 (10) C3—C2—C7—C6 −0.93 (18)
C3—N2—C1—N3 179.33 (11) N1—C2—C7—C6 −177.11 (12)
C3—N2—C1—N1 −0.81 (13) C5—C6—C7—C2 −0.26 (19)
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Acta Cryst. (2004). E60, o1583–o1585 Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
C6—H6···Oi 0.95 2.56 3.4982 (15) 169
C9—H9C···Oii 0.98 2.62 3.5932 (18) 175
N3—H1···N2iii 0.925 (18) 2.024 (18) 2.9402 (14) 170.1 (15)