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

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ISSN: 2056-9890

Crystal structures and supra­molecular features of 9,9-di­methyl-3,7-di­aza­bi­cyclo­[3.3.1]nonane-2,4,6,8-tetra­one, 3,7-di­aza­spiro­[bi­cyclo­[3.3.1]nonane-9,1′-cyclo­penta­ne]-2,4,6,8-tetra­one and 9-methyl-9-phenyl-3,7-di­aza­bi­cyclo­[3.3.1]nonane-2,4,6,8-tetra­one di­methyl­formamide monosolvate

aDepartment of Chemistry, Moscow State University, 1 Leninskie Gory, Moscow 119991, Russian Federation, and bInorganic Chemistry Department, Faculty of Science, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklay St., Moscow 117198, Russian Federation
*Correspondence e-mail: szv@org.chem.msu.ru

Edited by S. V. Lindeman, Marquette University, USA (Received 11 June 2017; accepted 25 June 2017; online 30 June 2017)

Compounds (I), C9H10N2O4, (II), C11H12N2O4, and (III), C14H12N2O4·C3H7NO represent 9,9-disubstituted-3,7-di­aza­bicyclo­[3.3.1]nonane-2,4,6,8-tetra­one deriv­atives with very similar mol­ecular geometries for the bicyclic framework: the dihedral angle between the planes of the imide groups is 74.87 (6), 73.86 (3) and 74.83 (6)° in (I)–(III), respectively. The dimethyl derivative (I) is positioned on a crystallographic twofold axis and its overall geometry deviates only slightly from idealized C2v symmetry. The spiro-cyclo­pentane derivative (II) and the phen­yl/methyl analog (III) retain only inter­nal Cs symmetry, which in the case of (II) coincides with crystallographic mirror symmetry. The cyclo­pentane moiety in (II) adopts an envelope conformation, with the spiro C atom deviating from the mean plane of the rest of the ring by 0.548 (2) Å. In compound (III), an N—H⋯O hydrogen bond is formed with the di­methyl­formamide solvent mol­ecule. In the crystal, both (I) and (II) form similar zigzag hydrogen-bonded ribbons through double inter­molecular N—H⋯O hydrogen bonds. However, whereas in (I) the ribbons are formed by two trans-arranged O=C—N—H amide fragments, the amide fragments are cis-positioned in (II). The formation of ribbons in (III) is apparently disrupted by participation of one of its N—H groups in hydrogen bonding with the solvent mol­ecule. As a result, the mol­ecules of (III) form zigzag chains rather than the ribbons through inter­molecular N—H⋯O hydrogen bonds. The crystal of (I) was a pseudo-merohedral twin.

1. Chemical context

Di­aza­bicyclo­nonane-tetra­ones are used in the synthesis of the sparteine subgroup of lupine alcaloids (Norcross et al., 2008[Norcross, N. R., Melbardis, J. P., Solera, M. F., Sephton, M. A., Kilner, C., Zakharov, L. N., Astles, P. C., Warriner, S. L. & Blakemore, P. R. (2008). J. Org. Chem. 73, 7939-7951.]) and are precursors in obtaining 3,7-di­aza­bicyclo­[3.3.1]nona­nes which have been studied in computer models as serine protease inhibitors (Vatsadze et al., 2016[Vatsadze, S. Z., Shulga, D. A., Loginova, Y. D., Vatsadze, I. A., Wang, L., Yu, H. & Kudryavtsev, K. V. (2016). Mendeleev Commun. 26, 212-213.]). They also have value as building blocks in the design of other biologically active compounds (Kudryavtsev et al., 2014[Kudryavtsev, K. V., Shulga, D. A., Chupakhin, V. I., Sinauridze, E. I., Ataullakhanov, F. I. & Vatsadze, S. Z. (2014). Tetrahedron, 70, 7854-7864.]), and in the synthesis of imaging agents for positron emission tomography (Medved'ko et al., 2016[Medved'ko, A. V., Egorova, B. V., Komarova, A. A., Rakhimov, R. D., Krut'ko, D. P., Kalmykov, S. N. & Vatsadze, S. Z. (2016). ACS Omega, 1, 854-867.]). In addition, they are good chelating ligands for 3d transition metals (Vatsadze et al., 2005[Vatsadze, S. Z., Tyurin, V. S., Zyk, N. V., Churakov, A. V., Kuz'mina, L. G., Avtomonov, E. V., Rakhimov, R. D. & Butin, K. P. (2005). Russ. Chem. Bull. 54, 1825-1835.]) including Cu (Vatsadze et al., 2014[Vatsadze, S. Z., Semashko, V. S., Manaenkova, M. A., Krut'ko, D. P., Nuriev, V. N., Rakhimov, R. D., Davlyatshin, D. I., Churakov, A. V., Howard, J. A. K., Maksimov, A. L., Li, W. & Yu, H. (2014). Russ. Chem. Bull. 63, 895-911.]).

[Scheme 1]

However, the crystal structures of this class of compounds have not been adequately characterized so far, as shown by a small number (eight) of similar structures found in the Cambridge Structural Database (CSD; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]). Moreover, their ability to form different supra­molecular structures depending on the substituents at the 9-position in the heterocycle, which we report in this work, has not been not reported before. A search in the CSD for the substructure 3,7-di­aza-2,4,6,8-tetra­oxobi­cyclo­[3.3.1]nonane yielded eight hits. Although there is a similarity in chemical structure of known related compounds (Horlein et al., 1981[Horlein, U., Schroder, T. & Born, L. (1981). Liebigs Ann. Chem. pp. 1699-1704.]; Norcross et al., 2008[Norcross, N. R., Melbardis, J. P., Solera, M. F., Sephton, M. A., Kilner, C., Zakharov, L. N., Astles, P. C., Warriner, S. L. & Blakemore, P. R. (2008). J. Org. Chem. 73, 7939-7951.]), their supra­molecular features are significantly different because of the impact of substituents and solvatation.

In this work, we have synthesized three 9,9-disubstituted-3,7-di­aza­bicyclo­[3.3.1]nonane-2,4,6,8-tetra­ones and show how groups bound to C9 as well as the presence of solvate mol­ecules affect their ability to form different hydrogen-bonding systems.

2. Structural commentary

Compounds (I)[link], C9H10N2O4, (II)[link], C11H12N2O4, and (III)[link], C14H12N2O4·C3H7NO represent 9,9-disubstituted-3,7-di­aza­bicyclo­[3.3.1]nonane-2,4,6,8-tetra­one derivatives and have very similar mol­ecular geometries (Figs. 1[link]–3[link][link]). In general, the 3,7-di­aza­bicyclo­[3.3.1]nonane-2,4,6,8-tetra­one skeleton exhibits idealized C2v (mm2) symmetry. The mol­ecule of (I)[link], containing two 9-methyl substituents, occupies a special position on a twofold axis [C2 (2)], and its geometry deviates only slightly from the perfectly symmetrical C2v. As a result of the presence of spiro-9-cyclo­pentane [in the case of (II)] and 9-phenyl and 9-methyl [in the case of (III)] substituents, the overall symmetry of these mol­ecules decreases to Cs (m). However, in the crystal, the intrinsic Cs symmetry remains only for the mol­ecule of (II)[link], which occupies a special position on a mirror plane. Compound (III)[link] crystallizes as a dimethyl formamide monosolvate, with the main mol­ecule occupying a general position.

[Figure 1]
Figure 1
The mol­ecular structure of (I)[link]. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as small spheres of arbitrary radius. [Symmetry code: (A) 1 + x, y, −z + [1\over2].]
[Figure 2]
Figure 2
The mol­ecular structure of (II)[link]. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as small spheres of arbitrary radius. [Symmetry code: (A) x, [1\over2] − y, z.]
[Figure 3]
Figure 3
The mol­ecular structure of (III)·DMF. Displacement ellipsoids are shown at the 50% probability level. H atoms are presented as small spheres of arbitrary radius. Dashed line indicates the intra­molecular N—H⋯O hydrogen bond.

The two imide fragments in the mol­ecules of (I)–(III) are almost planar (r.m.s. deviations are 0.013, 0.009 and 0.009/0.036 Å, respectively). The dihedral angles between the imide planes are 74.87 (6), 73.86 (3) and 74.83 (6)° for (I)–(III), respectively. Moreover, the four carbonyl carbon atoms in (I)–(III) are each coplanar with r.m.s. deviations of 0.018, 0.000, and 0.031 Å, respectively; the bridged carbon atom lies by 1.854 (3), 1.846 (1), and 1.858 (2) Å, respectively, above this plane in (I)–(III). The cyclo­pentane substituent in (II)[link] adopts an envelope conformation, with the C6 spiro-carbon atom deviating from the mean plane through the other ring atoms by 0.548 (2) Å.

Importantly, in (III)[link] the main mol­ecule forms a strong N7—H7⋯O5 hydrogen bond with the dimethyl formamide solvate mol­ecule (Table 3[link], Fig. 3[link]).

Table 3
Hydrogen-bond geometry (Å, °) for (III)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3⋯O1i 0.861 (19) 2.12 (2) 2.9650 (19) 168.3 (18)
N7—H7⋯O5 0.90 (2) 1.86 (2) 2.7682 (19) 178.6 (18)
Symmetry code: (i) [x+{\script{1\over 2}}, y, -z+{\script{1\over 2}}].

3. Supra­molecular features

In general, any compound of type (I)–(III) could form up to six inter­molecular hydrogen bonds utilizing two hydrogen-bond donor NH groups and four hydrogen-bond acceptor carbonyl oxygen atoms. In the literature, even the unsubstituted analogue (refcode GOHHER; Norcross et al., 2008[Norcross, N. R., Melbardis, J. P., Solera, M. F., Sephton, M. A., Kilner, C., Zakharov, L. N., Astles, P. C., Warriner, S. L. & Blakemore, P. R. (2008). J. Org. Chem. 73, 7939-7951.]) shows only four inter­molecular hydrogen bonds involving both imide fragments of bis­pidintetra­one with the formation of an infinite three-dimensional hydrogen-bonded network. If one of the nitro­gen atoms is alkyl­ated (for example, refcode BAHFIZ; Horlein et al., 1981[Horlein, U., Schroder, T. & Born, L. (1981). Liebigs Ann. Chem. pp. 1699-1704.]), the other one is involved in the formation of a doubly hydrogen-bonded dimer. When both nitro­gen atoms are functionalized [refcodes JIMWUY (Hametner et al., 2007[Hametner, C., Dangl, D., Mereiter, K., Marchetti, M. & Fröhlich, J. (2007). Heterocycles, 71, 2331.]), NAWLIH (Mereiter et al., 2014[Mereiter, K., Dangl, D. & Frohlich, J. (2014). Private communication (refcodes NAWLIH, NAWLON). CCDC, Cambridge, England.]), NAWLON et al., 2014[Mereiter, K., Dangl, D. & Frohlich, J. (2014). Private communication (refcodes NAWLIH, NAWLON). CCDC, Cambridge, England.]), PILXAK (Hametner et al., 2007[Hametner, C., Dangl, D., Mereiter, K., Marchetti, M. & Fröhlich, J. (2007). Heterocycles, 71, 2331.]), XAZGAH (Blakemore, et al., 2005[Blakemore, P. R., Kilner, C., Norcross, N. R. & Astles, P. C. (2005). Org. Lett. 7, 4721-4724.])], no hydrogen-bonds are observed.

Despite the geometrical similarity of compounds (I)-(III), they form different supra­molecular structures in the solid state. Thus, in the crystals of (I)[link] and (II)[link], the mol­ecules form the zigzag hydrogen-bonded ribbons by double N—H⋯O hydrogen bonds (Tables 1[link] and 2[link], Figs. 4[link] and 5[link]). The hydrogen-bonded ribbons in (I)[link] and (II)[link] are distinguished by the binding sites of the 3,7-di­aza­bicyclo­[3.3.1]nonane-2,4,6,8-tetra­one skeleton. According to symmetry, the ribbons in (I)[link] are formed by the two trans-arranged O=C—N—H amide fragments, whereas the binding O=C—N—H amide fragments in (II)[link] are cis disposed. As one of the two NH groups in (III)[link] is bonded to the dimethyl formamide solvate mol­ecule, the N—H⋯O hydrogen bonds form the zigzag chains rather than ribbons (Table 3[link], Fig. 6[link]).

Table 1
Hydrogen-bond geometry (Å, °) for (I)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3⋯O2i 0.90 (3) 2.01 (3) 2.906 (2) 173 (3)
Symmetry code: (i) -x+1, -y, -z+1.

Table 2
Hydrogen-bond geometry (Å, °) for (II)[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3⋯O1i 0.855 (14) 2.021 (14) 2.8718 (11) 173.7 (13)
Symmetry code: (i) -x+1, -y, -z+1.
[Figure 4]
Figure 4
The crystal structure of (I)[link], demonstrating the H-bonded zigzag-like ribbons propagating toward [001]. Dashed lines indicate the inter­molecular N—H⋯O hydrogen bonds.
[Figure 5]
Figure 5
The crystal structure of (II)[link], demonstrating the H-bonded zigzag-like ribbons propagating toward [010]. Dashed lines indicate the inter­molecular N—H⋯O hydrogen bonds.
[Figure 6]
Figure 6
The crystal structure of (III)·DMF, demonstrating the H-bonded zigzag-like chains propagating toward [100]. Dashed lines indicate the inter­molecular N—H⋯O hydrogen bonds.

4. Synthesis and crystallization

The title compounds (I)–(III) were synthesized (Fig. 7[link]) according to the procedure described earlier (Schon et al., 1998[Schön, U., Antel, J., Brückner, R., Messinger, J., Franke, R. & Gruska, A. (1998). J. Med. Chem. 41, 318-331.]).

[Figure 7]
Figure 7
Synthesis of (I)–(III) from 2-cyano­acetamide and ketones.

Di­nitrile subproducts were obtained by adding 2-cyano­acetamide to the corresponding ketone [(I) – acetone, (II)[link] – aceto­phenone, (III)[link] – cyclo­penta­none] in ethanol at room temperature. Then, the di­nitriles were heated to 393–413 K upon stirring in an acidic medium to complete dissolving. After 10–15 min, the mixture was poured into ice–water. The precipitated tetra­oxo-compounds were filtered off by suction, recrystallized from ethanol solution and finally dried. Single crystals suitable for X-ray diffraction study were obtained by recrystallization of the crude products from DMF solution.

5. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 4[link]. The hydrogen atoms of the amino groups were localized in the difference-Fourier maps and refined isotropically with fixed displacement parameters [Uiso(H) = 1.2Ueq(N)]. The other hydrogen atoms were placed in calculated positions with C—H = 0.95–1.00 Å and refined in the riding/rotating model with fixed isotropic displacement parameters [Uiso(H) = 1.5Ueq(C) for the CH3-groups and 1.2Ueq(C) for the other groups]. The crystal of (I)[link] was a pseudo-merohedral twin. The twin matrix is ([\overline{1}] 0 0 0 [\overline{1}] 0 0.775 0 1), and BASF = 0.180 (1).

Table 4
Experimental details

  (I) (II) (III)
Crystal data
Chemical formula C9H10N2O4 C11H12N2O4 C14H12N2O4·C3H7NO
Mr 210.19 236.23 345.35
Crystal system, space group Monoclinic, C2/c Orthorhombic, Pnma Orthorhombic, Pbca
Temperature (K) 100 120 120
a, b, c (Å) 11.4321 (17), 6.6263 (10), 12.4819 (19) 12.8058 (6), 11.4850 (6), 6.9058 (3) 7.7876 (5), 19.4656 (12), 21.7879 (13)
α, β, γ (°) 90, 110.788 (3), 90 90, 90, 90 90, 90, 90
V3) 884.0 (2) 1015.67 (8) 3302.8 (4)
Z 4 4 8
Radiation type Mo Kα Mo Kα Mo Kα
μ (mm−1) 0.13 0.12 0.10
Crystal size (mm) 0.30 × 0.20 × 0.15 0.30 × 0.20 × 0.20 0.22 × 0.20 × 0.18
 
Data collection
Diffractometer Bruker SMART 1K CCD Bruker SMART 1K CCD Bruker SMART 1K CCD
Absorption correction Multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.950, 0.970 0.960, 0.970 0.970, 0.975
No. of measured, independent and observed [I > 2σ(I)] reflections 4993, 1289, 1165 15297, 2181, 1782 41691, 5056, 3210
Rint 0.027 0.031 0.090
(sin θ/λ)max−1) 0.703 0.802 0.716
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.062, 0.184, 1.06 0.043, 0.119, 1.03 0.051, 0.124, 1.01
No. of reflections 1289 2181 5056
No. of parameters 74 85 235
H-atom treatment H atoms treated by a mixture of independent and constrained refinement H atoms treated by a mixture of independent and constrained refinement H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.55, −0.54 0.42, −0.23 0.33, −0.26
Computer programs: APEX2 (Bruker, 2005[Bruker (2005). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2001[Bruker (2001). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2014 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]).

Supporting information


Computing details top

For all compounds, data collection: APEX2 (Bruker, 2005); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

(I) 9,9-Dimethyl-3,7-diazabicyclo[3.3.1]nonane-2,4,6,8-tetraone top
Crystal data top
C9H10N2O4F(000) = 440
Mr = 210.19Dx = 1.579 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
a = 11.4321 (17) ÅCell parameters from 3269 reflections
b = 6.6263 (10) Åθ = 3.5–30.0°
c = 12.4819 (19) ŵ = 0.13 mm1
β = 110.788 (3)°T = 100 K
V = 884.0 (2) Å3Prism, colourless
Z = 40.30 × 0.20 × 0.15 mm
Data collection top
Bruker SMART 1K CCD
diffractometer
1165 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.027
φ and ω scansθmax = 30.0°, θmin = 1.8°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1616
Tmin = 0.950, Tmax = 0.970k = 99
4993 measured reflectionsl = 1717
1289 independent reflections
Refinement top
Refinement on F2Primary atom site location: difference Fourier map
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.062Hydrogen site location: mixed
wR(F2) = 0.184H atoms treated by a mixture of independent and constrained refinement
S = 1.06 w = 1/[σ2(Fo2) + (0.0846P)2 + 3.9571P]
where P = (Fo2 + 2Fc2)/3
1289 reflections(Δ/σ)max < 0.001
74 parametersΔρmax = 0.55 e Å3
0 restraintsΔρmin = 0.54 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. Refined as a 2-component twin.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.39535 (15)0.3325 (3)0.25497 (14)0.0103 (4)
H10.32430.41580.25950.012*
C20.43977 (16)0.1911 (3)0.35793 (14)0.0110 (4)
O20.36911 (13)0.1256 (2)0.40357 (12)0.0156 (3)
N30.56404 (14)0.1339 (2)0.39595 (13)0.0119 (4)
H30.591 (3)0.054 (4)0.458 (2)0.014*
C40.65231 (16)0.1966 (3)0.35040 (14)0.0109 (4)
O40.75961 (13)0.1393 (2)0.39060 (12)0.0161 (4)
C50.50000.4737 (4)0.25000.0107 (5)
C60.54703 (18)0.6086 (3)0.35697 (16)0.0147 (4)
H6A0.61540.69410.35320.022*
H6B0.57740.52390.42570.022*
H6C0.47830.69390.36030.022*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0104 (7)0.0099 (8)0.0096 (7)0.0002 (5)0.0026 (6)0.0002 (5)
C20.0117 (8)0.0105 (7)0.0094 (7)0.0007 (6)0.0021 (6)0.0012 (6)
O20.0148 (6)0.0192 (7)0.0135 (6)0.0021 (5)0.0058 (5)0.0027 (5)
N30.0131 (7)0.0114 (7)0.0106 (7)0.0004 (5)0.0035 (6)0.0024 (5)
C40.0119 (8)0.0105 (7)0.0093 (7)0.0000 (6)0.0026 (6)0.0020 (6)
O40.0131 (7)0.0200 (7)0.0139 (7)0.0037 (5)0.0031 (5)0.0006 (5)
C50.0107 (10)0.0100 (10)0.0114 (10)0.0000.0039 (8)0.000
C60.0148 (8)0.0129 (8)0.0160 (8)0.0011 (6)0.0049 (6)0.0039 (6)
Geometric parameters (Å, º) top
C1—C21.525 (2)N3—H30.90 (3)
C1—C4i1.527 (2)C4—O41.210 (2)
C1—C51.537 (2)C5—C61.537 (2)
C1—H11.0000C6—H6A0.9800
C2—O21.221 (2)C6—H6B0.9800
C2—N31.382 (2)C6—H6C0.9800
N3—C41.386 (2)
C2—C1—C4i105.89 (14)O4—C4—C1i122.81 (16)
C2—C1—C5112.14 (13)N3—C4—C1i116.17 (14)
C4i—C1—C5111.67 (12)C6i—C5—C6108.8 (2)
C2—C1—H1109.0C6—C5—C1i110.59 (9)
C4i—C1—H1109.0C6—C5—C1110.87 (10)
C5—C1—H1109.0C1i—C5—C1105.1 (2)
O2—C2—N3120.80 (17)C5—C6—H6A109.5
O2—C2—C1122.27 (16)C5—C6—H6B109.5
N3—C2—C1116.90 (15)H6A—C6—H6B109.5
C2—N3—C4125.92 (15)C5—C6—H6C109.5
C2—N3—H3117.3 (18)H6A—C6—H6C109.5
C4—N3—H3116.7 (18)H6B—C6—H6C109.5
O4—C4—N3120.97 (17)
C4i—C1—C2—O286.7 (2)C2—N3—C4—C1i3.3 (3)
C5—C1—C2—O2151.29 (17)C2—C1—C5—C6i178.06 (14)
C4i—C1—C2—N391.29 (17)C4i—C1—C5—C6i59.40 (19)
C5—C1—C2—N330.7 (2)C2—C1—C5—C661.11 (19)
O2—C2—N3—C4179.35 (16)C4i—C1—C5—C6179.77 (14)
C1—C2—N3—C41.3 (3)C2—C1—C5—C1i58.38 (11)
C2—N3—C4—O4179.26 (16)C4i—C1—C5—C1i60.28 (11)
Symmetry code: (i) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O2ii0.90 (3)2.01 (3)2.906 (2)173 (3)
Symmetry code: (ii) x+1, y, z+1.
(II) 3,7-Diazaspiro[bicyclo[3.3.1]nonane-9,1'-cyclopentane]-2,4,6,8-tetraone top
Crystal data top
C11H12N2O4Dx = 1.545 Mg m3
Mr = 236.23Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PnmaCell parameters from 4118 reflections
a = 12.8058 (6) Åθ = 3.2–33.9°
b = 11.4850 (6) ŵ = 0.12 mm1
c = 6.9058 (3) ÅT = 120 K
V = 1015.67 (8) Å3Prism, colourless
Z = 40.30 × 0.20 × 0.20 mm
F(000) = 496
Data collection top
Bruker SMART 1K CCD
diffractometer
1782 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.031
φ and ω scansθmax = 34.8°, θmin = 3.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1919
Tmin = 0.960, Tmax = 0.970k = 1718
15297 measured reflectionsl = 1010
2181 independent reflections
Refinement top
Refinement on F2Primary atom site location: difference Fourier map
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: mixed
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0631P)2 + 0.338P]
where P = (Fo2 + 2Fc2)/3
2181 reflections(Δ/σ)max < 0.001
85 parametersΔρmax = 0.42 e Å3
0 restraintsΔρmin = 0.23 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.40454 (6)0.09843 (6)0.57775 (10)0.01863 (16)
O20.56727 (6)0.10479 (6)0.00332 (11)0.02057 (17)
C10.35046 (9)0.25000.35970 (17)0.0114 (2)
H10.28310.25000.43300.014*
C20.41314 (6)0.14320 (7)0.41787 (12)0.01265 (16)
N30.48223 (6)0.10060 (7)0.28341 (11)0.01450 (16)
H30.5177 (10)0.0407 (13)0.3159 (19)0.017*
C40.49953 (7)0.14512 (8)0.09885 (13)0.01376 (16)
C50.43357 (9)0.25000.04181 (17)0.0130 (2)
H50.42320.25000.10170.016*
C60.32636 (9)0.25000.14282 (17)0.0130 (2)
C70.25898 (8)0.14463 (9)0.08181 (14)0.01871 (19)
H7A0.30340.07570.05710.022*
H7B0.20780.12510.18420.022*
C80.20315 (9)0.18259 (12)0.10339 (15)0.0277 (2)
H8A0.13070.15250.10510.033*
H8B0.24030.15250.21870.033*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0241 (3)0.0172 (3)0.0146 (3)0.0043 (2)0.0040 (2)0.0046 (2)
O20.0232 (3)0.0186 (3)0.0199 (3)0.0043 (2)0.0081 (3)0.0004 (3)
C10.0116 (4)0.0102 (4)0.0124 (4)0.0000.0003 (4)0.000
C20.0135 (3)0.0113 (3)0.0131 (3)0.0001 (3)0.0003 (3)0.0000 (3)
N30.0172 (3)0.0123 (3)0.0140 (3)0.0038 (2)0.0023 (2)0.0015 (2)
C40.0160 (4)0.0120 (3)0.0133 (3)0.0006 (3)0.0010 (3)0.0007 (3)
C50.0149 (5)0.0135 (5)0.0105 (4)0.0000.0001 (4)0.000
C60.0130 (5)0.0137 (5)0.0124 (5)0.0000.0017 (4)0.000
C70.0170 (4)0.0213 (4)0.0179 (4)0.0047 (3)0.0031 (3)0.0026 (3)
C80.0248 (5)0.0397 (6)0.0187 (4)0.0066 (4)0.0075 (4)0.0015 (4)
Geometric parameters (Å, º) top
O1—C21.2230 (11)C5—C61.5399 (17)
O2—C41.2103 (11)C5—H51.0000
C1—C21.5200 (11)C6—C71.5448 (12)
C1—C61.5292 (17)C7—C81.5287 (14)
C1—H11.0000C7—H7A0.9900
C2—N31.3727 (11)C7—H7B0.9900
N3—C41.3910 (11)C8—C8i1.549 (3)
N3—H30.855 (14)C8—H8A0.9900
C4—C51.5231 (11)C8—H8B0.9900
C2i—C1—C2107.61 (9)C1—C6—C5105.29 (10)
C2—C1—C6111.43 (6)C1—C6—C7112.32 (7)
C2—C1—H1108.8C5—C6—C7111.99 (7)
C6—C1—H1108.8C7i—C6—C7103.14 (10)
O1—C2—N3121.26 (8)C8—C7—C6105.43 (9)
O1—C2—C1122.03 (8)C8—C7—H7A110.7
N3—C2—C1116.69 (8)C6—C7—H7A110.7
C2—N3—C4126.26 (8)C8—C7—H7B110.7
C2—N3—H3116.9 (9)C6—C7—H7B110.7
C4—N3—H3116.8 (9)H7A—C7—H7B108.8
O2—C4—N3120.51 (8)C7—C8—C8i106.57 (6)
O2—C4—C5123.33 (9)C7—C8—H8A110.4
N3—C4—C5116.06 (8)C8i—C8—H8A110.4
C4i—C5—C4104.54 (10)C7—C8—H8B110.4
C4—C5—C6112.17 (7)C8i—C8—H8B110.4
C4—C5—H5109.3H8A—C8—H8B108.6
C6—C5—H5109.3
C2i—C1—C2—O189.14 (11)C2i—C1—C6—C7i62.03 (11)
C6—C1—C2—O1148.42 (9)C2—C1—C6—C7i177.76 (8)
C2i—C1—C2—N389.33 (10)C2i—C1—C6—C7177.76 (8)
C6—C1—C2—N333.11 (11)C2—C1—C6—C762.03 (11)
O1—C2—N3—C4179.14 (8)C4i—C5—C6—C158.65 (7)
C1—C2—N3—C40.66 (13)C4—C5—C6—C158.65 (7)
C2—N3—C4—O2175.36 (9)C4i—C5—C6—C7i63.69 (12)
C2—N3—C4—C51.04 (13)C4—C5—C6—C7i179.00 (8)
O2—C4—C5—C4i84.18 (12)C4i—C5—C6—C7179.00 (8)
N3—C4—C5—C4i92.10 (10)C4—C5—C6—C763.70 (12)
O2—C4—C5—C6154.04 (9)C1—C6—C7—C8155.71 (9)
N3—C4—C5—C629.68 (11)C5—C6—C7—C886.05 (10)
C2i—C1—C6—C560.10 (7)C7i—C6—C7—C834.55 (12)
C2—C1—C6—C560.11 (7)C6—C7—C8—C8i21.58 (8)
Symmetry code: (i) x, y+1/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O1ii0.855 (14)2.021 (14)2.8718 (11)173.7 (13)
Symmetry code: (ii) x+1, y, z+1.
(III) 9-Methyl-9-phenyl-3,7-diazabicyclo[3.3.1]nonane-2,4,6,8-tetraone dimethylformamide monosolvate top
Crystal data top
C14H12N2O4·C3H7NODx = 1.389 Mg m3
Mr = 345.35Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PbcaCell parameters from 2856 reflections
a = 7.7876 (5) Åθ = 2.3–26.0°
b = 19.4656 (12) ŵ = 0.10 mm1
c = 21.7879 (13) ÅT = 120 K
V = 3302.8 (4) Å3Prism, colourless
Z = 80.22 × 0.20 × 0.18 mm
F(000) = 1456
Data collection top
Bruker SMART 1K CCD
diffractometer
3210 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.090
φ and ω scansθmax = 30.6°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1111
Tmin = 0.970, Tmax = 0.975k = 2727
41691 measured reflectionsl = 3130
5056 independent reflections
Refinement top
Refinement on F2Primary atom site location: difference Fourier map
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: mixed
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.01 w = 1/[σ2(Fo2) + (0.0448P)2 + 1.1286P]
where P = (Fo2 + 2Fc2)/3
5056 reflections(Δ/σ)max < 0.001
235 parametersΔρmax = 0.33 e Å3
0 restraintsΔρmin = 0.26 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.91018 (15)0.32972 (6)0.24687 (5)0.0195 (3)
O21.28067 (16)0.39316 (7)0.39546 (6)0.0277 (3)
O31.05101 (18)0.54938 (6)0.41859 (6)0.0284 (3)
O40.71389 (17)0.48551 (6)0.25953 (6)0.0247 (3)
C10.7904 (2)0.39619 (8)0.33006 (7)0.0154 (3)
H10.67770.37460.31930.019*
C20.9331 (2)0.35860 (8)0.29593 (7)0.0156 (3)
N31.09219 (18)0.36122 (7)0.32247 (6)0.0169 (3)
H31.178 (2)0.3463 (10)0.3014 (9)0.020*
C41.1346 (2)0.39341 (9)0.37714 (7)0.0176 (3)
C50.9888 (2)0.42888 (8)0.41126 (8)0.0159 (3)
H51.01460.42800.45620.019*
C60.9822 (2)0.50346 (9)0.38999 (8)0.0197 (4)
N70.89576 (19)0.51620 (7)0.33590 (7)0.0196 (3)
H70.902 (3)0.5588 (10)0.3194 (9)0.024*
C80.7939 (2)0.46953 (9)0.30509 (8)0.0177 (3)
C90.8163 (2)0.39217 (8)0.40019 (7)0.0157 (3)
C100.8217 (2)0.31744 (8)0.42225 (7)0.0157 (3)
C110.7451 (2)0.26429 (9)0.38892 (8)0.0200 (4)
H110.69280.27400.35050.024*
C120.7444 (2)0.19734 (9)0.41138 (8)0.0229 (4)
H120.69120.16180.38830.027*
C130.8208 (2)0.18232 (9)0.46704 (8)0.0226 (4)
H130.82100.13650.48210.027*
C140.8969 (2)0.23430 (9)0.50061 (8)0.0218 (4)
H140.94960.22420.53890.026*
C150.8965 (2)0.30139 (9)0.47846 (8)0.0196 (4)
H150.94820.33680.50210.024*
C160.6721 (2)0.43004 (9)0.43480 (8)0.0205 (4)
H16A0.66580.47770.42050.031*
H16B0.69650.42950.47890.031*
H16C0.56230.40710.42700.031*
O50.91561 (18)0.64557 (7)0.28362 (6)0.0289 (3)
N10.84929 (19)0.65410 (7)0.18198 (7)0.0212 (3)
C170.8439 (2)0.67440 (9)0.24001 (8)0.0232 (4)
H170.77930.71460.24890.028*
C180.9381 (3)0.59137 (10)0.16458 (9)0.0284 (4)
H18A1.01810.57820.19720.043*
H18B1.00200.59910.12650.043*
H18C0.85410.55450.15830.043*
C190.7595 (3)0.69190 (10)0.13395 (9)0.0273 (4)
H19A0.69560.73010.15230.041*
H19B0.67950.66110.11280.041*
H19C0.84310.70990.10440.041*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0215 (6)0.0208 (6)0.0164 (6)0.0008 (5)0.0011 (5)0.0023 (5)
O20.0151 (6)0.0414 (8)0.0265 (7)0.0016 (6)0.0042 (5)0.0007 (6)
O30.0373 (8)0.0194 (7)0.0286 (7)0.0081 (6)0.0075 (6)0.0011 (5)
O40.0294 (7)0.0235 (7)0.0213 (6)0.0040 (5)0.0068 (5)0.0021 (5)
C10.0142 (8)0.0162 (8)0.0160 (8)0.0006 (6)0.0027 (6)0.0005 (6)
C20.0166 (8)0.0145 (8)0.0156 (8)0.0004 (6)0.0002 (6)0.0030 (6)
N30.0127 (7)0.0211 (7)0.0168 (7)0.0026 (6)0.0007 (5)0.0004 (6)
C40.0176 (8)0.0189 (8)0.0162 (8)0.0033 (6)0.0018 (6)0.0029 (7)
C50.0155 (8)0.0174 (8)0.0148 (8)0.0029 (6)0.0014 (6)0.0001 (6)
C60.0189 (8)0.0194 (8)0.0207 (9)0.0007 (7)0.0009 (7)0.0003 (7)
N70.0235 (8)0.0153 (7)0.0200 (7)0.0010 (6)0.0029 (6)0.0019 (6)
C80.0168 (8)0.0186 (8)0.0177 (8)0.0036 (6)0.0010 (6)0.0019 (7)
C90.0140 (8)0.0190 (8)0.0141 (8)0.0015 (6)0.0009 (6)0.0009 (6)
C100.0140 (8)0.0178 (8)0.0152 (8)0.0023 (6)0.0037 (6)0.0002 (6)
C110.0221 (9)0.0217 (9)0.0162 (8)0.0031 (7)0.0002 (7)0.0002 (7)
C120.0269 (9)0.0203 (9)0.0216 (9)0.0052 (7)0.0030 (7)0.0032 (7)
C130.0255 (10)0.0193 (9)0.0231 (9)0.0006 (7)0.0050 (7)0.0023 (7)
C140.0220 (9)0.0249 (9)0.0185 (8)0.0002 (7)0.0006 (7)0.0027 (7)
C150.0198 (9)0.0208 (9)0.0183 (8)0.0028 (7)0.0003 (7)0.0007 (7)
C160.0168 (8)0.0246 (9)0.0200 (8)0.0004 (7)0.0015 (7)0.0014 (7)
O50.0420 (8)0.0229 (7)0.0218 (7)0.0009 (6)0.0041 (6)0.0037 (5)
N10.0230 (8)0.0195 (7)0.0210 (7)0.0020 (6)0.0005 (6)0.0007 (6)
C170.0286 (10)0.0169 (8)0.0240 (9)0.0006 (7)0.0012 (8)0.0011 (7)
C180.0328 (11)0.0249 (10)0.0276 (10)0.0060 (8)0.0064 (8)0.0001 (8)
C190.0317 (11)0.0259 (10)0.0244 (9)0.0014 (8)0.0075 (8)0.0049 (8)
Geometric parameters (Å, º) top
O1—C21.2209 (19)C11—H110.9500
O2—C41.205 (2)C12—C131.382 (3)
O3—C61.214 (2)C12—H120.9500
O4—C81.213 (2)C13—C141.382 (2)
C1—C21.524 (2)C13—H130.9500
C1—C81.528 (2)C14—C151.392 (2)
C1—C91.543 (2)C14—H140.9500
C1—H11.0000C15—H150.9500
C2—N31.368 (2)C16—H16A0.9800
N3—C41.386 (2)C16—H16B0.9800
N3—H30.861 (19)C16—H16C0.9800
C4—C51.523 (2)O5—C171.237 (2)
C5—C61.525 (2)N1—C171.325 (2)
C5—C91.541 (2)N1—C181.454 (2)
C5—H51.0000N1—C191.458 (2)
C6—N71.380 (2)C17—H170.9500
N7—C81.380 (2)C18—H18A0.9800
N7—H70.90 (2)C18—H18B0.9800
C9—C101.533 (2)C18—H18C0.9800
C9—C161.540 (2)C19—H19A0.9800
C10—C151.392 (2)C19—H19B0.9800
C10—C111.398 (2)C19—H19C0.9800
C11—C121.392 (2)
C2—C1—C8105.18 (13)C12—C11—C10120.78 (16)
C2—C1—C9111.30 (13)C12—C11—H11119.6
C8—C1—C9113.43 (13)C10—C11—H11119.6
C2—C1—H1108.9C13—C12—C11120.33 (17)
C8—C1—H1108.9C13—C12—H12119.8
C9—C1—H1108.9C11—C12—H12119.8
O1—C2—N3121.31 (15)C12—C13—C14119.61 (17)
O1—C2—C1122.78 (15)C12—C13—H13120.2
N3—C2—C1115.87 (14)C14—C13—H13120.2
C2—N3—C4126.58 (15)C13—C14—C15120.16 (17)
C2—N3—H3117.7 (13)C13—C14—H14119.9
C4—N3—H3115.2 (13)C15—C14—H14119.9
O2—C4—N3120.51 (16)C10—C15—C14121.10 (16)
O2—C4—C5122.95 (15)C10—C15—H15119.5
N3—C4—C5116.53 (14)C14—C15—H15119.5
C4—C5—C6107.97 (14)C9—C16—H16A109.5
C4—C5—C9111.32 (13)C9—C16—H16B109.5
C6—C5—C9111.39 (14)H16A—C16—H16B109.5
C4—C5—H5108.7C9—C16—H16C109.5
C6—C5—H5108.7H16A—C16—H16C109.5
C9—C5—H5108.7H16B—C16—H16C109.5
O3—C6—N7121.43 (16)C17—N1—C18120.96 (15)
O3—C6—C5122.02 (15)C17—N1—C19121.26 (15)
N7—C6—C5116.55 (15)C18—N1—C19117.71 (15)
C6—N7—C8125.29 (15)O5—C17—N1125.66 (17)
C6—N7—H7118.5 (13)O5—C17—H17117.2
C8—N7—H7116.2 (13)N1—C17—H17117.2
O4—C8—N7121.65 (16)N1—C18—H18A109.5
O4—C8—C1121.45 (15)N1—C18—H18B109.5
N7—C8—C1116.88 (14)H18A—C18—H18B109.5
C10—C9—C16108.70 (13)N1—C18—H18C109.5
C10—C9—C5111.53 (13)H18A—C18—H18C109.5
C16—C9—C5109.69 (13)H18B—C18—H18C109.5
C10—C9—C1111.25 (13)N1—C19—H19A109.5
C16—C9—C1111.43 (13)N1—C19—H19B109.5
C5—C9—C1104.20 (13)H19A—C19—H19B109.5
C15—C10—C11118.01 (15)N1—C19—H19C109.5
C15—C10—C9120.04 (14)H19A—C19—H19C109.5
C11—C10—C9121.86 (14)H19B—C19—H19C109.5
C8—C1—C2—O188.55 (18)C4—C5—C9—C16179.36 (13)
C9—C1—C2—O1148.23 (15)C6—C5—C9—C1658.79 (18)
C8—C1—C2—N389.02 (16)C4—C5—C9—C159.96 (16)
C9—C1—C2—N334.20 (19)C6—C5—C9—C160.61 (16)
O1—C2—N3—C4178.71 (15)C2—C1—C9—C1058.45 (17)
C1—C2—N3—C41.1 (2)C8—C1—C9—C10176.82 (13)
C2—N3—C4—O2178.77 (16)C2—C1—C9—C16179.93 (13)
C2—N3—C4—C50.6 (2)C8—C1—C9—C1661.69 (18)
O2—C4—C5—C687.7 (2)C2—C1—C9—C561.86 (16)
N3—C4—C5—C691.58 (17)C8—C1—C9—C556.52 (17)
O2—C4—C5—C9149.71 (16)C16—C9—C10—C1577.40 (18)
N3—C4—C5—C931.0 (2)C5—C9—C10—C1543.7 (2)
C4—C5—C6—O396.53 (19)C1—C9—C10—C15159.54 (15)
C9—C5—C6—O3140.95 (17)C16—C9—C10—C1199.18 (17)
C4—C5—C6—N782.61 (18)C5—C9—C10—C11139.75 (16)
C9—C5—C6—N739.9 (2)C1—C9—C10—C1123.9 (2)
O3—C6—N7—C8170.25 (17)C15—C10—C11—C120.2 (2)
C5—C6—N7—C810.6 (2)C9—C10—C11—C12176.84 (16)
C6—N7—C8—O4175.77 (16)C10—C11—C12—C130.4 (3)
C6—N7—C8—C15.8 (2)C11—C12—C13—C140.5 (3)
C2—C1—C8—O487.35 (18)C12—C13—C14—C150.0 (3)
C9—C1—C8—O4150.80 (15)C11—C10—C15—C140.7 (2)
C2—C1—C8—N791.04 (16)C9—C10—C15—C14177.42 (15)
C9—C1—C8—N730.8 (2)C13—C14—C15—C100.6 (3)
C4—C5—C9—C1060.15 (17)C18—N1—C17—O53.0 (3)
C6—C5—C9—C10179.28 (13)C19—N1—C17—O5179.89 (18)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O1i0.861 (19)2.12 (2)2.9650 (19)168.3 (18)
N7—H7···O50.90 (2)1.86 (2)2.7682 (19)178.6 (18)
Symmetry code: (i) x+1/2, y, z+1/2.
 

Acknowledgements

The synthesis, purification and crystallization of compounds (I)–(III) were funded by RSF (grant No. 16–13-00114). This work was financially supported in part by the Ministry of Education and Science of the Russian Federation (the Agreement number 02.a03.21.0008).

References

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