Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807048301/cf2149sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807048301/cf2149Isup2.hkl |
CCDC reference: 667311
Key indicators
- Single-crystal X-ray study
- T = 180 K
- Mean (C-C) = 0.002 Å
- Disorder in solvent or counterion
- R factor = 0.047
- wR factor = 0.137
- Data-to-parameter ratio = 20.1
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ? PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ? PLAT045_ALERT_1_C Calculated and Reported Z Differ by ............ 0.50 Ratio PLAT243_ALERT_4_C High 'Solvent' Ueq as Compared to Neighbors for C34B PLAT243_ALERT_4_C High 'Solvent' Ueq as Compared to Neighbors for C36B PLAT302_ALERT_4_C Anion/Solvent Disorder ......................... 40.00 Perc. PLAT432_ALERT_2_C Short Inter X...Y Contact O4 .. C4 .. 3.00 Ang.
Alert level G PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 6
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 7 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
For related compounds, see: Okuda et al. (2007); Sasaki et al. (2001). For related literature, see: Frisch et al. (1998); Becke (1993); Lee et al. (1988). Cg1, Cg2, Cg3 and Cg4 are the centroids of the oxadiazole ring and the C21–C26, C17–C20/C25/C26 and C5–C10 benzene rings, respectively.
To a methanol solution (15 ml) of N-[5-(1-naphthyl)pyrimidin-4-yl]acetamide oxime (139 mg, 0.5 mmol; Okuda et al., 2007), hydroxylamine hydrochloride (46.3 mg, 0.6 mmol) was added. The mixture was stirred at room temperature for 3.5 h. After evaporation of methanol, 20 ml of water was added to the residue then it was extracted with ethyl acetate. The organic layer was washed with brine, dried over Na2SO4 and evaporated. The residue was recrystallized from methanol to give N-[(Z)-2-(3-methyl[1,2,4]oxadiazol-5-yl)-2-(1-naphthyl)ethenyl]formamide oxime (m.p. 483–486 K). Single crystals of (I) were obtained by recrystallization from a toluene:1,4-dioxane (2:1 v/v) solution (m.p. 464–465 K). After drying (I) at 393 K under vacuum, the melting temperature changed to 483–486 K.
O-bound and N-bound H atoms were found in a difference Fourier map and refined isotropically (refined distances given in Table 1). Methyl H atoms were refined as riding, with C—H = 0.96 Å and with Uiso(H) = 1.5Ueq(C), allowing for rotation of the methyl group. Other H atoms were positioned geometrically (C—H = 0.93 or 0.97 Å) and refined as riding, with Uiso(H) = 1.2Ueq(C). Atoms except for O in the dioxane molecule are disordered over two positions with site-occupation factors of 0.775 (4) and 0.225 (4). For the minor disorder component, distance restraints [O—C = 1.43 (1), C33B···C36B = 2.27 (2) and C34B···C35B = 2.27 (2) Å] were applied and the C atoms were refined isotropically.
The ab initio molecular calculations were performed by using the GAUSSIAN98 package (Frisch et al., 1998) at the HF/6–31 G** and B3LYP/6–311 G** (Becke, 1993; Lee et al., 1988) levels of theory. Full optimizations were carried out and the resultant stable structures were confirmed by the vibrational analysis which shows only real frequencies for the optimized structures.
As part of our investigation to prepare anti-advanced glycation end-product (AGEs) agents, we have developed a pyrimidine ring-opening reaction accompanied by the formation of a 1,2,4-oxadiazole ring by the reaction of various 4-pyrimidinylamidines or their amide oximes with hydroxylamine hydrochloride (Sasaki et al., 2001). The title compound, (I), was prepared for that purpose. A methanol solution of the compound on silica gel thin-layer chromatography (TLC) gave a single spot but it changed to two spots after one day, suggesting that the compound changed to an equilibrium mixture of two compounds. A methanol solution of the related compound, N-[5-(1-naphthyl)pyrimidin-4-yl]acetamide oxime, (II), which is a reaction substrate of the above reaction, has also shown a similar TLC phenomenon. Recently, we have determined the crystal structure of (II) by X-ray diffraction and interpreted this phenomenon in terms of two diastereomers of this compound caused by two sets of atropisomers which might exist in the methanol solution (Okuda et al., 2007). In the present study, an X-ray crystal structure analysis of (I) was undertaken in order to obtain fundamental information about the TLC phenomenon.
In the asymmetric unit of (I), there are two crystallographically independent oxime molecules, A and B (Fig. 1). Each molecule has intramolecular N—H···O and N—H···N hydrogen bonds (Table 1), which make non-H atoms in the N-[(Z)-2-(3-methyl[1,2,4]oxadiazol-5-yl)-2-ethenyl]formamide oxime unit approximately coplanar; mean deviations from the defined plane are 0.0410 (12) and 0.0399 (12) Å for molecules A and B, respectively. Although bond lengths and angles of both molecules are essentially the same, the conformation of molecule A about the C1—C11 bond axis is quite different from that of B about C17—C27 as shown by torsion angles C2—C1—C11—C15 = 64.28 (17)° and C18—C17—C27—C31 = 122.24 (13)°. The dihedral angles between the naphthalene and the N-[(Z)-2-(3-methyl[1,2,4]oxadiazol-5-yl)-2-ethenyl]formamide oxime plane are 68.60 (2) and 57.88 (2)° for molecules A and B, respectively. Molecular orbital calculations at the HF/6–31 G** level of theory starting from geometries of A and B gave the same structure, the optimized torsion angle corresponding to C2—C1—C11—C15 or C18—C17—C27—C31 being 73.66°. The other stable structure was obtained as an atropisomer, the torsion angle being -73.66°.
In the crystal structure of (I), molecules A and B are connected to each other by O—H···N hydrogen bonds to form a dimer. Neighboring dimers related by a c glide plane are linked via C—H···O and C—H···N interactions, giving a molecular layer extending parallel to the (100) plane (Fig. 2). Adjacent layers are linked through a π-π stacking interaction between oxadiazole O1/N1/C13/N2/C12 rings which are approximately parallel to each other, forming a double layer structure (Fig. 3). The centroid-centroid [Cg1···Cg1v; symmetry code: (v) 1 - x, y, 3/2 - z] distance of the oxadiazole rings is 3.6234 (9) Å and the dihedral angle between the rings is 8.90 (6)°; the shortest distance is N2···C13v 3.398 (2) Å. The 1,4-dioxane molecules are placed in the void space between the molecular double layers (Fig. 3) and bound weakly through C—H···π interactions.
The oxime molecule of (I) gives only a set of atropisomers, which give the same spot on TLC. Therefore, for (I) we propose a different mechanism of the TLC phenomenon than we proposed for (II), based on the molecular structure. As shown in Fig. 4, in a methanol solution, equilibriation between compounds (Ia) and (Ib) is possible. We suggest the new spot on silica gel TLC is derived from (Ib). The compound, (Ib), is stable in the gas phase as confirmed by molecular orbital calculations at HF/6–31 G** and B3LYP/6–311 G** levels of theory, but the electric energy of (Ib) is much higher than that of (Ia). The differences between (Ia) and (Ib) calculated by B3LYP/6–311 G** and HF/6–31 G** are 56.64 and 70.49 kJ mol-1, respectively, which might be reduced in a methanol solution but could govern the crystallized product. The oxime fragment of (Ib) is planar and intramolecular N—H···N and N—H···O hydrogen bonds are observed (N—H 1.041, H···N 1.806, N···N 2.581 Å and N—H···N 128.00°; N—H 1.041, H···O 2.755, N···O 3.774 Å and N—H···O 166.00° calculated by B3LYP/6–311 G**).
For related compounds, see: Okuda et al. (2007); Sasaki et al. (2001). For related literature, see: Frisch et al. (1998); Becke (1993); Lee et al. (1988). Cg1, Cg2, Cg3 and Cg4 are the centroids of the oxadiazole ring and the C21–C26, C17–C20/C25/C26 and C5–C10 benzene rings, respectively.
Data collection: PROCESS-AUTO (Rigaku/MSC, 2004); cell refinement: PROCESS-AUTO (Rigaku/MSC, 2004); data reduction: CrystalStructure (Rigaku/MSC, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2004) and PLATON (Spek, 2003).
C16H14N4O2·0.5C4H8O2 | F(000) = 2848.00 |
Mr = 338.37 | Dx = 1.340 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71075 Å |
Hall symbol: -C 2yc | Cell parameters from 37777 reflections |
a = 25.0090 (8) Å | θ = 3.0–30.0° |
b = 21.1940 (5) Å | µ = 0.09 mm−1 |
c = 14.5843 (4) Å | T = 180 K |
β = 119.8098 (9)° | Plate, colorless |
V = 6707.4 (3) Å3 | 0.40 × 0.20 × 0.09 mm |
Z = 16 |
Rigaku R-AXIS RAPID diffractometer | Rint = 0.049 |
Detector resolution: 10.00 pixels mm-1 | θmax = 30.0° |
ω scans | h = −35→35 |
59998 measured reflections | k = −29→29 |
9746 independent reflections | l = −20→18 |
6472 reflections with I > 2σ(I) |
Refinement on F2 | 6 restraints |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.047 | w = 1/[σ2(Fo2) + (0.0753P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.137 | (Δ/σ)max < 0.001 |
S = 1.06 | Δρmax = 0.34 e Å−3 |
9746 reflections | Δρmin = −0.26 e Å−3 |
486 parameters |
C16H14N4O2·0.5C4H8O2 | V = 6707.4 (3) Å3 |
Mr = 338.37 | Z = 16 |
Monoclinic, C2/c | Mo Kα radiation |
a = 25.0090 (8) Å | µ = 0.09 mm−1 |
b = 21.1940 (5) Å | T = 180 K |
c = 14.5843 (4) Å | 0.40 × 0.20 × 0.09 mm |
β = 119.8098 (9)° |
Rigaku R-AXIS RAPID diffractometer | 6472 reflections with I > 2σ(I) |
59998 measured reflections | Rint = 0.049 |
9746 independent reflections |
R[F2 > 2σ(F2)] = 0.047 | 6 restraints |
wR(F2) = 0.137 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.34 e Å−3 |
9746 reflections | Δρmin = −0.26 e Å−3 |
486 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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 > 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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
O1 | 0.42380 (4) | 0.01354 (4) | 0.75815 (6) | 0.0352 (2) | |
O2 | 0.41029 (5) | 0.21271 (4) | 0.46330 (7) | 0.0392 (2) | |
O3 | 0.41661 (5) | 0.48641 (4) | −0.00821 (7) | 0.0430 (3) | |
O4 | 0.42264 (5) | 0.28375 (4) | 0.27960 (7) | 0.0440 (3) | |
O5 | 0.29391 (6) | 0.16225 (6) | 0.72011 (9) | 0.0597 (3) | |
O6 | 0.21126 (5) | 0.08213 (5) | 0.74108 (9) | 0.0561 (3) | |
N1 | 0.43588 (6) | 0.06251 (5) | 0.83317 (8) | 0.0384 (3) | |
N2 | 0.42091 (5) | 0.10367 (5) | 0.67926 (8) | 0.0309 (2) | |
N3 | 0.40594 (5) | 0.09366 (4) | 0.47936 (8) | 0.0294 (2) | |
N4 | 0.40493 (5) | 0.17833 (5) | 0.37562 (8) | 0.0329 (2) | |
N5 | 0.41912 (7) | 0.43814 (5) | −0.07412 (9) | 0.0464 (3) | |
N6 | 0.41671 (5) | 0.39517 (5) | 0.06469 (8) | 0.0297 (2) | |
N7 | 0.42236 (5) | 0.40251 (5) | 0.25948 (8) | 0.0307 (2) | |
N8 | 0.42385 (5) | 0.31816 (5) | 0.36409 (8) | 0.0343 (2) | |
C1 | 0.40128 (6) | −0.06603 (5) | 0.58731 (9) | 0.0285 (2) | |
C2 | 0.44715 (6) | −0.10320 (6) | 0.59038 (10) | 0.0354 (3) | |
H2 | 0.4803 | −0.0842 | 0.5890 | 0.042* | |
C3 | 0.44503 (7) | −0.16939 (6) | 0.59559 (11) | 0.0399 (3) | |
H3 | 0.4765 | −0.1936 | 0.5970 | 0.048* | |
C4 | 0.39731 (7) | −0.19811 (6) | 0.59850 (10) | 0.0374 (3) | |
H4 | 0.3965 | −0.2419 | 0.6022 | 0.045* | |
C5 | 0.29865 (7) | −0.19105 (6) | 0.59899 (11) | 0.0443 (3) | |
H5 | 0.2976 | −0.2348 | 0.6036 | 0.053* | |
C6 | 0.25218 (8) | −0.15604 (8) | 0.59526 (14) | 0.0562 (4) | |
H6 | 0.2197 | −0.1759 | 0.5977 | 0.067* | |
C7 | 0.25284 (7) | −0.08990 (8) | 0.58778 (14) | 0.0532 (4) | |
H7 | 0.2208 | −0.0662 | 0.5851 | 0.064* | |
C8 | 0.30048 (6) | −0.06020 (6) | 0.58438 (11) | 0.0402 (3) | |
H8 | 0.3001 | −0.0165 | 0.5785 | 0.048* | |
C9 | 0.35024 (6) | −0.09515 (5) | 0.58971 (9) | 0.0294 (2) | |
C10 | 0.34876 (6) | −0.16214 (5) | 0.59594 (9) | 0.0330 (3) | |
C11 | 0.40486 (6) | 0.00385 (5) | 0.58031 (9) | 0.0282 (2) | |
C12 | 0.41573 (6) | 0.04236 (5) | 0.66965 (9) | 0.0283 (2) | |
C13 | 0.43363 (6) | 0.11357 (6) | 0.78176 (9) | 0.0324 (3) | |
C14 | 0.44440 (7) | 0.17717 (6) | 0.83035 (11) | 0.0427 (3) | |
H14A | 0.4790 | 0.1965 | 0.8298 | 0.064* | |
H14B | 0.4528 | 0.1734 | 0.9019 | 0.064* | |
H14C | 0.4084 | 0.2028 | 0.7908 | 0.064* | |
C15 | 0.40228 (6) | 0.03038 (5) | 0.49375 (9) | 0.0294 (2) | |
H15 | 0.3977 | 0.0035 | 0.4399 | 0.035* | |
C16 | 0.40251 (6) | 0.11929 (5) | 0.39027 (9) | 0.0304 (3) | |
H16 | 0.3981 | 0.0919 | 0.3371 | 0.036* | |
C17 | 0.40241 (6) | 0.56352 (5) | 0.13817 (9) | 0.0278 (2) | |
C18 | 0.44426 (6) | 0.60021 (6) | 0.12689 (9) | 0.0321 (3) | |
H18 | 0.4776 | 0.5810 | 0.1266 | 0.038* | |
C19 | 0.43748 (7) | 0.66621 (6) | 0.11577 (10) | 0.0371 (3) | |
H19 | 0.4663 | 0.6900 | 0.1084 | 0.045* | |
C20 | 0.38901 (7) | 0.69542 (6) | 0.11579 (10) | 0.0387 (3) | |
H20 | 0.3851 | 0.7390 | 0.1084 | 0.046* | |
C21 | 0.29388 (8) | 0.68988 (7) | 0.12774 (12) | 0.0482 (4) | |
H21 | 0.2898 | 0.7335 | 0.1208 | 0.058* | |
C22 | 0.25137 (8) | 0.65588 (8) | 0.13840 (14) | 0.0568 (4) | |
H22 | 0.2189 | 0.6762 | 0.1398 | 0.068* | |
C23 | 0.25652 (7) | 0.58961 (8) | 0.14730 (13) | 0.0501 (4) | |
H23 | 0.2270 | 0.5665 | 0.1540 | 0.060* | |
C24 | 0.30426 (6) | 0.55902 (6) | 0.14627 (11) | 0.0379 (3) | |
H24 | 0.3065 | 0.5153 | 0.1514 | 0.045* | |
C25 | 0.35057 (6) | 0.59295 (5) | 0.13752 (9) | 0.0301 (2) | |
C26 | 0.34446 (6) | 0.66003 (6) | 0.12702 (10) | 0.0353 (3) | |
C27 | 0.41140 (6) | 0.49376 (5) | 0.15171 (9) | 0.0278 (2) | |
C28 | 0.41507 (6) | 0.45665 (5) | 0.07202 (9) | 0.0280 (2) | |
C29 | 0.41883 (6) | 0.38655 (6) | −0.02680 (9) | 0.0318 (3) | |
C30 | 0.41975 (7) | 0.32367 (6) | −0.07106 (11) | 0.0400 (3) | |
H30A | 0.3840 | 0.3001 | −0.0834 | 0.060* | |
H30B | 0.4562 | 0.3012 | −0.0219 | 0.060* | |
H30C | 0.4197 | 0.3290 | −0.1365 | 0.060* | |
C31 | 0.41560 (6) | 0.46548 (5) | 0.23863 (9) | 0.0293 (2) | |
H31 | 0.4137 | 0.4915 | 0.2883 | 0.035* | |
C32 | 0.42351 (6) | 0.37709 (5) | 0.34702 (9) | 0.0311 (3) | |
H32 | 0.4241 | 0.4047 | 0.3971 | 0.037* | |
C33A | 0.27222 (11) | 0.10533 (11) | 0.66026 (16) | 0.0487 (6) | 0.775 (4) |
H33A | 0.3002 | 0.0710 | 0.6981 | 0.058* | 0.775 (4) |
H33B | 0.2706 | 0.1104 | 0.5928 | 0.058* | 0.775 (4) |
C34A | 0.21015 (11) | 0.09049 (11) | 0.64279 (15) | 0.0478 (6) | 0.775 (4) |
H34A | 0.1821 | 0.1245 | 0.6034 | 0.057* | 0.775 (4) |
H34B | 0.1951 | 0.0522 | 0.6011 | 0.057* | 0.775 (4) |
C35A | 0.23431 (12) | 0.13985 (12) | 0.80186 (17) | 0.0511 (6) | 0.775 (4) |
H35A | 0.2364 | 0.1349 | 0.8697 | 0.061* | 0.775 (4) |
H35B | 0.2063 | 0.1743 | 0.7646 | 0.061* | 0.775 (4) |
C36A | 0.29672 (11) | 0.15494 (11) | 0.81857 (16) | 0.0534 (6) | 0.775 (4) |
H36A | 0.3117 | 0.1936 | 0.8592 | 0.064* | 0.775 (4) |
H36B | 0.3251 | 0.1212 | 0.8581 | 0.064* | 0.775 (4) |
C33B | 0.2450 (5) | 0.1294 (5) | 0.6334 (7) | 0.087 (4)* | 0.225 (4) |
H33C | 0.2548 | 0.1221 | 0.5777 | 0.104* | 0.225 (4) |
H33D | 0.2068 | 0.1530 | 0.6046 | 0.104* | 0.225 (4) |
C34B | 0.2399 (6) | 0.0672 (5) | 0.6810 (10) | 0.092 (4)* | 0.225 (4) |
H34C | 0.2153 | 0.0372 | 0.6257 | 0.110* | 0.225 (4) |
H34D | 0.2804 | 0.0492 | 0.7257 | 0.110* | 0.225 (4) |
C35B | 0.2557 (5) | 0.1152 (5) | 0.8304 (6) | 0.092 (4)* | 0.225 (4) |
H35C | 0.2939 | 0.0916 | 0.8671 | 0.110* | 0.225 (4) |
H35D | 0.2409 | 0.1242 | 0.8791 | 0.110* | 0.225 (4) |
C36B | 0.2647 (6) | 0.1766 (6) | 0.7824 (9) | 0.100 (4)* | 0.225 (4) |
H36C | 0.2250 | 0.1964 | 0.7379 | 0.120* | 0.225 (4) |
H36D | 0.2902 | 0.2058 | 0.8385 | 0.120* | 0.225 (4) |
H2O | 0.4108 (8) | 0.2538 (9) | 0.4437 (14) | 0.062 (5)* | |
H4O | 0.4161 (10) | 0.2433 (10) | 0.2957 (17) | 0.085 (7)* | |
H3N | 0.4099 (7) | 0.1200 (7) | 0.5301 (13) | 0.043 (4)* | |
H7N | 0.4220 (7) | 0.3771 (7) | 0.2131 (13) | 0.043 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0532 (6) | 0.0262 (4) | 0.0302 (4) | −0.0033 (4) | 0.0238 (4) | 0.0004 (3) |
O2 | 0.0666 (7) | 0.0240 (4) | 0.0340 (5) | −0.0025 (4) | 0.0304 (5) | −0.0008 (4) |
O3 | 0.0778 (8) | 0.0276 (4) | 0.0354 (5) | 0.0014 (4) | 0.0371 (5) | 0.0029 (4) |
O4 | 0.0800 (8) | 0.0252 (4) | 0.0388 (5) | 0.0017 (4) | 0.0387 (5) | 0.0006 (4) |
O5 | 0.0633 (8) | 0.0560 (7) | 0.0584 (7) | −0.0165 (6) | 0.0292 (6) | 0.0007 (5) |
O6 | 0.0558 (7) | 0.0542 (6) | 0.0612 (7) | −0.0083 (5) | 0.0312 (6) | 0.0046 (5) |
N1 | 0.0556 (7) | 0.0328 (6) | 0.0307 (5) | −0.0035 (5) | 0.0244 (5) | −0.0038 (4) |
N2 | 0.0426 (6) | 0.0246 (5) | 0.0293 (5) | −0.0032 (4) | 0.0209 (5) | −0.0018 (4) |
N3 | 0.0429 (6) | 0.0220 (5) | 0.0283 (5) | −0.0025 (4) | 0.0215 (5) | −0.0004 (4) |
N4 | 0.0472 (7) | 0.0272 (5) | 0.0288 (5) | −0.0010 (4) | 0.0223 (5) | −0.0003 (4) |
N5 | 0.0814 (10) | 0.0322 (6) | 0.0383 (6) | 0.0018 (6) | 0.0394 (7) | −0.0007 (5) |
N6 | 0.0383 (6) | 0.0255 (5) | 0.0296 (5) | 0.0017 (4) | 0.0201 (4) | 0.0011 (4) |
N7 | 0.0453 (6) | 0.0241 (5) | 0.0271 (5) | 0.0028 (4) | 0.0213 (5) | 0.0014 (4) |
N8 | 0.0500 (7) | 0.0287 (5) | 0.0278 (5) | 0.0011 (4) | 0.0220 (5) | 0.0007 (4) |
C1 | 0.0382 (7) | 0.0221 (5) | 0.0268 (5) | −0.0008 (4) | 0.0174 (5) | 0.0007 (4) |
C2 | 0.0426 (8) | 0.0288 (6) | 0.0405 (7) | 0.0003 (5) | 0.0250 (6) | 0.0017 (5) |
C3 | 0.0520 (9) | 0.0287 (6) | 0.0435 (7) | 0.0093 (6) | 0.0271 (7) | 0.0036 (5) |
C4 | 0.0588 (9) | 0.0210 (5) | 0.0323 (6) | 0.0018 (5) | 0.0226 (6) | 0.0033 (5) |
C5 | 0.0517 (9) | 0.0337 (7) | 0.0446 (8) | −0.0138 (6) | 0.0218 (7) | 0.0010 (6) |
C6 | 0.0486 (10) | 0.0535 (9) | 0.0716 (11) | −0.0178 (7) | 0.0336 (9) | −0.0003 (8) |
C7 | 0.0414 (9) | 0.0512 (9) | 0.0729 (11) | −0.0033 (7) | 0.0329 (8) | −0.0022 (8) |
C8 | 0.0396 (8) | 0.0327 (6) | 0.0483 (8) | −0.0029 (5) | 0.0218 (6) | −0.0019 (6) |
C9 | 0.0361 (7) | 0.0248 (5) | 0.0269 (5) | −0.0028 (5) | 0.0154 (5) | −0.0007 (4) |
C10 | 0.0457 (8) | 0.0249 (5) | 0.0269 (5) | −0.0058 (5) | 0.0170 (5) | −0.0003 (4) |
C11 | 0.0358 (7) | 0.0204 (5) | 0.0316 (6) | −0.0016 (4) | 0.0192 (5) | −0.0004 (4) |
C12 | 0.0340 (6) | 0.0250 (5) | 0.0291 (6) | −0.0012 (4) | 0.0182 (5) | 0.0018 (4) |
C13 | 0.0405 (7) | 0.0303 (6) | 0.0296 (6) | −0.0032 (5) | 0.0197 (5) | −0.0017 (5) |
C14 | 0.0615 (10) | 0.0321 (7) | 0.0373 (7) | −0.0055 (6) | 0.0267 (7) | −0.0092 (5) |
C15 | 0.0374 (7) | 0.0229 (5) | 0.0316 (6) | −0.0016 (4) | 0.0201 (5) | −0.0019 (4) |
C16 | 0.0418 (7) | 0.0264 (6) | 0.0280 (5) | −0.0011 (5) | 0.0212 (5) | −0.0011 (4) |
C17 | 0.0357 (6) | 0.0243 (5) | 0.0222 (5) | −0.0006 (4) | 0.0135 (5) | 0.0006 (4) |
C18 | 0.0381 (7) | 0.0293 (6) | 0.0291 (6) | −0.0013 (5) | 0.0169 (5) | 0.0022 (5) |
C19 | 0.0476 (8) | 0.0307 (6) | 0.0338 (6) | −0.0081 (5) | 0.0208 (6) | 0.0012 (5) |
C20 | 0.0571 (9) | 0.0226 (5) | 0.0357 (6) | −0.0022 (5) | 0.0224 (6) | 0.0006 (5) |
C21 | 0.0575 (10) | 0.0351 (7) | 0.0526 (8) | 0.0121 (6) | 0.0279 (8) | 0.0011 (6) |
C22 | 0.0501 (10) | 0.0554 (10) | 0.0716 (11) | 0.0152 (7) | 0.0355 (9) | 0.0022 (8) |
C23 | 0.0414 (9) | 0.0533 (9) | 0.0616 (9) | 0.0025 (7) | 0.0302 (8) | 0.0038 (7) |
C24 | 0.0383 (7) | 0.0335 (6) | 0.0424 (7) | 0.0000 (5) | 0.0205 (6) | 0.0025 (5) |
C25 | 0.0357 (7) | 0.0276 (6) | 0.0252 (5) | 0.0013 (5) | 0.0138 (5) | 0.0008 (4) |
C26 | 0.0460 (8) | 0.0278 (6) | 0.0308 (6) | 0.0032 (5) | 0.0181 (6) | 0.0002 (5) |
C27 | 0.0342 (6) | 0.0236 (5) | 0.0268 (5) | 0.0012 (4) | 0.0161 (5) | 0.0009 (4) |
C28 | 0.0320 (6) | 0.0275 (5) | 0.0253 (5) | 0.0013 (4) | 0.0149 (5) | 0.0050 (4) |
C29 | 0.0368 (7) | 0.0315 (6) | 0.0300 (6) | 0.0004 (5) | 0.0187 (5) | 0.0005 (5) |
C30 | 0.0525 (9) | 0.0335 (6) | 0.0408 (7) | −0.0007 (6) | 0.0283 (7) | −0.0061 (6) |
C31 | 0.0369 (7) | 0.0239 (5) | 0.0285 (6) | 0.0008 (4) | 0.0174 (5) | 0.0003 (4) |
C32 | 0.0429 (7) | 0.0269 (6) | 0.0255 (5) | 0.0012 (5) | 0.0186 (5) | 0.0026 (4) |
C33A | 0.0513 (13) | 0.0569 (12) | 0.0387 (10) | −0.0011 (10) | 0.0232 (9) | −0.0082 (9) |
C34A | 0.0467 (12) | 0.0533 (12) | 0.0371 (10) | −0.0093 (9) | 0.0161 (9) | −0.0142 (9) |
C35A | 0.0533 (13) | 0.0668 (14) | 0.0339 (9) | 0.0019 (11) | 0.0221 (9) | −0.0081 (10) |
C36A | 0.0543 (14) | 0.0576 (13) | 0.0370 (10) | −0.0090 (10) | 0.0141 (10) | −0.0139 (9) |
O1—C12 | 1.3493 (13) | C14—H14A | 0.96 |
O1—N1 | 1.4272 (13) | C14—H14B | 0.96 |
O2—N4 | 1.4191 (13) | C14—H14C | 0.96 |
O2—H2O | 0.918 (19) | C15—H15 | 0.93 |
O3—C28 | 1.3467 (13) | C16—H16 | 0.93 |
O3—N5 | 1.4263 (13) | C17—C18 | 1.3777 (16) |
O4—N8 | 1.4192 (13) | C17—C25 | 1.4346 (17) |
O4—H4O | 0.92 (2) | C17—C27 | 1.4937 (15) |
O5—C36A | 1.411 (2) | C18—C19 | 1.4087 (17) |
O5—C33B | 1.430 (7) | C18—H18 | 0.93 |
O5—C33A | 1.429 (2) | C19—C20 | 1.361 (2) |
O5—C36B | 1.453 (5) | C19—H19 | 0.93 |
O6—C34B | 1.417 (5) | C20—C26 | 1.4184 (19) |
O6—C35B | 1.409 (5) | C20—H20 | 0.93 |
O6—C34A | 1.431 (2) | C21—C22 | 1.356 (2) |
O6—C35A | 1.451 (2) | C21—C26 | 1.419 (2) |
N1—C13 | 1.3017 (16) | C21—H21 | 0.93 |
N2—C12 | 1.3066 (14) | C22—C23 | 1.411 (2) |
N2—C13 | 1.3809 (15) | C22—H22 | 0.93 |
N3—C15 | 1.3674 (14) | C23—C24 | 1.3652 (19) |
N3—C16 | 1.3711 (14) | C23—H23 | 0.93 |
N3—H3N | 0.892 (15) | C24—C25 | 1.4218 (17) |
N4—C16 | 1.2757 (14) | C24—H24 | 0.93 |
N5—C29 | 1.2949 (16) | C25—C26 | 1.4299 (16) |
N6—C28 | 1.3098 (14) | C27—C31 | 1.3583 (15) |
N6—C29 | 1.3738 (15) | C27—C28 | 1.4435 (15) |
N7—C31 | 1.3606 (14) | C29—C30 | 1.4859 (17) |
N7—C32 | 1.3727 (14) | C30—H30A | 0.96 |
N7—H7N | 0.861 (15) | C30—H30B | 0.96 |
N8—C32 | 1.2727 (14) | C30—H30C | 0.96 |
C1—C2 | 1.3738 (17) | C31—H31 | 0.93 |
C1—C9 | 1.4337 (16) | C32—H32 | 0.93 |
C1—C11 | 1.4904 (15) | C33A—C34A | 1.477 (3) |
C2—C3 | 1.4073 (17) | C33A—H33A | 0.97 |
C2—H2 | 0.93 | C33A—H33B | 0.97 |
C3—C4 | 1.359 (2) | C34A—H34A | 0.97 |
C3—H3 | 0.93 | C34A—H34B | 0.97 |
C4—C10 | 1.4184 (19) | C35A—C36A | 1.490 (3) |
C4—H4 | 0.93 | C35A—H35A | 0.97 |
C5—C6 | 1.357 (2) | C35A—H35B | 0.97 |
C5—C10 | 1.4155 (19) | C36A—H36A | 0.97 |
C5—H5 | 0.93 | C36A—H36B | 0.97 |
C6—C7 | 1.407 (2) | C33B—C34B | 1.523 (13) |
C6—H6 | 0.93 | C33B—H33C | 0.97 |
C7—C8 | 1.370 (2) | C33B—H33D | 0.97 |
C7—H7 | 0.93 | C34B—H34C | 0.97 |
C8—C9 | 1.4169 (18) | C34B—H34D | 0.97 |
C8—H8 | 0.93 | C35B—C36B | 1.545 (14) |
C9—C10 | 1.4244 (16) | C35B—H35C | 0.97 |
C11—C15 | 1.3540 (16) | C35B—H35D | 0.97 |
C11—C12 | 1.4440 (16) | C36B—H36C | 0.97 |
C13—C14 | 1.4839 (16) | C36B—H36D | 0.97 |
C12—O1—N1 | 106.15 (8) | C26—C21—H21 | 119.5 |
N4—O2—H2O | 102.5 (11) | C21—C22—C23 | 119.92 (14) |
C28—O3—N5 | 106.23 (9) | C21—C22—H22 | 120.0 |
N8—O4—H4O | 100.8 (13) | C23—C22—H22 | 120.0 |
C33A—O5—C36A | 109.92 (14) | C24—C23—C22 | 120.81 (14) |
C34A—O6—C35A | 108.15 (14) | C24—C23—H23 | 119.6 |
C33B—O5—C36B | 100.4 (6) | C22—C23—H23 | 119.6 |
C34B—O6—C35B | 105.8 (7) | C23—C24—C25 | 121.11 (13) |
C13—N1—O1 | 103.35 (9) | C23—C24—H24 | 119.4 |
C12—N2—C13 | 102.96 (9) | C25—C24—H24 | 119.4 |
C15—N3—C16 | 123.82 (10) | C24—C25—C26 | 117.64 (11) |
C15—N3—H3N | 118.3 (9) | C24—C25—C17 | 123.59 (11) |
C16—N3—H3N | 117.9 (9) | C26—C25—C17 | 118.76 (11) |
C16—N4—O2 | 110.11 (9) | C20—C26—C21 | 121.28 (12) |
C29—N5—O3 | 103.46 (9) | C20—C26—C25 | 119.33 (12) |
C28—N6—C29 | 103.27 (9) | C21—C26—C25 | 119.39 (12) |
C31—N7—C32 | 122.39 (10) | C31—C27—C28 | 120.30 (10) |
C31—N7—H7N | 119.0 (10) | C31—C27—C17 | 119.80 (10) |
C32—N7—H7N | 118.3 (10) | C28—C27—C17 | 119.90 (9) |
C32—N8—O4 | 109.83 (9) | N6—C28—O3 | 112.30 (10) |
C2—C1—C9 | 119.44 (11) | N6—C28—C27 | 128.68 (10) |
C2—C1—C11 | 119.63 (11) | O3—C28—C27 | 119.03 (10) |
C9—C1—C11 | 120.93 (10) | N5—C29—N6 | 114.74 (11) |
C1—C2—C3 | 121.33 (12) | N5—C29—C30 | 121.36 (11) |
C1—C2—H2 | 119.3 | N6—C29—C30 | 123.90 (11) |
C3—C2—H2 | 119.3 | C29—C30—H30A | 109.5 |
C4—C3—C2 | 120.37 (12) | C29—C30—H30B | 109.5 |
C4—C3—H3 | 119.8 | H30A—C30—H30B | 109.5 |
C2—C3—H3 | 119.8 | C29—C30—H30C | 109.5 |
C3—C4—C10 | 120.79 (11) | H30A—C30—H30C | 109.5 |
C3—C4—H4 | 119.6 | H30B—C30—H30C | 109.5 |
C10—C4—H4 | 119.6 | C27—C31—N7 | 125.79 (10) |
C6—C5—C10 | 121.06 (13) | C27—C31—H31 | 117.1 |
C6—C5—H5 | 119.5 | N7—C31—H31 | 117.1 |
C10—C5—H5 | 119.5 | N8—C32—N7 | 124.21 (11) |
C5—C6—C7 | 120.35 (14) | N8—C32—H32 | 117.9 |
C5—C6—H6 | 119.8 | N7—C32—H32 | 117.9 |
C7—C6—H6 | 119.8 | O5—C33A—C34A | 109.42 (17) |
C8—C7—C6 | 120.30 (15) | O5—C33A—H33A | 109.8 |
C8—C7—H7 | 119.8 | C34A—C33A—H33A | 109.8 |
C6—C7—H7 | 119.8 | O5—C33A—H33B | 109.8 |
C7—C8—C9 | 120.92 (13) | C34A—C33A—H33B | 109.8 |
C7—C8—H8 | 119.5 | H33A—C33A—H33B | 108.2 |
C9—C8—H8 | 119.5 | O6—C34A—C33A | 111.00 (16) |
C8—C9—C10 | 118.32 (11) | O6—C34A—H34A | 109.4 |
C8—C9—C1 | 122.82 (11) | C33A—C34A—H34A | 109.4 |
C10—C9—C1 | 118.84 (11) | O6—C34A—H34B | 109.4 |
C5—C10—C4 | 121.75 (11) | C33A—C34A—H34B | 109.4 |
C5—C10—C9 | 119.02 (12) | H34A—C34A—H34B | 108.0 |
C4—C10—C9 | 119.23 (11) | O6—C35A—C36A | 110.28 (17) |
C15—C11—C12 | 120.46 (10) | O6—C35A—H35A | 109.6 |
C15—C11—C1 | 119.99 (10) | C36A—C35A—H35A | 109.6 |
C12—C11—C1 | 119.38 (10) | O6—C35A—H35B | 109.6 |
N2—C12—O1 | 112.82 (10) | C36A—C35A—H35B | 109.6 |
N2—C12—C11 | 128.54 (10) | H35A—C35A—H35B | 108.1 |
O1—C12—C11 | 118.61 (10) | O5—C36A—C35A | 109.82 (17) |
N1—C13—N2 | 114.71 (11) | O5—C36A—H36A | 109.7 |
N1—C13—C14 | 122.31 (11) | C35A—C36A—H36A | 109.7 |
N2—C13—C14 | 122.98 (11) | O5—C36A—H36B | 109.7 |
C13—C14—H14A | 109.5 | C35A—C36A—H36B | 109.7 |
C13—C14—H14B | 109.5 | H36A—C36A—H36B | 108.2 |
H14A—C14—H14B | 109.5 | O5—C33B—C34B | 104.3 (8) |
C13—C14—H14C | 109.5 | O5—C33B—H33C | 110.9 |
H14A—C14—H14C | 109.5 | C34B—C33B—H33C | 110.9 |
H14B—C14—H14C | 109.5 | O5—C33B—H33D | 110.9 |
C11—C15—N3 | 125.07 (10) | C34B—C33B—H33D | 110.9 |
C11—C15—H15 | 117.5 | H33C—C33B—H33D | 108.9 |
N3—C15—H15 | 117.5 | O6—C34B—C33B | 105.8 (8) |
N4—C16—N3 | 124.16 (10) | O6—C34B—H34C | 110.6 |
N4—C16—H16 | 117.9 | C33B—C34B—H34C | 110.6 |
N3—C16—H16 | 117.9 | O6—C34B—H34D | 110.6 |
C18—C17—C25 | 119.43 (11) | C33B—C34B—H34D | 110.6 |
C18—C17—C27 | 120.08 (11) | H34C—C34B—H34D | 108.7 |
C25—C17—C27 | 120.49 (10) | O6—C35B—C36B | 103.1 (8) |
C17—C18—C19 | 121.28 (12) | O6—C35B—H35C | 111.1 |
C17—C18—H18 | 119.4 | C36B—C35B—H35C | 111.1 |
C19—C18—H18 | 119.4 | O6—C35B—H35D | 111.1 |
C20—C19—C18 | 120.51 (12) | C36B—C35B—H35D | 111.1 |
C20—C19—H19 | 119.7 | H35C—C35B—H35D | 109.1 |
C18—C19—H19 | 119.7 | O5—C36B—C35B | 109.7 (8) |
C19—C20—C26 | 120.68 (11) | O5—C36B—H36C | 109.7 |
C19—C20—H20 | 119.7 | C35B—C36B—H36C | 109.7 |
C26—C20—H20 | 119.7 | O5—C36B—H36D | 109.7 |
C22—C21—C26 | 121.10 (13) | C35B—C36B—H36D | 109.7 |
C22—C21—H21 | 119.5 | H36C—C36B—H36D | 108.2 |
C12—O1—N1—C13 | 0.02 (13) | C21—C22—C23—C24 | 0.6 (3) |
C28—O3—N5—C29 | −0.04 (15) | C22—C23—C24—C25 | 0.8 (2) |
C9—C1—C2—C3 | 0.15 (18) | C23—C24—C25—C26 | −1.63 (19) |
C11—C1—C2—C3 | −179.16 (11) | C23—C24—C25—C17 | 178.69 (13) |
C1—C2—C3—C4 | −0.5 (2) | C18—C17—C25—C24 | 178.56 (11) |
C2—C3—C4—C10 | 0.25 (19) | C27—C17—C25—C24 | −1.87 (17) |
C10—C5—C6—C7 | 0.3 (2) | C18—C17—C25—C26 | −1.12 (16) |
C5—C6—C7—C8 | −0.1 (3) | C27—C17—C25—C26 | 178.45 (10) |
C6—C7—C8—C9 | −0.9 (2) | C19—C20—C26—C21 | 179.66 (13) |
C7—C8—C9—C10 | 1.61 (19) | C19—C20—C26—C25 | −0.51 (19) |
C7—C8—C9—C1 | −179.46 (13) | C22—C21—C26—C20 | 179.94 (14) |
C2—C1—C9—C8 | −178.51 (12) | C22—C21—C26—C25 | 0.1 (2) |
C11—C1—C9—C8 | 0.79 (17) | C24—C25—C26—C20 | −178.65 (11) |
C2—C1—C9—C10 | 0.41 (17) | C17—C25—C26—C20 | 1.05 (17) |
C11—C1—C9—C10 | 179.71 (10) | C24—C25—C26—C21 | 1.18 (18) |
C6—C5—C10—C4 | −179.23 (14) | C17—C25—C26—C21 | −179.12 (11) |
C6—C5—C10—C9 | 0.5 (2) | C18—C17—C27—C31 | 122.24 (13) |
C3—C4—C10—C5 | −179.94 (12) | C25—C17—C27—C31 | −57.32 (16) |
C3—C4—C10—C9 | 0.32 (18) | C18—C17—C27—C28 | −58.27 (16) |
C8—C9—C10—C5 | −1.42 (17) | C25—C17—C27—C28 | 122.16 (12) |
C1—C9—C10—C5 | 179.60 (11) | C29—N6—C28—O3 | −0.57 (14) |
C8—C9—C10—C4 | 178.33 (11) | C29—N6—C28—C27 | 178.81 (13) |
C1—C9—C10—C4 | −0.64 (17) | N5—O3—C28—N6 | 0.40 (14) |
C2—C1—C11—C15 | 64.28 (17) | N5—O3—C28—C27 | −179.04 (11) |
C9—C1—C11—C15 | −115.02 (13) | C31—C27—C28—N6 | 6.9 (2) |
C2—C1—C11—C12 | −111.09 (13) | C17—C27—C28—N6 | −172.63 (12) |
C9—C1—C11—C12 | 69.62 (15) | C31—C27—C28—O3 | −173.80 (11) |
C13—N2—C12—O1 | 0.48 (14) | C17—C27—C28—O3 | 6.72 (17) |
C13—N2—C12—C11 | −177.37 (13) | O3—N5—C29—N6 | −0.33 (16) |
N1—O1—C12—N2 | −0.33 (14) | O3—N5—C29—C30 | 178.75 (12) |
N1—O1—C12—C11 | 177.76 (11) | C28—N6—C29—N5 | 0.57 (16) |
C15—C11—C12—N2 | 4.0 (2) | C28—N6—C29—C30 | −178.49 (13) |
C1—C11—C12—N2 | 179.29 (12) | C28—C27—C31—N7 | −1.07 (19) |
C15—C11—C12—O1 | −173.79 (11) | C17—C27—C31—N7 | 178.42 (11) |
C1—C11—C12—O1 | 1.55 (17) | C32—N7—C31—C27 | −177.01 (12) |
O1—N1—C13—N2 | 0.29 (15) | O4—N8—C32—N7 | −0.20 (18) |
O1—N1—C13—C14 | −179.27 (12) | C31—N7—C32—N8 | 173.02 (12) |
C12—N2—C13—N1 | −0.48 (15) | C36A—O5—C33A—C34A | 59.9 (2) |
C12—N2—C13—C14 | 179.08 (13) | C35A—O6—C34A—C33A | 58.7 (2) |
C12—C11—C15—N3 | −3.8 (2) | O5—C33A—C34A—O6 | −60.1 (2) |
C1—C11—C15—N3 | −179.08 (11) | C34A—O6—C35A—C36A | −57.9 (2) |
C16—N3—C15—C11 | −179.25 (12) | C33A—O5—C36A—C35A | −59.8 (3) |
O2—N4—C16—N3 | −1.23 (17) | O6—C35A—C36A—O5 | 59.3 (3) |
C15—N3—C16—N4 | 178.86 (12) | C36B—O5—C33B—C34B | −69.8 (9) |
C25—C17—C18—C19 | 0.65 (17) | C35B—O6—C34B—C33B | −71.7 (11) |
C27—C17—C18—C19 | −178.92 (11) | O5—C33B—C34B—O6 | 74.5 (11) |
C17—C18—C19—C20 | −0.10 (18) | C34B—O6—C35B—C36B | 65.7 (11) |
C18—C19—C20—C26 | 0.02 (19) | C33B—O5—C36B—C35B | 69.5 (10) |
C26—C21—C22—C23 | −1.0 (2) | O6—C35B—C36B—O5 | −67.7 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···N8 | 0.919 (19) | 1.92 (2) | 2.7733 (15) | 153.4 (18) |
O4—H4O···N4 | 0.93 (2) | 1.91 (2) | 2.7867 (15) | 157 (2) |
N3—H3N···O2 | 0.892 (16) | 2.195 (15) | 2.5413 (12) | 102.4 (12) |
N3—H3N···N2 | 0.892 (16) | 2.081 (17) | 2.7567 (15) | 131.7 (13) |
N7—H7N···O4 | 0.861 (16) | 2.200 (15) | 2.5337 (14) | 102.8 (13) |
N7—H7N···N6 | 0.861 (16) | 2.136 (17) | 2.7777 (16) | 130.9 (13) |
C4—H4···O4i | 0.93 | 2.50 | 3.0014 (16) | 114 |
C15—H15···N1ii | 0.93 | 2.60 | 3.4675 (18) | 155 |
C31—H31···N5iii | 0.93 | 2.45 | 3.3763 (17) | 175 |
C33A—H33A···Cg1 | 0.97 | 2.87 | 3.501 (3) | 123 |
C33A—H33B···Cg2iv | 0.97 | 2.93 | 3.804 (2) | 150 |
C34A—H34A···Cg3iv | 0.97 | 2.93 | 3.575 (2) | 125 |
C35A—H35A···Cg4i | 0.97 | 2.82 | 3.711 (2) | 153 |
C33B—H33C···Cg2iv | 0.97 | 2.73 | 3.528 (9) | 140 |
C35B—H35D···Cg4i | 0.97 | 2.69 | 3.408 (8) | 131 |
Symmetry codes: (i) x, −y, z+1/2; (ii) x, −y, z−1/2; (iii) x, −y+1, z+1/2; (iv) −x+1/2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C16H14N4O2·0.5C4H8O2 |
Mr | 338.37 |
Crystal system, space group | Monoclinic, C2/c |
Temperature (K) | 180 |
a, b, c (Å) | 25.0090 (8), 21.1940 (5), 14.5843 (4) |
β (°) | 119.8098 (9) |
V (Å3) | 6707.4 (3) |
Z | 16 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.40 × 0.20 × 0.09 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 59998, 9746, 6472 |
Rint | 0.049 |
(sin θ/λ)max (Å−1) | 0.703 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.047, 0.137, 1.06 |
No. of reflections | 9746 |
No. of parameters | 486 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.34, −0.26 |
Computer programs: PROCESS-AUTO (Rigaku/MSC, 2004), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), CrystalStructure (Rigaku/MSC, 2004) and PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···N8 | 0.919 (19) | 1.92 (2) | 2.7733 (15) | 153.4 (18) |
O4—H4O···N4 | 0.93 (2) | 1.91 (2) | 2.7867 (15) | 157 (2) |
N3—H3N···O2 | 0.892 (16) | 2.195 (15) | 2.5413 (12) | 102.4 (12) |
N3—H3N···N2 | 0.892 (16) | 2.081 (17) | 2.7567 (15) | 131.7 (13) |
N7—H7N···O4 | 0.861 (16) | 2.200 (15) | 2.5337 (14) | 102.8 (13) |
N7—H7N···N6 | 0.861 (16) | 2.136 (17) | 2.7777 (16) | 130.9 (13) |
C4—H4···O4i | 0.93 | 2.50 | 3.0014 (16) | 114 |
C15—H15···N1ii | 0.93 | 2.60 | 3.4675 (18) | 155 |
C31—H31···N5iii | 0.93 | 2.45 | 3.3763 (17) | 175 |
C33A—H33A···Cg1 | 0.97 | 2.87 | 3.501 (3) | 123 |
C33A—H33B···Cg2iv | 0.97 | 2.93 | 3.804 (2) | 150 |
C34A—H34A···Cg3iv | 0.97 | 2.93 | 3.575 (2) | 125 |
C35A—H35A···Cg4i | 0.97 | 2.82 | 3.711 (2) | 153 |
C33B—H33C···Cg2iv | 0.97 | 2.73 | 3.528 (9) | 140 |
C35B—H35D···Cg4i | 0.97 | 2.69 | 3.408 (8) | 131 |
Symmetry codes: (i) x, −y, z+1/2; (ii) x, −y, z−1/2; (iii) x, −y+1, z+1/2; (iv) −x+1/2, y−1/2, −z+1/2. |
Subscribe to Acta Crystallographica Section E: Crystallographic Communications
The full text of this article is available to subscribers to the journal.
- Information on subscribing
- Sample issue
- If you have already subscribed, you may need to register
As part of our investigation to prepare anti-advanced glycation end-product (AGEs) agents, we have developed a pyrimidine ring-opening reaction accompanied by the formation of a 1,2,4-oxadiazole ring by the reaction of various 4-pyrimidinylamidines or their amide oximes with hydroxylamine hydrochloride (Sasaki et al., 2001). The title compound, (I), was prepared for that purpose. A methanol solution of the compound on silica gel thin-layer chromatography (TLC) gave a single spot but it changed to two spots after one day, suggesting that the compound changed to an equilibrium mixture of two compounds. A methanol solution of the related compound, N-[5-(1-naphthyl)pyrimidin-4-yl]acetamide oxime, (II), which is a reaction substrate of the above reaction, has also shown a similar TLC phenomenon. Recently, we have determined the crystal structure of (II) by X-ray diffraction and interpreted this phenomenon in terms of two diastereomers of this compound caused by two sets of atropisomers which might exist in the methanol solution (Okuda et al., 2007). In the present study, an X-ray crystal structure analysis of (I) was undertaken in order to obtain fundamental information about the TLC phenomenon.
In the asymmetric unit of (I), there are two crystallographically independent oxime molecules, A and B (Fig. 1). Each molecule has intramolecular N—H···O and N—H···N hydrogen bonds (Table 1), which make non-H atoms in the N-[(Z)-2-(3-methyl[1,2,4]oxadiazol-5-yl)-2-ethenyl]formamide oxime unit approximately coplanar; mean deviations from the defined plane are 0.0410 (12) and 0.0399 (12) Å for molecules A and B, respectively. Although bond lengths and angles of both molecules are essentially the same, the conformation of molecule A about the C1—C11 bond axis is quite different from that of B about C17—C27 as shown by torsion angles C2—C1—C11—C15 = 64.28 (17)° and C18—C17—C27—C31 = 122.24 (13)°. The dihedral angles between the naphthalene and the N-[(Z)-2-(3-methyl[1,2,4]oxadiazol-5-yl)-2-ethenyl]formamide oxime plane are 68.60 (2) and 57.88 (2)° for molecules A and B, respectively. Molecular orbital calculations at the HF/6–31 G** level of theory starting from geometries of A and B gave the same structure, the optimized torsion angle corresponding to C2—C1—C11—C15 or C18—C17—C27—C31 being 73.66°. The other stable structure was obtained as an atropisomer, the torsion angle being -73.66°.
In the crystal structure of (I), molecules A and B are connected to each other by O—H···N hydrogen bonds to form a dimer. Neighboring dimers related by a c glide plane are linked via C—H···O and C—H···N interactions, giving a molecular layer extending parallel to the (100) plane (Fig. 2). Adjacent layers are linked through a π-π stacking interaction between oxadiazole O1/N1/C13/N2/C12 rings which are approximately parallel to each other, forming a double layer structure (Fig. 3). The centroid-centroid [Cg1···Cg1v; symmetry code: (v) 1 - x, y, 3/2 - z] distance of the oxadiazole rings is 3.6234 (9) Å and the dihedral angle between the rings is 8.90 (6)°; the shortest distance is N2···C13v 3.398 (2) Å. The 1,4-dioxane molecules are placed in the void space between the molecular double layers (Fig. 3) and bound weakly through C—H···π interactions.
The oxime molecule of (I) gives only a set of atropisomers, which give the same spot on TLC. Therefore, for (I) we propose a different mechanism of the TLC phenomenon than we proposed for (II), based on the molecular structure. As shown in Fig. 4, in a methanol solution, equilibriation between compounds (Ia) and (Ib) is possible. We suggest the new spot on silica gel TLC is derived from (Ib). The compound, (Ib), is stable in the gas phase as confirmed by molecular orbital calculations at HF/6–31 G** and B3LYP/6–311 G** levels of theory, but the electric energy of (Ib) is much higher than that of (Ia). The differences between (Ia) and (Ib) calculated by B3LYP/6–311 G** and HF/6–31 G** are 56.64 and 70.49 kJ mol-1, respectively, which might be reduced in a methanol solution but could govern the crystallized product. The oxime fragment of (Ib) is planar and intramolecular N—H···N and N—H···O hydrogen bonds are observed (N—H 1.041, H···N 1.806, N···N 2.581 Å and N—H···N 128.00°; N—H 1.041, H···O 2.755, N···O 3.774 Å and N—H···O 166.00° calculated by B3LYP/6–311 G**).