research communications
Crystal structures of (E)-2-amino-4-methylsulfanyl-6-oxo-1-(1-phenylethylideneamino)-1,6-dihydropyrimidine-5-carbonitrile and (E)-2-amino-4-methylsulfanyl-6-oxo-1-[1-(pyridin-2-yl)ethylideneamino]-1,6-dihydropyrimidine-5-carbonitrile
aChemistry of Natural & Microbial Products Department, National Research Center, Cairo, Egypt, bChemistry Department, Faculty of Science, Helwan University, Cairo, Egypt, and cInstitut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, D-38106 Braunschweig, Germany
*Correspondence e-mail: p.jones@tu-bs.de
The title compounds 3a, C14H13N5OS, and 3b, C13H12N6OS, both show an E configuration about the N=C bond and a planar NH2 group. The molecules, which only differ in the presence of a phenyl (in 3a) or pyridyl (in 3b) substituent, are closely similar except for the different orientations of these groups. The amino hydrogen atoms form classical hydrogen bonds; in 3a the acceptors are the oxygen atom and the cyano nitrogen atom, leading to ribbons of molecules parallel to the b axis, whereas in 3b the acceptors are the oxygen atom and the pyridyl nitrogen, leading to a layer structure perpendicular to (01).
Keywords: crystal structure; pyrimidinones; hydrogen bonds.
1. Chemical context
Dimethyl N-cyanodithioiminocarbonate (2) is an important starting material for the synthesis of various classes of heterocycles (Elgemeie & Mohamed, 2014), e.g. azoles, and azoloazines (Thomae et al., 2009). It has been used effectively in the synthesis of a range of antibacterial (Paget et al., 2006), anticancer (Hu et al., 2014) and other biologically significant products (Marsault et al., 2007).
Pyrimidinones are multipurpose et al., 2019; Elgemeie & Mohamed, 2019); they are important in pharmaceutical chemistry because of their pharmacological potential (Galmarini et al., 2003). Research in the pharmaceutical chemistry of pyrimidone derivatives has become an active field, since several pyrimidinone-based compounds have been extensively used as clinical drugs to treat numerous types of viruses with high therapeutic effectiveness (Simons et al., 2005); their biotic profile and synthetic availability have been attractive in their design and development as possible chemotherapeutics. In particular, pyrimidinone derivatives have recently become significant in the improvement of anti-coronavirus agents (Pruijssers et al., 2019).
that are common in and find diverse applications in drug planning (ElgemeieIn order to access this class of compounds, a variety of new synthetic methods has been developed (Xu et al., 2004). Recently, we have designed the syntheses of several pyrimidinone derivatives starting from activated (Elgemeie et al., 2015a,b; Abu-Zaied et al., 2020, 2021). As part of this program, the reactions of 2-cyano-N′-(1-phenylethylidene)acetohydrazide (1a) or 2-cyano-N′-(1-(pyridin-2-yl)ethylidene)acetohydrazide (1b) with 2 in KOH/EtOH were studied. These reactions gave products that were crystallized from DMF and identified by X-ray crystallography as the title compounds (3a,b). 1H NMR spectra of 3a showed SCH3 protons at δ 2.55 ppm and the free NH2 protons at δ 8.52 ppm. The formation of 3 from 1 and 2 is assumed to proceed via initial addition of the active methylene group of 1 to the double bond of 2, followed by elimination of CH3SH and via addition of the NH group to the cyano group.
2. Structural commentary
The structure determinations confirm the expected chemical structures of 3a and 3b; the respective molecules are shown in Figs. 1 and 2. In both compounds, the configuration about the double bond N2=C7 is E and the amino group is planar. The pyrimidine ring dimensions are closely similar; e.g. the shortest bonds are C2—N3, the narrowest angles are at C6 (which bears the oxo substituent) and the widest angles are at C4 (which bears the methylthio group). These and a selection of other dimensions are presented in Tables 1 and 2.
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The compounds differ chemically only in the phenyl/pyridyl substituents. A least-squares fit of the two molecules shows a moderate difference in the orientation of these groups (Fig. 3, Tables 1 and 2); this may be associated with the role of the pyridyl nitrogen as a hydrogen-bond acceptor in 3b (see below).
Whereas the immediate substituent atoms of the pyrimidine rings lie close to the ring plane for 3a [maximum deviation of 0.103 (2) Å for N6], the substituents O1 and C15 of 3b are more significantly displaced [by 0.203 (2) and 0.179 (3) Å, respectively, to the same side of the ring]. The interplanar angles between the six-membered rings are 56.49 (6)° for 3a and 63.12 (3)° for 3b.
Intramolecular hydrogen bonds N6—H062⋯N2 (not shown explicitly in Figs. 1 and 2) are observed in both molecules (Tables 3 and 4).
3. Supramolecular features
In both structures, the hydrogen atoms of the amino groups act as hydrogen bond donors (Tables 3 and 4). In 3a, neighbouring molecules are connected via the same 21 operator, leading to ribbons of molecules parallel to the b axis (Fig. 4). In 3b, one hydrogen bond is formed via a 21 and one via an n glide operator, leading to layers parallel to (01) (Fig. 5).
4. Database survey
A search of the Cambridge Database (ConQuest Version 2.0.5) for 6-oxopyrimidines with the same substitution pattern (N at C2, S at C4, cyano at C5 and N at N1) revealed only our previous structures (Elgemeie et al., 2015a,b; refcodes WUSMAA and WUSMUU); the substituents at N1 were NH-SO2-p-C6H4Br and N=CH-2-tht, respectively.
5. Synthesis and crystallization
General procedure for the synthesis of compounds 3: A mixture of the appropriate 2-cyano-N′-(1-arylethylidene)acetohydrazide (1) (0.01 mol), dimethyl N-cyanodithioiminocarbonate (2) (0.01 mol) and anhydrous potassium hydroxide (0.01 mol) was refluxed in ethanol (10 mL). The reaction mixture was then poured onto ice–water; the solid product thus formed was filtered off and recrystallized from DMF.
3a: According to the general procedure, 2-cyano-N′-(1-phenylethylidene)acetohydrazide (1a) was refluxed with 2 for 3 h. Compound 3a was afforded as a pale-yellow solid (92%); m.p. 498–501 K; IR (cm−1) υ 3719 and 3437 (NH2), 2202 (CN) and 1657 (C=O). 1H NMR (400 MHz, DMSO-d6): δ 2.20 (s, 3H, CH3), 2.55 (s, 3H, SCH3), 8.52 (s, br, 2H, NH2), 8.045–8.065 (d, J = 8 Hz, 2H, 2 CH), 7.59–7.62 (m, 1H, CH), 7.50–7.54 (m, 2H, 2 CH). Analysis calculated for C14H13N5OS (299.35): C, 56.17; H, 4.38; N, 23.40; O, 5.34; S, 10.71%. Found: C, 55.89; H, 4.25; N, 23.15; S, 10.52%.
3b: According to the general procedure, 2-cyano-N′-(1-(pyridin-2-yl)ethylidene)acetohydrazide (1b) was refluxed with 2 for 30 min. Compound 3b was afforded as a buff solid (80%); m.p. 649–652 K; IR (cm−1) υ 3774 (NH2), 2172 (CN) and 1635 (C=O). 1H NMR (400 MHz, DMSO-d6): δ 2.20 (s, 3H, CH3), 2.51 (s, 3H, SCH3), 8.54 (s, br, 2H, NH2), 8.73–8.74 (d, J = 4 Hz, 1H, CH), 8.29–8.31 (d, J = 8 Hz, 1H, CH), 7.95–8.00 (t, 1H, CH); 7.59–7.63 (t, J = 8 Hz, 1H, CH). Analysis calculated for C13H12N6OS (300.34): C, 51.99; H, 4.03; N, 27.98; O, 5.33; S, 10.68. Found: C, 51.73; H, 4.22; N, 27.71; S, 10.39%.
Crystals of 3a proved to be almost all twinned, by 180° rotation about c*. Data were collected from a twinned crystal, but the using the `HKLF 5' method was no better than satisfactory (wR2 ca 0.11). Finally, an untwinned crystal was discovered. Despite its less regular reflection shape, the results proved to be slightly better in terms of the wR2 value, and the results quoted here are for this untwinned crystal.
6. Refinement
Crystal data, data collection and structure . The NH hydrogen atoms were refined freely. The methyl groups were refined as idealized rigid groups allowed to rotate but not tip (AFIX 137; C—H 0.98 Å, H—C—H 109.5 °). The hydrogens of the aromatic rings were included using a riding model starting from calculated positions (C—Haromatic 0.95 Å). The U(H) values were fixed at 1.5 (for the methyl H) or 1.2 times the equivalent Uiso value of the parent carbon atoms.
details are summarized in Table 5
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Supporting information
https://doi.org/10.1107/S2056989021004126/jy2007sup1.cif
contains datablocks 3a, 3b, global. DOI:Structure factors: contains datablock 3a. DOI: https://doi.org/10.1107/S2056989021004126/jy20073asup2.hkl
Structure factors: contains datablock 3b. DOI: https://doi.org/10.1107/S2056989021004126/jy20073bsup3.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989021004126/jy20073asup4.cml
For both structures, data collection: CrysAlis PRO (Rigaku OD, 2021); cell
CrysAlis PRO (Rigaku OD, 2021); data reduction: CrysAlis PRO (Rigaku OD, 2021); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: XP (Siemens, 1994); software used to prepare material for publication: SHELXL2018/3 (Sheldrick, 2015b).C14H13N5OS | F(000) = 624 |
Mr = 299.35 | Dx = 1.425 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 12.15369 (18) Å | Cell parameters from 58984 reflections |
b = 14.9466 (2) Å | θ = 3.6–77.1° |
c = 7.68691 (16) Å | µ = 2.12 mm−1 |
β = 91.7607 (16)° | T = 100 K |
V = 1395.72 (4) Å3 | Plate, pale yellow |
Z = 4 | 0.2 × 0.2 × 0.02 mm |
Rigaku XtaLAB Synergy, Single source at home/near, HyPix diffractometer | 2958 independent reflections |
Radiation source: micro-focus sealed X-ray tube | 2842 reflections with I > 2σ(I) |
Detector resolution: 10.0000 pixels mm-1 | Rint = 0.061 |
ω scans | θmax = 77.7°, θmin = 3.6° |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021) | h = −15→15 |
Tmin = 0.636, Tmax = 1.000 | k = −18→18 |
104992 measured reflections | l = −9→9 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.040 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.106 | w = 1/[σ2(Fo2) + (0.0516P)2 + 0.8822P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max = 0.001 |
2958 reflections | Δρmax = 0.40 e Å−3 |
200 parameters | Δρmin = −0.35 e Å−3 |
0 restraints |
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. Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) 5.1729 (0.0067) x - 0.7702 (0.0093) y + 6.8408 (0.0022) z = 3.9095 (0.0048) * -0.0400 (0.0011) N1 * 0.0328 (0.0011) C2 * -0.0019 (0.0010) N3 * -0.0193 (0.0011) C4 * 0.0105 (0.0011) C5 * 0.0178 (0.0010) C6 0.0930 (0.0023) N2 0.1026 (0.0023) N6 -0.0462 (0.0020) S1 -0.0028 (0.0025) C15 0.0557 (0.0021) O1 Rms deviation of fitted atoms = 0.0241 - 2.6471 (0.0093) x + 12.8703 (0.0066) y - 3.4786 (0.0058) z = 3.0019 (0.0051) Angle to previous plane (with approximate esd) = 56.485 ( 0.063 ) * -0.0047 (0.0012) C9 * 0.0009 (0.0013) C10 * 0.0043 (0.0015) C11 * -0.0056 (0.0015) C12 * 0.0016 (0.0015) C13 * 0.0034 (0.0013) C14 Rms deviation of fitted atoms = 0.0038 |
x | y | z | Uiso*/Ueq | ||
N1 | 0.47431 (10) | 0.36271 (8) | 0.24782 (18) | 0.0248 (3) | |
N2 | 0.37697 (11) | 0.37729 (8) | 0.34251 (18) | 0.0264 (3) | |
C2 | 0.53906 (13) | 0.43583 (10) | 0.2177 (2) | 0.0253 (3) | |
N6 | 0.50093 (13) | 0.51489 (9) | 0.2657 (2) | 0.0299 (3) | |
H061 | 0.5387 (18) | 0.5609 (17) | 0.251 (3) | 0.043 (6)* | |
H062 | 0.441 (2) | 0.5174 (16) | 0.319 (3) | 0.050 (7)* | |
N3 | 0.63513 (11) | 0.43021 (8) | 0.13939 (17) | 0.0252 (3) | |
C4 | 0.67045 (12) | 0.34825 (10) | 0.1009 (2) | 0.0240 (3) | |
S1 | 0.79679 (3) | 0.33529 (3) | −0.00002 (6) | 0.03105 (14) | |
C5 | 0.61368 (12) | 0.26976 (9) | 0.1394 (2) | 0.0238 (3) | |
C6 | 0.50952 (13) | 0.27387 (9) | 0.2196 (2) | 0.0241 (3) | |
O1 | 0.45193 (9) | 0.21063 (7) | 0.26161 (15) | 0.0286 (3) | |
C7 | 0.28666 (13) | 0.35750 (9) | 0.2578 (2) | 0.0260 (3) | |
C8 | 0.27945 (15) | 0.32587 (13) | 0.0737 (2) | 0.0376 (4) | |
H8A | 0.343475 | 0.347475 | 0.011570 | 0.056* | |
H8B | 0.211966 | 0.349048 | 0.017032 | 0.056* | |
H8C | 0.278191 | 0.260323 | 0.071499 | 0.056* | |
C9 | 0.18442 (13) | 0.36712 (10) | 0.3563 (2) | 0.0275 (3) | |
C10 | 0.08665 (16) | 0.33019 (13) | 0.2925 (3) | 0.0387 (4) | |
H10 | 0.084914 | 0.300421 | 0.183268 | 0.046* | |
C11 | −0.00923 (16) | 0.33629 (15) | 0.3871 (3) | 0.0472 (5) | |
H11 | −0.075770 | 0.310997 | 0.341450 | 0.057* | |
C12 | −0.00802 (16) | 0.37845 (15) | 0.5449 (3) | 0.0459 (5) | |
H12 | −0.073084 | 0.381751 | 0.610018 | 0.055* | |
C13 | 0.08929 (16) | 0.41639 (15) | 0.6092 (3) | 0.0458 (5) | |
H13 | 0.090130 | 0.446323 | 0.718242 | 0.055* | |
C14 | 0.18491 (15) | 0.41128 (12) | 0.5170 (2) | 0.0351 (4) | |
H14 | 0.250819 | 0.437667 | 0.562552 | 0.042* | |
N4 | 0.68678 (12) | 0.11352 (9) | 0.0616 (2) | 0.0315 (3) | |
C15 | 0.65497 (12) | 0.18367 (10) | 0.0965 (2) | 0.0256 (3) | |
C16 | 0.83220 (16) | 0.44877 (12) | −0.0485 (3) | 0.0419 (4) | |
H16A | 0.792700 | 0.467742 | −0.155236 | 0.063* | |
H16B | 0.911681 | 0.453120 | −0.064728 | 0.063* | |
H16C | 0.811591 | 0.487512 | 0.048102 | 0.063* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0263 (6) | 0.0142 (6) | 0.0343 (7) | 0.0000 (5) | 0.0071 (5) | −0.0012 (5) |
N2 | 0.0272 (6) | 0.0182 (6) | 0.0342 (7) | 0.0009 (5) | 0.0066 (5) | −0.0017 (5) |
C2 | 0.0304 (8) | 0.0157 (7) | 0.0300 (8) | −0.0013 (6) | 0.0013 (6) | 0.0014 (6) |
N6 | 0.0334 (7) | 0.0140 (6) | 0.0427 (8) | −0.0005 (5) | 0.0080 (6) | −0.0015 (5) |
N3 | 0.0277 (6) | 0.0172 (6) | 0.0307 (7) | −0.0014 (5) | 0.0036 (5) | 0.0010 (5) |
C4 | 0.0250 (7) | 0.0202 (7) | 0.0268 (8) | −0.0008 (5) | 0.0001 (6) | 0.0017 (6) |
S1 | 0.0273 (2) | 0.0258 (2) | 0.0404 (3) | 0.00045 (14) | 0.00645 (16) | 0.00140 (15) |
C5 | 0.0268 (7) | 0.0155 (7) | 0.0292 (8) | 0.0015 (5) | 0.0020 (6) | 0.0003 (5) |
C6 | 0.0281 (7) | 0.0151 (6) | 0.0293 (8) | 0.0011 (5) | 0.0024 (6) | 0.0004 (5) |
O1 | 0.0321 (6) | 0.0147 (5) | 0.0395 (6) | −0.0013 (4) | 0.0085 (5) | 0.0017 (4) |
C7 | 0.0326 (8) | 0.0133 (6) | 0.0323 (8) | 0.0012 (6) | 0.0022 (6) | 0.0009 (6) |
C8 | 0.0372 (9) | 0.0407 (10) | 0.0347 (9) | 0.0056 (7) | −0.0016 (7) | −0.0074 (7) |
C9 | 0.0293 (8) | 0.0177 (7) | 0.0357 (8) | 0.0006 (6) | 0.0024 (6) | 0.0042 (6) |
C10 | 0.0386 (10) | 0.0376 (10) | 0.0398 (10) | −0.0085 (7) | −0.0007 (8) | 0.0043 (8) |
C11 | 0.0309 (9) | 0.0582 (13) | 0.0523 (12) | −0.0121 (8) | −0.0017 (8) | 0.0152 (10) |
C12 | 0.0310 (9) | 0.0529 (12) | 0.0544 (12) | 0.0046 (8) | 0.0113 (8) | 0.0105 (9) |
C13 | 0.0400 (10) | 0.0495 (11) | 0.0485 (11) | 0.0038 (9) | 0.0118 (8) | −0.0079 (9) |
C14 | 0.0317 (8) | 0.0314 (8) | 0.0423 (10) | 0.0003 (7) | 0.0055 (7) | −0.0062 (7) |
N4 | 0.0328 (7) | 0.0215 (7) | 0.0404 (8) | 0.0024 (5) | 0.0059 (6) | 0.0005 (6) |
C15 | 0.0254 (7) | 0.0206 (7) | 0.0310 (8) | −0.0006 (6) | 0.0029 (6) | 0.0020 (6) |
C16 | 0.0404 (10) | 0.0290 (9) | 0.0571 (12) | −0.0104 (7) | 0.0146 (8) | −0.0067 (8) |
N1—C2 | 1.3705 (19) | C11—C12 | 1.367 (3) |
N1—C6 | 1.4138 (18) | C12—C13 | 1.389 (3) |
N1—N2 | 1.4248 (17) | C13—C14 | 1.382 (3) |
N2—C7 | 1.293 (2) | N4—C15 | 1.152 (2) |
C2—N6 | 1.326 (2) | N6—H061 | 0.84 (2) |
C2—N3 | 1.333 (2) | N6—H062 | 0.84 (2) |
N3—C4 | 1.3343 (19) | C8—H8A | 0.9800 |
C4—C5 | 1.397 (2) | C8—H8B | 0.9800 |
C4—S1 | 1.7522 (16) | C8—H8C | 0.9800 |
S1—C16 | 1.7918 (19) | C10—H10 | 0.9500 |
C5—C15 | 1.424 (2) | C11—H11 | 0.9500 |
C5—C6 | 1.427 (2) | C12—H12 | 0.9500 |
C6—O1 | 1.2253 (18) | C13—H13 | 0.9500 |
C7—C9 | 1.482 (2) | C14—H14 | 0.9500 |
C7—C8 | 1.492 (2) | C16—H16A | 0.9800 |
C9—C10 | 1.386 (2) | C16—H16B | 0.9800 |
C9—C14 | 1.401 (2) | C16—H16C | 0.9800 |
C10—C11 | 1.395 (3) | ||
C2—N1—C6 | 123.03 (13) | C13—C14—C9 | 119.84 (17) |
C2—N1—N2 | 117.02 (12) | N4—C15—C5 | 178.96 (16) |
C6—N1—N2 | 118.81 (11) | C2—N6—H061 | 120.0 (16) |
C7—N2—N1 | 114.40 (13) | C2—N6—H062 | 119.2 (17) |
N6—C2—N3 | 120.02 (14) | H061—N6—H062 | 121 (2) |
N6—C2—N1 | 117.16 (14) | C7—C8—H8A | 109.5 |
N3—C2—N1 | 122.79 (13) | C7—C8—H8B | 109.5 |
C2—N3—C4 | 116.77 (13) | H8A—C8—H8B | 109.5 |
N3—C4—C5 | 124.02 (14) | C7—C8—H8C | 109.5 |
N3—C4—S1 | 119.47 (11) | H8A—C8—H8C | 109.5 |
C5—C4—S1 | 116.49 (11) | H8B—C8—H8C | 109.5 |
C4—S1—C16 | 101.93 (8) | C9—C10—H10 | 119.7 |
C4—C5—C15 | 122.01 (14) | C11—C10—H10 | 119.7 |
C4—C5—C6 | 120.40 (13) | C12—C11—H11 | 119.8 |
C15—C5—C6 | 117.57 (13) | C10—C11—H11 | 119.8 |
O1—C6—N1 | 120.40 (13) | C11—C12—H12 | 120.3 |
O1—C6—C5 | 127.05 (13) | C13—C12—H12 | 120.3 |
N1—C6—C5 | 112.55 (12) | C14—C13—H13 | 119.5 |
N2—C7—C9 | 115.63 (14) | C12—C13—H13 | 119.5 |
N2—C7—C8 | 125.04 (15) | C13—C14—H14 | 120.1 |
C9—C7—C8 | 119.32 (15) | C9—C14—H14 | 120.1 |
C10—C9—C14 | 118.69 (16) | S1—C16—H16A | 109.5 |
C10—C9—C7 | 120.25 (16) | S1—C16—H16B | 109.5 |
C14—C9—C7 | 121.04 (15) | H16A—C16—H16B | 109.5 |
C9—C10—C11 | 120.68 (19) | S1—C16—H16C | 109.5 |
C12—C11—C10 | 120.41 (18) | H16A—C16—H16C | 109.5 |
C11—C12—C13 | 119.33 (18) | H16B—C16—H16C | 109.5 |
C14—C13—C12 | 121.04 (19) | ||
C2—N1—N2—C7 | 118.94 (15) | N2—N1—C6—C5 | −173.87 (13) |
C6—N1—N2—C7 | −72.88 (18) | C4—C5—C6—O1 | −179.25 (16) |
C6—N1—C2—N6 | −173.38 (14) | C15—C5—C6—O1 | 2.5 (3) |
N2—N1—C2—N6 | −5.7 (2) | C4—C5—C6—N1 | 1.4 (2) |
C6—N1—C2—N3 | 8.5 (2) | C15—C5—C6—N1 | −176.89 (14) |
N2—N1—C2—N3 | 176.15 (14) | N1—N2—C7—C9 | 176.69 (12) |
N6—C2—N3—C4 | 177.46 (15) | N1—N2—C7—C8 | −2.8 (2) |
N1—C2—N3—C4 | −4.5 (2) | N2—C7—C9—C10 | −166.23 (15) |
C2—N3—C4—C5 | −0.7 (2) | C8—C7—C9—C10 | 13.2 (2) |
C2—N3—C4—S1 | −179.30 (11) | N2—C7—C9—C14 | 12.1 (2) |
N3—C4—S1—C16 | −7.90 (16) | C8—C7—C9—C14 | −168.47 (16) |
C5—C4—S1—C16 | 173.40 (13) | C14—C9—C10—C11 | −0.5 (3) |
N3—C4—C5—C15 | −179.67 (15) | C7—C9—C10—C11 | 177.85 (16) |
S1—C4—C5—C15 | −1.0 (2) | C9—C10—C11—C12 | −0.4 (3) |
N3—C4—C5—C6 | 2.1 (3) | C10—C11—C12—C13 | 1.0 (3) |
S1—C4—C5—C6 | −179.25 (12) | C11—C12—C13—C14 | −0.7 (3) |
C2—N1—C6—O1 | 174.16 (15) | C12—C13—C14—C9 | −0.1 (3) |
N2—N1—C6—O1 | 6.7 (2) | C10—C9—C14—C13 | 0.7 (3) |
C2—N1—C6—C5 | −6.5 (2) | C7—C9—C14—C13 | −177.59 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H061···O1i | 0.84 (2) | 2.24 (3) | 2.9899 (17) | 149 (2) |
N6—H062···N4i | 0.84 (2) | 2.33 (2) | 3.054 (2) | 144 (2) |
C8—H8A···O1ii | 0.98 | 2.52 | 3.279 (2) | 134 |
N6—H062···N2 | 0.84 (2) | 2.25 (2) | 2.6273 (19) | 108 (2) |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) x, −y+1/2, z−1/2. |
C13H12N6OS | F(000) = 624 |
Mr = 300.35 | Dx = 1.460 Mg m−3 |
Monoclinic, P21/n | Cu Kα radiation, λ = 1.54184 Å |
a = 13.4774 (5) Å | Cell parameters from 27720 reflections |
b = 7.6797 (3) Å | θ = 3.9–77.3° |
c = 14.2755 (6) Å | µ = 2.19 mm−1 |
β = 112.401 (5)° | T = 100 K |
V = 1366.04 (10) Å3 | Plate, orange |
Z = 4 | 0.12 × 0.08 × 0.02 mm |
Rigaku XtaLAB Synergy, Single source at home/near, HyPix diffractometer | 2905 independent reflections |
Radiation source: micro-focus sealed X-ray tube | 2813 reflections with I > 2σ(I) |
Detector resolution: 10.0000 pixels mm-1 | Rint = 0.042 |
ω scans | θmax = 77.6°, θmin = 3.8° |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021) | h = −17→17 |
Tmin = 0.782, Tmax = 1.000 | k = −9→9 |
54131 measured reflections | l = −18→18 |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.036 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.097 | w = 1/[σ2(Fo2) + (0.0483P)2 + 0.8192P] where P = (Fo2 + 2Fc2)/3 |
S = 1.07 | (Δ/σ)max = 0.001 |
2905 reflections | Δρmax = 0.33 e Å−3 |
200 parameters | Δρmin = −0.39 e Å−3 |
0 restraints |
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. Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane) - 6.6755 (0.0064) x + 6.5784 (0.0022) y + 0.7860 (0.0078) z = 2.0405 (0.0036) * 0.0570 (0.0009) N1 * -0.0128 (0.0009) C2 * -0.0287 (0.0009) N3 * 0.0218 (0.0009) C4 * 0.0224 (0.0009) C5 * -0.0598 (0.0009) C6 -0.2034 (0.0018) O1 -0.1436 (0.0019) N2 -0.0415 (0.0019) N6 0.0815 (0.0018) S1 -0.1786 (0.0031) C15 Rms deviation of fitted atoms = 0.0383 6.7262 (0.0067) x + 6.5062 (0.0024) y - 0.3110 (0.0086) z = 4.9821 (0.0009) Angle to previous plane (with approximate esd) = 63.117 ( 0.033 ) * -0.0062 (0.0009) C9 * -0.0031 (0.0009) N5 * 0.0095 (0.0010) C10 * -0.0064 (0.0011) C11 * -0.0026 (0.0011) C12 * 0.0087 (0.0010) C13 Rms deviation of fitted atoms = 0.0066 |
x | y | z | Uiso*/Ueq | ||
N1 | 0.24070 (9) | 0.52162 (15) | 0.34716 (8) | 0.0181 (2) | |
N2 | 0.25298 (10) | 0.51485 (15) | 0.25281 (9) | 0.0200 (2) | |
C2 | 0.32652 (10) | 0.58859 (17) | 0.42667 (10) | 0.0180 (3) | |
N6 | 0.40369 (9) | 0.66515 (16) | 0.40482 (9) | 0.0210 (2) | |
H061 | 0.4563 (16) | 0.711 (3) | 0.4535 (15) | 0.034 (5)* | |
H062 | 0.3927 (14) | 0.680 (2) | 0.3424 (15) | 0.026 (4)* | |
N3 | 0.33350 (9) | 0.58187 (16) | 0.52197 (8) | 0.0202 (2) | |
C4 | 0.25208 (11) | 0.50497 (18) | 0.53832 (10) | 0.0211 (3) | |
S1 | 0.25540 (3) | 0.50264 (6) | 0.66187 (3) | 0.03285 (13) | |
C5 | 0.16475 (10) | 0.42545 (18) | 0.46300 (10) | 0.0202 (3) | |
C6 | 0.15960 (10) | 0.41990 (17) | 0.36111 (10) | 0.0186 (3) | |
O1 | 0.09466 (7) | 0.34075 (13) | 0.28923 (7) | 0.0216 (2) | |
C7 | 0.17715 (10) | 0.58645 (17) | 0.17779 (10) | 0.0182 (3) | |
C8 | 0.08130 (10) | 0.68105 (18) | 0.17933 (10) | 0.0201 (3) | |
H8A | 0.016282 | 0.615319 | 0.140383 | 0.030* | |
H8B | 0.077686 | 0.796660 | 0.149146 | 0.030* | |
H8C | 0.086858 | 0.693400 | 0.249489 | 0.030* | |
C9 | 0.19145 (10) | 0.57067 (17) | 0.07948 (10) | 0.0189 (3) | |
N5 | 0.11472 (9) | 0.64664 (16) | −0.00075 (8) | 0.0220 (3) | |
C10 | 0.12509 (11) | 0.6336 (2) | −0.09027 (11) | 0.0259 (3) | |
H10 | 0.072632 | 0.688318 | −0.147422 | 0.031* | |
C11 | 0.20768 (12) | 0.5451 (2) | −0.10409 (11) | 0.0279 (3) | |
H11 | 0.210358 | 0.537126 | −0.169500 | 0.034* | |
C12 | 0.28675 (12) | 0.4679 (2) | −0.02112 (12) | 0.0262 (3) | |
H12 | 0.344761 | 0.406811 | −0.028270 | 0.031* | |
C13 | 0.27859 (11) | 0.48252 (18) | 0.07219 (11) | 0.0227 (3) | |
H13 | 0.331879 | 0.432958 | 0.130782 | 0.027* | |
C14 | 0.08272 (11) | 0.33814 (19) | 0.48529 (10) | 0.0227 (3) | |
N4 | 0.01756 (10) | 0.26795 (19) | 0.50465 (10) | 0.0308 (3) | |
C15 | 0.38704 (14) | 0.5880 (3) | 0.73425 (12) | 0.0390 (4) | |
H15A | 0.393874 | 0.704706 | 0.709543 | 0.058* | |
H15B | 0.441562 | 0.511218 | 0.726668 | 0.058* | |
H15C | 0.397265 | 0.594636 | 0.805906 | 0.058* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0166 (5) | 0.0247 (6) | 0.0125 (5) | 0.0003 (4) | 0.0049 (4) | 0.0006 (4) |
N2 | 0.0198 (5) | 0.0264 (6) | 0.0136 (5) | 0.0002 (4) | 0.0064 (4) | −0.0001 (4) |
C2 | 0.0157 (6) | 0.0207 (6) | 0.0162 (6) | 0.0028 (5) | 0.0045 (5) | 0.0002 (5) |
N6 | 0.0180 (5) | 0.0300 (6) | 0.0141 (5) | −0.0032 (5) | 0.0051 (4) | −0.0004 (5) |
N3 | 0.0187 (5) | 0.0270 (6) | 0.0146 (5) | −0.0012 (4) | 0.0059 (4) | 0.0002 (4) |
C4 | 0.0206 (6) | 0.0266 (7) | 0.0161 (6) | −0.0004 (5) | 0.0071 (5) | 0.0005 (5) |
S1 | 0.0295 (2) | 0.0535 (3) | 0.0176 (2) | −0.01433 (17) | 0.01126 (16) | −0.00596 (15) |
C5 | 0.0181 (6) | 0.0250 (7) | 0.0177 (6) | −0.0004 (5) | 0.0068 (5) | 0.0009 (5) |
C6 | 0.0153 (6) | 0.0214 (6) | 0.0172 (6) | 0.0028 (5) | 0.0040 (5) | 0.0017 (5) |
O1 | 0.0189 (4) | 0.0266 (5) | 0.0164 (4) | −0.0019 (4) | 0.0034 (4) | −0.0010 (4) |
C7 | 0.0172 (6) | 0.0201 (6) | 0.0162 (6) | −0.0032 (5) | 0.0050 (5) | −0.0006 (5) |
C8 | 0.0185 (6) | 0.0232 (6) | 0.0173 (6) | 0.0008 (5) | 0.0053 (5) | 0.0010 (5) |
C9 | 0.0183 (6) | 0.0204 (6) | 0.0171 (6) | −0.0035 (5) | 0.0059 (5) | −0.0020 (5) |
N5 | 0.0177 (5) | 0.0300 (6) | 0.0164 (5) | −0.0025 (5) | 0.0042 (4) | 0.0001 (4) |
C10 | 0.0208 (6) | 0.0387 (8) | 0.0156 (6) | −0.0042 (6) | 0.0041 (5) | 0.0003 (6) |
C11 | 0.0279 (7) | 0.0399 (8) | 0.0175 (6) | −0.0050 (6) | 0.0102 (6) | −0.0047 (6) |
C12 | 0.0254 (7) | 0.0300 (7) | 0.0262 (7) | −0.0011 (6) | 0.0133 (6) | −0.0040 (6) |
C13 | 0.0223 (7) | 0.0239 (7) | 0.0215 (7) | 0.0002 (5) | 0.0077 (5) | 0.0012 (5) |
C14 | 0.0208 (6) | 0.0270 (7) | 0.0191 (6) | −0.0003 (5) | 0.0061 (5) | 0.0000 (5) |
N4 | 0.0256 (6) | 0.0353 (7) | 0.0330 (7) | −0.0034 (5) | 0.0128 (5) | 0.0028 (6) |
C15 | 0.0344 (8) | 0.0639 (12) | 0.0189 (7) | −0.0177 (8) | 0.0104 (6) | −0.0091 (7) |
N1—C2 | 1.3747 (17) | N5—C10 | 1.3412 (18) |
N1—C6 | 1.4179 (17) | C10—C11 | 1.381 (2) |
N1—N2 | 1.4191 (16) | C11—C12 | 1.389 (2) |
N2—C7 | 1.2883 (18) | C12—C13 | 1.382 (2) |
C2—N3 | 1.3286 (17) | C14—N4 | 1.1503 (19) |
C2—N6 | 1.3312 (17) | N6—H061 | 0.86 (2) |
N3—C4 | 1.3425 (17) | N6—H062 | 0.853 (19) |
C4—C5 | 1.3963 (19) | C8—H8A | 0.9800 |
C4—S1 | 1.7473 (14) | C8—H8B | 0.9800 |
S1—C15 | 1.8023 (16) | C8—H8C | 0.9800 |
C5—C14 | 1.4287 (18) | C10—H10 | 0.9500 |
C5—C6 | 1.4303 (18) | C11—H11 | 0.9500 |
C6—O1 | 1.2263 (16) | C12—H12 | 0.9500 |
C7—C8 | 1.4896 (18) | C13—H13 | 0.9500 |
C7—C9 | 1.4925 (17) | C15—H15A | 0.9800 |
C9—N5 | 1.3486 (17) | C15—H15B | 0.9800 |
C9—C13 | 1.3934 (19) | C15—H15C | 0.9800 |
C2—N1—C6 | 122.76 (11) | C13—C12—C11 | 118.05 (14) |
C2—N1—N2 | 115.57 (10) | C12—C13—C9 | 119.36 (13) |
C6—N1—N2 | 119.21 (10) | N4—C14—C5 | 179.05 (15) |
C7—N2—N1 | 115.53 (11) | C2—N6—H061 | 118.1 (13) |
N3—C2—N6 | 120.03 (12) | C2—N6—H062 | 117.7 (12) |
N3—C2—N1 | 122.68 (12) | H061—N6—H062 | 123.4 (18) |
N6—C2—N1 | 117.28 (12) | C7—C8—H8A | 109.5 |
C2—N3—C4 | 116.84 (11) | C7—C8—H8B | 109.5 |
N3—C4—C5 | 124.29 (12) | H8A—C8—H8B | 109.5 |
N3—C4—S1 | 118.15 (10) | C7—C8—H8C | 109.5 |
C5—C4—S1 | 117.56 (10) | H8A—C8—H8C | 109.5 |
C4—S1—C15 | 102.47 (7) | H8B—C8—H8C | 109.5 |
C4—C5—C14 | 122.04 (12) | N5—C10—H10 | 118.1 |
C4—C5—C6 | 119.75 (12) | C11—C10—H10 | 118.1 |
C14—C5—C6 | 118.08 (12) | C10—C11—H11 | 120.4 |
O1—C6—N1 | 119.88 (12) | C12—C11—H11 | 120.4 |
O1—C6—C5 | 127.47 (12) | C13—C12—H12 | 121.0 |
N1—C6—C5 | 112.65 (11) | C11—C12—H12 | 121.0 |
N2—C7—C8 | 127.85 (12) | C12—C13—H13 | 120.3 |
N2—C7—C9 | 113.66 (12) | C9—C13—H13 | 120.3 |
C8—C7—C9 | 118.49 (11) | S1—C15—H15A | 109.5 |
N5—C9—C13 | 122.82 (12) | S1—C15—H15B | 109.5 |
N5—C9—C7 | 115.56 (12) | H15A—C15—H15B | 109.5 |
C13—C9—C7 | 121.62 (12) | S1—C15—H15C | 109.5 |
C10—N5—C9 | 116.89 (12) | H15A—C15—H15C | 109.5 |
N5—C10—C11 | 123.73 (13) | H15B—C15—H15C | 109.5 |
C10—C11—C12 | 119.12 (13) | ||
C2—N1—N2—C7 | −127.19 (13) | N2—N1—C6—C5 | 173.52 (11) |
C6—N1—N2—C7 | 70.10 (15) | C4—C5—C6—O1 | 172.14 (13) |
C6—N1—C2—N3 | −8.6 (2) | C14—C5—C6—O1 | −3.8 (2) |
N2—N1—C2—N3 | −170.61 (12) | C4—C5—C6—N1 | −8.43 (18) |
C6—N1—C2—N6 | 172.59 (12) | C14—C5—C6—N1 | 175.67 (12) |
N2—N1—C2—N6 | 10.56 (17) | N1—N2—C7—C8 | 2.8 (2) |
N6—C2—N3—C4 | 179.06 (12) | N1—N2—C7—C9 | −177.94 (10) |
N1—C2—N3—C4 | 0.26 (19) | N2—C7—C9—N5 | −178.88 (12) |
C2—N3—C4—C5 | 3.3 (2) | C8—C7—C9—N5 | 0.50 (17) |
C2—N3—C4—S1 | −177.08 (10) | N2—C7—C9—C13 | 1.27 (18) |
N3—C4—S1—C15 | −7.55 (14) | C8—C7—C9—C13 | −179.35 (12) |
C5—C4—S1—C15 | 172.11 (12) | C13—C9—N5—C10 | 0.3 (2) |
N3—C4—C5—C14 | 176.96 (13) | C7—C9—N5—C10 | −179.57 (12) |
S1—C4—C5—C14 | −2.67 (19) | C9—N5—C10—C11 | 1.3 (2) |
N3—C4—C5—C6 | 1.2 (2) | N5—C10—C11—C12 | −1.6 (2) |
S1—C4—C5—C6 | −178.41 (10) | C10—C11—C12—C13 | 0.4 (2) |
C2—N1—C6—O1 | −168.41 (12) | C11—C12—C13—C9 | 1.0 (2) |
N2—N1—C6—O1 | −7.00 (18) | N5—C9—C13—C12 | −1.4 (2) |
C2—N1—C6—C5 | 12.11 (17) | C7—C9—C13—C12 | 178.41 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H061···N5i | 0.86 (2) | 2.26 (2) | 3.0122 (17) | 146.2 (17) |
N6—H062···O1ii | 0.853 (19) | 2.307 (19) | 3.0886 (15) | 152.4 (17) |
C10—H10···O1iii | 0.95 | 2.40 | 3.2351 (17) | 147 |
N6—H062···N2 | 0.853 (19) | 2.228 (18) | 2.6091 (17) | 107.1 (14) |
Symmetry codes: (i) x+1/2, −y+3/2, z+1/2; (ii) −x+1/2, y+1/2, −z+1/2; (iii) −x, −y+1, −z. |
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