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

Mohamed-Ezzat, R.A.; Elgemeie, G.H.; Jones, P.G.

doi:10.1107/S2056989021004126

research communications

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 77| Part 5| May 2021| Pages 547-550

https://doi.org/10.1107/S2056989021004126

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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

Reham A. Mohamed-Ezzat,^a Galal H. Elgemeie ^b and Peter G. Jones ^c ^*

^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

Edited by J. Reibenspies, Texas A & M University, USA (Received 7 April 2021; accepted 17 April 2021; online 23 April 2021)

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 ( $[\overline{1}]$ 01).

Keywords: crystal structure; pyrimidinones; hydrogen bonds.

CCDC references: 2078221; 2078220

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, azines 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 heterocyclic compounds that are common in nucleic acids and find diverse applications in drug planning (Elgemeie 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 ).

In 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 nitriles (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 cyclization 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.

Table 1
Selected geometric parameters (Å, °) for 3a

N1—N2	1.4248 (17)	C4—S1	1.7522 (16)
C2—N3	1.333 (2)	S1—C16	1.7918 (19)

C7—N2—N1	114.40 (13)	C4—S1—C16	101.93 (8)
N3—C4—C5	124.02 (14)	N1—C6—C5	112.55 (12)

N1—N2—C7—C9	176.69 (12)	N2—C7—C9—C14	12.1 (2)
N2—C7—C9—C10	−166.23 (15)

Table 2
Selected geometric parameters (Å, °) for 3b

N1—N2	1.4191 (16)	C4—S1	1.7473 (14)
C2—N3	1.3286 (17)	S1—C15	1.8023 (16)

C7—N2—N1	115.53 (11)	C4—S1—C15	102.47 (7)
N3—C4—C5	124.29 (12)	N1—C6—C5	112.65 (11)

N1—N2—C7—C9	−177.94 (10)	N2—C7—C9—C13	1.27 (18)
N2—C7—C9—N5	−178.88 (12)

Figure 1
The structure of compound 3a in the crystal. Ellipsoids correspond to 50% probability levels.

Figure 2
The structure of compound 3b in the crystal. Ellipsoids correspond to 50% probability levels.

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).

Figure 3
A least-squares fit of the molecules of 3a (solid bonds) and 3b (dashed bonds; molecule inverted with respect to the deposited coordinates). Only the fitted atoms are labelled; their r.m.s. deviation is 0.16 Å.

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).

Table 3
Hydrogen-bond geometry (Å, °) for 3a

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) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Table 4
Hydrogen-bond geometry (Å, °) for 3b

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) $[x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) .

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 ( $[\overline{1}]$ 01) (Fig. 5).

Figure 4
Packing diagram of compound 3a viewed perpendicular to (102) in the region z ≃ 0.25. Dashed lines indicate classical hydrogen bonds. Hydrogen atoms not involved in such bonds are omitted for clarity.

Figure 5
Packing diagram of compound 3b viewed perpendicular to ( $[\overline{1}]$ 01). Dashed lines indicate classical hydrogen bonds. Hydrogen atoms not involved in such bonds are omitted for clarity.

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 refinement 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 refinement details are summarized in Table 5. 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—H_aromatic 0.95 Å). The U(H) values were fixed at 1.5 (for the methyl H) or 1.2 times the equivalent U_iso value of the parent carbon atoms.

Table 5
Experimental details

	3a	3b
Crystal data
Chemical formula	C₁₄H₁₃N₅OS	C₁₃H₁₂N₆OS
M_r	299.35	300.35
Crystal system, space group	Monoclinic, P2₁/c	Monoclinic, P2₁/n
Temperature (K)	100	100
a, b, c (Å)	12.15369 (18), 14.9466 (2), 7.68691 (16)	13.4774 (5), 7.6797 (3), 14.2755 (6)
β (°)	91.7607 (16)	112.401 (5)
V (Å³)	1395.72 (4)	1366.04 (10)
Z	4	4
Radiation type	Cu Kα	Cu Kα
μ (mm⁻¹)	2.12	2.19
Crystal size (mm)	0.2 × 0.2 × 0.02	0.12 × 0.08 × 0.02

Data collection
Diffractometer	Rigaku XtaLAB Synergy, Single source at home/near, HyPix	Rigaku XtaLAB Synergy, Single source at home/near, HyPix
Absorption correction	Multi-scan (CrysAlis PRO; Rigaku OD, 2021 $[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )	Multi-scan (CrysAlis PRO; Rigaku OD, 2021 $[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ )
T_min, T_max	0.636, 1.000	0.782, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	104992, 2958, 2842	54131, 2905, 2813
R_int	0.061	0.042
(sin θ/λ)_max (Å⁻¹)	0.634	0.633

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.040, 0.106, 1.06	0.036, 0.097, 1.07
No. of reflections	2958	2905
No. of parameters	200	200
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
Δρ_max, Δρ_min (e Å⁻³)	0.40, −0.35	0.33, −0.39
Computer programs: CrysAlis PRO (Rigaku OD, 2021 $[Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]$ ), SHELXT (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and XP (Siemens, 1994 ).

Supporting information

CCDC references: 2078221; 2078220

Crystal structure: contains datablocks 3a, 3b, global. DOI: https://doi.org/10.1107/S2056989021004126/jy2007sup1.cif

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

checkCIF report

Computing details top

For both structures, data collection: CrysAlis PRO (Rigaku OD, 2021); cell refinement: 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).

(E)-2-Amino-4-methylsulfanyl-6-oxo-1-(1-phenylethylideneamino)-1,6-dihydropyrimidine-5-carbonitrile (3a) top

Crystal data top

C₁₄H₁₃N₅OS	F(000) = 624
M_r = 299.35	D_x = 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

Data collection top

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	R_int = 0.061
ω scans	θ_max = 77.7°, θ_min = 3.6°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021)	h = −15→15
T_min = 0.636, T_max = 1.000	k = −18→18
104992 measured reflections	l = −9→9

Refinement top

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(F_o²) + (0.0516P)² + 0.8822P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max = 0.001
2958 reflections	Δρ_max = 0.40 e Å⁻³
200 parameters	Δρ_min = −0.35 e Å⁻³
0 restraints

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.

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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.

(E)-2-Amino-4-methylsulfanyl-6-oxo-1-[1-(pyridin-2-yl)ethylideneamino]-1,6-dihydropyrimidine-5-carbonitrile (3b) top

Crystal data top

C₁₃H₁₂N₆OS	F(000) = 624
M_r = 300.35	D_x = 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

Data collection top

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	R_int = 0.042
ω scans	θ_max = 77.6°, θ_min = 3.8°
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2021)	h = −17→17
T_min = 0.782, T_max = 1.000	k = −9→9
54131 measured reflections	l = −18→18

Refinement top

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(F_o²) + (0.0483P)² + 0.8192P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.001
2905 reflections	Δρ_max = 0.33 e Å⁻³
200 parameters	Δρ_min = −0.39 e Å⁻³
0 restraints

Special details top

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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.

References

Abu-Zaied, M. A., Elgemeie, G. H. & Mahmoud, N. M. (2021). Nucleosides Nucleotides Nucleic Acids, 40, 336–356. CAS PubMed Google Scholar
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Volume 77| Part 5| May 2021| Pages 547-550

https://doi.org/10.1107/S2056989021004126

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

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

References

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

3. Supramolecular features