research communications
Acta Cryst.(2017). E73, 467–471 https://doi.org/10.1107/S2056989017003243
467
Received 26 January 2017 Accepted 27 February 2017
Edited by H. Stoeckli-Evans, University of Neuchaˆtel, Switzerland
Keywords:crystal structure; diamino-pyrimidin(2-yl) derivatives; thioacteamide; hydrogen bonding; C—H interactions; offset
–interactions.
CCDC references:1534990; 1534989
Supporting information:this article has supporting information at journals.iucr.org/e
Crystal structures of
N
-(4-chlorophenyl)-2-[(4,6-di-aminopyrimidin-2-yl)sulfanyl]acetamide and
N
-(3-
chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)-sulfanyl]acetamide
S. Subasri,aTimiri Ajay Kumar,bBarij Nayan Sinha,b Venkatesan Jayaprakash,b Vijayan Viswanathanaand Devadasan Velmurugana*
aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025,
India, andbDepartment of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835 215,
Jharkhand, India. *Correspondence e-mail: shirai2011@gmail.com
The title compounds, C12H12ClN5OS, (I), and C12H12ClN5OS, (II), are 2-[(diaminopyrimidin-2-yl)sulfanyl]acetamides. Compound (II), crystallizes with two independent molecules (AandB) in the asymmetric unit. In each of the molecules, in both (I) and (II), an intramolecular N—H N hydrogen bond forms anS(7) ring motif. The pyrimidine ring is inclined to the benzene ring by 42.25 (14) in (I), and by 59.70 (16) and 62.18 (15) in molecules A and B,
respectively, of compound (II). In the crystal of (I), molecules are linked by pairs of N—H N hydrogen bonds, forming inversion dimers with an R2
2 (8) ring motif. The dimers are linkedviabifurcated N—H O and C—H O hydrogen bonds, forming corrugated layers parallel to theacplane. In the crystal of (II), theAmolecules are linked through N—H O and N—H Cl hydrogen bonds, forming layers parallel to (100). TheBmolecules are also linked by N—H O and N—H Cl hydrogen bonds, also forming layers parallel to (100). The parallel layers ofAandBmolecules are linkedviaN—H N hydrogen bonds, forming a three-dimensional structure.
1. Chemical context
Diaminopyrimidine derivatives are reported to be therapeutic agents towards anti-cancer activity, selectively inhibiting c-Fms kinase of M-CSF-dependent myeloid leukemia cells (Xu
et al., 2010). They have also shown antibacterial activity (Kandeelet al., 1994), are potential antimicrobial (Hollaet al., 2006) and anti-AIDS agents (Nogueraset al., 1993) and anti-viral agents (Hockova´ et al., 2003, 2004) and have shown promise as immunosuppressants (Blumenkopfet al., 2002). In
this connection, the title
2-[(4,6-diaminopyrimidin-2-yl)sulfanyl] based analogues have been synthesized as anti-viral agents against NS2B/NS3 Dengue protease. We report herein on the syntheses and crystal structures of the title compounds, (I) and (II).
2. Structural commentary
59.70 (16) and 62.18 (15)in moleculesAandB, respectively,
of compound (II). In compound (I), the N1—C7—C8—S1 torsion angle is 77.2 (3), while in molecule Aof compound
(II), N5—C6—C5—S1 is 85.2 (3), and in moleculeBN10—
C18—C17—S2 is 68.4 (3).
In compound (I), the intramolecular N1—H1A N2
hydrogen bond (Table 1) generates an S(7) ring motif, as shown in Fig. 1. Amine atoms N4 and N5 attached to the pyrimidine ring deviate by 0.018 (3) and 0.060 (3) A˚ , respec-tively. The chlorine atom Cl1 attached to the benzene ring deviates by 0.058 (1) A˚ .
In compound (II), intramolecular N5—H5 N4 and N10— H10 N9 hydrogen bonds (Table 2 and Fig. 2) in moleculesA
andB, respectively, also generateS(7) ring motifs. In molecule
A, the amine group atoms N1 and N2 attached to the pyrim-idine ring deviate by 0.006 (3) and 0.004 (3) A˚ , respectively. The chlorine atom Cl1 attached to the benzene ring deviates
by 0.013 (1) A˚ . In moleculeB, the amine group atoms N6 and N7 attached to the pyrimidine ring deviate by0.003 (3) and 0.050 (3) A˚ , respectively. Atom Cl2 attached to the benzene ring deviates by 0.074 (1) A˚ .
3. Supramolecular features
In the crystal of (I), molecules are linked by pairs of N—
H N hydrogen bonds, forming inversion dimers with an
R2
2(8) ring motif (Table 1 and Fig. 4). The dimers are linked by
via bifurcated N—H O and C—H O hydrogen bonds,
forming corrugated layers parallel to theacplane (Table 1 and Fig. 5).
In the crystal of (II), theAmolecules are linked through
N—H O and N—H Cl hydrogen bonds, forming layers
parallel to (100). Likewise theBmolecules are also linked by
N—H O and N—H Cl hydrogen bonds, forming layers
parallel to (100). The parallel layers of A and layers of B
molecules are linkedviaN—H N hydrogen bonds, forming a three-dimensional structure (Table 2 and Fig. 6).
468
Subasriet al. C12H12ClN5OS and C12H12ClN5OS Acta Cryst.(2017). E73, 467–471
[image:2.610.313.564.71.216.2] [image:2.610.50.292.147.365.2]research communications
Figure 2
[image:2.610.49.297.543.697.2]The molecular structure of the two independent molecules (AandB) of compound (II), with the atom labelling. Displacement ellipsoids are drawn at the 30% probability level. The intramolecular N—H N hydrogen bonds are shown as dashed lines (see Table 2).
Figure 3
An AutoMolFit (PLATON; Spek, 2009) view of molecule B(red) on moleculeA(back) of (II).
Figure 1
[image:2.610.314.566.563.710.2]4. Database survey
A search of the Cambridge Structural Database (Version 5.37, update May 2016; Groom et al., 2016) for 2-[(pyrimidine-2-yl)sulfanyl]-N-phenylacetamide yielded five hits. Three of these involve (4,6-diaminopyrmidin-2-yl) groups. They include the 2-chlorophenyl analogue, N -(2-chlorophenyl)-2-[(4,6-di-aminopyrimidin-2-yl)sulfanyl]acetamide (ARARUI; Subasri
et al., 2016). Here the pyrimidine and benzene rings are inclined to one another by 67.84 (6), compared to 42.25 (14)
in (I), and 59.70 (16) and 62.18 (15) in moleculesAandB,
respectively, of compound (II). As in the title compounds,
there is also an intramolecular N—H N hydrogen bond
present, stabilizing the folded conformation of the molecule.
research communications
Acta Cryst.(2017). E73, 467–471 Subasriet al. C
[image:3.610.44.296.92.152.2]12H12ClN5OS and C12H12ClN5OS
469
Figure 5 [image:3.610.313.564.93.196.2]The crystal packing of compound (I) viewed along theaaxis. H atoms not involved in hydrogen bonding (see Table 1), have been excluded for clarity.
Figure 4
The crystal packing of compound (I) viewed along thebaxis. H atoms not involved in hydrogen bonding (see Table 1), have been excluded for clarity.
Table 1
Hydrogen-bond geometry (A˚ ,) for (I).
D—H A D—H H A D A D—H A
N1—H1A N2 0.86 2.06 2.856 (3) 154
N5—H5A N3i 0.86 2.16 2.990 (3) 162
N4—H4B O1ii 0.86 2.22 2.969 (3) 146
C11—H11 O1ii 0.93 2.45 3.144 (3) 132
Symmetry codes: (i)x;y;zþ1; (ii)x1 2;y;zþ
1 2.
Table 2
Hydrogen-bond geometry (A˚ ,) for (II).
D—H A D—H H A D A D—H A
N5—H5 N4 0.86 2.25 2.962 (3) 140
N10—H10A N9 0.86 2.02 2.826 (3) 157
N1—H1B O1i 0.86 2.19 2.931 (4) 145
N2—H2B Cl1i 0.86 2.76 3.405 (3) 133
N6—H6A O2ii 0.86 2.51 3.340 (4) 162
N6—H6B Cl2iii 0.86 2.70 3.556 (3) 176
N7—H7B O2iii 0.86 2.24 3.002 (4) 148
N1—H1A N8iv 0.86 2.21 3.070 (4) 174
N7—H7A N3v 0.86 2.19 3.046 (4) 178
Symmetry codes: (i)x;yþ3
2;zþ12; (ii)xþ2;yþ1;z; (iii)x;yþ32;z12; (iv)
x1;yþ3
[image:3.610.372.511.243.709.2] [image:3.610.46.291.375.708.2]470
Subasriet al. C12H12ClN5OS and C12H12ClN5OS Acta Cryst.(2017). E73, 467–471
[image:4.610.49.565.91.367.2]research communications
Figure 6
The crystal packing of compound (II) viewed along thebaxis (colour code:Amolecules black,Bmolecules red). H atoms not involved in hydrogen bonding (see Table 2), have been excluded for clarity.
Table 3
Experimental details.
(I) (II)
Crystal data
Chemical formula C12H12ClN5OS C12H12ClN5OS
Mr 309.78 309.78
Crystal system, space group Orthorhombic,Pbca Monoclinic,P21/c
Temperature (K) 293 293
a,b,c(A˚ ) 18.2743 (12), 7.4835 (5), 19.8021 (12) 18.220 (2), 8.1180 (12), 19.628 (2)
,,(
) 90, 90, 90 90, 108.761 (8), 90
V(A˚3) 2708.1 (3) 2748.9 (6)
Z 8 8
Radiation type MoK MoK
(mm1) 0.44 0.43
Crystal size (mm) 0.280.250.18 0.310.220.16
Data collection
Diffractometer Bruker SMART APEXII area-detector Bruker SMART APEXII area-detector
Absorption correction Multi-scan (SADABS; Bruker, 2008) Multi-scan (SADABS; Bruker, 2008)
Tmin,Tmax 0.741, 0.863 0.742, 0.892
No. of measured, independent and observed [I> 2(I)] reflections
22685, 3372, 2007 25810, 6858, 3462
Rint 0.060 0.075
(sin/ )max(A˚
1) 0.669 0.668
Refinement
R[F2> 2(F2)],wR(F2),S 0.050, 0.161, 1.08 0.050, 0.155, 0.96
No. of reflections 3372 6858
No. of parameters 181 361
H-atom treatment H-atom parameters constrained H-atom parameters constrained
max,min(e A˚3) 0.42,0.69 0.42,0.42
[image:4.610.80.536.400.723.2]5. Synthesis and crystallization
Compound (I):
To a solution of 4,6-diamino-pyrimidine-2-sulfanyl (0.5 g; 3.52 mmol) in 25 ml of ethanol, was added potassium hydro-xide (0.2g; 3.52 mmol) and the mixture was refluxed for 30 min, after which 3.52 mmol of 2-chloro-N -(4-chlorophen-yl)acetamide derivative was added and refluxed for 4 h. At the end of the reaction (monitored by TLC), the ethanol was evaporatedin vacuoand cold water was added; the precipitate formed was filtered and dried to give compound (I) as a crystalline powder (yield 97%). Colourless block-like crystals were obtained from a solution in methanol and ethyl acetate (1:1) by slow evaporation of the solvents at room temperature.
Compound (II):
To a solution of 4,6-diamino-pyrimidine-2-thiol (0.5 g; 3.52 mmol) in 25 ml of ethanol was added potassium hydro-xide (0.2g; 3.52 mmol) and the mixture was refluxed for
30 min. Then 3.52 mmol of 2-chloro-N
-(3-chlorophen-yl)acetamide was added and refluxed for 3 h. At the end of the reaction (monitored by TLC), the ethanol was evaporatedin vacuoand cold water was added and the precipitate formed was filtered and dried to give compound (II) as a crystalline powder (yield 92%). Colourless block-like crystals were obtained from a solution in methanol and ethyl acetate (2:1) by slow evaporation of the solvents at room temperature.
6. Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. For both (I) and (II), hydrogen atoms were placed in calculated positions and refined as
riding: C—H = 0.93–0.97 A˚ and N—H = 0.86 A˚, withUiso(H) = 1.2Ueq(N,C).
Acknowledgements
The authors thank the TBI X-ray facility, CAS in Crystal-lography and Biophysics, University of Madras, India, for the data collection. SS and DV thank the UGC (SAP–CAS) for the departmental facilities. SS also thanks UGC for the award of a meritorious fellowship.
References
Blumenkopf, T. A., Mueller, E. E. & Roskamp, E. J. (2002).Google Patents. WO2001040215 A1. PCT/IB2000/001628.
Bruker (2008).SMART,SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016).Acta Cryst.B72, 171–179.
Hockova´, D., Holy´, A., Masojı´dkova´, M., Andrei, G., Snoeck, R., De Clercq, E. & Balzarini, J. (2003).J. Med. Chem.46, 5064–5073. Hockova´, D., Holy´, A. N., Masoj\?ı´dkova´, M., Andrei, G., Snoeck, R.,
De Clercq, E. & Balzarini, J. (2004).Bioorg. Med. Chem.12, 3197– 3202.
Holla, B. S., Mahalinga, M., Karthikeyan, M. S., Akberali, P. M. & Shetty, N. S. (2006).Bioorg. Med. Chem.14, 2040–2047.
Kandeel, M., El-Meligie, S., Omar, R., Roshdy, S. & Youssef, K. (1994).J. Pharm. Sci.3, 197–205.
Nogueras, M., Sa´nchez, A., Melguizo, M., Quijano, M. L. & Melgarejo, M. (1993).Bioorg. Med. Chem. Lett.3, 601–606. Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122.
Sheldrick, G. M. (2015).Acta Cryst.C71, 3–8. Spek, A. L. (2009).Acta Cryst.D65, 148–155.
Subasri, S., Timiri, A. K., Barji, N. S., Jayaprakash, V., Vijayan, V. & Velmurugan, D. (2016).Acta Cryst.E72, 1171–1175.
Xu, L. B., Sun, W., Liu, H. Y., Wang, L. L., Xiao, J. H., Yang, X. H. & Li, S. (2010).Chin. Chem. Lett.21, 1318–1321.
research communications
Acta Cryst.(2017). E73, 467–471 Subasriet al. C
supporting information
sup-1 Acta Cryst. (2017). E73, 467-471
supporting information
Acta Cryst. (2017). E73, 467-471 [https://doi.org/10.1107/S2056989017003243]
Crystal structures of
N
-(4-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide and
N
-(3-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide
S. Subasri, Timiri Ajay Kumar, Barij Nayan Sinha, Venkatesan Jayaprakash, Vijayan Viswanathan
and Devadasan Velmurugan
Computing details
For both compounds, data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction:
SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine
structure: SHELXL2016 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015) and PLATON (Spek, 2009).
(I) N-(4-Chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide
Crystal data
C12H12ClN5OS
Mr = 309.78
Orthorhombic, Pbca a = 18.2743 (12) Å
b = 7.4835 (5) Å
c = 19.8021 (12) Å
V = 2708.1 (3) Å3
Z = 8
F(000) = 1280
Dx = 1.520 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 3372 reflections
θ = 2.1–28.4°
µ = 0.44 mm−1
T = 293 K Block, colourless 0.28 × 0.25 × 0.18 mm
Data collection
Bruker SMART APEXII area-detector diffractometer
Radiation source: fine-focus sealed tube
ω and φ scans
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
Tmin = 0.741, Tmax = 0.863
22685 measured reflections
3372 independent reflections 2007 reflections with I > 2σ(I)
Rint = 0.060
θmax = 28.4°, θmin = 2.1°
h = −23→24
k = −9→9
l = −26→26
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.050
wR(F2) = 0.161
S = 1.08 3372 reflections 181 parameters
0 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
supporting information
sup-2 Acta Cryst. (2017). E73, 467-471
H-atom parameters constrained
w = 1/[σ2(F
o2) + (0.0795P)2 + 0.3384P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max < 0.001
Δρmax = 0.42 e Å−3
Δρmin = −0.69 e Å−3
Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x y z Uiso*/Ueq
supporting information
sup-3 Acta Cryst. (2017). E73, 467-471
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
C1 0.0401 (14) 0.061 (2) 0.0392 (13) 0.0034 (13) 0.0018 (11) 0.0079 (13) C2 0.0559 (17) 0.060 (2) 0.0414 (14) 0.0041 (15) 0.0078 (13) 0.0057 (14) C3 0.076 (2) 0.0448 (17) 0.0356 (13) −0.0015 (15) 0.0010 (13) 0.0034 (12) C4 0.0668 (19) 0.054 (2) 0.0478 (15) −0.0159 (15) −0.0061 (14) 0.0062 (15) C5 0.0508 (16) 0.056 (2) 0.0446 (15) −0.0121 (14) 0.0037 (12) 0.0070 (14) C6 0.0404 (14) 0.0481 (17) 0.0349 (12) 0.0039 (12) 0.0025 (10) 0.0061 (12) C7 0.0361 (13) 0.0500 (17) 0.0390 (13) 0.0010 (12) 0.0049 (11) 0.0045 (12) C8 0.0396 (14) 0.0560 (18) 0.0441 (14) −0.0070 (12) 0.0021 (11) −0.0017 (13) C9 0.0320 (12) 0.0451 (16) 0.0338 (11) 0.0015 (11) 0.0008 (9) −0.0041 (11) C10 0.0361 (13) 0.0442 (16) 0.0362 (12) −0.0026 (11) 0.0054 (10) −0.0040 (11) C11 0.0329 (13) 0.0544 (18) 0.0396 (13) −0.0040 (11) −0.0016 (11) −0.0011 (12) C12 0.0347 (13) 0.0466 (17) 0.0339 (12) 0.0035 (11) −0.0013 (10) −0.0046 (11) N1 0.0330 (11) 0.0617 (16) 0.0370 (11) 0.0029 (10) 0.0041 (9) 0.0006 (10) N2 0.0307 (10) 0.0526 (14) 0.0344 (10) 0.0011 (9) 0.0008 (9) 0.0016 (10) N3 0.0328 (11) 0.0517 (15) 0.0344 (10) −0.0028 (9) 0.0001 (8) 0.0007 (10) N4 0.0372 (12) 0.0783 (19) 0.0385 (11) −0.0016 (12) −0.0058 (10) 0.0095 (12) N5 0.0426 (13) 0.0767 (19) 0.0405 (11) −0.0161 (12) −0.0008 (10) 0.0088 (12) O1 0.0304 (10) 0.114 (2) 0.0538 (12) 0.0020 (11) 0.0062 (8) −0.0101 (12) S1 0.0312 (3) 0.0698 (5) 0.0363 (3) −0.0015 (3) −0.0016 (3) 0.0060 (3) CL1 0.1216 (9) 0.0854 (7) 0.0422 (4) −0.0171 (6) 0.0013 (4) −0.0090 (4)
Geometric parameters (Å, º)
C1—C6 1.390 (3) C8—H8B 0.9700 C1—C2 1.391 (4) C9—N2 1.327 (3) C1—H1 0.9300 C9—N3 1.329 (3) C2—C3 1.375 (4) C9—S1 1.771 (2) C2—H2 0.9300 C10—N5 1.338 (3) C3—C4 1.374 (4) C10—N3 1.359 (3) C3—CL1 1.739 (3) C10—C11 1.386 (3) C4—C5 1.378 (4) C11—C12 1.374 (4) C4—H4 0.9300 C11—H11 0.9300 C5—C6 1.393 (4) C12—N4 1.352 (3) C5—H5 0.9300 C12—N2 1.364 (3) C6—N1 1.403 (3) N1—H1A 0.8600 C7—O1 1.218 (3) N4—H4A 0.8600 C7—N1 1.337 (3) N4—H4B 0.8600 C7—C8 1.517 (4) N5—H5A 0.8600 C8—S1 1.807 (3) N5—H5B 0.8600 C8—H8A 0.9700
supporting information
sup-4 Acta Cryst. (2017). E73, 467-471
C3—C2—H2 120.2 N5—C10—N3 115.8 (2) C1—C2—H2 120.2 N5—C10—C11 123.1 (2) C4—C3—C2 120.9 (3) N3—C10—C11 121.1 (2) C4—C3—CL1 119.6 (2) C12—C11—C10 118.1 (2) C2—C3—CL1 119.5 (2) C12—C11—H11 121.0 C3—C4—C5 119.7 (3) C10—C11—H11 121.0 C3—C4—H4 120.2 N4—C12—N2 116.0 (2) C5—C4—H4 120.2 N4—C12—C11 122.3 (2) C4—C5—C6 120.7 (3) N2—C12—C11 121.7 (2) C4—C5—H5 119.7 C7—N1—C6 129.6 (2) C6—C5—H5 119.7 C7—N1—H1A 115.2 C1—C6—C5 119.0 (2) C6—N1—H1A 115.2 C1—C6—N1 123.7 (2) C9—N2—C12 114.7 (2) C5—C6—N1 117.2 (2) C9—N3—C10 115.3 (2) O1—C7—N1 124.8 (3) C12—N4—H4A 120.0 O1—C7—C8 121.3 (2) C12—N4—H4B 120.0 N1—C7—C8 113.9 (2) H4A—N4—H4B 120.0 C7—C8—S1 114.6 (2) C10—N5—H5A 120.0 C7—C8—H8A 108.6 C10—N5—H5B 120.0 S1—C8—H8A 108.6 H5A—N5—H5B 120.0 C7—C8—H8B 108.6 C9—S1—C8 103.73 (12) S1—C8—H8B 108.6
C6—C1—C2—C3 −0.4 (4) O1—C7—N1—C6 −2.5 (5) C1—C2—C3—C4 1.4 (5) C8—C7—N1—C6 176.8 (3) C1—C2—C3—CL1 −177.9 (2) C1—C6—N1—C7 −22.2 (5) C2—C3—C4—C5 −0.9 (5) C5—C6—N1—C7 161.4 (3) CL1—C3—C4—C5 178.4 (2) N3—C9—N2—C12 −2.0 (4) C3—C4—C5—C6 −0.5 (5) S1—C9—N2—C12 175.36 (19) C2—C1—C6—C5 −1.0 (4) N4—C12—N2—C9 176.9 (2) C2—C1—C6—N1 −177.3 (3) C11—C12—N2—C9 −3.5 (4) C4—C5—C6—C1 1.5 (4) N2—C9—N3—C10 4.2 (4) C4—C5—C6—N1 178.1 (3) S1—C9—N3—C10 −173.28 (19) O1—C7—C8—S1 −103.4 (3) N5—C10—N3—C9 −179.5 (2) N1—C7—C8—S1 77.2 (3) C11—C10—N3—C9 −1.0 (4) N5—C10—C11—C12 174.5 (3) N2—C9—S1—C8 17.9 (2) N3—C10—C11—C12 −3.8 (4) N3—C9—S1—C8 −164.3 (2) C10—C11—C12—N4 −174.2 (3) C7—C8—S1—C9 −88.3 (2) C10—C11—C12—N2 6.3 (4)
Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
supporting information
sup-5 Acta Cryst. (2017). E73, 467-471
N4—H4B···O1ii 0.86 2.22 2.969 (3) 146
C11—H11···O1ii 0.93 2.45 3.144 (3) 132
Symmetry codes: (i) −x, −y, −z+1; (ii) x−1/2, y, −z+1/2.
(II) N-(3-Chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide
Crystal data
C12H12ClN5OS
Mr = 309.78
Monoclinic, P21/c
a = 18.220 (2) Å
b = 8.1180 (12) Å
c = 19.628 (2) Å
β = 108.761 (8)°
V = 2748.9 (6) Å3
Z = 8
F(000) = 1280
Dx = 1.497 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 6858 reflections
θ = 1.2–28.4°
µ = 0.43 mm−1
T = 293 K Block, colourless 0.31 × 0.22 × 0.16 mm
Data collection
Bruker SMART APEXII area-detector diffractometer
Radiation source: fine-focus sealed tube
ω and φ scans
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
Tmin = 0.742, Tmax = 0.892
25810 measured reflections
6858 independent reflections 3462 reflections with I > 2σ(I)
Rint = 0.075
θmax = 28.4°, θmin = 1.2°
h = −24→24
k = −10→10
l = −26→26
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.050
wR(F2) = 0.155
S = 0.96 6858 reflections 361 parameters 0 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H-atom parameters constrained
w = 1/[σ2(F
o2) + (0.0646P)2 + 0.6656P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max = 0.001
Δρmax = 0.42 e Å−3
Δρmin = −0.42 e Å−3
Special details
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x y z Uiso*/Ueq
supporting information
sup-6 Acta Cryst. (2017). E73, 467-471
supporting information
sup-7 Acta Cryst. (2017). E73, 467-471
H7B 1.201739 0.741880 −0.292327 0.084* N8 1.22428 (13) 0.6664 (3) −0.13364 (12) 0.0461 (6) N9 1.11350 (14) 0.5443 (3) −0.11441 (12) 0.0479 (6) N10 1.05376 (13) 0.6562 (3) −0.00640 (12) 0.0448 (6) H10A 1.058236 0.620508 −0.046127 0.054* O1 0.46540 (13) 0.5750 (4) 0.06196 (11) 0.0714 (7) O2 1.11150 (13) 0.6397 (3) 0.11485 (11) 0.0643 (7) S1 0.36824 (4) 0.56020 (11) 0.18798 (4) 0.0463 (2) S2 1.23535 (4) 0.62488 (11) −0.00038 (4) 0.0492 (2) CL1 0.70803 (5) 0.80248 (14) 0.02776 (5) 0.0738 (3) CL2 0.89352 (5) 1.01784 (12) 0.10723 (5) 0.0649 (3)
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
supporting information
sup-8 Acta Cryst. (2017). E73, 467-471
N10 0.0414 (13) 0.0570 (18) 0.0359 (13) −0.0045 (12) 0.0126 (11) −0.0002 (12) O1 0.0594 (14) 0.113 (2) 0.0437 (13) 0.0075 (14) 0.0188 (11) 0.0222 (14) O2 0.0714 (15) 0.0839 (18) 0.0362 (12) 0.0075 (14) 0.0152 (11) −0.0032 (12) S1 0.0464 (4) 0.0585 (6) 0.0351 (4) 0.0021 (4) 0.0146 (3) −0.0024 (4) S2 0.0415 (4) 0.0653 (6) 0.0391 (4) −0.0092 (4) 0.0107 (3) 0.0047 (4) CL1 0.0698 (6) 0.0948 (8) 0.0647 (6) −0.0090 (5) 0.0327 (5) 0.0072 (5) CL2 0.0665 (5) 0.0756 (7) 0.0602 (5) 0.0000 (5) 0.0308 (4) −0.0049 (5)
Geometric parameters (Å, º)
C1—N1 1.348 (4) C15—N7 1.336 (4) C1—N3 1.360 (3) C15—N8 1.348 (4) C1—C2 1.389 (4) C16—N8 1.320 (3) C2—C3 1.372 (4) C16—N9 1.331 (4) C2—H2 0.9300 C16—S2 1.766 (3) C3—N2 1.355 (4) C17—C18 1.508 (4) C3—N4 1.362 (3) C17—S2 1.808 (3) C4—N3 1.327 (3) C17—H17A 0.9700 C4—N4 1.332 (4) C17—H17B 0.9700 C4—S1 1.766 (3) C18—O2 1.223 (3) C5—C6 1.510 (4) C18—N10 1.346 (4) C5—S1 1.800 (3) C19—C24 1.388 (4) C5—H5A 0.9700 C19—C20 1.387 (4) C5—H5B 0.9700 C19—N10 1.405 (4) C6—O1 1.215 (3) C20—C21 1.378 (4) C6—N5 1.346 (4) C20—H20 0.9300 C7—C12 1.383 (4) C21—C22 1.378 (4) C7—C8 1.386 (4) C21—H21 0.9300 C7—N5 1.411 (4) C22—C23 1.378 (4) C8—C9 1.374 (5) C22—H22 0.9300 C8—H8 0.9300 C23—C24 1.383 (4) C9—C10 1.361 (5) C23—CL2 1.736 (3) C9—H9 0.9300 C24—H24 0.9300 C10—C11 1.366 (5) N1—H1A 0.8600 C10—H10 0.9300 N1—H1B 0.8600 C11—C12 1.387 (4) N2—H2A 0.8600 C11—CL1 1.736 (3) N2—H2B 0.8600 C12—H12 0.9300 N5—H5 0.8600 C13—N9 1.346 (4) N6—H6A 0.8600 C13—N6 1.352 (4) N6—H6B 0.8600 C13—C14 1.378 (4) N7—H7A 0.8600 C14—C15 1.398 (4) N7—H7B 0.8600 C14—H14 0.9300 N10—H10A 0.8600
supporting information
sup-9 Acta Cryst. (2017). E73, 467-471
supporting information
sup-10 Acta Cryst. (2017). E73, 467-471
N1—C1—C2—C3 178.0 (3) N10—C19—C24—C23 178.0 (3) N3—C1—C2—C3 −0.6 (4) N4—C4—N3—C1 2.2 (5) C1—C2—C3—N2 179.3 (3) S1—C4—N3—C1 −175.7 (2) C1—C2—C3—N4 3.1 (4) N1—C1—N3—C4 179.5 (3) S1—C5—C6—O1 −93.7 (3) C2—C1—N3—C4 −1.9 (4) S1—C5—C6—N5 85.2 (3) N3—C4—N4—C3 0.1 (4) C12—C7—C8—C9 2.3 (5) S1—C4—N4—C3 177.8 (2) N5—C7—C8—C9 −178.8 (3) N2—C3—N4—C4 −179.4 (3) C7—C8—C9—C10 −1.9 (6) C2—C3—N4—C4 −2.9 (4) C8—C9—C10—C11 0.6 (6) O1—C6—N5—C7 2.0 (5) C9—C10—C11—C12 0.3 (6) C5—C6—N5—C7 −176.9 (3) C9—C10—C11—CL1 −179.8 (3) C12—C7—N5—C6 −20.0 (5) C8—C7—C12—C11 −1.4 (5) C8—C7—N5—C6 161.1 (3) N5—C7—C12—C11 179.7 (3) N9—C16—N8—C15 2.3 (5) C10—C11—C12—C7 0.1 (5) S2—C16—N8—C15 −174.2 (2) CL1—C11—C12—C7 −179.8 (2) N7—C15—N8—C16 177.1 (3) N9—C13—C14—C15 1.8 (5) C14—C15—N8—C16 −2.7 (5) N6—C13—C14—C15 179.0 (3) N8—C16—N9—C13 0.1 (5) C13—C14—C15—N7 −178.9 (3) S2—C16—N9—C13 176.4 (2) C13—C14—C15—N8 0.8 (5) N6—C13—N9—C16 −179.7 (3) S2—C17—C18—O2 −112.5 (3) C14—C13—N9—C16 −2.2 (5) S2—C17—C18—N10 68.4 (3) O2—C18—N10—C19 4.6 (5) C24—C19—C20—C21 −0.7 (4) C17—C18—N10—C19 −176.3 (3) N10—C19—C20—C21 −178.3 (3) C24—C19—N10—C18 1.4 (5) C19—C20—C21—C22 0.5 (5) C20—C19—N10—C18 178.8 (3) C20—C21—C22—C23 −0.1 (5) N3—C4—S1—C5 −172.4 (2) C21—C22—C23—C24 −0.1 (5) N4—C4—S1—C5 9.5 (3) C21—C22—C23—CL2 177.2 (2) C6—C5—S1—C4 −88.7 (2) C22—C23—C24—C19 −0.1 (4) N8—C16—S2—C17 −172.9 (2) CL2—C23—C24—C19 −177.5 (2) N9—C16—S2—C17 10.3 (3) C20—C19—C24—C23 0.6 (4) C18—C17—S2—C16 −86.9 (2)
Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
N5—H5···N4 0.86 2.25 2.962 (3) 140 N10—H10A···N9 0.86 2.02 2.826 (3) 157 N1—H1B···O1i 0.86 2.19 2.931 (4) 145
N2—H2B···Cl1i 0.86 2.76 3.405 (3) 133
N6—H6A···O2ii 0.86 2.51 3.340 (4) 162
N6—H6B···Cl2iii 0.86 2.70 3.556 (3) 176
N7—H7B···O2iii 0.86 2.24 3.002 (4) 148
N1—H1A···N8iv 0.86 2.21 3.070 (4) 174
N7—H7A···N3v 0.86 2.19 3.046 (4) 178
