organic compounds ActaCrystallographicaSectionE (cid:5)=0.55mm(cid:4)1 0.40(cid:5)0.20(cid:5)0.20mm Structure Reports T=294K Online Datacollection ISSN1600-5368 RigakuR-AXISRAPID 9506measuredreflections diffractometer 1296independentreflections Absorptioncorrection:multi-scan 962reflectionswithI>2(cid:2)(I) 2-Chloropyrimidin-4-amine (CrystalClear;Rigaku,2007) R =0.038 int T =0.840,T =0.888 min max Gerard A. van Albada,a Mohamed Ghazzali,b* Khalid Refinement Al-Farhanb and Jan Reedijka,b R[F2>2(cid:2)(F2)]=0.035 Hatomstreatedbyamixtureof wR(F2)=0.092 independentandconstrained aLeidenInstituteofChemistry,LeidenUniversity,POBox9502,2300RALeiden, S=1.14 refinement TheNetherlands,andbDepartmentofChemistry,FacultyofScience,KingSaud 1296reflections (cid:2)(cid:6) =0.17eA˚(cid:4)3 max University,POBox2455,Riyadh11451,SaudiArabia 82parameters (cid:2)(cid:6)min=(cid:4)0.27eA˚(cid:4)3 Correspondencee-mail:[email protected] 2restraints Received7December2011;accepted27December2011 Table 1 Keyindicators:single-crystalX-raystudy;T=294K;mean(cid:2)(C–C)=0.003A˚; Hydrogen-bondgeometry(A˚,(cid:3)). Rfactor=0.035;wRfactor=0.092;data-to-parameterratio=15.8. D—H(cid:2)(cid:2)(cid:2)A D—H H(cid:2)(cid:2)(cid:2)A D(cid:2)(cid:2)(cid:2)A D—H(cid:2)(cid:2)(cid:2)A N2—H2A(cid:2)(cid:2)(cid:2)N3i 0.90(2) 2.17(2) 3.069(2) 174(2) Inthetitlepyrimidinederivative,C H ClN ,the2-chloroand 4 4 3 N2—H2B(cid:2)(cid:2)(cid:2)N1ii 0.87(2) 2.16(2) 3.024(2) 170(2) 4-amino substituents almost lie in the mean plane of the Symmetrycodes:(i)(cid:4)x;(cid:4)yþ1;(cid:4)zþ1;(ii)x;(cid:4)yþ1;zþ1. pyrimidinering,withdeviationsof0.003(1)A˚ fortheClatom, 2 2 and 0.020(1)A˚ for the N atom. In the crystal, molecules are Data collection: CrystalClear (Rigaku, 2007); cell refinement: linked via pairs of N—H(cid:2)(cid:2)(cid:2)N hydrogen bonds, forming CrystalClear;datareduction:CrystalClear;program(s)usedtosolve inversion dimers. These dimers are further linked via N— structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine H(cid:2)(cid:2)(cid:2)N hydrogen bonds, forming an undulating two-dimen- structure: SHELXL97 (Sheldrick, 2008); molecular graphics: sional network lyingparallel to (100). DIAMOND(Brandenburg,2007);softwareusedtopreparematerial forpublication:publCIF(Westrip,2010). Related literature The authors are indebted to the Deanship of Scientific Forcompoundsrelatedtopyrimidin-4-amine,see:VanAlbada Research,CollegeofScienceResearchCenter,forsupporting et al. (1999, 2003); Van Meervelt & Uytterhoeven (2003); this work. The Distinguished Scientist Fellowship Program Kozˇı´sˇeketal.(2005).Fortheagriculturalandpharmaceutical (DSFP) at King Saud University is gratefully acknowledged. relevance of 2-chloropyrimidin-4-amine, see: Zunszain et al. (2005).Forgraph-setanalysisofhydrogenbonds,see:Etteret Supplementary data and figures for this paper are available from the al.(1990);Bernstein et al.(1995). IUCrelectronicarchives(Reference:ZJ2047). References Bernstein,J.,Davis,R.E.,Shimoni,L.&Chang,N.-L.(1995).Angew.Chem. Int.Ed.Engl.34,1555–1573. Brandenburg,K.(2007).DIAMOND.CrystalImpactGbR,Bonn,Germany. Etter,M.C.,MacDonald,J.C.&Bernstein,J.(1990).ActaCryst.B46,256–262. Kozˇı´sˇek, J., D´ıaz, J. G., Fronc, M. & Svoboda, I. (2005). Acta Cryst. E61, m1150–m1152. Rigaku(2007).CrystalClear.Rigaku/MSCInc.,TheWoodlands,Texas,USA. Sheldrick,G.M.(2008).ActaCryst.A64,112–122. VanAlbada,G.A.,Komaei,S.A.,Kooijman,H.,Spek,A.L.&Reedijk,J. (1999).Inorg.Chim.Acta,287,226–231. Experimental VanAlbada,G.A.,Roubeau,O.,Mutikainen,I.,Turpeinen,U.&Reedijk,J. (2003).NewJ.Chem.27,1693–1697. Crystaldata VanMeervelt,L.&Uytterhoeven,K.(2003).Z.Kristallogr.NewCryst.Struct. CHClN c=12.7608(7)A˚ 218,481–482. M4 =4129.355 (cid:3)=100.886(2)(cid:3) Westrip,S.P.(2010).J.Appl.Cryst.43,920–925. Mronoclinic,P2=c V=569.70(5)A˚3 Zunszain, P. A., Federico, C., Sechi, M., Al-Damluji, S. & Ganellin, C. R. a=3.83162(191)A˚ Z=4 (2005).Bioorg.Med.Chem.13,3681–3689. b=11.8651(7)A˚ MoK(cid:4)radiation o302 A.VanAlbadaetal. doi:10.1107/S1600536811055863 ActaCryst.(2012).E68,o302 supplementary materials supplementary materials Acta Cryst. (2012). E68, o302 [ doi:10.1107/S1600536811055863 ] 2-Chloropyrimidin-4-amine G. van Albada, M. Ghazzali, K. Al-Farhan and J. Reedijk Comment The molecule of 2-chloropyrimidin-4-amine is relevant for agrochemistry as a plant growth regulator and as a pharmaceutical intermediate (Zunszain et al. 2005). It could also be an interesting precursor for chelating ligands after chlorine substitution. Pyrimidin-amines are interesting bridging ligands, as they contain two nitrogen coordination donor atoms, and an amine as a hydrogen bond donor group (Van Albada et al. 1999, 2003). The ligands pyrimidin-4-amine and 2-amine can easily bridge two metal ions (Kožíšek et al. 2005). With the presence of two donor atoms, the title compound might serve as a building block in the formation of coordination polymers. Due to the position of a chloride atom in-between the two donor N atoms of the pyrimidin-4-amine, the bridging would be likely to change. In fact, coordination complexes with the 2-chloropyrimidin-4-amine are yet unreachable. We here present the molecular structure of this compound, (Figure 1). The 2-chloropyrimidin-4-amine molecule is nearly planar, with r.m.s. deviation of the pyrimidine heterocyclic non-hy- drogen atoms is 0.002 (2) Å. In the crystal, molecules are arranged with two N—H···N hydrogen bond motifs, where the amine group serves as a twofold donor of the hydrogen atoms for the two pyrimidine nitrogen atoms. Considering graph-set 2 analysis (Etter et al., 1990; Bernstein et al., 1995), the descriptors are R (8) loops and C(5) chain motifs along the [001] 2 and [010] vectors, respectively. The network can be described as a wobbled two-dimensional network extending in the (100) plane, (Figure 2). It is worth to note that the related pyrimidin-4-amine molecule (Van Meervelt et al. 2003), crystallizes in the orthorhombic Pcab space group and exhibits only the N—H···N hydrogen bond with C(5) chain motif of a one-di- mensional zigzag chain. Experimental The ligand was used as commercially available. 0.5 mg of the compound was dissolved in 10 ml of methanol. The solution was stand at room temperature in a closed vessel. After two weeks, colourless blocks appeared and separated by filtration. Refinement Carbon-bound H-atoms were placed in ideal calculated positions [aromatic C—H 0.93 Å, U (H) = 1.2U (C)] and refined iso eq as riding atoms. The amine H-atoms were constrained into their positions using two distance restraints [N—H 0.91 Å, U (H) = 1.2U (N)]. iso eq sup-1 supplementary materials Figures Fig. 1. Atomic numbering scheme and thermal ellipsoidal (50% probability level) of the title compound. Hydrogen atoms are presented as spheres of arbitrary radii. 2 Fig. 2. bc-plane projection showing the N—H···N hydrogen bonds as dotted line of R (8) 2 loop (presented in blue color), and C(5) chain (presented in red color). Symmetry codes: (i) - x, -y + 1, -z + 1; (ii) x, -y + 1/2, z + 1/2. 2-Chloropyrimidin-4-amine Crystal data C4H4ClN3 F(000) = 264 Mr = 129.55 Dx = 1.510 Mg m−3 Monoclinic, P21/c Mo Kα radiation, λ = 0.71075 Å Hall symbol: -P 2ybc Cell parameters from 342 reflections a = 3.83162 (19) Å θ = 3.3–27.5° b = 11.8651 (7) Å µ = 0.55 mm−1 c = 12.7608 (7) Å T = 294 K β = 100.886 (2)° Block, colourless V = 569.70 (5) Å3 0.40 × 0.20 × 0.20 mm Z = 4 Data collection Rigaku R-AXIS RAPID 1296 independent reflections diffractometer Radiation source: fine-focus sealed tube 962 reflections with I > 2σ(I) graphite Rint = 0.038 ω scans θmax = 27.5°, θmin = 3.3° Absorption correction: multi-scan h = −4→4 (CrystalClear; Rigaku, 2007) Tmin = 0.840, Tmax = 0.888 k = −15→15 9506 measured reflections l = −16→16 sup-2 supplementary materials Refinement Primary atom site location: structure-invariant direct Refinement on F2 methods Least-squares matrix: full Secondary atom site location: difference Fourier map Hydrogen site location: inferred from neighbouring R[F2 > 2σ(F2)] = 0.035 sites H atoms treated by a mixture of independent and wR(F2) = 0.092 constrained refinement w = 1/[σ2(Fo2) + (0.0422P)2 + 0.0697P] S = 1.14 where P = (Fo2 + 2Fc2)/3 1296 reflections (Δ/σ)max < 0.001 82 parameters Δρmax = 0.17 e Å−3 2 restraints Δρmin = −0.27 e Å−3 Special details 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 mat- rix. 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, convention- al 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. 2 Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å ) x y z Uiso*/Ueq Cl1 0.05814 (13) 0.43867 (4) 0.20898 (3) 0.0586 (2) N1 0.3425 (4) 0.25622 (13) 0.29987 (11) 0.0500 (4) N2 0.2112 (5) 0.37262 (14) 0.59166 (12) 0.0522 (4) H2B 0.277 (5) 0.3340 (17) 0.6504 (14) 0.065 (6)* H2A 0.103 (5) 0.4395 (14) 0.5959 (17) 0.061 (6)* C2 0.2035 (4) 0.35294 (14) 0.32044 (13) 0.0419 (4) N3 0.1530 (4) 0.39673 (11) 0.41103 (10) 0.0407 (3) C4 0.2612 (4) 0.33227 (13) 0.49910 (12) 0.0400 (4) C5 0.4177 (5) 0.22616 (15) 0.48826 (14) 0.0480 (4) H5 0.4961 0.1806 0.5473 0.058* C6 0.4495 (5) 0.19310 (16) 0.38937 (16) 0.0531 (5) H6 0.5506 0.1230 0.3818 0.064* 2 Atomic displacement parameters (Å ) U11 U22 U33 U12 U13 U23 Cl1 0.0718 (4) 0.0665 (4) 0.0379 (3) 0.0003 (2) 0.0113 (2) 0.0060 (2) sup-3 supplementary materials N1 0.0570 (9) 0.0502 (9) 0.0447 (9) 0.0005 (7) 0.0143 (7) −0.0103 (7) N2 0.0775 (11) 0.0455 (9) 0.0345 (8) 0.0079 (8) 0.0130 (7) 0.0007 (7) C2 0.0431 (9) 0.0456 (9) 0.0379 (9) −0.0055 (7) 0.0101 (7) −0.0045 (7) N3 0.0496 (8) 0.0380 (7) 0.0357 (7) −0.0010 (6) 0.0112 (6) −0.0019 (6) C4 0.0439 (9) 0.0395 (9) 0.0372 (8) −0.0034 (7) 0.0092 (7) −0.0013 (7) C5 0.0533 (10) 0.0429 (10) 0.0472 (10) 0.0047 (8) 0.0075 (8) 0.0027 (8) C6 0.0550 (11) 0.0442 (10) 0.0610 (12) 0.0047 (8) 0.0132 (9) −0.0092 (9) Geometric parameters (Å, °) Cl1—C2 1.7518 (17) C2—N3 1.315 (2) N1—C2 1.312 (2) N3—C4 1.358 (2) N1—C6 1.363 (2) C4—C5 1.412 (2) N2—C4 1.322 (2) C5—C6 1.349 (2) N2—H2B 0.874 (15) C5—H5 0.9300 N2—H2A 0.902 (16) C6—H6 0.9300 C2—N1—C6 112.47 (15) N2—C4—C5 123.11 (16) C4—N2—H2B 120.6 (14) N3—C4—C5 119.33 (15) C4—N2—H2A 121.3 (14) C6—C5—C4 117.77 (16) H2B—N2—H2A 118 (2) C6—C5—H5 121.1 N1—C2—N3 130.85 (16) C4—C5—H5 121.1 N1—C2—Cl1 115.10 (12) C5—C6—N1 123.94 (17) N3—C2—Cl1 114.05 (13) C5—C6—H6 118.0 C2—N3—C4 115.64 (14) N1—C6—H6 118.0 N2—C4—N3 117.56 (15) Hydrogen-bond geometry (Å, °) D—H···A D—H H···A D···A D—H···A N2—H2A···N3i 0.90 (2) 2.17 (2) 3.069 (2) 174.(2) N2—H2B···N1ii 0.87 (2) 2.16 (2) 3.024 (2) 170.(2) Symmetry codes: (i) −x, −y+1, −z+1; (ii) x, −y+1/2, z+1/2. sup-4 supplementary materials Fig. 1 sup-5 supplementary materials Fig. 2 sup-6