Buy article online - an online subscription or single-article purchase is required to access this article.
Download citation
Download citation
link to html
The mol­ecules of the title compound, C13H18N6O2S2, lie across twofold rotation axes in the space group C2/c. Although the pyrimidine ring is effectively planar, the bridging methyl­ene C atom is displaced from the plane of the pyrimidine ring by 0.213 (2) Å, while the C-C-C angle at the bridging C atom is 120.3 (2)°. The mol­ecule contains two symmetry-related N-H...O hydrogen bonds, generating S(8) motifs, and inter­moecular N-H...O hydrogen bonds link the mol­ecules into a ribbon of edge-fused rings.

Supporting information


Crystallographic Information File (CIF)
Contains datablocks global, I


Structure factor file (CIF format)
Contains datablock I

CCDC reference: 964768

Introduction top

Pyrimidino­nes have attracted considerable attention in synthetic organic chemistry because of their wide range of biological activities (Kappe 2000), while multicomponent reactions are gaining importance in organic and medicinal chemistry because of their capacity to generate multifunctionalized products. We have now obtained the unexpected product 5,5'-methyl­enebis[6-amino-3-methyl-2-methyl­sulfanylpyrimidin-4(3H)-one], (I), from a reaction involving a 4-amino­pyrimidin-6-one, paraformaldehyde and tetra­lone which was intended to produce the corresponding 6,9-di­hydro­benzo[h]pyrimido[4,5-b]quinolin-8(5H)-one. In the event, the tetra­lone played no part in the reaction, which was a simple condensation between the pyrimidinone and paraformaldehyde, and the product (I) can, in fact, be prepared in satisfactory yield without the presence of tetra­lone. Methyl­endi­pyrimidinone derivatives such as (I) can be used as multifunctionalized precursors in the synthesis of more complex heterocyclic compounds.

Experimental top

Synthesis and crystallization top

A mixture of 6-amino-3-methyl-2-(methyl­sulfanyl)pyrimidin-4(3H)-one (1.0 mmol) and paraformaldehyde (5.0 mmol) in di­methyl­formamide (5.0 ml) was heated under reflux for 5 h, after which time the product started to crystallize. The mixture was allowed to cool to ambient temperature, and the resulting solid product was collected by filtration and washed with methanol. Orange crystals suitable for single-crystal X-ray diffraction were selected directly from the crystallized product [yield 70%, m.p. >573 K (decomposition)]. MS (70 eV) m/z (%): 354 (100, M+), 339 (28), 249 (57), 201 (16), 184 (55), 150 (19), 88 (83), 57 (18).

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 1. All H atoms were located in difference maps. H atoms bonded to C atoms were then treated as riding atoms in geometrically idealized positions, with C—H = 0.98 (CH3) or 0.99 Å (CH2) and Uiso(H) = kUeq(C), where k = 1.2 for the H atoms bonded to atom C51 and k = 1.5 for the methyl groups, which were permitted to rotate but not to tilt. The H atoms bonded to atom N61 were permitted to ride at the positions located in a difference map, with Uiso(H) = 1.2Ueq(N), giving the N—H distances shown in Table 2. The reflection 200, which had been badly attenuated by the beam-stop, was omitted from the data set.

Results and discussion top

The molecules of the title compound, (I) (Fig. 1), lie across twofold rotation axes in the space group C2/c, and the reference molecule was selected as one lying across the axis along (1/2, y, 1/4). The molecule of (I) contains two symmetry-related N—H···O hydrogen bonds (Table 2), which produce a pair of edge-fused S(8) rings (Bernstein et al., 1995) (Fig. 1). The intra­molecular N—H···O hydrogen bond and the inter­molecular N—H···O hydrogen bond, discussed below, have similar and fairly short N···O distances and in both the N—H···O unit deviates only slightly from linearity; accordingly, both hydrogen bonds can be regarded as fairly strong for their type. However, apart from the inter­molecular hydrogen bond, there are no direction-specific inter­molecular inter­actions in the crystal structure of (I).

Despite the high degree of substitution on the pyrimidine ring, this ring is effectively planar, with a maximum deviation from the mean plane of the six ring atoms of only 0.026 (2) Å for atom C5. This ring planarity is in marked contrast to the puckered rings often found for highly substituted pyrimidine rings, particularly for those carrying substituents at each of positions 4, 5 and 6 (Melguizo et al., 2003; Quesada et al., 2003, 2004; Low et al., 2007; Trilleras et al., 2007; Cobo et al., 2008). Indeed, with the exception of the central atom C51, discussed below, the maximum deviations of any of the substituent atoms from the mean plane of the pyrimidine ring are 0.060 (2) Å for atom N61 and 0.059 (1) Å for atom S21. Although atom S21 is almost coplanar with the ring, the adjacent atom C21 is displaced from the ring plane by 0.408 (2) Å, consistent with the torsion angles (Table 1) involving this atom.

A striking feature of the molecular geometry is the wide C—C—C angle at the central C51 atom (Table 2), although the C5—C51 distance is entirely typical of its type [mean value (Allen et al., 1987) = 1.510 Å and upper quartile value = 1.518 Å]. This angle is associated with a displacement of atom C51 from the mean plane of the ring by 0.213 (3) Å in the sense which gives a smaller C—C—C angle than would be the case of C51 were coplanar with the ring. By contrast, the central C—C—C angle in di­phenyl­methane, Ph2CH2, is entirely normal at 112.4 (7)° (Barnes et al., 1981), while the C—C—C angle in propane, determined on isolated molecules in the gas phase, is 112 (1)° (Iijima, 1972). While X—CH2X bond angles which are significantly larger than the ideal tetra­hedral value are uncommon, the value found here is not without precedent. For example, in methyl­enebis(1,3,5-tri­methyl-4-imidazolin-2-one), (II) (see Scheme), which crystallizes with Z' = 2 (Glidewell et al., 1979), the central C—C—C angles in the two independent molecules are 113.1 (8) and 116.9 (8)°. However, if the substituent X is based upon an element from the second row of the Periodic Table, substanti­ally larger X—CH2X angles have been observed: thus, in CH2(PSePh2)2, the central P—C—P angle in 117.9 (6)° (Carroll & Titus, 1977) and in CH2(SiPh3)2, the central Si—C—Si angle is 128.8 (7)° (Glidewell & Liles, 1982). If the central –CH2– unit is replaced by one of its isoelectronic analogues, i.e. –NH– or –O–, similar behaviour is observed; thus, the C—O—C angle in O(CPh3)2 is 127.9 (1)° (Glidewell & Liles, 1978), while in HN(SiPh3)2, the central Si—N—Si angle is as large as 138.1 (4)° (Glidewell & Holden, 1981). All these observations, and others on similar compounds, are most straightforwardly inter­preted in terms of steric repulsions between the substituents dominated, but not exclusively controlled, by the nonbonded contacts between the α-atoms denoted as X above.

Anomalously large C—C—C angles have also been reported at the bridging methine C atom in compound (III) (see Scheme), where the C—C—C angle at the bridging C atom is 127.8 (3)° (Insuasty et al., 2012) and in compounds (IV)–(X), where the corresponding angles are all close to 130° (Delgado et al., 2005, 2006). In (III), there is a short and repulsive intra­molecular N···S contact, with a similar C—H···S contact in each of (IV)–(X). The surprising feature in all of these molecules is the effective planarity of their molecular skeletons. Rather than using a rotation of the imidazole or aryl ring about the single bond linking it to the bridging atom, which might intuitively seem to be least energetic pathway, the steric stress is instead relieved in every case by an expansion of the central C—C—C angle.

The structural metrics of simple molecular systems characterized by bond angles which are significantly larger than those expected from the VSEPR (valence shell electron pair repulsion) model (Gillespie & Nyholm, 1957; Gillespie, 1972) have been successfully analysed in steric terms (Bartell, 1960; Burdett, 1980) by recognizing that, for geometrical purposes, atoms within molecules can be treated as hard incompressible entities (Bartell, 1960), which do not, however behave as spherical objects, as judged by the angular variation of the limiting contact distances in molecular crystals (Nyburg & Faerman, 1985). In the present compound, (I), there are no other direction-specific inter­actions between the molecules, as noted above, and the mutual disposition and orientation of the two pyrimidine rings appears to be controlled by the hydrogen bonds. Accordingly, the steric strain around atom C51 can be relieved by three plausible means, or by some combination of them: (i) the C5—C51 bond length could become perturbed from its normal value, although this is probably the most energy-expensive option; (ii) the C5—C51—C5i angle [symmetry code: (i) -x+1, y, -z+1/2] could be widened; or (iii) atom C51 could be displaced from the plane of the pyrimidine ring. Since the C5—C51 bond is of normal length, this leaves a combination of angle enlargement and atom displacement available for the relief of steric strain. Given the separation of atoms C5 and C5i, confining atom C51 to the plane of the pyrimidine ring would require a central C—C—C angle of 133.5°, associated with a C5—C51 bond length of only 1.21 Å; hence the observed combination of a less extreme C5—C51—C5i angle and the displacement of atom C51 from the plane of the pyrimidine ring.

The molecules of (I) are linked by a second N—H···O hydrogen bond (Table 3) to produce a molecular ribbon consisting of edge-fused running parallel to the [101] direction, in which molecules lying across the series of twofold rotation axes along (0.5n, y, 0.5n-1/4) alternate with centrosymmetric R42(8) rings centred at (0.5n+1/4, y, 0.5n), where n represents an integer in each case (Fig. 2). Two ribbons of this type, related to one another by the C-centring operation, pass through each unit cell, but there are no direction-specific inter­actions between adjacent ribbons.

Related literature top

For related literature, see: Barnes et al. (1981); Bartell (1960); Bernstein et al. (1995); Burdett (1980); Carroll & Titus (1977); Cobo et al. (2008); Delgado et al. (2005, 2006); Gillespie (1972); Glidewell & Holden (1981); Glidewell & Liles (1978, 1982); Iijima (1972); Insuasty et al. (2012); Kappe (2000); Low et al. (2007); Melguizo et al. (2003); Nyburg & Faerman (1985); Quesada et al. (2003, 2004); Trilleras et al. (2007).

Computing details top

Data collection: COLLECT (Hooft, 1998); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
Fig. 1. The molecular structure of compound (I), showing the atom-labelling scheme and the intramolecular N—H···O hydrogen bonds. Displacement ellipsoids are drawn at the 30% probability level. [Symmetry code: (i) -x+1, y, -z+1/2.]

Fig. 2. Part of the crystal structure of compound (I), showing the formation of a ribbon of edge-fused hydrogen-bonded S(8) and R42(8) rings parallel to the [101] direction. For the sake of clarity, H atoms bonded to C atoms have been omitted. The S21 atoms marked with an asterisk (*), a hash (#), a dollar sign ($), an ampersand (&) or an `at' sign (@) are at the symmetry positions (-x+1, y, -z+1/2), (x+1/2, -y+1/2, z+1/2), (x+1, y, z+1), (-x+3/2, -y+1/2, -z+1) and (-x+2, y, -z+3/2), respectively.
5,5'-Methylenebis[6-amino-3-methyl-2-methylsulfanylpyrimidin-4(3H)-one] top
Crystal data top
C13H18N6O2S2F(000) = 744
Mr = 354.47Dx = 1.536 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1763 reflections
a = 19.862 (6) Åθ = 2.9–27.5°
b = 7.4877 (19) ŵ = 0.37 mm1
c = 14.236 (5) ÅT = 120 K
β = 133.61 (2)°Block, orange
V = 1533.0 (10) Å30.31 × 0.24 × 0.16 mm
Z = 4
Data collection top
Bruker–Nonius KappaCCD
1763 independent reflections
Radiation source: Bruker–Nonius FR591 rotating anode1442 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.041
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 2.9°
ϕ & ω scansh = 2525
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
k = 99
Tmin = 0.895, Tmax = 0.944l = 1818
10706 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.113H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0598P)2 + 1.8314P]
where P = (Fo2 + 2Fc2)/3
1763 reflections(Δ/σ)max = 0.001
107 parametersΔρmax = 0.43 e Å3
0 restraintsΔρmin = 0.47 e Å3
Crystal data top
C13H18N6O2S2V = 1533.0 (10) Å3
Mr = 354.47Z = 4
Monoclinic, C2/cMo Kα radiation
a = 19.862 (6) ŵ = 0.37 mm1
b = 7.4877 (19) ÅT = 120 K
c = 14.236 (5) Å0.31 × 0.24 × 0.16 mm
β = 133.61 (2)°
Data collection top
Bruker–Nonius KappaCCD
1763 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
1442 reflections with I > 2σ(I)
Tmin = 0.895, Tmax = 0.944Rint = 0.041
10706 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0410 restraints
wR(F2) = 0.113H-atom parameters constrained
S = 1.07Δρmax = 0.43 e Å3
1763 reflectionsΔρmin = 0.47 e Å3
107 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
N10.40451 (10)0.2749 (2)0.37455 (14)0.0221 (3)
C20.47983 (12)0.2819 (2)0.49776 (17)0.0210 (4)
N30.56632 (10)0.2293 (2)0.55153 (14)0.0218 (3)
C40.57747 (13)0.1544 (2)0.47152 (18)0.0213 (4)
C50.49617 (13)0.1386 (2)0.33850 (18)0.0213 (4)
C60.41280 (13)0.2054 (2)0.29338 (17)0.0218 (4)
S210.47580 (3)0.36659 (6)0.60877 (4)0.02434 (17)
C210.35233 (14)0.3784 (3)0.5089 (2)0.0300 (4)
C310.64794 (13)0.2467 (3)0.69125 (18)0.0275 (4)
O410.65766 (9)0.10876 (18)0.52349 (13)0.0255 (3)
C510.50000.0381 (4)0.25000.0227 (5)
N610.33348 (11)0.2033 (2)0.16687 (15)0.0274 (4)
Atomic displacement parameters (Å2) top
N10.0212 (8)0.0270 (8)0.0231 (8)0.0010 (6)0.0171 (7)0.0002 (6)
C20.0212 (9)0.0221 (9)0.0242 (9)0.0003 (7)0.0174 (8)0.0019 (7)
N30.0201 (8)0.0269 (8)0.0210 (7)0.0007 (6)0.0152 (7)0.0017 (6)
C40.0231 (9)0.0211 (9)0.0260 (9)0.0003 (7)0.0193 (8)0.0029 (7)
C50.0236 (9)0.0215 (9)0.0249 (9)0.0014 (7)0.0191 (8)0.0014 (7)
C60.0214 (9)0.0236 (9)0.0238 (9)0.0031 (7)0.0169 (8)0.0007 (7)
S210.0246 (3)0.0302 (3)0.0237 (3)0.00031 (19)0.0187 (2)0.00003 (18)
C210.0258 (9)0.0410 (12)0.0284 (10)0.0040 (9)0.0207 (9)0.0012 (9)
C310.0218 (9)0.0393 (11)0.0226 (9)0.0013 (8)0.0157 (8)0.0027 (8)
O410.0209 (7)0.0334 (8)0.0252 (7)0.0021 (6)0.0170 (6)0.0029 (6)
C510.0239 (12)0.0239 (13)0.0262 (13)0.0000.0195 (11)0.000
N610.0207 (8)0.0409 (10)0.0232 (8)0.0014 (7)0.0162 (7)0.0023 (7)
Geometric parameters (Å, º) top
N1—C21.303 (2)C21—H21A0.9800
N1—C61.377 (2)C21—H21B0.9800
C2—N31.370 (2)C21—H21C0.9800
C2—S211.7553 (19)C31—H31A0.9800
N3—C41.417 (2)C31—H31B0.9800
N3—C311.467 (2)C31—H31C0.9800
C4—O411.255 (2)C51—C5i1.514 (2)
C4—C51.410 (3)C51—H51A0.9900
C5—C61.392 (3)C51—H51B0.9900
C5—C511.514 (2)N61—H61A0.8798
C6—N611.346 (2)N61—H61B0.8800
S21—C211.798 (2)
C2—N1—C6117.02 (16)H21A—C21—H21B109.5
N1—C2—N3124.99 (16)S21—C21—H21C109.5
N1—C2—S21120.24 (14)H21A—C21—H21C109.5
N3—C2—S21114.76 (13)H21B—C21—H21C109.5
C2—N3—C4119.68 (15)N3—C31—H31A109.5
C2—N3—C31121.27 (15)N3—C31—H31B109.5
C4—N3—C31119.04 (15)H31A—C31—H31B109.5
O41—C4—C5125.50 (17)N3—C31—H31C109.5
O41—C4—N3118.18 (16)H31A—C31—H31C109.5
C5—C4—N3116.32 (16)H31B—C31—H31C109.5
C6—C5—C4119.04 (17)C5—C51—C5i120.3 (2)
C6—C5—C51121.42 (15)C5—C51—H51A107.2
C4—C5—C51119.40 (15)C5i—C51—H51A107.2
N61—C6—N1114.86 (17)C5—C51—H51B107.2
N61—C6—C5122.35 (17)C5i—C51—H51B107.2
N1—C6—C5122.77 (17)H51A—C51—H51B106.9
C2—S21—C21100.96 (10)C6—N61—H61A123.8
C6—N1—C2—N31.6 (3)O41—C4—C5—C518.4 (3)
C6—N1—C2—S21179.46 (13)N3—C4—C5—C51171.97 (16)
N1—C2—N3—C42.6 (3)C2—N1—C6—N61179.08 (17)
S21—C2—N3—C4178.35 (13)C2—N1—C6—C52.3 (3)
N1—C2—N3—C31178.27 (18)C4—C5—C6—N61176.56 (18)
S21—C2—N3—C310.8 (2)C51—C5—C6—N617.9 (3)
C2—N3—C4—O41179.51 (16)C4—C5—C6—N14.9 (3)
C31—N3—C4—O411.4 (3)C51—C5—C6—N1170.59 (18)
C2—N3—C4—C50.2 (2)N1—C2—S21—C2111.36 (18)
C31—N3—C4—C5178.98 (16)N3—C2—S21—C21169.56 (14)
O41—C4—C5—C6175.99 (17)C4—C5—C51—C5i102.25 (17)
N3—C4—C5—C63.6 (2)C6—C5—C51—C5i82.24 (17)
Symmetry code: (i) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
N61—H61A···O41i0.882.052.921 (3)173
N61—H61B···O41ii0.882.072.917 (3)162
Symmetry codes: (i) x+1, y, z+1/2; (ii) x1/2, y+1/2, z1/2.

Experimental details

Crystal data
Chemical formulaC13H18N6O2S2
Crystal system, space groupMonoclinic, C2/c
Temperature (K)120
a, b, c (Å)19.862 (6), 7.4877 (19), 14.236 (5)
β (°) 133.61 (2)
V3)1533.0 (10)
Radiation typeMo Kα
µ (mm1)0.37
Crystal size (mm)0.31 × 0.24 × 0.16
Data collection
DiffractometerBruker–Nonius KappaCCD
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.895, 0.944
No. of measured, independent and
observed [I > 2σ(I)] reflections
10706, 1763, 1442
(sin θ/λ)max1)0.650
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.113, 1.07
No. of reflections1763
No. of parameters107
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.43, 0.47

Computer programs: COLLECT (Hooft, 1998), DIRAX/LSQ (Duisenberg et al., 2000), EVALCCD (Duisenberg et al., 2003), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Selected geometric parameters (Å, º) top
C5—C511.514 (2)
C5—C51—C5i120.3 (2)
N1—C2—S21—C2111.36 (18)C4—C5—C51—C5i102.25 (17)
N3—C2—S21—C21169.56 (14)C6—C5—C51—C5i82.24 (17)
Symmetry code: (i) x+1, y, z+1/2.
Hydrogen-bond geometry (Å, º) top
N61—H61A···O41i0.882.052.921 (3)173
N61—H61B···O41ii0.882.072.917 (3)162
Symmetry codes: (i) x+1, y, z+1/2; (ii) x1/2, y+1/2, z1/2.

Subscribe to Acta Crystallographica Section C: Structural Chemistry

The full text of this article is available to subscribers to the journal.

If you have already registered and are using a computer listed in your registration details, please email for assistance.

Buy online

You may purchase this article in PDF and/or HTML formats. For purchasers in the European Community who do not have a VAT number, VAT will be added at the local rate. Payments to the IUCr are handled by WorldPay, who will accept payment by credit card in several currencies. To purchase the article, please complete the form below (fields marked * are required), and then click on `Continue'.
E-mail address* 
Repeat e-mail address* 
(for error checking) 

Format*   PDF (US $40)
   HTML (US $40)
   PDF+HTML (US $50)
In order for VAT to be shown for your country javascript needs to be enabled.

VAT number 
(non-UK EC countries only) 

Terms and conditions of use
Contact us

Follow Acta Cryst. C
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds