Crystal structure of ethyl 2-phenyl-4-(prop-2-yn-1-yl­oxy)-5,6,7,8-tetra­hydro­pyrido[4′,3′:4,5]thieno[2,3-d]pyrimidine-7-carboxyl­ate

Mehmet Akkurt; Victoria A Smolenski; Shaaban K Mohamed; Jerry P Jasinski; Essam K Ahmed; Mustafa R Albayati

doi:10.1107/S2056989015018447

. 2015 Oct 10;71(Pt 11):o836–o837. doi: 10.1107/S2056989015018447

Crystal structure of ethyl 2-phenyl-4-(prop-2-yn-1-yloxy)-5,6,7,8-tetrahydropyrido[4′,3′:4,5]thieno[2,3-d]pyrimidine-7-carboxylate

Mehmet Akkurt ^a, Victoria A Smolenski ^b, Shaaban K Mohamed ^c,^d, Jerry P Jasinski ^b, Essam K Ahmed ^d, Mustafa R Albayati ^e,^*

PMCID: PMC4645036 PMID: 26594553

Abstract

In the title compound, C₂₁H₁₉N₃O₃S, the 5,6,7,8-tetrahydropyridine ring adopts a half-chair conformation. The fused-thieno[2,3-d]pyrimidine ring system is essentially planar (r.m.s. deviation = 0.001 Å) and forms a dihedral angle of 2.66 (6)° with the attached phenyl ring. The three-dimensional crystal packing is stabilized by C—H⋯O and C—H⋯N hydrogen bonds and C—H⋯π interactions.

Keywords: crystal structure, thieno-pyrimidine, tetrahydropyridine ring, hydrogen bonding, C—H⋯π interactions

Related literature

For general chemistry background to heterocyclic thieno[2,3-d]pyrimidines, see: Litvinov (2004 ▸). For the diversity of biological activities of thieno-pyrimidine derivatives, see: Nasr & Gineinah (2002 ▸); Bhuiyan et al. (2005 ▸); Chambhare et al. (2003 ▸); Alagarsamy et al. (2006 ▸). Kapustina et al. (1992 ▸). For related structures, see: Liu et al. (2005 ▸); Ren et al. (2006 ▸).

Experimental

Crystal data

C₂₁H₁₉N₃O₃S
M _r = 393.45
Monoclinic,
a = 13.143 (2) Å
b = 8.013 (2) Å
c = 17.880 (2) Å
β = 96.129 (14)°
V = 1872.3 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.20 mm⁻¹
T = 296 K
0.28 × 0.14 × 0.08 mm

Data collection

Agilent Xcalibur, Eos, Gemini diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014 ▸) T _min = 0.834, T _max = 1.000
14345 measured reflections
6319 independent reflections
4721 reflections with I > 2σ(I)
R _int = 0.032

Refinement

R[F ² > 2σ(F ²)] = 0.044
wR(F ²) = 0.117
S = 1.04
6319 reflections
254 parameters
H-atom parameters constrained
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2014 ▸); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS2014 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▸); software used to prepare material for publication: PLATON (Spek, 2009 ▸).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015018447/tk5390sup1.cif

e-71-0o836-sup1.cif^{(28.5KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015018447/tk5390Isup2.hkl

e-71-0o836-Isup2.hkl^{(346.3KB, hkl)}

Click here for additional data file.^{(7.4KB, cml)}

Supporting information file. DOI: 10.1107/S2056989015018447/tk5390Isup3.cml

Click here for additional data file.^{(1.1MB, tif)}

. DOI: 10.1107/S2056989015018447/tk5390fig1.tif

View of the title compound with the atom numbering scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level.

Click here for additional data file.^{(3.7MB, tif)}

a . DOI: 10.1107/S2056989015018447/tk5390fig2.tif

The molecular packing viewed down a axis. H atoms not involved in H bonding are omitted for clarity.

CCDC reference: 1429186

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

Cg1 and Cg4 are the centroids of the S1,C9C11/C15 and C1C6 rings, respectively.

DHA	DH	HA	D A	DHA
C14H14AO2ⁱ	0.97	2.44	3.294(2)	146
C21H21N2ⁱⁱ	0.93	2.55	3.418(2)	156
C12H12B Cg4ⁱⁱⁱ	0.97	2.80	3.6643(17)	149
C19H19A Cg1^iv	0.97	2.92	3.6736(18)	136

Open in a new tab

Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

JPJ acknowledges the NSF–MRI program (grant No·CHE-1039027) for funds to purchase the X-ray diffractometer.

supplementary crystallographic information

S1. Comment

Thieno[2,3-d]pyrimidines are a large group of heterocyclic compounds (Litvinov, 2004), and some of them showed antiviral (Nasr & Gineinah, 2002), antimicrobial (Bhuiyan et al., 2005; Chambhare et al., 2003), and antibacterial properties (Alagarsamy et al., 2006). Fused tri- and tetracyclic thieno[2,3-d]pyrimidin-4-ones are synthesized by many methods and among them some compounds have fungicidal, antibacterial, and anti-inflammatory activities (Kapustina et al., 1992). In this context, and following to our on-going study of bio-active molecules, we report here the synthesis and crystal structure of the title compound.

In the title compound (Fig. 1), the 5,6,7,8-tetrahydropyridine ring (N3/C11/-C15) adopts a half-chair conformation [the puckering parameters are Q_T = 0.4662 (14) Å, θ = 50.06 (17) ° and φ = 30.8 (2) °]. The fused-thieno[2,3-d]pyrimidine ring system (S1/N1/N2C7-C11/C15) is essentially planar (r.m.s. deviation = 0.001 Å) and forms a dihedral angle of 2.66 (6)° with the attached phenyl ring (C1–C6). The C8–O1–C19–C20, C13–N3–C16–O2 and N3–C16–O3–C17 torsion angles are −166.90 (12), −174.90 (13) and 179.78 (12)°, respectively. All bond lengths and angles in the title molecule are normal and comparable with those previously reported for related structures (Liu et al., 2005; Ren et al., 2006).

In the crystal, molecules are linked by C—H···O, C—H···N and C—H···π hydrogen bonds, forming a three dimensional network (Fig. 2 & Table 1).

S2. Experimental

Propargyl bromide (1.1 g, 9 mmol) was added to a suspension of ethyl 4-hydroxy-2-phenyl-5,6-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidine-7(8H)-carboxylate (1.07 g, 3 mmol) and K₂CO₃ (0.82 g, 6 mmol) in DMF (15 ml), and stirred at room temperature for 6 h. The excess solvent was evaporated to dryness in vacuo. The residue was diluted with water and then extracted with CH₂Cl₂ (3 x 30 ml). The combined organic extracts were dried over anhydrous Na₂SO₄, filtered and evaporated under reduced pressure to give colourless crystals in a sufficient quality for X-ray diffraction.