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. 2020 Feb 28;5(Pt 2):x200257. doi: 10.1107/S2414314620002576

1,3-Bis(2-oxoprop­yl)thymine

Bogdan Doboszewski a, Alexander Y Nazarenko b,*, Fábio da Paixão Soares a
Editor: O Blacquec
PMCID: PMC9462178  PMID: 36340837

In the title compound, C11H14N2O4, the two 2-oxopropyl groups are nearly perpendicular to the planar thymine unit. One methyl group of the oxopropyl substituent is disordered. In the crystal, C—H⋯O inter­actions help to connect the mol­ecules into (001) layers.

Keywords: crystal structure, thymine, substituted nucleobase, 2-oxoprop­yl

Abstract

In the title compound [systematic name: 5-methyl-1,3-bis­(2-oxoprop­yl)pyrimidine-2,4(1H,3H)-dione], C11H14N2O4, the two 2-oxopropyl groups are nearly perpendicular to the planar thymine unit. One methyl group of oxopropyl substituent is disordered. In the crystal, C—H⋯O inter­actions help to connect the mol­ecules into (001) layers. graphic file with name x-05-x200257-scheme1-3D1.jpg

Structure description

Nucleoside analogs play an important role in combating viral diseases and neoplasms; this is demonstrated by the pharmacological success of drugs such as Zidovudine, Stavudine, Lamivudine, and around 20 others belonging to this group of compounds (Adamska et al., 2016 ▸; Krim et al., 2012 ▸; Negrón-Silva et al., 2013 ▸; Thakur et al., 2014 ▸). We performed the transformation of N 1,N 3-bis­propargyl thymine and uracyl, which furnished N 1,N 3-bis-(2-oxopro-1-yl) derivatives; these compounds offer ample possibilities of further functionalization via C or O alkyl­ation of their enolates, or via reductive amination, among others.

In the title compound (Fig. 1 ▸), the thymine unit is nearly planar, with the largest deviation from the mean plane being less than 0.03 Å. The two essentially planar 2-oxopropyl substituents are almost perpendicular to the thymine unit; the dihedral angles between the mean plane of the six-membered ring and those of the 2-oxopropyl fragments with atoms C1 and C7 are 77.96 (1) and 82.92 (1)°, respectively. Rotational disorder was observed for the C1 methyl group of the 2-oxopropyl substituent.

Figure 1.

Figure 1

Numbering scheme for the title compound, shown with 50% probability displacement ellipsoids.

There are no usual hydrogen bonds in this structure. Attractive C—H⋯O inter­actions (Table 1 ▸), involving all oxygen atoms of the mol­ecule, help to organize the mol­ecules in a layer parallel to the (001) plane. These layers are packed in the three-dimensional crystal by van der Waals forces, mainly between hydrogen atoms (Fig. 2 ▸).

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C3—H3A⋯O2i 0.97 (1) 2.56 (1) 3.304 (2) 134 (1)
C3—H3B⋯O4ii 0.97 (1) 2.45 (1) 3.3820 (19) 160 (1)
C5—H5B⋯O3iii 0.96 (1) 2.50 (1) 3.353 (2) 148 (1)
C7—H7A⋯O1iv 0.96 (1) 2.54 (1) 3.2576 (19) 131 (1)
C7—H7B⋯O3iii 0.96 (1) 2.50 (1) 3.370 (2) 150 (1)
C8—H8⋯O4ii 0.96 (1) 2.50 (1) 3.3213 (19) 144 (1)

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

Figure 2.

Figure 2

Packing of the title compound, viewed along [010].

Synthesis and crystallization

As N1,N3-bis­propargyl thymine can be prepared in yields exceeding 80%, we used it as a starting material to obtain the title compound (1) via addition of water catalyzed by silica-supported HgSO4/H2SO4 (Mello et al., 2010 ▸). This furnished the necessary 1 (R f 0.30, EtOAc neat, more polar than N1,N3-bis-propargylthymine, R f 0.70, hexane-EtOAc) by simple filtration of the solids and crystallization from ethyl acetate. The product formed well-resolved crystals suitable for X-ray analysis. Compound 1: m.p. 408–412 K (EtOAc). 1H NMR (300 MHz, DMSO-d 6): 7.47 (broadened s, 1H, H6), 4.66 and 4.64 (two s, total of 4H, NCH2), 2.16 and 2.14 (two s, total of 6H, COCH3), 1.80 (broadened s, 3H, C5CH3). 13C NMR (75 MHz, DMSO-d 6): 201.8 and 201.3 (two COCH3), 162.0 and 150.6 (C2, 4), 140.8 (C6), 107.3 (C5), 56.9 and 49.7 (two CH2), 27.1 and 26.8 (two COCH3), 12.4 (C5CH3).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. Methyl group C1 is disordered.

Table 2. Experimental details.

Crystal data
Chemical formula C11H14N2O4
M r 238.24
Crystal system, space group Monoclinic, P21/c
Temperature (K) 173
a, b, c (Å) 13.9490 (9), 4.9891 (3), 17.3647 (11)
β (°) 105.693 (4)
V (Å3) 1163.41 (13)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.2 × 0.15 × 0.08
 
Data collection
Diffractometer Bruker PHOTON-100 CMOS
Absorption correction Multi-scan (SADABS; Krause et al., 2015 ▸)
T min, T max 0.769, 0.862
No. of measured, independent and observed [I > 2σ(I)] reflections 18736, 2458, 1889
R int 0.051
(sin θ/λ)max (Å−1) 0.632
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.042, 0.103, 1.03
No. of reflections 2458
No. of parameters 163
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.21, −0.19

Computer programs: APEX2 (Bruker, 2013 ▸) SAINT (Bruker, 2016 ▸), SHELXT (Sheldrick, 2015a ▸), SHELXL (Sheldrick, 2015b ▸) and OLEX2 (Dolomanov et al., 2009 ▸).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314620002576/zq4039sup1.cif

x-05-x200257-sup1.cif (589.5KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314620002576/zq4039Isup2.hkl

x-05-x200257-Isup2.hkl (197KB, hkl)

Supporting information file. DOI: 10.1107/S2414314620002576/zq4039Isup3.cdx

Supporting information file. DOI: 10.1107/S2414314620002576/zq4039Isup4.cml

CCDC reference: 1986083

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

Acknowledgments

Financial support from the State University of New York for acquisition and maintenance of the X-ray diffractometer is gratefully acknowledged.

full crystallographic data

Crystal data

C11H14N2O4 Dx = 1.360 Mg m−3
Mr = 238.24 Melting point: 412 K
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
a = 13.9490 (9) Å Cell parameters from 2683 reflections
b = 4.9891 (3) Å θ = 3.0–25.8°
c = 17.3647 (11) Å µ = 0.11 mm−1
β = 105.693 (4)° T = 173 K
V = 1163.41 (13) Å3 Plate, colourless
Z = 4 0.2 × 0.15 × 0.08 mm
F(000) = 504

Data collection

Bruker PHOTON-100 CMOS diffractometer 2458 independent reflections
Radiation source: sealedtube 1889 reflections with I > 2σ(I)
Detector resolution: 10.4 pixels mm-1 Rint = 0.051
ω scans θmax = 26.7°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Krause et al., 2015) h = −17→17
Tmin = 0.769, Tmax = 0.862 k = −6→6
18736 measured reflections l = −21→21

Refinement

Refinement on F2 Primary atom site location: dual
Least-squares matrix: full Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.042 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103 H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 1/[σ2(Fo2) + (0.0421P)2 + 0.5355P] where P = (Fo2 + 2Fc2)/3
2458 reflections (Δ/σ)max < 0.001
163 parameters Δρmax = 0.21 e Å−3
0 restraints Δρmin = −0.18 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.
Refinement. Methylene hydrogen atoms are refined with riding coordinates and with Uiso(H) = 1.2 Uiso(C); methyl hydrogen atoms are refined as rotating idealized methyl groups and with Uiso(H) = 1.5 Uiso(C).

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

x y z Uiso*/Ueq Occ. (<1)
O1 0.83624 (10) 0.9143 (2) 0.36977 (7) 0.0433 (3)
O2 0.63791 (8) 1.2059 (2) 0.24695 (7) 0.0361 (3)
O3 0.92187 (8) 0.9349 (2) 0.18756 (7) 0.0378 (3)
O4 0.50121 (8) 1.2301 (2) 0.06408 (7) 0.0364 (3)
N1 0.62809 (9) 0.8661 (3) 0.15811 (7) 0.0258 (3)
N2 0.78007 (9) 1.0765 (3) 0.21574 (7) 0.0244 (3)
C1 0.35466 (13) 1.0758 (5) 0.09457 (13) 0.0579 (6)
H1A 0.333498 1.262010 0.097365 0.087* 0.43 (3)
H1B 0.343268 0.974481 0.139636 0.087* 0.43 (3)
H1C 0.316192 0.995262 0.044202 0.087* 0.43 (3)
H1D 0.328474 0.892492 0.090103 0.087* 0.57 (3)
H1E 0.318704 1.180021 0.047833 0.087* 0.57 (3)
H1F 0.345780 1.159240 0.143267 0.087* 0.57 (3)
C2 0.46300 (11) 1.0691 (3) 0.09839 (9) 0.0285 (4)
C3 0.52141 (11) 0.8459 (3) 0.14837 (10) 0.0291 (4)
H3A 0.50906 (19) 0.8483 (3) 0.2009 (7) 0.035*
H3B 0.4978 (3) 0.675 (2) 0.1234 (3) 0.035*
C4 0.67906 (11) 1.0595 (3) 0.20955 (9) 0.0252 (3)
C5 0.83796 (11) 1.2601 (3) 0.27622 (8) 0.0261 (3)
H5A 0.8008 (5) 1.422 (2) 0.27574 (8) 0.031*
H5B 0.8985 (8) 1.3054 (7) 0.26324 (18) 0.031*
C6 0.86268 (11) 1.1388 (3) 0.35899 (9) 0.0266 (3)
C7 0.91998 (12) 1.3150 (3) 0.42473 (9) 0.0316 (4)
H7A 0.8774 (5) 1.456 (2) 0.4341 (5) 0.047*
H7B 0.9756 (8) 1.392 (2) 0.4098 (3) 0.047*
H7C 0.9440 (8) 1.2108 (12) 0.4727 (6) 0.047*
C8 0.67438 (11) 0.7030 (3) 0.11540 (9) 0.0259 (3)
H8 0.6350 (7) 0.574 (2) 0.0796 (7) 0.031*
C9 0.77188 (11) 0.7166 (3) 0.12144 (8) 0.0250 (3)
C10 0.83202 (11) 0.9100 (3) 0.17581 (9) 0.0254 (3)
C11 0.82282 (13) 0.5375 (4) 0.07549 (10) 0.0347 (4)
H11A 0.7752 (6) 0.398 (2) 0.0469 (7) 0.052*
H11B 0.8811 (8) 0.449 (2) 0.1132 (4) 0.052*
H11C 0.8461 (8) 0.6461 (12) 0.0358 (6) 0.052*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0613 (9) 0.0324 (7) 0.0357 (7) −0.0108 (6) 0.0122 (6) 0.0031 (5)
O2 0.0298 (6) 0.0419 (7) 0.0409 (7) −0.0006 (5) 0.0169 (5) −0.0137 (6)
O3 0.0215 (6) 0.0471 (8) 0.0452 (7) 0.0015 (5) 0.0095 (5) −0.0046 (6)
O4 0.0377 (7) 0.0335 (7) 0.0383 (7) −0.0051 (5) 0.0108 (5) 0.0024 (5)
N1 0.0200 (6) 0.0270 (7) 0.0309 (7) −0.0016 (5) 0.0079 (5) −0.0025 (6)
N2 0.0212 (6) 0.0294 (7) 0.0234 (6) −0.0016 (5) 0.0073 (5) −0.0028 (5)
C1 0.0299 (10) 0.0888 (17) 0.0564 (12) 0.0140 (10) 0.0142 (9) 0.0332 (12)
C2 0.0279 (8) 0.0338 (9) 0.0241 (7) −0.0036 (7) 0.0075 (6) −0.0053 (7)
C3 0.0213 (8) 0.0303 (9) 0.0366 (9) −0.0047 (6) 0.0093 (6) −0.0001 (7)
C4 0.0221 (7) 0.0288 (8) 0.0260 (7) −0.0009 (6) 0.0086 (6) 0.0001 (6)
C5 0.0242 (8) 0.0285 (8) 0.0255 (8) −0.0042 (6) 0.0064 (6) −0.0023 (6)
C6 0.0237 (8) 0.0296 (8) 0.0278 (8) 0.0008 (6) 0.0091 (6) 0.0004 (7)
C7 0.0313 (9) 0.0361 (9) 0.0262 (8) −0.0022 (7) 0.0058 (6) 0.0011 (7)
C8 0.0302 (8) 0.0248 (8) 0.0227 (7) −0.0013 (6) 0.0074 (6) −0.0010 (6)
C9 0.0295 (8) 0.0249 (8) 0.0217 (7) 0.0038 (6) 0.0087 (6) 0.0028 (6)
C10 0.0222 (8) 0.0304 (8) 0.0246 (7) 0.0038 (6) 0.0081 (6) 0.0050 (6)
C11 0.0383 (9) 0.0361 (10) 0.0340 (9) 0.0054 (8) 0.0168 (7) −0.0022 (8)

Geometric parameters (Å, º)

O1—C6 1.2093 (19) C2—C3 1.508 (2)
O2—C4 1.2191 (18) C3—H3A 0.972 (12)
O3—C10 1.2205 (18) C3—H3B 0.972 (12)
O4—C2 1.2066 (19) C5—H5A 0.958 (12)
N1—C3 1.4551 (19) C5—H5B 0.958 (12)
N1—C4 1.3749 (19) C5—C6 1.511 (2)
N1—C8 1.3742 (19) C6—C7 1.491 (2)
N2—C4 1.3864 (18) C7—H7A 0.962 (10)
N2—C5 1.4612 (19) C7—H7B 0.962 (10)
N2—C10 1.4027 (19) C7—H7C 0.962 (10)
C1—H1A 0.9800 C8—H8 0.959 (17)
C1—H1B 0.9800 C8—C9 1.337 (2)
C1—H1C 0.9800 C9—C10 1.449 (2)
C1—H1D 0.9800 C9—C11 1.499 (2)
C1—H1E 0.9800 C11—H11A 0.997 (11)
C1—H1F 0.9800 C11—H11B 0.997 (11)
C1—C2 1.495 (2) C11—H11C 0.997 (11)
C4—N1—C3 117.21 (12) H3A—C3—H3B 107.8
C8—N1—C3 120.74 (13) O2—C4—N1 122.08 (13)
C8—N1—C4 122.02 (12) O2—C4—N2 122.48 (14)
C4—N2—C5 116.53 (12) N1—C4—N2 115.44 (13)
C4—N2—C10 125.13 (13) N2—C5—H5A 109.2
C10—N2—C5 117.87 (12) N2—C5—H5B 109.2
H1A—C1—H1B 109.5 N2—C5—C6 111.84 (13)
H1A—C1—H1C 109.5 H5A—C5—H5B 107.9
H1A—C1—H1D 141.1 C6—C5—H5A 109.2
H1A—C1—H1E 56.3 C6—C5—H5B 109.2
H1A—C1—H1F 56.3 O1—C6—C5 121.18 (14)
H1B—C1—H1C 109.5 O1—C6—C7 123.40 (14)
H1B—C1—H1D 56.3 C7—C6—C5 115.42 (13)
H1B—C1—H1E 141.1 C6—C7—H7A 109.5
H1B—C1—H1F 56.3 C6—C7—H7B 109.5
H1C—C1—H1D 56.3 C6—C7—H7C 109.5
H1C—C1—H1E 56.3 H7A—C7—H7B 109.5
H1C—C1—H1F 141.1 H7A—C7—H7C 109.5
H1D—C1—H1E 109.5 H7B—C7—H7C 109.5
H1D—C1—H1F 109.5 N1—C8—H8 118.5
H1E—C1—H1F 109.5 C9—C8—N1 122.96 (14)
C2—C1—H1A 109.5 C9—C8—H8 118.5
C2—C1—H1B 109.5 C8—C9—C10 118.83 (14)
C2—C1—H1C 109.5 C8—C9—C11 123.13 (14)
C2—C1—H1D 109.5 C10—C9—C11 118.03 (13)
C2—C1—H1E 109.5 O3—C10—N2 120.12 (14)
C2—C1—H1F 109.5 O3—C10—C9 124.33 (14)
O4—C2—C1 122.64 (16) N2—C10—C9 115.55 (12)
O4—C2—C3 122.26 (14) C9—C11—H11A 109.5
C1—C2—C3 115.10 (14) C9—C11—H11B 109.5
N1—C3—C2 113.07 (13) C9—C11—H11C 109.5
N1—C3—H3A 109.0 H11A—C11—H11B 109.5
N1—C3—H3B 109.0 H11A—C11—H11C 109.5
C2—C3—H3A 109.0 H11B—C11—H11C 109.5
C2—C3—H3B 109.0
O4—C2—C3—N1 6.9 (2) C5—N2—C4—O2 6.5 (2)
N1—C8—C9—C10 0.5 (2) C5—N2—C4—N1 −173.64 (13)
N1—C8—C9—C11 179.45 (14) C5—N2—C10—O3 −5.4 (2)
N2—C5—C6—O1 0.6 (2) C5—N2—C10—C9 175.01 (12)
N2—C5—C6—C7 −178.80 (12) C8—N1—C3—C2 −103.59 (16)
C1—C2—C3—N1 −173.11 (16) C8—N1—C4—O2 179.34 (15)
C3—N1—C4—O2 1.3 (2) C8—N1—C4—N2 −0.5 (2)
C3—N1—C4—N2 −178.54 (13) C8—C9—C10—O3 178.02 (15)
C3—N1—C8—C9 179.04 (14) C8—C9—C10—N2 −2.5 (2)
C4—N1—C3—C2 74.43 (17) C10—N2—C4—O2 178.41 (14)
C4—N1—C8—C9 1.1 (2) C10—N2—C4—N1 −1.7 (2)
C4—N2—C5—C6 79.50 (16) C10—N2—C5—C6 −93.04 (15)
C4—N2—C10—O3 −177.28 (14) C11—C9—C10—O3 −1.0 (2)
C4—N2—C10—C9 3.2 (2) C11—C9—C10—N2 178.53 (13)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
C3—H3A···O2i 0.97 (1) 2.56 (1) 3.304 (2) 134 (1)
C3—H3B···O4ii 0.97 (1) 2.45 (1) 3.3820 (19) 160 (1)
C5—H5B···O3iii 0.96 (1) 2.50 (1) 3.353 (2) 148 (1)
C7—H7A···O1iv 0.96 (1) 2.54 (1) 3.2576 (19) 131 (1)
C7—H7B···O3iii 0.96 (1) 2.50 (1) 3.370 (2) 150 (1)
C8—H8···O4ii 0.96 (1) 2.50 (1) 3.3213 (19) 144 (1)

Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) x, y−1, z; (iii) −x+2, y+1/2, −z+1/2; (iv) x, y+1, z.

References

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  2. Bruker (2013). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.
  3. Bruker (2016). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
  4. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.
  5. Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10. [DOI] [PMC free article] [PubMed]
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  7. Mello, R., Alcalde-Aragonés, A. & González-Núñez, M. E. (2010). Tetrahedron Lett. 51, 4281–4283.
  8. Negrón-Silva, G. E., González-Olvera, R., Angeles-Beltrán, D., Maldonado-Carmona, N., Espinoza-Vázquez, A., Palomar-Pardavé, M. E., Romero-Romo, M. A. & Santillan, R. (2013). Molecules, 18, 4613–4627. [DOI] [PMC free article] [PubMed]
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  10. Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.
  11. Thakur, R. K., Mishra, A., Ramakrishna, K. K. G., Mahar, R., Shukla, S. K., Srivastava, A. K. & Tripathi, R. P. (2014). Tetrahedron, 70, 8462–8473.

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2414314620002576/zq4039sup1.cif

x-05-x200257-sup1.cif (589.5KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S2414314620002576/zq4039Isup2.hkl

x-05-x200257-Isup2.hkl (197KB, hkl)

Supporting information file. DOI: 10.1107/S2414314620002576/zq4039Isup3.cdx

Supporting information file. DOI: 10.1107/S2414314620002576/zq4039Isup4.cml

CCDC reference: 1986083

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


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