1,3-Bis(2-oxoprop­yl)thymine

Doboszewski, B.; Nazarenko, A.Y.; Soares, F. da P.

doi:10.1107/S2414314620002576

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 5| Part 2| February 2020| x200257

https://doi.org/10.1107/S2414314620002576

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1,3-Bis(2-oxopropyl)thymine

Bogdan Doboszewski,^a Alexander Y. Nazarenko ^b ^* and Fábio da Paixão Soares ^a

^aDepartamento de Química, Universidade Federal Rural de Pernambuco, 52171-900 Recife, PE, Brazil, and ^bChemistry Department, State University of New York, College at Buffalo, 1300 Elmwood Ave, Buffalo, NY 14222-1095, USA
^*Correspondence e-mail: nazareay@buffalostate.edu

Edited by O. Blacque, University of Zürich, Switzerland (Received 15 February 2020; accepted 24 February 2020; online 28 February 2020)

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.

Keywords: crystal structure; thymine; substituted nucleobase; 2-oxopropyl.

CCDC reference: 1986083

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 N¹,N³-bispropargyl thymine and uracyl, which furnished N¹,N³-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
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⋯O1^iv	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) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) x, y-1, z; (iii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) x, y+1, z.

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-d₆): 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-d₆): 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[F² > 2σ(F²)], wR(F²), 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
Δρ_max, Δρ_min (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 ).

Structural data

CCDC reference: 1986083

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314620002576/zq4039sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314620002576/zq4039Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314620002576/zq4039Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2414314620002576/zq4039Isup4.cml

checkCIF report

Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

5-Methyl-1,3-bis(2-oxopropyl)pyrimidine-2,4(1H,3H)-dione top

Crystal data top

C₁₁H₁₄N₂O₄	D_x = 1.360 Mg m⁻³
M_r = 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 top

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

Refinement top

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(F_o²) + (0.0421P)² + 0.5355P] where P = (F_o² + 2F_c²)/3
2458 reflections	(Δ/σ)_max < 0.001
163 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.18 e Å⁻³

Special details top

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 U_iso(H) = 1.2 U_iso(C); methyl hydrogen atoms are refined as rotating idealized methyl groups and with U_iso(H) = 1.5 U_iso(C).

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

	x	y	z	U_iso*/U_eq	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) top

	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) top

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) top

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···O1^iv	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.

Acknowledgements

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

References

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