organic papers
Acta Cryst.(2005). E61, o2665–o2667 doi:10.1107/S1600536805022774 Xionget al. C
6H6N2O4
o2665
Acta Crystallographica Section E Structure Reports Online
ISSN 1600-5368
1-(Carboxymethyl)uracil
Jing Xiong,* Miao-Chang Liu and Ji-Xin Yuan
School of Chemistry and Materials Science, Wenzhou Normal College, Wenzhou 325027, People’s Republic of China
Correspondence e-mail: theresa_xiong@yahoo.com.cn
Key indicators
Single-crystal X-ray study T= 298 K
Mean(C–C) = 0.010 A˚ Rfactor = 0.066 wRfactor = 0.148 Data-to-parameter ratio = 8.3
For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.
#2005 International Union of Crystallography
Printed in Great Britain – all rights reserved
In the title compound, C6H6N2O4, the planar carboxyl group
makes a dihedral angle of 74.61 (2) with the uracil plane. In
the crystal structure, intermolecular N—H O and O— H O hydrogen bonds link the molecules into a three-dimensional network.
Comment
Thymine and uracil are important nucleobases in biology; they contribute to a wide range of biochemical processes, such as complementary base pairing in genetic information storage and transfer, molecular recognition and for some enzyme reactions (Bazzicalupiet al., 2001; Hondaet al., 2002; Leiroset al., 2003). As a result, great efforts have been undertaken to investigate thymine, uracil and their derivatives (Joliboiset al., 1998; Koikeet al., 1998). In a continuation of our research in this field, we present here the synthesis and crystal structure of the title compound, namely 1-(carboxymethyl)uracil, (I).
In (I) (Fig. 1), the carboxyl group (C6/O3/O4/H4) and uracil ring (C1–C4/N1/N2) are each almost planar, with r.m.s. deviations of 0.0196 and 0.0093 A˚ , respectively. The dihedral angle between their mean planes is 74.61 (2). Moreover, the
C—N bond lengths in the uracil ring (Table 1) range from 1.369 (9) to 1.382 (8) A˚ , which are shorter than a C—N single bond length (ca1.443 A˚ ) (Jinet al., 2004), but longer than a typical C N bond length (ca 1.269 A˚ ), indicating delocali-zation. On the other hand, the conjugation of O2/C2/C3/C4
[image:1.610.221.446.605.722.2]Received 24 June 2005 Accepted 15 July 2005 Online 23 July 2005
Figure 1
results in a decrease of the C2—C3 bond length [1.419 (10) A˚ ]. In the crystal structure (Fig. 2), intermolecular N—H O and O—H O hydrogen bonds (Table 2) link each molecule with the four adjacent molecules to form a three-dimensional network. This hydrogen-bonding motif can be described in graph-set notation asR44(20) andR22(8) (Huet al., 2005).
Experimental
Bromoacetic acid (45 mmol, 6.25 g) in water (10 ml) was added to a solution of uracil (30 mmol, 3.33 g), potassium hydroxide (11.5 mmol, 6.41 g) and water (20 ml) at 313 K. The mixture was cooled after 2 h reaction and the pH was adjusted to 5.5 using hydrochloric acid. The precipitate was filtered off and the pH of the filtrate was adjusted to 1, again using hydrochloric acid, and the solution was cooled for 6 h in a refrigerator and then filtered. The precipitate was washed with water and dried to obtain the title compound. Single crystals were obtained by recrystallization from anhydrous ethanol.
Crystal data
C6H6N2O4 Mr= 170.13
Monoclinic,Pc a= 5.0999 (8) A˚
b= 4.6273 (8) A˚
c= 15.0106 (19) A˚
= 107.093 (5) V= 338.58 (9) A˚3 Z= 2
Dx= 1.669 Mg m
3
MoKradiation Cell parameters from 861
reflections
= 2.8–24.8
= 0.14 mm1 T= 298 (2) K Rod, colourless 0.210.110.10 mm
Data collection
Bruker APEX area-detector diffractometer
’and!scans
Absorption correction: multi-scan (SADABS; Bruker, 2002)
Tmin= 0.971,Tmax= 0.983
3071 measured reflections
621 independent reflections 607 reflections withI> 2(I)
Rint= 0.035
max= 25.2 h=6!6
k=5!5
l=17!18
Refinement
Refinement onF2 R[F2> 2(F2)] = 0.066 wR(F2) = 0.148 S= 1.26 621 reflections 75 parameters
H atoms treated by a mixture of independent and constrained refinement
w= 1/[2(F
o2) + (0.0727P)2
+ 0.2892P]
whereP= (Fo2+ 2Fc2)/3
(/)max< 0.001 max= 0.30 e A˚
3 min=0.31 e A˚
3
Table 1
Selected bond lengths (A˚ ).
O1—C1 1.217 (7) O2—C2 1.227 (8) N1—C4 1.371 (8) N1—C1 1.374 (8)
N2—C1 1.369 (9) N2—C2 1.382 (8) C2—C3 1.419 (10)
Table 2
Hydrogen-bond geometry (A˚ ,).
D—H A D—H H A D A D—H A
O4—H4 O2i
0.82 (2) 1.76 (3) 2.553 (7) 160 (7) N2—H2 O3ii
0.84 (2) 2.00 (3) 2.828 (7) 169 (7)
Symmetry codes: (i)xþ1;yþ2;zþ1
2; (ii)x;yþ1;z 1 2.
H atoms attached to N and O atoms were located in a difference Fourier map, and refined with O—H and N—H distances restrained to 0.82 (2) and 0.85 (2) A˚ , respectively, and withUiso= 1.2Ueq(parent
atom). The other H atoms were positioned geometrically and allowed to ride on their parent atoms at distances of Csp2—H = 0.93 A˚ , with
Uiso = 1.2Ueq(parent atom), and Csp 3
—H = 0.97 A˚ , with Uiso =
1.5Ueq(parent atom). Due to the absence of any significant
anom-alous scatterers in the molecule, the Friedel pairs were merged before the final refinement
Data collection:SMART(Bruker, 2002); cell refinement:SAINT (Bruker, 2002); data reduction:SAINT; program(s) used to solve structure:SHELXS97(Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2002); software used to prepare material for publication:SHELXL97.
We are grateful for funding to Wenzhou Technology Project Foundation of China (No. S2004A004), Zhejiang Provincial Natural Science Foundation of China (No. Y404118) and National Natural Science Foundation of China (No. 20471043).
References
Bazzicalupi, C., Bencini, A., Berni, E., Ciattini, S., Bianchi, A., Giorgi, C., Paoletti, P. & Valtancoli, B. (2001). Inorg. Chim. Acta, 317, 259– 267.
Bruker (2002).SADABS (Version 2.03), SAINT (Version 6.02), SMART
(Version 5.62) andSHELXTL(Version 6.10). Bruker AXS Inc., Madison, Winsonsin, USA.
Honda, T., Inagawa, H., Fukushima, M., Moriyama, A. & Soma, G. I. (2002).
Clin. Chim. Acta,322, 59–66.
Hu, M.-L., Cheng, Y.-Q., Wang, S., Yuan, J.-X. & Cai, X.-Q. (2005).Acta Cryst.
E61, o1196–o1197.
Jin, Z.-M., Li, L., Li, M.-C., Hu, M.-L. & Shen, L. (2004).Acta Cryst.C60, o642–o643.
organic papers
o2666
Xionget al. C [image:2.610.313.567.74.318.2]6H6N2O4 Acta Cryst.(2005). E61, o2665–o2667
Figure 2
Jolibois, F., D’Ham, C., Grand, A., Subra, R. & Cadet, J. (1998). J. Mol. Struct.(Theochem),427, 143–155.
Koike, T., Gotoh, T., Aoki, S., Kimura, E. & Shiro, M. (1998).Inorg. Chim. Acta,270, 424–432.
Leiros, I., Moe, E., Lanes, O., Smalas, A. O. & Willassen, N. P. (2003).Acta Cryst.D59, 1357–1365.
Sheldrick, G. M. (1997). SHELXS97 and SHELXL97. University of Go¨ttingen, Germany.
organic papers
Acta Cryst.(2005). E61, o2665–o2667 Xionget al. C
supporting information
sup-1 Acta Cryst. (2005). E61, o2665–o2667
supporting information
Acta Cryst. (2005). E61, o2665–o2667 [https://doi.org/10.1107/S1600536805022774]
1-(Carboxymethyl)uracil
Jing Xiong, Miao-Chang Liu and Ji-Xin Yuan
1-(Carboxymethyl)uracil
Crystal data
C6H6N2O4 Mr = 170.13 Monoclinic, Pc
Hall symbol: P -2yc
a = 5.0999 (8) Å
b = 4.6273 (8) Å
c = 15.0106 (19) Å
β = 107.093 (5)°
V = 338.58 (9) Å3 Z = 2
F(000) = 176
Dx = 1.669 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 861 reflections
θ = 2.8–24.8°
µ = 0.14 mm−1 T = 298 K Rod, colourless 0.21 × 0.11 × 0.10 mm
Data collection
Bruker APEX area-detector diffractometer
Radiation source: fine-focus sealed tube Graphite monochromator
φ and ω scans
Absorption correction: multi-scan (SADABS; Bruker, 2002)
Tmin = 0.971, Tmax = 0.983
3071 measured reflections 621 independent reflections 607 reflections with I > 2σ(I)
Rint = 0.035
θmax = 25.2°, θmin = 2.8° h = −6→6
k = −5→5
l = −17→18
Refinement
Refinement on F2
Least-squares matrix: full
R[F2 > 2σ(F2)] = 0.066 wR(F2) = 0.148 S = 1.27 621 reflections 75 parameters 4 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ2(F
o2) + (0.0727P)2 + 0.2892P]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max < 0.001
Δρmax = 0.30 e Å−3
Δρmin = −0.31 e Å−3
Special details
supporting information
sup-2 Acta Cryst. (2005). E61, o2665–o2667
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2,
conventional 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.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x y z Uiso*/Ueq
O1 0.9156 (10) 0.3732 (10) 0.5139 (3) 0.0398 (13) O2 0.4403 (10) 0.9587 (11) 0.2833 (3) 0.0396 (13) O3 0.9652 (10) 0.5312 (11) 0.7798 (3) 0.0373 (12) O4 0.9946 (9) 0.8467 (10) 0.6727 (3) 0.0341 (12) N1 0.5691 (10) 0.6351 (11) 0.5402 (3) 0.0252 (12) N2 0.6688 (11) 0.6708 (13) 0.3997 (4) 0.0292 (13) C1 0.7309 (12) 0.5479 (13) 0.4864 (4) 0.0246 (14) C2 0.4686 (13) 0.8753 (13) 0.3631 (5) 0.0275 (14) C3 0.3159 (13) 0.9613 (16) 0.4239 (5) 0.0297 (15) H3 0.1790 1.1003 0.4051 0.036* C4 0.3702 (12) 0.8410 (14) 0.5085 (5) 0.0292 (15) H4A 0.2685 0.8998 0.5476 0.035* C5 0.6290 (14) 0.5115 (14) 0.6334 (4) 0.0306 (15) H5A 0.6522 0.3044 0.6290 0.037* H5B 0.4720 0.5430 0.6562 0.037* C6 0.8787 (12) 0.6316 (13) 0.7031 (4) 0.0231 (13) H2 0.741 (14) 0.593 (14) 0.362 (4) 0.028* H4 1.139 (9) 0.873 (15) 0.715 (4) 0.028*
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
O1 0.039 (3) 0.037 (3) 0.041 (3) 0.013 (2) 0.009 (2) 0.007 (2) O2 0.043 (3) 0.048 (3) 0.030 (2) 0.015 (3) 0.014 (2) 0.015 (3) O3 0.042 (3) 0.041 (3) 0.028 (2) −0.009 (2) 0.0091 (19) 0.013 (2) O4 0.040 (3) 0.032 (2) 0.027 (2) −0.015 (2) 0.006 (2) 0.003 (2) N1 0.026 (3) 0.023 (3) 0.027 (3) −0.001 (2) 0.008 (2) −0.001 (2) N2 0.034 (3) 0.036 (3) 0.020 (3) 0.008 (3) 0.012 (2) −0.003 (2) C1 0.019 (3) 0.017 (3) 0.031 (3) 0.001 (3) −0.002 (2) −0.009 (3) C2 0.027 (3) 0.021 (3) 0.033 (4) 0.001 (3) 0.006 (3) −0.002 (3) C3 0.026 (3) 0.026 (3) 0.038 (4) 0.002 (3) 0.011 (3) 0.000 (3) C4 0.027 (4) 0.029 (3) 0.035 (3) −0.010 (3) 0.015 (3) −0.008 (3) C5 0.039 (4) 0.022 (3) 0.032 (3) −0.003 (3) 0.012 (3) 0.004 (3) C6 0.032 (3) 0.017 (3) 0.027 (3) 0.003 (3) 0.019 (3) 0.007 (3)
Geometric parameters (Å, º)
supporting information
sup-3 Acta Cryst. (2005). E61, o2665–o2667
O4—C6 1.306 (7) C3—C4 1.339 (10) O4—H4 0.82 (2) C3—H3 0.9300 N1—C4 1.371 (8) C4—H4A 0.9300 N1—C1 1.374 (8) C5—C6 1.497 (10) N1—C5 1.459 (8) C5—H5A 0.9700 N2—C1 1.369 (9) C5—H5B 0.9700
C6—O4—H4 104 (5) C4—C3—H3 120.2 C4—N1—C1 120.8 (5) C2—C3—H3 120.2 C4—N1—C5 122.0 (5) C3—C4—N1 122.9 (6) C1—N1—C5 117.1 (5) C3—C4—H4A 118.6 C1—N2—C2 126.9 (5) N1—C4—H4A 118.6 C1—N2—H2 116 (5) N1—C5—C6 114.9 (5) C2—N2—H2 116 (5) N1—C5—H5A 108.6 O1—C1—N2 122.6 (6) C6—C5—H5A 108.6 O1—C1—N1 122.3 (6) N1—C5—H5B 108.6 N2—C1—N1 115.1 (5) C6—C5—H5B 108.6 O2—C2—N2 117.7 (6) H5A—C5—H5B 107.5 O2—C2—C3 127.6 (6) O3—C6—O4 123.6 (6) N2—C2—C3 114.7 (6) O3—C6—C5 121.7 (6) C4—C3—C2 119.6 (6) O4—C6—C5 114.7 (5)
C2—N2—C1—O1 −178.3 (6) N2—C2—C3—C4 −1.0 (9) C2—N2—C1—N1 1.9 (9) C2—C3—C4—N1 −0.1 (10) C4—N1—C1—O1 177.3 (6) C1—N1—C4—C3 2.1 (9) C5—N1—C1—O1 0.7 (9) C5—N1—C4—C3 178.6 (6) C4—N1—C1—N2 −2.9 (8) C4—N1—C5—C6 −101.4 (7) C5—N1—C1—N2 −179.5 (5) C1—N1—C5—C6 75.2 (7) C1—N2—C2—O2 −179.2 (7) N1—C5—C6—O3 −173.2 (5) C1—N2—C2—C3 0.0 (9) N1—C5—C6—O4 5.4 (8) O2—C2—C3—C4 178.1 (7)
Hydrogen-bond geometry (Å, º)
D—H···A D—H H···A D···A D—H···A
O4—H4···O2i 0.82 (2) 1.76 (3) 2.553 (7) 160 (7)
N2—H2···O3ii 0.84 (2) 2.00 (3) 2.828 (7) 169 (7)