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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

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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

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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

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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 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

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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)

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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)

Figure

Figure 1
Figure 2

References

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