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Crystallography Reports, Vol. 47, No. 3, 2002, pp. 428­432. Translated from Kristallografiya, Vol. 47, No. 3, 2002, pp. 473­477. Original Russian Text Copyright © 2002 by Rybakov, Babaev, Chernyshev.

STRUCTURES OF ORGANIC COMPOUNDS

X-ray Mapping in Heterocyclic Design: VII. Diffraction Study of the Structure of N-Pyridoneacetic Acid and the Product of Its Intramolecular Dehydration
V. B. Rybakov, E. V. Babaev, and V. V. Chernyshev
Faculty of Chemistry, Moscow State University, Vorob'evy gory, Moscow, 119899 Russia e-mail: rybakov@biocryst.phys.msu.su
Received July 25, 2001

Abstract--The structure of pyridoneacetic acid C7H7N1O3 (I) is determined by the single-crystal X-ray diffraction technique. The crystals of I are monoclinic, a = 7.4502(15) å, b = 10.006(6) å, c = 9.960(3) å, = 109.96(2)°, Z = 4, and space group P21/c. The structure of pyridoneacetic acid is solved by the direct method and refined by the least-squares procedure in the anisotropic approximation to R = 0.0387. The structure of the product of its intramolecular dehydration, C7H6N1O2B1F4 (II), is determined by the grid search procedure and refined by the Reitveld method (Rp = 0.045, Rwp = 0.58, Re = 0.026, and 2 = 4.69). The crystals of II are monoclinic, a = 10.4979(3) å, b = 11.4467(3) å, c = 7.6027(1) å, = 100.83(2)°, Z = 4, and space group P21/n. The system of two conjugated heterocycles is planar. © 2002 MAIK "Nauka / Interperiodica".

INTRODUCTION This study continues our structural investigations of heterocyclic compounds that are able to enter readily into reactions of ring transformation [1­12]. In this paper, we concentrate on the structural study of pyridoneacetic acid, C7H7N1O3 (I), and the product of its intramolecular dehydration (cyclization), namely, 2-oxo-2,3-dihydrooxazolo[1,2-a]pyridinium tetrafluoO NH
(1) KOH (2) ClCH2COO­K+ (3) H+

roborate, C7H6N1O2B1F4 (II). There are no data on the structures of I and II in the Cambridge Structural Database [13]. Pyridoneacetic acid I was synthesized by alkylation of pyridone with chloracetic acid in the presence of an alkali. The cyclization of pyridone I into the oxazolopyridinium salt II was achieved by its treatment with acetic anhydride and the following careful addition of tetrafluoroboric acid
O N
Ac2O HBF4

O N+ II O BF4
­

I

COOH

.

EXPERIMENTAL The unit cell parameters of I (C7H7NO3) were determined and refined using 25 reflections in the range 14° 16° on an Enraf­Nonius CAD4 automated diffractometer [14] (MoK, graphite monochromator). Crystals I are monoclinic, a = 7.4502(15) å, b = 10.006(6) å, c = 9.960(3) å, = 109.96(2)°, V = 697.9(5) å3 , dcalcd = 1.457 g/cm3 , µ(Mo) = 0.116 mm­1, Z = 4, and space group P21/c. A set of 1745 reflections with I 2(I) was collected from a crystal no larger than 0.48 â 0.48 â 0.06 mm in size in the range 2.98° 28.97° on the same diffractometer ( scan mode) at room temperature. The primary processing of the set of diffraction data was performed with the WinGX98 pro-

gram package [15]. The structure was solved by the direct method and refined by the least-squares procedure in the anisotropic approximation using the SHELX97 program package [16]. All the hydrogen atoms of the molecule were located from the electrondensity difference synthesis and refined in the isotropic approximation. The final discrepancy factors are R1 = 0.0387 and wR2 = 0.0793. The residual electron density lies between max = 0.124 and min = ­0.132 e/å3 . The atomic coordinates and thermal parameters are listed in Table 1. The diffraction experiment for C7H6N1O2B1F4 (II) was performed on an XRD7 automated powder diffractometer (Seifert-FPM, Freiburg) (CuK, Ni filter) in

1063-7745/02/4703-0428$22.00 © 2002 MAIK "Nauka / Interperiodica"


X-RAY MAPPING IN HETEROCYCLIC DESIGN Table 1. Atomic coordinates (â 104) and isotropic thermal parameters (å2 â 103) for molecule I Atom N(1) C(2) O(2) C(3) C(4) C(5) C(6) C(7) C(8) O(81) O(82) H(3) H(4) H(5) H(6) H(7A) H(7B) H(82) x 6745(2) 6691(2) 5112(1) 8427(2) 10 050(3) 10 030(3) 8396(3) 4980(2) 4411(2) 2943(2) 5628(2) 8440(20) 11 190(30) 11 170(30) 8190(30) 3960(20) 5130(20) 5090(30) y 1982(1) 955(1) 701(1) 281(2) 636(2) 1702(2) 2349(2) 2696(2) 3690(1) 4305(1) 3828(1) ­ 421(19) 100(20) 1910(20) 3100(20) 2079(16) 3178(18) 4480(20) z 502(1) 1403(1) 1553(1) 2085(2) 1854(2) 937(2) 288(2) ­ 217(2) 706(1) 226(1) 2001(1) 2727(19) 2324(19) 760(20) ­ 370(20) ­ 588(15) ­1010(20) 2460(20) Ueq/Uiso 34(1) 34(1) 42(1) 46(1) 57(1) 61(1) 49(1) 38(1) 33(1) 55(1) 41(1) 56(5) 63(5) 78(6) 73(6) 38(4) 60(5) 80(6)

429

Table 2. Atomic coordinates (â104) and isotropic thermal parameters (å2) for molecule II Atom N(1) C(2) C(3) C(4) C(5) C(6) C(7) C(8) O(2) O(8) B F(1) F(2) F(3) F(4) H(3) H(4) H(5) H(6) H(7A) H(7B) x 9(7) 1313(10) 1830(8) 942(11) ­ 401(10) ­ 883(10) ­ 282(10) 1095(12) 2001(6) 1417(6) 961(17) 1134(8) 966(9) 1927(6) ­101(6) 2697(71) 1254(75) ­ 991(77) ­1779(70) ­ 786(69) ­ 729(71) y 2021(8) 1858(9) 715(9) ­153(8) 83(8) 1182(10) 3240(10) 3721(7) 2839(6) 4710(5) 3254(15) 4387(5) 2664(5) 2763(5) 3003(6) 596(66) ­ 915(56) ­ 543(60) 1333(71) 3358(66) 3638(60) z 8178(11) 8553(16) 8354(14) 7795(13) 7412(13) 7607(14) 8468(12) 9063(14) 9089(8) 9476(8) 3844(24) 3513(10) 2345(7) 4970(8) 4395(9) 8610(82) 7655(96) 7033(85) 7369(96) 9425(90) 7401(78) Biso 1.56(7) 1.56 1.56 1.56 1.56 1.56 1.56 1.56 1.56 1.56 3.7(5) 2.78(8) 2.78 2.78 2.78 4.0 4.0 4.0 4.0 4.0 4.0

0.02° steps. Compound II is very unstable and tends to undergo self-condensation. Because of the high hygroscopicity and instability of compound II, the powder to be studied was placed in a cell inside a dry box filled
I, pulse â 10 1.8
4

with argon and then was isolated from the atmospheric moisture with a thin polyester film. The unit cell parameters were determined with the ITO indexing program [17] in the range of angles 12° 2 150° and indices

0.9

â5

0

10

20

30

40

50

60

70

80 2, deg

Fig. 1. Experimental and difference (Reitveld refinement) spectra for II. CRYSTALLOGRAPHY REPORTS Vol. 47 No. 3 2002


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RYBAKOV et al.

(2) 1.353
1.401(3)

1.409(2)

C(4) C(3)
1.374(2)

1.261(2)

O(2)

C(2)

C(5)

1.3 35( 3)

9(2) 1.36

1.452(2)

C(6)

N(1) C(7)
1.509(2) 1.306(2)

1.203(2)

O(81)

C(8) O(82)
Fig. 2. Molecular structure, atomic numbering, and interatomic distances in I.

) 14 4( 37 1.

C(3)

1.4 35 (15 )

12) 56( 1.3

1.385(12)

O(2)
1.358(12)

1) 1.206(1

C(4)
1.411(16)

C(2)

C(8)
15 34( 16)

O(8)

1.3 74( 15)

) (13 55 1.3

1 454(14)

C(5) C(6)

N(1) C(7)

Fig. 3. Molecular structure, atomic numbering, and interatomic distances in II.

0 h 6; 0 k 7; and -5 l 5. The space group was determined from the systematic absences of reflections. Crystals II are monoclinic, a = 10.4979(3) å, b = 11.4467(3) å, c = 7.6027(1) å, = 100.83(3)°, V = 897.3(1) å3 , dcalcd = 1.6502 g/cm3 , µ(Cu) = 15.369 cm­1, Z = 4, and space group P21/n. The data of the NMR spectroscopic study of II were used as preliminary structural data. The initial geometrical model of the molecule was constructed using semiempirical and empirical methods with the MOPAC 6.0 [18] and PCMODEL [19] programs. The structure was solved according to the grid search procedure [20]

based on the given molecular fragments. The full-profile refinement of the structure was performed by the Reitveld method with the MRIA program [21]. The pseudo-Voigt function was used as a profile function, and the background was approximated by the Chebyshev polynomials of the fifth order. The texture parameters were refined within the March­Dollase model [22] in the [010] direction. In the refinement, the thermal parameters of the non-hydrogen atoms of the cation were averaged. The thermal parameters of the fluorine atoms of the anion were also averaged. The final parameters of the refinement had the following values:
CRYSTALLOGRAPHY REPORTS Vol. 47 No. 3 2002


X-RAY MAPPING IN HETEROCYCLIC DESIGN Table 3. Parameters of interatomic contacts [24] in I D­H C(7)­H(7A) C(3)­H(3) C(4)­H(4) C(4)­H(4) C(5)­H(5) C(6)­H(6) C(7)­H(7B) C(7)­H(7B) C(7)­H(7B) O(82)­H(82) d(D­H) 0.95(2) 0.95(2) 0.98(2) 0.98(2) 0.95(2) 0.97(2) 0.96(2) 0.96(2) 0.96(2) 0.96(2) d(D A) 2.643(2) 3.322(2) 3.315(2) 3.526(2) 3.612(3) 3.481(3) 3.377(3) 3.626(2) 3.339(2) 2.535(2) d(H A) 2.44(2) 2.60(2) 2.80(2) 2.57(2) 2.87(2) 2.75(2) 2.87(2) 2.67(2) 2.93(2) 1.61(2) DHA 92(1) 134(1) 114(1) 166(2) 136(2) 132(2) 114(1) 172(2) 107(1) 162(2) A O(2) O(81) O(81) O(82) O(81) O(81) O(81) O(2) O(82) O(2) Symmetry code (x, y, z (1 ­ x, (x + 1, (2 ­ x, (x + 1, (1 ­ x, (1 ­ x, (x, 1/2 (x, 1/2 (1 ­ x, ) y ­ 1/2, 1/2 1/2 ­ y, z + y ­ 1/2, 1/2 y, z) 1 ­ y, ­z) 1 ­ y, ­z) ­ y, z ­ 1/2) ­ y, z ­ 1/2) y + 1/2, 1/2 ­ z) 1/2) ­ z)

431

­ z)

Note: D is a donor atom, A is an acceptor atom, and H is a hydrogen atom (the d distances and angles are given in å and degrees, respectively).

Table 4. Parameters of interatomic contacts [24] in II D­H C(7)­H(7B) C(6)­H(6) C(6)­H(6) C(6)­H(6) C(6)­H(6) C(7)­H(7A) C(5)­H(5) C(4)­H(4) C(3)­H(3) C(3)­H(3) C(4)­H(4) C(4)­H(4) C(3)­H(3) C(7)­H(7A) C(7)­H(7A) C(7)­H(7B) d(D­H) 0.97(6) 0.94(7) 0.94(7) 0.94(7) 0.94(7) 0.99(8) 0.96(7) 0.95(7) 0.91(7) 0.91(7) 0.95(7) 0.95(7) 0.91(7) 0.99(8) 0.99(8) 0.97(6) d(D A) 3.15(1) 3.49(1) 3.33(1) 3.53(1) 3.40(1) 3.53(1) 3.21(1) 3.69(1) 3.29(1) 3.26(1) 3.49(1) 3.63(1) 3.49(1) 3.17(1) 3.06(1) 3.15(1) d(H A) 2.60(7) 2.88(7) 2.75(7) 2.63(8) 2.80(8) 2.82(8) 2.47(7) 2.98(7) 2.87(7) 2.68(7) 2.81(7) 2.84(8) 2.78(7) 2.50(8) 2.72(6) 2.38(7) DHA 116(4) 124(6) 121(5) 162(6) 122(6) 129(5) 134(5) 133(5) 110(5) 123(5) 129(5) 142(5) 136(6) 126(5) 101(4) 136(5) A F(4) O(8) O(2) F(1) F(3) F(3) F(2) F(4) O(8) F(1) F(3) O(2) F(4) O(8) F(2) F(1) Symmetry code (x, y, z) (x ­ 1/2, 1/2 ­ y, z ­ 1/2) (x ­ 1/2, 1/2 ­ y, z ­ 1/2) (x ­ 1/2, 1/2 ­ y, z + 1/2) (x ­ 1/2, 1/2 ­ y, z + 1/2) (x ­ 1/2, 1/2 ­ y, z + 1/2) (­ x, ­ y, 1 ­ z) (­ x, ­ y, 1 ­ z) (1/2 ­ x, y ­ 1/2, 3/2 + z) (1/2 ­ x, y ­ 1/2, 3/2 + z) (1/2 ­ x, y ­ 1/2, 3/2 + z) (1/2 ­ x, y ­ 1/2, 3/2 + z) (x + 1/2, 1/2 ­ y, z + 1/2) (­ x, 1 ­ y, 2 ­ z) (x, y, 1 + z) (­ x, 1 ­ y, 1 ­ z)

Note: D is a donor atom, A is an acceptor atom, and H is a hydrogen atom (the d distances and angles are given in å and degrees, respectively).

Rp = 0.045, Rwp = 0.58, Re = 0.026, and 2 = 4.69, where Rp = |Io ­ Ic |/Io, Rwp = w |Io ­ Ic |/wIo, Re = Io /Io, Io is the observed intensity, and Ic is the calculated intensity. The observed and difference X-ray diffraction patterns are shown in Fig. 1. The atomic coordinates and isotropic thermal parameters are listed in Table 2. The molecular structures of I and II with the atomic numberings are shown in Figs. 2 and 3, respectively. The drawings were obtained with the PLUTON96 program [23].
CRYSTALLOGRAPHY REPORTS Vol. 47 No. 3 2002

RESULTS AND DISCUSSION Earlier, we studied the structures of the N-substituted pyridones-2 containing the phenacyl [3] and para-nitrophenacyl [8] groups at the nitrogen atom. The structure of the pyridine fragment in molecule I is similar to those in the pyridones studied earlier. The O(2) and C(7) atoms lie in the plane of the heterocycle. In the pyridine fragment (Fig. 2), formally single and double bonds alternate to form the quasi-diene structural fragment C(3)=C(4)­C(5)=C(6). The C(2)­N(1)­C(7)­C(8) tor-


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RYBAKOV et al. 2. E. V. Babaev, S. V. Bozhenko, D. A. Maiboroda, et al., Bull. Soc. Chim. Belg. 106 (11), 631 (1997). 3. S. G. Zhukov, V. B. Rybakov, E. V. Babaev, et al., Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 53, 1909 (1997). 4. E. V. Babaev, S. V. Bozhenko, S. G. Zhukov, and V. B. Rybakov, Khim. Geterotsikl. Soedin., No. 8, 1105 (1997). 5. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 44, 1067 (1999) [Crystallogr. Rep. 44, 997 (1999)]. 6. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 45, 108 (2000) [Crystallogr. Rep. 45, 103 (2000)]. 7. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 45, 292 (2000) [Crystallogr. Rep. 45, 261 (2000)]. 8. E. V. Babaev, V. B. Rybakov, S. G. Zhukov, and I. A. Orlova, Khim. Geterotsikl. Soedin., No. 4, 542 (1999). 9. S. G. Zhukov, E. V. Babaev, V. V. Chernyshev, et al., Z. Kristallogr. 215, 306 (2000). 10. V. B. Rybakov, S. G. Zhukov, K. Yu. Pasichnichenko, and E. V. Babaev, Koordin. Khim. 26 (9), 714 (2000). 11. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, and E. J. Sonneveld, Kristallografiya 46 (3), 435 (2001) [Crystallogr. Rep. 46, 385 (2001)]. 12. V. B. Rybakov, S. I. Troyanov, E. V. Babaev, et al., Kristallografiya 46 (6), 1069 (2001) [Crystallogr. Rep. 46, 986 (2001)]. 13. F. H. Allen and O. Kennard, Chem. Design Automat. News 8 (1), 31 (1993). 14. Enraf­Nonius CAD4 Software: Version 5.0 (Enraf­Nonius, Delft, The Netherlands, 1989). 15. L. J. Farrugia, WinGX98: X-ray Crystallographic Programs for Windows (Univ. of Glasgow, Glasgow, 1998). 16. G. M. Sheldrick, SHELX97: Program for the Solution and Refinement of Crystal Structures (Univ. of GÆttingen, GÆttingen, 1997). 17. J. W. Visser, J. Appl. Crystallogr. 2, 89 (1969). 18. J. J. P. Stewart, MOPAC 6.0. QCPE Program No. 455 (Indiana Univ., Department of Chemistry, Bloomington, 1990). 19. PCMODEL 7.0. Molecular Modeling Software for the Windows95/NT (Sarena Software, Bloomington, 1999). 20. V. V. Chernyshev and Y. Schenk, Z. Kristallogr. 213, 1 (1998). 21. V. B. Zlokazov and V. V. Chernyshev, J. Appl. Crystallogr. 25, 447 (1992). 22. W. A. Dollase, J. Appl. Crystallogr. 19, 267 (1986). 23. A. L. Spek, PLUTON96: Molecular Graphics Program (Univ. of Utrecht, The Netherlands, 1996). 24. M. Nardelli, J. Appl. Crystallogr. 28, 659 (1995).

sion angle is equal to 77.2(2)°, which rules out the formation of the O(2)···H(82)­O(82) intramolecular hydrogen bond. A similar molecular structure is observed in 1,2-dihydro-2-imino-1-carboxymethylpyridine [5], in which the planes of the carboxyl group and the pyridine ring form a dihedral angle of 80.81(5)°. In crystal structure I, a network of intermolecular hydrogen bonds is observed. The parameters of the hydrogen bonds are listed in Table 3. The heterocyclic cation II has a planar structure. The largest atomic deviation from the plane of the bicyclic fragment is 0.01 å. The O(8) atom lies in this plane. It is interesting to reveal structural changes that accompany the I II cyclization. As was noted above, the bond lengths in the six-membered ring of molecule I alternate. Upon cyclization, the diene-like structure is retained but the bond alternation becomes less pronounced (due to the stronger bond delocalization in the cation). At the same time, upon cyclization, the carbonyl fragment of the amide group loses the double-bond character. Most likely, this indicates significant charge localization at the nitrogen atom of the cation.
1.35 1.41

O
1.26 1.41

1.37

1.44

1.36

O

1.39

1.40

N
1.34 1.37

N+ COOH

1.21

O

The aforementioned specific structural feature of cation II suggests that no aromatization occurs in the bicyclic fragment formed from the monocycle. A system of intermolecular contacts involving the hydrogen, oxygen, and fluorine atoms is formed in crystal structure II (Table 4). These contacts were calculated using the PARST95 program [24]. The mean B­F bond length in the tetrahedral anion is 1.321(19) å. ACKNOWLEDGMENTS We are grateful to Professor E. Kemnitz (Humboldt UniversitÄt, Berlin), who kindly allowed us to perform the diffractometric experiment. The synthetic part of this study was supported by the Russian Foundation for Basic Research, project no. 9903-33076. We also acknowledge the support of this Foundation in the payment of the license for using the Cambridge Structural Database, project no. 99-0790133. REFERENCES
1. E. V. Babaev, A. V. Efimov, S. G. Zhukov, and V. B. Rybakov, Khim. Geterotsikl. Soedin., No. 7, 983 (1998).

Translated by I. Polyakova

CRYSTALLOGRAPHY REPORTS

Vol. 47

No. 3

2002