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Crystallography Reports, Vol. 45, No. 1, 2000, pp. 103­104. Translated from Kristallografiya, Vol. 45, No. 1, 2000, pp. 108­110. Original Russian Text Copyright © 2000 by Rybakov, Zhukov, Babaev, Mazina, Aslanov.

STRUCTURES OF ORGANIC COMPOUNDS

X-ray Mapping in Heterocyclic Design: II. Diffractometric Study of Crystalline 2-Oxo-2,3Dihydroimidazo[1,2-a]pyridine Hydrochloride
V. B. Rybakov, S. G. Zhukov, E. V. Babaev, O. S. Mazina, and L. A. Aslanov
Chemistry Department, Moscow State University, Vorob'evy gory, Moscow, 119899 Russia e-mail: rybakov@biocryst.phys.msu.su
Received May 13, 1999

Abstract--The crystal structure of 2-oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride, C7H7ClN2O, is determined by X-ray diffraction. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0408. The alternation of bond lengths in the molecule is inconsiderable, but does not disappear completely, since no aromatization occurs upon formation of the bicycle from the molecule. This structural change is apparently due to the increased conjugation of the NH group with the pyridine residue of the bicycle. One of the specific structural features of the salt is the formation of the N+­H···Cl­ hydrogen bond (N­H, 0.792 å; H···Cl, 2.260 å; and N­H···Cl, 171.2°). © 2000 MAIK "Nauka / Interperiodica".

This work continues a series of investigations of heterocyclic compounds that enter into reactions of cyclization and ring transformation [1­5]. The structure of 1,2-dihydro-2-imino-1-carboxymethylpyridine (I) was studied in the preceding paper [5]. In the present work, we determined the structure of a product of its cyclization, 2-oxo-2,3-dihydroimidazo[1,2a]pyridine hydrochloride (II). The I II cyclization was first carried out by Reindel in 1924 [6]. However, the compound obtained was by mistake assigned the structure of pyrrolo[2,3b]pyridine. Tschitschibabin showed [7] that, in the course of cyclization, the imidazolone fragment is formed. No data on the crystal structure of II is present in the Cambridge Structural Database [8]. The synthesis of II was performed according to the procedure described in [6]
+ NH2 O

The crystal data are a = 7.121(2) å, b = 7.621(2) å, c = 8.312(2) å, = 65.69(2)°, = 67.45(2)°, = 70.24(2)°, V = 370.9(2) å3 , dcalcd = 1.528 g/cm3 , µ(Mo) = 0.450 mm­1, Z = 2, and space group P 1 . A set of 2187 unique reflections with I 2(I) was collected in the range 26° on the same diffractometer by the -scan technique. The processing of the diffraction data measured was performed with the WinGX96 program package [10]. The coordinates of the non-hydrogen atoms were found by the direct method, and the structure was refined in the anisotropic approximation by the least-squares procedure using the SHELX97 program package [11]. All the hydrogen atoms were located from the difference synthesis of electron density and

HCl O­ N II

H+ N O. Cl­
C(6) 1.383(4) 1.371(4) C(5) 1.382(3)

1.362(3) 1.377(3) N(3) C(4) 1.346(3) 1.466(3) C(2) 1.514(3) C(1) O(2) 1.199(3)

N I

Recrystallization from a 1 : 1 isopropanol­water solution yields transparent colorless crystals with a platelike habit. EXPERIMENTAL Crystals II, C7H7ClN2O, are triclinic. The unit-cell parameters were determined and refined on a CAD4 automated diffractometer using 25 reflections in the range 11°­14° [9] (MoK, graphite monochromator).

C(7) 1.359(4)

N(9) 1.350(3) C(8)

The structure of the molecule studied and atomic numbering.

1063-7745/00/4501-0103 $20.00 © 2000 MAIK "Nauka / Interperiodica"


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RYBAKOV et al.

Atomic coordinates (â 104) and equivalent (isotropic) thermal parameters Ueq/Uiso (å2 â 103) for molecule II Atom Cl C(1) C(2) O(2) N(3) C(4) C(5) C(6) C(7) C(8) N(9) H(11) H(12) H(3) H(5) H(6) H(7) H(8) x 3283(1) 1527(5) 1959(4) 1793(3) 2584(3) 2623(3) 3171(4) 3022(4) 2365(4) 1866(4) 2016(3) 2420(39) 108(49) 2762(43) 3563(40) 3492(40) 2256(44) 1490(39) y 1424(1) 8296(3) 7252(3) 7963(3) 5279(3) 4945(3) 3200(3) 3304(4) 5090(4) 6783(4) 6668(2) 9159(37) 8941(42) 4332(42) 2025(38) 2152(39) 5137(42) 8035(38) z 8058(1) 2928(3) 4782(3) 5889(3) 4961(3) 3459(3) 3088(3) 1453(4) 219(4) 613(3) 2226(2) 2174(35) 3078(39) 5847(40) 3951(36) 1119(35) ­ 911(42) ­119(35) Ueq/Uiso 44(1) 40(1) 40(1) 58(1) 40(1) 34(1) 42(1) 44(1) 43(1) 38(1) 31(1) 41(7) 55(8) 51(8) 40(6) 47(7) 62(8) 41(7)

It is interesting to reveal the structural changes upon the I II cyclization. As we already noted in [5], the bond lengths in the ring of I distinctly alternate: actually, molecule I contains a quazi-diene fragment. In the course of cyclization, the bonds in the six-membered fragment tend to become equal, and the alternation of bond lengths in II becomes inconsiderable.
1 35 1 40 1 35 1 42 1 33 + NH2 O 1 37 1 38 1 38

H+ N O. Cl­

1 36

N I

O

­

1 36

N II

This structural feature is remarkable, since no aromatization occurs upon formation of the bicycle from the monocycle. The above structural change is apparently due to the increased conjugation of the NH group with the pyridine residue of the bicycle. Another structural feature of salt II is the formation of the N(3)+­H(3)···Cl­ hydrogen bond [N(3)­H(3), 0.79 å; H(3)···Cl, 2.26 å; and N(3)­H(3)···Cl, 171°]. ACKNOWLEDGMENTS This work was supported by the Russian Foundation for Basic Research, project no. 99-03-33076a. We also acknowledge the support of this Foundation in the payment of the licence for using the Cambridge Structural Database, project no. 99-07-90133. REFERENCES
1. E. V. Babaev, A. V. Efimov, S. G. Zhukov, et al., Khim. Geterotsikl. Soedin., No. 7, 983 (1998). 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, et al., Khim. Geterotsikl. Soedin., No. 8, 1105 (1997). 5. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 44 (6), 1067 (1999). 6. F. Reindel, Chem. Ber. 57, 1381 (1924). 7. A. E. Tschitschibabin, Chem. Ber. 57, 2092 (1925). 8. F. H. Allen and O. Kennard, Chem. Des. Autom. News 8, 31 (1993). 9. Enraf­Nonius, CAD4 Software: Version 5.0 (Enraf­ Nonius, Delft, 1989). 10. L. J. Farrugia, WinGX96: An Integrated System of Publicly Available Windows Programs for the Solution, Refinement, and Analysis of Single-Crystal X-ray Diffraction Data (Univ. of Glasgow, Glasgow, 1996). 11. G. M. Sheldrick, SHELX97: Programs for the Solution and Refinement of Crystal Structures (Univ. of GÆttingen, GÆttingen, 1997). 12. A. L. Spek, PLUTON96: Molecular Graphics Program (Univ. of Utrecht, Utrecht, 1996).

included in the refinement in the isotropic approximation. The final discrepancy factors are R1 = 0.0408 and wR2 = 0.0930. The atomic coordinates and thermal parameters are listed in the table. The residual electron density lies between max = 0.253 and min = ­0.255 e/å3 . The organic cation shown in the figure was drawn with the PLUTON96 program [12]. RESULTS AND DISCUSSION The chloride anion serves as a counterion in compound II. The heterocyclic cation is planar. The largest atomic deviation from the plane of the bicycle is 0.011(2) å. In theory, three tautomeric forms of II are possible: A, B, and C
H+ N N A N N+ B OH N C O H+ N OH .

However, the C(1)­C(2) bond (figure) is a single C-C bond (1.51 å), which eliminates the C tautomer. The C(2)­O(2) bond is the normal double bond C=O (1.20 å), which eliminates the B tautomer. Therefore, the structure of cation II is unambiguously described by the A tautomer.

Translated by I. Polyakova
CRYSTALLOGRAPHY REPORTS Vol. 45 No. 1 2000