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Crystallography Reports, Vol. 45, No. 2, 2000, pp. 261­263. Translated from Kristallografiya, Vol. 45, No. 2, 2000, pp. 292­294. Original Russian Text Copyright © 2000 by Rybakov, Zhukov, Babaev, Mazina, Aslanov.

STRUCTURES OF ORGANIC COMPOUNDS

X-ray Mapping in Heterocyclic Design: III. Diffractometric Study of the Crystal Structure of 1-Methyl-2-Oxo-2,3Dihydroimidazo[1,2-a]pyridinium Bromide
V. B. Rybakov, S. G. Zhukov, E. V. Babaev, O. S. Mazina, and L. A. Aslanov
Chemistry Department, Moscow State University, Vorob'evy gory, GSP-3, Moscow, 119899 Russia
Received May 13, 1999

Abstract--The crystal structure of 1-methyl-2-oxo-2,3-dihydroimidazo[1,2-a]pyridinium bromide C8H9BrN2O is determined by X-ray diffraction. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0599. The geometry of the pyridinium fragment observed in the molecule corresponds to the limited number of centers at which the positive charge can be delocalized. Apparently, this delocalization predominantly occurs in the NCN fragment of the imidazole ring and only slightly affects the pyridine moiety of the molecule. © 2000 MAIK "Nauka / Interperiodica".

Earlier [1, 2], we performed structural studies characterizing the transformation of pyridine I into imidazopyridine II. This work continues our investigations into the structure of the compounds obtained by consecutive transformations of compounds I and II. Formally, compound II is the hydrochloride of instable free base III. Compound III, which readily enters into the reactions with electrophilic chemical agents, can be prepared by a reaction between sodium methylate and salt II [3]. The object of the present work was compound IV (a homolog of salt II), which was obtained by the reaction between salt II and the base followed by the methylation (without isolation of intermediate compound III):
+ NH2 O

EXPERIMENTAL Salt IV was initially isolated as the perchlorate according to the procedure described in [3]; however, we failed to prepare the satisfactory crystals of the isolated perchlorate and transformed the compound into the bromide salt. For this purpose, an aqueous solution of the perchlorate was treated by a saturated KBr solution. The precipitate of potassium perchlorate was filtered off, and the aqueous solution of bromide IV was evaporated to dryness. The dry residue was recrystallized from a 1 : 1 isopropanol­water solution and used for the X-ray diffraction analysis. Transparent colorless crystals of bromide IV have a platelike habit. Crystals of bromide IV, C8H9BrN2O, are monoclinic. The unit cell parameters were determined and refined on a CAD4 automated diffractometer using 25 reflections in the range 11°­13° [5] (MoK, graphite monochromator). The crystal data are a = 7.806(1) å, b = 6.404(1) å, c = 8.812(1) å, = 97.44(2)°, V = 436.8(1) å3 , dcalcd = 1.742 g/cm3 , µ(Mo) = 4.656 mm­1, Z = 2, and space group P21/m. A set of 934 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 [6]. The structure was solved by the direct method and refined in the anisotropic approximation by the least-squares procedure using the SHELX97 program package [7]. All the hydrogen atoms were located from the difference synthesis of electron density and included in the refinement in the isotropic approximation. The final discrepancy factors are R1 = 0.0599 and wR2 = 0.1374. The atomic coordinates and thermal parameters are listed in the table. The residual electron density lies between max = 1.304 and min

N O­ N III O

N I

HCl Me ONa

(1) Me2SO4 (2) NaClO4 (3) KBr

H N N II

+

CH3 O N N IV
+

Cl­

O Br
­

We determined the crystal structure of salt IV by X-ray diffraction analysis. Up to now, according to the data of the Cambridge Structural Database [4], the X-ray structure analysis of this compound has not been performed.

1063-7745/00/4502-0261$20.00 © 2000 MAIK "Nauka / Interperiodica"


262

RYBAKOV et al.

Atomic coordinates (â 104) and equivalent (isotropic) thermal parameters Ueq/Uiso (å2 â 103) Atom Br C(1) C(2) O(2) N(3) C(3) C(4) C(5) C(6) C(7) C(8) N(9) H(11) H(31) H(32) H(5) H(6) H(7) H(8) x 4404(1) 2386(4) 741(4) 578(3) ­ 612(3) ­2432(4) ­12(4) ­ 913(4) 52(5) 1835(5) 2690(4) 1725(3) 3050(24) ­2694(46) ­2983(35) ­2147(41) ­ 667(47) 2640(51) 3737(36) y 7500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 2500 1310(36) 2500 1197(49) 2500 2500 2500 2500 z 7737(1) 8644(4) 9354(3) 10 698(3) 8179(3) 8381(4) 6777(3) 5322(4) 4116(4) 4360(4) 5811(4) 7007(3) 8835(22) 9425(46) 7881(34) 5161(38) 3032(49) 3670(50) 6017(34) Ueq/Uiso 42(1) 35(1) 36(1) 53(1) 31(1) 45(1) 23(1) 31(1) 33(1) 35(1) 31(1) 26(1) 20(5) 53(12) 69(9) 33(9) 69(15) 65(13) 17(8)

the mirror plane. In the crystals of compound IV (in distinction to II), hydrogen bonds are absent. A comparison of the geometries of the NH derivative II and the homologous NCH3 derivative IV reveals that introduction of the methyl group results only in a slight lengthening of the C(4)­N(3) bond in compound IV as compared to II. The lengths of all the other skeleton bonds in II and IV are virtually identical. This result supports our conclusion [2] that compound II actually exists in the NH tautomeric form, since its structure and geometry coincide with those of the NCH3 derivative IV. Cations II and IV can be represented by three resonance structures--A, B, and C (R = H or CH3)
R N N A
+

R N O N
+

R N O N
+

O

B

C

= ­1.265 e/å3 . Cation IV shown in the figure was drawn with the PLUTON96 program [8]. RESULTS AND DISCUSSION The bromide anion serves as a counterion in salt IV. The heterocyclic cation occupies a special position in

Ê(3) 1.454(4) 1.380(5) Ê(5) Ê(6) 1.380(5) 1.380(4) 1.377(4) Ê(4) 1.345(4) N(3) 1.380(4) 1.208(4) Ê(2) O(2) 1.499(5) Ê(1)

Consider the C(6)C(7)C(8) fragment (distinguished by heavy lines in structures A and B). In II and IV, the mean C(6)­C(7) bond length is 1.381(4) å, whereas the length of the adjacent C(7)­C(8) bond is 1.362(4) å. These bond lengths in the C(6)C(7)C(8) fragment are consistent with resonance structures A and B, but contradict structure C, which implies the reverse ratio of the bond lengths: the C(6)­C(7) bond should be shorter than the C(7)­C(8) bond. Of the two structures A and B, the latter structure is preferential for IV, since, bearing the positive charge, the nitrogen atom of the pyridine fragment should attract the bromide anion; that is, the N(9)···Br distance should be shorter than the N(3)···Br distance, which is the case in crystal structure IV [3.833(1) and 5.112(2) å, respectively]. In structure II [2], the chloride anion approaches the N(3) atom rather than the N(9) atom [the shortest distances, other than hydrogen bonds, are N(3)···Cl = 3.045(2) å and N(9)···Cl = 5.025(2) å], indicating that structure A is preferential for II. A partial fixation of the geometry of the pyridine fragment results in a limited number of centers at which the positive charge can be delocalized. Apparently, this delocalization predominantly occurs in the N(9)C(4)N(3) fragment of the imidazole ring and only slightly affects the pyridine ring. 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.
CRYSTALLOGRAPHY REPORTS Vol. 45 No. 2 2000

Ê(7) 1.364(4) ãr

N(9) 1.372(4) Ê(8) 1.468(4)

Structure of the heterocyclic cation IV.


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263

REFERENCES
1. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 44, 1067 (1999) [Crystallogr. Rep. 44, 997 (1999)]. 2. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 45, 108 (2000) [Crystallogr. Rep. 45, 103 (2000)]. 3. E. D. Sych and L. T. Gorb, Ukr. Khim. Zh., No. 9, 961 (1996). 4. F. H. Allen and O. Kennard, Chem. Des. Autom. News 8, 31 (1993).

5. Enraf­Nonius. CAD4 Software: Version 5.0 (Enraf­ Nonius, Delft, 1989). 6. 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). 7. G. M. Sheldrick, SHELX97: Programs for the Solution and Refinement of Crystal Structures (Univ. of GÆttingen, GÆttingen, 1997). 8. A. L. Spek, PLUTON96: Molecular Graphics Program (Univ. of Utrecht, Utrecht, 1996).

Translated by I. Polyakova

CRYSTALLOGRAPHY REPORTS

Vol. 45

No. 2

2000