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Crystallography Reports, Vol. 46, No. 6, 2001, pp. 986988. Translated from Kristallografiya, Vol. 46, No. 6, 2001, pp. 10691071. Original Russian Text Copyright © 2001 by Rybakov, Troyanov, Babaev, Mazina, Aslanov.

STRUCTURE OF ORGANIC COMPOUNDS

X-ray Mapping in Heterocyclic Design: V. Diffractometric Study of the Crystal Structure of 2-Hydroxy-3-Trifluoracetylimidazo[1,2-a]pyridine Hydrochloride at 180 K
V. B. Rybakov, S. I. Troyanov, 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 November 23, 2000

Abstract--The crystal structure of 2-hydroxy-3-trifluoracetylimidazo[1,2-a]pyridine hydrochloride C9H6F3ClN2O2 is determined by X-ray diffraction at 180 K. The structure is solved by the direct method and refined by the least-squares procedure to R = 0.0296. The alternation of bond lengths in the six-membered fragment of the molecule is observed. One of the specific features of the crystal structure is the formation of a system of the NH···Cl (N··· Cl, 3.09 å; NH, 0.83 å; H··· Cl, 2.33 å; and NH··· Cl, 153°) and OH··· Cl (O··· Cl, 2.87 å; OH, 0.95 å; H··· Cl, 1.92 å; and OH··· Cl, 178°) hydrogen bonds in which the chlorine atoms are related to the reference atom by different symmetry transformations. © 2001 MAIK "Nauka / Interperiodica".

INTRODUCTION This work continues the series of our investigations of heterocyclic compounds that are able to enter into the reactions of cyclization and ring transformation [18]. Earlier [6], we described the structure of 2oxo-2,3-dihydroimidazo[1,2-a]pyridine hydrochloride C7H7ClN2O (I). This salt was used as a starting substance for preparation of 2-hydroxy-3-trifluoracetylimidazo[1,2-a]pyridine hydrochloride C9H6F3ClN2O2 (II). Compound II was prepared by the reaction between I and trifluoracetic anhydride
H+ N N O Cl
(CF3CO)2O

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) C(10) O(10) C(11) F(1) F(2) F(3) H(2) H(3) H(5) H(6) H(7) H(8) x 4755(1) 3540(1) 3885(1) 3887(1) 4231(1) 4123(1) 4354(1) 4148(1) 3721(1) 3501(1) 3704(1) 3099(1) 2867(1) 2904(1) 2773(1) 2434(1) 3305(1) 4186(9) 4488(8) 4635(7) 4300(7) 3585(8) 3208(7) y 1286(1) 4336(3) 6417(3) 7359(2) 7391(2) 6006(3) 6330(3) 4654(3) 2694(3) 2434(3) 4117(2) 2626(3) 733(2) 3220(3) 5869(2) 1766(2) 2518(2) 8630(40) 8570(40) 7800(40) 4780(40) 1560(40) 1230(30) z 1458(1) 2447(1) 2227(1) 1538(1) 2873(1) 3505(1) 4286(1) 4803(1) 4548(1) 3778(1) 3262(1) 2024(1) 2301(1) 1149(1) 1006(1) 885(1) 743(1) 1523(12) 2893(10) 4407(10) 5344(10) 4901(11) 3562(9) Ueq/Uiso 31(1) 20(1) 20(1) 25(1) 21(1) 21(1) 26(1) 30(1) 31(1) 26(1) 20(1) 22(1) 31(1) 26(1) 34(1) 45(1) 35(1) 49(5) 37(5) 31(4) 36(4) 37(4) 29(4)

N

H+ N Cl OH O CF3

I II Colorless crystals of the prismatic habit precipitated in the reaction vessel. The crystals removed from the mother liquor cracked within 30 s. Because of the high volatility of trifluoracetic anhydride, the X-ray-quality crystals were chosen under the flow of cooled nitrogen with a binocular microscope in polarized light. According to the data of the Cambridge Structural Database [9], the X-ray structure analysis of II has not been performed. EXPERIMENTAL Crystals of compound II are monoclinic. The unit cell parameters were determined and refined at

1063-7745/01/4606-0986$21.00 © 2001 MAIK "Nauka / Interperiodica"

X-RAY MAPPING IN HETEROCYCLIC DESIGN

987

1.402(2)

1.379(2)

1.369(2)

1.368(2)

C(5)
1 405(2)

C(6)
1.376(2)

1 365(2)

C(4)
1.431(2)

N(3)
400(2)

1.304(2)

1.376(2)

1.562(2)

1.219(2)

C(10)

1 332(2)

C(11)

1 337(2)
1.337(2)

C(8)

1.438(2)

C(7)

N(9)

1

C(2) C(1)

O(2) F(3)

O(10)

F(1)

F(2)
Structure of heterocyclic cation II.

180(2) K on an IPDS automated diffractometer using 1097 reflections in the range 5°25° (MoK, graphite monochromator). The crystal data are a = 23.761(5) å, b = 4.856(1) å, c = 17.713(4) å, = 100.41(3)°, V = 2010.1(7) å3 , Z = 8, space group C2/c, dcalcd = 1.762 g/cm3 , and µ(Mo) = 0.415 mm1. A set of 4505 reflections with I 2(I) was collected on the same diffractometer and at the same temperature by the -scan technique in the range 3.16°26.19°. The diffraction data measured were processed with the X-RED-107 program package. The non-hydrogen atoms were located by the direct method and refined in the anisotropic approximation by the least-squares procedure according to the SHELX97 program package [10]. All the hydrogen atoms were located from the difference Fourier syntheses of electron density. The structure was refined by the least-squares procedure in the anisotropic approximation (isotropic, for H atoms) to R1 = 0.0296 (wR2 = 0.0642). The atomic coordinates and isotropic thermal parameters that are equivalent to the corresponding anisotropic parameters are listed in the table. The residual (maximum and minimum) electron densities are max = 0.240 and min = 0.184 e/å3 . The drawing of the cation with the atomic numbering (see figure) was obtained with the PLUTON96 program [11]. RESULTS AND DISCUSSION The chloride ion serves as a counterion in compound II. The heterocyclic cation is planar: the largest
CRYSTALLOGRAPHY REPORTS Vol. 46 No. 6 2001

atomic deviation from the plane of the bicyclic fragment is 0.015(1) å. The cations of salts I and II can be represented by one of the three structures (R = H or COCF3):
H+ N N H O R N R H+ N OH N H
+

N OH R

A

B

C

In our earlier work [6], we found that the structure of salt I is of the A type. The localization of the protons at the N(3) and O(2) atoms and the absence of a proton at the C(1) atom suggest that the structure of salt II (which is prepared by acylation of I) should be unambiguously assigned to the B-type structure rather than to the C type. It is of interest to reveal the structural changes upon the I II acylation. A comparison of the bond lengths in the cations studied shows that the quasidiene character of the C(5)C(6)C(7)C(8) moiety of the six-membered heterocycle in II is pronounced more than that in I. Protonation of the exocyclic O atom results in a redistribution of the bond lengths in the fivemembered ring. In particular, the C(2)O(2) bond lengthens and the C(1)C(2) bond shortens. This is consistent with the expected bond-length distribution in the ketonic compound I and the enolic compound II. We conclude that

988

RYBAKOV et al.

the attachment of the COCF3 group to the C(1) atom in the ketonic A form increases the acidity of the remaining proton and stabilizes the enolic B form. Since the C(1)C(10) bond (heterocycleacyl) is rather long (1.44 å), the COCF3 group in II is apparently weakly conjugated with the enolic fragment.
1.37 1.38 1.36 1.38

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). 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 (6), 1067 (1999) [Crystallogr. Rep. 44, 997 (1999)]. 6. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 45 (1), 108 (2000) [Crystallogr. Rep. 45, 103 (2000)]. 7. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, et al., Kristallografiya 45 (2), 292 (2000) [Crystallogr. Rep. 45, 261 (2000)]. 8. V. B. Rybakov, S. G. Zhukov, E. V. Babaev, and E. J. Sonneveld, Kristallografiya 46 (3), 435 (2001) [Crystallogr. Rep. 46, 385 (2001)]. 9. F. H. Allen and O. Kennard, Chem. Des. Autom. News 8, 31 (1993). 10. G. M. Sheldrick, SHELX97: Programs for the Solution and Refinement of Crystal Structures, GÆttingen: Univ. of GÆttingen, 1997. 11. A. L. Spek, PLUTON96: Molecular Graphics Program, Utrecht: Univ. of Utrecht, 1996.

H+ N
1.36 1.20 1.51

1.38

1.40

H+ N
1.37 1.30 1.40

N Cl

O

1.41 1.38

N Cl

OH

R

I (the A form)

II (the B form; R = COCF3)

Another specific structural feature of II is the formation of the hydrogen-bond system. The N(3)H(3)···Cl hydrogen bond, in which the chlorine atom is related to the reference atom by the (1 x, 1 + y, 1/2 z) symmetry transformation, is characterized by the following parameters: N(3)···Cl, 3.09 å; N(3)H(3), 0.83 å; H(3)···Cl, 2.33 å; and N(3)H(3)···Cl, 153°. In the O(2)H(2)···Cl hydrogen bond [O(2)···Cl, 2.87 å; O(2)H(2), 0.95 å; H(2)···Cl, 1.92 å; and O(2) H(2)···Cl, 178°], the chlorine atom is related to the reference atom by the (x, 1 + y, z) symmetry transformation. ACKNOWLEDGMENTS We are grateful to Professor E. Kemnitz (InstitÝt fÝr Chemie, 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 to use the

Translated by I. Polyakova

CRYSTALLOGRAPHY REPORTS

Vol. 46

No. 6

2001