The structure of the title compound, C10H12BrNO3, is

reported. The ribose sugar has a C3'-endo pucker and

the exocyclic torsion angle 05'--C5'---C4'--C3' adopts

a gauche + value of 61.0 (9) °

Bernadette, JV

Capaldi, DC

Neidle, S

Reese, CB

UCL Discovery

S. LAKSHMI et al. 407 CIA--C2A--C3A 110.0 (2) C IB-----C2B-----C3B 110.4 (3) CgA---C2A--O11A 109.0 (2) CgB---C2B---O11B 109.3 (3) C3A---C2A---O11A 105.5 (2) C3B--C2B--O11B 105.1 (2) C3A---C2A---CgA 110.6 (2) C3B---C2B---C8B II1.1 (3) C2A---C3A---C4A 112.9 (3) C2B----C3B---C4B 113.1 (3) C3A----C4A---425A 112.1 (4) C3B---C4B---C5B 111.5 (4) C4A----C5A---C6A 110.1 (4) C4B----C5B---C6B 110.5 (4) C IA--C6A----C5A 111.9 (3) C 1B--C6B----C5B 113.2 (3) CIA---C21A---OI 2A 122.0 (3) C1B---C2rB----OI2B 121.9 (3) CIA----C21A--C31A 118.3 (3) C1B----C21B-----C31B 118.4 (3) C31A--C21A---~12A 119.6 (3) C31B---C21B----OI2B 119.6 (3) C2~A----C3'A---C4~A 123.8 (3) C2'B--C3'B----C4~B 124.6 (3) C31A---C41A---C7A 121.8 (3) C3'B---C41B---C7B 122.8 (3) C3rA---C4'A---C5~A 121.2 (3) C3~B----C4~B---C5rB 120.6 (3) C51A---C41A--C7A 117.0 (3) C51B---C41B---C7B ! 16.6 (3) C41A----C51A---C61A 111.9 (3) C41B----C51B----C61B 112.4 (4) CIA---C61A---C51A 113.2 (2) C1B----C61B---C51B 113.8 (3) C2A---CgA----C9A 113.6 (3) C2B---CgB----C9B 115.3 (3) CgA--C9A----CIOA 178.6 (4) CgB---C9B---CIOB 178.1 (4) Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Lakshmi, S., Subramanian, K., Rajagopalan, K., Koellner, G. & Steiner, Th. (1995). Acta Cryst. C51, 2327-2329. Nardelli, M. (1983). Comput. Chem. 7, 95-98. Nasipuri, D. (1992). In Stereochemistry of Organic Compounds - Principles and Applications. New Delhi: Wiley Eastern. Sheldrick, G. M. (1985). SHELXS86. Program for the Solution of Crystal Structures. University of G6ttingen, Germany. Sheldrick, G. M. (1993). SHELXL93. Program for the Refinement ofCrystal Structures. University of G6ttingen, Germany. Table 3. Ring-puckering parameters according to Cremer & Pople (1975) Q (~,) 0 (o) qo (o) Molecule A Ring 1 0.580 (3) 177.0 (3) 154 (6) Ring 2 0.460 (3) 126.8 (4) 109.2 (5) Molecule B Ring 1 0.573 (4) 2.6 (4) 350 (9) Ring 2 0.449 (3) 52.8 (4) 311.5 (6) Table 4. Hydrogen-bond parameters (,4, o) D--H...O D--H H...O D-.-O Hnorm"" O D--Hnorm"" "O OIIA--H- • .O12A 0.78 (4) 1.93 (4) 2.668 (4) 1.75 154 OllB--H...O12B 0.91 (8) 2.03 (3) 2.659 (4) !.99 124 CIOA--H. • .OIIB 0.89 (4) 2.54 (5) 3.413 (4) 2.37 162 C10B--H-"OIIA 0.92(3) 2.50(5) 3.414(5) 2.36 164 The structure was solved by direct methods. The initial R index for the model was 0.19. After a few cycles of full-matrix refinement the R index dropped to 0.12. All H atoms were located from difference Fourier maps and refined isotropically. The Flack X parameter refined to -0 .16  (32). Data collection: CAD-4 Software (Enraf-Nonius, 1989). Cell refinement: SDP (Frenz, 1978). Program(s) used to solve structure: SHELXS86 (Sheldrick, 1985). Program(s) used to refine structure: SHELXL93 (Sheldrick, 1993). Molecular graphics: ORTEPII (Johnson, 1976). Software used to prepare material for publication: PARST (Nardelli, 1983). Lists of structure factors, anisotropic displacement parameters, H- atom coordinates and complete geometry have been deposited with the IUCr (Reference: KA1129). Copies may be obtained through The Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CH 1 2HU, England. References Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358. Desiraju, G. R. (1991). Acc. Chem. Res. 24, 290-296. Enraf-Nonius (1989). CAD-4 Software. Version 5.0. Enraf-Nonius, Delft, The Netherlands. Frenz, B. A. (1978). The Enraf-Nonius CAD-4 SDP - a Real-Time System for Concurrent X-ray Data Collection and Crystal Structure Solution. Computing in Crystallography, edited by H. Schenk, R. Olthof-Hazekamp, H. van Koningsveld & G. C. Bassi, pp. 64-71. Delft University Press. Acta Cryst. (1996). C52, 407-409 The a -Pyr idy l  Nuc leos ide  Ana logue  2 -Bromo-5- (2 -deoxy-c~-a - r ibo furanosy l ) -  pyr id ine  STEPHEN NEIDLE, a* DANIEL C. CAPALDI, b JOSEPH V. BERNADETTE b AND COLIN B. REESE b aCRC Biomolecular Structure Unit, The Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, England, and bDepartment of Chemistry, King's College, Strand, London WC2R 2LS, England. E-mail: steve@iris5. icr.ac.uk (Received 19 July 1995; accepted 20 September 1995) Abstract The structure of the title compound, C10H12BrNO3, is reported. The ribose sugar has a C3'-endo pucker and the exocyclic torsion angle 05'--C5'---C4'--C3' adopts a gauche +value of 61.0 (9) °. Comment The determination of the structure of the title compound, (I), was undertaken in order to unequivocally assign the a-conformation at the C I' atom following its synthe- sis as part of a project aimed at developing modified nucleosides for DNA triple-strand recognition. The de- tails of the conformational features are being employed in molecular-modelling studies on triple helices with non-standard bases. HO--CH2 o H o .  Br (i) 01996 International Union of Crystallography Printed in Great Britain - all rights reserved Acta Crystallographica Section C ISSN 0108-2701 ©1996 408 C10H12BrNO3 The structure and conformation of (I) show overall similarity to those of the non-brominated parent com- pound (II) (Ford, Neidle, Eaton, Millican & Mann, 1987). The C1 ' - -C5  bond length [1.515 (7)k,] is close to that in (II) [1.510 (5) /k] and is significantly longer than the average glycosidic bond in standard nucleosides (1.46/~). It is also slightly longer than the C I '~C bond in analogues of the c~-anomer of the antibiotic show- domycin (Neidle, Kaye & Reese, 1990), which have an average bond length of 1.493/~. These differences result in changes in the bond geometry of the furanose ring compared with that in standard nucleosides. The conformational features of (I) are mostly similar to those found in (II) (Ford et al., 1987). The furan- ose sugar ring in the title compound has a C3'-endo pucker with a pseudorotation parameter P of 5.9 (7) °, compared with a value of 324.5 (5) ° and a C2'-exo pucker in (II). The orientation of the pyridine ring with respect o the sugar is very similar in the two structures, with values for the pseudo-glycosidic torsion angle O4 ' - -C1 ' - - -C5- -C6  of 135.0 (6) ° in (I) and 126.2 (5) ° in (II). The exocyclic torsion angle O5 ' - -C5 ' - -C4 ' - -  C3' adopts a gauche + value of 61.0(9) ° in the title compound, whereas in the non-brominated compound it has a less common (Neidle, 1994) trans value of 177.2(5) °. The gauche + value predominates in right- handed oligo- and polynucleotides. 0 (~) f-~ C3 C2 ~.~ Br 04' C4 ~ N V l  C4' k ~,C / '  (-J "~ 03' Fig. 1. Two orthogonal views of the title structure with displacement ellipsoids hown at the 50% probability level and H atoms drawn as small circles of arbitrary radii. Exper imenta l  Details of the synthesis of (I) will be published elsewhere. Crystal data C10HI2BrNO3 Mo Koe radiation Mr = 274.1 A = 0.7107 Monoclinic Cell parameters from 250 P21 reflections a = 7.686 (3) A, 0 = 2-22 ° b = 7.2420 (10) ~ # = 3.747 mm -I c -- 9.9240 (10) A, T = 293 (2) K /3 = 98.31 (2) ° Prism V = 546.6 (2)A, 3 0.5 x 0.2 x 0.1 mm Z = 2 Colourless Dx = 1.666 Mg m -3 Data collection Enraf-Nonius FAST diffrac- tometer MADNESS (Enraf-Nonius, 1990) scans Absorption correction: none 2486 measured reflections 1509 independent reflections 1426 observed reflections [1 > 2o'(/)1 Rint = 0 .0686 0ma,, = 24.75 ° h = -8  ---+ 8 k=-8- -+ 8 1 = -11 ~ 8 Refinement Refinement on F 2 R[F 2 > 20.(F2)] = 0.0434 wR(F 2) = 0.1139 S = 0.909 1509 reflections 136 parameters H atoms treated using a riding model; Uiso values refined w = 1/[0.2(Fo 2) + (0.1000e) 2] where P = (Fo 2 + 2F~)/3 (A/0.)max < 0.001 Apmax = 0.649 e A, -3 Apmin = -0.518 e A, -3 Extinction correction: none Atomic scattering factors from International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.4) Absolute configuration: Flack (1983) parameter = -0.02 (2) Table 1. Fractional atomic coordinates and equivalent isotropic displacement parameters (i{ 2 ) . . . .  * * Ueq = ( I /3 )E ,~)Uua i aj ai.aj. x y z Ueq Br -0.17728 (6) -0.32905 (10) -0.65133 (5) 0.0494 (3) N1 0.1762 (7) -0.3998 (7) -0.6064 (5) 0.0411 (12) C2 0.0467 (7) -0.3470 (11) -0.5408 (5) 0.0358 (13) C3 0.0616 (7) -0.3069 (11) -0.4052 (5) 0.0383 (14) C4 0.2287 (8) -0.3128 (13) -0.3318 (5) 0.0410 (13) C5 0.3702 (7) -0.3607 (8) -0.3948 (5) 0.0331 (14) C6 0.3361 (7) -0.4054 (8) -0.5301 (6) 0.0373 (14) CI' 0.5557 (8) -0.3624 (10) -0.3184 (6) 0.044 (2) C2' 0.5944 (10) -0.5220 (12) -0.2204 (8) 0.050 (2) C3' 0.7276 (8) -0.4396 (11) -0.1074 (7) 0.045 (2) 03' 0.7344 (7) -0.5361 (10) 0.0154 (5) 0.073 (2) 04' 0.5822 (6) -0.1994 (7) -0.2377 (5) 0.0523 (14) C4' 0.6576 (9) -0.2457 (10) -0.1029 (7) 0.043 (2) C5' 0.7831 (I0) -0.0928 (12) -0.0492 (7) 0.056 (2) 05' 0.9213 (6) -0.0741 (8) -0.1308 (4) 0.0583 (13) Data collection: MADNESS (Enraf-Nonius, 1990). Cell re- finement: MADNESS. Data reduction: MADNESS. Program(s) STEPHEN NEIDLE et al. 409 used to solve structure: SHELXS86 (Sheldrick, 1990). Pro- gram(s) used to refine structure: SHELXL93 (Sheldrick, 1993). Molecular graphics: ORTEX (McArdle, 1993). The authors are grateful to the Cancer Research Campaign for grants (to SN and CBR) in support of this work. X-ray data were collected at the EPSRC Crystallographic Service, University of Wales, Cardiff; Professor M. B. Hursthouse is thanked for providing access to this facility. Lists of structure factors, anisotropic displacement parameters, H- atom coordinates, bond distances and angles involving non-H atoms, and torsion angles have been deposited with the IUCr (Reference: AS1213). Copies may be obtained through The Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England. References Enraf-Nonius (1990). MADNESS. Program for Area-Detector Data Interpretation. Enraf-Nonius, Delft, The Netherlands. Hack, H. D. (1983). Acta Cryst. A39, 876-881. Ford, K. G., Neidle, S., Eaton, M. A. W., Millican, T. A. & Mann, J. (1987). Acta Cryst. C43, 1988-1990. McArdle, P. (1993). J. Appl. Cryst. 26, 752. Neidle, S. (1994). In DNA Structure and Recognition. Oxford University Press. Neidle, S., Kaye, A. & Reese, C. B. (1990). Acta Cryst. B46, 426--431. Sheldrick, G. M. (1990). Acta Cryst. A46, 467--473. Sheldrick, G. M. (1993). SHELX93. Program for the Refinement of Crystal Structures. University of G6ttingen, Germany. Acta Cryst. (1996). C52, 409-411 2-Phenylquinol ine-4-carboxyl ic Acid ANTHONY C. BLACKBURN, ALLISON J. DOBSON AND ROGER E. GERKIN Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA. E-mail: rgerkin@magnus.acs. ohio-state.edu (Received 19 July 1995; accepted 25 September 1995) Abstract In 2-phenylquinoline-4-carboxylic acid, C16HllNO2, hydrogen bonding occurs only between a carboxy O- atom donor and the ring N atom, which acts as an ac- ceptor. The carboxy H atom is ordered in this structure. The dihedral angle between the plane of the carboxy group and the best-fit mean quinoline plane is 53.6 (1) °. All bond distances and angles within the quinoline core, the carboxy group and the phenyl group fall within the normal ranges. The structure is described in space group P212121 ©1996 International Union of Crystallography Printed in Great Britain - all rights reserved Comment As part of a continuing series of investigations of hydro- gen bonding in organic solids, we describe here the structure of 2-phenylquinoline-4-carboxylic acid,(I), the structure of which has not been reported previously. COOH (I) The title molecule is shown in Fig. 1 with the numbering system and a stereoview of the structure is presented in Fig. 2. Selected bond lengths and angles are compiled in Table 2 and these data support the assignment of hydrogen bonds for this structure in which atom O(1) is the sole donor and the N atom of the quinoline moiety is the sole acceptor. Consistent with this, the carboxy H-atom position is ordered in this structure. Takusagawa, Hirotsu & Shimada (1973) presented graphically a smooth curvilinear correlation between the N--Hcarboxy distance and the C--N----Cring bond angle based upon their data for four pyridine dicarbox- ylic acids, namely, dipicolinic monohydrate, dinicotinic, cinchomeronic and quinolinic. In these acids, the N m I-l~arboxy distances ranged from 0.89(4) to 2.17(6)A, while the C--N---C.dng angles ranged from 116.8(4) to 125.3(2) ° . Although corresponding data obtained subsequently for isonicotinic acid (pyridine-4-carboxylic acid) (Takusagawa & Shimada, 1976) conform well to that correlation, those for both nicotinic acid (pyridine- 3-carboxylic acid) (Kutoglu & Scheringer, 1983) and the present compound o not. It thus appears that the degree of correlation shown initially was largely fortuitous. All bond distances and angles within the quinoline core, the carboxy group and the phenyl group fall within the normal ranges. The mean deviation of the quinoline core atoms from the least-squares best- fit plane through them is 0.022 (3)/~, the maximum deviation being 0.040(3)A, for atom C(7). For the phenyl gr.oup, the corresponding mean deviation is 0.004 (3)A, the maximum deviation being 0.006 (3)A for atom C(13). The dihedral angle between these two planes is 37.0(1) °. The dihedral angle between the best-fit quinoline plane and the carboxy group plane is 53.6(1) °. Apart from the hydrogen bonding, four of the five closest approaches between molecules in this structure are between the carboxy H atom, H(1), of one mol- ecule and atoms H(17), C(2), C(9) and C(17) of two other molecules; the fifth close approach occurs between atom O(1) and an H(17) atom. These five approach distances are all at least 0.12/k less than the sums of the corresponding van der Waals radii. Acta Crystallographica Section CISSN 0108-2701 ©1996 

The alpha-pyridyl nucleoside analogue 2-bromo-5-(2-deoxy-alpha-D-ribofuranosyl)pyridine

http://discovery.ucl.ac.uk/1367923/1/as1213.pdf

The alpha-pyridyl nucleoside analogue 2-bromo-5-(2-deoxy-alpha-D-ribofuranosyl)pyridine

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