The crystal structure of C12H17N304 has been determined.

This modified base is in a syn conformation

with respect to the deoxyribose sugar, which adopts a

distorted C3'/04'-endo pucker

Capaldi, DC

Neidle, S

Reese, CB

Roselt, PD

UCL Discovery

2332 N I~.C2H406P- ,  3NH,~.C2H306p2- .C2H406 P - ,  2NH~.C2H306 P2-  and  3NH~.C2H206p3- .H20 P---O1 P----O2 P--O3 P----O4 O2---C2 O5---C1 O6----421 C1---C2 O 1--P---4)2 O 1--P-----4)3 O I --P----O4 O2--P---Q3 O2--P---(M 03--P---04 C2--02--P 02--C2--C lO5---CI--4)6 O5--C 1---C2 O6---C 1--C2 O 1 --P--O2---C 2 O3--P---O2---C2 O4---P---O2----C2 P---O2---C2--C 1 O5---C 1---C2---O2 O6---C 1---C2--O2 Table 9. Selected geometry (A, O )for phosphoglycolate moieties (I) .508 (2) .596 (2) .496 (2) .563 (2) .425 (2) .212 (2) .309 (2) .510 (2) 103.9 (1) 115.6(1) 109.4 (1) 110.7 (1) 105.2 (1) 111.3 (1) 120.1 (2) 112.8 (2) 124.7 (2) 124.7 (2) 110.5 (2) --164.4 (1) 70.9 (2) --49.4 (2) -93.4 (2) -6.0 (2) 174.9 (2) (IIA) (IIB) (IIIA) (IIIB) (IV) 1.506 (2) 1.493 (2) 1.562 (1) 1.552 (1) 1.518 (2) 1.594 (2) 1.580 (2) 1.600 (1) 1.599 (1) 1.625 (2) 1.501 (2) 1.502 (2) 1.506 (1) 1.514 (1) 1.507 (2) 1.558 (2) 1.577 (2) 1.504 (1) 1.498 (1) 1.521 (2) 1.420 (2) 1.422 (2) 1.430 (2) 1.421 (2) 1.426 (2) 1.207 (3) 1.227 (3) 1.242 (2) 1.244 (2) 1.252 (2) 1.309 (2) 1.285 (2) 1.267 (2) 1.267 (2) 1.259 (2) 1.493 (3) 1.516 (3) 1.513 (2) 1.513 (2) 1.517 (2) 104.7(1) 105.1 (1) 99.7(1) 98.8(I) 103.3(I) 116.1 (1) 117.8(1) 111.6(1) 112.2(1) 112.9(1) 108.4(1) 111.4 (1) III.8(I) 113.0(I) If3.0(1) 109.9(1) 110.2(I) 110.1 (I) 109.1 (I) 107.4 (1) 106.2(1) 106.4(1) 108.9(1) 110.7 (1) 106.9(I) 110.9 (1) 105.5 (l) 113.9(1) 112.2 (l) 112.6(1) 121.1 (2) 124.6 (2) 117.9 (I) 118.7 (1) 116.4 (2) ll3.1 (2) 108.6(2) ll0.3 (l) 110.4 (l) ll0.8 (2) 124.5 (3) 124.8(2) 126.2 (1) 126.6 (1) 125.1 (2) 123.9(3) 120.1 (2) 120.4(1) 120.2 (l) 119.5 (2) 111.3 (2) 115.2(2) 113.3 (l) ll3.1 (l) 115.4(2) -162.8 (2) -161.6 (2) -166.5(1) -178.9 (l) 176.5 (2) 71.8 (2) --33.8 (2) 76.1 (1) 63.8 (1) 57.0 (2) -48.2 (2) 80.2 (2) --49.4 (I) -60.1 (1) --64.1 (2) -109.0(2) 153.4(2) 171.3(1) 172.5(1) 179.5(2) -- 1.1 (8) -7 .9  (3) - 11.8 (2) -- 1.9 (2) 1.6 (3) --175.1 (2) 172.5(2) 170.2(1) 177.8(1) -178.6(2) The collection of data at low temperature was carded out using an Oxford Cryosystem cooler for all compounds. In the case of (II), an additional peak near O5A was found on a difference map. It was interpreted in terms of the disordering of this atom over the sites O5A and 051A. For all compounds, data collection: KM4 Software (Ku- mar Diffraction, 1989); cell refinement: KM4 Software; data reduction: KM4 Software; program(s) used to solve struc- ture: SHELXS86 (Sheldrick, 1985); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: ORTEPII (Johnson, 1976). Financial support was received from KBN grant No. 2 P303 078 07. Lists of structure factors, anisotropic displacement parameters, H- atom coordinates and complete geometry have been deposited with the IUCr (Reference: MU1249). Copies may be obtained through The Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England. Acta Cryst. (1996). C52, 2332-2334 4-Amino-l-(2-deoxy-/~-D-ribofuranosyl)-6,7- dihydro- 1H,5H-cyclopentapyrimidine-2-one STEPHEN NEIDLE, a DANIEL C. CAPALDI ,  b COLIN B. REESE b AND PETER D. ROSELT b aCRC Biomolecular Structure Unit, The Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, England, and bDepartment of Chemistry, King's College London, Strand, London WC2R 2LS, England. E-mail: steve @ iris5, icr. ac. uk (Received 10 November 1995; accepted 21 February 1996) References Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA. Kuma Diffraction (1989). Kuma KM4 User's Guide. Version 3.1. Kuma Diffraction, Wroctaw, Poland. Lis, T. (1993). Acta Cryst. C49, 696-705. Lis, T. (1994). Acta Cryst. C50, 181-185. Lis, T. (1995). Acta Cryst. C51, 997-1001. Lis, T. & Starynowicz, P. (1995). Abstracts of Polish Chemical So- ciety Meeting, Lublin, S-7 K-2. Zaktad Wydawniczo-Poligraficzny Politechniki Lubelskiej, Lublin. (In Polish.) Sheldrick, G. M. (1985). SHELXS86. Program for the Solution of Crystal Structures. University of G6ningen, Germany. Sheldrick, G. M. (1993). SHELXL93. Program for Crystal Structure Refinement. University of G6ttingen, Germany. © 1996 International Union of Crystallography Printed in Great Britain - all rights reserved Abstract The crystal structure of C12H17N304 has been deter- mined. This modified base is in a syn conformation with respect to the deoxyribose sugar, which adopts a distorted C3'/04'-endo pucker. Comment The crystal structure of this modified nucleoside, (I), was determined as part of a project to assess the effect of the bulky cyclopentene ring on the conformation of cytosine itself, and ultimately on DNA structures when incorporated into an oligonucleotide. Results from these studies will be reported elsewhere. This is the first reported crystal structure of a cytosine derivative with a cyclic aliphatic group attached at the 5 and 6 positions. Acta Crystallographica Section C ISSN 0108-2701 © 1996 STEPHEN NEIDLE et aL 2333 ,NH2 / HO 0) The molecule adopts a syn conformation about the glycosidic bond, with a value of 64.4(3) ° for the glycosidic angle (O4' - -C1 ' - -N1- -C2) .  This is unusual for pyrimidines, which are normally observed in the anti conformation (Neidle, 1994). Molecular-mechanics energy calculations using the HYPERCHEM program (Hypercube Inc., 1994) indicate that the crystallographic syn conformation and the anti conformation, produced by a rotation of 180 ° about the glycosidic angle, differ by 1.7 kcal mole- l (1 kcal = 4.184 kJ), with the former having the lower energy. The anti conformation results in close contacts between the H atoms on C7 and C2'/C3' of the furanose ring. This could be relieved by sugar repuckering, which occurred on molecular- mechanics minimizations of the two conformations, syn and anti. The difference in energies for the two conformers was then only 0.2 kcal mole - l  , albeit still in favour of the syn conformation. Equivalent calculations on cytosine itself show the anti conformation to be favoured by 1.3 kcal mole - l ,  suggesting that the cyclo- pentenyl derivation has resulted in a slight shift towards a syn conformational preference. The deoxyribose sugar has a distorted pucker interme- diate between C3'-endo and 04'-endo, with a pseudo- rotation phase angle, P, of 56.2 ° and a maximum degree of pucker of 39.9 °. The exocyclic torsion angle 05 ' - -  N3 05' c ,~CC3 '  c2'. - "~ Fig. 1. A view of the title structure. Displacement ellipsoids are shown at the 50% probability level. H atoms have been drawn as small circles of arbitrary radius. C5' - -C4 ' - -C3 ' ,  with a value of 53.6 (4) °, is in the com- mon gauche + domain. Bond lengths and angles for the cytosine base agree closely with standard values (Clowney et al., 1996; Gelbin et al., 1996), as do most of the values for the sugar ring and its substituents. A few, such as the C l 'm C2' distance, differ by several e.s.d.'s. This may be a consequence of the well established ependence of nucleoside sugar geometry on pucker type. The cytosine base is significantly non-planar with the substituent atom N4 deviating by 0.093 (2)A from the least-squares plane defined by N1,C2,O2,N3,C4,N4,- C5,C6, and an r.m.s, deviation for the six non-H ring atoms and two substituent atoms of 0.066 ,~. The cyclo- pentene ring is closely coplanar, with a r.m.s, deviation of 0.020 A and no ring atom deviating by more than 0.028 (2)A from the least-squares plane. The dihedral angle between this plane and that of the cytosine ring is 8.0 (1)°. Experimental The title compound was crystallized by slow evaporation from ethanolic solution. Details of the synthesis will be published elsewhere. Crystal data CI2HI7N304 Mo Ka radiation Mr = 267.29 A = 0.71073 ,~, Orthorhombic Cell parameters from 250 P2t 2~ 21 reflections a = 9.543 (4) ,~, 0 = 2-22 ° b = 10.2790(10,) ,~, # = 0.112 mm -1 c = 12.231 (5) A T = 293 (2) K V = 1199.8 (7) ~3 Prismatic Z=4 0.3 x 0.1 x 0.06 mm Dx = 1.480 Mg m -3 Colourless Dm not measured Data collection Enraf-Nonius FAST diffrac- tometer to scans in 0.2 ° steps Absorption correction: none 5215 measured reflections 1875 independent reflections 1541 observed reflections [I > 2cr(~)] Rim = 0.0354 0max = 24.89 °h = -10 ~ 10 k = -10 ~ 11 l = - 10 ---, 14 Refinement Refinement on F 2 R[F 2 > 2~r(F2)] = 0.0493 wR(F 2) = 0.1124 S = 0.969 1875 reflections 240 parameters H atoms riding, Uiso refined w = l/[a2(F 2) + (0.1291P) 2] where P = (Fo 2 + 2F2)/3 (A/o')max < 0.001 Apma~ = 0.45 e ,~,-3 Apmin -0.30 e ,~-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) 2334 CI2HI7N304 Table 1. Fractional atomic coordinates and equivalent isotropic displacement parameters (t~ 2 ) Ueq = ( I /3)Ei~jUoa~ af ai.a j. x y Z Ueq N1 -0.0878 (2) 0.8283 (3) -0.0201 (2) 0.0177 (6) C2 -0.0158 (3) 0.8987 (3) 0.0608 (2) 0.0183 (8) 02 0.0318 (2) 0.8405 (2) 0.1410 (2) 0.0232 (5) N3 --0.0031 (3) 1.0298 (3) 0.0495 (2) 0.0179 (6) C4 -0.0611 (3) 1.0916 (3) -0.0364 (3) 0.0171 (7) N4 --0.0627 (3) 1.2209 (3) -0.0380 (2) 0.0273 (7) C5 --0.1159 (3) 1.0206 (3) -0.1265 (2) 0.0172 (7) C6 -0.1295 (3) 0.8901 (3) -0.1147 (2) 0.0163 (7) C7 -0.1862 (3) 0.8253 (3) -0.2145 (3) 0.0209 (8) C8 -0.2018 (4) 0.9385 (3) -0.2969 (3) 0.0291 (9) C9 -0.1633 (3) 1.0651 (3) -0.2384 (3) 0.0230 (8) CI' -0.1263 (4) 0.6926 (3) -0.0010 (3) 0.0212 (8) C2' -0.0065 (4) 0.5982 (3) 0.0265 (3) 0.0218 (8) C3' -0.0480 (3) 0.5404 (3) 0.1370 (3) 0.0199 (7) 03' -0.0104 (2) 0.4071 (2) 0.1433 (2) 0.0277 (6) 04' -0.2240 (2) 0.6866 (2) 0.0869 (2) 0.0221 (6) C4' -0.2062 (3) 0.5622 (3) 0.1375 (3) 0.0204 (7) C5' -0.2788 (3) 0.5585 (3) 0.2481 (3) 0.0235 (8) 05' -0.2226 (2) 0.6426 (2) 0.3296 (2) 0.0268 (6) Table 2. Selected geometric parameters (A, o) C2--N1--C1'--O4' 64.4 (3) C 1'--O4'--C4'--C3' 39.6 (3) O#--CIt--C2'--C3 ' 0.1 (3) C2'--C3t--C4'--O4 ~ -37.8 (3) C1'--C2'--C3t--C4 t 22.4 (3) O4'---C4'--C5~--O5 ' -65.5 (3) C2'---Cll---O4'---C4 ' --24.6 (3) C3'---C4t---C5'--O5 ' 53.6 (4) The assignment of absolute configuration was made on chemical grounds, with the base having a/3-configuration with respect o the deoxyribose sugar. Data collection: MADNES (Pflugrath & Messerschmidt, 1990); further details from Darr, Drake, Hursthouse & Malik (1993). Cell refinement: MADNES. Data reduction: MADNES. Program(s) used to solve structure: SHELXS86 (Sheldrick, 1990). Program(s) used to refine structure: SHELXL93 (Sheldrick, 1993). Molecular graphics: ORTEX (McArdle, 1993). Software used to prepare material for publication: SHELXL93. Neidle, S. (1994). DNA Structure and Recognition. Oxford University Press. Pflugrath, J. W. & Messerschmidt, A. (1990). MADNES. Munich Area Detector Systems. Enraf-Nonius, Delft, The Netherlands. Sheldrick, G. M. (1990). Acta Cryst. A46, 467-473. Sheldrick, G. M. (1993). SHELXL93. Program for Crystal Structure Refinement. University of G6ttingen, Germany. Acta Cryst. (1996). C52, 2334-2337 (E)-2,2,5,5-Tetramethyl-3,4-bis[4-(tribromo- methyl)phenyl]hex-3-ene JAMES E. GANO,* KRIS'7~ KIRSCHBAUM AND PADMANAB- HAN SEKHER Department ofChemistry, University of Toledo, Toledo, OH 43606, USA. E-mail: jgano @ uoft02, utoledo, edu (Received 19 July 1995: accepted I February 1996) Abstract Steric repulsion of the ten-butyl groups of the title com- pound, C24H26Br6, causes the phenyl rings to rotate out of the plane of the central double bond eliminating the conjugation between the three 7r systems, yet the cen- tral double bond is normal, 1.33 (1)A. The molecules pack together to maximize Br...Br and ten-butyl...ten- butyl interactions forming 'planes' of Br atoms and tert- butyl groups. The results are supplemented by MOPAC calculations. We 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 and complete geometry have been deposited with the IUCr (Reference: BM1048). Copies may be obtained through The Managing Editor, International Union of Crystallography, 5 Abbey Square, Chester CHI 2HU, England. References Clowney, L., Jain, S. C., Srinivasan, A. R., Westbrook, J., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 509-518. Darr, J. A., Drake, S. R., Hursthouse, M. B. & Malik, K. M. A. (1993). lnorg. Chem. 32, 5704-5708. Gelbin, A., Schneider, B., Clowney, L., Hsiel, S.-H., Olson, W. K. & Berman, H. M. (1996). J. Am. Chem. Soc. 118, 519-529. Hypercube Inc. (1994). HYPERCHEM. Program for Molecular Modeling. Version 4. Hypercube Inc., Waterloo, Ontario, Canada. McArdle, P. (1993). J. Appl. Cryst. 26, 752. © 1996 International Union of Crystallography Printed in Great Britain - all rights reserved Comment Stilbenes bearing tert-butyl groups on the central C atoms have received significant attention because of their unusual geometry (Gano, Park, Pinkerton & Lenoir, 1990, 1991; Gano, Park, Subramaniam, Lenoir & Gleiter, 1991; Laali, Gano, Lenoir & Gundlach, 1994; Lenoir, Gano & McTague, 1986). Although the crystal structure of a Z isomer appeared some time ago (Gano, Park, Pinkerton & Lenoir, 1991), crystal- lographic information on the E isomers has proven to be elusive (Ermer, 1977). Herein is provided the first report of a crystallographic investigation of an (E)-di- tert-butylstilbene, (E)-2,2,5,5-tetramethyl-3,4-bis[4-(tri- bromomethyl)phenyl]hex-3-ene, (la). Stilbene (la) was prepared by bromination of stilbene (lb), whose prepa- ration followed the procedure for preparation of the par- ent sfilbene (lc) (Lenoir et al., 1986). Recrystallization of (la) from chloroform pro- duced crystals suitable for X-ray diffraction measure- ments. Although the results immediately suggested that additional rotational isomers were needed to accommo- Acta Crystallographica Section C ISSN 0108-2701 © 1996 

4-amino-1-(2-deoxy-beta-D-ribofuranosyl)-6,7-dihydro-1H,5H-cyclopentapyrimidine-2-one

http://discovery.ucl.ac.uk/1367854/1/bm1048.pdf

4-amino-1-(2-deoxy-beta-D-ribofuranosyl)-6,7-dihydro-1H,5H-cyclopentapyrimidine-2-one

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UCL Discovery