X-Ray-Diffraction Study and Determination of Absolute Configuration of the Anticancer Drug S( ) Cyclophosphamide (Endoxan, Cytoxan, NSC-26271)
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1 X-Ray-Diffraction Study and Determination of Absolute Configuration of the Anticancer Drug S( ) Cyclophosphamide (Endoxan, Cytoxan, NSC-26271) D. A. Adamiak and W. Saenger A bteilung Chemie, M ax-planck-institut für experim entelle Medizin, Göttingen R. Kinas and W. J. Stec Centre of M olecular and M acrom olecular Studies, Polish Academy of Sciences, Lodz (Z. Naturforsch. 32 c, [1977]; received May 31, 1977) S ( ) Cyclophosphamide, Absolute Configuration, X-Ray Diffraction Methods (-) Cyclophosphamide (1) crystallized from tetrachlorom ethane in the triclinic space group P I with cell dimensions a = (4) Ä, b = (4) Ä, c = (4) A, a = (2), ß = (2), y = (2). T hree molecules are contained in the u nit cell. The X-ray analysis was based on diffractom eter m easurem ent of 2635 independent reflections and the structure was solved by Patterson and direct methods. The final R and R w factors after full-m atrix least-squares refine m ent are and , respectively. The absolute configuration is S based on Ham ilton s 7?-factor ratio test. The oxazaphosphorinane ring exists in a chair form with the bis-/?-chloroethylamino group in equatorial position and about perpendicular to and bisecting the O P N plane. I I The structure is sim ilar to that found in racemic 1 except a different conformation about one ethylamino N C bond. Introduction Cyclophosphamide (1, Cytoxan, Endoxan, NSC26271, 2 - (bis-/?-chloroethyl) am ino- 2 - o x o -1,3,2 oxazaphosphorinane is a powerful, clinically tested and applied cancerostatic a g e n t1. The stereoselective consumption of I by h u m an s2 and differentiated cytotoxic activity of its enantiomeric form s 3 against ADJ/PC6 plasma cell tum our in m ice4 suggest that the configuration around phosphorous atom is an im portant factor in the metabolic process of 1. These results prompted us to carry out the below described single crystal X-ray analysis of ( ) 1 in order to supply inform ation about structure func tion relationships. An X-ray study of racemic 1 has been described previously 5. Experim ental (-) 1 crystallized from tetrachloromethane in the form of stout, irregular prisms. Space group sym metry and cell constants were derived by photo graphic and diffractom eter techniques and are gathered in Table I. Owing to rather high therm al Requests for reprints should be sent to Prof. Dr. W. Saen ger, A bteilung Chemie, M ax-planck-institut für E xperi m entelle Medizin, Herm ann-rein-str. 3, D-3400 Göttingen. T able I. Crystallographic data. Chemical form ula: C7H 15N20 2C12P Space g roup: P 1 Cell constants: a = (4) Ä b = (4) Ä c = (4) Ä a = (2) Ä ß = (2) Ä y = (2) Ä Z = 3 Z?cal g/cm 3 motion of the molecules in the crystal lattice, the X-ray intensities fell of rapidly with glancing angle 0 and therefore only 2635 data could be collected (@max = 5 8 ) using an automated STOE four circle diffractometer equipped with a fine focus tube (Cu K,,,, N i-filter). Data were corrected for geometri cal factors but not for absorption (size of crystal only 0.3 x 0.3 X 0.5 mm3), standard deviations were assigned according to counting statistics6 and the data were finally converted to normalized structure amplitudes. The structure was solved by direct methods (M ULTAN7), 'but since only the positions of P and Cl atoms were apparent from an E-map, they were confirmed against a sharpened Patterson map and then successive Fourier maps were calcu lated which finally allowed us to deduce the whole structure. In order to establish the absolute con- Dieses Werk wurde im Jahr 2013 vom Verlag Zeitschrift für Naturforschung in Zusammenarbeit mit der Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.v. digitalisiert und unter folgender Lizenz veröffentlicht: Creative Commons Namensnennung-Keine Bearbeitung 3.0 Deutschland Lizenz. This work has been digitalized and published in 2013 by Verlag Zeitschrift für Naturforschung in cooperation with the Max Planck Society for the Advancement of Science under a Creative Commons Attribution-NoDerivs 3.0 Germany License. Zum ist eine Anpassung der Lizenzbedingungen (Entfall der Creative Commons Lizenzbedingung Keine Bearbeitung ) beabsichtigt, um eine Nachnutzung auch im Rahmen zukünftiger wissenschaftlicher Nutzungsformen zu ermöglichen. On it is planned to change the License Conditions (the removal of the Creative Commons License condition no derivative works ). This is to allow reuse in the area of future scientific usage.
2 D. A. Adamiak et al. X-Ray Structure of Cyclophosphamide 673 figuration of ( )1, coordinates and anisotropic temperature factors were refined by least squares techniques8 for both models (x, y, z) and the enantiomorph (x, y, 2) with proper inclusion of anomalous scattering contributions from Cl and P atoms 9. Final weighted discrepancy indices R w = [ 2 w(\foi,\ - \ F ',u 1 ) «, Foi, 12 ] 1/2 are 7.28% for model (x, y, z) and 6.77% for model (x, y, z)*. On the basis of Hamilton s Ä-factor ratio te s t10, model (x, y, 2) can be excluded at a significance level < , see Table II. of ( )1 is presented in Fig. 1. The configuration around the phosphorous atom is S, the complete description of the molecule is S( )cyclophosphamide. The packing of the molecules within the unit cell is described in the stereo view Fig. 2. C3 Table II. Determination of the absolute configuration of ( ) 1 using Hamilton s significance test. For both models 1 (x,y,z ) and 2 (x,y,z ) the R-factors a re : Model 1. R t = R w 1 = Model 2. R 2 = R w2 = where R = 2 F 0bs ^ c a l / 2 F 0bs RW = [ 2 w ( Fobs I - 1F cal I) 2/ 2 w Fobs 2] ^ R and R w are a measure of the agreement between a set of observed structure amplitudes F 0bs and a set of calculated structure amplitudes F Cai; w is a set of weights; m>=1/o 2, where a2 is the variance of Fobs The Ä-factor ratios are: # = R2/R 1 = #W = Ryft/Rwl = In our case for the dimension of hypothesis, 6 = 1; the num ber of reflections, n = 2635; the number of refined param eters, n = 376; and significance level, a = # b,n -m,a = #1,2259,0.005 = From the table of significance points of the R-iactor ratio 10 for 6 = 1, a = 0.005, /V=2000 and 7V2 = 3000 we get: #1,2000, #1,3000,0.005 = Since N 1 = m n= 2259 is between 2000 and 3000 the value was obtained using the following form ula10: for Nq< N 1< N 2 Fig. 1. A plot of S ( - ) I showing therm al ellipsoids of the atoms the 20% probability level. a) * b Nl,a - N (Afl-N~) X UN' ~ NJ N* ;Rb N2'a + {N2 N1)N0 #b,n0,a]. Both /M aotor ratios # and # w are greater than the #-factor ratio of Therefore for N l = 2259 and a = 0.005, model 2 can be rejected at a level < (99.5% probability). b) Results and Discussion Final atomic coordinates for ( ) 1 are listed in Table III. Tables IV to VI display geometrical data calculated from the entries in Table III. The structure * A list of observed and calculated structure factors may be obtained from the authors. Fig. 2. Schematic drawing of a view along the N P bond in a) S (-) 1 of this crystal structure and in b) the structure of racemic ( ± ) 1. Note that in a) the two /?-chloroethyl groups are related by m symmetry while diad symmetry is observed in b ). It is remarkable that within the unit cell ( = the asymmetric unit in this space group) three independent molecules are assembled which show identical conformations with torsion angles not deviating more
3 674 D. A. Adamiak e t a l. X-Ray Structure of Cyclophosphamide than 3 o. The molecules are linked via hydrogen bonds N (6) H - * 0 ( 7 " ), Ä; N (6') H- 0 ( 7 ), Ä and N (6 ") H- - 0 ( 7 '), Ä, i. e. each molecule acts simultaneously as a hydrogen bond donor and acceptor. The cyclophosphamide molecules in the present investigation have sim ilar geometry as discussed for the crystal structure of the racem ate5 with only onetorsion angle different. The 1,3,2-oxazaphosphorinane rings display chair conform ation with the bis-/?-chloroethylamino substituent in equatiorial orientation. The latter is approximately perpendicu lar tot he 0 ( 2 ) P (1) N (6) plane, the torsion angles with the C (9) N (8) C ( l l ) planes being 83.4, 85.6, and 86.1 for molecules, A, B and C. This conformation results from partial double bond character of the P N (8) bond which is shortened by Ä with respeot to a normal single bond of Ä. Similarly, the configuration about N (8 ) is nearly planar, with the sum of angles around N (8) at Further it is noticeable that the P ( l ) N (6) distance, Ä, indicates partial double bond character as well, i. e. the hydrogen atom at N (6) is rather acidic. Table III. Fractional atomic coordinates and anisotropic tem perature factors of the non-hydrogen atoms with standard de viations in parantheses. T em perature factors are in the form T exp [ (/?11h 2+ /? 22k2+ /? 33l2+ 2 /? 12h k -f 2/?13h l+ 2 /? 23k l ) ]. Atom PI 02 C3 C4 C5 N6 07 N8 C9 CIO C ll C12 CL1 CL2 P I' 02' C3' C4' C5' N 6' 07' N 8' C9' CIO' C ll' C12' CL1' CL2' P I" 02" C3" C4" C5" N 6" 07" N8" C9" CIO" C ll" C12" CL1" CL2" X ( 4 ) ( 8 ) (1 5 ) (1 7 ) (1 4 ) (9) (9) (1 0 ) (1 3 ) (1 4 ) (1 3 ) (1 9 ) (4 ) ( 5 ) (4 ) (9 ) (1 6 ) (1 6 ) (1 4 ) (1 0 ) ( 9 ) (1 1 ) (1 2 ) (1 2 ) (1 7 ) ( 1 8 ) (4 ) (4 ) (0 ) ( 9 ) (1 6 ) (1 9 ) (1 6 ) (1 0 ) (1 1 ) (12) (1 3 ) (1 4 ) (1 7 ) (1 6 ) (4) ( 5 ) Y ( 3 ) ( 9 ) (1 6 ) (1 7 ) (1 4 ) ( 1 0 ) ( 8 ) (9) ( 1 1 ) (1 3 ) ( 1 3 ) ( 1 7 ) (4 ) ( 4 ) (4 ).1617(9).1563(17).0658(18) ( 1 6 ) (1 1 ) (1 2 ).0191(13).0456(14) ( 1 4 ).0595(17) (1 5 ) ( 4 ) ( 5 ) ( 0 ) ( 9 ) ( 1 4 ) (1 7 ) (1 4 ) ( 1 0 ) ( 1 0 ) ( 1 1 ) (1 4 ) ( 1 4 ) (1 9 ) ( 1 7 ).0912(4) ( 5 ) Z ( 4 ) (9 ) (1 7 ) (1 5 ) (1 5 ) (9 ) ( 9 ) ( 1 0 ) (12) (1 4 ) ( 1 4 ) (20) (4 ) (4) ( 4 ).7392 (9) (1 8 ) (1 5 ) (1 3 ) (1 1 ) (1 1 ) ( 1 1 ) (1 3 ) (1 4 ) (1 9 ) ( 2 1 ) (4) (4) (0) (9) ( 1 4 ) ( 1 5 ) ( 1 5 ) (1 1 ) (1 1 ).0605(11).0943(14).2284(14).1332(18).2539(20).2703 (4).3384(5) B (11) 166(5) 153(14) 182(23) 226(27) 174(19) 130(14) 259(16) 173(15) 211(19) 224 (22) 258(19) 311(32) 183(5) 260 (8) 122(4) 175(14) 197 (24) 196(23) 159(20) 138(15) 107(13) 123(15) 112(16) 96(16) 203(27) 273(31) 152(5) 214(7) 202(5) 159(13) 255(25) 343(35) 238(25) 152(15) 307(18) 257 (20) 173(18) 197(21) 198(27) 186(24) 230(6) 313(8) B (22) 117(4) 213(15) 234(25) 265(27) 172(19) 213(16) 127(12) 137(13) 141(15) 125(17) 288(19) 227(27) 164(5) 234 (7) 184 (5) 170(14) 260 (28) 297(31) 233 (25) 172(16) 380(23) 288 (22) 181(20) 195(21) 219(28) 143(22) 238(6) 361 (9) 151(4) 180(14) 150(20) 261(27) 172(21) 146(15) 219(16) 182(16) 189(19) 184 (20) 363(38) 263(28) 186(5) 293(8) B (33) B (12) B (13) B (23) 148 (4) 189(15) 245 (27) 154(21) 187 (22) 143(13) 202(15) 154(14) 161(17) (21) 419(21) 355(39) 182 (5) 157 (6) 147 (5) 152(14) 291 (32) 164(22) 102(17) 144(16) 230(19) 118(15) 139(19) 179(22) 228(29) 304(36) (6) 212(7) 196(5) 154(13) 149(21) 173(23) 219(24) 184(17) 284(19) 202(17) 192(20) 148(20) 210(28) 271(31) 194(5) 284(8) 45 (4) 96(12) 79(20) 36(22) 56(17) 89(12) 37(11) 2 2 (12) 90(14) 83(16) 185 (16) 184(26) 56(4) 82 (6) 75(4) 108(13) 145(23) 127(23) 97(19) 76(13) 115(15) 115(15) 47(15) 51(16) 71(23) 70(22) 101(5) 144(6) 110(4) 75(11) 97(19) 199 (27) 119(19) 69(12) 187(15) 149(16) 109(17) 107(17) 115(27) 103(22) 124(5) 192(7) 63 (4) 83(12) 144 (22) 115(21) 74(18) 69(11) 100(14) 60(13) 103(16) 126(19) 228(17) 165 (31) 100(5) 8 6 (6) 65(4) 66(13) 119(24) 90 (20) 32(16) 58(13) 83(14) 66(13) 58(15) 47(16) 7(24) 105 (29) 97(5) 147(6) 130(5) 83(11) 56(19) 177(25) 151(22) 89(14) 211(17) 169(16) 126(17) 89(18) 96(24) 104 (24) 110(5) 190(7) 69 (4) 111(13) 116(22) 106(21) 109(18) (12) 74(12) 84(12) 89(14) 82(16) 255(17) 171(29) 79(5) 92(5) 80(4) 86(13) 208 (26) 165 (23) 78(18) 74(14) 157(18) 108(16) 66(17) 92(19) 106(26) 100 (24) 141(5) 160(7) 109(4) 73(12) 44(17) 138(22) 111(19) 89(13) 191(15) 135(15) 126(17) 62(17) 4(27) 88(26) 110(4) 214(7)
4 675 D. A. Adamiak e t d l. X-Ray Structure of Cyclophosphamide Table IV. Fractional atomic coordinates for the hydrogen atoms. Atom H3 1 H3 2 H4 1 H4 2 H5 1 H5 2 H6 1 H9 1 H9 2 H ll 1 H ll 2 H12 1 H12 2 H10 1 H10 2 H 3' 1 H 3' 2 H 4' 1 H 4' 2 H 5' 1 H 5' 2 H 6' 1 H 9' 1 H 9' 2 H l l '1 H l l '2 H10' 1 H 1 0 '2 H 1 2 '1 H 3" 1 H 3" 2 H 4" 1 H 4" 2 H 5" 1 H 5" 2 H 6" 1 H 9" 1 H 9" 2 H 10"l H10"2 H ll" l H ll" 2 H 12"l X Y Z Fig. 3. A stereo view of the structure along a-axis. The bis-/?-chloroethylamino group displays nearly mirror-symmetry, Fig. 2. The torsion angles about the N - C bonds, P ( l ) - N ( 8 ) - C ( 9 ) - C ( 1 0 ) and P ( l ) N ( 8 ) - 'C ( l l ) C (12) are opposite, at 104 and 97 but the orientations about the ethyl bonds, N CH2 CH2 Cl, are both tr a n s. From the close structural relationship between the three S ( ) 1 molecules one could conclude that they exist in a rather constrained conformation. A comparison with the crystal structure of the racemic ( ± ) 1 (Tables V VII) shows that the six-membered oxazaphosphorinane ring and its substituents N (8 ), C(9) and C ( l l ) have nearly identical geometry but the conformation about the N (8) C(9) bond is different, with the torsion angle P ( l ) N (8) C(9) C (10) at 103. This brings the two /?-diloroethyl groups into a propellerjike orientation with nearly twofold rotational symmetry, Fig. 2. Thus the oxazaphosphorinane moiety appears to be rather rigid but rotation does accur about the N C bonds. Table V. Bond distances (A), with standard deviations in parentheses. Bond Mole cule A Mole cule B M ole cule C Ref. 5 P ( D - 0 (2) 0 (2) - C(3) C(3) C (4) C (4) C (5) C(5) N ( 6) N (6) - - P ( l ) P ( l ) - 0 (7 ) P ( l ) - N ( 8) N (8) C(9) C(9) C(10) C (1) C l l N (8) - C ( l l) C ( l l ) - -C (1 2 ) C (12) -- C l (11) 1.453(24) (20) 1.474(26) 1.431(21) 1.659(10) 1.474(06) 1.650(13) 1.476(11) 1.551(22) 1.812(10) 1.622(16) 1.335(27) 1.956(18) 1.580(10) 1.486(23) (27) 1.495(23) 1.477(21) 1.606(13) 1.510(10) 1.648(13) 1.487(17) 1.473(22) 1.832(14) (25) 1.418(25) 1.931(24) 1.613(07) 1.469(20) 1.485(22) 1.520(19) 1.475(22) 1.644(11) 1.477(12) 1.652(13) 1.444(20) 1.530(12) 1.770(16) 1.565(27) 1.384(21) 1.918(23) 1.580(4) 1.466(4) 1.520(10) 1.488(8) 1.481(7) 1.623(5) 1.466(4) 1.623(5) 1.457(7) 1.512(8) 1.769(6) (6) 1.513(7) 1.798(5)
5 676 D. A. Adamiak et al. X-Ray Structure of Cyclophosphamide Table VI. Bond angles ( ) with standard deviations in parentheses. Angle Molecule A Molecule B Molecule C Ref. 5l 0 (2) - P ( l) N (6) (0.5) (0.6) (0.5) (0.2) 0 (2) - P ( l ) - 0 (7 ) (0.6) (0.6) (0.5) (0.2) 0 (2) - P ( l) N (8) (0.5) (0.6) (0.5) (0.2) N (6) -P ( l) 0 (7 ) (0.6) (0.7) (0.6) (0.3) N (6) P ( l) N (8) (0.5) (0.6) (0.6) (0.2) 0 ( 7 ) - P ( l) N (8) (0.6) (0.7) (0.6) (0.2) P (1) 0 (2) - C(3) (0.9) (0.9) (0.8) (0.4) 0 (2) C(3) C(4) (1.3) (1.4) (1.2) (0.5) C(3) C(4) C (5) (1.4) (1.4) (1.4) (0.6) C (4) C(5) N (6) (1.2) (1.2) (1.3) (0.5) P ( l ) - N (6) C(5) (0.9) (1.9) (0.9) (0.4) P ( l ) - N (8) C(9) (0.9) (1.0) (1.0) (0.4) P ( i) - N (8) C ( ll) (0.8) (1-0) (1.0) (0.4) C(9) N (8)' C ( ll) (1.0) (1.2) (1.2) (0.5) N (8) - C (9) C(10) (1.0) (1.1) (1.2) (0.5) C(9) - C (10)-- C l (1.0) (1.0) (1.0) (0.5) N (8) - -C(11) - ( 12) 98.4 (1.2) (1.4) (1.5) (0.4) C ( ll) - C ( 12) - C l (1.3) (1-3) (1.3) (0.4) Table 7. Torsional angles * ( ) and standard deviations in parentheses. Angles Molecule A Molecule B Molecule C Ref. 5 P ( D - 0 (2) C ( 3 ) - C (4) (1.5) ) (1.4) P(i) N (6) C(5) C(4) 44.2 (1.6) ) 45.6 (1.6) 45.8 P(i) N (8) C(9) C (10) (1.1) ) (1.2) P(i) N (8) C ( ll) -- ( 12) 97.2 (1.3) ) 97.4 (1.4) (2) - P(l) N (6) C(5) (1-1) ) (1.1) (2) - P(l) - N (8) - C(9) (1.0) ) (1.1) (2) - P (1) - N (8) C ( ll) 95.0 (0.9) ) 94.9 (1-1) (2) - C(3) C(4) C(5) 61.9 (1.7) ) 64.3 (1.6) 61.9 C(3) 0 (2). P(l) N (6) 49.6 (1.1) ) 50.9 (1.0) 44.9 C(3) C (2) P ( l) - 0 (7 ) (1.1) ) (1.0) C(3) 0 (2) - P(l) - N (8) (1.0) ) (1-0) C(3) C(4) C(5) N (6) (1.8) ) (1.9) 55.0 C (5)< N (6) P(l) - 0 (7 ) 83.5 (1.1) ) 82.1 (1-1) 88.0 C (5) N (6) - P (l)- N (8) (1.0) ) (1.0) N (6) P(l) ~ N (8) - -C(9) 43.9 (1.1) ) 42.1 (1.2) 44.9 N (6) P(l) - N (8) - - C ( ll) (0.9) ) (1.1) ( 7 ) - P (1)1 N (8) - "C (9) (0.9) ) (1-0) ( 7 ) - P (1) N (8_) - (11) (1.0) ) (1.3) 0.9 N (8) C (9) C (10) - C l l (0.9) ) (1-0) N (8) - -C ( ll) C (12) Cl (0.9) ) (1.0) C (9 )~ N (8) - - C (ll) -C (1 2 ) (1.4) ) (1.6) C (10) - C ( 9 ) - - N (8) - C ( l l ) 95.6 (1.2) ) 94.3 (1.5) * Definition: The angles A B C D are defined zero when the bonds A B and C D are cis planar. They are counted positive when, looking along the central B C bond, the far bond is rotated clockwise with respect to the near bond. D.A.A. gratefully acknowledges a fellowship from Alexander von Humboldt Stiftung. The calculations were carried out using the UNIVAC 1108 computer of the Gesellschaft für wissenschaftliche Datenverarbeitung, Göttingen, and were supported in part by the Deutsche Forschungsgemeinschaft. 1 Symposium on Cyclophosphamide in Pediatric Neoplasia, Cancer Chemotherapy Reports 51, No. 6 [1967]. 2 P. J. Cox, P. B. Farm er, A. B. Foster, E. D. Gilby, and M. Jarm an, Cancer Treatment Report 60, 483 [1976]. 3 R. Kinas, K. Pankiewicz, and W. J. Stec, Bull. Acad. Pol. Sei., Serie Sciences Chimiques XIII, [1975]. 4 P. K. Cox, P. B. Farm er, M. Jarm an, M. Jones, W. J. Stec, and R. Kinas, Biochem. Pharmacol. 25, [1976].
6 D. A. Adamiak et al. X-Ray Structure of Cyclophosphamide 677 J. C. Clardy, J. A. Mosbo, and J. G. Verkade, Phosphorus [1974] and references cited therein. G. W. Stout and L. H. Jensen, X-Ray Structure Determ i nation, p. 457; The Macmillan Co., New York P. Main, G. Germain, and M. M. Woolfson, MULTAN, a system of computer programs for the automatic solution of non-centric structures, York, Louvain 1970; Acta Crystallogr. B 26, [1970]. 8 W. R. Busing, K. O. Martin, and H. A. Levy, ORFLS, a FORTRAN Crystallographic least squares program, USAEC Report ORNL-TM-305, Oak Ridge National Laboratory, Oak Ridge, Tenn International Tables for X-Ray Crystallography, Vol. Ill, p 202 and 214, The Kynoch Press, Birmingham W. C. Hamilton, Acta Crystallogr. 18, [1965]. International Tables for X-Ray Crystallography, Vol. iv, p , The Kynoch Press, Birmingham 1974.
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