7401
Crystal and Molecular Structure of 3,N4-Ethenocytidine Hydrochloride. A Study of the Dimensions and Molecular Interactions of the Fluorescent +Cytidine System Andrew H. -J. Wang, Jorge R. Barrio, and Iain C. Paul* Contributionfrom the Department of Chemistry, School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801. Received March 3, 1976
Abstract: The crystal structure of 3,N4-ethenocytidine hydrochloride (1, e-Cyd.HC1) has been determined to provide the molecular dimensions of this fluorescent analogue of a cytosine nucleoside and to probe its capability for molecular interaction. The crystals of 1 are monoclinic, with a = 6.330 ( l ) , b = 16.968 (2), c = 6.695 (1) A, and p = 115’ 22 (l)’, and there are two C IlH14N305+C1- entities in the space group P21. The structure has been refined to an R factor of 0.045 on 1675 nonzero reflections (Mo Ka). The t-cytosine moiety is slightly nonplanar with a maximum deviation of 0.037 from the best plane through the ten nonhydrogen atoms; there are some minor differences in bond lengths and angles from those found in protonated unbridged cytosine derivatives. The arrangement about the glycosyl bond is anti (XC-N = 42.6’) and the ribose ring exists in the C(2’)-endo or the C(2’)-endo-C-(3’)-exo conformation. The C(4’)-C(5’) exocyclic bond is in a gauche-gauche arrangement. There appears to be a C(6)-H(6)- - -0(5’) intramolecular hydrogen bond. The N - H bond in the base and the three hydroxyl groups in the sugar are involved in an intermolecular hydrogen bonding arrangement in which the chloride anion acts as an acceptor for three hydrogen bonds. Translationally equivalent t-cytosine bases crystallize such that a chloride anion lies between them in the plane of the rings in a fashion similar to that observed for other unbridged cytosine salts. This arrangement results in some short H- - -C1- and H- - -0 contacts. This packing also results in another CI- lying 3.21 8, above the plane of the t-cytosine cation. This latter type of “ion pair” interaction is quite common in anhydrous halide salts of nucleic acid bases and nucleosides. There is no base-base overlap.
The systematic examination of the interactions of coenzyme analogues, together with a comparison of their kinetic behavior relative to the natural substrate, provides information concerning the nature of the binding sites of the functioning enzymes. Analogues have been used in the past, e.g., in studies of the mechanisms of enzyme action] and of the evolution of enzyme s t r ~ c t u r e s . * Recent -~ progress in the determination of the three-dimensional structure of enzymes5 has increased understanding of the mechanisms of enzyme action6 Fluorescent substrate analogues of cytosine nucleotides, obtained by reaction of cytosine derivatives with chloroaceta l d e h ~ d e , ~have - ’ ~ been shown to replace the natural substrates in several enzymatic reactions. The introduction of the second ring on the cytosine portion gives the new molecule a similar spatial outline and similar potential binding areas to those of the corresponding adenine nucleotides (Figure 1). Indeed, the chloroacetaldehyde-modified cytosine nucleotides mimic the structural features of the natural coenzymes and replace adenosine nucleotides in enzymatic phosphorylation9 and photophosphorylation.’ I Since various substituted e C y d compounds are readily ac~ e s s i b l e ~and ~ ~ ~in’ view * of the observations concerning the behavior of c-cytidine coenzyme analogues, we undertook a n x-ray study of 3,N4-ethenocytidine hydrochloride (1, t-Cyd.HCl).8,13This study should provide the molecular dimensions of the c-cytidine molecule and allow examination of the molecular interactions of 1 in the crystalline state.
H
c1-
HO OH 1
HO OH 3’
2
w
Knowledge of the structure of the coenzyme binding sites of the enzyme and the molecular dimensions of 3,N4-ethenocytidine should aid in the correlation of the activity of the modified cytidine nucleotides and the spatial dimensions of the enzymes. In order to facilitate comparisons with related cytidine compounds, the conventional atom numbering for cytidine, as shown in 2, is used in this paper. This paper is the second in a series on the structure of chloroacetaldehydemodified nucleosides. Previously, a derivative of e-adenosine was reported.I4
Experimental Section +Cytidine hydrochloride8 was recrystallized from ethanol-water by standing at room temperature. The crystals are colorless, transparent, elongated, rectangular-shaped plates. Crystal data: C I I H ~ ~ N ~ O ~ + mol . C I wt - ; 303.7; monoclinic; a = 6.330 ( l ) , b = 16.968 (2), c = 6.695 (1) 8,; /3 = 115’ 22 (I)’; V = 649.8 A3;Dmeasd = 1.54 g cm-3; z = 2; Dcalcd = 1.55 g F(000) = 316; p (Mo Ka) = 3.2 cm-I; systematic absences for OkO when k = 2 n 1; the space group is either P21 or P 2 l / m . Since the compound is optically active, the former must be the correct space group. The density was measured by flotation in a mixture of hexane and carbon tetrachloride and the cell dimensions were obtained by a least-squares fit to the hand-centered settings for 12 reflections on a Picker FACS-1 diffractometer (Mo K a l , X = 0.70926 A). A crystal with dimensions ca. 0.40 X 0.30 X 0.25 mm was used for data collection. The general procedures for data collection were essentially the same as described previously,I5 except that Nb-filtered Mo K E (X = 0.7107 A) radiation was used. The octants of data, hkl and zkl, were measured to 28 = 70’ (sin 0/X = 0.807). N o evidence for crystal deterioration or loss of intensity was noted. Out of 2961 possible independent reflections, 1675 were considered to be nonzero, using a 3u criterion based on counting statistics. The data were corrected for Lorentz and polarization effects but not for absorption; the maximum and minimum transmission factors (based on intensities) were estimated to be 0.86 and 0.90. The structure was solved by the heavy atom method based on chlorine. The hydrogen atoms were located from a difference map. Full-matrix, least-squares refinement of positional and anisotropic thermal parameters for the nonhydrogen atoms and of positional and isotropic thermal parameters for the hydrogen atoms converged with
+
Wang, Barrio, Paul / 3,N4-Ethenocytidine Hydrochloride
7402 Table I. Final Atomic Coordinates in the c-Cyd-HCI Structure. Standard Deviations in Parentheses Atoms
Figure 1 . Overlay of the line representations of the N(9)-substituted adenine and N( I)-substituted t-cytidine showing similar polarities at various points. Drawing similar to one depicted in ref 78.
valuesforRand R2,Rz = [Zw(lFoI - ) ~ ~ ) ) 2 / Z w l F , 1 2 ] ' / 2 , ~ f 0 . 0 4 5 and 0.037, respectively. The final value of Z w A 2 / ( N 0 - NV), where N O is the number of observations and NV is the number of variables, is 1.55. All reflections were assigned weights using a program written by DieterichI6 using the scheme proposed by Corfield et al." A final difference map showed a negative peak of 1 electron/A3 near the center of the position occupied by the chloride ion.'* There were also some peaks and troughs with electron densities of 0.2-0.3 electron/A3. Most of these peaks lie close to the midpoint between two atoms which are covalently bonded and may be due a t least in part to the effect of the valence electrons. A final structure-factor calculation showed no significant abnormality for any individual reflection. The final values for the atomic coordinates and thermal parameters are listed in Tables I and II.I9 The scattering curves for CI-, C, N, and 0 used in the analysis were taken from the compilation by Cromer and Mann;20that for hydrogen was the one calculated by Stewart et aLzl The curve for CI- was corrected for the effects of anomalous dispersion.22
Results and Discussion Molecular Dimensions of the +Cytosine Ring. A stereoscopic view of the t-CydH+ cation is shown in Figure 2. The bond lengths and angles involving the nonhydrogen atoms are given in Figure 3. The distances and angles involving hydrogen atoms have been deposited. An analysis23of thermal vibrations of the €-cytosine ring system showed that it could be treated as a moderately good rigid body (root mean square A of U ( i , j )is 0.0019 and resulted in adjustments to the bond lengths of a maximum of 0.006 A for N(4)-C(7) and an average change of 0.003 A. In subsequent discussions, the unadjusted values are used. The cytosine ring system is bridged between N(3) and N(4) by the etheno group; N(4) has an attached hydrogen atom. This is the first example of an x-ray analysis on a cytosine ring with an t bridge. It is well e ~ t a b l i s h e dthat ~ ~ substitution a t nitrogen has a definite effect on the lengths and angles in pyrimidine rings. In 1971, Viswamitra et al.25compiled the bond lengths and angles found in x-ray structures of unsubstituted cytosine bases, neutral N(1)mbstituted cytosine bases, and in protonated N ( 1)-substituted cytosine derivatives. We have brought this compilation up to date (Dec 1975),26and we compare the dimensions found for the above three types with those found for the t-cytosine ring system in Figure 4. In the earlier comparison the greatest differences between the protonated [Figure 4 (c)] and neutral species [Figure 4(a) and (b)] were in the N(4)-C(4)-N(3)-C(2)-0(2) region of the heterocyclic base. With the new and considerably expanded structural data, the differences are generally similar to those described before. It should be pointed out that some of the dimensions, particularly those involving peripheral atoms, could be significantly influenced by hydrogen bonding. Thus, in addition to experimental errors, one could anticipate some
w2)
Journal of the American Chemical Society
/ 98:23 /
X
0.21 124 (16) 1.1163 (5) 1.2071 (6) 1.4072 (4) 1.0383 (5) 0.8137 (6) 0.7130 (6) 0.7317 (6) 0.8859 (6) 0.8738 (8) 1.0749 (8) 1.2751 (6) 1.2405 (6) 1.3328 (6) 1.2442 (7) 1.0129 (7) 1.2294 (4) 1.3455 (5) 1.5805 (5) 0.8226 (5) 0.556 (9) 0.585 (6) 0.863 (8) 0.836 (7) 1.207 (9) 1.423 (6) 1.069 (5) 1.275 (6) 1.353 (6) 0.974 (7) 1.034 (7) 1.463 (8) 1.617 (7) 0.834 (9)
Y
Z
0.11675 (16) 0.1790 (4) 0.3787 (5) 0.5167 (4) 0.4129 (5) 0.2629 (6) 0.3521 (6) 0.0621 (6) 0.0259 (6) 0.5596 (8) 0.5996 (7) 0. I260 (6) 0.1498 (5) -0.0081 (6) -0.1973 (6) -0.3908 (6) -0.0954 (4) 0.3669 (4) 0.1060 (5) -0.3327 (5) 0.268 (7) -0.026 (6) -0.106 (8) 0.648 (6) 0.736 (8) 0.231 (6) 0.082 (5) -0.048 (5) -0.252 (6) -0.478 (7) -0.451 (7) 0.402 (8) 0.028 (7) -0.261 (9)
0.50000" 0.2967 (2) 0.3355 (2) 0.3319 (2) 0.3799 (2) 0.3888 (2) 0.4377 (2) 0.3488 (2) 0.3030 (2) 0.4600 (3) 0.4247 (2) 0.2456 (2) 0.1582 (2) 0.1244 (2) 0.1844 (2) 0.1671 (3) 0.2591 (2) 0.1300 (2) 0.1241 (2) 0.1587 (2) 0.447 (3) 0.350 (2) 0.263 (3) 0.492 (3) 0.424 (3) 0.258 (2) 0.145 (2) 0.074 (2) 0.192 (2) 0.220 (3) 0.125 (3) 0.137 (3) 0.093 (3) 0.126 (3)
'' This coordinate was held constant in the refinement to determine the origin in t h e y direction. differences within a particular class. The complete list of data including maximum and minimum values for each dimension is included in the microfilm edition of the Journal. The agreement between the values found for the t-CydH+ cation [Figure 4 (d)] and in N(1)-substituted and protonated cytosine structures (Fig. 4c) is quite good, with the greatest differences involving the C(2)-N(3) bond (longer in t-CydH+), the C(4)-C(5) bond (shorter), the C(4)-N(4) bond (longer), and the N( 1)-C(6) bond (longer). In both protonated species [Figure 4(c) and (d)], the C(2)-0(2) distance is less than in the uncharged forms [Figure 4(a) and (b)]. The inferred decrease in this distance upon protonation in the t-Cyd series is accompanied by an increase in the C - 0 stretching frequencies in the infrared spectra.53There are also significant changes in the internal ring bond angles a t N ( l ) , C(2), C(4), and C(5). The two bond angles external to the six-membered ring at C(4) are greatly different from each other [133.1 (4) and 106.8 (3)O] in the t-CydH+ cation. The two main contributors to the resonance hybrid of the t-CydH+ cation would appear to be 3 and 4.
November 10, 1976
3
4
7403 Table 11. Final Thermal Parameters, Expressed in the Form Exp[-(P] 1h2 Thermal Parameters Exp[-(Bo sin2 0 / A 2 ) ]
PI I 0.0208 (3) 0.0139 (8) 0.0171 (11) 0.0196 (8) 0.0167 (9) 0.0152 ( I O ) 0.0205 (1 0) 0.0109 ( 1 1) 0.0158 (10) 0.0318 (16) 0.0274 ( 1 4) 0.0134 ( I O ) 0.0149 ( 1 1) 0.0165 (10) 0.0171 (12) 0.0235 (14) 0.0228 (9) 0.0157 (9) 0.0166 (8) 0.0182 (9)
+ P22k* + P3312 + 2P12hk + 2P13hl + 2023kl)l and Isotropic PI2
033
P22
0.00212 (3) 0.0015 (1) 0.0017 (1) 0.0029 ( I ) 0.0017 (1) 0.0017 (1) 0.0022 (1) 0.0027 (2) 0.0022 ( I ) 0.0025 (2) 0.0026 (2) 0.0019 ( I ) 0.0018 ( I ) 0.0020 (1) 0.0026 (2) 0.0027 (2) 0.00189 (9) 0.0029 ( I ) 0.0043 ( I ) 0.0027 ( I )
0.00053 (9) -0.0000 (2) -0.0003 (3) 0.0013 ( 3 ) 0.0007 (3) -0.0002 (3) 0.0017 (3) 0.0002 (3) -0.0011 (3) 0.0019 (4) 0.0022 (4) -0.0004 (3) -0.0003 (3) -0.0003 (3) -0.0010 (3) -0.0016 (4) -0.0009 (2) -0.0003 (3) 0.0016 (3) -0.0002 (3)
0.0217 (3) 0.0142 (8) 0.0131 (9) 0.0155 (7) 0.0138 (8) 0.0208 ( I O ) 0.0250 (1 1) 0.0191 ( I 1) 0.0180 ( I O ) 0.0224 (1 3) 0.0161 (11) 0.0132 (9) 0.0147 (10) 0.0148 (10) 0.0153 (10) 0.0156(11) 0.0157 (7) 0.0147 (7) 0.0216 (9) 0.0173 (8)
PI3
P33
0.0103 (2) 0.0052 (7) 0.0064 (9) 0.0039 (6) 0.0060 (7) 0.0090 (9) 0.0130 ( I O ) 0.0026 (9) 0.0062 (9) 0.01 52 ( 1 2) 0.0082 ( 1 1) 0.0067 (8) 0.0073 (8) 0.0067 (9) 0.0093 (9) 0.0093 ( 1 0) 0.0108 (6) 0.0063 (7) 0.0072 (7) 0.0072 (7)
BdA?)
BdA2 1 H(j) H(6) H(7) H(8) NH(4) H(1’) H(2’)
0.00045 (9) -0.0010 (2) -0.0004 (3) -0.0013 (2) 0.0002 ( 2 ) 0.0007 (3) 0.0003 (3) -0.0001 (3) -0.0012 (3) -0.0007 (4) -0.0008 (3) -0.0007 (3) -0.0005 (3) -0.0012 (3) -0.0009 (3) -0.0008 (4) -0.0002 (2) 0.0008 (2) -0.0029 (3) 0.0009 (3)
OH(2‘) H(3‘) OH(3’) H(4‘) H (5’A) H(5’B) OH(5‘)
2.8 (9) 5.2 (1.1) 3.7 (9) 5.4 (1.2) 4.4 ( 1 . 1 ) 1.9 (7) 1 . 1 (6)
3.9 (1.3) 2.1 (7) 4.0 ( 1 .O) 1.6 (7) 4.2 ( 1 .O) 2.8 (9) 4.9 ( I . 5 )
e
8
Figure 2. Stereoscopic view of the e-Cyd cation. The percentage probability of the ellipsoids is 20%.
The t-cytosine moiety is slightly, but significantly, nonplanar (Table 111), with a maximum deviation of 0.037 A from the best plane through the ten atoms which were included in the plane calculation. The C ( 1’) atom is practically coplanar with the €-cytosine ring, as was the case in the c-adenosine derivative.14 The pyrimidine ring is slightly nonplanar with atoms deviating from the plane by distances of -0.020 to f0.018 A. The five atoms of the etheno ring are coplanar as was also observed in the study of the c-adenosine cation.I4 The best planes through the two rings of the t-cytosine moiety are inclined a t an angle of l o 27’. The N M R spectra (1 00 MHz) of both the e-CydH+ cation and its free base in either D2O or MezSO-ds clearly show a long-range coupling between H(5) and H(8) with a coupling constant of 0.6 Coupling constants of this magnitude occur for essentially planar configurations and fall off rapidly with large departures from
planarity. From these data, near planarity of the free base of e C y d can be inferred. Molecular Dimensions of the Ribose Ring. The best fouratom plane in the ribose ring contains the atoms C ( 1’), C(3’), C(4’), and O( 1’) with C(2’) lying 0.594 A on the same side as C(5’) (Table 111). The conformation of the ribose is thus C(2’)-endo, which is one of the common puckering modes for pyrimidine nucleosides and nucleotide^.^^-^^ When referred to the three-atom plane, C ( l’), O( l’), and C(4’), the puckering of the ribose ring is C(2’)-endo-C(3’)-exo (2T3)55with C(2’) and C(3’) lying on the same and opposite sides of the plane as the C(5’) atom a t distances of 0.466 and -0.169 A, respectively. Using the pseudorotation rotation introduced by Altona and S ~ n d a r a l i n g a m , ~the ’ values of T~ and P are -38.7 and 170.5’, respectively. The values for the torsion angles around the ring are O(l’)-C(l’)-C(2’)-C(3’), 36.1’; C(l’)-C(2’)Wang, Barrio, Paul
/ 3,N4-Ethenocytidine Hydrochloride
1404 Table 111. Least-Squares Planes for the Base and Sugar and the Deviations of the Atoms from Planes I-VI in ..&a,b Atoms N(1) C(2)
O(2) N(3) C(4) N(4) C(5) (26) (27) C(8) C(10 C(2') (33') C(4') O(1') C(5')
I
11
-0.008 0.009 0.018
-0.002
-0.025
-0.020
0.01I
0.025 0.007 -0.01 2
-0.002 -0.037
257
