1-(β-D-Erythrofuranos­yl)cytidine (β-erythrocytidine)

1-(β-D-Erythrofuranosyl)cytidine, C₈H₁₁N₃O₄, (I), a derivative of β-cytidine, (II), lacks an exocyclic hydroxy­methyl (–CH₂OH) substituent at C4′ and crystallizes in a global conformation different from that observed for (II). In (I), the β-D-erythrofuranosyl ring assumes an E₃ conformation (C3′-exo; S, i.e. south), and the N-glycoside bond conformation is syn. In contrast, (II) contains a β-D-ribofuranosyl ring in a ³T₂ conformation (N, i.e. north) and an anti-N-glycoside linkage. These crystallographic properties mimic those found in aqueous solution by NMR with respect to furan­ose conformation. Removal of the –CH₂OH group thus affects the global conformation of the aldofuranosyl ring. These results provide further support for S/syn–anti and N/anti correlations in pyrimidine nucleosides. The crystal structure of (I) was determined at 200 K.

S1. Comment

Tetrofuranose-containing nucleosides and their phosphate esters have attracted attention recently as building blocks in the preparation of novel oligonucleotides (Schoning et al., 2000; Kempeneers et al., 2004). Oligonucleotides containing β-tetrofuranosyl rings, which lack the exocyclic C5' hydroxymethyl group found in β-ribofuranosyl rings, are necessarily assembled via 2'→3'-phosphodiester linkages. The trans-O2',O3' configuration found in L-threo derivatives (TNA) mimics backbones formed from conventional 3'→5' linkages (Wilds et al., 2002), whereas the cis-O2',O3' configuration found in erythro building blocks presumably results in oligonucleotides with considerably different structures and topologies.

Nucleoside conformation in solution is affected significantly by removal of the furanose exocyclic hydroxymethyl functionality. NMR investigations of β-erythronucleosides have revealed very different J_HH, J_CH and J_CC values, indicative of a major shift in the preferred conformation of the furanose ring relative to that observed in the corresponding β-ribonucleosides (Kline & Serianni, 1992). For example, the endocyclic ³J_H1',H2', ³J_H2',H3' and ³J_H3',H4' values are 5.6, 4.6 and 3.3 Hz to (to H4'S) in β-erythrocytidine, (I), whereas the corresponding values in β-cytidine, (II), are 3.9, 5.3 and 6.0 Hz, respectively. Pseudorotational analysis (Rao et al., 1981) of these J couplings reveals a highly preferred S (south) furanose conformation in (I) (79%; P = 186.4°; τ_m = 40°), whereas a similar analysis for (II) reveals a preferred N (north) conformation (58%; P = 21.8°; τ_m = 38°) (Fig. 1). The different preferred furanose conformations were expected to affect N-glycoside conformation in (I) and (II), but NMR data were unavailable to address this question.

A comparison of the low-temperature crystal structure of (I) determined here (Fig. 2) with that of (II) (Ward, 1993) shows differences in furanose conformation nearly identical to those observed in solution. Removal of the exocyclic CH₂OH group stabilizes S conformations, with E₃ (C3'-exo) preferred in (I) (P = 197.8°; τ_m = 44°) and ³T₂ preferred in (II) (P = 7.7°; τ_m = 39°) (Fig. 1 and Table 1). These results can be explained based on a preferred quasi-equatorial orientation of the bulkier CH₂OH substituent in (II), which is achievable in N conformations like ³T₂. While the pseudorotational phase angles P differ significantly, the puckering amplitudes, τ_m, are similar in (I) and (II) (Table 1). Endocyclic C1—C2 and C2—C3 bond lengths in (I) are larger by ~0.01 Å, whereas r_C3,C4 in (I) and (II) are more similar (Δ = 0.004 Å) (Table 1).

The change in the furanose conformation caused by removal of the CH₂OH substituent is accompanied by a significant change in the N-glycoside conformation. In (I), the nitrogen base is oriented syn/+sc, with the C2—O2 bond oriented above the furanose ring, corresponding to an O4'—C1'—N1—C2 torsion angle of 60.8 (2)° (Table 1). In contrast, the N-glycoside conformation is anti/ap in (II) [O4'—C1'—N1—C2 torsion angle -162.6 (3)°], orienting the C6—H6 bond above the furanose ring; the C1'—N1 bond is rotated almost 180° in (II) relative to (I). A correlation between the N-glycoside and furanose conformations is thus evident (Saenger, 1984). ³E Conformations leave the top face of the furanose ring unhindered by the CH₂OH group, but the resulting quasi-axial orientation of the C3'—H3' bond interferes with a syn N-glycoside conformation which would place atom O2 in close proximity with atom H3'. An anti N-glycoside conformation eliminates this apparently unfavourable arrangement. The E₃ conformation is achievable in (I) because it lacks the directing influence of an exocyclic CH₂OH. In this ring geometry, the top face of the furanose ring is largely unhindered, allowing the more sterically demanding syn geometry about the N-glycoside.

Recent statistical analyses of nucleoside and nucleotide crystal structures (Gelbin et al., 1996) have shown that N furanose conformations (C3'-endo) almost exclusively prefer anti N-glycosyl torsions, while S forms (C2'-endo) adopt both anti and syn geometries. Within the C2'-endo/syn group, virtually all structures were purine nucleosides. In this respect, (I) deviates from expectation. These results suggest that (I) could be useful in the development of NMR probes of N-glycoside conformation [e.g. DESERT [Acronym in full?] experiments (Akasaka et al., 1975), with either H1' or H6 deuterated], or trans-glycoside ³J_C2',C2/6 studies (Kline & Serianni, 1990), potentially serving as a pyrimidine nucleoside reference structure in which a syn N-glycoside may be adopted to some extent in aqueous solution.

The crystal structure of β-erythrouridine, (III), has been reported recently (Czechtizky & Vasella, 2001), and some structural parameters are shown in Table 1. Like (I), the furanose conformation in (III) is E₃. By comparison, the crystal structure of β-uridine, (IV) (Green et al., 1975), shows ³E conformations for the β-ribofuranose ring in two independent forms. Thus, for pyrimidine nucleosides, the erythro- and ribofuranose rings show a consistent difference in their preferred conformation. However, the N-glycoside conformation in (III) is anti/-ac (O4'—C1'—N1—C2 = -131.4°) (Table 1), unlike that found for (I), and an anti/ap N-glycoside conformation is observed in the related compound (IV) (O4'—C1'—N1—C2 torsion angles are -164.41° and -152.96° in the two forms). Thus, the syn conformation observed in (I) may be partly caused by crystal packing forces.

Since the furanose conformations are similar in (I) and (III), the differences in the structural parameters in these structures can be attributed mainly to different N-glycosyl conformations, especially for bond lengths and angles in the vicinity of the anomeric C atom. For example, r_C1',C2' and the O4'—C1'—N1 bond angle are considerably larger in (I) (Table 1). The C1'—N1 and C1'—O4' bond lengths, however, are similar in both structures. It is noteworthy that r_C2',O2' < r_C3',O3' in both (I) and (III), whereas these bond lengths are identical in (II). Presumably, the quasi-axial and quasi-equatorial orientations of the C3'—O3' and C2'—O2' bonds, respectively, in (I) and (III), are responsible for this difference, with the former orientation expected to generate a longer bond (Podlasek et al., 1996). The C—O bond lengths, however, will be modulated by differences in hydrogen bonding in the crystal, and these secondary effects may complicate interpretations based solely on bond orientation.

The hydrogen bonding in the crystal structures of (I) and (II) also differs. In (I), atoms O2' and O3' each serve as a donor and a mono-acceptor, and atom O4' is not involved in hydrogen bonding. In (II), atoms O2', O3' and O4' behave similarly, and atom O5' serves only as a donor. In (III), however, atoms O2' and O3' serve only as acceptors, but like (I) and (II), atom O4' is not involved in hydrogen bonding. In the nitrogen base, the C4' NH₂ group serves as a donor in two hydrogen bonds, and atom N3 serves as a hydrogen-bond acceptor in both (I) and (II). The C2 carbonyl serves as a single acceptor in (I) and a double acceptor in (II). In (III), the C2 carbonyl serves as a single acceptor, the C4 carbonyl as a dual acceptor and atom N3 as a donor. An interesting intermolecular hydrogen-bonding pattern is observed in (I), wherein atoms O2' and O3' of one molecule serve as donors to the C4'-NH₂ and N3 atoms of a second molecule in the crystal lattice. This hydrogen-bonding pattern suggests modes of recognition between nucleosides involving direct base–sugar interactions. This pattern is not observed in (II) and (III).

The structure of (I) forms a hydrogen-bonded bilayer about the ab plane (Fig. 3). Each sheet is formed via three types of hydrogen bonds, N4—H4A···O3'(x + 1, y + 1, z), N4—H4B···O2'(x + 1, y, z) and O3'—H3'···N3(x - 1, y, z). The layers are joined by hydrogen bonding between O2'—H2'O and O2(-x, y + 1/2, -z) of opposite sheets. Details of the hydrogen bonding are summarized in Table 2.

Related literature

For related literature, see: Akasaka et al. (1975); Czechtizky & Vasella (2001); Gelbin et al. (1996); Green et al. (1975); Kempeneers et al. (2004); Kline & Serianni (1990, 1992); Podlasek et al. (1996); Rao et al. (1981); Saenger (1984); Schoning et al. (2000); Ward (1993); Wilds et al. (2002).

S2. Experimental

Compound (I) was prepared as described previously by Kline & Serianni (1992) and was crystallized from hot ethanol.

S3. Refinement

H atoms attached to carbon were placed at calculated geometries and allowed to ride on the position of the parent atom, with C—H = 0.95–1.00 Å. Hydroxy H atoms were located at the position that maximizes the electron density and this was coupled with a rotating-group refinement; O—H = 0.84 Å. The two H atoms of N4 were located in a difference map and freely refined, including a parameter for isotropic thermal motion, in subsequent cycles of least-squares refinement; N—H = 0.84 (3)–0.87 (4) Å. For other H atoms, U_iso(H) = 1.2U_eq(C) or 1.5U_eq(O). [Please check added distances]

Computing details

Data collection: APEX2 (Bruker, 2006); cell refinement: APEX2 and SAINT (Bruker, 2006); data reduction: SAINT and XPREP (Sheldrick, 2003); program(s) used to solve structure: XS (Sheldrick, 2001); program(s) used to refine structure: XL (Sheldrick, 2001); molecular graphics: XP (Sheldrick, 1998); software used to prepare material for publication: enCIFer (Allen et al., 2004).

Figures

	Fig. 1. The pseudorotational itinerary of an aldofuranose ring. E and T denote envelope and twist forms, respectively. The preferred furanose conformations in crystalline (I) and (II) are highlighted.
	Fig. 2. A plot of (I). Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 3. A packing diagram for (I), viewed down b axis, illustrating the hydrogen-bonded bilayers. Dasehed lines denote hydrogen bonds.

1-(β-D-Erythrofuranosyl)cytidine

Crystal data

C8H11N3O4	F(000) = 224
Mr = 213.20	Dx = 1.599 Mg m^−3
Monoclinic, P21	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2yb	Cell parameters from 4223 reflections
a = 8.5473 (10) Å	θ = 5.3–68.3°
b = 6.2423 (7) Å	µ = 1.11 mm^−1
c = 9.1325 (11) Å	T = 200 K
β = 114.701 (4)°	Plate, colourless
V = 442.68 (9) Å^3	0.30 × 0.20 × 0.03 mm
Z = 2

Data collection

Bruker SMART APEX CCD area-detector diffractometer	1269 independent reflections
Radiation source: fine-focus sealed tube, Siemens KFFCU2K-90	1242 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
Detector resolution: 8.33 pixels mm^-1	θmax = 69.6°, θmin = 5.3°
ϕ and ω scans	h = −10→10
Absorption correction: multi-scan (Sheldrick, 2004)	k = −6→7
Tmin = 0.731, Tmax = 0.967	l = −10→10
5338 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.028	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.076	w = 1/[σ^2(Fo^2) + (0.0428P)^2 + 0.1356P] where P = (Fo^2 + 2Fc^2)/3
S = 1.09	(Δ/σ)max < 0.001
1269 reflections	Δρmax = 0.24 e Å^−3
146 parameters	Δρmin = −0.21 e Å^−3
1 restraint	Absolute structure: Flack (1983), with how many Friedel pairs?
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: 0.1 (2)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. The structure forms a hydrogen-bonded bilayer about the ab-plane. Each sheet is made by hydrogen bonding between N3—H3A and O2 by (x + 1, y, z) and O3—H3 and N2 by (x - 1, y, z). The layers are joined by hydrogen bonding between O2—H2 and O4 of opposite sheets (-x, y + 1/2, -z).

Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
N1	0.1448 (2)	0.7247 (3)	0.29260 (19)	0.0199 (4)
N3	0.3708 (2)	0.7236 (3)	0.20676 (19)	0.0204 (4)
N4	0.5564 (2)	1.0060 (4)	0.2635 (3)	0.0281 (4)
H4A	0.585 (4)	1.136 (7)	0.299 (4)	0.050 (9)*
H4B	0.603 (3)	0.946 (6)	0.210 (3)	0.031 (7)*
O4'	0.02373 (16)	0.4246 (3)	0.36761 (15)	0.0229 (3)
O2'	−0.26822 (17)	0.7967 (3)	0.08930 (17)	0.0236 (3)
H2'O	−0.2509	0.8626	0.0173	0.035*
O3'	−0.33947 (16)	0.4622 (3)	0.26457 (15)	0.0221 (3)
H3'O	−0.4241	0.5427	0.2155	0.033*
O2	0.17056 (17)	0.4582 (3)	0.13373 (17)	0.0264 (4)
C1'	−0.0114 (2)	0.6310 (4)	0.2975 (2)	0.0190 (4)
H1'	−0.0472	0.7246	0.3669	0.023*
C2'	−0.1669 (2)	0.6085 (3)	0.1317 (2)	0.0188 (4)
H2'	−0.1253	0.5744	0.0470	0.023*
C3'	−0.2565 (2)	0.4129 (3)	0.1623 (2)	0.0198 (4)
H3'	−0.3360	0.3420	0.0600	0.024*
C4'	−0.1012 (2)	0.2762 (4)	0.2579 (2)	0.0234 (5)
H4'A	−0.1308	0.1634	0.3182	0.028*
H4'B	−0.0557	0.2074	0.1860	0.028*
C2	0.2282 (2)	0.6269 (4)	0.2070 (2)	0.0183 (4)
C4	0.4221 (2)	0.9141 (4)	0.2769 (2)	0.0200 (4)
C5	0.3399 (2)	1.0154 (4)	0.3648 (2)	0.0245 (5)
H5	0.3785	1.1497	0.4162	0.029*
C6	0.2048 (2)	0.9131 (4)	0.3724 (2)	0.0206 (4)
H6	0.1501	0.9732	0.4345	0.025*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0193 (7)	0.0219 (10)	0.0216 (7)	−0.0023 (7)	0.0114 (6)	−0.0018 (7)
N3	0.0176 (7)	0.0221 (10)	0.0230 (7)	0.0004 (7)	0.0102 (6)	−0.0001 (7)
N4	0.0252 (9)	0.0242 (12)	0.0412 (10)	−0.0070 (8)	0.0201 (8)	−0.0076 (10)
O4'	0.0200 (6)	0.0235 (8)	0.0247 (6)	−0.0020 (6)	0.0089 (5)	0.0063 (6)
O2'	0.0255 (6)	0.0228 (8)	0.0287 (7)	0.0051 (6)	0.0174 (5)	0.0079 (7)
O3'	0.0193 (6)	0.0240 (8)	0.0263 (6)	0.0013 (6)	0.0127 (5)	0.0031 (7)
O2	0.0282 (7)	0.0226 (9)	0.0363 (7)	−0.0080 (7)	0.0213 (6)	−0.0121 (7)
C1'	0.0186 (9)	0.0216 (12)	0.0211 (9)	−0.0013 (8)	0.0125 (7)	0.0001 (9)
C2'	0.0191 (8)	0.0195 (11)	0.0207 (9)	−0.0009 (8)	0.0113 (8)	−0.0001 (9)
C3'	0.0208 (8)	0.0190 (12)	0.0220 (8)	−0.0038 (8)	0.0113 (7)	−0.0019 (9)
C4'	0.0229 (9)	0.0196 (12)	0.0316 (11)	−0.0014 (9)	0.0152 (8)	0.0017 (9)
C2	0.0191 (8)	0.0202 (11)	0.0186 (9)	0.0003 (8)	0.0108 (7)	0.0008 (9)
C4	0.0161 (8)	0.0222 (12)	0.0196 (8)	−0.0007 (8)	0.0054 (7)	0.0037 (8)
C5	0.0246 (10)	0.0190 (12)	0.0296 (10)	−0.0033 (8)	0.0109 (8)	−0.0062 (10)
C6	0.0208 (8)	0.0231 (12)	0.0186 (8)	0.0017 (8)	0.0089 (7)	−0.0022 (9)

Geometric parameters (Å, º)

N1—C6	1.366 (3)	O2—C2	1.234 (3)
N1—C2	1.399 (3)	C1'—C2'	1.548 (3)
N1—C1'	1.475 (2)	C1'—H1'	1.0000
N3—C4	1.335 (3)	C2'—C3'	1.528 (3)
N3—C2	1.361 (3)	C2'—H2'	1.0000
N4—C4	1.335 (3)	C3'—C4'	1.512 (3)
N4—H4A	0.87 (4)	C3'—H3'	1.0000
N4—H4B	0.84 (3)	C4'—H4'A	0.9900
O4'—C1'	1.414 (3)	C4'—H4'B	0.9900
O4'—C4'	1.452 (3)	C4—C5	1.417 (3)
O2'—C2'	1.414 (3)	C5—C6	1.347 (3)
O2'—H2'O	0.8400	C5—H5	0.9500
O3'—C3'	1.422 (2)	C6—H6	0.9500
O3'—H3'O	0.8400
C6—N1—C2	120.56 (16)	O3'—C3'—C2'	111.88 (17)
C6—N1—C1'	117.92 (17)	C4'—C3'—C2'	99.78 (15)
C2—N1—C1'	121.52 (18)	O3'—C3'—H3'	112.3
C4—N3—C2	120.60 (17)	C4'—C3'—H3'	112.3
C4—N4—H4A	119 (2)	C2'—C3'—H3'	112.3
C4—N4—H4B	120 (2)	O4'—C4'—C3'	104.69 (18)
H4A—N4—H4B	120 (3)	O4'—C4'—H4'A	110.8
C1'—O4'—C4'	108.24 (14)	C3'—C4'—H4'A	110.8
C2'—O2'—H2'O	109.5	O4'—C4'—H4'B	110.8
C3'—O3'—H3'O	109.5	C3'—C4'—H4'B	110.8
O4'—C1'—N1	110.56 (16)	H4'A—C4'—H4'B	108.9
O4'—C1'—C2'	107.04 (16)	O2—C2—N3	122.16 (17)
N1—C1'—C2'	115.12 (15)	O2—C2—N1	119.61 (17)
O4'—C1'—H1'	108.0	N3—C2—N1	118.23 (19)
N1—C1'—H1'	108.0	N3—C4—N4	117.48 (19)
C2'—C1'—H1'	108.0	N3—C4—C5	121.90 (18)
O2'—C2'—C3'	114.65 (15)	N4—C4—C5	120.6 (2)
O2'—C2'—C1'	111.69 (17)	C6—C5—C4	117.1 (2)
C3'—C2'—C1'	100.67 (15)	C6—C5—H5	121.4
O2'—C2'—H2'	109.8	C4—C5—H5	121.4
C3'—C2'—H2'	109.8	C5—C6—N1	121.34 (18)
C1'—C2'—H2'	109.8	C5—C6—H6	119.3
O3'—C3'—C4'	107.56 (15)	N1—C6—H6	119.3
C4'—O4'—C1'—N1	−127.06 (16)	O3'—C3'—C4'—O4'	−74.70 (18)
C4'—O4'—C1'—C2'	−0.97 (18)	C2'—C3'—C4'—O4'	42.12 (17)
C6—N1—C1'—O4'	−120.29 (18)	C4—N3—C2—O2	174.86 (18)
C2—N1—C1'—O4'	60.8 (2)	C4—N3—C2—N1	−4.6 (3)
C6—N1—C1'—C2'	118.28 (19)	C6—N1—C2—O2	−178.96 (18)
C2—N1—C1'—C2'	−60.6 (3)	C1'—N1—C2—O2	−0.1 (3)
O4'—C1'—C2'—O2'	149.12 (15)	C6—N1—C2—N3	0.5 (3)
N1—C1'—C2'—O2'	−87.6 (2)	C1'—N1—C2—N3	179.42 (17)
O4'—C1'—C2'—C3'	27.00 (18)	C2—N3—C4—N4	−175.86 (19)
N1—C1'—C2'—C3'	150.32 (17)	C2—N3—C4—C5	5.1 (3)
O2'—C2'—C3'—O3'	−47.3 (2)	N3—C4—C5—C6	−1.2 (3)
C1'—C2'—C3'—O3'	72.69 (18)	N4—C4—C5—C6	179.72 (19)
O2'—C2'—C3'—C4'	−160.84 (16)	C4—C5—C6—N1	−2.9 (3)
C1'—C2'—C3'—C4'	−40.83 (18)	C2—N1—C6—C5	3.3 (3)
C1'—O4'—C4'—C3'	−26.19 (19)	C1'—N1—C6—C5	−175.65 (19)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···O3′^i	0.87 (4)	2.20 (4)	2.982 (3)	150 (3)
N4—H4B···O2′^ii	0.84 (3)	2.08 (3)	2.912 (3)	177 (2)
O2′—H2′O···O2^iii	0.84	1.88	2.699 (2)	166
O3′—H3′O···N3^iv	0.84	2.06	2.825 (2)	151

Symmetry codes: (i) x+1, y+1, z; (ii) x+1, y, z; (iii) −x, y+1/2, −z; (iv) x−1, y, z.