2′-Deoxy-5-methylisocytidine

In the title compound, 2-amino-1-(2-deoxy-β-D-erythro-pento­furan­osyl)-5-methyl­pyrimidin-4(1H)-one, C₁₀H₁₅N₃O₄, the conformation of the N-glycosidic bond is syn and the 2-deoxy­ribo­furan­ose moiety adopts an unusual ^OT₁ sugar pucker. The orientation of the exocyclic C4′—C5′ bond is +sc (+gauche).

S1. Comment

Transposition of the amino and oxo groups in the canonical nucleic acid base cytosine results in isocytosine. This nucleobase can form a Watson-Crick base pair with isoguanine, forming a DNA with antiparallel (aps) chain orientation (Switzer et al., 1989, 1993; Tor & Dervan, 1993; Roberts et al., 1995; Horn et al., 1995). More interestingly, isocytosine or 5-methylisocytosine can form a reverse Watson-Crick base pair with the canonical DNA base guanine, which then results in parallel (ps) DNA (Sugiyama et al., 1996; Seela et al., 1998; Seela, He & Wei, 1999; Seela, Wei et al., 1999).

2'-Deoxyisocytidine, (Ia), proved to be problematic in oligonucleotide synthesis. It is deaminated under the normal deprotection conditions (concentrated ammonia, elevated temperature; Switzer et al., 1989), and it was found to be an acid-labile pyrimidine nucleoside (Roberts et al., 1997; Dekker, 1960). Only when a rather labile protecting group is chosen for compound (Ia), as well as for the other nucleosides used in the solid-phase synthesis, can intact oligonucleotides be isolated. Another approach that circumvents this problem was the use of the 5-methyl derivative of 2'-deoxyisocytosine [5miC_d, (Ib)] as a substitute (Tor & Dervan, 1993; Jurczyk et al., 1998; Bukowska & Kusmierek, 1996). Many oligonucleotides containing compound (Ib) were prepared and the base-pairing properties were studied in parallel and in antiparallel DNA (Seela, He & Wei, 1999). As it has recently been shown that the base-pairing properties of (Ib) are similar to those of (Ia), it was decided to elucidate the molecular structure of the title 5-methyl derivative, (Ib). \sch

The structure of (Ib) is shown in Fig. 1. Similar to the significant nonplanarity of the pyrimidine ring of 2'-deoxy-5-methylcytidine [5 m dC, (II)] (Sato, 1988), the nucleobase of (Ib) is somewhat nonplanar. The deviations of its C and N atoms from the least-squares plane are in the range of 0.036 (3) to −0.043 (3) Å [N1 = −0.040 (3), C2 = 0.035 (3), N3= 0.009 (3), C4 = −0.043 (3), C5 = 0.036 (3) and C6 = 0.005 (3) Å].

Bond lengths and angles are summarized in Table 1. The glycosidic bond length (N1—C1') of 1.478 (5) Å is 0.017 (8) Å longer than the corresponding bond length in (II). The most distinct feature of the conformation of (Ib), different from other pyrimidine nucleosides, is the syn conformation of its glycosidic bond, which corresponds to a torsion angle χ_CN (O4'-C1'-N1—C2) = 58.2 (5)° (Table 1). The glycosidic torsion angle in pyrimidine nucleosides is generally found to be anti; very few syn structures are known (Saenger, 1989). For example, (II) has an anti glycosidic bond with χ_CN = −131.7°. 4-Thiouridine hydrate (Saenger & Scheit, 1970) was the first pyrimidine nucleoside found to exist in the syn conformation in the crystalline state, with χ_CN = 76.8°. 2'-Deoxy-2'-(R)-phenylsulfinyl-uridine (Hata et al., 1991) also adopts a syn conformation, with χ_CN = 61.6°. The dihydro analogue of (Ib), the ribonucleoside 5,6-dihydroisocytidine monohydrate, which also has the amino group at the 2-position, adopts the usual anti conformation, with χ_CN = 107.6° (Kojic-Prodic et al., 1976). The reason for the preference of a syn conformer of (Ib) is a bifurcated hydrogen bond formed between the 2-amino group of the base and atoms O4' and O5' of the sugar moiety. The 2-amino group is located above the 2'-deoxyribofuranose moiety, as shown in Fig. 1.

The next major conformational parameter of interest is the pucker of the deoxyribofuranose moiety of (Ib). Its phase angle of pseudorotation, P, is 102.4 (6)°. The following two points are noteworthy. Firstly, the P value of (Ib) lies outside the preferred pseudorotation range of nucleosides: the C3'-endo domain is in the region P = 340–40° (North) and the C2'-endo domain is in the region P = 140–200° (South); thus, the P value of (Ib) corresponds to a sugar pucker mode of ^OT₁, which is also shown in Fig. 1. Secondly, in contrast with the standard sugars, where the average value of Ψ_m is 38.6 (3)° (Saenger, 1984), the maximum puckering amplitude in (Ib) of only 26.1 (1)° is significantly smaller. This indicates that the sugar moiety of (Ib) is flattened compared with those of the normal nucleoside sugar moieties. Such cases are also found in cyclic nucleosides, where the sugar conformation and the puckering amplitude are often constrained (Saenger, 1989). The conformation about the C5'-C4' bond is +sc (+gauche) (Saenger, 1984), with a torsion angle γ (O5'-C5'-C4'-C3') of 62.7 (4)°. For comparison, the sugar ring of (II) is puckered in a typical C2'-endo envelope form (P = 161.5°), with a normal maximum amplitude Ψ_m = 37.9°. Furthermore, the oxygen O5' is located out of the sugar ring, with γ = 178.6° (Sato, 1988).

The hydrogen-bond pattern of (Ib) is summarized in Table 2. The intramolecular bifurcated hydrogen bond (N2—H22···O5' and N2—H22···O4'), which does not exist in molecule (II), is particularly important. This hydrogen bond stabilizes the syn conformation of the pyrimidine moiety and restricts the conformation of the sugar ring in a way similar to the cyclic nucleosides.

Beside this important intramolecular hydrogen bond, there are three intermolecular hydrogen bonds responsible for the packing of the molecules in (Ib) (Table 2). The O3'-H3'···O4ⁱⁱ bond connects molecules parallel to the c axis to form infinite chains [symmetry code: (ii) x, y, z − 1]. Three of these chains placed around the threefold axis form triple strands. Each molecule of the first chain of a strand forms O5'-H5'···O4ⁱⁱⁱ and N2—H21···O5'ⁱ hydrogen bonds with molecules of the second chain [symmetry codes: (i) 2/3 − y, 4/3 + x − y, 1/3 + z; (iii) 2/3 − y, 4/3 + x − y, z − 2/3]. At the same time, atoms O5' and O4 accept hydrogen bonds from two molecules of the third chain. The second chain donates hydrogen bonds to the third chain. The triple strands are not connected to each other. Fig. 2 shows the crystal packing of (Ib) along the threefold c axis.

S2. Experimental

Compound (Ib) was synthesized from 2,5'-anhydrothymidine (Watanabe et al., 1978) according to the procedure reported by Kowollik & Langen (1968), and was crystallized from acetone/MeOH (8:2).

S3. Refinement

In the absence of suitable anomalous scatterers, the measured Friedel data could not be used to determine the absolute structure. Therefore, Friedel reflections were merged. However, comparison with the known configuration of the parent molecule indicates that the proposed configuration is correct. All H atoms were located in difference Fourier syntheses. Nevertheless, all H atoms, except hydroxyl- and amino-H, were generated in idealized positions and refined using a riding model, with displacement parameters fixed at 1.5 times the (equivalent) isotropic displacement parameters of the parent atoms. The coordinates and displacement parameters of amino- and hydroxyl-H atoms were refined freely (If this statement of H-atom treatment is correct, please provide s.u.s for *all* parameters involving the amino- and hydroxyl-H atoms, for Tables 1 and 2 and for the supplementary data).

Computing details

Data collection: XSCANS (Siemens, 1996); cell refinement: XSCANS; data reduction: SHELXTL (Sheldrick, 1997); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL93 (Sheldrick, 1993); molecular graphics: SHELXTL and DIAMOND (Brandenburg, 1999); software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. A perspective view of (Ib) showing the bifurcated intramolecular hydrogen bond, which stabilizes the syn conformation of the glycosidic bond. Displacement ellipsoids are drawn at the 25% probability level and H atoms are shown as spheres of an arbitrary size.
	Fig. 2. The arrangement of the molecules in (Ib) around a crystallographic 31 axis. Intermolecular hydrogen bonds are represented by dashed lines. H atoms and intramolecular hydrogen bonds are omitted for clarity.

2-amino-1-(2-deoxy-β-D-erythro-pentofuranosyl)-5-methylpyrimidin-4(1H)-one

Crystal data

C10H15N3O4	Dx = 1.417 Mg m^−3
Mr = 241.25	Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3	Cell parameters from 41 reflections
Hall symbol: R 3	θ = 2.4–12.3°
a = 16.611 (3) Å	µ = 0.11 mm^−1
c = 10.6471 (13) Å	T = 293 K
V = 2544.4 (7) Å^3	Prism, colourless
Z = 9	0.51 × 0.17 × 0.11 mm
F(000) = 1152

Data collection

Siemens P4 diffractometer	892 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.037
Graphite monochromator	θmax = 25.0°, θmin = 2.4°
2θ/ω scans	h = −17→17
Absorption correction: empirical (using intensity measurements) (SHELXTL; Sheldrick, 1997)	k = −19→19
Tmin = 0.914, Tmax = 0.988	l = −12→12
2165 measured reflections	3 standard reflections every 97 reflections
975 independent reflections	intensity decay: none

Refinement

Refinement on F^2	Hydrogen site location: difference Fourier map
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.039	Calculated w = 1/[σ^2(Fo^2) + (0.0489P)^2 + 2.6081P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.096	(Δ/σ)max < 0.001
S = 1.05	Δρmax = 0.46 e Å^−3
975 reflections	Δρmin = −0.21 e Å^−3
163 parameters	Extinction correction: SHELXL93 (Sheldrick, 1993), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.0018 (5)
Primary atom site location: structure-invariant direct methods

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. Refinement on F² for ALL reflections except for 0 with very negative F² or flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating _R_factor_obs 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	0.1514 (2)	0.5532 (2)	0.7336 (3)	0.041 (1)
C2	0.0972 (3)	0.5885 (3)	0.7775 (3)	0.037 (1)
N2	0.0663 (3)	0.6285 (3)	0.6981 (3)	0.050 (1)
H21	0.033	0.651	0.731	0.04 (1)*
H22	0.084	0.636	0.617	0.06 (1)*
N3	0.0740 (2)	0.5835 (2)	0.8966 (3)	0.043 (1)
C4	0.1062 (3)	0.5460 (3)	0.9826 (3)	0.041 (1)
O4	0.0809 (2)	0.5396 (2)	1.0944 (2)	0.054 (1)
C5	0.1721 (3)	0.5180 (3)	0.9441 (4)	0.044 (1)
C5A	0.2163 (4)	0.4860 (4)	1.0404 (4)	0.064 (1)
H5A1	0.256	0.537	1.094	0.097*
H5A2	0.252	0.464	0.999	0.097*
H5A3	0.169	0.437	1.090	0.097*
C6	0.1902 (3)	0.5210 (3)	0.8212 (4)	0.046 (1)
H6	0.230	0.501	0.794	0.069*
C1'	0.1625 (3)	0.5391 (3)	0.5990 (3)	0.046 (1)
H1'	0.207	0.517	0.591	0.069*
C2'	0.0726 (4)	0.4715 (3)	0.5323 (4)	0.069 (2)
H2'1	0.068	0.412	0.524	0.104*
H2'2	0.019	0.464	0.579	0.104*
C3'	0.0770 (3)	0.5125 (3)	0.4056 (4)	0.052 (1)
H3'1	0.022	0.519	0.391	0.076*
O3'	0.0824 (3)	0.4539 (3)	0.3140 (3)	0.080 (1)
H3'	0.105	0.491	0.225	0.11 (2)*
C4'	0.1658 (3)	0.6084 (3)	0.4075 (3)	0.045 (1)
H4'	0.213	0.606	0.355	0.068*
O4'	0.1982 (2)	0.6251 (2)	0.5358 (2)	0.044 (1)
C5'	0.1553 (3)	0.6889 (3)	0.3643 (4)	0.046 (1)
H5'2	0.215	0.746	0.365	0.070*
H5'1	0.131	0.678	0.279	0.070*
O5'	0.0935 (2)	0.6987 (2)	0.4467 (2)	0.044 (1)
H5'	0.093	0.754	0.429	0.10 (2)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.046 (3)	0.054 (2)	0.032 (2)	0.032 (2)	0.000 (1)	−0.000 (1)
C2	0.038 (2)	0.046 (2)	0.032 (2)	0.024 (2)	−0.003 (1)	−0.003 (2)
N2	0.063 (2)	0.076 (3)	0.032 (2)	0.051 (2)	0.008 (2)	0.006 (2)
N3	0.051 (2)	0.059 (2)	0.031 (2)	0.037 (2)	−0.000 (1)	−0.001 (1)
C4	0.048 (2)	0.050 (2)	0.032 (2)	0.029 (2)	−0.005 (2)	−0.004 (2)
O4	0.069 (2)	0.081 (2)	0.029 (1)	0.052 (2)	0.003 (1)	0.003 (1)
C5	0.046 (2)	0.056 (2)	0.037 (2)	0.030 (2)	−0.005 (2)	−0.002 (2)
C5A	0.078 (3)	0.093 (4)	0.048 (2)	0.062 (3)	−0.008 (2)	0.004 (2)
C6	0.048 (2)	0.056 (2)	0.048 (2)	0.037 (2)	0.003 (2)	0.004 (2)
C1'	0.061 (2)	0.051 (2)	0.036 (2)	0.035 (2)	0.011 (2)	0.008 (2)
C2'	0.085 (4)	0.049 (3)	0.038 (2)	0.006 (2)	0.011 (2)	−0.007 (2)
C3'	0.056 (2)	0.043 (2)	0.054 (2)	0.025 (2)	−0.008 (2)	−0.007 (2)
O3'	0.136 (4)	0.063 (2)	0.041 (2)	0.049 (2)	−0.006 (2)	−0.008 (2)
C4'	0.050 (2)	0.058 (2)	0.032 (2)	0.030 (2)	0.009 (2)	0.004 (2)
O4'	0.0385 (1)	0.048 (2)	0.043 (1)	0.018 (1)	−0.002 (1)	0.004 (1)
C5'	0.050 (2)	0.047 (2)	0.035 (2)	0.018 (2)	0.008 (2)	0.008 (2)
O5'	0.051 (2)	0.044 (2)	0.040 (1)	0.026 (1)	0.006 (1)	0.009 (1)

Geometric parameters (Å, º)

N1—C2	1.378 (5)	C1'—C2'	1.523 (7)
N1—C6	1.384 (5)	C1'—H1'	0.98
N1—C1'	1.478 (5)	C2'—C3'	1.496 (6)
C2—N3	1.316 (4)	C2'—H2'1	0.97
C2—N2	1.328 (5)	C2'—H2'2	0.97
N2—H21	0.878	C3'—O3'	1.412 (5)
N2—H22	0.896	C3'—C4'	1.539 (6)
N3—C4	1.358 (5)	C3'—H3'1	0.98
C4—O4	1.249 (4)	O3'—H3'	1.090
C4—C5	1.445 (5)	C4'—O4'	1.444 (4)
C5—C6	1.339 (6)	C4'—C5'	1.505 (6)
C5—C5A	1.504 (5)	C4'—H4'	0.98
C5A—H5A1	0.96	C5'—O5'	1.420 (5)
C5A—H5A2	0.96	C5'—H5'2	0.97
C5A—H5A3	0.96	C5'—H5'1	0.97
C6—H6	0.93	O5'—H5'	0.946
C1'—O4'	1.413 (5)
C2—N1—C6	117.7 (3)	N1—C1'—H1'	108.9
C2—N1—C1'	123.8 (3)	C2'—C1'—H1'	108.9
C6—N1—C1'	118.2 (3)	C3'—C2'—C1'	106.2 (3)
N3—C2—N2	118.0 (3)	C3'—C2'—H2'1	110.5
N3—C2—N1	122.3 (3)	C1'—C2'—H2'1	110.5
N2—C2—N1	119.7 (3)	C3'—C2'—H2'2	110.5
C2—N2—H21	116.1	C1'—C2'—H2'2	110.5
C2—N2—H22	120.2	H2'1—C2'—H2'2	108.7
H21—N2—H22	123.5	O3'—C3'—C2'	108.3 (4)
C2—N3—C4	120.5 (3)	O3'—C3'—C4'	111.4 (4)
O4—C4—N3	119.2 (3)	C2'—C3'—C4'	105.2 (3)
O4—C4—C5	121.3 (3)	O3'—C3'—H3'1	110.6
N3—C4—C5	119.4 (3)	C2'—C3'—H3'1	110.6
C6—C5—C4	117.3 (3)	C4'—C3'—H3'1	110.6
C6—C5—C5A	122.6 (4)	C3'—O3'—H3'	109.8
C4—C5—C5A	120.2 (4)	O4'—C4'—C5'	108.5 (3)
C5—C5A—H5A1	109.5	O4'—C4'—C3'	106.5 (3)
C5—C5A—H5A2	109.5	C5'—C4'—C3'	116.1 (3)
H5A1—C5A—H5A2	109.5	O4'—C4'—H4'	108.5
C5—C5A—H5A3	109.5	C5'—C4'—H4'	108.5
H5A1—C5A—H5A3	109.5	C3'—C4'—H4'	108.5
H5A2—C5A—H5A3	109.5	C1'—O4'—C4'	109.2 (3)
C5—C6—N1	122.2 (4)	O5'—C5'—C4'	108.9 (3)
C5—C6—H6	118.9	O5'—C5'—H5'2	109.9
N1—C6—H6	118.9	C4'—C5'—H5'2	109.9
O4'—C1'—N1	108.9 (3)	O5'—C5'—H5'1	109.9
O4'—C1'—C2'	106.5 (3)	C4'—C5'—H5'1	109.9
N1—C1'—C2'	114.5 (4)	H5'2—C5'—H5'1	108.3
O4'—C1'—H1'	108.9	C5'—O5'—H5'	110.2
C6—N1—C2—N3	−7.1 (6)	C6—N1—C1'—O4'	−128.3 (4)
C1'—N1—C2—N3	166.4 (4)	C2—N1—C1'—C2'	−60.9 (5)
C6—N1—C2—N2	173.3 (4)	C6—N1—C1'—C2'	112.6 (5)
C1'—N1—C2—N2	−13.2 (6)	O4'—C1'—C2'—C3'	19.4 (5)
N2—C2—N3—C4	−177.8 (4)	N1—C1'—C2'—C3'	139.8 (4)
N1—C2—N3—C4	2.6 (6)	C1'—C2'—C3'—O3'	113.6 (4)
C2—N3—C4—O4	−177.8 (3)	C1'—C2'—C3'—C4'	−5.6 (5)
C2—N3—C4—C5	4.8 (6)	O3'—C3'—C4'—O4'	−126.9 (4)
O4—C4—C5—C6	175.3 (4)	C2'—C3'—C4'—O4'	−9.7 (5)
N3—C4—C5—C6	−7.4 (6)	C5'—C4'—C3'—O3'	112.3 (4)
O4—C4—C5—C5A	−3.9 (6)	C2'—C3'—C4'—C5'	−130.6 (4)
N3—C4—C5—C5A	173.4 (4)	N1—C1'—O4'—C4'	−150.4 (3)
C4—C5—C6—N1	2.8 (6)	C4'—O4'—C1'—C2'	−26.4 (4)
C5A—C5—C6—N1	−178.0 (4)	C5'—C4'—O4'—C1'	148.3 (3)
C5—C6—N1—C2	4.1 (6)	C3'—C4'—O4'—C1'	22.8 (4)
C1'—N1—C6—C5	−169.8 (4)	O4'—C4'—C5'—O5'	−57.1 (4)
O4'—C1'—N1—C2	58.2 (5)	O5'—C5'—C4'—C3'	62.7 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H21···O5′^i	0.88	2.12	2.977 (4)	167
N2—H22···O5′	0.90	2.06	2.864 (4)	149
N2—H22···O4′	0.90	2.18	2.814 (4)	127
O3′—H3′···O4^ii	1.09	1.75	2.744 (4)	149
O5′—H5′···O4^iii	0.95	1.78	2.694 (4)	161

Symmetry codes: (i) −y+2/3, x−y+4/3, z+1/3; (ii) x, y, z−1; (iii) −y+2/3, x−y+4/3, z−2/3.