N,3'-cyclo-5'-O-Cyano-methyl-thymidine.

The title compound, C(19)H(20)N(4)O(4), is a cyclo-nucleoside with a C-N linkage. The furan-ose ring adopts a twist C3'-endo/C2'-exo (close to (3)T(2)) conformation with a pseudorotational phase angle (P) of 8.1° and puckering amplitude (v(m)) of 30.6°. The orientation of the pyrimidine ring with respect to the sugar group is anti. One intra-molecular C-H⋯O hydrogen bond is observed. The packing features an N-H⋯O hydrogen bond.

Related literature

For nucleosides, see: Kaur et al. (2007 ▶); Imanishi & Satoshi (2002 ▶); Len et al. (2008 ▶); Mieczkowski et al. (2010 ▶); Sanger (1984 ▶); Altona & Sundaralingam (1972 ▶, 1973 ▶); Zhou & Chattopadhyaya (2009 ▶).

Experimental

Crystal data

C19H20N4O4

M = 368.39

Orthorhombic,

a = 10.1682 (7) Å

b = 11.0867 (8) Å

c = 15.8882 (11) Å

V = 1791.1 (2) Å3

Z = 4

Mo Kα radiation

μ = 0.10 mm−1

T = 295 K

0.15 × 0.11 × 0.09 mm

Data collection

Bruker SMART 1000 diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T min = 0.985, T max = 0.991

10105 measured reflections

2036 independent reflections

1756 reflections with I > 2σ(I)

R int = 0.031

Refinement

R[F 2 > 2σ(F 2)] = 0.034

wR(F 2) = 0.079

S = 1.04

2036 reflections

249 parameters

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.18 e Å−3

Δρmin = −0.15 e Å−3

Data collection: SMART (Bruker, 1998 ▶); cell refinement: SAINT (Bruker, 1998 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008 ▶).

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810019379/om2332sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810019379/om2332Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C19H20N4O4	F(000) = 776
Mr = 368.39	Dx = 1.366 Mg m−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 2856 reflections
a = 10.1682 (7) Å	θ = 2.2–26.1°
b = 11.0867 (8) Å	µ = 0.10 mm−1
c = 15.8882 (11) Å	T = 295 K
V = 1791.1 (2) Å3	Block, colourless
Z = 4	0.15 × 0.11 × 0.09 mm

Bruker SMART 1000 diffractometer	2036 independent reflections
Radiation source: fine-focus sealed tube	1756 reflections with I > 2σ(I)
graphite	Rint = 0.031
Detector resolution: 9.00 pixels mm-1	θmax = 26.1°, θmin = 2.2°
φ and ω scans	h = −12→10
Absorption correction: multi-scan (SADABS; Bruker, 2001)	k = −13→13
Tmin = 0.985, Tmax = 0.991	l = −19→18
10105 measured reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.079	H atoms treated by a mixture of independent and constrained refinement
S = 1.04	w = 1/[σ2(Fo2) + (0.0361P)2 + 0.3497P] where P = (Fo2 + 2Fc2)/3
2036 reflections	(Δ/σ)max < 0.001
249 parameters	Δρmax = 0.18 e Å−3
0 restraints	Δρmin = −0.15 e Å−3

Experimental. (See detailed section in the paper)

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

Refinement. 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.

	x	y	z	Uiso*/Ueq
O1	0.26037 (18)	0.41221 (14)	0.18977 (11)	0.0419 (4)
O2	0.2659 (2)	0.16696 (16)	−0.04016 (11)	0.0476 (5)
O3	0.01006 (15)	0.29016 (14)	0.30360 (10)	0.0331 (4)
O4	−0.26649 (17)	0.29459 (15)	0.27577 (11)	0.0414 (4)
N1	0.0436 (2)	0.04989 (18)	0.20934 (13)	0.0322 (5)
H1	0.034 (2)	−0.023 (2)	0.1935 (14)	0.027 (6)*
N2	0.16403 (18)	0.22763 (16)	0.20033 (12)	0.0280 (4)
N3	0.2616 (2)	0.29017 (17)	0.07452 (12)	0.0345 (5)
N4	−0.5475 (2)	0.1380 (3)	0.2508 (2)	0.0720 (8)
C1	0.2157 (3)	0.4766 (2)	−0.00647 (16)	0.0382 (6)
C2	0.2429 (3)	0.5985 (2)	−0.01234 (16)	0.0434 (7)
H2	0.3247	0.6274	0.0044	0.052*
C3	0.1488 (3)	0.6782 (2)	−0.04317 (17)	0.0481 (7)
H3	0.1688	0.7598	−0.0476	0.058*
C4	0.0270 (3)	0.6379 (3)	−0.06705 (17)	0.0493 (7)
H4	−0.0360	0.6917	−0.0867	0.059*
C5	−0.0002 (3)	0.5186 (3)	−0.0617 (2)	0.0651 (9)
H5	−0.0823	0.4903	−0.0784	0.078*
C6	0.0925 (3)	0.4386 (3)	−0.0316 (2)	0.0612 (9)
H6	0.0715	0.3571	−0.0282	0.073*
C7	0.3192 (3)	0.3888 (2)	0.02538 (17)	0.0415 (6)
H7A	0.3665	0.3554	−0.0222	0.050*
H7B	0.3819	0.4321	0.0601	0.050*
C8	0.2318 (3)	0.1800 (2)	0.03381 (15)	0.0343 (5)
C9	0.1612 (2)	0.0937 (2)	0.08223 (15)	0.0316 (5)
C10	0.1238 (2)	0.12081 (19)	0.16251 (15)	0.0277 (5)
C11	0.2314 (2)	0.3165 (2)	0.15690 (15)	0.0314 (5)
C12	0.1264 (3)	−0.0252 (2)	0.04249 (17)	0.0399 (6)
H12A	0.1788	−0.0880	0.0672	0.060*
H12B	0.1433	−0.0215	−0.0169	0.060*
H12C	0.0349	−0.0420	0.0518	0.060*
C13	0.1405 (2)	0.2471 (2)	0.29099 (15)	0.0301 (5)
H13	0.2054	0.3027	0.3149	0.036*
C14	0.1430 (2)	0.1270 (2)	0.33571 (15)	0.0348 (6)
H14A	0.1374	0.1356	0.3964	0.042*
H14B	0.2197	0.0794	0.3210	0.042*
C15	0.0176 (2)	0.0765 (2)	0.29797 (14)	0.0317 (5)
H15	−0.0133	0.0051	0.3285	0.038*
C16	−0.0762 (2)	0.1842 (2)	0.30890 (15)	0.0315 (5)
H16	−0.1137	0.1809	0.3657	0.038*
C17	−0.1865 (2)	0.1961 (2)	0.24724 (16)	0.0350 (5)
H17A	−0.1524	0.2125	0.1914	0.042*
H17B	−0.2376	0.1223	0.2452	0.042*
C18	−0.3794 (3)	0.3126 (3)	0.22543 (18)	0.0475 (7)
H18A	−0.3540	0.3150	0.1666	0.057*
H18B	−0.4192	0.3895	0.2395	0.057*
C19	−0.4758 (3)	0.2153 (3)	0.23850 (19)	0.0499 (7)

	U11	U22	U33	U12	U13	U23
O1	0.0471 (11)	0.0284 (9)	0.0502 (10)	−0.0092 (9)	0.0064 (9)	−0.0036 (8)
O2	0.0649 (13)	0.0443 (11)	0.0336 (10)	0.0056 (10)	0.0107 (9)	0.0019 (8)
O3	0.0327 (9)	0.0251 (8)	0.0416 (9)	0.0000 (7)	0.0067 (8)	−0.0025 (7)
O4	0.0349 (9)	0.0366 (9)	0.0525 (11)	0.0061 (8)	0.0015 (8)	−0.0049 (8)
N1	0.0373 (12)	0.0202 (10)	0.0391 (12)	−0.0018 (9)	0.0062 (9)	−0.0028 (9)
N2	0.0299 (10)	0.0229 (9)	0.0313 (10)	−0.0010 (8)	0.0031 (8)	−0.0003 (8)
N3	0.0366 (11)	0.0300 (10)	0.0368 (11)	−0.0005 (9)	0.0073 (9)	0.0067 (9)
N4	0.0401 (15)	0.0722 (18)	0.104 (2)	−0.0030 (14)	0.0069 (16)	−0.0095 (18)
C1	0.0470 (16)	0.0323 (13)	0.0354 (13)	−0.0036 (11)	0.0094 (12)	0.0060 (10)
C2	0.0494 (16)	0.0363 (14)	0.0445 (15)	−0.0087 (14)	0.0147 (13)	−0.0039 (11)
C3	0.075 (2)	0.0226 (12)	0.0470 (16)	0.0023 (13)	0.0218 (15)	0.0018 (12)
C4	0.063 (2)	0.0403 (16)	0.0445 (16)	0.0120 (14)	0.0054 (14)	0.0070 (12)
C5	0.0517 (18)	0.0491 (19)	0.094 (3)	−0.0004 (15)	−0.0155 (19)	0.0119 (17)
C6	0.0521 (19)	0.0343 (15)	0.097 (3)	−0.0099 (13)	−0.0142 (18)	0.0167 (16)
C7	0.0393 (14)	0.0401 (15)	0.0451 (16)	−0.0067 (12)	0.0080 (12)	0.0072 (12)
C8	0.0381 (13)	0.0304 (12)	0.0345 (13)	0.0092 (11)	0.0015 (11)	0.0026 (10)
C9	0.0340 (13)	0.0279 (12)	0.0330 (13)	0.0035 (10)	0.0009 (10)	−0.0009 (10)
C10	0.0262 (11)	0.0210 (11)	0.0359 (13)	0.0043 (9)	−0.0012 (10)	0.0011 (9)
C11	0.0281 (12)	0.0247 (11)	0.0416 (13)	0.0001 (9)	0.0025 (11)	0.0023 (10)
C12	0.0511 (16)	0.0314 (13)	0.0373 (14)	0.0026 (12)	−0.0013 (13)	−0.0036 (11)
C13	0.0291 (12)	0.0286 (12)	0.0327 (12)	−0.0011 (9)	0.0008 (10)	−0.0021 (10)
C14	0.0342 (14)	0.0377 (13)	0.0325 (13)	0.0012 (11)	−0.0003 (11)	0.0055 (11)
C15	0.0353 (13)	0.0267 (12)	0.0329 (13)	−0.0023 (10)	0.0058 (11)	0.0048 (10)
C16	0.0342 (12)	0.0276 (12)	0.0326 (12)	−0.0039 (10)	0.0080 (10)	0.0007 (10)
C17	0.0332 (13)	0.0281 (12)	0.0437 (14)	−0.0007 (10)	0.0063 (11)	−0.0036 (11)
C18	0.0406 (15)	0.0482 (16)	0.0539 (17)	0.0105 (13)	0.0022 (13)	0.0076 (13)
C19	0.0331 (14)	0.0575 (18)	0.0592 (18)	0.0073 (14)	0.0008 (13)	−0.0053 (15)

O1—C11	1.219 (3)	C5—C6	1.380 (4)
O2—C8	1.234 (3)	C5—H5	0.9300
O3—C13	1.424 (3)	C6—H6	0.9300
O3—C16	1.468 (3)	C7—H7A	0.9700
O4—C18	1.413 (3)	C7—H7B	0.9700
O4—C17	1.435 (3)	C8—C9	1.422 (3)
N1—C10	1.355 (3)	C9—C10	1.365 (3)
N1—C15	1.463 (3)	C9—C12	1.504 (3)
N1—H1	0.85 (2)	C12—H12A	0.9600
N2—C11	1.384 (3)	C12—H12B	0.9600
N2—C10	1.390 (3)	C12—H12C	0.9600
N2—C13	1.476 (3)	C13—C14	1.509 (3)
N3—C11	1.376 (3)	C13—H13	0.9800
N3—C8	1.415 (3)	C14—C15	1.517 (3)
N3—C7	1.466 (3)	C14—H14A	0.9700
N4—C19	1.142 (4)	C14—H14B	0.9700
C1—C6	1.381 (4)	C15—C16	1.539 (3)
C1—C2	1.382 (4)	C15—H15	0.9800
C1—C7	1.520 (4)	C16—C17	1.495 (3)
C2—C3	1.392 (4)	C16—H16	0.9800
C2—H2	0.9300	C17—H17A	0.9700
C3—C4	1.370 (4)	C17—H17B	0.9700
C3—H3	0.9300	C18—C19	1.472 (4)
C4—C5	1.354 (4)	C18—H18A	0.9700
C4—H4	0.9300	C18—H18B	0.9700
C13—O3—C16	107.23 (16)	O1—C11—N2	121.7 (2)
C18—O4—C17	112.91 (19)	N3—C11—N2	115.7 (2)
C10—N1—C15	121.4 (2)	C9—C12—H12A	109.5
C10—N1—H1	117.2 (16)	C9—C12—H12B	109.5
C15—N1—H1	117.0 (16)	H12A—C12—H12B	109.5
C11—N2—C10	122.47 (19)	C9—C12—H12C	109.5
C11—N2—C13	117.56 (19)	H12A—C12—H12C	109.5
C10—N2—C13	119.92 (19)	H12B—C12—H12C	109.5
C11—N3—C8	124.78 (19)	O3—C13—N2	109.69 (18)
C11—N3—C7	115.9 (2)	O3—C13—C14	104.21 (18)
C8—N3—C7	119.09 (19)	N2—C13—C14	109.15 (19)
C6—C1—C2	117.4 (3)	O3—C13—H13	111.2
C6—C1—C7	121.9 (2)	N2—C13—H13	111.2
C2—C1—C7	120.6 (2)	C14—C13—H13	111.2
C1—C2—C3	120.4 (3)	C13—C14—C15	97.21 (19)
C1—C2—H2	119.8	C13—C14—H14A	112.3
C3—C2—H2	119.8	C15—C14—H14A	112.3
C4—C3—C2	120.8 (3)	C13—C14—H14B	112.3
C4—C3—H3	119.6	C15—C14—H14B	112.3
C2—C3—H3	119.6	H14A—C14—H14B	109.9
C5—C4—C3	119.1 (3)	N1—C15—C14	107.63 (19)
C5—C4—H4	120.5	N1—C15—C16	112.16 (19)
C3—C4—H4	120.5	C14—C15—C16	100.96 (18)
C4—C5—C6	120.6 (3)	N1—C15—H15	111.8
C4—C5—H5	119.7	C14—C15—H15	111.8
C6—C5—H5	119.7	C16—C15—H15	111.8
C5—C6—C1	121.6 (3)	O3—C16—C17	109.88 (18)
C5—C6—H6	119.2	O3—C16—C15	104.13 (17)
C1—C6—H6	119.2	C17—C16—C15	117.36 (19)
N3—C7—C1	112.2 (2)	O3—C16—H16	108.4
N3—C7—H7A	109.2	C17—C16—H16	108.4
C1—C7—H7A	109.2	C15—C16—H16	108.4
N3—C7—H7B	109.2	O4—C17—C16	106.58 (19)
C1—C7—H7B	109.2	O4—C17—H17A	110.4
H7A—C7—H7B	107.9	C16—C17—H17A	110.4
O2—C8—N3	118.5 (2)	O4—C17—H17B	110.4
O2—C8—C9	125.3 (2)	C16—C17—H17B	110.4
N3—C8—C9	116.2 (2)	H17A—C17—H17B	108.6
C10—C9—C8	119.9 (2)	O4—C18—C19	110.9 (2)
C10—C9—C12	121.3 (2)	O4—C18—H18A	109.5
C8—C9—C12	118.8 (2)	C19—C18—H18A	109.5
N1—C10—C9	123.6 (2)	O4—C18—H18B	109.5
N1—C10—N2	115.7 (2)	C19—C18—H18B	109.5
C9—C10—N2	120.6 (2)	H18A—C18—H18B	108.0
O1—C11—N3	122.6 (2)	N4—C19—C18	177.4 (3)
C6—C1—C2—C3	−0.5 (4)	C8—N3—C11—O1	179.1 (2)
C7—C1—C2—C3	178.7 (2)	C7—N3—C11—O1	−6.0 (3)
C1—C2—C3—C4	1.0 (4)	C8—N3—C11—N2	−1.7 (3)
C2—C3—C4—C5	−1.1 (4)	C7—N3—C11—N2	173.2 (2)
C3—C4—C5—C6	0.8 (5)	C10—N2—C11—O1	176.3 (2)
C4—C5—C6—C1	−0.3 (6)	C13—N2—C11—O1	−6.4 (3)
C2—C1—C6—C5	0.2 (5)	C10—N2—C11—N3	−2.9 (3)
C7—C1—C6—C5	−179.0 (3)	C13—N2—C11—N3	174.4 (2)
C11—N3—C7—C1	−80.4 (3)	C16—O3—C13—N2	85.9 (2)
C8—N3—C7—C1	94.8 (3)	C16—O3—C13—C14	−30.8 (2)
C6—C1—C7—N3	−35.9 (4)	C11—N2—C13—O3	99.4 (2)
C2—C1—C7—N3	145.0 (2)	C10—N2—C13—O3	−83.3 (2)
C11—N3—C8—O2	−179.0 (2)	C11—N2—C13—C14	−147.0 (2)
C7—N3—C8—O2	6.3 (3)	C10—N2—C13—C14	30.3 (3)
C11—N3—C8—C9	2.4 (3)	O3—C13—C14—C15	48.7 (2)
C7—N3—C8—C9	−172.4 (2)	N2—C13—C14—C15	−68.4 (2)
O2—C8—C9—C10	−177.0 (2)	C10—N1—C15—C14	−35.7 (3)
N3—C8—C9—C10	1.5 (3)	C10—N1—C15—C16	74.5 (3)
O2—C8—C9—C12	1.4 (4)	C13—C14—C15—N1	70.8 (2)
N3—C8—C9—C12	179.9 (2)	C13—C14—C15—C16	−46.9 (2)
C15—N1—C10—C9	173.5 (2)	C13—O3—C16—C17	−126.6 (2)
C15—N1—C10—N2	−8.5 (3)	C13—O3—C16—C15	−0.1 (2)
C8—C9—C10—N1	172.0 (2)	N1—C15—C16—O3	−84.0 (2)
C12—C9—C10—N1	−6.3 (4)	C14—C15—C16—O3	30.3 (2)
C8—C9—C10—N2	−5.9 (3)	N1—C15—C16—C17	37.7 (3)
C12—C9—C10—N2	175.7 (2)	C14—C15—C16—C17	152.0 (2)
C11—N2—C10—N1	−171.3 (2)	C18—O4—C17—C16	−176.96 (19)
C13—N2—C10—N1	11.5 (3)	O3—C16—C17—O4	−67.2 (2)
C11—N2—C10—C9	6.8 (3)	C15—C16—C17—O4	174.11 (18)
C13—N2—C10—C9	−170.4 (2)	C17—O4—C18—C19	71.4 (3)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O3i	0.85 (2)	2.12 (2)	2.938 (2)	161 (2)
C6—H6···O2	0.93	2.89	3.492 (3)	123

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O3i	0.85 (2)	2.12 (2)	2.938 (2)	161 (2)
C6—H6⋯O2	0.93	2.89	3.492 (3)	123

Symmetry code: (i) .