Methyl 1-de­oxy-1-(N¹-thymin­yl)-β-D-psicofuran­oside

In the structure of the title compound, C₁₂H₁₈N₂O₇, the furanosyl ring adopts the S-type sugar pucker with the following pseudorotational parameters: P_S = 159.6° (C2′-endo according to the designation of the ribofuran­ose ring of natural nucleosides; C3′-endo according to the numbering of the title compound) and ν_max = 35.9°. The conformation around the C5′—C6′ bond is ap (gauche–trans; gt; −g), with a torsion angle γ of −170.3 (2)°. The structure of the thymine base is very similar to that of thymidine. There are intermolecular N—H...O and O—H...O hydrogen bonds.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.044
• wR factor = 0.132
• Data-to-parameter ratio = 12.2

checkCIF/PLATON results

No syntax errors found



Alert level C
STRVA01_ALERT_2_C           Chirality of atom sites is inverted?
           From the CIF: _refine_ls_abs_structure_Flack    1.700
           From the CIF: _refine_ls_abs_structure_Flack_su    1.400
PLAT032_ALERT_4_C Std. Uncertainty in Flack Parameter too High ...       1.40
PLAT033_ALERT_2_C Flack Parameter Value Deviates 2 * su from zero.       1.70
PLAT380_ALERT_4_C Check Incorrectly? Oriented X(sp2)-Methyl Moiety        C50
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          4

Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
            correct. If it is not, please give the correct count in the
            _publ_section_exptl_refinement section of the submitted CIF.
           From the CIF: _diffrn_reflns_theta_max           30.00
           From the CIF: _reflns_number_total               2335
           Count of symmetry unique reflns         2362
           Completeness (_total/calc)             98.86%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured         0
           Fraction of Friedel pairs measured     0.000
           Are heavy atom types Z>Si present         no
PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature        293 K
PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature .        293 K
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3'    = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4'    = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5'    = .          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   5 ALERT level C = Check and explain
   6 ALERT level G = General alerts; check

   5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

In a search of new approaches to the synthesis of conformationally rigid 1,3-anhydro-β-D-psicofuranosyl nucleosides, we have briefly reported on the condensation of methyl 1,3-anhydro-4,6-di-O-toluoyl -β-D-psicofuranoside (I, scheme 1) with persilylated thymine (Roivainen et al., 2002). Conventional work-up of the reaction mixture followed by deprotection of the product gave thymine nucleoside, structure of which was tentatively proposed as 1-(1,3-anhydro -β-D-psicofuranosyl)thymine (II).

Later on, careful comparison of the NMR spectroscopy data for isolated compound with those for 9-(1,3-anhydro-β-D-psicofuranosyl)adenine (Roivainen et al., 2002), 1-(1,3-anhydro-β-D-psicofuranosyl)uracil (Kulak et al., 2005) and 1-(1,3-anhydro-β-D-psicofuranosyl)thymine (II) (Pradeepkumar et al., 2004), as well as the CD spectroscopy data for isolated compound with those for uracil and thymine nucleosides (Miles et al., 1967, 1970; Kulak et al., 2005) showed essential differences pointing to the unusual structure of the former. We have, therefore, undertaken the determination of the crystal and molecular structure of isolated thymime derivative. Recently, we have determined the single-crystal X-ray structure of 9-(1,3-anhydro-β-D-psicofuranosyl)adenine (Roivainen et al., 2006).

The molecular structure of the new glycoside (Fig.1) was found to be methyl 1-deoxy-1-(N¹-thyminyl)-β-D-psicofuranoside (III). It became obvious that its formation from methyl glycoside (I) and persilylated thymine results from nucleophilic attack of the nitrogen-atom N1 of the base onto the carbon atom C1' of the sugar.

As might be expected, the structure of the thymine base of (III) was found to be very similar to that of thymidine (Young et al., 1969; Chekhlov, 1995). The C1'-N1 bond length of 1.464 (2) Å is shorter than the glycosidic bond length of thymidine by 0.016 Å (Young et al., 1969; Chekhlov, 1995). The furanosyl ring of (III) in the solid state adopts the S-type sugar pucker with the following pseudorotational parameters: P_S = 159.6° (C2'-endo according to the designation of the ribofuranose ring of natural nucleosides; C3'-endo; according to the atom numbering indicated in Fig. 1) and ν_max = 35.9°. The conformation around the C5'-C6' bond is ap (gauche,trans; gt;-g) with a torsion angle γ of -170.3 (2)°. It is noteworthy that the C5'-O5' bond is longer than O5'-C2' as it is the case for the most nucleosides (Seela et al., 1999; Roivainen et al., 2006).

In solid state the molecules are linked to each other via four hydrogen bonds of different strengths. From the thymine base the oxygen atoms (O2, O4) act as acceptors and the NH-group (N3) as donor of hydrogen bonds. From the sugar moiety the hydroxyl group of O4' acts as donor and the hydroxyl groups of O3' and O6' as donor as well as acceptor groups. In summary, a three dimensional hydrogen bonding scheme results (Fig. 2).

Related literature

For related literature, see: Chekhlov (1995); Kulak et al. (2005); Miles et al. (1967, 1970); Pradeepkumar et al. (2004); Roivainen et al. (2002, 2006); Seela et al. (1999); Young et al. (1969).

S2. Experimental

The synthesis of compound (I) has been described earlier (Roivainen et al., 2002). Samples for X-ray analyses were crystallized from a mixture of methanol and propanol-2. Single crystals suitable for X-ray diffraction were selected directly from the sample as prepared.

S3. Refinement

In the absence of suitable anomalous scattering, Friedel equivalents could not be used to determine the absolute structure. Therefore, Friedel equivalents were merged before the final refinements.

The known configuration of the parent molecule was used to define the enantiomer employed in this structure refinement.

All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms bonded to carbon were placed in geometrically idealized positions (C—H=0.93–0.98 Å) and constrained to ride on their parent atoms with a common isotropic displament parameter. The hydrogen atoms of the OH und NH groups were first refined with the restriction of a common O—H and N—H bond length (DFIX). After refinement the positions of these hydrogen atoms were also constrained (AFIX 3).

Computing details

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

Figures

	Fig. 1. The molecular structure of nucleoside (III) with the numbering scheme used. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as spheres of arbitrary size.
	Fig. 2. Part of the crystal structure of nucleoside (III) showing the main structural features of the hydrogen bonding scheme. Dotted lines indicate hydrogen bonds. Symmetry codes for the generation of the different molecules are as follows: 1) 1 - x, -1/2 + y, 1/2 - y; 2) 1 - x, y, z; 3) -x, 1/2 + y,1/2 - z; 4) 1 - x, 1/2 + y, 1/2 - y; 5) 1/2 + x, 3/2 - y, 1 - z; 6) -1/2 + x, 3/2 - y, 1 - z; 7) -1/2 + x, 1/2 - y, 1 - z; 8) 1/2 + x, 1/2 - y, 1 - z; 9) -1 + x, y,z; 10) -x,-1/2 + y, 1/2 - z.
	Fig. 3. The structures of (I), (II) and (III).

Methyl 1-deoxy-1-(N¹-thyminyl)-β-D-psicofuranoside

Crystal data

C12H18N2O7	F(000) = 640
Mr = 302.28	Dx = 1.427 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 65 reflections
a = 5.7476 (7) Å	θ = 5.5–12.4°
b = 15.6207 (12) Å	µ = 0.12 mm^−1
c = 15.6735 (12) Å	T = 293 K
V = 1407.2 (2) Å^3	Needle, colourless
Z = 4	0.35 × 0.16 × 0.16 mm

Data collection

Siemens P4 diffractometer	Rint = 0.021
Radiation source: fine-focus sealed tube	θmax = 30.0°, θmin = 1.8°
Graphite monochromator	h = −8→1
2θ/ω scans	k = −21→1
3072 measured reflections	l = −1→22
2335 independent reflections	3 standard reflections every 97 reflections
2102 reflections with I > 2σ(I)	intensity decay: 0.4%

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.044	w = 1/[σ^2(Fo^2) + (0.0728P)^2 + 0.2397P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.132	(Δ/σ)max < 0.001
S = 1.05	Δρmax = 0.25 e Å^−3
2335 reflections	Δρmin = −0.22 e Å^−3
192 parameters	Extinction correction: SHELXTL (Sheldrick, 1997), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.021 (4)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983)
Secondary atom site location: difference Fourier map	Absolute structure parameter: 1.7 (14)

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 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	0.1653 (3)	0.49559 (9)	0.48231 (10)	0.0332 (4)
C2	0.2349 (5)	0.57613 (13)	0.45747 (13)	0.0383 (5)
O2	0.4073 (4)	0.58835 (11)	0.41307 (12)	0.0553 (5)
N3	0.0962 (5)	0.64153 (11)	0.48671 (14)	0.0487 (5)
H3	0.1333	0.6923	0.4706	0.075 (3)*
C4	−0.0964 (5)	0.63477 (13)	0.53910 (15)	0.0443 (5)
O4	−0.2060 (5)	0.69882 (12)	0.56133 (16)	0.0728 (7)
C5	−0.1533 (4)	0.54875 (13)	0.56644 (13)	0.0369 (4)
C50	−0.3524 (5)	0.53625 (19)	0.62618 (18)	0.0531 (6)
H501	−0.4222	0.5906	0.6387	0.075 (3)*
H502	−0.2973	0.5106	0.6781	0.075 (3)*
H503	−0.4658	0.4994	0.6002	0.075 (3)*
C6	−0.0208 (4)	0.48472 (12)	0.53712 (12)	0.0339 (4)
H6	−0.0562	0.4294	0.5547	0.075 (3)*
C1'	0.2955 (4)	0.42076 (12)	0.45255 (12)	0.0328 (4)
H1'1	0.3118	0.3804	0.4992	0.075 (3)*
H1'2	0.4502	0.4386	0.4354	0.075 (3)*
C2'	0.1763 (4)	0.37591 (12)	0.37717 (11)	0.0304 (4)
O2'	0.1290 (3)	0.43351 (11)	0.30982 (10)	0.0426 (4)
C3'	−0.0556 (4)	0.33227 (13)	0.39528 (12)	0.0349 (4)
H3'	−0.1868	0.3719	0.3893	0.075 (3)*
O3'	−0.0464 (4)	0.29518 (10)	0.47810 (10)	0.0512 (5)
H3O	−0.1711	0.2672	0.4789	0.075 (3)*
C4'	−0.0604 (4)	0.26182 (13)	0.32716 (13)	0.0339 (4)
H4'	−0.1183	0.2847	0.2729	0.075 (3)*
O4'	−0.1915 (3)	0.18980 (10)	0.35188 (11)	0.0466 (4)
H4O	−0.3134	0.1845	0.3229	0.075 (3)*
C5'	0.1973 (4)	0.23823 (13)	0.31950 (13)	0.0350 (4)
H5'	0.2278	0.1885	0.3559	0.075 (3)*
O5'	0.3284 (3)	0.30973 (10)	0.35161 (10)	0.0390 (3)
C6'	0.2637 (5)	0.21586 (19)	0.22929 (16)	0.0491 (6)
H6'1	0.1545	0.1745	0.2063	0.075 (3)*
H6'2	0.2585	0.2667	0.1939	0.075 (3)*
O6'	0.4901 (4)	0.18126 (19)	0.22886 (14)	0.0791 (8)
H6O	0.5052	0.1505	0.1853	0.075 (3)*
C22'	0.3241 (6)	0.4601 (2)	0.26075 (16)	0.0610 (8)
H221	0.2739	0.4990	0.2170	0.075 (3)*
H222	0.3957	0.4110	0.2349	0.075 (3)*
H223	0.4345	0.4882	0.2972	0.075 (3)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0448 (9)	0.0214 (6)	0.0335 (7)	−0.0003 (7)	0.0067 (7)	0.0013 (5)
C2	0.0525 (12)	0.0267 (8)	0.0356 (9)	−0.0049 (9)	−0.0002 (9)	0.0056 (7)
O2	0.0691 (12)	0.0419 (9)	0.0549 (10)	−0.0134 (9)	0.0151 (10)	0.0100 (7)
N3	0.0715 (14)	0.0209 (7)	0.0536 (10)	−0.0022 (9)	0.0011 (11)	0.0046 (7)
C4	0.0599 (14)	0.0256 (8)	0.0475 (11)	0.0090 (10)	−0.0042 (11)	−0.0010 (8)
O4	0.0989 (18)	0.0346 (9)	0.0848 (14)	0.0265 (11)	0.0097 (15)	−0.0036 (9)
C5	0.0430 (11)	0.0318 (9)	0.0360 (9)	0.0022 (9)	−0.0012 (9)	−0.0047 (7)
C50	0.0507 (14)	0.0545 (13)	0.0540 (13)	0.0041 (12)	0.0113 (12)	−0.0138 (11)
C6	0.0456 (11)	0.0241 (7)	0.0319 (8)	−0.0033 (8)	0.0051 (8)	−0.0018 (6)
C1'	0.0391 (10)	0.0285 (8)	0.0307 (8)	0.0054 (8)	0.0002 (8)	−0.0003 (7)
C2'	0.0338 (9)	0.0290 (8)	0.0285 (7)	0.0049 (7)	0.0042 (7)	0.0003 (6)
O2'	0.0471 (9)	0.0461 (8)	0.0345 (7)	−0.0037 (7)	−0.0035 (7)	0.0128 (6)
C3'	0.0367 (10)	0.0297 (8)	0.0382 (9)	0.0025 (8)	0.0077 (8)	−0.0010 (7)
O3'	0.0813 (13)	0.0363 (8)	0.0361 (7)	−0.0176 (9)	0.0171 (9)	−0.0027 (6)
C4'	0.0340 (9)	0.0319 (8)	0.0359 (9)	0.0023 (8)	0.0013 (8)	−0.0009 (7)
O4'	0.0498 (9)	0.0383 (8)	0.0517 (9)	−0.0087 (7)	−0.0008 (8)	−0.0014 (7)
C5'	0.0361 (10)	0.0345 (9)	0.0345 (8)	0.0073 (8)	−0.0021 (8)	−0.0082 (7)
O5'	0.0323 (7)	0.0406 (7)	0.0440 (7)	0.0080 (6)	−0.0010 (6)	−0.0156 (6)
C6'	0.0446 (12)	0.0605 (15)	0.0423 (10)	0.0053 (12)	0.0000 (10)	−0.0230 (11)
O6'	0.0506 (11)	0.122 (2)	0.0651 (12)	0.0234 (13)	−0.0032 (10)	−0.0587 (14)
C22'	0.074 (2)	0.0713 (17)	0.0374 (10)	−0.0288 (17)	0.0071 (13)	0.0091 (11)

Geometric parameters (Å, º)

N1—C2	1.376 (2)	C2'—C3'	1.524 (3)
N1—C6	1.382 (3)	O2'—C22'	1.422 (3)
N1—C1'	1.464 (2)	C3'—O3'	1.423 (2)
C2—O2	1.226 (3)	C3'—C4'	1.534 (3)
C2—N3	1.375 (3)	C3'—H3'	0.9800
N3—C4	1.382 (4)	O3'—H3O	0.8389
N3—H3	0.8600	C4'—O4'	1.408 (3)
C4—O4	1.232 (3)	C4'—C5'	1.531 (3)
C4—C5	1.448 (3)	C4'—H4'	0.9800
C5—C6	1.338 (3)	O4'—H4O	0.8389
C5—C50	1.491 (3)	C5'—O5'	1.438 (3)
C50—H501	0.9600	C5'—C6'	1.505 (3)
C50—H502	0.9600	C5'—H5'	0.9800
C50—H503	0.9600	C6'—O6'	1.409 (4)
C6—H6	0.9300	C6'—H6'1	0.9700
C1'—C2'	1.535 (3)	C6'—H6'2	0.9700
C1'—H1'1	0.9700	O6'—H6O	0.8389
C1'—H1'2	0.9700	C22'—H221	0.9600
C2'—O5'	1.412 (2)	C22'—H222	0.9600
C2'—O2'	1.413 (2)	C22'—H223	0.9600
C2—N1—C6	120.86 (17)	C2'—O2'—C22'	116.0 (2)
C2—N1—C1'	119.41 (18)	O3'—C3'—C2'	108.65 (18)
C6—N1—C1'	119.69 (15)	O3'—C3'—C4'	110.10 (16)
O2—C2—N3	122.86 (19)	C2'—C3'—C4'	101.94 (16)
O2—C2—N1	122.5 (2)	O3'—C3'—H3'	111.9
N3—C2—N1	114.6 (2)	C2'—C3'—H3'	111.9
C2—N3—C4	127.30 (17)	C4'—C3'—H3'	111.9
C2—N3—H3	116.4	C3'—O3'—H3O	101.2
C4—N3—H3	116.4	O4'—C4'—C5'	110.30 (17)
O4—C4—N3	121.0 (2)	O4'—C4'—C3'	113.03 (17)
O4—C4—C5	123.7 (3)	C5'—C4'—C3'	102.12 (17)
N3—C4—C5	115.31 (19)	O4'—C4'—H4'	110.4
C6—C5—C4	117.6 (2)	C5'—C4'—H4'	110.4
C6—C5—C50	123.7 (2)	C3'—C4'—H4'	110.4
C4—C5—C50	118.7 (2)	C4'—O4'—H4O	112.1
C5—C50—H501	109.5	O5'—C5'—C6'	112.1 (2)
C5—C50—H502	109.5	O5'—C5'—C4'	107.02 (15)
H501—C50—H502	109.5	C6'—C5'—C4'	112.00 (19)
C5—C50—H503	109.5	O5'—C5'—H5'	108.5
H501—C50—H503	109.5	C6'—C5'—H5'	108.5
H502—C50—H503	109.5	C4'—C5'—H5'	108.5
C5—C6—N1	124.18 (18)	C2'—O5'—C5'	110.08 (15)
C5—C6—H6	117.9	O6'—C6'—C5'	109.1 (2)
N1—C6—H6	117.9	O6'—C6'—H6'1	109.9
N1—C1'—C2'	112.45 (17)	C5'—C6'—H6'1	109.9
N1—C1'—H1'1	109.1	O6'—C6'—H6'2	109.9
C2'—C1'—H1'1	109.1	C5'—C6'—H6'2	109.9
N1—C1'—H1'2	109.1	H6'1—C6'—H6'2	108.3
C2'—C1'—H1'2	109.1	C6'—O6'—H6O	108.6
H1'1—C1'—H1'2	107.8	O2'—C22'—H221	109.5
O5'—C2'—O2'	111.93 (16)	O2'—C22'—H222	109.5
O5'—C2'—C3'	105.49 (15)	H221—C22'—H222	109.5
O2'—C2'—C3'	104.80 (17)	O2'—C22'—H223	109.5
O5'—C2'—C1'	106.05 (16)	H221—C22'—H223	109.5
O2'—C2'—C1'	111.72 (16)	H222—C22'—H223	109.5
C3'—C2'—C1'	116.81 (16)
C6—N1—C2—O2	175.6 (2)	C1'—C2'—O2'—C22'	74.0 (2)
C1'—N1—C2—O2	−2.3 (3)	O5'—C2'—C3'—O3'	80.69 (18)
C6—N1—C2—N3	−4.2 (3)	O2'—C2'—C3'—O3'	−161.01 (16)
C1'—N1—C2—N3	177.94 (19)	C1'—C2'—C3'—O3'	−36.8 (2)
O2—C2—N3—C4	−177.7 (2)	O5'—C2'—C3'—C4'	−35.54 (19)
N1—C2—N3—C4	2.1 (4)	O2'—C2'—C3'—C4'	82.75 (18)
C2—N3—C4—O4	179.6 (3)	C1'—C2'—C3'—C4'	−153.02 (17)
C2—N3—C4—C5	0.9 (4)	O3'—C3'—C4'—O4'	36.9 (3)
O4—C4—C5—C6	179.6 (3)	C2'—C3'—C4'—O4'	152.08 (17)
N3—C4—C5—C6	−1.8 (3)	O3'—C3'—C4'—C5'	−81.6 (2)
O4—C4—C5—C50	−1.2 (4)	C2'—C3'—C4'—C5'	33.6 (2)
N3—C4—C5—C50	177.4 (2)	O4'—C4'—C5'—O5'	−141.60 (16)
C4—C5—C6—N1	−0.3 (3)	C3'—C4'—C5'—O5'	−21.2 (2)
C50—C5—C6—N1	−179.4 (2)	O4'—C4'—C5'—C6'	95.2 (2)
C2—N1—C6—C5	3.6 (3)	C3'—C4'—C5'—C6'	−144.4 (2)
C1'—N1—C6—C5	−178.6 (2)	O2'—C2'—O5'—C5'	−90.3 (2)
C2—N1—C1'—C2'	−100.1 (2)	C3'—C2'—O5'—C5'	23.1 (2)
C6—N1—C1'—C2'	82.0 (2)	C1'—C2'—O5'—C5'	147.67 (17)
N1—C1'—C2'—O5'	175.76 (15)	C6'—C5'—O5'—C2'	122.23 (19)
N1—C1'—C2'—O2'	53.6 (2)	C4'—C5'—O5'—C2'	−0.9 (2)
N1—C1'—C2'—C3'	−67.1 (2)	O5'—C5'—C6'—O6'	69.4 (3)
O5'—C2'—O2'—C22'	−44.8 (3)	C4'—C5'—C6'—O6'	−170.3 (2)
C3'—C2'—O2'—C22'	−158.6 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O4^i	0.86	2.00	2.842 (3)	167
O3′—H3O···O3′^ii	0.84	2.46	3.2745 (16)	163
O4′—H4O···O6′^iii	0.84	1.86	2.662 (3)	160
O6′—H6O···O2^iv	0.84	1.89	2.721 (2)	170

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