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In the structure of the title compound, C11H13N5O4, the glycosidic torsion angle, χ, is −107.1 (2)° [nucleic acid nomenclature used throughout the manuscript; IUPAC–IUB Joint Commision on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9–15], indicating the anti conformation. The furanosyl ring adopts an N-type sugar pucker with the following pseudorotational parameters: PN = 50.5 (2)° and νmax = 34.9 (1)°. The conformation around the C5′—C6′ bond is ap (gauche,trans; gt; −g), with a torsion angle γ of 176.28 (19)°. The 1′,2′-oxetane ring is not planar but folded along C3′...C1′, with an angle of 9.6 (1)°.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270106037759/fa3039sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270106037759/fa3039Isup2.hkl
Contains datablock I

CCDC reference: 628520

Comment top

In recent years conformationally rigid 1,3-anhydro-β-D-psicofuranosyl nucleosides have attracted much attention as constituents of oligonucleotides, the exciting biochemical and biophysical properties of which have been investigated in detail by Chattopadhyaya and co-workers (Bogucka et al., 2005, and references therein); however, structural data have not heretofore been published. Recently, we described the synthesis of the anhydro nucleoside (I) (Roivainen et al., 2002), and deduced its structure from UV and NMR spectroscopic data to be consistent with that of (I) in the scheme below. Its single-crystal X-ray structure (Fig. 1), which we determined in order to confirm this assignment, is reported here.

Selected geometric parameters for the anhydro nucleoside (I) are given in Table 1. As might be expected, the structures of the adenine bases of (I) and adenosine (II) (Lai & Marsh, 1972), which represents the conformationally unrigid counterpart to (I), are very similar. The orientation of the almost planar adenine base of (I) relative to the sugar ring is anti, with glycosyl torsion angle χ (C4—N9—C2'—O5') (IUPAC–IUB Joint Commission on Biochemical Nomenclature, 1983) of −107.1 (2)° and differs substantially from that of −170.1° found for adenosine. The furanosyl ring of nucleoside (I) in the solid state adopts the N-type sugar pucker with following pseudorotational parameters: PN = 50.5 (2)° (C5'-exo) and νmax = 34.9 (1)°. The N-conformation was also found in the crystal structure of adenosine, although through somewhat different pseudorotational parameters, viz. PN = 7.2° (C2'-exo/C3'-endo; 3T2) and νmax = 36.0° (Lai & Marsh, 1972). It is noteworthy that the insertion of the 1',2'-oxetane ring into the molecule of adenosine did not lead to an essential change of bond distances within the furanose ring (the deviations are ±0.007 Å for all bonds, but the C5'—C4' bond was shorter by 0.014 Å than the relevant C3'—C4' bond of adenosine). Thus, the C5'—O5' bond [1.450 (2) Å] is longer than O5'—C2' [1.418 (2) Å], in accordance with an analogous correlation in most purine nucleosides (Seela et al., 1999). The 1',2'-oxetane ring itself is not planar but folded along C3'—C1' with an angle of 9.6 (1)°.

The glycosidic bond length of the nucleoside (I) C2'—N9 of 1.438 (2) Å is shorter than that of adenosine by 0.028 Å (Lai & Marsh, 1972). The conformations around the exocyclic C5'—C6' bond in the solid state of the nucleoside (I) and the corresponding C4'—C5' bond of adenosine are similar, viz. ap (gauche,trans; gt;-g), with torsion angles γ of 176.28 (19) and 177.0°, respectively.

In the extended structure all molecules are linked together via a three-dimensional network of hydrogen bonds. The main intermolecular feature, an eight-membered ring (Fig. 2), consists of the hydroxy groups O6' and O4' of two different molecules and the amino group N6 and atom N1 of a third molecule. Whereas the hydroxy groups function both as donors and as acceptors of hydrogen bonds, atom N1 serves only as an acceptor and the NH2– group as a donor. Three of the four intermolecular hydrogen bonds are found within this ring system. The fourth connects a fourth, exocyclic molecule with the NH2-groups inside the eight-membered supramolecular ring. The geometric details of all four hydrogen bonds are given in Table 2. As can be seen from the donor–acceptor distances, which are in the range 2.633 (3) to 3.043 (2) Å, only the hydrogen bond between the hydroxyl groups is relatively strong, whereas the other three are weaker.

Experimental top

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

Refinement top

In the absence of suitable anomalous scattering atoms, refinement of the Flack (1983) parameter (Flack, 1983) led to an inconclusive result. All H atoms were initially found in a difference Fourier synthesis. In order to maximize the data/parameter ratio, the H atoms bonded to C atoms were placed in geometrically idealized positions (C—H = 0.93–0.98 Å) and constrained to ride on their parent atoms. In order to describe the hydrogen-bonding scheme as well as possible, the positions of the H atoms of the OH und NH2 groups were first allowed to refine restrained to common O—H and N—H bond lengths (DFIX). After refinement, the positions of these H atoms were also constrained (AFIX 3) to ride on their parent atoms.

Computing details top

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

Figures top
[Figure 1] Fig. 1. A perspective view of nucleoside (I), with the numbering scheme used. All non-H atoms were drawn as displacement ellipsoids at the 50% probability level and H atoms are shown as spheres of small arbitrary size.
[Figure 2] Fig. 2. Part of the crystal structure of nucleoside (I), showing the main structural features of the hydrogen-bonding scheme. [Symmetry codes for the generation of the different molecules are as follows: (1) x, y, z; (2) 2 − x, −1/2 + y, 1 − z; (3) 1 + x, y, 1 + z; (4) 1 − x, 1/2 + y, 1 − z.]
9-(1,3-Anhydro-β-D-psicofuranosyl)adenine top
Crystal data top
C11H13N5O4F(000) = 292
Mr = 279.26Dx = 1.518 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 32 reflections
a = 5.4154 (5) Åθ = 4.3–12.5°
b = 9.8941 (8) ŵ = 0.12 mm1
c = 11.4431 (12) ÅT = 293 K
β = 94.970 (14)°Plate, colourless
V = 610.82 (10) Å30.35 × 0.22 × 0.08 mm
Z = 2
Data collection top
Bruker P4
diffractometer
1686 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.023
Graphite monochromatorθmax = 30.0°, θmin = 1.8°
ω scansh = 07
2053 measured reflectionsk = 130
1878 independent reflectionsl = 1616
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.041 w = 1/[σ2(Fo2) + (0.0627P)2 + 0.0578P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.109(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.24 e Å3
1878 reflectionsΔρmin = 0.23 e Å3
186 parametersExtinction correction: SHELXTL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
5 restraintsExtinction coefficient: 0.037 (8)
Primary atom site location: structure-invariant direct methodsAbsolute structure: based on known absolute configuration of the chemical entity
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.7 (13)
Crystal data top
C11H13N5O4V = 610.82 (10) Å3
Mr = 279.26Z = 2
Monoclinic, P21Mo Kα radiation
a = 5.4154 (5) ŵ = 0.12 mm1
b = 9.8941 (8) ÅT = 293 K
c = 11.4431 (12) Å0.35 × 0.22 × 0.08 mm
β = 94.970 (14)°
Data collection top
Bruker P4
diffractometer
1686 reflections with I > 2σ(I)
2053 measured reflectionsRint = 0.023
1878 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.041H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.109Δρmax = 0.24 e Å3
S = 1.04Δρmin = 0.23 e Å3
1878 reflectionsAbsolute structure: based on known absolute configuration of the chemical entity
186 parametersAbsolute structure parameter: 0.7 (13)
5 restraints
Special details top

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 (Å2) top
xyzUiso*/Ueq
N11.0645 (4)0.0648 (2)0.70622 (17)0.0413 (5)
C21.0944 (5)0.1224 (3)0.6016 (2)0.0421 (6)
H211.22350.18440.60150.047 (2)*
N30.9656 (4)0.1035 (2)0.49783 (19)0.0380 (5)
C40.7818 (4)0.0143 (2)0.50832 (17)0.0287 (4)
C50.7304 (4)0.0553 (2)0.60914 (17)0.0310 (4)
C60.8844 (4)0.0297 (2)0.71232 (18)0.0338 (5)
N60.8554 (4)0.0924 (2)0.81362 (17)0.0451 (5)
H610.74590.15620.81370.047 (2)*
H620.96130.07570.87310.047 (2)*
N70.5259 (4)0.1393 (2)0.58820 (16)0.0398 (5)
C80.4570 (4)0.1198 (3)0.47760 (18)0.0370 (5)
H810.32270.16420.43850.047 (2)*
N90.6010 (3)0.02752 (19)0.42329 (14)0.0289 (4)
C1'0.6795 (4)0.1284 (2)0.25069 (18)0.0320 (4)
H1'10.81070.11230.19980.047 (2)*
H1'20.73070.19420.31080.047 (2)*
O4'0.1036 (3)0.00909 (19)0.05149 (12)0.0359 (4)
H4'O0.20090.05010.01520.047 (2)*
C2'0.5720 (3)0.0016 (2)0.29920 (16)0.0269 (4)
C3'0.3213 (4)0.0476 (3)0.24248 (17)0.0305 (4)
H3'0.201 (6)0.081 (3)0.297 (3)0.047 (2)*
O3'0.4400 (3)0.15917 (17)0.18710 (13)0.0354 (4)
C5'0.4817 (4)0.1302 (2)0.13100 (17)0.0312 (4)
H5'0.56360.08100.07090.047 (2)*
C4'0.2366 (4)0.0606 (2)0.15315 (17)0.0310 (4)
H4'0.13150.12550.19040.047 (2)*
O5'0.6307 (3)0.12337 (17)0.24239 (12)0.0329 (3)
O6'0.6916 (5)0.3373 (2)0.08697 (17)0.0678 (7)
H6'O0.76720.36530.15710.047 (2)*
C6'0.4583 (6)0.2775 (3)0.0989 (2)0.0508 (7)
H6'10.35550.28650.02550.047 (2)*
H6'20.37710.32500.15900.047 (2)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0474 (11)0.0458 (12)0.0282 (9)0.0127 (10)0.0103 (7)0.0002 (9)
C20.0437 (12)0.0482 (14)0.0324 (10)0.0160 (11)0.0086 (9)0.0036 (10)
N30.0368 (10)0.0447 (11)0.0311 (8)0.0070 (9)0.0043 (7)0.0037 (8)
C40.0300 (9)0.0324 (10)0.0227 (8)0.0009 (8)0.0037 (7)0.0010 (7)
C50.0358 (10)0.0345 (10)0.0212 (8)0.0046 (9)0.0052 (7)0.0001 (7)
C60.0419 (11)0.0342 (11)0.0236 (8)0.0020 (9)0.0073 (8)0.0032 (8)
N60.0622 (13)0.0448 (12)0.0253 (8)0.0159 (10)0.0141 (8)0.0034 (8)
N70.0449 (10)0.0455 (11)0.0273 (8)0.0133 (9)0.0059 (7)0.0027 (8)
C80.0373 (11)0.0451 (13)0.0271 (9)0.0105 (10)0.0055 (7)0.0016 (9)
N90.0308 (8)0.0343 (9)0.0203 (7)0.0023 (7)0.0045 (6)0.0007 (6)
C1'0.0318 (10)0.0347 (11)0.0285 (9)0.0015 (9)0.0028 (7)0.0012 (8)
O4'0.0340 (7)0.0461 (9)0.0255 (6)0.0034 (7)0.0096 (5)0.0043 (7)
C2'0.0272 (8)0.0330 (10)0.0196 (7)0.0040 (8)0.0027 (6)0.0024 (7)
C3'0.0269 (9)0.0408 (11)0.0234 (8)0.0083 (8)0.0006 (7)0.0009 (8)
O3'0.0407 (8)0.0323 (8)0.0312 (7)0.0048 (6)0.0089 (6)0.0019 (6)
C5'0.0356 (10)0.0348 (11)0.0220 (8)0.0046 (9)0.0040 (7)0.0005 (8)
C4'0.0281 (9)0.0402 (11)0.0236 (8)0.0014 (9)0.0042 (7)0.0021 (8)
O5'0.0359 (7)0.0338 (8)0.0271 (7)0.0106 (6)0.0077 (5)0.0054 (6)
O6'0.1016 (17)0.0658 (14)0.0316 (8)0.0446 (14)0.0198 (9)0.0164 (9)
C6'0.0721 (18)0.0414 (14)0.0354 (12)0.0086 (13)0.0157 (12)0.0089 (10)
Geometric parameters (Å, º) top
N1—C21.349 (3)C1'—H1'10.9700
N1—C61.357 (3)C1'—H1'20.9700
C2—N31.337 (3)O4'—C4'1.409 (2)
C2—H210.9300O4'—H4'O0.9115
N3—C41.343 (3)C2'—O5'1.418 (2)
C4—N91.383 (2)C2'—C3'1.533 (3)
C4—C51.392 (3)C3'—O3'1.451 (3)
C5—N71.389 (3)C3'—C4'1.523 (3)
C5—C61.408 (3)C3'—H3'1.00 (3)
C6—N61.336 (3)C5'—O5'1.450 (2)
N6—H610.8666C5'—C6'1.506 (4)
N6—H620.8665C5'—C4'1.536 (3)
N7—C81.302 (3)C5'—H5'0.9800
C8—N91.383 (3)C4'—H4'0.9800
C8—H810.9300O6'—C6'1.412 (4)
N9—C2'1.438 (2)O6'—H6'O0.9117
C1'—O3'1.463 (3)C6'—H6'10.9700
C1'—C2'1.535 (3)C6'—H6'20.9700
C2—N1—C6118.60 (19)O5'—C2'—C3'107.53 (16)
N3—C2—N1129.5 (2)N9—C2'—C3'119.45 (16)
N3—C2—H21115.3O5'—C2'—C1'116.03 (16)
N1—C2—H21115.3N9—C2'—C1'119.60 (17)
C2—N3—C4110.3 (2)C3'—C2'—C1'86.02 (16)
N3—C4—N9128.23 (19)O3'—C3'—C4'111.13 (16)
N3—C4—C5127.01 (18)O3'—C3'—C2'90.96 (15)
N9—C4—C5104.76 (18)C4'—C3'—C2'105.38 (18)
N7—C5—C4111.52 (17)O3'—C3'—H3'111 (2)
N7—C5—C6131.1 (2)C4'—C3'—H3'118.5 (19)
C4—C5—C6117.3 (2)C2'—C3'—H3'116.2 (18)
N6—C6—N1120.23 (19)C3'—O3'—C1'91.80 (15)
N6—C6—C5122.6 (2)O5'—C5'—C6'106.79 (18)
N1—C6—C5117.2 (2)O5'—C5'—C4'104.89 (16)
C6—N6—H61118.1C6'—C5'—C4'114.8 (2)
C6—N6—H62118.2O5'—C5'—H5'110.1
H61—N6—H62123.0C6'—C5'—H5'110.1
C8—N7—C5103.66 (19)C4'—C5'—H5'110.1
N7—C8—N9114.16 (18)O4'—C4'—C3'113.7 (2)
N7—C8—H81122.9O4'—C4'—C5'114.41 (17)
N9—C8—H81122.9C3'—C4'—C5'102.24 (15)
C4—N9—C8105.90 (16)O4'—C4'—H4'108.7
C4—N9—C2'130.66 (18)C3'—C4'—H4'108.7
C8—N9—C2'122.95 (17)C5'—C4'—H4'108.7
O3'—C1'—C2'90.40 (15)C2'—O5'—C5'108.25 (15)
O3'—C1'—H1'1113.6C6'—O6'—H6'O112.3
C2'—C1'—H1'1113.6O6'—C6'—C5'111.8 (3)
O3'—C1'—H1'2113.6O6'—C6'—H6'1109.3
C2'—C1'—H1'2113.6C5'—C6'—H6'1109.3
H1'1—C1'—H1'2110.8O6'—C6'—H6'2109.3
C4'—O4'—H4'O109.5C5'—C6'—H6'2109.3
O5'—C2'—N9106.95 (17)H6'1—C6'—H6'2107.9
C6—N1—C2—N31.9 (5)C8—N9—C2'—C1'161.9 (2)
N1—C2—N3—C41.1 (4)O3'—C1'—C2'—O5'100.92 (17)
C2—N3—C4—N9176.7 (2)O3'—C1'—C2'—N9128.49 (18)
C2—N3—C4—C52.4 (3)O3'—C1'—C2'—C3'6.66 (15)
N3—C4—C5—N7179.9 (2)O5'—C2'—C3'—O3'109.34 (17)
N9—C4—C5—N70.6 (3)N9—C2'—C3'—O3'128.69 (19)
N3—C4—C5—C60.7 (4)C1'—C2'—C3'—O3'6.72 (15)
N9—C4—C5—C6178.6 (2)O5'—C2'—C3'—C4'2.9 (2)
C2—N1—C6—N6177.6 (3)N9—C2'—C3'—C4'119.1 (2)
C2—N1—C6—C53.7 (4)C1'—C2'—C3'—C4'118.96 (17)
N7—C5—C6—N62.2 (4)C4'—C3'—O3'—C1'113.95 (17)
C4—C5—C6—N6178.7 (2)C2'—C3'—O3'—C1'7.04 (16)
N7—C5—C6—N1176.5 (3)C2'—C1'—O3'—C3'7.03 (16)
C4—C5—C6—N12.5 (3)O3'—C3'—C4'—O4'48.4 (2)
C4—C5—N7—C80.1 (3)C2'—C3'—C4'—O4'145.60 (17)
C6—C5—N7—C8178.9 (3)O3'—C3'—C4'—C5'75.4 (2)
C5—N7—C8—N90.5 (3)C2'—C3'—C4'—C5'21.7 (2)
N3—C4—N9—C8179.9 (2)O5'—C5'—C4'—O4'156.69 (19)
C5—C4—N9—C80.9 (2)C6'—C5'—C4'—O4'86.5 (2)
N3—C4—N9—C2'7.9 (4)O5'—C5'—C4'—C3'33.3 (2)
C5—C4—N9—C2'172.8 (2)C6'—C5'—C4'—C3'150.12 (19)
N7—C8—N9—C40.9 (3)N9—C2'—O5'—C5'148.35 (16)
N7—C8—N9—C2'173.6 (2)C3'—C2'—O5'—C5'18.9 (2)
C4—N9—C2'—O5'107.1 (2)C1'—C2'—O5'—C5'75.3 (2)
C8—N9—C2'—O5'63.7 (2)C6'—C5'—O5'—C2'155.3 (2)
C4—N9—C2'—C3'130.6 (2)C4'—C5'—O5'—C2'33.1 (2)
C8—N9—C2'—C3'58.6 (3)O5'—C5'—C6'—O6'60.5 (3)
C4—N9—C2'—C1'27.4 (3)C4'—C5'—C6'—O6'176.28 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H61···O3i0.872.092.932 (3)166
N6—H62···O4ii0.872.223.043 (2)159
O4—H4O···O6iii0.911.752.633 (3)162
O6—H6O···N1iv0.911.872.782 (3)175
Symmetry codes: (i) x+1, y+1/2, z+1; (ii) x+1, y, z+1; (iii) x+1, y1/2, z; (iv) x+2, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC11H13N5O4
Mr279.26
Crystal system, space groupMonoclinic, P21
Temperature (K)293
a, b, c (Å)5.4154 (5), 9.8941 (8), 11.4431 (12)
β (°) 94.970 (14)
V3)610.82 (10)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.35 × 0.22 × 0.08
Data collection
DiffractometerBruker P4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
2053, 1878, 1686
Rint0.023
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.041, 0.109, 1.04
No. of reflections1878
No. of parameters186
No. of restraints5
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.24, 0.23
Absolute structureBased on known absolute configuration of the chemical entity
Absolute structure parameter0.7 (13)

Computer programs: XSCANS (Siemens, 1996), SHELXTL (Sheldrick, 1997), SHELXTL.

Selected geometric parameters (Å, º) top
N9—C2'1.438 (2)C2'—O5'1.418 (2)
C1'—O3'1.463 (3)C2'—C3'1.533 (3)
C1'—C2'1.535 (3)C3'—O3'1.451 (3)
O4'—C4'1.409 (2)C5'—O5'1.450 (2)
C8—N9—C2'122.95 (17)O3'—C3'—C4'111.13 (16)
O5'—C2'—N9106.95 (17)O3'—C3'—C2'90.96 (15)
N9—C2'—C3'119.45 (16)C3'—O3'—C1'91.80 (15)
O5'—C2'—C1'116.03 (16)O5'—C5'—C4'104.89 (16)
N9—C2'—C1'119.60 (17)C3'—C4'—C5'102.24 (15)
C3'—C2'—C1'86.02 (16)C2'—O5'—C5'108.25 (15)
C2—N3—C4—N9176.7 (2)C3'—C2'—O5'—C5'18.9 (2)
N7—C5—C6—N62.2 (4)C1'—C2'—O5'—C5'75.3 (2)
N3—C4—N9—C8179.9 (2)C6'—C5'—O5'—C2'155.3 (2)
C4—N9—C2'—O5'107.1 (2)C4'—C5'—O5'—C2'33.1 (2)
N9—C2'—O5'—C5'148.35 (16)C4'—C5'—C6'—O6'176.28 (19)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H61···O3'i0.872.092.932 (3)165.7
N6—H62···O4'ii0.872.223.043 (2)158.8
O4'—H4'O···O6'iii0.911.752.633 (3)162.2
O6'—H6'O···N1iv0.911.872.782 (3)174.9
Symmetry codes: (i) x+1, y+1/2, z+1; (ii) x+1, y, z+1; (iii) x+1, y1/2, z; (iv) x+2, y+1/2, z+1.
 

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