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Hydrated sodium cytidine-5'-monophosphate, 2Na+·C9H12N3O8P2-·6.5H2O, crystallizes in the monoclinic space group P21. The asymmetric unit contains two independent anions, four cations and 13 water mol­ecules. Both mol­ecules have approximately identical conformations.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801016786/cv6066sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536801016786/cv6066Isup2.hkl
Contains datablock I

CCDC reference: 156696

Key indicators

  • Single-crystal X-ray study
  • T = 173 K
  • Mean [sigma](C-C) = 0.015 Å
  • H-atom completeness 49%
  • Disorder in solvent or counterion
  • R factor = 0.061
  • wR factor = 0.186
  • Data-to-parameter ratio = 7.1

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
PLAT_302 Alert C Anion/Solvent Disorder ....................... 18.00 Perc. General Notes
FORMU_01 There is a discrepancy between the atom counts in the _chemical_formula_sum and _chemical_formula_moiety. This is usually due to the moiety formula being in the wrong format. Atom count from _chemical_formula_sum: C9 H25 N3 Na2 O14.5 P1 Atom count from _chemical_formula_moiety:C9 H43 N3 Na2 O14.5 P1 FORMU_01 There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data. Atom count from _chemical_formula_sum:C9 H25 N3 Na2 O14.5 P1 Atom count from the _atom_site data: C9 H12 N3 Na2 O14.5 P1 CELLZ_01 From the CIF: _cell_formula_units_Z 4 From the CIF: _chemical_formula_sum C9 H25 N3 Na2 O14.50 P TEST: Compare cell contents of formula and atom_site data atom Z*formula cif sites diff C 36.00 36.00 0.00 H 100.00 48.00 52.00 N 12.00 12.00 0.00 Na 8.00 8.00 0.00 O 58.00 58.00 0.00 P 4.00 4.00 0.00 Difference between formula and atom_site contents detected. WARNING: H atoms missing from atom site list. Is this intentional? CHEMW_03 From the CIF: _cell_formula_units_Z 4 From the CIF: _chemical_formula_weight 484.27 TEST: Calculate formula weight from _atom_site_* atom mass num sum C 12.01 9.00 108.10 H 1.01 12.00 12.10 N 14.01 3.00 42.02 O 16.00 14.50 231.99 Na 22.99 2.00 45.98 P 30.97 1.00 30.97 Calculated formula weight 471.16 The ratio of given/expected molecular weight as calculated from the _atom_site* data lies outside the range 0.99 <> 1.01 REFLT_03 From the CIF: _diffrn_reflns_theta_max 24.98 From the CIF: _reflns_number_total 3756 Count of symmetry unique reflns 3787 Completeness (_total/calc) 99.18% 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 yes WARNING: Large fraction of Friedel related reflns may be needed to determine absolute structure
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check

Comment top

Cytidine 5'-monophosphate (5'-CMP) is one of the four common ribonucleotides which make up ribonucleic acids (RNA's). The crystal structure of the sodium salt of cytidine 5'-monophosphate 6.5 hydrate provides valuable information on the interaction mechanisms of alkaline metal ions with water and nucleotides.

Previous studies have been done on the barium salt of cytidine 5'-monophosphate 8.5 hydrate (Hogle et al., 1980), and some information on the crystal data of disodium cytidine 5'-monophosphate were indicated by these authors. Nevertheless, the molecular structure and conformational parameters have not been published yet to our knowledge. Nishimura et al. (1986), indicated that the crystal structure of this salt was not solved. Difficulties in growing single crystals of this mononucleotide would be the reason. Despite these difficulties, single crystals have been obtained and the corresponding crystal structure has been determined in this work.

The two independent molecules of 5'-CMP show similar conformation. The sugar puckers (Saenger, 1984; Landolt-Bornstein, 1989), are C2'-en (2T1) in which the C2 and C11 atoms are displaced by 0.559 (11) and -0.576 (10) Å, respectively, from the least-squares planes of the ribose rings. The cytosine rings are nearly planar, the deviations of the ring atoms defining the least-squares planes from the corresponding least-squares planes are less than 0.025 Å. The torsion angles χ [O7—C1—N1—-C6 = -125.1 (10) and O15—C10—N4–C15 = -130.2 (9)] about the glycosyl C1—N1 and C10—N4 linkages adopt values corresponding to an anti conformation, and the orientations γ [O4—C5—C4—C3 = 48.9 (12) and O12—C14—C13—C12 = 47.6 (12)] about the exocyclic C5—C4 and C14—C13 bonds are +sc (gauche, gauche). These orientations are similar to the ones observed in the barium salt of 5'-CMP (Hogle et al., 1980). The ribose pseudo-rotation phase angles are P = 161.5 (11) (2T1) and 157.1 (9)° (2T1) and the degree of pucker τm = 36.9 (6) and 38.2 (6)°, respectively.

The nucleotides are bridged via the phosphate groups forming chains running along the [101] direction. The undisordered NaO6 polyhedra bridge parallel chains via the phosphate groups. This packing leaves channels in the structure along b which are filled with the disordered Na ions coordinated by water molecules.

Three of the Na+ ions are coordinated to six ligands forming distorted octahedra, while in the case of disodium guanosine 5'- phosphate heptahydrate (Barnes & Hankinson, 1982), only two octahedra are distorted and two are fairly regular. The forth Na+ ion is penta-coordinated with two waters, O9 of the phosphate group, and with the cytidine base through atoms N2 and O8. Besides the O8, N2 and N5 atoms of the cytidine bases and the O5, O13 and O14 atoms of the ribose rings, the oxygen atoms O1 and O9 of the phosphate group are involved in the Na+ coordination. A similar situation with the O atoms of the phosphate group taking part in the Na+ coordination was observed in disodium guanosine 5'-monophosphate heptahydrate (Kattl et al., 1981). In the present hydrated crystal structure, the Na+ ions are either partly or completely surrounded by water-O atoms. They also show strong affinity for the negatively charged phosphate groups. The Na2+ ion is surrounded by six water-O atoms and was found to be disordered over two sites together with the O30 water atom.

The O—H groups of the ribose rings form intermolecular H-bonds with three oxygen atoms of the phosphate groups, while one O—H ribose group is H-bonded to one water molecule. Atom N6 of the cytidine base is connected by hydrogen bonding to the positionally disordered water molecule. There are two intramolecular hydrogen bonds which connect ribose atoms C1 and C10 with the oxygen atoms O8 and O16 which are attached to the cytidine bases. One ribose ring is stabilized by an intramolecular hydrogen bond between its O—H groups. Details of the hydrogen-bonding system is given in Table 2.

Experimental top

The disodium salt of cytidine 5'-monophosphate hexahydrate purchased from Sigma Chemical was crystallized by slow evaporation from a water–methanol solution using three recrystallization processes.

Refinement top

The H atoms of the nucleotide molecules and H atoms belonging to three water molecules were fixed at ideal positions and refined isotropically. The disordered atoms Na2 and O29 were split into Na5 and O30 and refined isotropically.

Computing details top

Data collection: CAD-4-PC Software (Enraf-Nonius, 1992); cell refinement: CAD-4-PC Software; data reduction: CAD-4-PC Software; program(s) used to solve structure: SHELXTL97 (Sheldrick, 1997) and SIR97 (Altomare et al., 1997); program(s) used to refine structure: SHELXTL97; molecular graphics: DIAMOND (Pennington, 1999); software used to prepare material for publication: SHELXTL97 and PLATON (Spek, 1999).

Figures top
[Figure 1] Fig. 1. Molecular structure showing 50% probability displacement ellipsoids. H atoms are omitted for clarity.
[Figure 2] Fig. 2. Packing diagram viewed down the b axis. Note the alternate nucleotide and solvent layers and the channels in the structure which are formed along the b direction.
Hydrated sodium cytidine-5'-monophosphate top
Crystal data top
2Na+·C9H4N3O8P2·6.5H6OF(000) = 1012
Mr = 484.27Dx = 1.600 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71070 Å
a = 14.042 (2) ÅCell parameters from 25 reflections
b = 8.924 (2) Åθ = 13–26°
c = 16.091 (3) ŵ = 0.26 mm1
β = 94.410 (2)°T = 173 K
V = 2010.4 (7) Å3Prism, colourless
Z = 40.35 × 0.35 × 0.30 mm
Data collection top
Enraf-Nonius CAD-4
diffractometer
Rint = 0.094
Radiation source: fine-focus sealed tubeθmax = 25.0°, θmin = 1.5°
Graphite monochromatorh = 1616
ω/2θ scansk = 010
3930 measured reflectionsl = 019
3756 independent reflections2 standard reflections every 60 min
2202 reflections with I > 2σ(I) intensity decay: 2%
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)] = 0.061 w = 1/[σ2(Fo2) + (0.1092P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.186(Δ/σ)max < 0.001
S = 1.05Δρmax = 0.53 e Å3
3756 reflectionsΔρmin = 0.41 e Å3
531 parametersExtinction correction: SHELXTL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.016 (3)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.1 (3)
Crystal data top
2Na+·C9H4N3O8P2·6.5H6OV = 2010.4 (7) Å3
Mr = 484.27Z = 4
Monoclinic, P21Mo Kα radiation
a = 14.042 (2) ŵ = 0.26 mm1
b = 8.924 (2) ÅT = 173 K
c = 16.091 (3) Å0.35 × 0.35 × 0.30 mm
β = 94.410 (2)°
Data collection top
Enraf-Nonius CAD-4
diffractometer
Rint = 0.094
3930 measured reflections2 standard reflections every 60 min
3756 independent reflections intensity decay: 2%
2202 reflections with I > 2σ(I)
Refinement top
R[F2 > 2σ(F2)] = 0.061H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.186Δρmax = 0.53 e Å3
S = 1.05Δρmin = 0.41 e Å3
3756 reflectionsAbsolute structure: Flack (1983)
531 parametersAbsolute structure parameter: 0.1 (3)
1 restraint
Special details top

Geometry. Least-square planes and deviations from them calculated using PLATON software (Speck, 1999)

PLANE NUMBER 1 - CYTIDINE BASE ===============

MOLECULE 1

EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S -0.428 (2) 0.8659 (14) -0.259 (4) -1.67 (2)

ATOM DIST(A) N1 DEFINING -0.013 (9) C9 DEFINING -0.009 (12) C8 DEFINING 0.022 (12) C7 DEFINING 0.010 (10) N3 DEFINING -0.027 (9) N2 DEFINING 0.023 (9) C6 DEFINING -0.005 (12) O8 DEFINING -0.001 (9) C1 NON-DEFINING -0.087 (11)

MOLECULE 2

EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S 0.185 (3) 0.8716 (14) 0.454 (2) 7.37 (5)

ATOM DIST(A) N4 DEFINING 0.041 (9) C18 DEFINING -0.011 (11) C17 DEFINING -0.011 (11) C16 DEFINING -0.028 (11) N6 DEFINING 0.039 (9) N5 DEFINING -0.019 (9) C15 DEFINING -0.018 (11) O16 DEFINING 0.007 (9) C10 NON-DEFINING 0.168 (11)

PLANE NUMBER 2 - RIBOSE RINGS ===============

MOLECULE 1

EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S 0.607 (5) 0.587 (6) -0.536 (5) -2.021 (13)

ATOM DIST(A) O7 DEFINING 0.001 (7) C1 DEFINING 0.000 (10) C3 DEFINING 0.000 (10) C4 DEFINING -0.001 (10) C2 NON-DEFINING 0.559 (11)

MOLECULE 2

EQUATION OF PLANE AS PX+QY+RZ=S, XYZ IN FRACTIONAL UNITS P Q R S 0.665 (4) 0.609 (6) -0.432 (5) 3.44 (6)

ATOM DIST(A) O15 DEFINING -0.016 (7) C10 DEFINING 0.010 (11) C12 DEFINING -0.010 (10) C13 DEFINING -0.016 (10) C11 NON-DEFINING -0.576 (11)

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*/UeqOcc. (<1)
P10.16968 (18)0.0823 (3)0.06490 (16)0.0229 (6)
P20.39336 (18)0.1952 (3)0.63987 (15)0.0198 (6)
Na10.0835 (3)0.0826 (6)0.2672 (3)0.0423 (12)
Na20.4120 (7)0.3703 (14)0.0182 (6)0.048 (3)*0.50
Na30.1728 (3)0.1896 (9)0.5255 (3)0.0670 (19)
Na40.2335 (3)0.3538 (5)0.3429 (3)0.0396 (12)
Na50.4356 (7)0.2826 (15)0.0085 (6)0.054 (3)*0.50
O10.0873 (5)0.1337 (8)0.1248 (4)0.0286 (18)
O20.1901 (5)0.0816 (8)0.0701 (5)0.0314 (18)
O30.2581 (5)0.1764 (9)0.0737 (4)0.0292 (18)
O40.1371 (5)0.1059 (9)0.0279 (4)0.0312 (18)
O50.0680 (5)0.0977 (9)0.1924 (5)0.036 (2)
H50.12270.06370.17850.053*
O60.1200 (5)0.1802 (10)0.1454 (5)0.044 (2)
H60.14220.25440.11820.066*
O70.1006 (5)0.2005 (9)0.1957 (4)0.0313 (18)
O80.0725 (5)0.0252 (11)0.3942 (5)0.042 (2)
O90.3346 (5)0.2469 (9)0.5628 (4)0.0317 (19)
O100.3747 (5)0.2880 (9)0.7162 (4)0.0298 (18)
O110.3837 (5)0.0294 (8)0.6580 (4)0.0281 (18)
O120.5036 (5)0.2166 (8)0.6217 (5)0.0293 (18)
O130.7240 (5)0.0249 (8)0.4688 (5)0.0317 (18)
H13A0.73770.07810.47890.038*
O140.6850 (5)0.3037 (10)0.4262 (4)0.037 (2)
H140.68980.40890.41840.044*
O150.7016 (5)0.3083 (8)0.6201 (4)0.0264 (16)
O160.9300 (5)0.0809 (11)0.6144 (4)0.039 (2)
O170.2537 (5)0.1368 (10)0.2495 (4)0.039 (2)
O180.1935 (5)0.5996 (10)0.2992 (5)0.046 (2)
O190.0759 (5)0.2665 (11)0.3748 (5)0.046 (2)
O200.3957 (7)0.4302 (10)0.2318 (6)0.063 (3)
O210.3753 (5)0.1765 (11)0.1244 (5)0.044 (2)
O220.4998 (5)0.1758 (10)0.7342 (5)0.042 (2)
O230.2795 (7)0.5301 (11)0.0977 (6)0.065 (3)
O240.1118 (6)0.1267 (12)0.6513 (6)0.056 (3)
O250.5326 (7)0.0222 (13)0.8897 (6)0.063 (3)
O260.4106 (7)0.2112 (16)0.0395 (7)0.088 (4)
O270.4537 (10)0.072 (2)0.0972 (8)0.113 (5)
O280.0438 (6)0.3623 (12)0.5052 (5)0.057 (3)
O290.2885 (13)0.247 (3)0.0494 (12)0.056 (5)*0.50
O300.2644 (12)0.311 (2)0.0210 (11)0.048 (5)*0.50
N10.1389 (6)0.0166 (11)0.2694 (5)0.026 (2)
N20.2150 (6)0.1356 (11)0.3870 (5)0.030 (2)
N30.3610 (6)0.2396 (11)0.3805 (5)0.033 (2)
H3A0.41070.26420.35330.040*
H3B0.36010.26180.43380.040*
N40.7813 (5)0.0935 (11)0.6599 (5)0.024 (2)
N50.9086 (6)0.0274 (11)0.7379 (5)0.029 (2)
N60.8829 (6)0.1274 (11)0.8657 (5)0.030 (2)
H6A0.84490.15070.90470.036*
H6B0.94430.14820.87280.036*
C10.0603 (7)0.0722 (13)0.2309 (6)0.026 (2)
H10.01770.10420.27470.031*
C20.0006 (8)0.0061 (14)0.1604 (6)0.030 (3)
H20.04290.06730.12650.036*
C30.0375 (7)0.1284 (13)0.1101 (6)0.028 (3)
H30.05190.10110.05010.034*
C40.0429 (7)0.2419 (13)0.1200 (6)0.027 (2)
H40.01460.34310.12850.032*
C50.1067 (8)0.2517 (15)0.0498 (7)0.037 (3)
H5A0.16300.31440.06670.044*
H5B0.07180.29940.00090.044*
C60.1405 (7)0.0579 (14)0.3526 (6)0.027 (3)
C70.2890 (7)0.1704 (12)0.3421 (6)0.026 (2)
C80.2888 (8)0.1321 (14)0.2578 (6)0.031 (3)
H80.33980.16020.22540.037*
C90.2141 (7)0.0546 (14)0.2248 (6)0.028 (3)
H90.21310.02460.16810.034*
C100.7490 (7)0.1859 (13)0.5880 (6)0.022 (2)
H100.80540.22170.55920.027*
C110.6787 (7)0.1107 (13)0.5261 (6)0.024 (2)
H110.63320.04750.55580.028*
C120.6279 (7)0.2492 (12)0.4889 (6)0.023 (2)
H120.56170.22490.46550.028*
C130.6269 (6)0.3559 (13)0.5593 (6)0.023 (2)
H130.64280.45810.53900.028*
C140.5355 (7)0.3652 (13)0.6035 (7)0.029 (3)
H14A0.54710.42280.65590.035*
H14B0.48570.41770.56760.035*
C150.8771 (7)0.0448 (13)0.6700 (7)0.029 (3)
C160.8475 (7)0.0606 (13)0.7956 (6)0.026 (2)
C170.7488 (7)0.0167 (13)0.7859 (6)0.027 (3)
H170.70630.03870.82740.032*
C180.7201 (7)0.0548 (13)0.7177 (6)0.027 (2)
H180.65450.08040.70820.032*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
P10.0229 (13)0.0223 (15)0.0238 (14)0.0026 (13)0.0027 (11)0.0012 (13)
P20.0233 (13)0.0162 (14)0.0205 (13)0.0012 (12)0.0061 (10)0.0010 (12)
Na10.034 (2)0.051 (3)0.043 (3)0.012 (2)0.0094 (19)0.005 (3)
Na30.034 (3)0.129 (6)0.039 (3)0.001 (4)0.007 (2)0.007 (4)
Na40.042 (3)0.031 (3)0.048 (3)0.001 (2)0.018 (2)0.000 (2)
O10.023 (4)0.027 (5)0.035 (4)0.002 (3)0.002 (3)0.003 (3)
O20.035 (4)0.018 (4)0.042 (5)0.001 (4)0.008 (3)0.009 (4)
O30.018 (3)0.033 (5)0.037 (4)0.003 (3)0.000 (3)0.001 (4)
O40.039 (4)0.022 (5)0.034 (4)0.013 (4)0.011 (3)0.002 (3)
O50.031 (4)0.034 (5)0.042 (4)0.012 (4)0.006 (3)0.009 (4)
O60.033 (4)0.038 (5)0.063 (5)0.022 (4)0.022 (4)0.027 (4)
O70.035 (4)0.030 (5)0.028 (4)0.007 (4)0.006 (3)0.007 (4)
O80.033 (4)0.064 (6)0.028 (4)0.011 (4)0.007 (4)0.006 (4)
O90.029 (4)0.039 (5)0.027 (4)0.006 (4)0.003 (3)0.002 (4)
O100.031 (4)0.026 (5)0.033 (4)0.009 (4)0.005 (3)0.003 (4)
O110.033 (4)0.021 (4)0.031 (4)0.003 (3)0.006 (3)0.004 (3)
O120.021 (3)0.018 (4)0.051 (4)0.003 (3)0.016 (3)0.004 (4)
O130.035 (4)0.013 (4)0.048 (5)0.000 (3)0.012 (4)0.000 (4)
O140.049 (5)0.037 (5)0.026 (4)0.003 (4)0.014 (3)0.012 (4)
O150.030 (4)0.019 (4)0.030 (4)0.002 (3)0.001 (3)0.001 (3)
O160.023 (4)0.065 (7)0.031 (4)0.011 (4)0.008 (3)0.012 (4)
O170.029 (4)0.049 (5)0.039 (4)0.005 (4)0.010 (3)0.003 (4)
O180.038 (4)0.042 (6)0.059 (5)0.007 (4)0.011 (4)0.011 (5)
O190.038 (5)0.049 (6)0.051 (5)0.002 (4)0.004 (4)0.002 (4)
O200.073 (7)0.029 (6)0.090 (7)0.017 (5)0.037 (6)0.013 (5)
O210.036 (4)0.053 (6)0.041 (4)0.000 (4)0.002 (3)0.003 (5)
O220.037 (4)0.050 (6)0.041 (4)0.018 (4)0.007 (4)0.010 (4)
O230.081 (7)0.038 (6)0.078 (7)0.003 (5)0.026 (6)0.012 (5)
O240.053 (5)0.059 (7)0.058 (5)0.013 (5)0.011 (5)0.008 (5)
O250.052 (6)0.077 (8)0.058 (6)0.022 (5)0.003 (5)0.001 (6)
O260.061 (7)0.098 (10)0.099 (9)0.001 (7)0.023 (6)0.016 (8)
O270.118 (11)0.137 (15)0.085 (9)0.021 (10)0.000 (8)0.008 (9)
O280.059 (5)0.056 (7)0.057 (6)0.002 (5)0.009 (5)0.010 (5)
N10.026 (5)0.029 (6)0.024 (5)0.009 (4)0.001 (4)0.005 (4)
N20.023 (5)0.038 (6)0.029 (5)0.006 (4)0.000 (4)0.003 (4)
N30.028 (5)0.040 (7)0.032 (5)0.001 (5)0.004 (4)0.004 (5)
N40.020 (4)0.028 (5)0.024 (4)0.004 (4)0.001 (4)0.004 (4)
N50.027 (5)0.038 (6)0.021 (5)0.002 (4)0.006 (4)0.006 (4)
N60.030 (5)0.032 (6)0.028 (5)0.004 (4)0.000 (4)0.008 (4)
C10.032 (6)0.028 (6)0.018 (5)0.011 (6)0.007 (4)0.000 (5)
C20.033 (6)0.028 (7)0.030 (6)0.008 (5)0.005 (5)0.002 (5)
C30.026 (5)0.035 (7)0.024 (5)0.010 (5)0.003 (4)0.001 (5)
C40.029 (6)0.015 (5)0.036 (6)0.010 (5)0.002 (5)0.004 (5)
C50.040 (7)0.039 (8)0.031 (6)0.002 (6)0.007 (5)0.003 (6)
C60.025 (6)0.040 (7)0.016 (5)0.006 (5)0.004 (4)0.005 (5)
C70.016 (5)0.018 (6)0.042 (6)0.002 (5)0.001 (5)0.002 (5)
C80.033 (6)0.033 (7)0.026 (6)0.011 (6)0.002 (5)0.003 (5)
C90.029 (5)0.034 (7)0.021 (5)0.002 (5)0.004 (4)0.006 (5)
C100.017 (5)0.028 (6)0.021 (5)0.001 (5)0.004 (4)0.003 (5)
C110.031 (6)0.019 (6)0.023 (5)0.008 (5)0.012 (4)0.000 (5)
C120.020 (5)0.026 (6)0.024 (5)0.004 (5)0.006 (4)0.006 (5)
C130.021 (5)0.027 (6)0.020 (5)0.004 (5)0.004 (4)0.007 (5)
C140.023 (5)0.022 (6)0.044 (7)0.003 (5)0.010 (5)0.000 (5)
C150.020 (5)0.032 (7)0.033 (6)0.003 (5)0.006 (5)0.004 (6)
C160.023 (5)0.027 (7)0.029 (6)0.007 (5)0.008 (4)0.005 (5)
C170.027 (6)0.030 (7)0.026 (6)0.007 (5)0.015 (5)0.006 (5)
C180.020 (5)0.033 (6)0.028 (5)0.001 (5)0.004 (4)0.009 (5)
Geometric parameters (Å, º) top
P1—O21.494 (8)O15—C101.399 (13)
P1—O31.515 (7)O15—C131.442 (11)
P1—O11.518 (7)O16—C151.247 (12)
P1—O41.609 (7)O24—Na1vi2.334 (11)
P1—Na13.385 (5)O25—Na2vii2.357 (14)
P2—O91.507 (7)O25—Na5vii2.410 (16)
P2—O111.516 (8)O26—Na5v2.350 (15)
P2—O101.521 (7)O26—Na2v2.643 (15)
P2—O121.609 (7)O27—Na2v2.966 (19)
Na1—O12.334 (8)O29—O300.79 (2)
Na1—O24i2.334 (11)N1—C91.364 (13)
Na1—O192.381 (10)N1—C61.388 (13)
Na1—O172.434 (8)N1—C11.457 (13)
Na1—N5ii2.512 (10)N2—C61.337 (14)
Na1—Na43.489 (6)N2—C71.346 (13)
Na2—Na50.940 (13)N3—C71.300 (13)
Na2—O302.27 (2)N3—H3B0.8800
Na2—O25iii2.357 (14)N3—H3A0.8800
Na2—O292.38 (2)N4—C181.358 (12)
Na2—O212.458 (13)N4—C151.412 (12)
Na2—O232.602 (15)N4—C101.464 (13)
Na2—O26iv2.643 (15)N5—C151.316 (13)
Na2—O27iv2.966 (19)N5—C161.345 (13)
Na3—O242.326 (10)N5—Na1viii2.512 (10)
Na3—O92.361 (9)N6—C161.337 (13)
Na3—O282.382 (11)N6—H6B0.8800
Na3—N22.400 (10)N6—H6A0.8800
Na3—O82.855 (10)C1—C21.528 (15)
Na3—C63.022 (11)C1—H11.0000
Na4—O14v2.306 (9)C2—C31.521 (16)
Na4—O192.364 (9)C2—H21.0000
Na4—O182.384 (10)C3—C41.516 (15)
Na4—O13v2.413 (9)C3—H31.0000
Na4—O172.455 (9)C4—C51.498 (15)
Na4—O202.868 (12)C4—H41.0000
Na5—O292.24 (2)C5—H5A0.9900
Na5—O26iv2.350 (15)C5—H5B0.9900
Na5—O272.36 (2)C7—C81.399 (14)
Na5—O25iii2.410 (16)C8—C91.333 (15)
Na5—O212.430 (13)C8—H80.9500
Na5—O302.44 (2)C9—H90.9500
O4—C51.422 (15)C10—C111.505 (14)
O5—C21.392 (13)C10—H101.0000
O5—H50.8400C11—C121.527 (15)
O6—C31.407 (12)C11—H111.0000
O6—H60.8400C12—C131.481 (15)
O7—C11.415 (13)C12—H121.0000
O7—C41.457 (11)C13—C141.516 (14)
O8—C61.242 (12)C13—H131.0000
O12—C141.437 (13)C14—H14A0.9900
O13—C111.389 (12)C14—H14B0.9900
O13—Na4iv2.413 (9)C16—C171.437 (14)
O13—H13A0.9500C17—C181.307 (15)
O14—C121.422 (11)C17—H170.9500
O14—Na4iv2.306 (9)C18—H180.9500
O14—H140.9500
O2—P1—O3112.0 (4)P2—O9—Na3126.7 (4)
O2—P1—O1113.6 (4)C14—O12—P2117.8 (6)
O3—P1—O1111.3 (4)C11—O13—Na4iv117.7 (6)
O2—P1—O4104.4 (4)C11—O13—H13A121.1
O3—P1—O4107.9 (4)Na4iv—O13—H13A121.1
O1—P1—O4107.0 (4)C12—O14—Na4iv122.4 (7)
O2—P1—Na190.2 (3)C12—O14—H14118.8
O3—P1—Na198.3 (3)Na4iv—O14—H14118.8
O1—P1—Na136.0 (3)C10—O15—C13108.8 (7)
O4—P1—Na1141.9 (3)Na1—O17—Na491.1 (3)
O9—P2—O11113.9 (4)Na4—O19—Na194.6 (3)
O9—P2—O10112.3 (4)Na5—O21—Na222.2 (3)
O11—P2—O10110.6 (4)Na3—O24—Na1vi140.5 (5)
O9—P2—O12106.7 (4)Na2vii—O25—Na5vii22.7 (3)
O11—P2—O12104.6 (4)Na5v—O26—Na2v20.7 (3)
O10—P2—O12108.0 (4)Na5—O27—Na2v105.5 (6)
O1—Na1—O24i135.7 (4)O30—O29—Na595 (2)
O1—Na1—O19125.1 (4)O30—O29—Na272 (2)
O24i—Na1—O1998.2 (3)Na5—O29—Na223.2 (4)
O1—Na1—O1784.1 (3)O29—O30—Na288 (2)
O24i—Na1—O1791.0 (3)O29—O30—Na566 (2)
O19—Na1—O1786.4 (3)Na2—O30—Na522.7 (4)
O1—Na1—N5ii87.4 (3)C9—N1—C6119.0 (9)
O24i—Na1—N5ii94.1 (4)C9—N1—C1120.3 (9)
O19—Na1—N5ii99.8 (3)C6—N1—C1120.7 (8)
O17—Na1—N5ii171.4 (3)C6—N2—C7120.6 (9)
O1—Na1—P122.47 (18)C6—N2—Na3104.3 (6)
O24i—Na1—P1118.4 (3)C7—N2—Na3135.0 (7)
O19—Na1—P1133.8 (3)C7—N3—H3B120.0
O17—Na1—P167.2 (2)C7—N3—H3A120.0
N5ii—Na1—P1104.2 (2)H3B—N3—H3A120.0
O1—Na1—Na4103.8 (2)C18—N4—C15119.4 (9)
O24i—Na1—Na4103.0 (3)C18—N4—C10120.7 (8)
O19—Na1—Na442.5 (2)C15—N4—C10119.9 (8)
O17—Na1—Na444.7 (2)C15—N5—C16119.3 (9)
N5ii—Na1—Na4140.0 (3)C15—N5—Na1viii109.6 (7)
P1—Na1—Na498.95 (15)C16—N5—Na1viii131.1 (7)
Na5—Na2—O3088.7 (11)C16—N6—H6B120.0
Na5—Na2—O25iii81.8 (10)C16—N6—H6A120.0
O30—Na2—O25iii95.6 (6)H6B—N6—H6A120.0
Na5—Na2—O2969.6 (11)O7—C1—N1107.2 (8)
O30—Na2—O2919.3 (6)O7—C1—C2106.6 (8)
O25iii—Na2—O2989.4 (6)N1—C1—C2114.9 (9)
Na5—Na2—O2177.3 (10)O7—C1—H1109.3
O30—Na2—O2183.3 (6)N1—C1—H1109.3
O25iii—Na2—O21159.1 (7)C2—C1—H1109.3
O29—Na2—O2182.6 (6)O5—C2—C3115.8 (9)
Na5—Na2—O23153.4 (11)O5—C2—C1110.4 (8)
O30—Na2—O2368.4 (6)C3—C2—C1100.6 (10)
O25iii—Na2—O23112.6 (6)O5—C2—H2109.8
O29—Na2—O2387.7 (6)C3—C2—H2109.8
O21—Na2—O2386.6 (4)C1—C2—H2109.8
Na5—Na2—O26iv61.8 (10)O6—C3—C4111.5 (9)
O30—Na2—O26iv149.3 (8)O6—C3—C2108.1 (9)
O25iii—Na2—O26iv88.6 (5)C4—C3—C2104.1 (8)
O29—Na2—O26iv131.2 (8)O6—C3—H3111.0
O21—Na2—O26iv82.3 (5)C4—C3—H3111.0
O23—Na2—O26iv137.1 (6)C2—C3—H3111.0
Na5—Na2—O27iv119.2 (11)O7—C4—C5108.6 (8)
O30—Na2—O27iv152.0 (8)O7—C4—C3106.3 (8)
O25iii—Na2—O27iv87.2 (5)C5—C4—C3116.3 (9)
O29—Na2—O27iv169.9 (8)O7—C4—H4108.5
O21—Na2—O27iv103.7 (5)C5—C4—H4108.5
O23—Na2—O27iv84.8 (5)C3—C4—H4108.5
O26iv—Na2—O27iv58.3 (5)O4—C5—C4110.0 (10)
O24—Na3—O9104.0 (3)O4—C5—H5A109.7
O24—Na3—O2887.1 (4)C4—C5—H5A109.7
O9—Na3—O28127.0 (5)O4—C5—H5B109.7
O24—Na3—N2153.3 (5)C4—C5—H5B109.7
O9—Na3—N288.8 (3)H5A—C5—H5B108.2
O28—Na3—N2104.0 (3)O8—C6—N2120.6 (9)
O24—Na3—O8109.0 (4)O8—C6—N1120.0 (9)
O9—Na3—O8135.2 (3)N2—C6—N1119.4 (9)
O28—Na3—O884.5 (3)O8—C6—Na370.3 (6)
N2—Na3—O849.6 (3)N2—C6—Na350.3 (5)
O24—Na3—C6131.9 (4)N1—C6—Na3169.1 (8)
O9—Na3—C6113.1 (3)N3—C7—N2117.3 (9)
O28—Na3—C693.8 (3)N3—C7—C8121.3 (10)
N2—Na3—C625.4 (3)N2—C7—C8121.3 (9)
O8—Na3—C624.2 (2)C9—C8—C7117.1 (10)
O14v—Na4—O1999.8 (3)C9—C8—H8121.5
O14v—Na4—O18150.6 (3)C7—C8—H8121.5
O19—Na4—O1897.5 (3)C8—C9—N1122.5 (10)
O14v—Na4—O13v67.6 (3)C8—C9—H9118.7
O19—Na4—O13v104.7 (3)N1—C9—H9118.7
O18—Na4—O13v85.0 (3)O15—C10—N4106.0 (7)
O14v—Na4—O1780.6 (3)O15—C10—C11106.6 (7)
O19—Na4—O1786.3 (3)N4—C10—C11114.8 (9)
O18—Na4—O17124.4 (3)O15—C10—H10109.8
O13v—Na4—O17147.6 (3)N4—C10—H10109.8
O14v—Na4—O2095.8 (3)C11—C10—H10109.8
O19—Na4—O20154.0 (3)O13—C11—C10112.0 (8)
O18—Na4—O2077.9 (3)O13—C11—C12114.2 (8)
O13v—Na4—O20100.4 (3)C10—C11—C1299.3 (9)
O17—Na4—O2075.9 (3)O13—C11—H11110.3
O14v—Na4—Na196.9 (3)C10—C11—H11110.3
O19—Na4—Na142.9 (2)C12—C11—H11110.3
O18—Na4—Na1111.9 (2)O14—C12—C13111.2 (9)
O13v—Na4—Na1143.1 (3)O14—C12—C11106.4 (8)
O17—Na4—Na144.23 (19)C13—C12—C11104.6 (8)
O20—Na4—Na1114.8 (2)O14—C12—H12111.4
Na2—Na5—O2987.2 (11)C13—C12—H12111.4
Na2—Na5—O26iv97.5 (11)C11—C12—H12111.4
O29—Na5—O26iv173.0 (9)O15—C13—C12106.3 (8)
Na2—Na5—O27162.9 (12)O15—C13—C14107.2 (8)
O29—Na5—O2776.6 (8)C12—C13—C14116.9 (9)
O26iv—Na5—O2799.1 (6)O15—C13—H13108.7
Na2—Na5—O25iii75.5 (10)C12—C13—H13108.7
O29—Na5—O25iii91.7 (7)C14—C13—H13108.7
O26iv—Na5—O25iii94.6 (5)O12—C14—C13109.5 (9)
O27—Na5—O25iii99.1 (5)O12—C14—H14A109.8
Na2—Na5—O2180.6 (10)C13—C14—H14A109.8
O29—Na5—O2186.4 (6)O12—C14—H14B109.8
O26iv—Na5—O2189.3 (5)C13—C14—H14B109.8
O27—Na5—O21103.7 (6)H14A—C14—H14B108.2
O25iii—Na5—O21156.0 (7)O16—C15—N5122.8 (9)
Na2—Na5—O3068.7 (10)O16—C15—N4116.9 (9)
O29—Na5—O3018.8 (6)N5—C15—N4120.2 (9)
O26iv—Na5—O30163.9 (8)N6—C16—N5117.7 (9)
O27—Na5—O3095.4 (7)N6—C16—C17120.4 (9)
O25iii—Na5—O3090.0 (6)N5—C16—C17121.8 (10)
O21—Na5—O3080.5 (5)C18—C17—C16117.2 (9)
P1—O1—Na1121.5 (4)C18—C17—H17121.4
C5—O4—P1117.5 (7)C16—C17—H17121.4
C2—O5—H5109.5C17—C18—N4121.9 (10)
C3—O6—H6109.5C17—C18—H18119.1
C1—O7—C4109.0 (7)N4—C18—H18119.1
C6—O8—Na385.5 (6)
O7—C1—N1—C6125.1 (10)O15—C10—N4—C15130.2 (9)
C4—O7—C1—C222.6 (10)C13—O15—C10—C1126.0 (10)
O7—C1—C2—C335.2 (10)O15—C10—C11—C1237.0 (9)
C1—C2—C3—C434.0 (10)C10—C11—C12—C1334.2 (9)
C2—C3—C4—O722.2 (10)C11—C12—C13—O1520.7 (10)
C3—C4—O7—C10.1 (13)C12—C13—O15—C103.0 (10)
O4—C5—C4—C348.9 (12)O12—C14—C13—C1247.6 (12)
C5—C4—C3—O6144.8 (9)C14—C13—C12—O14146.9 (9)
P1—O4—C5—C4156.4 (7)P2—O12—C14—C13160.1 (7)
Symmetry codes: (i) x, y, z1; (ii) x1, y, z1; (iii) x+1, y+1/2, z+1; (iv) x+1, y+1/2, z; (v) x+1, y1/2, z; (vi) x, y, z+1; (vii) x+1, y1/2, z+1; (viii) x+1, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O29vii0.882.263.07 (2)153
N6—H6A···O30vii0.882.052.913 (19)169
N3—H3A···O22iii0.882.032.890 (11)166
N3—H3B···O90.882.142.986 (10)161
O5—H5···O60.842.242.678 (12)113
O5—H5···O23ix0.842.493.288 (12)160
O6—H6···O2ix0.841.772.602 (11)175
N6—H6B···O1viii0.882.012.863 (11)163
O13—H13A···O9vii0.951.952.651 (11)128
O14—H14···O11iii0.951.882.573 (11)128
C1—H1···O81.002.322.760 (13)105
C5—H5B···O10.992.532.993 (13)108
C10—H10···O161.002.282.711 (13)105
Symmetry codes: (iii) x+1, y+1/2, z+1; (vii) x+1, y1/2, z+1; (viii) x+1, y, z+1; (ix) x, y1/2, z.

Experimental details

Crystal data
Chemical formula2Na+·C9H4N3O8P2·6.5H6O
Mr484.27
Crystal system, space groupMonoclinic, P21
Temperature (K)173
a, b, c (Å)14.042 (2), 8.924 (2), 16.091 (3)
β (°) 94.410 (2)
V3)2010.4 (7)
Z4
Radiation typeMo Kα
µ (mm1)0.26
Crystal size (mm)0.35 × 0.35 × 0.30
Data collection
DiffractometerEnraf-Nonius CAD-4
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
3930, 3756, 2202
Rint0.094
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.061, 0.186, 1.05
No. of reflections3756
No. of parameters531
No. of restraints1
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.53, 0.41
Absolute structureFlack (1983)
Absolute structure parameter0.1 (3)

Computer programs: CAD-4-PC Software (Enraf-Nonius, 1992), CAD-4-PC Software, SHELXTL97 (Sheldrick, 1997) and SIR97 (Altomare et al., 1997), DIAMOND (Pennington, 1999), SHELXTL97 and PLATON (Spek, 1999).

Selected geometric parameters (Å, º) top
Na3—O242.326 (10)Na4—O172.455 (9)
Na3—O92.361 (9)Na4—O202.868 (12)
Na3—O282.382 (11)Na5—O292.24 (2)
Na3—N22.400 (10)Na5—O26ii2.350 (15)
Na3—O82.855 (10)Na5—O272.36 (2)
Na4—O14i2.306 (9)Na5—O25iii2.410 (16)
Na4—O192.364 (9)Na5—O212.430 (13)
Na4—O182.384 (10)Na5—O302.44 (2)
Na4—O13i2.413 (9)
O7—C1—N1—C6125.1 (10)O15—C10—N4—C15130.2 (9)
C4—O7—C1—C222.6 (10)C13—O15—C10—C1126.0 (10)
O7—C1—C2—C335.2 (10)O15—C10—C11—C1237.0 (9)
C1—C2—C3—C434.0 (10)C10—C11—C12—C1334.2 (9)
C2—C3—C4—O722.2 (10)C11—C12—C13—O1520.7 (10)
C3—C4—O7—C10.1 (13)C12—C13—O15—C103.0 (10)
O4—C5—C4—C348.9 (12)O12—C14—C13—C1247.6 (12)
C5—C4—C3—O6144.8 (9)C14—C13—C12—O14146.9 (9)
P1—O4—C5—C4156.4 (7)P2—O12—C14—C13160.1 (7)
Symmetry codes: (i) x+1, y1/2, z; (ii) x+1, y+1/2, z; (iii) x+1, y+1/2, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···O29iv0.87942.25843.07 (2)153.26
N6—H6A···O30iv0.87942.04552.913 (19)168.63
N3—H3A···O22iii0.87962.02992.890 (11)165.50
N3—H3B···O90.88132.13752.986 (10)161.28
O5—H5···O60.84002.24182.678 (12)112.47
O5—H5···O23v0.84002.48763.288 (12)159.58
O6—H6···O2v0.84041.76452.602 (11)174.65
N6—H6B···O1vi0.88072.00962.863 (11)162.88
O13—H13A···O9iv0.95051.95322.651 (11)128.42
O14—H14···O11iii0.95021.88092.573 (11)127.61
C1—H1···O81.00052.32282.760 (13)105.27
C5—H5B···O10.99062.52842.993 (13)108.44
C10—H10···O161.00022.27812.711 (13)104.77
Symmetry codes: (iii) x+1, y+1/2, z+1; (iv) x+1, y1/2, z+1; (v) x, y1/2, z; (vi) x+1, y, z+1.
 

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