Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536801016786/cv6066sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536801016786/cv6066Isup2.hkl |
CCDC reference: 156696
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.
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.
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).
2Na+·C9H4N3O8P2−·6.5H6O | F(000) = 1012 |
Mr = 484.27 | Dx = 1.600 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71070 Å |
a = 14.042 (2) Å | Cell parameters from 25 reflections |
b = 8.924 (2) Å | θ = 13–26° |
c = 16.091 (3) Å | µ = 0.26 mm−1 |
β = 94.410 (2)° | T = 173 K |
V = 2010.4 (7) Å3 | Prism, colourless |
Z = 4 | 0.35 × 0.35 × 0.30 mm |
Enraf-Nonius CAD-4 diffractometer | Rint = 0.094 |
Radiation source: fine-focus sealed tube | θmax = 25.0°, θmin = 1.5° |
Graphite monochromator | h = −16→16 |
ω/2θ scans | k = 0→10 |
3930 measured reflections | l = 0→19 |
3756 independent reflections | 2 standard reflections every 60 min |
2202 reflections with I > 2σ(I) | intensity decay: 2% |
Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
Least-squares matrix: full | H 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 = 1.05 | Δρmax = 0.53 e Å−3 |
3756 reflections | Δρmin = −0.41 e Å−3 |
531 parameters | Extinction correction: SHELXTL97, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
1 restraint | Extinction coefficient: 0.016 (3) |
Primary atom site location: structure-invariant direct methods | Absolute structure: Flack (1983) |
Secondary atom site location: difference Fourier map | Absolute structure parameter: 0.1 (3) |
2Na+·C9H4N3O8P2−·6.5H6O | V = 2010.4 (7) Å3 |
Mr = 484.27 | Z = 4 |
Monoclinic, P21 | Mo Kα radiation |
a = 14.042 (2) Å | µ = 0.26 mm−1 |
b = 8.924 (2) Å | T = 173 K |
c = 16.091 (3) Å | 0.35 × 0.35 × 0.30 mm |
β = 94.410 (2)° |
Enraf-Nonius CAD-4 diffractometer | Rint = 0.094 |
3930 measured reflections | 2 standard reflections every 60 min |
3756 independent reflections | intensity decay: 2% |
2202 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.061 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.186 | Δρmax = 0.53 e Å−3 |
S = 1.05 | Δρmin = −0.41 e Å−3 |
3756 reflections | Absolute structure: Flack (1983) |
531 parameters | Absolute structure parameter: 0.1 (3) |
1 restraint |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
P1 | 0.16968 (18) | −0.0823 (3) | −0.06490 (16) | 0.0229 (6) | |
P2 | 0.39336 (18) | 0.1952 (3) | 0.63987 (15) | 0.0198 (6) | |
Na1 | 0.0835 (3) | −0.0826 (6) | −0.2672 (3) | 0.0423 (12) | |
Na2 | 0.4120 (7) | 0.3703 (14) | −0.0182 (6) | 0.048 (3)* | 0.50 |
Na3 | 0.1728 (3) | 0.1896 (9) | 0.5255 (3) | 0.0670 (19) | |
Na4 | 0.2335 (3) | −0.3538 (5) | −0.3429 (3) | 0.0396 (12) | |
Na5 | 0.4356 (7) | 0.2826 (15) | 0.0085 (6) | 0.054 (3)* | 0.50 |
O1 | 0.0873 (5) | −0.1337 (8) | −0.1248 (4) | 0.0286 (18) | |
O2 | 0.1901 (5) | 0.0816 (8) | −0.0701 (5) | 0.0314 (18) | |
O3 | 0.2581 (5) | −0.1764 (9) | −0.0737 (4) | 0.0292 (18) | |
O4 | 0.1371 (5) | −0.1059 (9) | 0.0279 (4) | 0.0312 (18) | |
O5 | −0.0680 (5) | 0.0977 (9) | 0.1924 (5) | 0.036 (2) | |
H5 | −0.1227 | 0.0637 | 0.1785 | 0.053* | |
O6 | −0.1200 (5) | −0.1802 (10) | 0.1454 (5) | 0.044 (2) | |
H6 | −0.1422 | −0.2544 | 0.1182 | 0.066* | |
O7 | 0.1006 (5) | −0.2005 (9) | 0.1957 (4) | 0.0313 (18) | |
O8 | 0.0725 (5) | 0.0252 (11) | 0.3942 (5) | 0.042 (2) | |
O9 | 0.3346 (5) | 0.2469 (9) | 0.5628 (4) | 0.0317 (19) | |
O10 | 0.3747 (5) | 0.2880 (9) | 0.7162 (4) | 0.0298 (18) | |
O11 | 0.3837 (5) | 0.0294 (8) | 0.6580 (4) | 0.0281 (18) | |
O12 | 0.5036 (5) | 0.2166 (8) | 0.6217 (5) | 0.0293 (18) | |
O13 | 0.7240 (5) | 0.0249 (8) | 0.4688 (5) | 0.0317 (18) | |
H13A | 0.7377 | −0.0781 | 0.4789 | 0.038* | |
O14 | 0.6850 (5) | 0.3037 (10) | 0.4262 (4) | 0.037 (2) | |
H14 | 0.6898 | 0.4089 | 0.4184 | 0.044* | |
O15 | 0.7016 (5) | 0.3083 (8) | 0.6201 (4) | 0.0264 (16) | |
O16 | 0.9300 (5) | 0.0809 (11) | 0.6144 (4) | 0.039 (2) | |
O17 | 0.2537 (5) | −0.1368 (10) | −0.2495 (4) | 0.039 (2) | |
O18 | 0.1935 (5) | −0.5996 (10) | −0.2992 (5) | 0.046 (2) | |
O19 | 0.0759 (5) | −0.2665 (11) | −0.3748 (5) | 0.046 (2) | |
O20 | 0.3957 (7) | −0.4302 (10) | −0.2318 (6) | 0.063 (3) | |
O21 | 0.3753 (5) | 0.1765 (11) | −0.1244 (5) | 0.044 (2) | |
O22 | 0.4998 (5) | −0.1758 (10) | 0.7342 (5) | 0.042 (2) | |
O23 | 0.2795 (7) | 0.5301 (11) | −0.0977 (6) | 0.065 (3) | |
O24 | 0.1118 (6) | 0.1267 (12) | 0.6513 (6) | 0.056 (3) | |
O25 | 0.5326 (7) | −0.0222 (13) | 0.8897 (6) | 0.063 (3) | |
O26 | 0.4106 (7) | −0.2112 (16) | 0.0395 (7) | 0.088 (4) | |
O27 | 0.4537 (10) | 0.072 (2) | 0.0972 (8) | 0.113 (5) | |
O28 | 0.0438 (6) | 0.3623 (12) | 0.5052 (5) | 0.057 (3) | |
O29 | 0.2885 (13) | 0.247 (3) | 0.0494 (12) | 0.056 (5)* | 0.50 |
O30 | 0.2644 (12) | 0.311 (2) | 0.0210 (11) | 0.048 (5)* | 0.50 |
N1 | 0.1389 (6) | 0.0166 (11) | 0.2694 (5) | 0.026 (2) | |
N2 | 0.2150 (6) | 0.1356 (11) | 0.3870 (5) | 0.030 (2) | |
N3 | 0.3610 (6) | 0.2396 (11) | 0.3805 (5) | 0.033 (2) | |
H3A | 0.4107 | 0.2642 | 0.3533 | 0.040* | |
H3B | 0.3601 | 0.2618 | 0.4338 | 0.040* | |
N4 | 0.7813 (5) | 0.0935 (11) | 0.6599 (5) | 0.024 (2) | |
N5 | 0.9086 (6) | −0.0274 (11) | 0.7379 (5) | 0.029 (2) | |
N6 | 0.8829 (6) | −0.1274 (11) | 0.8657 (5) | 0.030 (2) | |
H6A | 0.8449 | −0.1507 | 0.9047 | 0.036* | |
H6B | 0.9443 | −0.1482 | 0.8728 | 0.036* | |
C1 | 0.0603 (7) | −0.0722 (13) | 0.2309 (6) | 0.026 (2) | |
H1 | 0.0177 | −0.1042 | 0.2747 | 0.031* | |
C2 | 0.0006 (8) | 0.0061 (14) | 0.1604 (6) | 0.030 (3) | |
H2 | 0.0429 | 0.0673 | 0.1265 | 0.036* | |
C3 | −0.0375 (7) | −0.1284 (13) | 0.1101 (6) | 0.028 (3) | |
H3 | −0.0519 | −0.1011 | 0.0501 | 0.034* | |
C4 | 0.0429 (7) | −0.2419 (13) | 0.1200 (6) | 0.027 (2) | |
H4 | 0.0146 | −0.3431 | 0.1285 | 0.032* | |
C5 | 0.1067 (8) | −0.2517 (15) | 0.0498 (7) | 0.037 (3) | |
H5A | 0.1630 | −0.3144 | 0.0667 | 0.044* | |
H5B | 0.0718 | −0.2994 | 0.0009 | 0.044* | |
C6 | 0.1405 (7) | 0.0579 (14) | 0.3526 (6) | 0.027 (3) | |
C7 | 0.2890 (7) | 0.1704 (12) | 0.3421 (6) | 0.026 (2) | |
C8 | 0.2888 (8) | 0.1321 (14) | 0.2578 (6) | 0.031 (3) | |
H8 | 0.3398 | 0.1602 | 0.2254 | 0.037* | |
C9 | 0.2141 (7) | 0.0546 (14) | 0.2248 (6) | 0.028 (3) | |
H9 | 0.2131 | 0.0246 | 0.1681 | 0.034* | |
C10 | 0.7490 (7) | 0.1859 (13) | 0.5880 (6) | 0.022 (2) | |
H10 | 0.8054 | 0.2217 | 0.5592 | 0.027* | |
C11 | 0.6787 (7) | 0.1107 (13) | 0.5261 (6) | 0.024 (2) | |
H11 | 0.6332 | 0.0475 | 0.5558 | 0.028* | |
C12 | 0.6279 (7) | 0.2492 (12) | 0.4889 (6) | 0.023 (2) | |
H12 | 0.5617 | 0.2249 | 0.4655 | 0.028* | |
C13 | 0.6269 (6) | 0.3559 (13) | 0.5593 (6) | 0.023 (2) | |
H13 | 0.6428 | 0.4581 | 0.5390 | 0.028* | |
C14 | 0.5355 (7) | 0.3652 (13) | 0.6035 (7) | 0.029 (3) | |
H14A | 0.5471 | 0.4228 | 0.6559 | 0.035* | |
H14B | 0.4857 | 0.4177 | 0.5676 | 0.035* | |
C15 | 0.8771 (7) | 0.0448 (13) | 0.6700 (7) | 0.029 (3) | |
C16 | 0.8475 (7) | −0.0606 (13) | 0.7956 (6) | 0.026 (2) | |
C17 | 0.7488 (7) | −0.0167 (13) | 0.7859 (6) | 0.027 (3) | |
H17 | 0.7063 | −0.0387 | 0.8274 | 0.032* | |
C18 | 0.7201 (7) | 0.0548 (13) | 0.7177 (6) | 0.027 (2) | |
H18 | 0.6545 | 0.0804 | 0.7082 | 0.032* |
U11 | U22 | U33 | U12 | U13 | U23 | |
P1 | 0.0229 (13) | 0.0223 (15) | 0.0238 (14) | 0.0026 (13) | 0.0027 (11) | 0.0012 (13) |
P2 | 0.0233 (13) | 0.0162 (14) | 0.0205 (13) | −0.0012 (12) | 0.0061 (10) | −0.0010 (12) |
Na1 | 0.034 (2) | 0.051 (3) | 0.043 (3) | 0.012 (2) | 0.0094 (19) | −0.005 (3) |
Na3 | 0.034 (3) | 0.129 (6) | 0.039 (3) | −0.001 (4) | 0.007 (2) | 0.007 (4) |
Na4 | 0.042 (3) | 0.031 (3) | 0.048 (3) | 0.001 (2) | 0.018 (2) | 0.000 (2) |
O1 | 0.023 (4) | 0.027 (5) | 0.035 (4) | 0.002 (3) | −0.002 (3) | 0.003 (3) |
O2 | 0.035 (4) | 0.018 (4) | 0.042 (5) | 0.001 (4) | 0.008 (3) | 0.009 (4) |
O3 | 0.018 (3) | 0.033 (5) | 0.037 (4) | 0.003 (3) | 0.000 (3) | −0.001 (4) |
O4 | 0.039 (4) | 0.022 (5) | 0.034 (4) | −0.013 (4) | 0.011 (3) | −0.002 (3) |
O5 | 0.031 (4) | 0.034 (5) | 0.042 (4) | 0.012 (4) | 0.006 (3) | −0.009 (4) |
O6 | 0.033 (4) | 0.038 (5) | 0.063 (5) | −0.022 (4) | 0.022 (4) | −0.027 (4) |
O7 | 0.035 (4) | 0.030 (5) | 0.028 (4) | 0.007 (4) | −0.006 (3) | −0.007 (4) |
O8 | 0.033 (4) | 0.064 (6) | 0.028 (4) | −0.011 (4) | 0.007 (4) | −0.006 (4) |
O9 | 0.029 (4) | 0.039 (5) | 0.027 (4) | −0.006 (4) | 0.003 (3) | 0.002 (4) |
O10 | 0.031 (4) | 0.026 (5) | 0.033 (4) | 0.009 (4) | 0.005 (3) | −0.003 (4) |
O11 | 0.033 (4) | 0.021 (4) | 0.031 (4) | −0.003 (3) | 0.006 (3) | 0.004 (3) |
O12 | 0.021 (3) | 0.018 (4) | 0.051 (4) | 0.003 (3) | 0.016 (3) | 0.004 (4) |
O13 | 0.035 (4) | 0.013 (4) | 0.048 (5) | 0.000 (3) | 0.012 (4) | 0.000 (4) |
O14 | 0.049 (5) | 0.037 (5) | 0.026 (4) | 0.003 (4) | 0.014 (3) | 0.012 (4) |
O15 | 0.030 (4) | 0.019 (4) | 0.030 (4) | 0.002 (3) | −0.001 (3) | 0.001 (3) |
O16 | 0.023 (4) | 0.065 (7) | 0.031 (4) | 0.011 (4) | 0.008 (3) | 0.012 (4) |
O17 | 0.029 (4) | 0.049 (5) | 0.039 (4) | 0.005 (4) | 0.010 (3) | 0.003 (4) |
O18 | 0.038 (4) | 0.042 (6) | 0.059 (5) | 0.007 (4) | 0.011 (4) | 0.011 (5) |
O19 | 0.038 (5) | 0.049 (6) | 0.051 (5) | −0.002 (4) | 0.004 (4) | 0.002 (4) |
O20 | 0.073 (7) | 0.029 (6) | 0.090 (7) | −0.017 (5) | 0.037 (6) | −0.013 (5) |
O21 | 0.036 (4) | 0.053 (6) | 0.041 (4) | 0.000 (4) | −0.002 (3) | −0.003 (5) |
O22 | 0.037 (4) | 0.050 (6) | 0.041 (4) | 0.018 (4) | 0.007 (4) | 0.010 (4) |
O23 | 0.081 (7) | 0.038 (6) | 0.078 (7) | −0.003 (5) | 0.026 (6) | −0.012 (5) |
O24 | 0.053 (5) | 0.059 (7) | 0.058 (5) | −0.013 (5) | 0.011 (5) | 0.008 (5) |
O25 | 0.052 (6) | 0.077 (8) | 0.058 (6) | 0.022 (5) | −0.003 (5) | −0.001 (6) |
O26 | 0.061 (7) | 0.098 (10) | 0.099 (9) | 0.001 (7) | −0.023 (6) | 0.016 (8) |
O27 | 0.118 (11) | 0.137 (15) | 0.085 (9) | −0.021 (10) | 0.000 (8) | −0.008 (9) |
O28 | 0.059 (5) | 0.056 (7) | 0.057 (6) | 0.002 (5) | 0.009 (5) | −0.010 (5) |
N1 | 0.026 (5) | 0.029 (6) | 0.024 (5) | −0.009 (4) | 0.001 (4) | 0.005 (4) |
N2 | 0.023 (5) | 0.038 (6) | 0.029 (5) | 0.006 (4) | 0.000 (4) | 0.003 (4) |
N3 | 0.028 (5) | 0.040 (7) | 0.032 (5) | −0.001 (5) | 0.004 (4) | −0.004 (5) |
N4 | 0.020 (4) | 0.028 (5) | 0.024 (4) | −0.004 (4) | −0.001 (4) | 0.004 (4) |
N5 | 0.027 (5) | 0.038 (6) | 0.021 (5) | 0.002 (4) | −0.006 (4) | −0.006 (4) |
N6 | 0.030 (5) | 0.032 (6) | 0.028 (5) | 0.004 (4) | 0.000 (4) | 0.008 (4) |
C1 | 0.032 (6) | 0.028 (6) | 0.018 (5) | −0.011 (6) | 0.007 (4) | 0.000 (5) |
C2 | 0.033 (6) | 0.028 (7) | 0.030 (6) | −0.008 (5) | 0.005 (5) | 0.002 (5) |
C3 | 0.026 (5) | 0.035 (7) | 0.024 (5) | −0.010 (5) | 0.003 (4) | −0.001 (5) |
C4 | 0.029 (6) | 0.015 (5) | 0.036 (6) | −0.010 (5) | 0.002 (5) | −0.004 (5) |
C5 | 0.040 (7) | 0.039 (8) | 0.031 (6) | −0.002 (6) | 0.007 (5) | 0.003 (6) |
C6 | 0.025 (6) | 0.040 (7) | 0.016 (5) | 0.006 (5) | −0.004 (4) | −0.005 (5) |
C7 | 0.016 (5) | 0.018 (6) | 0.042 (6) | 0.002 (5) | −0.001 (5) | −0.002 (5) |
C8 | 0.033 (6) | 0.033 (7) | 0.026 (6) | −0.011 (6) | 0.002 (5) | 0.003 (5) |
C9 | 0.029 (5) | 0.034 (7) | 0.021 (5) | −0.002 (5) | 0.004 (4) | 0.006 (5) |
C10 | 0.017 (5) | 0.028 (6) | 0.021 (5) | −0.001 (5) | −0.004 (4) | −0.003 (5) |
C11 | 0.031 (6) | 0.019 (6) | 0.023 (5) | 0.008 (5) | 0.012 (4) | 0.000 (5) |
C12 | 0.020 (5) | 0.026 (6) | 0.024 (5) | −0.004 (5) | 0.006 (4) | 0.006 (5) |
C13 | 0.021 (5) | 0.027 (6) | 0.020 (5) | −0.004 (5) | −0.004 (4) | 0.007 (5) |
C14 | 0.023 (5) | 0.022 (6) | 0.044 (7) | 0.003 (5) | 0.010 (5) | 0.000 (5) |
C15 | 0.020 (5) | 0.032 (7) | 0.033 (6) | −0.003 (5) | −0.006 (5) | 0.004 (6) |
C16 | 0.023 (5) | 0.027 (7) | 0.029 (6) | −0.007 (5) | 0.008 (4) | −0.005 (5) |
C17 | 0.027 (6) | 0.030 (7) | 0.026 (6) | 0.007 (5) | 0.015 (5) | −0.006 (5) |
C18 | 0.020 (5) | 0.033 (6) | 0.028 (5) | 0.001 (5) | 0.004 (4) | 0.009 (5) |
P1—O2 | 1.494 (8) | O15—C10 | 1.399 (13) |
P1—O3 | 1.515 (7) | O15—C13 | 1.442 (11) |
P1—O1 | 1.518 (7) | O16—C15 | 1.247 (12) |
P1—O4 | 1.609 (7) | O24—Na1vi | 2.334 (11) |
P1—Na1 | 3.385 (5) | O25—Na2vii | 2.357 (14) |
P2—O9 | 1.507 (7) | O25—Na5vii | 2.410 (16) |
P2—O11 | 1.516 (8) | O26—Na5v | 2.350 (15) |
P2—O10 | 1.521 (7) | O26—Na2v | 2.643 (15) |
P2—O12 | 1.609 (7) | O27—Na2v | 2.966 (19) |
Na1—O1 | 2.334 (8) | O29—O30 | 0.79 (2) |
Na1—O24i | 2.334 (11) | N1—C9 | 1.364 (13) |
Na1—O19 | 2.381 (10) | N1—C6 | 1.388 (13) |
Na1—O17 | 2.434 (8) | N1—C1 | 1.457 (13) |
Na1—N5ii | 2.512 (10) | N2—C6 | 1.337 (14) |
Na1—Na4 | 3.489 (6) | N2—C7 | 1.346 (13) |
Na2—Na5 | 0.940 (13) | N3—C7 | 1.300 (13) |
Na2—O30 | 2.27 (2) | N3—H3B | 0.8800 |
Na2—O25iii | 2.357 (14) | N3—H3A | 0.8800 |
Na2—O29 | 2.38 (2) | N4—C18 | 1.358 (12) |
Na2—O21 | 2.458 (13) | N4—C15 | 1.412 (12) |
Na2—O23 | 2.602 (15) | N4—C10 | 1.464 (13) |
Na2—O26iv | 2.643 (15) | N5—C15 | 1.316 (13) |
Na2—O27iv | 2.966 (19) | N5—C16 | 1.345 (13) |
Na3—O24 | 2.326 (10) | N5—Na1viii | 2.512 (10) |
Na3—O9 | 2.361 (9) | N6—C16 | 1.337 (13) |
Na3—O28 | 2.382 (11) | N6—H6B | 0.8800 |
Na3—N2 | 2.400 (10) | N6—H6A | 0.8800 |
Na3—O8 | 2.855 (10) | C1—C2 | 1.528 (15) |
Na3—C6 | 3.022 (11) | C1—H1 | 1.0000 |
Na4—O14v | 2.306 (9) | C2—C3 | 1.521 (16) |
Na4—O19 | 2.364 (9) | C2—H2 | 1.0000 |
Na4—O18 | 2.384 (10) | C3—C4 | 1.516 (15) |
Na4—O13v | 2.413 (9) | C3—H3 | 1.0000 |
Na4—O17 | 2.455 (9) | C4—C5 | 1.498 (15) |
Na4—O20 | 2.868 (12) | C4—H4 | 1.0000 |
Na5—O29 | 2.24 (2) | C5—H5A | 0.9900 |
Na5—O26iv | 2.350 (15) | C5—H5B | 0.9900 |
Na5—O27 | 2.36 (2) | C7—C8 | 1.399 (14) |
Na5—O25iii | 2.410 (16) | C8—C9 | 1.333 (15) |
Na5—O21 | 2.430 (13) | C8—H8 | 0.9500 |
Na5—O30 | 2.44 (2) | C9—H9 | 0.9500 |
O4—C5 | 1.422 (15) | C10—C11 | 1.505 (14) |
O5—C2 | 1.392 (13) | C10—H10 | 1.0000 |
O5—H5 | 0.8400 | C11—C12 | 1.527 (15) |
O6—C3 | 1.407 (12) | C11—H11 | 1.0000 |
O6—H6 | 0.8400 | C12—C13 | 1.481 (15) |
O7—C1 | 1.415 (13) | C12—H12 | 1.0000 |
O7—C4 | 1.457 (11) | C13—C14 | 1.516 (14) |
O8—C6 | 1.242 (12) | C13—H13 | 1.0000 |
O12—C14 | 1.437 (13) | C14—H14A | 0.9900 |
O13—C11 | 1.389 (12) | C14—H14B | 0.9900 |
O13—Na4iv | 2.413 (9) | C16—C17 | 1.437 (14) |
O13—H13A | 0.9500 | C17—C18 | 1.307 (15) |
O14—C12 | 1.422 (11) | C17—H17 | 0.9500 |
O14—Na4iv | 2.306 (9) | C18—H18 | 0.9500 |
O14—H14 | 0.9500 | ||
O2—P1—O3 | 112.0 (4) | P2—O9—Na3 | 126.7 (4) |
O2—P1—O1 | 113.6 (4) | C14—O12—P2 | 117.8 (6) |
O3—P1—O1 | 111.3 (4) | C11—O13—Na4iv | 117.7 (6) |
O2—P1—O4 | 104.4 (4) | C11—O13—H13A | 121.1 |
O3—P1—O4 | 107.9 (4) | Na4iv—O13—H13A | 121.1 |
O1—P1—O4 | 107.0 (4) | C12—O14—Na4iv | 122.4 (7) |
O2—P1—Na1 | 90.2 (3) | C12—O14—H14 | 118.8 |
O3—P1—Na1 | 98.3 (3) | Na4iv—O14—H14 | 118.8 |
O1—P1—Na1 | 36.0 (3) | C10—O15—C13 | 108.8 (7) |
O4—P1—Na1 | 141.9 (3) | Na1—O17—Na4 | 91.1 (3) |
O9—P2—O11 | 113.9 (4) | Na4—O19—Na1 | 94.6 (3) |
O9—P2—O10 | 112.3 (4) | Na5—O21—Na2 | 22.2 (3) |
O11—P2—O10 | 110.6 (4) | Na3—O24—Na1vi | 140.5 (5) |
O9—P2—O12 | 106.7 (4) | Na2vii—O25—Na5vii | 22.7 (3) |
O11—P2—O12 | 104.6 (4) | Na5v—O26—Na2v | 20.7 (3) |
O10—P2—O12 | 108.0 (4) | Na5—O27—Na2v | 105.5 (6) |
O1—Na1—O24i | 135.7 (4) | O30—O29—Na5 | 95 (2) |
O1—Na1—O19 | 125.1 (4) | O30—O29—Na2 | 72 (2) |
O24i—Na1—O19 | 98.2 (3) | Na5—O29—Na2 | 23.2 (4) |
O1—Na1—O17 | 84.1 (3) | O29—O30—Na2 | 88 (2) |
O24i—Na1—O17 | 91.0 (3) | O29—O30—Na5 | 66 (2) |
O19—Na1—O17 | 86.4 (3) | Na2—O30—Na5 | 22.7 (4) |
O1—Na1—N5ii | 87.4 (3) | C9—N1—C6 | 119.0 (9) |
O24i—Na1—N5ii | 94.1 (4) | C9—N1—C1 | 120.3 (9) |
O19—Na1—N5ii | 99.8 (3) | C6—N1—C1 | 120.7 (8) |
O17—Na1—N5ii | 171.4 (3) | C6—N2—C7 | 120.6 (9) |
O1—Na1—P1 | 22.47 (18) | C6—N2—Na3 | 104.3 (6) |
O24i—Na1—P1 | 118.4 (3) | C7—N2—Na3 | 135.0 (7) |
O19—Na1—P1 | 133.8 (3) | C7—N3—H3B | 120.0 |
O17—Na1—P1 | 67.2 (2) | C7—N3—H3A | 120.0 |
N5ii—Na1—P1 | 104.2 (2) | H3B—N3—H3A | 120.0 |
O1—Na1—Na4 | 103.8 (2) | C18—N4—C15 | 119.4 (9) |
O24i—Na1—Na4 | 103.0 (3) | C18—N4—C10 | 120.7 (8) |
O19—Na1—Na4 | 42.5 (2) | C15—N4—C10 | 119.9 (8) |
O17—Na1—Na4 | 44.7 (2) | C15—N5—C16 | 119.3 (9) |
N5ii—Na1—Na4 | 140.0 (3) | C15—N5—Na1viii | 109.6 (7) |
P1—Na1—Na4 | 98.95 (15) | C16—N5—Na1viii | 131.1 (7) |
Na5—Na2—O30 | 88.7 (11) | C16—N6—H6B | 120.0 |
Na5—Na2—O25iii | 81.8 (10) | C16—N6—H6A | 120.0 |
O30—Na2—O25iii | 95.6 (6) | H6B—N6—H6A | 120.0 |
Na5—Na2—O29 | 69.6 (11) | O7—C1—N1 | 107.2 (8) |
O30—Na2—O29 | 19.3 (6) | O7—C1—C2 | 106.6 (8) |
O25iii—Na2—O29 | 89.4 (6) | N1—C1—C2 | 114.9 (9) |
Na5—Na2—O21 | 77.3 (10) | O7—C1—H1 | 109.3 |
O30—Na2—O21 | 83.3 (6) | N1—C1—H1 | 109.3 |
O25iii—Na2—O21 | 159.1 (7) | C2—C1—H1 | 109.3 |
O29—Na2—O21 | 82.6 (6) | O5—C2—C3 | 115.8 (9) |
Na5—Na2—O23 | 153.4 (11) | O5—C2—C1 | 110.4 (8) |
O30—Na2—O23 | 68.4 (6) | C3—C2—C1 | 100.6 (10) |
O25iii—Na2—O23 | 112.6 (6) | O5—C2—H2 | 109.8 |
O29—Na2—O23 | 87.7 (6) | C3—C2—H2 | 109.8 |
O21—Na2—O23 | 86.6 (4) | C1—C2—H2 | 109.8 |
Na5—Na2—O26iv | 61.8 (10) | O6—C3—C4 | 111.5 (9) |
O30—Na2—O26iv | 149.3 (8) | O6—C3—C2 | 108.1 (9) |
O25iii—Na2—O26iv | 88.6 (5) | C4—C3—C2 | 104.1 (8) |
O29—Na2—O26iv | 131.2 (8) | O6—C3—H3 | 111.0 |
O21—Na2—O26iv | 82.3 (5) | C4—C3—H3 | 111.0 |
O23—Na2—O26iv | 137.1 (6) | C2—C3—H3 | 111.0 |
Na5—Na2—O27iv | 119.2 (11) | O7—C4—C5 | 108.6 (8) |
O30—Na2—O27iv | 152.0 (8) | O7—C4—C3 | 106.3 (8) |
O25iii—Na2—O27iv | 87.2 (5) | C5—C4—C3 | 116.3 (9) |
O29—Na2—O27iv | 169.9 (8) | O7—C4—H4 | 108.5 |
O21—Na2—O27iv | 103.7 (5) | C5—C4—H4 | 108.5 |
O23—Na2—O27iv | 84.8 (5) | C3—C4—H4 | 108.5 |
O26iv—Na2—O27iv | 58.3 (5) | O4—C5—C4 | 110.0 (10) |
O24—Na3—O9 | 104.0 (3) | O4—C5—H5A | 109.7 |
O24—Na3—O28 | 87.1 (4) | C4—C5—H5A | 109.7 |
O9—Na3—O28 | 127.0 (5) | O4—C5—H5B | 109.7 |
O24—Na3—N2 | 153.3 (5) | C4—C5—H5B | 109.7 |
O9—Na3—N2 | 88.8 (3) | H5A—C5—H5B | 108.2 |
O28—Na3—N2 | 104.0 (3) | O8—C6—N2 | 120.6 (9) |
O24—Na3—O8 | 109.0 (4) | O8—C6—N1 | 120.0 (9) |
O9—Na3—O8 | 135.2 (3) | N2—C6—N1 | 119.4 (9) |
O28—Na3—O8 | 84.5 (3) | O8—C6—Na3 | 70.3 (6) |
N2—Na3—O8 | 49.6 (3) | N2—C6—Na3 | 50.3 (5) |
O24—Na3—C6 | 131.9 (4) | N1—C6—Na3 | 169.1 (8) |
O9—Na3—C6 | 113.1 (3) | N3—C7—N2 | 117.3 (9) |
O28—Na3—C6 | 93.8 (3) | N3—C7—C8 | 121.3 (10) |
N2—Na3—C6 | 25.4 (3) | N2—C7—C8 | 121.3 (9) |
O8—Na3—C6 | 24.2 (2) | C9—C8—C7 | 117.1 (10) |
O14v—Na4—O19 | 99.8 (3) | C9—C8—H8 | 121.5 |
O14v—Na4—O18 | 150.6 (3) | C7—C8—H8 | 121.5 |
O19—Na4—O18 | 97.5 (3) | C8—C9—N1 | 122.5 (10) |
O14v—Na4—O13v | 67.6 (3) | C8—C9—H9 | 118.7 |
O19—Na4—O13v | 104.7 (3) | N1—C9—H9 | 118.7 |
O18—Na4—O13v | 85.0 (3) | O15—C10—N4 | 106.0 (7) |
O14v—Na4—O17 | 80.6 (3) | O15—C10—C11 | 106.6 (7) |
O19—Na4—O17 | 86.3 (3) | N4—C10—C11 | 114.8 (9) |
O18—Na4—O17 | 124.4 (3) | O15—C10—H10 | 109.8 |
O13v—Na4—O17 | 147.6 (3) | N4—C10—H10 | 109.8 |
O14v—Na4—O20 | 95.8 (3) | C11—C10—H10 | 109.8 |
O19—Na4—O20 | 154.0 (3) | O13—C11—C10 | 112.0 (8) |
O18—Na4—O20 | 77.9 (3) | O13—C11—C12 | 114.2 (8) |
O13v—Na4—O20 | 100.4 (3) | C10—C11—C12 | 99.3 (9) |
O17—Na4—O20 | 75.9 (3) | O13—C11—H11 | 110.3 |
O14v—Na4—Na1 | 96.9 (3) | C10—C11—H11 | 110.3 |
O19—Na4—Na1 | 42.9 (2) | C12—C11—H11 | 110.3 |
O18—Na4—Na1 | 111.9 (2) | O14—C12—C13 | 111.2 (9) |
O13v—Na4—Na1 | 143.1 (3) | O14—C12—C11 | 106.4 (8) |
O17—Na4—Na1 | 44.23 (19) | C13—C12—C11 | 104.6 (8) |
O20—Na4—Na1 | 114.8 (2) | O14—C12—H12 | 111.4 |
Na2—Na5—O29 | 87.2 (11) | C13—C12—H12 | 111.4 |
Na2—Na5—O26iv | 97.5 (11) | C11—C12—H12 | 111.4 |
O29—Na5—O26iv | 173.0 (9) | O15—C13—C12 | 106.3 (8) |
Na2—Na5—O27 | 162.9 (12) | O15—C13—C14 | 107.2 (8) |
O29—Na5—O27 | 76.6 (8) | C12—C13—C14 | 116.9 (9) |
O26iv—Na5—O27 | 99.1 (6) | O15—C13—H13 | 108.7 |
Na2—Na5—O25iii | 75.5 (10) | C12—C13—H13 | 108.7 |
O29—Na5—O25iii | 91.7 (7) | C14—C13—H13 | 108.7 |
O26iv—Na5—O25iii | 94.6 (5) | O12—C14—C13 | 109.5 (9) |
O27—Na5—O25iii | 99.1 (5) | O12—C14—H14A | 109.8 |
Na2—Na5—O21 | 80.6 (10) | C13—C14—H14A | 109.8 |
O29—Na5—O21 | 86.4 (6) | O12—C14—H14B | 109.8 |
O26iv—Na5—O21 | 89.3 (5) | C13—C14—H14B | 109.8 |
O27—Na5—O21 | 103.7 (6) | H14A—C14—H14B | 108.2 |
O25iii—Na5—O21 | 156.0 (7) | O16—C15—N5 | 122.8 (9) |
Na2—Na5—O30 | 68.7 (10) | O16—C15—N4 | 116.9 (9) |
O29—Na5—O30 | 18.8 (6) | N5—C15—N4 | 120.2 (9) |
O26iv—Na5—O30 | 163.9 (8) | N6—C16—N5 | 117.7 (9) |
O27—Na5—O30 | 95.4 (7) | N6—C16—C17 | 120.4 (9) |
O25iii—Na5—O30 | 90.0 (6) | N5—C16—C17 | 121.8 (10) |
O21—Na5—O30 | 80.5 (5) | C18—C17—C16 | 117.2 (9) |
P1—O1—Na1 | 121.5 (4) | C18—C17—H17 | 121.4 |
C5—O4—P1 | 117.5 (7) | C16—C17—H17 | 121.4 |
C2—O5—H5 | 109.5 | C17—C18—N4 | 121.9 (10) |
C3—O6—H6 | 109.5 | C17—C18—H18 | 119.1 |
C1—O7—C4 | 109.0 (7) | N4—C18—H18 | 119.1 |
C6—O8—Na3 | 85.5 (6) | ||
O7—C1—N1—C6 | −125.1 (10) | O15—C10—N4—C15 | −130.2 (9) |
C4—O7—C1—C2 | −22.6 (10) | C13—O15—C10—C11 | −26.0 (10) |
O7—C1—C2—C3 | 35.2 (10) | O15—C10—C11—C12 | 37.0 (9) |
C1—C2—C3—C4 | −34.0 (10) | C10—C11—C12—C13 | −34.2 (9) |
C2—C3—C4—O7 | 22.2 (10) | C11—C12—C13—O15 | 20.7 (10) |
C3—C4—O7—C1 | 0.1 (13) | C12—C13—O15—C10 | 3.0 (10) |
O4—C5—C4—C3 | 48.9 (12) | O12—C14—C13—C12 | 47.6 (12) |
C5—C4—C3—O6 | 144.8 (9) | C14—C13—C12—O14 | 146.9 (9) |
P1—O4—C5—C4 | −156.4 (7) | P2—O12—C14—C13 | −160.1 (7) |
Symmetry codes: (i) x, y, z−1; (ii) x−1, y, z−1; (iii) −x+1, y+1/2, −z+1; (iv) −x+1, y+1/2, −z; (v) −x+1, y−1/2, −z; (vi) x, y, z+1; (vii) −x+1, y−1/2, −z+1; (viii) x+1, y, z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O29vii | 0.88 | 2.26 | 3.07 (2) | 153 |
N6—H6A···O30vii | 0.88 | 2.05 | 2.913 (19) | 169 |
N3—H3A···O22iii | 0.88 | 2.03 | 2.890 (11) | 166 |
N3—H3B···O9 | 0.88 | 2.14 | 2.986 (10) | 161 |
O5—H5···O6 | 0.84 | 2.24 | 2.678 (12) | 113 |
O5—H5···O23ix | 0.84 | 2.49 | 3.288 (12) | 160 |
O6—H6···O2ix | 0.84 | 1.77 | 2.602 (11) | 175 |
N6—H6B···O1viii | 0.88 | 2.01 | 2.863 (11) | 163 |
O13—H13A···O9vii | 0.95 | 1.95 | 2.651 (11) | 128 |
O14—H14···O11iii | 0.95 | 1.88 | 2.573 (11) | 128 |
C1—H1···O8 | 1.00 | 2.32 | 2.760 (13) | 105 |
C5—H5B···O1 | 0.99 | 2.53 | 2.993 (13) | 108 |
C10—H10···O16 | 1.00 | 2.28 | 2.711 (13) | 105 |
Symmetry codes: (iii) −x+1, y+1/2, −z+1; (vii) −x+1, y−1/2, −z+1; (viii) x+1, y, z+1; (ix) −x, y−1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | 2Na+·C9H4N3O8P2−·6.5H6O |
Mr | 484.27 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 173 |
a, b, c (Å) | 14.042 (2), 8.924 (2), 16.091 (3) |
β (°) | 94.410 (2) |
V (Å3) | 2010.4 (7) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.26 |
Crystal size (mm) | 0.35 × 0.35 × 0.30 |
Data collection | |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3930, 3756, 2202 |
Rint | 0.094 |
(sin θ/λ)max (Å−1) | 0.594 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.061, 0.186, 1.05 |
No. of reflections | 3756 |
No. of parameters | 531 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.53, −0.41 |
Absolute structure | Flack (1983) |
Absolute structure parameter | 0.1 (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).
Na3—O24 | 2.326 (10) | Na4—O17 | 2.455 (9) |
Na3—O9 | 2.361 (9) | Na4—O20 | 2.868 (12) |
Na3—O28 | 2.382 (11) | Na5—O29 | 2.24 (2) |
Na3—N2 | 2.400 (10) | Na5—O26ii | 2.350 (15) |
Na3—O8 | 2.855 (10) | Na5—O27 | 2.36 (2) |
Na4—O14i | 2.306 (9) | Na5—O25iii | 2.410 (16) |
Na4—O19 | 2.364 (9) | Na5—O21 | 2.430 (13) |
Na4—O18 | 2.384 (10) | Na5—O30 | 2.44 (2) |
Na4—O13i | 2.413 (9) | ||
O7—C1—N1—C6 | −125.1 (10) | O15—C10—N4—C15 | −130.2 (9) |
C4—O7—C1—C2 | −22.6 (10) | C13—O15—C10—C11 | −26.0 (10) |
O7—C1—C2—C3 | 35.2 (10) | O15—C10—C11—C12 | 37.0 (9) |
C1—C2—C3—C4 | −34.0 (10) | C10—C11—C12—C13 | −34.2 (9) |
C2—C3—C4—O7 | 22.2 (10) | C11—C12—C13—O15 | 20.7 (10) |
C3—C4—O7—C1 | 0.1 (13) | C12—C13—O15—C10 | 3.0 (10) |
O4—C5—C4—C3 | 48.9 (12) | O12—C14—C13—C12 | 47.6 (12) |
C5—C4—C3—O6 | 144.8 (9) | C14—C13—C12—O14 | 146.9 (9) |
P1—O4—C5—C4 | −156.4 (7) | P2—O12—C14—C13 | −160.1 (7) |
Symmetry codes: (i) −x+1, y−1/2, −z; (ii) −x+1, y+1/2, −z; (iii) −x+1, y+1/2, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···O29iv | 0.8794 | 2.2584 | 3.07 (2) | 153.26 |
N6—H6A···O30iv | 0.8794 | 2.0455 | 2.913 (19) | 168.63 |
N3—H3A···O22iii | 0.8796 | 2.0299 | 2.890 (11) | 165.50 |
N3—H3B···O9 | 0.8813 | 2.1375 | 2.986 (10) | 161.28 |
O5—H5···O6 | 0.8400 | 2.2418 | 2.678 (12) | 112.47 |
O5—H5···O23v | 0.8400 | 2.4876 | 3.288 (12) | 159.58 |
O6—H6···O2v | 0.8404 | 1.7645 | 2.602 (11) | 174.65 |
N6—H6B···O1vi | 0.8807 | 2.0096 | 2.863 (11) | 162.88 |
O13—H13A···O9iv | 0.9505 | 1.9532 | 2.651 (11) | 128.42 |
O14—H14···O11iii | 0.9502 | 1.8809 | 2.573 (11) | 127.61 |
C1—H1···O8 | 1.0005 | 2.3228 | 2.760 (13) | 105.27 |
C5—H5B···O1 | 0.9906 | 2.5284 | 2.993 (13) | 108.44 |
C10—H10···O16 | 1.0002 | 2.2781 | 2.711 (13) | 104.77 |
Symmetry codes: (iii) −x+1, y+1/2, −z+1; (iv) −x+1, y−1/2, −z+1; (v) −x, y−1/2, −z; (vi) x+1, y, z+1. |
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.