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Acta Cryst. (2013). E69, m464-m465    [ doi:10.1107/S1600536813019260 ]

Poly[[[mu]-bis(4-nitrophenyl) phosphato-[kappa]2O,O']sodium]

A. Gerus and T. Lis

Abstract top

The title compound, [Na(C12H8N2O8P)], consists of one Na+ cation and one bis(p-nitrophenyl)phosphate anion with a considerable distortion of the phosphate tetrahedron due to the presence of two P-O ester bonds. The anion bridges five Na+ cations whereby each cation is chelated by the nitro O atoms of one anion and bonded via a nitro O atom and phosphate O atoms to four other anions. This bridging arrangement leads to the formation of double layers parallel to (001). Adjacent layers are linked through weak C-H...O hydrogen bonds.

Comment top

Phosphate diester hydrolysis is a reaction of continuing interest since such process is of fundamental biological importance. Currently, there is much interest in developing artificial nucleases that hydrolyze the phosphate diester bonds in RNA and DNA (Sredhera & Cowan, 2001; Belousoff et al., 2009; Branum et al., 2001). Thus, there have been numerous model studies devoted to understanding how metalloenzymes hydrolyze phosphate diesters (Mancin et al., 2005; Liu et al., 2004). In most cases the substrate of choice is the "activated" phosphate diester bis(p-nitrophenyl)phosphate (BNPP). It is considered as an activated phosphate diester because the p-nitro groups draw electron density away from the phosphorus atom as well as help to stabilize the negatively charged leaving group (Jurek & Martell, 1999). For this reason the bis(p-nitrophenyl)phosphate anion is a popular model substrate for kinetic studies of the hydrolytic cleavage of the phosphodiester bond similar to DNA (Chang et al., 2009; Oh et al., 1996).

BNPP is commercially available as a sodium salt. There are many references concerning solid state studies of BNPP acting as a ligand in complexes or as an anion in salts. The first publications referring to BNPP describe salts of local anesthetics (Sax et al., 1970, 1971; Pletcher et al., 1972; Yoo et al., 1975). The structure of BNPP has been observed also in many macrocyclic complexes (Král et al., 2006; Bazzicalupi et al., 2004; Fry et al., 2003; Warden et al., 2005). Here we report the structure of BNPP as a sodium salt, [Na(C12H8N2O8P)], (I).

Compound (I) crystallizes with one bis(p-nitrophenyl)phosphate anion (Fig. 1) and one sodium cation in the asymmetric unit. The phenyl rings are almost coplanar. The interplanar angle between two phenyl rings amounts to 2.36 (3)°. The nitro group O1—N1—O2 is rotated 2.00 (4)° from the phenyl ring C1—C6 and the second nitro group O3—N2—O4 is rotated 9.01 (4)° from the phenyl ring C11—C61. The phosphate group is highly distorted from the ideal tetrahedral geometry (Table 1). In the anion there are two shorter P—O bonds of 1.4733 (8) Å and 1.4834 (7) Å, and two longer P—O ester bonds lengths of 1.6266 (8) Å and 1.6287 (12) Å. The shortest bond is P–O31. A little longer than the P–O31 bond is the P–O41 bond, bridging Na+ ions. Both O11 and O21 atoms involved in longer ester bonds are attached to aryl rings. The average P—O distance is 1.55 Å, but individual P—O bonds in the structure of compound (I) show how much the phosphate group is deformed. In previous reports containing BNPP anions the most similar deviations for P—O ester bond length in the phosphate group has been observed for these four examples (Sax et al., 1970, 1971; Pletcher et al., 1972; Yoo et al., 1975).

The bond angles in the phosphate group distinctly deviate from the ideal value of 109.5°. The average value for the O–P–O angle is 108.9°, however, individual angles show considerable deviations. The smallest angle is 92.20 (4)° for O11—P1—O21, that is ArO—P—OAr. This deviation can be correlated with the corresponding bond lengths. Such a small angle has not been observed in any previous report of a BNPP structure. The most comparabler value of an O—P—O angle is 95.3 (2)° (Bond et al., 1985). The largest angle is 119.67 (5)° for O31—P—O41, and the four remaining angles are about 110°.

In (I), the coordination geometry of Na+ ion is irregular, with an overall coordination number of six [5 + 1] . The Na+ ion is coordinated by five symmetry-related BNPP anions via oxygen atoms. It is chelated by one anion in a bidentate mode (via O1 and O2), and coordinated by four anions in a monodentate manner (via O31iv, O4iii, O41v and O41vi) (Fig. 2). The Na—O distances are in the range 2.2386 (10) to 2.9377 (18) Å (Table 2). In the structure there is also a short Na···Na distance of 3.253 (2) Å, and two sodium cations are bridged by two O atoms (denoted as O41 in Fig. 2), forming a dimeric sub-structure with a four-membered ring (Figs. 2 and 4). The cations and anions are arranged in double layers parallel to (001) (Figs. 3 and 4). Adjacent layers are linked through weak C—H···O hydrogen bonds existing between H atoms of the aromatic rings and nitro O atoms (Fig. 3, Table 2).

Related literature top

For hydrolytic cleavage of the phosphodiester bond in bis(p-nitrophenyl)phosphate (BNPP) and related systems, see: Belousoff et al. (2009); Branum et al. (2001); Chang et al. (2009); Liu et al. (2004); Mancin et al. (2005); Oh et al. (1996); Sredhera & Cowan (2001). For crystal structures containing the BNPP entity, see: Bazzicalupi et al. (2004); Bond et al. (1985); Fry et al. (2003); Jurek & Martell (1999); Král et al. (2006); Pletcher et al. (1972) Sax et al. (1970, 1971); Warden et al. (2005); Yoo et al. (1975).

Experimental top

The bis(p-nitrophenyl)phosphate sodium salt was purchased from Sigma-Aldrich. Yellow crystals were obtained after several days by slow evaporation of an aqueous solution.

Refinement top

All H atoms were introduced in geometrically calculated positions, with C—H = 0.95 A ° and Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The molecular structure and numbering scheme for the BNPP anion. Displacement ellipsoids are shown at the 50% probability level.
[Figure 2] Fig. 2. Coordination sphere of the Na+ cation in (I). Displacement ellipsoids are shown at the 50% probability level. [Symmetry codes: (iii) x + 1, y + 2, z; (iv) x, y + 1, z; (v) x + 1, y + 1, z; (vi) -x + 1, -y + 2, -z + 1; (viii) -x + 2, -y + 3, -z + 1; (xi) -x + 1, -y + 1, -z + 1; (xii) -x + 2, -y + 2, -z + 1].
[Figure 3] Fig. 3. Projection of (I) along [100] showing the double layers. Dashed lines indicate C—H···O hydrogen bonds. Displacement ellipsoids are shown at the 50% probability level.
[Figure 4] Fig. 4. The packing diagram for crystal of the title salt (I). Displacement ellipsoids are shown at 50% probability level.
Poly[[µ-bis(4-nitrophenyl) phosphato-κ2O,O']sodium] top
Crystal data top
[Na(C12H8N2O8P)]Z = 2
Mr = 362.16F(000) = 368
Triclinic, P1Dx = 1.806 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.963 (2) ÅCell parameters from 8925 reflections
b = 9.844 (3) Åθ = 3.2–37.5°
c = 11.213 (3) ŵ = 0.29 mm1
α = 103.93 (3)°T = 100 K
β = 105.83 (3)°Block, yellow
γ = 106.38 (3)°0.30 × 0.27 × 0.25 mm
V = 666.1 (3) Å3
Data collection top
Agilent Xcalibur (Onyx with CCD camera)
diffractometer
6748 independent reflections
Radiation source: fine-focus sealed tube5542 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.014
ω and π scansθmax = 37.6°, θmin = 3.2°
Absorption correction: analytical
(CrysAlis PRO; Agilent, 2011)
h = 1110
Tmin = 0.918, Tmax = 0.931k = 1615
13418 measured reflectionsl = 1915
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.030Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.090H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0486P)2 + 0.1337P]
where P = (Fo2 + 2Fc2)/3
6748 reflections(Δ/σ)max = 0.001
217 parametersΔρmax = 0.66 e Å3
0 restraintsΔρmin = 0.33 e Å3
Crystal data top
[Na(C12H8N2O8P)]γ = 106.38 (3)°
Mr = 362.16V = 666.1 (3) Å3
Triclinic, P1Z = 2
a = 6.963 (2) ÅMo Kα radiation
b = 9.844 (3) ŵ = 0.29 mm1
c = 11.213 (3) ÅT = 100 K
α = 103.93 (3)°0.30 × 0.27 × 0.25 mm
β = 105.83 (3)°
Data collection top
Agilent Xcalibur (Onyx with CCD camera)
diffractometer
6748 independent reflections
Absorption correction: analytical
(CrysAlis PRO; Agilent, 2011)
5542 reflections with I > 2σ(I)
Tmin = 0.918, Tmax = 0.931Rint = 0.014
13418 measured reflectionsθmax = 37.6°
Refinement top
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.090Δρmax = 0.66 e Å3
S = 1.07Δρmin = 0.33 e Å3
6748 reflectionsAbsolute structure: ?
217 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
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
P10.19163 (3)0.36887 (2)0.291283 (19)0.00783 (4)
O10.52988 (11)1.11256 (7)0.18582 (7)0.01642 (12)
O20.66594 (11)1.15233 (7)0.39510 (6)0.01488 (11)
O30.28509 (13)0.46498 (7)0.15506 (8)0.02195 (14)
O40.14079 (12)0.34783 (8)0.36644 (7)0.01817 (13)
O110.18884 (10)0.45097 (6)0.18143 (6)0.01210 (10)
O210.02554 (10)0.20680 (6)0.18007 (6)0.01107 (10)
O310.40483 (10)0.36277 (7)0.34892 (6)0.01340 (11)
O410.08681 (9)0.42769 (7)0.37940 (6)0.01131 (10)
N10.55665 (11)1.06716 (8)0.27967 (7)0.01084 (11)
N20.18533 (12)0.34891 (8)0.25185 (8)0.01290 (12)
C10.28334 (12)0.60309 (8)0.21207 (7)0.00932 (12)
C20.24915 (13)0.65553 (9)0.10570 (8)0.01132 (12)
H20.16540.58620.01870.014*
C30.33698 (13)0.80825 (9)0.12681 (8)0.01110 (12)
H30.31440.84480.05510.013*
C40.45900 (12)0.90670 (8)0.25538 (8)0.00970 (12)
C50.49639 (13)0.85587 (9)0.36171 (8)0.01053 (12)
H50.58150.92550.44840.013*
C60.40903 (13)0.70311 (9)0.34079 (8)0.01043 (12)
H60.43410.66690.41260.013*
C110.01420 (12)0.07325 (8)0.20306 (8)0.00914 (11)
C210.14071 (13)0.05705 (9)0.09256 (8)0.01090 (12)
H210.19020.04920.00770.013*
C310.19405 (13)0.19754 (9)0.10643 (8)0.01187 (13)
H310.27900.28670.03200.014*
C410.11984 (13)0.20435 (9)0.23230 (8)0.01057 (12)
C510.00777 (13)0.07667 (9)0.34263 (8)0.01163 (13)
H510.05790.08540.42710.014*
C610.06168 (13)0.06395 (9)0.32862 (8)0.01120 (12)
H610.14890.15260.40330.013*
Na0.75570 (5)1.41177 (4)0.39243 (3)0.01082 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
P10.00772 (8)0.00661 (8)0.00894 (8)0.00226 (6)0.00311 (6)0.00274 (6)
O10.0212 (3)0.0124 (3)0.0172 (3)0.0056 (2)0.0065 (2)0.0091 (2)
O20.0167 (3)0.0091 (2)0.0144 (3)0.0027 (2)0.0032 (2)0.0020 (2)
O30.0321 (4)0.0079 (3)0.0231 (3)0.0030 (3)0.0129 (3)0.0025 (2)
O40.0225 (3)0.0154 (3)0.0206 (3)0.0075 (2)0.0087 (3)0.0116 (2)
O110.0172 (3)0.0066 (2)0.0100 (2)0.00113 (19)0.0046 (2)0.00292 (18)
O210.0137 (2)0.0062 (2)0.0103 (2)0.00136 (19)0.00201 (19)0.00335 (18)
O310.0084 (2)0.0132 (3)0.0176 (3)0.0045 (2)0.0038 (2)0.0042 (2)
O410.0108 (2)0.0121 (2)0.0121 (2)0.00466 (19)0.00572 (19)0.00352 (19)
N10.0107 (3)0.0084 (3)0.0147 (3)0.0041 (2)0.0052 (2)0.0049 (2)
N20.0142 (3)0.0093 (3)0.0190 (3)0.0054 (2)0.0094 (2)0.0063 (2)
C10.0102 (3)0.0068 (3)0.0107 (3)0.0024 (2)0.0041 (2)0.0031 (2)
C20.0127 (3)0.0092 (3)0.0100 (3)0.0020 (2)0.0031 (2)0.0035 (2)
C30.0123 (3)0.0092 (3)0.0111 (3)0.0031 (2)0.0036 (2)0.0044 (2)
C40.0101 (3)0.0072 (3)0.0122 (3)0.0031 (2)0.0044 (2)0.0038 (2)
C50.0119 (3)0.0078 (3)0.0106 (3)0.0031 (2)0.0035 (2)0.0025 (2)
C60.0123 (3)0.0086 (3)0.0097 (3)0.0031 (2)0.0037 (2)0.0035 (2)
C110.0094 (3)0.0073 (3)0.0110 (3)0.0029 (2)0.0039 (2)0.0036 (2)
C210.0126 (3)0.0084 (3)0.0101 (3)0.0025 (2)0.0036 (2)0.0028 (2)
C310.0136 (3)0.0082 (3)0.0124 (3)0.0025 (2)0.0054 (3)0.0024 (2)
C410.0121 (3)0.0074 (3)0.0142 (3)0.0040 (2)0.0068 (2)0.0046 (2)
C510.0130 (3)0.0104 (3)0.0118 (3)0.0040 (2)0.0040 (2)0.0053 (2)
C610.0130 (3)0.0086 (3)0.0099 (3)0.0024 (2)0.0027 (2)0.0031 (2)
Na0.00911 (14)0.00915 (14)0.01433 (15)0.00301 (11)0.00447 (12)0.00451 (12)
Geometric parameters (Å, º) top
P1—O311.4733 (8)C2—C31.3861 (12)
P1—O411.4834 (7)C2—H20.9500
P1—O111.6266 (8)C3—C41.3908 (14)
P1—O211.6287 (12)C3—H30.9500
O1—N11.2282 (10)C4—C51.3895 (12)
O1—Na2.9377 (18)C5—C61.3867 (12)
O2—N11.2399 (12)C5—H50.9500
O2—Na2.4618 (11)C6—H60.9500
O3—N21.2288 (12)C11—C611.3976 (12)
O4—N21.2335 (11)C11—C211.3995 (14)
O4—Nai2.3853 (11)C21—C311.3857 (12)
O11—C11.3663 (11)C21—H210.9500
O21—C111.3668 (10)C31—C411.3894 (12)
O31—Naii2.2386 (10)C31—H310.9500
O41—Naiii2.3135 (9)C41—C511.3862 (14)
O41—Naiv2.4065 (14)C51—C611.3877 (12)
N1—C41.4552 (12)C51—H510.9500
N2—C411.4560 (12)C61—H610.9500
C1—C21.3987 (12)Na—Nav3.253 (2)
C1—C61.3998 (14)
O31—P1—O41119.67 (5)C1—C6—H6120.6
O31—P1—O11110.86 (4)O21—C11—C61123.21 (8)
O41—P1—O11110.02 (4)O21—C11—C21116.04 (7)
O31—P1—O21110.48 (5)C61—C11—C21120.74 (8)
O41—P1—O21110.21 (4)C31—C21—C11120.28 (8)
O11—P1—O2192.20 (4)C31—C21—H21119.9
N1—O1—Na83.76 (6)C11—C21—H21119.9
N1—O2—Na106.72 (6)C21—C31—C41118.15 (8)
N2—O4—Nai116.10 (7)C21—C31—H31120.9
C1—O11—P1123.69 (6)C41—C31—H31120.9
C11—O21—P1123.67 (6)C51—C41—C31122.37 (8)
P1—O31—Naii157.93 (4)C51—C41—N2117.95 (8)
P1—O41—Naiii143.20 (5)C31—C41—N2119.61 (8)
P1—O41—Naiv129.49 (4)C41—C51—C61119.45 (8)
Naiii—O41—Naiv87.11 (4)C41—C51—H51120.3
O1—N1—O2122.74 (7)C61—C51—H51120.3
O1—N1—C4119.12 (8)C51—C61—C11119.01 (8)
O2—N1—C4118.13 (8)C51—C61—H61120.5
O1—N1—Na72.71 (6)C11—C61—H61120.5
O2—N1—Na50.43 (5)O31vi—Na—O41vii165.08 (3)
C4—N1—Na167.00 (5)O31vi—Na—O4viii99.55 (4)
O3—N2—O4123.14 (8)O41vii—Na—O4viii81.55 (4)
O3—N2—C41119.25 (8)O31vi—Na—O41iv101.98 (5)
O4—N2—C41117.59 (8)O41vii—Na—O41iv92.89 (4)
O11—C1—C2115.91 (8)O4viii—Na—O41iv80.28 (4)
O11—C1—C6123.34 (8)O31vi—Na—O284.38 (4)
C2—C1—C6120.75 (7)O41vii—Na—O292.94 (4)
C3—C2—C1120.25 (8)O4viii—Na—O2172.26 (3)
C3—C2—H2119.9O41iv—Na—O2105.55 (4)
C1—C2—H2119.9O31vi—Na—O174.29 (5)
C2—C3—C4118.44 (8)O41vii—Na—O193.25 (4)
C2—C3—H3120.8O4viii—Na—O1128.23 (3)
C4—C3—H3120.8O41iv—Na—O1151.44 (3)
C5—C4—C3121.88 (8)O2—Na—O146.28 (3)
C5—C4—N1118.65 (8)O31vi—Na—N176.99 (4)
C3—C4—N1119.43 (8)O41vii—Na—N194.92 (4)
C6—C5—C4119.77 (8)O4viii—Na—N1151.70 (3)
C6—C5—H5120.1O41iv—Na—N1128.02 (4)
C4—C5—H5120.1O2—Na—N122.85 (2)
C5—C6—C1118.90 (8)O1—Na—N123.53 (2)
C5—C6—H6120.6
O31—P1—O11—C174.91 (8)C4—C5—C6—C10.33 (12)
O41—P1—O11—C159.73 (8)O11—C1—C6—C5179.42 (7)
O21—P1—O11—C1172.18 (6)C2—C1—C6—C51.12 (12)
O31—P1—O21—C1153.96 (7)P1—O21—C11—C618.66 (11)
O41—P1—O21—C1180.51 (7)P1—O21—C11—C21172.40 (6)
O11—P1—O21—C11167.21 (6)O21—C11—C21—C31178.45 (7)
P1—O11—C1—C2174.63 (6)C61—C11—C21—C310.52 (12)
P1—O11—C1—C65.90 (11)C11—C21—C31—C410.45 (12)
O11—C1—C2—C3179.50 (7)C21—C31—C41—C511.26 (12)
C6—C1—C2—C31.01 (12)C21—C31—C41—N2175.67 (7)
C1—C2—C3—C40.09 (12)O3—N2—C41—C51174.72 (8)
C2—C3—C4—C50.72 (12)O4—N2—C41—C516.77 (11)
C2—C3—C4—N1178.70 (7)O3—N2—C41—C318.22 (12)
O1—N1—C4—C5177.82 (7)O4—N2—C41—C31170.30 (8)
O2—N1—C4—C51.43 (11)C31—C41—C51—C611.08 (12)
O1—N1—C4—C30.23 (11)N2—C41—C51—C61175.90 (7)
O2—N1—C4—C3179.48 (7)C41—C51—C61—C110.07 (12)
C3—C4—C5—C60.60 (12)O21—C11—C61—C51178.18 (7)
N1—C4—C5—C6178.60 (7)C21—C11—C61—C510.71 (12)
Symmetry codes: (i) x1, y2, z; (ii) x, y1, z; (iii) x1, y1, z; (iv) x+1, y+2, z+1; (v) x+2, y+3, z+1; (vi) x, y+1, z; (vii) x+1, y+1, z; (viii) x+1, y+2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O3ix0.952.503.1865 (15)129
C21—H21···O1x0.952.533.3337 (18)142
Symmetry codes: (ix) x, y, z; (x) x, y+1, z.
Selected geometric parameters (Å, º) top
P1—O311.4733 (8)O2—Na2.4618 (11)
P1—O411.4834 (7)O4—Nai2.3853 (11)
P1—O111.6266 (8)O31—Naii2.2386 (10)
P1—O211.6287 (12)O41—Naiii2.3135 (9)
O1—Na2.9377 (18)O41—Naiv2.4065 (14)
O31—P1—O41119.67 (5)O31—P1—O21110.48 (5)
O31—P1—O11110.86 (4)O41—P1—O21110.21 (4)
O41—P1—O11110.02 (4)O11—P1—O2192.20 (4)
Symmetry codes: (i) x1, y2, z; (ii) x, y1, z; (iii) x1, y1, z; (iv) x+1, y+2, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···O3v0.952.503.1865 (15)129.4
C21—H21···O1vi0.952.533.3337 (18)142.3
Symmetry codes: (v) x, y, z; (vi) x, y+1, z.
Acknowledgements top

We thank Professor Dr Jerzy Lisowski for helpful discussions during preparation of this article.

references
References top

Agilent (2011). CrysAlis PRO. Agilent Technologies, Yarnton, England.

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