3-Pyridyl­methyl­phospho­nic acid monohydrate

The title mol­ecule, C₆H₈NO₃P·H₂O, has a zwitterionic structure. The crystal-packing properties are influenced by the presence of water mol­ecules in the crystal lattice and are stabilized by stacking interactions between pyridyl rings. Hydro­gen bonds link the mol­ecules in a three-dimensional network.

Key indicators

• Single-crystal X-ray study
• T = 293 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.052
• wR factor = 0.146
• Data-to-parameter ratio = 11.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

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S1. Comment

The investigation presented in this paper is part of systematic studies of organophosphorus derivatives of pyridine. Now we describe the crystal structure of 3-pyridylmethylphosphonic acid monohydrate, (I). In previous papers, the structures of 2-pyridylmethylphosphonic acid, (II) (Gałdecki & Wolf, 1990), and 4-pyridylmethylphosphonic acid monohydrate, (III) (Wolf et al., 1996), were reported. Knowledge of the structure of these compounds will help to design and synthesize new platinum(II) complexes of cytotoxic activity using them as ligands. Platinum(II) complexes of phosphonate ligands exhibit significant antitumour activity (Klenner et al., 1993; Bloemink et al., 1994).

The title molecule exists as a zwitterion. Negative charge is spread over the O2—P1—O3 fragment of the phosphonic group while the positive charge, formally located on the N atom, is delocalized on the pyridyl ring.

The most interesting feature of (I) is the significant difference between the P1—O2 and P1—O3 bond lengths, which is as large as 10σ, while the corresponding values in the previous reported structures, (II) and (III), are not significantly different, 1.500 (4) and 1.507 (3) Å, and 1.506 (2) and 1.5039 (14) Å, respectively. However, both mentioned values of bond distances P1—O2 and P1—O3 in (I) are contained within the range of the delocalized bond lengths 1.473–1.534 Å (mean value 1.501 Å) for aminophosphonic acids (Choi & McPartlin, 2000).

Analysis of the structural data indicates that the coordination around P atom is nearly tetrahedral, with the angles varying from 105.03 (10) to 116.84 (11)°.

Table 2 presents the hydrogen-bonding geometry and C—H···O interactions, with H···O contacts significantly less than the sum of the van der Waals radii (Taylor & Kennard, 1982).

The crystal-packing properties are influenced by presence of the water molecules in the crystal lattice. The solvent water molecule is a donor of two hydrogen bonds and is involved in two C—H···O interactions.

Considering the above P—O distances, it must be noticed that they correspond to three different environments (in order of decreasing bond distances): O1 is protonated and a donor in one O—H···O interaction; O2 is an acceptor in two (O—H···O and N—H···O) interactions; O3 is an acceptor in three (two O—H···O and one C—H···O) interactions.

Apart from the typical hydrogen bonds, aromatic π–π-stacking interactions between pyridyl rings are found. They additionally stabilize the molecular packing of (I). The distances between the centroids of the pyridyl rings are Cg1···Cg2(1 - x, 1 - y, 1 - z) = 3.738 (4) Å and Cg1···Cg3(-x, 1 - y, 1 - z) = 4.021 (4) Å. The perpendicular distances between the rings are 3.514 (4) and 3.459 (4) Å, respectively.

The conformation of the non-H skeleton of the title molecule is described by the torsion angles summarized in Table 1.

S2. Experimental

The title compound was synthesized in one step by the acidolysis of diethyl 3-pyridylmethylphosphonate with hydrobromic acid in acetic acid (Wasilewski et al., 1976; Ochocki et al., 1997) and was recrystallized from a water/ethanol mixture (1:1 by volume). The purity of the product was confirmed by ¹H NMR analysis.

S3. Refinement

H atoms from pyridyl and methylidene groups, except H1, were geometrically placed and refined using a riding model with isotropic displacement parameters equal to 1.2U_eq of the attached C atom. H atoms, which are involved in the hydrogen bonds, were located from the difference map and refined isotropically. The H401 and H402 atoms of the solvent water molecule were refined with the O—H distance restrained to 0.95 (3) Å (U_iso = 1.5U_eq of atom O4).

Computing details

Data collection: KM-4 Data Collection Program (Kuma, 1998); cell refinement: KM4 Data Collection Program; data reduction: DATAPROC (Kuma, 1996); program(s) used to solve structure: SHELXS86 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEX (McArdle, 1995); software used to prepare material for publication: PARST97 (Nardelli, 1996b).

Figures

Fig. 1. The structure of the title compound with the atom-labeling scheme. Displacement ellipsoids are drawn at the 40% probability level.

3-pyridylmethylphosphonic acid monohydrate

Crystal data

C6H8NO3P·H2O	F(000) = 400
Mr = 191.12	Dx = 1.549 Mg m^−3
Monoclinic, P21/n	Cu Kα radiation, λ = 1.54178 Å
a = 7.0554 (7) Å	Cell parameters from 24 reflections
b = 14.0106 (13) Å	θ = 20.0–37.8°
c = 8.5228 (15) Å	µ = 2.84 mm^−1
β = 103.444 (12)°	T = 293 K
V = 819.40 (18) Å^3	Cylinder, colourless
Z = 4	0.15 mm (radius)

Data collection

Kuma KM-4 diffractometer	1302 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.061
Graphite monochromator	θmax = 67.1°, θmin = 6.2°
ω scans	h = −7→8
Absorption correction: for a cylinder mounted on the ϕ axis (CYCLABS; Nardelli, 1996a)	k = −16→16
Tmin = 0.491, Tmax = 0.527	l = 0→10
2917 measured reflections	3 standard reflections every 150 reflections
1410 independent reflections	intensity decay: <3%

Refinement

Refinement on F^2	Hydrogen site location: difference Fourier map
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.052	w = 1/[σ^2(Fo^2) + (0.078P)^2 + 0.3766P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.146	(Δ/σ)max = 0.007
S = 1.11	Δρmax = 0.44 e Å^−3
1410 reflections	Δρmin = −0.42 e Å^−3
124 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
2 restraints	Extinction coefficient: 0.025 (2)
Primary atom site location: structure-invariant direct methods

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
P1	0.20789 (9)	0.28625 (4)	0.87719 (7)	0.0352 (4)
O1	0.0880 (3)	0.21576 (12)	0.7493 (2)	0.0451 (6)
H11	0.006 (5)	0.238 (3)	0.691 (4)	0.061 (11)*
O2	0.3056 (3)	0.22375 (11)	1.0179 (2)	0.0449 (6)
O3	0.0871 (3)	0.36656 (12)	0.9132 (2)	0.0505 (6)
C1	0.3987 (4)	0.33214 (19)	0.7905 (3)	0.0456 (7)
H101	0.4835	0.3722	0.8697	0.055*
H102	0.4759	0.2790	0.7670	0.055*
C2	0.3281 (4)	0.38905 (18)	0.6388 (3)	0.0369 (6)
C3	0.3093 (4)	0.48717 (18)	0.6441 (3)	0.0389 (6)
H3	0.3427	0.5188	0.7426	0.047*
N1	0.2431 (3)	0.53678 (15)	0.5080 (2)	0.0406 (6)
H1	0.239 (5)	0.600 (3)	0.519 (4)	0.056 (9)*
C4	0.1930 (4)	0.4961 (2)	0.3627 (3)	0.0444 (7)
H4	0.1458	0.5331	0.2713	0.053*
C5	0.2117 (4)	0.3996 (2)	0.3496 (3)	0.0463 (7)
H5	0.1799	0.3703	0.2490	0.056*
C6	0.2785 (4)	0.34601 (18)	0.4876 (3)	0.0427 (7)
H6	0.2904	0.2802	0.4793	0.051*
O4	0.2249 (4)	0.55319 (19)	0.9842 (3)	0.0759 (8)
H401	0.117 (6)	0.587 (3)	1.013 (6)	0.114*
H402	0.190 (7)	0.487 (2)	0.978 (6)	0.114*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.0428 (6)	0.0281 (5)	0.0314 (5)	0.0006 (2)	0.0016 (3)	0.0014 (2)
O1	0.0513 (13)	0.0342 (11)	0.0417 (11)	−0.0025 (8)	−0.0057 (9)	−0.0005 (7)
O2	0.0562 (13)	0.0340 (9)	0.0367 (10)	−0.0037 (8)	−0.0053 (9)	0.0066 (7)
O3	0.0627 (14)	0.0397 (10)	0.0495 (11)	0.0107 (8)	0.0138 (9)	−0.0029 (7)
C1	0.0408 (15)	0.0431 (14)	0.0490 (15)	0.0009 (12)	0.0026 (11)	0.0070 (11)
C2	0.0340 (13)	0.0356 (12)	0.0421 (13)	−0.0006 (10)	0.0110 (9)	0.0026 (10)
C3	0.0440 (15)	0.0348 (13)	0.0403 (13)	−0.0029 (10)	0.0145 (10)	−0.0033 (10)
N1	0.0473 (14)	0.0318 (12)	0.0452 (12)	0.0004 (9)	0.0160 (9)	0.0032 (8)
C4	0.0485 (17)	0.0458 (15)	0.0393 (13)	−0.0001 (11)	0.0113 (11)	0.0062 (10)
C5	0.0545 (18)	0.0467 (15)	0.0380 (13)	−0.0050 (12)	0.0115 (11)	−0.0063 (11)
C6	0.0456 (16)	0.0345 (12)	0.0492 (15)	−0.0004 (11)	0.0137 (11)	−0.0040 (10)
O4	0.0752 (18)	0.0786 (17)	0.0845 (17)	−0.0270 (14)	0.0403 (13)	−0.0273 (14)

Geometric parameters (Å, º)

P1—O3	1.4860 (18)	C3—H3	0.9300
P1—O2	1.5150 (17)	N1—C4	1.334 (3)
P1—O1	1.5655 (18)	N1—H1	0.89 (3)
P1—C1	1.799 (3)	C4—C5	1.366 (4)
O1—H11	0.74 (3)	C4—H4	0.9300
C1—C2	1.502 (3)	C5—C6	1.383 (4)
C1—H101	0.9700	C5—H5	0.9300
C1—H102	0.9700	C6—H6	0.9300
C2—C3	1.383 (4)	O4—H401	0.97 (3)
C2—C6	1.392 (3)	O4—H402	0.95 (3)
C3—N1	1.340 (3)
O3—P1—O2	116.84 (11)	N1—C3—C2	120.2 (2)
O3—P1—O1	112.23 (12)	N1—C3—H3	119.9
O2—P1—O1	105.03 (10)	C2—C3—H3	119.9
O3—P1—C1	109.52 (12)	C4—N1—C3	123.1 (2)
O2—P1—C1	106.60 (12)	C4—N1—H1	121 (2)
O1—P1—C1	105.92 (12)	C3—N1—H1	116 (2)
P1—O1—H11	115 (3)	N1—C4—C5	119.3 (2)
C2—C1—P1	114.42 (17)	N1—C4—H4	120.4
C2—C1—H101	108.7	C5—C4—H4	120.4
P1—C1—H101	108.7	C4—C5—C6	119.2 (2)
C2—C1—H102	108.7	C4—C5—H5	120.4
P1—C1—H102	108.7	C6—C5—H5	120.4
H101—C1—H102	107.6	C5—C6—C2	121.0 (2)
C3—C2—C6	117.1 (2)	C5—C6—H6	119.5
C3—C2—C1	121.0 (2)	C2—C6—H6	119.5
C6—C2—C1	121.9 (2)	H401—O4—H402	106 (4)
O3—P1—C1—C2	−58.1 (2)	C2—C3—N1—C4	−0.2 (4)
O2—P1—C1—C2	174.66 (18)	C3—N1—C4—C5	−1.0 (4)
O1—P1—C1—C2	63.2 (2)	N1—C4—C5—C6	1.3 (4)
P1—C1—C2—C3	93.1 (3)	C4—C5—C6—C2	−0.5 (4)
P1—C1—C2—C6	−86.7 (3)	C3—C2—C6—C5	−0.6 (4)
C6—C2—C3—N1	0.9 (4)	C1—C2—C6—C5	179.3 (2)
C1—C2—C3—N1	−178.9 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H11···O2^i	0.74 (3)	1.87 (3)	2.598 (3)	170 (4)
N1—H1···O2^ii	0.89 (3)	1.78 (3)	2.644 (3)	163 (3)
O4—H401···O3^iii	0.97 (3)	1.82 (4)	2.787 (4)	171 (4)
O4—H402···O3	0.95 (3)	1.87 (3)	2.806 (3)	166 (3)
C3—H3···O4	0.93	2.44	3.227 (4)	142
C1—H101···O4^iv	0.97	2.38	3.309 (4)	159
C4—H4···O3^v	0.93	2.44	3.313 (3)	156

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