[(4,4-Dimethyl-2-oxo-1,3-oxazolidin-3-yl)methyl]phosphonic acid

The title compound, C₆H₁₂NO₅P, was synthesized as an inter­mediate phase in a search for new N-(phosphono­methyl)glycine derivatives. The mol­ecules are held together by O-H...O hydrogen bonds, forming chains along the b axis in the crystal structure. The observed mol­ecular structure is compared with that calculated by the density functional theory method.

S1. Comment

The herbicidal activities of derivatives of N-(phosphonomethyl)glycine (glyphosate) were reported by Baird et al. (1971). These compounds have also been effective in suppressing tumour growth and have been investigated as potential lead compounds with anticancer, antiviral and antibacterial activities (Kafarski & Lejczak, 1991; Alonso et al., 2000; Camden, 1999, 2000). Recently, we synthesized a series of five new α-aminophosphonic acids and investigated their genotoxic and antiproliferative activities (Naydenova et al., 2006). Among the aforesaid five compounds, only for compound (I) were were able to obtain crystals suitable for X-ray diffraction. In this paper, we report the crystal structure of (I) and compare its geometric parameters with those optimized by density functional theory (DFT) calculations. Such a comparison is required in order to verify whether the DFT method could be employed for investigating the molecular structures of the other four compounds in the series.

The molecular structure of (I) is shown in Fig. 1. The structural features of the 2-oxazolidinone ring are comparable with those of similar compounds (Rios et al., 2002; Eknoian et al., 1998). The ring has an envelope conformation, with atom C4 deviating by 0.416 (6) Å from the plane defined by the other four atoms (N3/C2/O1/C5). The P1—C8 bond length of 1.811 (4) Å and the N3—C8—P1 angle of 113.5 (2)° are comparable with the corresponding values found for the glyphosate molecule [1.817 (3) Å and 111.7 (2)°, respectively; Sheldrick & Morr (1981)]. The similarity in P1—O4 and P1—O5 bond distances (Table 1) corresponds to the fact that there is no transfer of an H atom from the acid moiety to the N atom.

Symmetrically equivalent molecules, generated by a 2₁ screw axis, are linked through O—H···O hydrogen bonds (Table 2), forming a chain parallel to the b axis (Fig. 2). In the chain, the molecules face one another in such a way that the phosphonic acid moieties form the inner side of the chain, whereas the 2-oxazolidinone groups are outside it. Additional weak C—H···O interactions link the chains into `pseudo-layers' parallel to the (100) plane. It is worth noting that polar interactions exist inside the pseudo-layers, whereas non-polar ones are found outside them.

The values of the bond lengths and angles calculated by the DFT method are in good agreement with the experimental data (Table 1), the differences not exceeding 0.06 Å for the bond lengths and 3° for the valence angles. This shows that an envelope conformation of the 2-oxazolidinone ring is most probable, with atom C4 displaced by 0.322 Å from the least-squares plane formed by the other four atoms. The major difference between the computed and experimental structures is in the value of the torsion angle N3—C8—P1—O4 [−78.2 and −63.6 (3)°, respectively]. Consequently, the intramolecular interaction between the oxazolidinone and phosphonic parts, O4—H4···O2, is more pronounced in the calculated structure than in the experimental one [O4—O2 = 2.727 and 3.250 (4) Å, respectively].

S2. Experimental

Compound (I) was prepared according to the method of Naydenova et al. (2006). Crystals of (I) suitable for single-crystal X-ray diffraction were grown as colourless needles by slow evaporation of an aqueous solution at 277 K.

S3. Refinement

Methyl H atoms were constrained to an ideal geometry, with C—H = 0.96 Å and U_iso(H) = 1.5U_eq(C), but were allowed to rotate freely about their parent C—C bonds. The other H atoms were placed in calculated positions, with C—H_methylene = 0.97 and O—H_hydroxy = 0.82 Å, and constrained to ride on their parent atoms, with U_iso(H) = 1.2U_eq(C,O).

DFT calculations at the B3LYP/6311++G(d,p) level of theory using GAUSSIAN03 (Frisch et al., 2004) were performed. Optimizations started from the X-ray geometry of (I) and were followed by optimization of all geometric variables (bond lengths and angles), without any symmetry constraint.

Computing details

Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

	Fig. 1. The molecular structure of (I), the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
	Fig. 2. A view of the chain of (I), along the b axis. H atoms have been omitted except for those involved in O—H···O hydrogen bonds (dotted lines). [Symmetry codes: (i) 1 − x, 1/2 + y, 3/2 − z; (ii) x, y − 1, z.]

[(4,4-dimethyl-2-oxo-1,3-oxazolidin-3-yl)methyl]phosphonic acid

Crystal data

C6H12NO5P	F(000) = 440
Mr = 209.14	Dx = 1.502 Mg m^−3
Monoclinic, P21/c	Melting point = 430–431 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 9.2775 (13) Å	Cell parameters from 22 reflections
b = 6.7213 (16) Å	θ = 18.2–19.6°
c = 14.875 (2) Å	µ = 0.29 mm^−1
β = 94.614 (11)°	T = 290 K
V = 924.6 (3) Å^3	Prism, colourless
Z = 4	0.24 × 0.24 × 0.22 mm

Data collection

Enraf–Nonius CAD-4 diffractometer	Rint = 0.096
Radiation source: fine-focus sealed tube	θmax = 30.0°, θmin = 2.2°
Graphite monochromator	h = 0→13
ω/2θ scans	k = −9→9
5096 measured reflections	l = −20→20
2661 independent reflections	3 standard reflections every 120 min
1642 reflections with I > 2σ(I)	intensity decay: 1%

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.067	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.192	H-atom parameters constrained
S = 0.98	w = 1/[σ^2(Fo^2) + (0.0712P)^2 + 1.849P] where P = (Fo^2 + 2Fc^2)/3
2661 reflections	(Δ/σ)max < 0.001
118 parameters	Δρmax = 0.29 e Å^−3
0 restraints	Δρmin = −0.34 e Å^−3

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
C2	0.7930 (4)	0.9278 (5)	0.7173 (3)	0.0350 (8)
C4	0.7711 (4)	0.7504 (6)	0.5822 (2)	0.0370 (8)
C5	0.7180 (5)	0.9636 (6)	0.5695 (3)	0.0454 (9)
H5A	0.7572	1.0240	0.5175	0.054*
H5B	0.6132	0.9678	0.5612	0.054*
C6	0.6654 (7)	0.5990 (8)	0.5410 (3)	0.0706 (16)
H6A	0.7044	0.4678	0.5508	0.106*
H6B	0.6490	0.6231	0.4774	0.106*
H6C	0.5756	0.6098	0.5685	0.106*
C7	0.9209 (5)	0.7264 (9)	0.5490 (3)	0.0655 (14)
H7A	0.9843	0.8262	0.5762	0.098*
H7B	0.9149	0.7410	0.4846	0.098*
H7C	0.9580	0.5968	0.5651	0.098*
C8	0.8128 (4)	0.5680 (5)	0.7373 (2)	0.0335 (8)
H8A	0.8864	0.6011	0.7851	0.040*
H8B	0.8523	0.4664	0.7001	0.040*
N3	0.7806 (3)	0.7447 (4)	0.68248 (19)	0.0320 (6)
O1	0.7700 (3)	1.0657 (4)	0.65187 (19)	0.0460 (7)
O2	0.8228 (3)	0.9740 (4)	0.79589 (18)	0.0447 (7)
O3	0.5438 (3)	0.4027 (4)	0.71827 (19)	0.0480 (7)
O4	0.6050 (3)	0.6255 (4)	0.85285 (17)	0.0394 (6)
H4	0.5778	0.7249	0.8244	0.059*
O5	0.7195 (3)	0.3065 (4)	0.85448 (17)	0.0433 (7)
H5	0.7562	0.2172	0.8265	0.065*
P1	0.65676 (10)	0.46742 (13)	0.78740 (6)	0.0310 (2)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C2	0.0339 (17)	0.0291 (18)	0.042 (2)	−0.0012 (14)	0.0048 (15)	−0.0029 (14)
C4	0.048 (2)	0.0336 (18)	0.0295 (17)	0.0002 (16)	0.0018 (15)	0.0004 (14)
C5	0.061 (3)	0.040 (2)	0.0363 (19)	0.004 (2)	0.0054 (17)	0.0049 (17)
C6	0.113 (5)	0.055 (3)	0.040 (2)	−0.031 (3)	−0.017 (3)	0.004 (2)
C7	0.074 (3)	0.079 (4)	0.047 (3)	0.023 (3)	0.022 (2)	0.002 (2)
C8	0.0361 (18)	0.0293 (18)	0.0345 (17)	0.0033 (13)	−0.0013 (14)	−0.0011 (13)
N3	0.0369 (16)	0.0266 (14)	0.0323 (15)	0.0007 (12)	0.0022 (12)	−0.0028 (12)
O1	0.0648 (19)	0.0280 (14)	0.0455 (15)	0.0002 (12)	0.0061 (13)	0.0018 (11)
O2	0.0574 (17)	0.0343 (14)	0.0413 (14)	0.0011 (13)	−0.0030 (12)	−0.0123 (12)
O3	0.0542 (18)	0.0395 (15)	0.0479 (16)	−0.0148 (13)	−0.0103 (13)	0.0014 (13)
O4	0.0483 (15)	0.0331 (13)	0.0369 (13)	0.0100 (12)	0.0029 (11)	0.0000 (11)
O5	0.0668 (19)	0.0274 (13)	0.0351 (13)	0.0136 (12)	0.0011 (12)	0.0020 (10)
P1	0.0384 (5)	0.0230 (4)	0.0309 (4)	0.0000 (4)	−0.0017 (3)	0.0010 (3)

Geometric parameters (Å, º)

C2—O2	1.220 (4)	C7—H7A	0.9600
C2—N3	1.336 (4)	C7—H7B	0.9600
C2—O1	1.348 (4)	C7—H7C	0.9600
C4—N3	1.487 (4)	C8—N3	1.459 (4)
C4—C6	1.509 (6)	C8—P1	1.811 (4)
C4—C7	1.520 (6)	C8—H8A	0.9700
C4—C5	1.523 (6)	C8—H8B	0.9700
C5—O1	1.453 (5)	O3—P1	1.473 (3)
C5—H5A	0.9700	O4—P1	1.543 (3)
C5—H5B	0.9700	O4—H4	0.8200
C6—H6A	0.9600	O5—P1	1.552 (3)
C6—H6B	0.9600	O5—H5	0.8200
C6—H6C	0.9600
O2—C2—N3	127.7 (4)	H7A—C7—H7B	109.5
O2—C2—O1	121.8 (3)	C4—C7—H7C	109.5
N3—C2—O1	110.5 (3)	H7A—C7—H7C	109.5
N3—C4—C6	112.0 (3)	H7B—C7—H7C	109.5
N3—C4—C7	110.0 (3)	N3—C8—P1	113.5 (2)
C6—C4—C7	112.2 (4)	N3—C8—H8A	108.9
N3—C4—C5	98.1 (3)	P1—C8—H8A	108.9
C6—C4—C5	113.0 (4)	N3—C8—H8B	108.9
C7—C4—C5	110.8 (4)	P1—C8—H8B	108.9
O1—C5—C4	104.9 (3)	H8A—C8—H8B	107.7
O1—C5—H5A	110.8	C2—N3—C8	121.7 (3)
C4—C5—H5A	110.8	C2—N3—C4	111.2 (3)
O1—C5—H5B	110.8	C8—N3—C4	125.1 (3)
C4—C5—H5B	110.8	C2—O1—C5	107.8 (3)
H5A—C5—H5B	108.8	P1—O4—H4	109.5
C4—C6—H6A	109.5	P1—O5—H5	109.5
C4—C6—H6B	109.5	O3—P1—O4	113.82 (17)
H6A—C6—H6B	109.5	O3—P1—O5	116.85 (16)
C4—C6—H6C	109.5	O4—P1—O5	101.15 (14)
H6A—C6—H6C	109.5	O3—P1—C8	111.73 (17)
H6B—C6—H6C	109.5	O4—P1—C8	107.57 (16)
C4—C7—H7A	109.5	O5—P1—C8	104.69 (16)
C4—C7—H7B	109.5
O3—P1—C8—N3	62.0 (3)	P1—C8—N3—C4	−106.1 (3)
O4—P1—C8—N3	−63.6 (3)	C8—N3—C2—O2	−4.4 (6)
O5—P1—C8—N3	−170.7 (2)	O1—C2—N3—C4	9.9 (4)
P1—C8—N3—C2	91.6 (4)	C2—O1—C5—C4	−23.0 (4)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4···O3^i	0.82	1.73	2.503 (4)	157
O5—H5···O2^ii	0.82	1.82	2.609 (4)	162
C5—H5A···O5^iii	0.97	2.68	3.553 (4)	151
C6—H6B···O4^iii	0.96	2.52	3.365 (4)	147

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