Charge density study of hydrogen [(2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate

The crystal structure and charge density of hydrogen (2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate, C₅H₉N₄O₃P·H₂O, have been determined by means of single-crystal X-ray diffraction. Diffraction data were collected at 105 K with Mo Kα radiation to a resolution of sin θ/λ = 1.08 Å⁻¹. A four-circle diffractometer equipped with a CCD area detector was used to collect 50 161 reflections over 3 d. 6082 unique reflections with I > 3σ(I) were used in the multipole model to map the deformation electron density and gave the final statistical factors R(F) = 0.0329, wR(F) = 0.0235 and g.o.f. = 1.37. Structure determination revealed that two O atoms in the crystal structure of the title compound act as hydrogen-bond acceptors for more than one hydrogen bond. Examination of deformation electron density maps showed preferential polarization of the lone-pair electron density of the two O atoms into the shortest hydrogen bonds.

Computing details

Data collection: COLLECT (Nonius BV, 1997-2000); cell refinement: HKL SCALEPACK (Otwinowski & Minor 1997); data reduction: HKL DENZO and SCALEPACK (Otwinowski & Minor 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: JANA2000 (Petricek & Dusek, 2000); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: JANA2000 (Petricek & Dusek, 2000).

hydrogen-[(2,4-diaminopyrimidin-1-io)methyl]phosphonate monohydrate

Crystal data

C5H9N4O3P·H2O	F(000) = 464
Mr = 222.15	Dx = 1.638 Mg m^−3
Monoclinic, P21/n	Mo Kα radiation, λ = 0.71069 Å
a = 5.8389 (2) Å	Cell parameters from 21482 reflections
b = 19.3579 (5) Å	θ = 1–50°
c = 8.0338 (3) Å	µ = 0.30 mm^−1
β = 97.203 (2)°	T = 105 K
V = 900.88 (5) Å^3	Prism, translucent colourless
Z = 4	0.3 × 0.2 × 0.2 mm

Data collection

Nonius KappaCCD diffractometer	6076 reflections with > 3σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.037
Graphite monochromator	θmax = 50.5°, θmin = 3.3°
Detector resolution: 9.1 pixels mm^-1	h = 0→12
CCD rotation scans	k = 0→42
34544 measured reflections	l = −17→16
9362 independent reflections

Refinement

Refinement on F	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F > 3σ(F)] = 0.033	H atoms treated by a mixture of independent and constrained refinement
wR(F) = 0.022	Weighting scheme based on measured s.u.'s w = 1/σ^2(F)
S = 1.37	(Δ/σ)max = 0.003
9362 reflections	Δρmax = 0.93 e Å^−3
368 parameters	Δρmin = −1.25 e Å^−3
0 restraints	Extinction correction: isotropic
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.026 (2)

Special details

Geometry. During the least squares refinement H atoms were shifted repeatedly so that the X—H distances (where X is the relevant heavy atom) corresponded to the values determined from neutron diffraction studies (Allen, 1986; Dahaoui et al., 1999). The neutron diffraction lengths of bonds C(sp³)-H, C(sp²)-H, N—H, O(hydroxyl)-H and O(water)-H were 1.085, 1.076, 1.032, 1.070 and 0.096 Å, respectively.

Refinement. Refinement in JANA2000 was based on F. Reflection file was imported from SHELX. In the final cycle of multipole refinement (Hansen & Coppens, 1978) the following parameters were refined: P_v, P_lm±, U^ij parameters of all atoms and positions and κ parameters of non-H atoms. The multipole expansion was truncated at octopole level for all non-H atoms and at dipole level for all H atoms. Other parameters were treated as follows: H atoms were shifted along the X—H bond vectors (where X is the relevant heavy atom) to average bond-distance values determined from neutron diffraction studies (Allen, 1986; Dahaoui et al., 1999). In the last refinement cycle the H atom positions were fixed and isotropic extinction coefficient was refined. κ parameters of non-H atoms and κ, parameters of all atoms were refined separately in the previous cycles of multipole refinement. Total number of all refined parameters was 368.

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

	x	y	z	Uiso*/Ueq
P1	0.200373 (17)	0.250975 (5)	0.793413 (13)	0.01040 (3)
O1	0.12354 (7)	0.17748 (2)	0.80948 (6)	0.01541 (11)
O2	0.13278 (8)	0.28505 (2)	0.62532 (6)	0.01534 (10)
O3	0.46994 (8)	0.25944 (3)	0.83675 (6)	0.01438 (11)
N1	0.05339 (9)	0.37694 (3)	0.89726 (5)	0.01121 (9)
C2	0.22777 (9)	0.42402 (2)	0.93384 (5)	0.01069 (9)
N2	0.41445 (10)	0.40775 (3)	1.03948 (7)	0.01451 (11)
N3	0.21824 (10)	0.48739 (3)	0.86660 (6)	0.01156 (9)
C4	0.03274 (9)	0.50591 (3)	0.75930 (6)	0.01183 (10)
N4	0.02685 (8)	0.56820 (3)	0.68987 (7)	0.01606 (11)
C5	−0.15870 (9)	0.45986 (3)	0.72092 (6)	0.01350 (10)
C6	−0.13942 (8)	0.39624 (3)	0.79033 (6)	0.01277 (10)
C7	0.07225 (8)	0.30393 (2)	0.94846 (6)	0.01199 (10)
O4	−0.12231 (8)	0.10517 (3)	1.02510 (6)	0.01841 (11)
H21	0.533339	0.446907	1.066205	0.029 (3)*
H22	0.431189	0.362999	1.109759	0.032 (3)*
H41	−0.117712	0.580518	0.607738	0.031 (3)*
H42	0.164629	0.601913	0.708183	0.028 (3)*
H5	−0.311782	0.474452	0.639752	0.041 (2)*
H6	−0.270379	0.356977	0.769913	0.036 (2)*
H71	0.170591	0.29812	1.071509	0.037 (2)*
H72	−0.101545	0.284708	0.952404	0.039 (2)*
H3	0.532744	0.239634	0.958281	0.049 (3)*
H401	−0.198478	0.144498	1.065917	0.027 (2)*
H402	−0.027646	0.130343	0.95666	0.036 (3)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
P1	0.01082 (5)	0.01008 (5)	0.00995 (5)	−0.00046 (4)	−0.00014 (3)	−0.00108 (4)
O1	0.01614 (18)	0.00995 (15)	0.0200 (2)	−0.00174 (13)	0.00190 (15)	−0.00286 (14)
O2	0.01754 (19)	0.01864 (18)	0.00898 (17)	0.00142 (14)	−0.00175 (14)	0.00006 (14)
O3	0.01050 (18)	0.01894 (19)	0.01321 (19)	−0.00094 (14)	−0.00037 (15)	0.00092 (15)
N1	0.01043 (17)	0.00935 (15)	0.01357 (15)	−0.00144 (14)	0.00035 (15)	−0.00062 (13)
C2	0.01009 (17)	0.00936 (15)	0.01209 (16)	−0.00090 (13)	−0.00075 (15)	−0.00011 (13)
N2	0.0129 (2)	0.01159 (16)	0.0173 (2)	−0.00210 (15)	−0.00470 (18)	0.00251 (16)
N3	0.01123 (17)	0.00949 (15)	0.01319 (15)	−0.00132 (14)	−0.00150 (16)	0.00083 (13)
C4	0.01170 (17)	0.01065 (16)	0.01261 (16)	−0.00030 (15)	−0.00057 (15)	0.00085 (14)
N4	0.01500 (19)	0.01264 (17)	0.0194 (2)	−0.00105 (15)	−0.00227 (17)	0.00470 (15)
C5	0.01125 (17)	0.01253 (17)	0.01581 (17)	−0.00080 (15)	−0.00192 (15)	0.00013 (14)
C6	0.01047 (17)	0.01171 (16)	0.01547 (17)	−0.00177 (14)	−0.00102 (16)	−0.00110 (14)
C7	0.01423 (18)	0.01000 (15)	0.01208 (18)	−0.00172 (13)	0.00296 (15)	−0.00068 (13)
O4	0.01739 (17)	0.0175 (2)	0.01999 (18)	−0.00082 (15)	0.0010 (2)	−0.00015 (16)

Geometric parameters (Å, º)

P1—O1	1.5022 (4)	N3—C4	1.3455 (7)
P1—O2	1.5103 (5)	C4—N4	1.3272 (7)
P1—O3	1.5774 (5)	C4—C5	1.4328 (7)
P1—C7	1.8427 (5)	N4—H41	1.032
O3—H3	1.070	N4—H42	1.032
N1—C2	1.3706 (7)	C5—C6	1.3507 (7)
N1—C6	1.3793 (7)	C5—H5	1.076
N1—C7	1.4723 (7)	C6—H6	1.076
C2—N2	1.3326 (7)	C7—H71	1.085
C2—N3	1.3387 (7)	C7—H72	1.085
N2—H21	1.032	O4—H401	0.960
N2—H22	1.032	O4—H402	0.960
O1—P1—O2	116.30 (2)	N4—C4—C5	119.76 (4)
O1—P1—O3	112.33 (2)	C4—N4—H41	117.04
O1—P1—C7	108.53 (2)	C4—N4—H42	122.41
O2—P1—O3	107.08 (3)	H41—N4—H42	120.37
O2—P1—C7	106.19 (2)	C4—C5—C6	117.13 (4)
O3—P1—C7	105.75 (2)	C4—C5—H5	122.24
C2—N1—C6	118.67 (4)	C6—C5—H5	120.63
C2—N1—C7	123.43 (4)	N1—C6—C5	121.56 (5)
C6—N1—C7	117.43 (4)	N1—C6—H6	114.37
N1—C2—N2	120.38 (4)	C5—C6—H6	124.07
N1—C2—N3	122.05 (4)	P1—C7—N1	111.57 (3)
N2—C2—N3	117.57 (5)	P1—C7—H71	110.18
C2—N2—H21	115.73	P1—C7—H72	106.83
C2—N2—H22	124.10	N1—C7—H71	111.50
H21—N2—H22	119.19	N1—C7—H72	107.45
C2—N3—C4	119.47 (5)	H71—C7—H72	109.15
N3—C4—N4	119.18 (5)	H401—O4—H402	96.76
N3—C4—C5	121.05 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H21···N3^i	1.032	1.954	2.9804 (7)	172.9
N2—H22···O1^ii	1.032	2.000	2.8729 (7)	140.6
N4—H41···O4^iii	1.032	1.807	2.8374 (7)	176.3
N4—H42···O1^iv	1.032	1.932	2.9392 (7)	164.4
O3—H3···O2^ii	1.070	1.474	2.5431 (7)	176.3
O4—H401···O2^v	0.960	1.782	2.7383 (8)	173.6
O4—H402···O1	0.960	1.809	2.7648 (7)	173.6

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