Experimental electron density of urea–phosphoric acid (1/1) at 100 K

Rodrigues, B.L.; Tellgren, R.; Fernandes, N.G.

doi:10.1107/S0108768101004359

Experimental electron density of urea–phosphoric acid (1/1) at 100 K

B. L. Rodrigues, R. Tellgren and N. G. Fernandes

The deformation electron density of the urea–phosphoric acid adduct has been studied from 100 K X-ray and neutron diffraction experiments. Data were interpreted according to the Hirshfeld model. The long hydrogen bonds show characteristics of electrostatic interaction. Deformation density maps on the short hydrogen bond shows hydrogen more strongly bonded to urea than to phosphoric acid, and peak maxima at almost midway between the two O—H bonds.

Keywords: electron density; hydrogen bonding; urea–phosphoric acid.

Read article Similar articles

Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768101004359/ca0006sup1.cif Contains datablocks global, neutron, X-ray
	Structure factor file (CIF format) https://doi.org/10.1107/S0108768101004359/ca0006neutronsup2.hkl Contains datablock neutron
	Structure factor file (CIF format) https://doi.org/10.1107/S0108768101004359/ca0006X-raysup3.hkl Contains datablock X-ray

CCDC references: 166508; 166509

Computing details top

Data collection: XSCANS(Siemens, 1991) for X-ray. Cell refinement: XSCANS(Siemens, 1991) for X-ray. Data reduction: ARACOR (Lundgren, 1982) for neutron; P4red(Lundgren, 1982) for X-ray. Program(s) used to solve structure: DUPALS (Lundgren, 1982) for neutron. Program(s) used to refine structure: DUPALS (Lundgren, 1982) for neutron; DUPALS(Lundgren, 1982) for X-ray. Molecular graphics: ORTEP 3(Burnet & Johnson, 1996) for neutron; ORTEP-3 (Burnet and Johnson, 1996) and FOPLOT(Lundgren, 1982) for X-ray. For both compounds, software used to prepare material for publication: Ms-DOS 6.0 editor.

Figures top

(neutron) urea phosphate top

Crystal data top

CH₇N₂O₅P	F(000) = 656
M_r = 159	D_x = 1.820 Mg m⁻³
Orthorhombic, Pbca	Neutron radiation, λ = 1.207 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 9 reflections
a = 17.43 (2) Å	θ = 18.9–30.9°
b = 7.43 (2) Å	µ = 2.23 mm⁻¹
c = 8.97 (2) Å	T = 100 K
V = 1161 (4) Å³	Prismatic, colorless
Z = 8	3.8 × 2.2 × 1.0 mm

Data collection top

Huber four circle diffractometer	1579 reflections with I > −3σ(I)
Radiation source: Studsvik (Sweden) reactor	R_int = 0.017
Cu(220) double system monochromator	θ_max = 52°, θ_min = 1°
θ–2θ scans	h = −22→0
Absorption correction: analytical ?	k = −9→0
T_min = 0.55, T_max = 0.66	l = 0→11
1762 measured reflections	3 standard reflections every each 30 reflections reflections
1599 independent reflections	intensity decay: less than 2

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Refined anisotropically
R[F² > 2σ(F²)] = 0.053	w = 1/[σ²(F_o²)]
wR(F²) = 0.053	(Δ/σ)_max = 0.001
S = 1.35	Δρ_max = 0.38 e Å⁻³
1579 reflections	Δρ_min = −0.19 e Å⁻³
151 parameters	Extinction correction: see text

Crystal data top

CH₇N₂O₅P	V = 1161 (4) Å³
M_r = 159	Z = 8
Orthorhombic, Pbca	Neutron radiation, λ = 1.207 Å
a = 17.43 (2) Å	µ = 2.23 mm⁻¹
b = 7.43 (2) Å	T = 100 K
c = 8.97 (2) Å	3.8 × 2.2 × 1.0 mm

Data collection top

Huber four circle diffractometer	1579 reflections with I > −3σ(I)
Absorption correction: analytical ?	R_int = 0.017
T_min = 0.55, T_max = 0.66	3 standard reflections every each 30 reflections reflections
1762 measured reflections	intensity decay: less than 2
1599 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.053	0 restraints
wR(F²) = 0.053	Refined anisotropically
S = 1.35	Δρ_max = 0.38 e Å⁻³
1579 reflections	Δρ_min = −0.19 e Å⁻³
151 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
P	0.31097 (8)	0.2798 (2)	0.3096 (2)	0.0081 (7)
O1	0.33979 (8)	0.0912 (2)	0.3620 (2)	0.0117 (7)
O2	0.27752 (8)	0.3861 (2)	0.4378 (1)	0.0101 (6)
O3	0.24495 (8)	0.2515 (2)	0.1954 (2)	0.0118 (7)
O4	0.37978 (8)	0.3693 (2)	0.2372 (2)	0.0114 (7)
O5	0.44844 (8)	0.6367 (2)	0.3098 (2)	0.0121 (7)
N1	0.50979 (5)	0.7845 (1)	0.4931 (1)	0.0131 (5)
N2	0.39770 (5)	0.6329 (1)	0.5442 (1)	0.0143 (5)
C	0.45156 (6)	0.6836 (2)	0.4487 (1)	0.0092 (6)
H1	0.2975 (1)	0.0091 (3)	0.3944 (3)	0.024 (1)
H3	0.2591 (1)	0.1980 (4)	0.0962 (3)	0.023 (1)
H4	0.4113 (1)	0.5116 (4)	0.2826 (3)	0.025 (1)
H11	0.5526 (2)	0.8112 (4)	0.4195 (3)	0.026 (1)
H12	0.5142 (2)	0.8217 (4)	0.6004 (3)	0.029 (1)
H21	0.3520 (1)	0.5595 (4)	0.5086 (3)	0.027 (1)
H22	0.3995 (2)	0.6734 (4)	0.6509 (3)	0.031 (1)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P	0.0093 (7)	0.0093 (7)	0.0058 (7)	0.0003 (5)	−0.0007 (5)	−0.0007 (6)
O1	0.0121 (6)	0.0090 (6)	0.0139 (7)	0.0005 (6)	−0.0020 (5)	0.0010 (5)
O2	0.0129 (6)	0.0109 (6)	0.0064 (6)	0.0007 (5)	0.0005 (5)	−0.0008 (5)
O3	0.0108 (6)	0.0161 (6)	0.0084 (7)	0.0009 (5)	−0.0016 (5)	−0.0032 (6)
O4	0.0130 (6)	0.0106 (6)	0.0104 (7)	−0.0029 (5)	0.0030 (5)	−0.0013 (5)
O5	0.0155 (7)	0.0135 (7)	0.0074 (7)	−0.0038 (5)	0.0005 (5)	−0.0009 (5)
N1	0.0131 (4)	0.0143 (4)	0.0117 (5)	−0.0033 (3)	0.0001 (4)	−0.0024 (4)
N2	0.0144 (5)	0.0175 (5)	0.0111 (5)	−0.0047 (4)	0.0039 (3)	−0.0027 (4)
C	0.0103 (5)	0.0097 (5)	0.0077 (6)	−0.0002 (4)	0.0001 (4)	0.0002 (4)
H1	0.025 (1)	0.019 (1)	0.028 (1)	−0.002 (1)	−0.001 (1)	0.003 (1)
H3	0.023 (1)	0.030 (1)	0.017 (1)	0.000 (1)	−0.002 (1)	−0.005 (1)
H4	0.029 (1)	0.028 (1)	0.018 (1)	0.004 (1)	0.006 (1)	0.001 (1)
H11	0.025 (1)	0.028 (1)	0.024 (1)	−0.007 (1)	0.005 (1)	−0.000 (1)
H12	0.032 (1)	0.037 (1)	0.017 (1)	−0.009 (1)	−0.001 (1)	−0.008 (1)
H21	0.022 (1)	0.034 (1)	0.026 (1)	−0.011 (1)	0.003 (1)	−0.003 (1)
H22	0.034 (1)	0.043 (2)	0.016 (1)	−0.008 (1)	0.007 (1)	−0.008 (1)

Geometric parameters (Å, º) top

P—O1	1.562 (2)	N1—H12	1.004 (3)
P—O2	1.512 (2)	N2—H21	1.017 (3)
P—O4	1.517 (2)	N2—H22	1.003 (3)
P—O3	1.554 (2)	O1—H1	1.000 (3)
C—O5	1.295 (2)	O3—H3	1.005 (3)
C—N1	1.323 (1)	O4—H4	1.259 (3)
C—N2	1.325 (1)	O5—H4	1.160 (3)
N1—H11	1.016 (3)

O1—P—O2	111.4 (1)	C—N1—H11	118.6 (2)
O1—P—O3	108.3 (1)	C—N1—H12	120.2 (2)
O1—P—O4	105.5 (1)	H11—N1—H12	120.8 (2)
O2—P—O3	106.6 (1)	C—N2—H21	120.4 (2)
O2—P—O4	113.6 (1)	C—N2—H22	120.5 (2)
O3—P—O4	111.3 (1)	H21—N2—H22	119.0 (2)
P—O1—H1	113.5 (2)	O5—C—N1	118.3 (1)
P—O3—H3	117.0 (2)	O5—C—N2	121.0 (1)
P—O4—H4	125.1 (2)	N1—C—N2	120.8 (1)
C—O5—H4	116.2 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	1.000 (3)	1.643 (3)	2.639 (2)	174.4 (3)
O3—H3···O2ⁱⁱ	1.005 (3)	1.584 (3)	2.589 (2)	177.4 (3)
O4—H4···O5	1.259 (3)	1.160 (3)	2.410 (2)	170.2 (3)
N1—H11···O4ⁱⁱⁱ	1.016 (3)	1.885 (3)	2.893 (2)	171.4 (2)
N1—H12···O5^iv	1.004 (3)	2.221 (3)	3.090 (2)	143.9 (2)
N2—H21···O2	1.017 (3)	1.936 (3)	2.943 (2)	170.1 (2)
N2—H22···O5^iv	1.003 (4)	2.180 (3)	3.064 (2)	146.2 (2)

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

(X-ray) urea phosphate top

Crystal data top

CH₇N₂O₅P	F(000) = 656.0
M_r = 159.0	D_x = 1.815 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 98 reflections
a = 17.4527 (7) Å	θ = 12–20°
b = 7.4465 (5) Å	µ = 0.43 mm⁻¹
c = 8.9589 (4) Å	T = 100 K
V = 1164.31 (9) Å³	Almost spherical, colorless
Z = 8	0.19 mm (radius)

Data collection top

SIEMENS P4 diffractometer	7257 reflections with I > 0.0σ(I)
Radiation source: sealed tube	R_int = 0.013
Graphite monochromator	θ_max = 60°, θ_min = 1°
θ–2θ scans	h = −1→41
Absorption correction: analytical ?	k = −1→17
T_min = 0.87, T_max = 0.89	l = −1→21
8472 measured reflections	3 standard reflections every each 400 reflections reflections
7433 independent reflections	intensity decay: 1.1%

Refinement top

Refinement on F²	Hydrogen fixed from neutron
Least-squares matrix: full	w = 1/[σ²(F_o²) + 0.0068F_o² + 34.9λ/sen(θ)-0.00055F_o²λ/sen(θ)]
R[F² > 2σ(F²)] = 0.058	(Δ/σ)_max = 0.001
wR(F²) = 0.053	Δρ_max = 0.61 e Å⁻³
S = 0.69	Δρ_min = −0.62 e Å⁻³
7257 reflections	Extinction correction: see text
215 parameters

Crystal data top

CH₇N₂O₅P	V = 1164.31 (9) Å³
M_r = 159.0	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 17.4527 (7) Å	µ = 0.43 mm⁻¹
b = 7.4465 (5) Å	T = 100 K
c = 8.9589 (4) Å	0.19 mm (radius)

Data collection top

SIEMENS P4 diffractometer	7257 reflections with I > 0.0σ(I)
Absorption correction: analytical ?	R_int = 0.013
T_min = 0.87, T_max = 0.89	3 standard reflections every each 400 reflections reflections
8472 measured reflections	intensity decay: 1.1%
7433 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.058	215 parameters
wR(F²) = 0.053	Hydrogen fixed from neutron
S = 0.69	Δρ_max = 0.61 e Å⁻³
7257 reflections	Δρ_min = −0.62 e Å⁻³

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
P	0.311006 (9)	0.27977 (2)	0.30966 (2)	0.00835
O1	0.33980 (3)	0.09073 (8)	0.36199 (7)	0.01296
O2	0.27739 (3)	0.38618 (8)	0.43782 (6)	0.01059
O3	0.24492 (3)	0.25128 (8)	0.19524 (6)	0.01337
O4	0.37975 (4)	0.36869 (8)	0.23724 (6)	0.01262
O5	0.44835 (4)	0.63663 (8)	0.30980 (8)	0.01380
N1	0.50967 (4)	0.78421 (9)	0.49287 (7)	0.01389
N2	0.39746 (4)	0.63295 (9)	0.54387 (8)	0.01559
C	0.45132 (4)	0.68355 (8)	0.44853 (9)	0.00993
H1	0.29755	0.00911	0.39445	0.02384
H3	0.25912	0.19804	0.09619	0.02348
H4	0.41127	0.51156	0.28258	0.02507
H11	0.55260	0.81118	0.41950	0.02600
H12	0.51423	0.82167	0.60044	0.02865
H21	0.35197	0.55954	0.50861	0.02731
H22	0.39954	0.67336	0.65086	0.03132

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
P	0.00824 (6)	0.00962 (6)	0.00719 (6)	−0.00015 (4)	0.00004 (4)	−0.00067 (4)
O1	0.0111 (2)	0.0101 (1)	0.0177 (2)	0.0003 (1)	−0.0007 (1)	0.0010 (1)
O2	0.0124 (1)	0.0119 (1)	0.0075 (1)	0.0007 (1)	0.0010 (1)	−0.0009 (1)
O3	0.0107 (1)	0.0200 (2)	0.0094 (1)	0.0013 (1)	−0.0023 (1)	−0.0037 (1)
O4	0.0129 (2)	0.0132 (2)	0.0117 (2)	−0.0032 (1)	0.0040 (1)	−0.0022 (1)
O5	0.0168 (2)	0.0160 (2)	0.0086 (1)	−0.0057 (2)	0.0008 (1)	−0.0005 (1)
N1	0.0119 (2)	0.0167 (2)	0.0131 (2)	−0.0041 (2)	0.0004 (1)	−0.0019 (2)
N2	0.0142 (2)	0.0204 (3)	0.0121 (2)	−0.0060 (2)	0.0046 (2)	−0.0036 (2)
C	0.0096 (2)	0.0105 (2)	0.0097 (2)	−0.0006 (1)	0.0002 (1)	−0.0000 (1)
H1	0.024998	0.018751	0.027763	−0.002416	−0.000650	0.003265
H3	0.023347	0.030052	0.017041	0.000250	−0.001957	−0.005255
H4	0.028995	0.028516	0.017700	0.003885	0.006139	0.001524
H11	0.025276	0.028459	0.024263	−0.007124	0.005188	−0.000453
H12	0.031773	0.036946	0.017236	−0.008599	−0.001259	−0.008311
H21	0.021820	0.034235	0.025889	−0.010745	0.002788	−0.003251
H22	0.034504	0.043219	0.016248	−0.008118	0.006685	−0.008459

Geometric parameters (Å, º) top

P—O1	1.566 (1)	O3—H3	1.003 (1)
P—O2	1.513 (1)	O4—H4	1.265 (1)
P—O4	1.516 (1)	H4—O5	1.160 (1)
P—O3	1.558 (1)	N1—H11	1.017 (1)
C—N1	1.325 (1)	N1—H12	1.006 (1)
C—N2	1.325 (1)	N2—H21	1.014 (1)
C—O5	1.292 (1)	N2—H22	1.005 (1)
O1—H1	0.999 (1)

O1—P—O2	111.58 (3)	C—N1—H11	118.95 (6)
O1—P—O3	108.19 (3)	C—N1—H12	120.29 (7)
O1—P—O4	105.46 (3)	H11—N1—H12	120.41 (7)
O2—P—O3	106.48 (3)	C—N2—H21	120.52 (7)
O2—P—O4	113.75 (3)	C—N2—H22	120.26 (7)
O3—P—O4	111.33 (3)	H21—N2—H22	119.12 (7)
P—O1—H1	113.40 (5)	O5—C—N1	118.17 (7)
P—O3—H3	116.95 (4)	O5—C—N2	120.98 (6)
P—O4—H4	125.04 (4)	N1—C—N2	120.85 (7)
C—O5—H4	116.22 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	0.999 (1)	1.643 (1)	2.639 (1)	174.58 (4)
O3—H3···O2ⁱⁱ	1.003 (1)	1.584 (1)	2.586 (1)	177.31 (4)
O4—H4···O5	1.265 (1)	1.160 (1)	2.416 (1)	170.25 (4)
N1—H11···O4ⁱⁱⁱ	1.017 (1)	1.884 (1)	2.893 (1)	171.35 (4)
N1—H12···O5^iv	1.006 (1)	2.222 (1)	3.091 (1)	143.73 (4)
N2—H21···O2	1.014 (1)	1.940 (1)	2.945 (1)	170.27 (4)
N2—H22···O5^iv	1.005 (1)	2.181 (1)	3.067 (1)	146.20 (5)

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

Experimental details

	(neutron)	(X-ray)
Crystal data
Chemical formula	CH₇N₂O₅P	CH₇N₂O₅P
M_r	159	159.0
Crystal system, space group	Orthorhombic, Pbca	Orthorhombic, Pbca
Temperature (K)	100	100
a, b, c (Å)	17.43 (2), 7.43 (2), 8.97 (2)	17.4527 (7), 7.4465 (5), 8.9589 (4)
V (Å³)	1161 (4)	1164.31 (9)
Z	8	8
Radiation type	Neutron, λ = 1.207 Å	Mo Kα
µ (mm⁻¹)	2.23	0.43
Crystal size (mm)	3.8 × 2.2 × 1.0	0.19 (radius)

Data collection
Diffractometer	Huber four circle diffractometer	SIEMENS P4 diffractometer
Absorption correction	Analytical	Analytical
T_min, T_max	0.55, 0.66	0.87, 0.89
No. of measured, independent and observed reflections	1762, 1599, 1579 [I > −3σ(I)]	8472, 7433, 7257 [I > 0.0σ(I)]
R_int	0.017	0.013
(sin θ/λ)_max (Å⁻¹)	0.653	1.218

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.053, 0.053, 1.35	0.058, 0.053, 0.69
No. of reflections	1579	7257
No. of parameters	151	215
No. of restraints	0	?
H-atom treatment	Refined anisotropically	Hydrogen fixed from neutron
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.19	0.61, −0.62

Computer programs: XSCANS(Siemens, 1991), ARACOR (Lundgren, 1982), P4red(Lundgren, 1982), DUPALS (Lundgren, 1982), DUPALS(Lundgren, 1982), ORTEP 3(Burnet & Johnson, 1996), ORTEP-3 (Burnet and Johnson, 1996) and FOPLOT(Lundgren, 1982), Ms-DOS 6.0 editor.

Selected geometric parameters (Å, º) for (neutron) top

P—O1	1.562 (2)	N1—H12	1.004 (3)
P—O2	1.512 (2)	N2—H21	1.017 (3)
P—O4	1.517 (2)	N2—H22	1.003 (3)
P—O3	1.554 (2)	O1—H1	1.000 (3)
C—O5	1.295 (2)	O3—H3	1.005 (3)
C—N1	1.323 (1)	O4—H4	1.259 (3)
C—N2	1.325 (1)	O5—H4	1.160 (3)
N1—H11	1.016 (3)

O1—P—O2	111.4 (1)	C—N1—H11	118.6 (2)
O1—P—O3	108.3 (1)	C—N1—H12	120.2 (2)
O1—P—O4	105.5 (1)	H11—N1—H12	120.8 (2)
O2—P—O3	106.6 (1)	C—N2—H21	120.4 (2)
O2—P—O4	113.6 (1)	C—N2—H22	120.5 (2)
O3—P—O4	111.3 (1)	H21—N2—H22	119.0 (2)
P—O1—H1	113.5 (2)	O5—C—N1	118.3 (1)
P—O3—H3	117.0 (2)	O5—C—N2	121.0 (1)
P—O4—H4	125.1 (2)	N1—C—N2	120.8 (1)
C—O5—H4	116.2 (2)

Hydrogen-bond geometry (Å, º) for (neutron) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···O2ⁱ	1.000 (3)	1.643 (3)	2.639 (2)	174.4 (3)
O3—H3···O2ⁱⁱ	1.005 (3)	1.584 (3)	2.589 (2)	177.4 (3)
O4—H4···O5	1.259 (3)	1.160 (3)	2.410 (2)	170.2 (3)
N1—H11···O4ⁱⁱⁱ	1.016 (3)	1.885 (3)	2.893 (2)	171.4 (2)
N1—H12···O5^iv	1.004 (3)	2.221 (3)	3.090 (2)	143.9 (2)
N2—H21···O2	1.017 (3)	1.936 (3)	2.943 (2)	170.1 (2)
N2—H22···O5^iv	1.003 (4)	2.180 (3)	3.064 (2)	146.2 (2)

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

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page