Literature DB >> 23634070

2-Amino-4-methyl-pyrimidinium dihydrogen phosphate.

Sajesh P Thomas1, Jyothi Sunkari.   

Abstract

A charge-assisted hydrogen-bonding network involving N-H⋯O and O-H⋯O hydrogen bonds stabilizes the crystal of the title salt, C5H8N3 (+)·H2PO4 (-). The dihydrogen phosphate anions form one-dimensional chains along [100], via O-H⋯O hydrogen bonds. The 2-amino-4-methyl-pyrimidinium cations are linked to these chains by means of two different kinds of N-H⋯O hydrogen bonds. Neighbouring chains are linked via C-H⋯N and C-H⋯O hydrogen bonds forming two-dimensional slab-like networks lying parallel to (01-1).

Entities:  

Year:  2013        PMID: 23634070      PMCID: PMC3629583          DOI: 10.1107/S160053681300648X

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

Intriguing anion clusters formed by the supra­molecular assembly of dihydrogen phosphates have been investigated recently (see: Hossain et al., 2012 ▶). Methyl­pyrimidine derivatives are known to be synthetic precursors to many bioactive pyrimidine derivatives (see: Xue et al., 1993 ▶). Metal complexes of pyrimidines (see: Zhu et al., 2008 ▶) and their proton transfer complexes with mineral acids are reported (see: Aakeroy et al., 2003 ▶). The infinite O—H⋯O hydrogen-bond chain present in this material is a structural feature suggestive of possible proton conducting behaviour (see: Haile et al., 2001 ▶).

Experimental

Crystal data

C5H8N3H2PO4 M = 207.13 Triclinic, a = 6.1720 (2) Å b = 7.5616 (3) Å c = 9.9216 (4) Å α = 100.562 (3)° β = 99.821 (3)° γ = 102.279 (4)° V = 434.07 (3) Å3 Z = 2 Mo Kα radiation μ = 0.31 mm−1 T = 295 K 0.25 × 0.20 × 0.18 mm

Data collection

Oxford Xcalibur Eos (Nova) CCD detector diffractometer Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 ▶) T min = 0.928, T max = 0.947 9718 measured reflections 1717 independent reflections 1546 reflections with I > 2σ(I) R int = 0.027

Refinement

R[F 2 > 2σ(F 2)] = 0.031 wR(F 2) = 0.088 S = 1.08 1717 reflections 125 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.21 e Å−3 Δρmin = −0.34 e Å−3 Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis PRO (Oxford Diffraction, 2006 ▶); data reduction: CrysAlis RED (Oxford Diffraction, 2006 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶) and WinGX (Farrugia, 2012 ▶); molecular graphics: Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: PLATON (Spek, 2009 ▶). Click here for additional data file. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S160053681300648X/ds2227sup1.cif Click here for additional data file. Structure factors: contains datablock(s) I. DOI: 10.1107/S160053681300648X/ds2227Isup2.hkl Click here for additional data file. Supplementary material file. DOI: 10.1107/S160053681300648X/ds2227Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C5H8N3+·H2PO4Z = 2
Mr = 207.13F(000) = 216
Triclinic, P1Least Squares Treatment of 25 SET4 setting angles.
Hall symbol: -P 1Dx = 1.585 Mg m3
a = 6.1720 (2) ÅMo Kα radiation, λ = 0.71073 Å
b = 7.5616 (3) ÅCell parameters from 326 reflections
c = 9.9216 (4) Åθ = 2.8–26.0°
α = 100.562 (3)°µ = 0.31 mm1
β = 99.821 (3)°T = 295 K
γ = 102.279 (4)°Block, colourless
V = 434.07 (3) Å30.25 × 0.20 × 0.18 mm
Oxford Xcalibur Eos (Nova) CCD detector diffractometer1717 independent reflections
Radiation source: Enhance (Mo) X-ray Source1546 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.027
ω scansθmax = 26.0°, θmin = 2.8°
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)h = −7→7
Tmin = 0.928, Tmax = 0.947k = −9→9
9718 measured reflectionsl = −12→12
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.031Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.088H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.0449P)2 + 0.1805P] where P = (Fo2 + 2Fc2)/3
1717 reflections(Δ/σ)max < 0.001
125 parametersΔρmax = 0.21 e Å3
0 restraintsΔρmin = −0.34 e Å3
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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.
xyzUiso*/Ueq
N10.1136 (3)0.3869 (2)1.11795 (16)0.0405 (5)
N2−0.0464 (2)0.1740 (2)0.90738 (15)0.0332 (4)
N30.3480 (2)0.2530 (2)0.99937 (15)0.0326 (4)
C10.1379 (3)0.2712 (2)1.00803 (17)0.0293 (5)
C2−0.0146 (3)0.0613 (2)0.79698 (18)0.0341 (5)
C30.2007 (3)0.0371 (3)0.7852 (2)0.0407 (6)
C40.3796 (3)0.1362 (3)0.88869 (19)0.0386 (6)
C5−0.2202 (4)−0.0381 (3)0.6843 (2)0.0507 (7)
P10.28422 (7)0.48498 (6)0.64883 (4)0.0283 (1)
O10.0685 (2)0.31898 (17)0.59152 (14)0.0418 (4)
O20.4901 (2)0.39299 (18)0.64980 (12)0.0365 (4)
O30.2949 (2)0.5709 (2)0.79898 (13)0.0439 (4)
O40.29115 (19)0.61556 (16)0.55043 (13)0.0336 (4)
H1N0.230600.449201.182400.0490*
H2N−0.019300.400201.125100.0490*
H30.21960−0.044700.708300.0490*
H3N0.464 (4)0.319 (3)1.071 (2)0.048 (6)*
H40.525000.123900.883800.0460*
H5A−0.31890−0.126200.719500.0760*
H5B−0.17500−0.102100.605200.0760*
H5C−0.298900.050200.655800.0760*
H1−0.033700.354200.548500.0630*
H20.532400.392800.575800.0550*
U11U22U33U12U13U23
N10.0258 (7)0.0530 (9)0.0348 (8)0.0121 (7)0.0011 (6)−0.0069 (7)
N20.0252 (7)0.0384 (8)0.0319 (7)0.0049 (6)0.0049 (6)0.0030 (6)
N30.0238 (7)0.0423 (8)0.0309 (7)0.0087 (6)0.0047 (6)0.0069 (6)
C10.0241 (8)0.0338 (8)0.0303 (8)0.0081 (6)0.0052 (6)0.0081 (7)
C20.0327 (9)0.0334 (8)0.0331 (9)0.0033 (7)0.0079 (7)0.0048 (7)
C30.0410 (10)0.0435 (10)0.0373 (10)0.0132 (8)0.0140 (8)0.0003 (8)
C40.0315 (9)0.0494 (10)0.0403 (10)0.0173 (8)0.0134 (8)0.0103 (8)
C50.0393 (11)0.0546 (12)0.0424 (11)−0.0023 (9)0.0047 (8)−0.0077 (9)
P10.0201 (2)0.0388 (3)0.0242 (2)0.0076 (2)0.0030 (2)0.0046 (2)
O10.0294 (7)0.0421 (7)0.0492 (8)0.0029 (5)−0.0041 (6)0.0177 (6)
O20.0300 (6)0.0563 (8)0.0293 (6)0.0201 (6)0.0081 (5)0.0126 (6)
O30.0298 (7)0.0705 (9)0.0280 (7)0.0165 (6)0.0057 (5)−0.0015 (6)
O40.0238 (6)0.0396 (6)0.0379 (7)0.0078 (5)0.0066 (5)0.0106 (5)
P1—O31.4964 (13)N1—H2N0.8600
P1—O11.5623 (14)N1—H1N0.8600
P1—O21.5725 (14)N3—H3N0.90 (2)
P1—O41.5098 (13)C2—C51.492 (3)
O1—H10.8200C2—C31.401 (3)
O2—H20.8200C3—C41.347 (3)
N1—C11.319 (2)C3—H30.9300
N2—C21.329 (2)C4—H40.9300
N2—C11.349 (2)C5—H5C0.9600
N3—C11.348 (2)C5—H5A0.9600
N3—C41.347 (2)C5—H5B0.9600
P1···H3Ni2.89 (2)C2···C1ix3.481 (2)
P1···H2Nii3.1000C2···O13.099 (2)
P1···H1iii2.8900C3···O13.257 (2)
P1···H1Ni3.0600C4···O23.395 (2)
P1···H2iv2.8800C5···O13.277 (3)
O1···C33.257 (2)C5···H4viii2.9800
O1···C53.277 (3)H1···P1iii2.8900
O1···O4iii2.6100 (18)H1···O4iii1.8000
O1···C23.099 (2)H1···H1iii2.5500
O2···N1i3.000 (2)H1N···H2i2.5200
O2···C43.395 (2)H1N···H3N2.2400
O2···O4iv2.5843 (17)H1N···P1i3.0600
O3···N1ii2.845 (2)H1N···O2i2.1400
O3···N3i2.6276 (19)H2···O4iv1.8000
O4···O1iii2.6100 (18)H2···H1Ni2.5200
O4···O2iv2.5843 (17)H2···H2iv2.4500
O1···H5Bv2.5800H2···P1iv2.8800
O2···H1Ni2.1400H2N···P1ii3.1000
O3···H3Ni1.73 (2)H2N···O3ii2.0100
O3···H2Nii2.0100H3···O4x2.9100
O4···H2iv1.8000H3···H5B2.3900
O4···H1iii1.8000H3N···H1N2.2400
O4···H3vi2.9100H3N···P1i2.89 (2)
O4···H5Avii2.8000H3N···O3i1.73 (2)
N1···O2i3.000 (2)H4···N2xi2.5500
N1···O3ii2.845 (2)H4···C5xi2.9800
N3···O3i2.6276 (19)H5A···O4xii2.8000
N2···H4viii2.5500H5B···H32.3900
C1···C2ix3.481 (2)H5B···O1v2.5800
O3—P1—O4115.79 (8)N2—C1—N3121.54 (15)
O1—P1—O3109.84 (8)N2—C2—C3122.14 (16)
O1—P1—O4109.55 (7)N2—C2—C5116.73 (17)
O1—P1—O2104.78 (7)C3—C2—C5121.13 (17)
O2—P1—O4110.13 (7)C2—C3—C4117.84 (18)
O2—P1—O3106.13 (7)N3—C4—C3120.03 (18)
P1—O1—H1109.00C2—C3—H3121.00
P1—O2—H2109.00C4—C3—H3121.00
C1—N2—C2117.90 (15)C3—C4—H4120.00
C1—N3—C4120.52 (15)N3—C4—H4120.00
H1N—N1—H2N120.00C2—C5—H5B109.00
C1—N1—H1N120.00C2—C5—H5C109.00
C1—N1—H2N120.00C2—C5—H5A109.00
C1—N3—H3N117.5 (15)H5A—C5—H5C109.00
C4—N3—H3N121.9 (15)H5B—C5—H5C109.00
N1—C1—N3118.80 (16)H5A—C5—H5B110.00
N1—C1—N2119.66 (17)
C2—N2—C1—N1178.81 (15)C4—N3—C1—N20.1 (2)
C2—N2—C1—N3−1.3 (2)C1—N3—C4—C30.3 (3)
C1—N2—C2—C32.1 (2)N2—C2—C3—C4−1.7 (3)
C1—N2—C2—C5−177.38 (16)C5—C2—C3—C4177.75 (19)
C4—N3—C1—N1−179.98 (18)C2—C3—C4—N30.4 (3)
D—H···AD—HH···AD···AD—H···A
O1—H1···O4iii0.821.802.6100 (18)168
N1—H1N···O2i0.862.143.000 (2)177
O2—H2···O4iv0.821.802.5843 (17)161
N1—H2N···O3ii0.862.012.845 (2)163
N3—H3N···O3i0.90 (2)1.73 (2)2.6276 (19)173 (2)
C4—H4···N2xi0.932.553.463 (2)166
C5—H5B···O1v0.962.583.531 (3)171
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A D—HH⋯A DA D—H⋯A
O1—H1⋯O4i 0.821.802.6100 (18)168
N1—H1N⋯O2ii 0.862.143.000 (2)177
O2—H2⋯O4iii 0.821.802.5843 (17)161
N1—H2N⋯O3iv 0.862.012.845 (2)163
N3—H3N⋯O3ii 0.90 (2)1.73 (2)2.6276 (19)173 (2)
C4—H4⋯N2v 0.932.553.463 (2)166
C5—H5B⋯O1vi 0.962.583.531 (3)171

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) ; (vi) .

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