Literature DB >> 21837054

A second triclinic polymorph of (1-ammonio-1-phosphono-eth-yl)phospho-nate.

Natalia V Tsaryk1, Anatolij V Dudko, Alexandra N Kozachkova, Vasily I Pekhnyo.   

Abstract

The asymmetric unit of the second polymorph of the title compound, C(2)H(9)NO(6)P(2), contains one mol-ecule existing as a zwitterion. The N atom of the ammonio group is protonated and one of the phospho-nic acid groups is deprotonated. Bond lengths and angles are similar in both polymorphs. Besides the differences in cell parameters, the most significant structural difference between this structure and that of the first polymorph [Dudko, Bon, Kozachkova, Tsarik & Pekhno (2008 ▶), Ukr. Khim. Zh.74, 104-106] is the presence of strong symmetric hydrogen bonds between neighbouring phospho-nate groups. H atoms involved in these hydrogen bonds are located at inversion centres and O⋯O distances are observed in the range 2.458 (5)-2.523 (5) Å. These bonds and additional O-H⋯O and N-H⋯O hydrogen bonds inter-link the mol-ecules, giving a three-dimensional supromolecular network.

Entities:  

Year:  2011        PMID: 21837054      PMCID: PMC3151912          DOI: 10.1107/S1600536811022239

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


Related literature

For the original polymorph, see: Dudko et al. (2008 ▶). For similar bis­phospho­nates, see: Fernández et al. (2003 ▶); Li et al. (2009 ▶). For general background on the usage of organic diphospho­nic acids as chelating agents in metal extraction and as drugs to prevent calcification and inhibit bone resorption, see: Matczak-Jon & Videnova-Adrabinska (2005 ▶); Matkovskaya et al. (2001 ▶). For examples of symmetrical O—H⋯O hydrogen bonds, see Catti & Ferraris (1976 ▶); Meot-Ner (2005 ▶). For bond-length data, see: Allen et al. (1987 ▶).

Experimental

Crystal data

C2H9NO6P2 M = 205.04 Triclinic, a = 5.5674 (11) Å b = 5.9023 (12) Å c = 11.385 (2) Å α = 82.334 (10)° β = 82.145 (9)° γ = 78.148 (10)° V = 360.56 (12) Å3 Z = 2 Mo Kα radiation μ = 0.59 mm−1 T = 296 K 0.56 × 0.16 × 0.09 mm

Data collection

Bruker APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2007 ▶) T min = 0.734, T max = 0.949 4331 measured reflections 1401 independent reflections 861 reflections with I > 2σ(I) R int = 0.058

Refinement

R[F 2 > 2σ(F 2)] = 0.049 wR(F 2) = 0.122 S = 1.06 1401 reflections 116 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.45 e Å−3 Δρmin = −0.43 e Å−3 Data collection: APEX2 (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811022239/im2293sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811022239/im2293Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811022239/im2293Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C2H9NO6P2Z = 2
Mr = 205.04F(000) = 212
Triclinic, P1Dx = 1.889 Mg m3
Hall symbol: -P 1Melting point: 551 K
a = 5.5674 (11) ÅMo Kα radiation, λ = 0.71073 Å
b = 5.9023 (12) ÅCell parameters from 1315 reflections
c = 11.385 (2) Åθ = 3.6–25.3°
α = 82.334 (10)°µ = 0.59 mm1
β = 82.145 (9)°T = 296 K
γ = 78.148 (10)°Needle, colourless
V = 360.56 (12) Å30.56 × 0.16 × 0.09 mm
Bruker APEXII CCD diffractometer1401 independent reflections
Radiation source: fine-focus sealed tube861 reflections with I > 2σ(I)
graphiteRint = 0.058
φ and ω scansθmax = 26.0°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2007)h = −6→6
Tmin = 0.734, Tmax = 0.949k = −7→7
4331 measured reflectionsl = −12→14
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.049Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.122H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.0387P)2 + 0.6717P] where P = (Fo2 + 2Fc2)/3
1401 reflections(Δ/σ)max < 0.001
116 parametersΔρmax = 0.45 e Å3
0 restraintsΔρmin = −0.43 e Å3
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.
xyzUiso*/Ueq
P10.4512 (2)−0.0726 (2)0.18108 (11)0.0243 (4)
P20.2798 (2)0.2733 (2)0.36756 (11)0.0266 (4)
O10.3269 (6)−0.1949 (6)0.1024 (3)0.0327 (9)
H1O0.337 (11)−0.133 (11)0.034 (5)0.049*
O20.6470 (5)0.0492 (6)0.1152 (3)0.0337 (9)
O30.5438 (7)−0.2366 (6)0.2838 (4)0.0475 (11)
H3O0.531 (12)−0.379 (12)0.301 (6)0.071*
O40.5260 (5)0.3445 (5)0.3268 (3)0.0236 (8)
O50.2923 (6)0.0865 (7)0.4724 (3)0.0344 (9)
H5O0.50000.00000.50000.052*
O60.0723 (6)0.4792 (7)0.3914 (3)0.0421 (10)
H6O0.00000.50000.50000.063*
N1−0.0104 (8)0.0192 (9)0.2928 (4)0.0287 (11)
H1A−0.086 (10)−0.025 (9)0.237 (5)0.043*
H1B−0.151 (10)0.102 (10)0.316 (5)0.043*
H1C0.030 (10)−0.091 (10)0.342 (5)0.043*
C10.1979 (8)0.1433 (8)0.2439 (4)0.0195 (10)
C20.1069 (9)0.3297 (8)0.1441 (4)0.0278 (12)
H2A0.08270.25560.07760.042*
H2B0.22760.42650.11910.042*
H2C−0.04640.42350.17300.042*
U11U22U33U12U13U23
P10.0236 (7)0.0195 (7)0.0316 (7)−0.0033 (5)−0.0072 (6)−0.0066 (6)
P20.0204 (7)0.0387 (9)0.0230 (7)−0.0080 (6)−0.0030 (5)−0.0074 (6)
O10.038 (2)0.028 (2)0.037 (2)−0.0124 (17)−0.0077 (18)−0.0095 (17)
O20.0203 (18)0.045 (2)0.042 (2)−0.0155 (16)0.0069 (16)−0.0208 (18)
O30.065 (3)0.016 (2)0.068 (3)−0.0036 (19)−0.042 (2)0.002 (2)
O40.0182 (16)0.0200 (18)0.0344 (19)−0.0022 (13)−0.0056 (14)−0.0091 (15)
O50.0272 (19)0.055 (2)0.0241 (18)−0.0172 (17)−0.0077 (15)0.0035 (17)
O60.0231 (19)0.067 (3)0.034 (2)0.0124 (18)−0.0057 (16)−0.0270 (19)
N10.017 (2)0.036 (3)0.033 (3)−0.009 (2)−0.006 (2)0.005 (2)
C10.016 (2)0.022 (3)0.022 (2)−0.0064 (19)−0.0040 (19)0.000 (2)
C20.031 (3)0.023 (3)0.027 (3)0.000 (2)−0.007 (2)−0.001 (2)
P1—O21.490 (3)O5—H5O1.229 (0)
P1—O31.493 (4)O6—H6O1.261 (0)
P1—O11.533 (4)N1—C11.502 (6)
P1—C11.831 (5)N1—H1A0.90 (6)
P2—O41.510 (3)N1—H1B0.86 (6)
P2—O51.512 (4)N1—H1C0.82 (6)
P2—O61.520 (3)C1—C21.534 (6)
P2—C11.840 (4)C2—H2A0.9600
O1—H1O0.81 (6)C2—H2B0.9600
O3—H3O0.85 (7)C2—H2C0.9600
O2—P1—O3111.7 (2)C1—N1—H1B118 (4)
O2—P1—O1114.3 (2)H1A—N1—H1B87 (4)
O3—P1—O1110.8 (2)C1—N1—H1C113 (4)
O2—P1—C1109.0 (2)H1A—N1—H1C110 (5)
O3—P1—C1106.5 (2)H1B—N1—H1C111 (6)
O1—P1—C1103.86 (19)N1—C1—C2107.8 (4)
O4—P2—O5112.46 (18)N1—C1—P1107.2 (3)
O4—P2—O6112.8 (2)C2—C1—P1109.4 (3)
O5—P2—O6111.7 (2)N1—C1—P2107.4 (3)
O4—P2—C1107.07 (18)C2—C1—P2111.7 (3)
O5—P2—C1106.2 (2)P1—C1—P2113.1 (2)
O6—P2—C1105.98 (19)C1—C2—H2A109.5
P1—O1—H1O110 (4)C1—C2—H2B109.5
P1—O3—H3O128 (4)H2A—C2—H2B109.5
P2—O5—H5O115.9 (0)C1—C2—H2C109.5
P2—O6—H6O115.1 (0)H2A—C2—H2C109.5
C1—N1—H1A115 (3)H2B—C2—H2C109.5
O2—P1—C1—N1171.5 (3)O4—P2—C1—N1166.1 (3)
O3—P1—C1—N1−67.9 (3)O5—P2—C1—N145.8 (3)
O1—P1—C1—N149.2 (3)O6—P2—C1—N1−73.2 (4)
O2—P1—C1—C254.9 (4)O4—P2—C1—C2−76.0 (3)
O3—P1—C1—C2175.5 (3)O5—P2—C1—C2163.7 (3)
O1—P1—C1—C2−67.4 (3)O6—P2—C1—C244.7 (4)
O2—P1—C1—P2−70.3 (3)O4—P2—C1—P148.0 (3)
O3—P1—C1—P250.3 (3)O5—P2—C1—P1−72.4 (3)
O1—P1—C1—P2167.4 (2)O6—P2—C1—P1168.7 (2)
D—H···AD—HH···AD···AD—H···A
O1—H1O···O2i0.81 (6)1.70 (6)2.507 (5)170 (6)
O3—H3O···O4ii0.85 (7)1.63 (7)2.475 (5)175 (7)
O5—H5O···O5iii1.23 (1)1.23 (1)2.458 (5)180 (0)
O6—H6O···O6iv1.26 (1)1.26 (1)2.523 (6)180.(1)
N1—H1A···O2v0.90 (6)2.11 (6)2.929 (6)150 (5)
N1—H1B···O4v0.86 (6)2.06 (6)2.896 (5)165 (5)
N1—H1C···O6ii0.82 (6)2.50 (6)3.196 (6)145 (5)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O1—H1O⋯O2i0.81 (6)1.70 (6)2.507 (5)170 (6)
O3—H3O⋯O4ii0.85 (7)1.63 (7)2.475 (5)175 (7)
O5—H5O⋯O5iii1.23 (1)1.23 (1)2.458 (5)180 (0)
O6—H6O⋯O6iv1.26 (1)1.26 (1)2.523 (6)180 (1)
N1—H1A⋯O2v0.90 (6)2.11 (6)2.929 (6)150 (5)
N1—H1B⋯O4v0.86 (6)2.06 (6)2.896 (5)165 (5)
N1—H1C⋯O6ii0.82 (6)2.50 (6)3.196 (6)145 (5)

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

  4 in total

Review 1.  The ionic hydrogen bond.

Authors:  Michael Meot-Ner
Journal:  Chem Rev       Date:  2005-01       Impact factor: 60.622

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Two members of the bisphosphonate class of drugs: a zwitterion and a molecular compound.

Authors:  Daniel Fernández; Daniel Vega; Javier A Ellena
Journal:  Acta Crystallogr C       Date:  2003-05-10       Impact factor: 1.172

4.  Hydroxonium 1-ammonio-ethane-1,1-diyl-diphospho-nate.

Authors:  Ming Li; Wen Wen; Wuzu Ha; Liang Chang
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2009-03-19
  4 in total
  2 in total

1.  Crystal structure of bis-[(1-ammonio-1-phosphono-eth-yl)phospho-nato]tetra-aqua-cadmium dihydrate: a powder X-ray diffraction study.

Authors:  Mwaffak Rukiah; Thaer Assaad
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2015-03-07

2.  Tetra-methyl-ammonium hydrogen terephthalate.

Authors:  Leila Dolatyari; Samad Shoghpour Bayraq; Sara Sharifi; Ali Ramazani; Ali Morsali; Hadi Amiri Rudbari
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2012-09-26
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.