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Bis(3-carbamoylpyridin-1-ium) phosphite mono­hydrate

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aInstitute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
*Correspondence e-mail: fabry@fzu.cz

Edited by E. V. Boldyreva, Russian Academy of Sciences, Russia (Received 11 July 2018; accepted 6 August 2018; online 21 August 2018)

Two of the constituent mol­ecules in the title structure, 2C6H7N2O+·HPO32−·H2O, i.e. the phosphite anion and the water mol­ecule, are situated on a symmetry plane. The mol­ecules are held together by moderate N—H⋯O and O—H⋯N, and weak O—H⋯O and C—H⋯Ocarbon­yl hydrogen bonds in which the amide and secondary amine groups, and the water molecules are involved. The structural features are usual, among them the H atom bonded to the P atom avoids hydrogen bonding.

1. Chemical context

Nicotinamide (pyridine-2-carboxamide) is a biologically important mol­ecule, being the active part of vitamin B3 and nicotinamide adenine dinucleotide (NAD) (e.g. Wald, 1991[Wald, N. (1991). Lancet, 338, 131-137.]; Williamson et al., 1967[Williamson, D. H., Lund, P. & Krebs, H. A. (1967). Biochem J. 103, 514-527.]).

[Scheme 1]

However, inter­est in the preparation of the title hydrated salt was called for with respect to an investigation of the configuration of the –NH2 group and its dependence on its environment.

It was hoped that 3-carbamoyl­pyridine (nicotinamide) would make a salt or a co-crystal with phospho­rous acid, H3PO3. It is difficult to predict which of these two forms would be prefererred, because of a small difference of ΔpKa = pKa(base) − pKa(acid) (Childs et al., 2007[Childs, S. L., Stahly, G. P. & Park, A. (2007). Mol. Pharm. 4, 323-338.]). [The pKa values for 3-carbamoyl­pyridine and H3PO3 are 3.3 and 1.3 (first degree), respectively (CRC Handbook, 2009[CRC Handbook (2009). CRC Handbook of Chemistry and Physics, 90th ed., edited by D. R. Lidl, pp. 8-40 and 8-45. Boca Raton, London, New York: CRC Press.]).]

2. Structural commentary

The title molecules are shown in Fig. 1[link]. The resulting structure turned out to be a monohydrated salt. Table 1[link] lists the hydrogen bonds, which are shown in Fig. 2[link]. The secondary amine hydrogen H1n1 is involved in the strongest hydrogen bond present in the structure (N1—H1n1⋯O3i). Its parameters indicate that this hydrogen bond is situated on the boundary between strong and moderate hydrogen bonds (Gilli & Gilli, 2009[Gilli, G. & Gilli, P. (2009). The Nature of the Hydrogen Bond, p. 61. New York: Oxford University Press Inc.]). The amide hydrogen H1n2 is donated to the water oxygen, while H2n2 is donated to atom O3 of the phosphite anion. Atom O2 is an acceptor of water hydrogen H1ow. Water hydrogen H2ow is donated to a pair of O3 atoms. The carbonyl oxygen O1 is an acceptor of two weak C—H⋯O hydrogen bonds, namely C3—H1c3⋯O1ii and C4—H1c4⋯O1iii. The water oxygen atom is also an acceptor of hydrogen H1c2 (see Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H1c2⋯Owi 0.95 2.64 3.5777 (14) 168
C3—H1c3⋯O1ii 0.95 2.56 3.4790 (17) 164
C4—H1c4⋯O1iii 0.95 2.56 3.1948 (13) 125
N1—H1n1⋯O3iv 1.053 (15) 1.455 (15) 2.508 (3) 178.1 (14)
N2—H1n2⋯Owi 0.849 (16) 2.140 (16) 2.9513 (13) 159.8 (18)
N2—H2n2⋯O3v 0.889 (18) 1.955 (18) 2.823 (3) 165.2 (15)
Ow—H1ow⋯O2vi 0.84 (2) 1.82 (2) 2.657 (4) 172 (2)
Ow—H2ow⋯O3 0.96 (3) 2.42 (2) 3.263 (3) 146.8 (9)
Ow—H2ow⋯O3vii 0.96 (3) 2.42 (2) 3.263 (3) 146.8 (9)
Symmetry codes: (i) [-x+{\script{3\over 2}}, -y+2, z+{\script{1\over 2}}]; (ii) x, y+1, z-1; (iii) [-x+{\script{3\over 2}}, -y+1, z-{\script{1\over 2}}]; (iv) [-x+{\script{3\over 2}}, -y+2, z-{\script{1\over 2}}]; (v) [-x+{\script{3\over 2}}, -y+1, z+{\script{1\over 2}}]; (vi) x, y, z-1; (vii) -x+1, y, z.
[Figure 1]
Figure 1
The title mol­ecule, with anisotropic atomic displacement ellipsoids shown at the 50% probability level (PLATON; Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).
[Figure 2]
Figure 2
View of the title structure. C, H, N, O and P atoms are represented by gray, small gray, blue, red and violet circles, respectively. [Symmetry codes: (i) −x + 1, y, z; (ii) x, y − 1, z; (iii) x, y − 1, z; (iv) −x + [{3\over 2}], −y + 1, z − [{1\over 2}]; (v) −x + 2, y − 1, z; (vi) −x + [{3\over 2}], −y + 1, z + [{1\over 2}]; (vii) x − [{1\over 2}], −y + 1, z − [{1\over 2}]; (viii) x, y − 1, z − 1.] The hydrogen bonds are shown as yellow dashed lines (DIAMOND; Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]).

Phosphite and fluoro­phospho­nate, as well hydrogen phosphite and hydrogen fluoro­phospho­nate, are similar mol­ecules. Either mol­ecule can be involved, not only in isostructural compounds, but even in mixed crystals (Fábry et al., 2012[Fábry, J., Fridrichová, M., Dušek, M., Fejfarová, K. & Krupková, R. (2012). Acta Cryst. C68, o76-o83.]). Similarity regarding not only the shape of the mol­ecules but also the avoidance both of P-bonded fluorines and hydrogens of involvement in strong or moderate hydrogen bonds (Matulková et al., 2017[Matulková, I., Fábry, J., Němec, I., Císařová, I. & Vaněk, P. (2017). Acta Cryst. B73, 1114-1124.]). The latter article shows a plot of the dependence of P—F distance on the longest P—O distance in flouro­phospho­nate and hydrogen fluoro­phospho­nate mol­ecules. The P—F distance tends to be longer in [FPO3]2− than in [HFPO3]. Fig. 3[link] shows a similar plot for the phosphites and hydrogen phosphites between both mol­ecules despite the larger spread of P—H distances in phosphite mol­ecules because of the lower accuracy of the H-atom determinations by X-ray diffraction experiments. The reason why the P—H bond tends to be longer follows from the conservation of the overall bond valence sum of the central P5+ or P3+ atom. It is worth pointing out that the tabulated value of the bond valence parameter for the P—H bond seems to yield too high values. For example, for the important values of the P—H distances, i.e. 1.28, 1.33 and 1.37 Å (cf. Fig. 3[link]), the bond valences (Brese & O'Keeffe, 1991[Brese, N. E. & O'Keeffe, M. (1991). Acta Cryst. B47, 192-197.]) are 1.42, 1.24 and 1.11, respectively. The P—H bond valence parameters are going to be checked as part of future work.

[Figure 3]
Figure 3
The dependence of the longest P—O distance (Å) on the P—H distance (Å) in hydrogen phosphites (red circles); phosphites are represented by black squares and the title phosphite structure by a green triangle.

The C—NH2 group tends to be fairly planar for short C—N bonds (Fábry et al., 2014[Fábry, J., Dušek, M., Vaněk, P., Rafalovskyi, I., Hlinka, J. & Urban, J. (2014). Acta Cryst. C70, 1153-1160.]). In agreement with a short C—N bond length [C6—N2 = 1.3232 (18) Å] in the title structure, the best plane through C6/N2/H1n2/H2n2 reveals a maximum deviation of about 0.05 (2) Å for each hydrogen, while ξ2 = 12.6.

3. Supra­molecular features

In the crystal, the most important graph-set motif (Etter et al., 1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]) present is an R43(10) ring motif, which is composed of atoms P1—O3⋯H2n2iv—N2iv—H1n2iv⋯Ow⋯H1n2vii—N2vii—H2n2vii⋯O3i (Table 1[link] and Fig. 2[link]; symmetry codes are given in the figure cation). The phosphite anion and the water mol­ecule are linked by Owater—H⋯Ophosphite hydrogen bonds, forming chains propagating along [001]. The cations are linked to these chains via N—H⋯O hydrogen bonds, forming layers parallel to the bc plane, as shown in Fig. 2[link]. The layers are linked by C—H⋯O hydrogen bonds, resulting in the formation of a supra­molecular three-dimensional structure.

4. Database survey

The applied crystallographic databases were the Cambridge Crystallographic Database (Version 5.39, with updates to May 2018; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) and the Inorganic Crystal Structure Database (June 2018; ICSD, 2018[ICSD (2018). Inorganic Crystal Structure Database. FIZ-Karlsruhe, Germany. https://www.fiz-karlsruhe.de/fiz/products/icsd/welcome.html.]). The search was carried out for all phosphites or hydrogen phosphites with a cation of one kind.

5. Synthesis and crystallization

The title structure was prepared by slow evaporation of a water solution (18 ml) of equimolar amounts of nicotinamide (1.49 g) and phospho­rous acid (1 g). Colourless crystals were isolated after two months.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. All the H atoms were discernible in the difference electron-density map. The aryl H atoms were constrained by the constraints C—H = 0.95 Å and Uiso(H) = 1.2Ueq(C). Water hydrogen H2ow was refined freely, while H1ow was restrained with a distance restraint of 0.84 Å with elasticity 0.02 Å (Müller, 2009[Müller, P. (2009). Crystallogr. Rev. 15, 57-83.]), and with Uiso(H) = 1.5Ueq(O). The hydrogens of the primary amine N2 group and the secondary amine N1 group were constrained by Uiso(H) = 1.2Ueq(N). The P—H hydrogen was refined isotropically. Three reflections, i.e. 95[\overline{2}], 10,5,[\overline{2}] and 11,5,[\overline{2}], were discarded from the refinement because |I(obs) − I(calc)|/σ(I) > 20.

Table 2
Experimental details

Crystal data
Chemical formula 2C6H7N2O+·HPO32−·H2O
Mr 344.3
Crystal system, space group Orthorhombic, Pmn21
Temperature (K) 95
a, b, c (Å) 22.9297 (4), 4.5910 (1), 7.0900 (1)
V3) 746.37 (2)
Z 2
Radiation type Cu Kα
μ (mm−1) 2.01
Crystal size (mm) 0.45 × 0.16 × 0.06
 
Data collection
Diffractometer Rigaku OD SuperNova Dual source diffractometer with an AtlasS2 detector
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2017[Rigaku OD (2017). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, Oxfordshire, England.])
Tmin, Tmax 0.599, 0.831
No. of measured, independent and observed [I > 3σ(I)] reflections 10796, 1592, 1588
Rint 0.021
(sin θ/λ)max−1) 0.630
 
Refinement
R[F > 3σ(F)], wR(F), S 0.019, 0.054, 2.21
No. of reflections 1592
No. of parameters 181
No. of restraints 1
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.14, −0.15
Absolute structure Since the Flack parameter turned out to equal to 0.012(13) in the final stage of refinement it was set to 0. 726 Friedel pairs used in the refinement.
Absolute structure parameter 0.0
Computer programs: CrysAlis PRO (Rigaku OD, 2017[Rigaku OD (2017). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, Oxfordshire, England.]), SIR2014 (Burla et al., 2015[Burla, M. C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Cuocci, C., Giacovazzo, C., Mallamo, M., Mazzone, A. & Polidori, G. (2015). J. Appl. Cryst. 48, 306-309.]), JANA2006 (Petříček et al., 2014[Petříček, V., Dušek, M. & Palatinus, L. (2014). Z. Kristallogr. 229, 345-352.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); extinction correction according to Becker & Coppens (1974[Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147.]).

Since the phosphite oxygens revealed large displacement ellipsoids, the anharmonic displacement parameters upto the fourth grade were included for atoms P1, O2 and O3. (The refinement with the harmonic approximation resulted in Robs = 0.0242, Rwobs = 0.0773, Rall = 0.0243, Rwall = 0.0774 and S = 3.13, with number of parameters = 127. With application of anharmonic approximation, Robs = 0.0188, Rwobs = 0.0535, Rall = 0.0188, Rwall = 0.0535 and S = 2.21, with number of parameters = 181. The respective values of the third- and fourth-order components of the displacement tensor are given in the CIF.)

Refinement with the assumption of the presence of inversion twinning resulted in a Flack parameter of 0.012 (13) (726 Friedel pairs used in the refinement). Therefore, the crystal was considered as single-domained in the final stage of the refiement, the results of which are presented here.

Supporting information


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2017); cell refinement: CrysAlis PRO (Rigaku OD, 2017); data reduction: CrysAlis PRO (Rigaku OD, 2017); program(s) used to solve structure: SIR2014 (Burla et al., 2015); program(s) used to refine structure: JANA2006 (Petříček et al., 2014); molecular graphics: PLATON (Spek, 2009) and DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al., 2014).

Bis(3-carbamoylpyridin-1-ium) phosphite monohydrate top
Crystal data top
2C6H7N2O+·HPO32·H2OF(000) = 360
Mr = 344.3Dx = 1.532 Mg m3
Orthorhombic, Pmn21Cu Kα radiation, λ = 1.54184 Å
Hall symbol: P -2x;-2yac;2zacCell parameters from 9530 reflections
a = 22.9297 (4) Åθ = 6.5–75.9°
b = 4.5910 (1) ŵ = 2.01 mm1
c = 7.0900 (1) ÅT = 95 K
V = 746.37 (2) Å3Plate, colourless
Z = 20.45 × 0.16 × 0.06 mm
Data collection top
Rigaku OD SuperNova Dual source
diffractometer with an AtlasS2 detector
1592 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source1588 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.021
Detector resolution: 5.2027 pixels mm-1θmax = 76.3°, θmin = 3.9°
ω/ scansh = 2828
Absorption correction: multi-scan
(CrysAlis PRO; Rigaku OD, 2017)
k = 55
Tmin = 0.599, Tmax = 0.831l = 88
10796 measured reflections
Refinement top
Refinement on F2Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0004I2)
R[F > 3σ(F)] = 0.019(Δ/σ)max = 0.035
wR(F) = 0.054Δρmax = 0.14 e Å3
S = 2.21Δρmin = 0.15 e Å3
1592 reflectionsExtinction correction: B-C type 1 Lorentzian isotropic (Becker & Coppens, 1974)
181 parametersExtinction coefficient: 910 (160)
1 restraintAbsolute structure: Since the Flack parameter turned out to equal to 0.012(13) in the final stage of refinement it was set to 0. 726 Friedel pairs used in the refinement.
22 constraintsAbsolute structure parameter: 0.0
H atoms treated by a mixture of independent and constrained refinement
Special details top

Refinement. This part differs from the original article by Thanigaimani et al. (2006). It also differs from the refinement by Thanigaimani et al. (2006) by a different threshold for the consideration of the observed diffractions: F2 > 3sigma(F2) has been used as criterion for observed diffractions by JANA2006 which was used for the calculation of the corrected structural model.

Three diffractions 9 5 -2, 10 5 -2, 11 5 -2 were discarded from the refinement because |I(obs)-I(calc)|/σ(I) > 20.

Since the Flack parameter turned out to equal to 0.012 (13) in the final stage of refinement it was set to 0. 726 Friedel pairs used in the refinement.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.84788 (5)0.8441 (2)0.47478 (18)0.0157 (3)
C20.88464 (4)1.0560 (2)0.40131 (18)0.0159 (3)
H1c20.9169851.1210480.4736570.0191*
N10.87528 (4)1.1699 (2)0.23035 (17)0.0168 (2)
H1n10.9056 (7)1.320 (3)0.175 (2)0.0202*
C30.82992 (5)1.0852 (2)0.1232 (2)0.0169 (3)
H1c30.8241691.1701760.0024560.0202*
C40.79162 (5)0.8751 (2)0.1879 (2)0.0178 (3)
H1c40.7595520.8146680.1125530.0213*
C50.80087 (4)0.7536 (2)0.36522 (18)0.0168 (3)
H1c50.775040.6086150.4116230.0201*
C60.85727 (5)0.7074 (3)0.66613 (19)0.0173 (3)
O10.82199 (4)0.52392 (19)0.72395 (16)0.0271 (2)
N20.90344 (4)0.7930 (2)0.76358 (18)0.0202 (3)
H1n20.9281 (7)0.917 (3)0.724 (3)0.0243*
H2n20.9105 (7)0.698 (4)0.871 (3)0.0243*
P10.50.3758 (3)0.7085 (2)0.0181 (6)
H1p10.50.092 (5)0.698 (4)0.034 (6)*
O20.50.4732 (8)0.9100 (6)0.0287 (14)
O30.55414 (11)0.4668 (5)0.5974 (3)0.0350 (8)
Ow0.50.7861 (2)0.22531 (19)0.0219 (3)
H1ow0.50.672 (5)0.132 (3)0.0328*
H2ow0.50.658 (6)0.332 (4)0.0328*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0143 (4)0.0170 (5)0.0159 (5)0.0034 (3)0.0021 (4)0.0004 (4)
C20.0157 (4)0.0167 (5)0.0152 (5)0.0009 (4)0.0018 (4)0.0008 (4)
N10.0174 (4)0.0158 (4)0.0172 (4)0.0004 (3)0.0006 (4)0.0018 (4)
C30.0183 (4)0.0170 (5)0.0153 (5)0.0020 (4)0.0026 (4)0.0000 (4)
C40.0163 (4)0.0189 (5)0.0182 (5)0.0008 (3)0.0032 (4)0.0018 (4)
C50.0142 (4)0.0177 (5)0.0184 (5)0.0001 (4)0.0019 (3)0.0001 (4)
C60.0176 (5)0.0183 (5)0.0161 (5)0.0013 (4)0.0026 (3)0.0014 (4)
O10.0275 (4)0.0331 (4)0.0207 (4)0.0115 (3)0.0015 (4)0.0082 (4)
N20.0179 (4)0.0265 (5)0.0162 (4)0.0015 (4)0.0011 (3)0.0072 (4)
P10.0192 (11)0.0147 (7)0.0205 (12)000.0018 (8)
O20.038 (3)0.040 (2)0.008 (2)000.0080 (19)
O30.0349 (14)0.0382 (15)0.0318 (15)0.0234 (11)0.0241 (13)0.0182 (12)
Ow0.0283 (5)0.0185 (5)0.0188 (5)000.0010 (5)
Geometric parameters (Å, º) top
C1—C21.3884 (15)C5—H1c50.95
C1—C51.3920 (16)C6—O11.2379 (15)
C1—C61.5103 (18)C6—N21.3237 (16)
C2—H1c20.95N2—H1n20.849 (16)
C2—N11.3375 (17)N2—H2n20.889 (18)
N1—H1n11.053 (15)H1n2—H2n21.50 (2)
N1—C31.3455 (16)P1—H1p11.30 (3)
H1n1—O3i1.455 (15)P1—O21.497 (4)
C3—H1c30.9501P1—O31.528 (3)
C3—C41.3827 (15)P1—O3ii1.528 (3)
C4—H1c40.95Ow—H1ow0.84 (2)
C4—C51.3917 (18)Ow—H2ow0.96 (3)
C2—C1—C5118.02 (11)C1—C5—H1c5119.91
C2—C1—C6122.79 (10)C4—C5—H1c5119.91
C5—C1—C6119.19 (10)C1—C6—O1119.15 (11)
C1—C2—H1c2119.45C1—C6—N2117.36 (10)
C1—C2—N1121.10 (10)O1—C6—N2123.49 (13)
H1c2—C2—N1119.45C6—N2—H1n2124.0 (12)
C2—N1—H1n1119.1 (9)C6—N2—H2n2116.4 (11)
C2—N1—C3121.51 (10)H1n2—N2—H2n2119.2 (16)
H1n1—N1—C3119.3 (9)H1p1—P1—O2110.6 (13)
N1—H1n1—O3i178.1 (14)H1p1—P1—O3104.1 (7)
N1—C3—H1c3119.82H1p1—P1—O3ii104.1 (7)
N1—C3—C4120.37 (12)O2—P1—O3114.21 (12)
H1c3—C3—C4119.82O2—P1—O3ii114.21 (12)
C3—C4—H1c4120.58O3—P1—O3ii108.64 (15)
C3—C4—C5118.82 (11)H1n1iii—O3—P1120.3 (6)
H1c4—C4—C5120.59H1ow—Ow—H2ow104 (2)
C1—C5—C4120.18 (10)
Symmetry codes: (i) x+3/2, y+2, z1/2; (ii) x+1, y, z; (iii) x+3/2, y+2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H1c2···Owiii0.952.643.5777 (14)167.77
C3—H1c3···O1iv0.952.563.4790 (17)163.62
C4—H1c4···O1v0.952.563.1948 (13)124.74
N1—H1n1···O3i1.053 (15)1.455 (15)2.508 (3)178.1 (14)
N2—H1n2···Owiii0.849 (16)2.140 (16)2.9513 (13)159.8 (18)
N2—H2n2···O3vi0.889 (18)1.955 (18)2.823 (3)165.2 (15)
Ow—H1ow···O2vii0.84 (2)1.82 (2)2.657 (4)172 (2)
Ow—H2ow···O30.96 (3)2.42 (2)3.263 (3)146.8 (9)
Ow—H2ow···O3ii0.96 (3)2.42 (2)3.263 (3)146.8 (9)
Symmetry codes: (i) x+3/2, y+2, z1/2; (ii) x+1, y, z; (iii) x+3/2, y+2, z+1/2; (iv) x, y+1, z1; (v) x+3/2, y+1, z1/2; (vi) x+3/2, y+1, z+1/2; (vii) x, y, z1.
 

Acknowledgements

The author expresses the gratitude for the support of the Ministry of Education of the Czech Republic. Dr Michal Dušek from the Institute of Physics is thanked for careful data collection.

Funding information

Funding for this research was provided by: Ministry of Education of the Czech Republic (grant No. NPU I-LO1603).

References

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