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

Fábry, J.

doi:10.1107/S2056989018011192

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Volume 74| Part 9| September 2018| Pages 1295-1298

https://doi.org/10.1107/S2056989018011192

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

Jan Fábry ^a ^*

^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⋯O_carbonyl 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.

Keywords: crystal structure; hydrogen bonding; phosphite.

CCDC reference: 1860376

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 ; Williamson et al., 1967 ).

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 ΔpK_a = pK_a(base) − pK_a(acid) (Childs et al., 2007 ). [The pK_a values for 3-carbamoylpyridine and H₃PO₃ are 3.3 and 1.3 (first degree), respectively (CRC Handbook, 2009 ).]

2. Structural commentary

The title molecules are shown in Fig. 1. The resulting structure turned out to be a monohydrated salt. Table 1 lists the hydrogen bonds, which are shown in Fig. 2. 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 ). 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).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O3^iv	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⋯O3^v	0.889 (18)	1.955 (18)	2.823 (3)	165.2 (15)
Ow—H1ow⋯O2^vi	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⋯O3^vii	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
The title molecule, with anisotropic atomic displacement ellipsoids shown at the 50% probability level (PLATON; Spek, 2009

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

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 ). 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 ). 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 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), the bond valences (Brese & O'Keeffe, 1991 ) 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
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 ). 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 ) present is an R₄³(10) ring motif, which is composed of atoms P1—O3⋯H2n2^iv—N2^iv—H1n2^iv⋯Ow⋯H1n2^vii—N2^vii—H2n2^vii⋯O3ⁱ (Table 1 and Fig. 2; symmetry codes are given in the figure cation). The phosphite anion and the water molecule are linked by O_water—H⋯O_phosphite 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. 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 ) and the Inorganic Crystal Structure Database (June 2018; ICSD, 2018 ). 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. 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 U_iso(H) = 1.2U_eq(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 ), and with U_iso(H) = 1.5U_eq(O). The hydrogens of the primary amine N2 group and the secondary amine N1 group were constrained by U_iso(H) = 1.2U_eq(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
M_r	344.3
Crystal system, space group	Orthorhombic, Pmn2₁
Temperature (K)	95
a, b, c (Å)	22.9297 (4), 4.5910 (1), 7.0900 (1)
V (Å³)	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 $[Rigaku OD (2017). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, Oxfordshire, England.]$ )
T_min, T_max	0.599, 0.831
No. of measured, independent and observed [I > 3σ(I)] reflections	10796, 1592, 1588
R_int	0.021
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (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 ), JANA2006 (Petříček et al., 2014 ), PLATON (Spek, 2009 ) and DIAMOND (Brandenburg & Putz, 2005 ); extinction correction according to Becker & Coppens (1974 ).

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 R_obs = 0.0242, Rw_obs = 0.0773, R_all = 0.0243, Rw_all = 0.0774 and S = 3.13, with number of parameters = 127. With application of anharmonic approximation, R_obs = 0.0188, Rw_obs = 0.0535, R_all = 0.0188, Rw_all = 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

CCDC reference: 1860376

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989018011192/eb2010sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018011192/eb2010Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989018011192/eb2010Isup3.smi

Supporting information file. DOI: https://doi.org/10.1107/S2056989018011192/eb2010Isup4.cml

checkCIF report

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⁻·H₂O	F(000) = 360
M_r = 344.3	D_x = 1.532 Mg m⁻³
Orthorhombic, Pmn2₁	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: P -2x;-2yac;2zac	Cell parameters from 9530 reflections
a = 22.9297 (4) Å	θ = 6.5–75.9°
b = 4.5910 (1) Å	µ = 2.01 mm⁻¹
c = 7.0900 (1) Å	T = 95 K
V = 746.37 (2) Å³	Plate, colourless
Z = 2	0.45 × 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 Source	1588 reflections with I > 3σ(I)
Mirror monochromator	R_int = 0.021
Detector resolution: 5.2027 pixels mm^-1	θ_max = 76.3°, θ_min = 3.9°
ω/ scans	h = −28→28
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2017)	k = −5→5
T_min = 0.599, T_max = 0.831	l = −8→8
10796 measured reflections

Refinement top

Refinement on F²	Weighting 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) = 0.054	Δρ_max = 0.14 e Å⁻³
S = 2.21	Δρ_min = −0.15 e Å⁻³
1592 reflections	Extinction correction: B-C type 1 Lorentzian isotropic (Becker & Coppens, 1974)
181 parameters	Extinction coefficient: 910 (160)
1 restraint	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.
22 constraints	Absolute 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

	x	y	z	U_iso*/U_eq
C1	0.84788 (5)	0.8441 (2)	0.47478 (18)	0.0157 (3)
C2	0.88464 (4)	1.0560 (2)	0.40131 (18)	0.0159 (3)
H1c2	0.916985	1.121048	0.473657	0.0191*
N1	0.87528 (4)	1.1699 (2)	0.23035 (17)	0.0168 (2)
H1n1	0.9056 (7)	1.320 (3)	0.175 (2)	0.0202*
C3	0.82992 (5)	1.0852 (2)	0.1232 (2)	0.0169 (3)
H1c3	0.824169	1.170176	0.002456	0.0202*
C4	0.79162 (5)	0.8751 (2)	0.1879 (2)	0.0178 (3)
H1c4	0.759552	0.814668	0.112553	0.0213*
C5	0.80087 (4)	0.7536 (2)	0.36522 (18)	0.0168 (3)
H1c5	0.77504	0.608615	0.411623	0.0201*
C6	0.85727 (5)	0.7074 (3)	0.66613 (19)	0.0173 (3)
O1	0.82199 (4)	0.52392 (19)	0.72395 (16)	0.0271 (2)
N2	0.90344 (4)	0.7930 (2)	0.76358 (18)	0.0202 (3)
H1n2	0.9281 (7)	0.917 (3)	0.724 (3)	0.0243*
H2n2	0.9105 (7)	0.698 (4)	0.871 (3)	0.0243*
P1	0.5	0.3758 (3)	0.7085 (2)	0.0181 (6)
H1p1	0.5	0.092 (5)	0.698 (4)	0.034 (6)*
O2	0.5	0.4732 (8)	0.9100 (6)	0.0287 (14)
O3	0.55414 (11)	0.4668 (5)	0.5974 (3)	0.0350 (8)
Ow	0.5	0.7861 (2)	0.22531 (19)	0.0219 (3)
H1ow	0.5	0.672 (5)	0.132 (3)	0.0328*
H2ow	0.5	0.658 (6)	0.332 (4)	0.0328*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0143 (4)	0.0170 (5)	0.0159 (5)	0.0034 (3)	0.0021 (4)	−0.0004 (4)
C2	0.0157 (4)	0.0167 (5)	0.0152 (5)	0.0009 (4)	−0.0018 (4)	−0.0008 (4)
N1	0.0174 (4)	0.0158 (4)	0.0172 (4)	0.0004 (3)	−0.0006 (4)	0.0018 (4)
C3	0.0183 (4)	0.0170 (5)	0.0153 (5)	0.0020 (4)	−0.0026 (4)	0.0000 (4)
C4	0.0163 (4)	0.0189 (5)	0.0182 (5)	0.0008 (3)	−0.0032 (4)	−0.0018 (4)
C5	0.0142 (4)	0.0177 (5)	0.0184 (5)	−0.0001 (4)	0.0019 (3)	−0.0001 (4)
C6	0.0176 (5)	0.0183 (5)	0.0161 (5)	0.0013 (4)	0.0026 (3)	0.0014 (4)
O1	0.0275 (4)	0.0331 (4)	0.0207 (4)	−0.0115 (3)	−0.0015 (4)	0.0082 (4)
N2	0.0179 (4)	0.0265 (5)	0.0162 (4)	−0.0015 (4)	−0.0011 (3)	0.0072 (4)
P1	0.0192 (11)	0.0147 (7)	0.0205 (12)	0	0	−0.0018 (8)
O2	0.038 (3)	0.040 (2)	0.008 (2)	0	0	−0.0080 (19)
O3	0.0349 (14)	0.0382 (15)	0.0318 (15)	−0.0234 (11)	0.0241 (13)	−0.0182 (12)
Ow	0.0283 (5)	0.0185 (5)	0.0188 (5)	0	0	−0.0010 (5)

Geometric parameters (Å, º) top

C1—C2	1.3884 (15)	C5—H1c5	0.95
C1—C5	1.3920 (16)	C6—O1	1.2379 (15)
C1—C6	1.5103 (18)	C6—N2	1.3237 (16)
C2—H1c2	0.95	N2—H1n2	0.849 (16)
C2—N1	1.3375 (17)	N2—H2n2	0.889 (18)
N1—H1n1	1.053 (15)	H1n2—H2n2	1.50 (2)
N1—C3	1.3455 (16)	P1—H1p1	1.30 (3)
H1n1—O3ⁱ	1.455 (15)	P1—O2	1.497 (4)
C3—H1c3	0.9501	P1—O3	1.528 (3)
C3—C4	1.3827 (15)	P1—O3ⁱⁱ	1.528 (3)
C4—H1c4	0.95	Ow—H1ow	0.84 (2)
C4—C5	1.3917 (18)	Ow—H2ow	0.96 (3)

C2—C1—C5	118.02 (11)	C1—C5—H1c5	119.91
C2—C1—C6	122.79 (10)	C4—C5—H1c5	119.91
C5—C1—C6	119.19 (10)	C1—C6—O1	119.15 (11)
C1—C2—H1c2	119.45	C1—C6—N2	117.36 (10)
C1—C2—N1	121.10 (10)	O1—C6—N2	123.49 (13)
H1c2—C2—N1	119.45	C6—N2—H1n2	124.0 (12)
C2—N1—H1n1	119.1 (9)	C6—N2—H2n2	116.4 (11)
C2—N1—C3	121.51 (10)	H1n2—N2—H2n2	119.2 (16)
H1n1—N1—C3	119.3 (9)	H1p1—P1—O2	110.6 (13)
N1—H1n1—O3ⁱ	178.1 (14)	H1p1—P1—O3	104.1 (7)
N1—C3—H1c3	119.82	H1p1—P1—O3ⁱⁱ	104.1 (7)
N1—C3—C4	120.37 (12)	O2—P1—O3	114.21 (12)
H1c3—C3—C4	119.82	O2—P1—O3ⁱⁱ	114.21 (12)
C3—C4—H1c4	120.58	O3—P1—O3ⁱⁱ	108.64 (15)
C3—C4—C5	118.82 (11)	H1n1ⁱⁱⁱ—O3—P1	120.3 (6)
H1c4—C4—C5	120.59	H1ow—Ow—H2ow	104 (2)
C1—C5—C4	120.18 (10)

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C2—H1c2···Owⁱⁱⁱ	0.95	2.64	3.5777 (14)	167.77
C3—H1c3···O1^iv	0.95	2.56	3.4790 (17)	163.62
C4—H1c4···O1^v	0.95	2.56	3.1948 (13)	124.74
N1—H1n1···O3ⁱ	1.053 (15)	1.455 (15)	2.508 (3)	178.1 (14)
N2—H1n2···Owⁱⁱⁱ	0.849 (16)	2.140 (16)	2.9513 (13)	159.8 (18)
N2—H2n2···O3^vi	0.889 (18)	1.955 (18)	2.823 (3)	165.2 (15)
Ow—H1ow···O2^vii	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···O3ⁱⁱ	0.96 (3)	2.42 (2)	3.263 (3)	146.8 (9)

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

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).

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