Pyridinium nitrate at 120 K

Batsanov, A.S.

doi:10.1107/S160053680403017X

organic compounds

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ISSN: 2056-9890

Volume 60| Part 12| December 2004| Pages o2426-o2428

https://doi.org/10.1107/S160053680403017X

Pyridinium nitrate at 120 K

Andrei S. Batsanov ^a ^*

^aDepartment of Chemistry, University of Durham, South Road, Durham DH1 3LE, England
^*Correspondence e-mail: a.s.batsanov@durham.ac.uk

(Received 15 November 2004; accepted 19 November 2004; online 27 November 2004)

The structural unit of pyridinium nitrate, C₅H₆N⁺·NO₃⁻, is a pyridinium–nitrate ion pair, held together by a strong N—H⋯O hydrogen bond.

Comment

The present paper reports the low-temperature study of the title compound, (I). For the introduction and the room-temperature results, see the preceeding paper (Batsanov, 2004 ).

Cooling of (I) from 290 to 120 K resulted in an approximately 4% decrease of the unit-cell volume, which was shown (by fast determinations at 160, 200 and 250 K) to be practically linear in this range. It is noteworthy that, whilst at room temperature β > 90°, on cooling it decreases, passing through 90° at 250 K. Therefore, in the present report, the non-standard cell setting with β < 90° is used, for compatibility with the room-temperature data (Serewicz et al., 1965 ; Batsanov, 2004).

The structure at 120 K (Fig. 1) is similar to that at room temperature (see Table 1), with the anisotropic displacement parameters approximately three times lower [U_eq of non-H atoms averaging 0.08 (1) Å² at 290 K versus 0.027 (5) Å² at 120 K]. The asymmetric unit comprises one pyridinium cation and one nitrate anion, the ionic nature of which is proven by the location of H atoms. Both ions are planar, and the dihedral angle between them increases from 13.7 (1)° at 290 K to 21.1 (1)° at 120 K. This change can be best approximated as a rotation of the anion around atom O1, which is hydrogen bonded to the cation (Table 2). The deviations of the nitrate anion atoms from the pyridine ring plane illustrate this point, viz. O1 −0.302 (4), O2 0.081 (6), O3 0.174 (5) and N2 −0.006 (5) Å at 290 K versus O1 −0.265 (4), O2 0.274 (5), O3 0.496 (4) and N2 0.173 (4) Å at 120 K.

The ion pair is held together by a strong (Steiner, 2002 ) and nearly linear N1—H1⋯O1 hydrogen bond (Table 2). The N1⋯O1 distance decreases from 2.787 (3) Å at 290 K to 2.699 (2) Å at 120 K; cf. 2.730 (3) Å in the structure of PyH⁺·MeSO₃⁻ at 173 K (Bolte et al., 2001 ) and 2.664 (4)–2.698 (4) Å in PyH⁺·F₃CCO₂⁻, (II), at 183 K (Palmore & McBride-Wieser, 1997 ). In (I), the ion pair is further stabilized by a weak (Desiraju & Steiner, 1999 ) hydrogen bond (C2—H2⋯O3) involving the ortho H atom, thus producing a seven-membered ring. This motif can be described by the graph set R₂²(7), according to Etter et al. (1990 ) and Bernstein et al. (1995 ). The same motif is realised in the structure of (II), where the C(ortho)—H⋯O bonds are substantially stronger: the C⋯O distances range from 3.175 (4) to 3.214 (4) Å versus 3.229 (3) Å in (I), and the H⋯O distances (for the C—H bond lengths corrected to 1.08 Å) from 2.28 (3) to 2.42 (4) Å versus 2.55 (3) Å in (I). The weaker bonding in (I) can be easily explained, as atom H2 participates in a bifurcated hydrogen bond, with O3 of the same ion pair and with O2 of an adjacent ion pair. The latter bond is evidently the stronger, with the C⋯O distance shorter by 0.15 Å. No such competition is possible in (II), which contains no O atoms not involved in intra-pair hydrogen bonds.

In fact, all H atoms in (I) participate in inter-pair C—H⋯O contacts which are shorter than the sum of van der Waals radii (Rowland & Taylor, 1996 ), correspond to the stabilizing part of the potential curve (Desiraju & Steiner, 1999) and can be interpreted as weak hydrogen bonds (Table 2).

Due to protonation of N1, the C2—N1—C6 angle in (I) is widened in comparison with the neutral pyridine molecule [116.6 (2)°; Mootz & Wusson, 1981 ] and coincides with those in PyH⁺·MeSO₃⁻ and (II).

Figure 1
The molecular structure of (I

) at 120 K. Displacement ellipsoids are drawn at the 50% probability level. The dashed and dotted lines indicate strong and weak hydrogen bonds, respectively.

Experimental

The crystals of (I) were grown by slow evaporation, at room temperature, of an aqueous solution of equimolar amounts of pyridine and nitric acid.

Crystal data

C₅H₆N⁺·NO₃⁻
M_r = 142.12
Monoclinic, P2₁/c
a = 3.7756 (9) Å
b = 12.336 (3) Å
c = 13.353 (3) Å
β = 88.60 (1)°
V = 621.8 (4) Å³
Z = 4
D_x = 1.521 Mg m⁻³
Mo Kα radiation
Cell parameters from 851 reflections
θ = 10.4–24.9°
μ = 0.13 mm⁻¹
T = 120 (1) K
Plate, colourless
0.42 × 0.37 × 0.03 mm

Data collection

Bruker SMART 1K CCD area-detector diffractometer
ω scans
Absorption correction: none
3711 measured reflections
1408 independent reflections
1006 reflections with I > 2σ(I)
R_int = 0.065
θ_max = 27.5°
h = −4 → 4
k = −10 → 15
l = −17 → 17

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.049
wR(F²) = 0.128
S = 1.04
1408 reflections
115 parameters
All H-atom parameters refined
w = 1/[σ²(F_o²) + (0.045P)² + 0.4158P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

N1—C2	1.339 (3)
N1—C6	1.343 (3)
C2—C3	1.373 (3)
C3—C4	1.389 (3)
C4—C5	1.383 (3)
C5—C6	1.370 (3)
O1—N2	1.272 (2)
O2—N2	1.237 (2)
O3—N2	1.245 (2)

C2—N1—C6	122.2 (2)
N1—C2—C3	120.3 (2)
C2—C3—C4	118.7 (2)
C5—C4—C3	119.8 (2)
C6—C5—C4	119.5 (2)
N1—C6—C5	119.6 (2)
O2—N2—O3	121.32 (18)
O2—N2—O1	119.44 (18)
O3—N2—O1	119.24 (17)

Table 2
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1	0.97 (3)	1.74 (3)	2.699 (2)	171 (3)
N1—H1⋯O3	0.97 (3)	2.47 (3)	3.160 (3)	128 (2)
C2—H2⋯O3	0.93 (2)	2.63 (2)	3.229 (3)	122.4 (18)
C2—H2⋯O2ⁱ	0.93 (2)	2.50 (2)	3.076 (3)	119.9 (18)
C3—H3⋯O2ⁱⁱ	0.96 (2)	2.62 (2)	3.272 (3)	125.3 (17)
C4—H4⋯O3ⁱⁱⁱ	0.94 (2)	2.65 (2)	3.244 (3)	121.5 (16)
C5—H5⋯O3ⁱⁱⁱ	0.97 (2)	2.61 (2)	3.240 (3)	122.8 (18)
C6—H6⋯O1^iv	0.97 (2)	2.38 (2)	3.215 (3)	143.1 (19)
C6—H6⋯O2^iv	0.97 (2)	2.60 (2)	3.384 (3)	137.8 (18)
Symmetry codes: (i) $[-x,y-{\script{1\over 2}},{\script{3\over 2}}-z]$ ; (ii) $[1-x,y-{\script{1\over 2}},{\script{3\over 2}}-z]$ ; (iii) $[1+x,{\script{1\over 2}}-y,z-{\script{1\over 2}}]$ ; (iv) -x,1-y,1-z.

All H atoms were refined in an isotropic approximation without constraints.

Data collection: SMART (Bruker, 1997 ); cell refinement: SAINT (Bruker, 2001 ); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S160053680403017X/lh6319sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S160053680403017X/lh6319Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 1997); cell refinement: SMART (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXTL (Bruker, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

pyridinium nitrate top

Crystal data top

C₅H₆N⁺·NO₃⁻	F(000) = 296
M_r = 142.12	D_x = 1.521 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 851 reflections
a = 3.7756 (9) Å	θ = 10.4–24.9°
b = 12.336 (3) Å	µ = 0.13 mm⁻¹
c = 13.353 (3) Å	T = 120 K
β = 88.60 (1)°	Plate, colourless
V = 621.8 (4) Å³	0.42 × 0.37 × 0.03 mm
Z = 4

Data collection top

Bruker SMART 1K CCD area-detector diffractometer	1006 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.065
Graphite monochromator	θ_max = 27.5°, θ_min = 2.3°
Detector resolution: 8 pixels mm^-1	h = −4→4
ω scans	k = −10→15
3711 measured reflections	l = −17→17
1408 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.049	Hydrogen site location: difference Fourier map
wR(F²) = 0.128	All H-atom parameters refined
S = 1.04	w = 1/[σ²(F_o²) + (0.045P)² + 0.4158P] where P = (F_o² + 2F_c²)/3
1408 reflections	(Δ/σ)_max < 0.001
115 parameters	Δρ_max = 0.24 e Å⁻³
0 restraints	Δρ_min = −0.32 e Å⁻³

Special details top

Experimental. The data collection nominally covered over a hemisphere of reciprocal space, by a combination of 3 sets of ω scans; each set at different φ and/or 2θ angles and each scan (5 sec/frame exposure) covering 0.3° in ω. Crystal to detector distance 4.42 cm. Crystals are stable in dry air but deteriorate in atmospheric air.

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.

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

	x	y	z	U_iso*/U_eq
N1	0.3911 (5)	0.31297 (14)	0.54178 (14)	0.0221 (4)
H1	0.269 (8)	0.374 (2)	0.573 (2)	0.055 (9)*
C2	0.4522 (5)	0.22606 (18)	0.59896 (16)	0.0235 (5)
H2	0.371 (6)	0.2287 (19)	0.6656 (18)	0.024 (6)*
C3	0.6197 (6)	0.13673 (18)	0.55879 (16)	0.0245 (5)
H3	0.659 (6)	0.074 (2)	0.6001 (18)	0.028 (6)*
C4	0.7247 (5)	0.13889 (18)	0.45835 (17)	0.0239 (5)
H4	0.827 (6)	0.0772 (18)	0.4280 (16)	0.018 (5)*
C5	0.6606 (6)	0.23012 (18)	0.40145 (17)	0.0248 (5)
H5	0.733 (6)	0.2309 (19)	0.3315 (19)	0.030 (6)*
C6	0.4892 (5)	0.31687 (19)	0.44450 (16)	0.0247 (5)
H6	0.437 (6)	0.3826 (19)	0.4075 (18)	0.028 (6)*
O1	0.0001 (4)	0.48032 (13)	0.61332 (11)	0.0286 (4)
O2	−0.1078 (5)	0.56343 (14)	0.75376 (12)	0.0361 (4)
O3	0.1735 (4)	0.41066 (14)	0.75319 (12)	0.0346 (4)
N2	0.0216 (5)	0.48502 (14)	0.70817 (13)	0.0232 (4)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0182 (8)	0.0201 (9)	0.0281 (10)	−0.0005 (7)	−0.0019 (7)	−0.0046 (8)
C2	0.0223 (10)	0.0284 (11)	0.0198 (10)	−0.0039 (9)	−0.0014 (8)	−0.0014 (9)
C3	0.0223 (11)	0.0233 (11)	0.0281 (11)	−0.0006 (9)	−0.0050 (8)	0.0032 (9)
C4	0.0174 (10)	0.0228 (11)	0.0314 (12)	0.0005 (8)	−0.0009 (8)	−0.0057 (9)
C5	0.0194 (10)	0.0333 (12)	0.0219 (10)	−0.0020 (9)	−0.0006 (8)	−0.0020 (9)
C6	0.0216 (10)	0.0262 (12)	0.0264 (11)	−0.0020 (9)	−0.0032 (9)	0.0038 (9)
O1	0.0367 (9)	0.0300 (9)	0.0193 (7)	0.0086 (7)	−0.0016 (6)	−0.0021 (7)
O2	0.0441 (10)	0.0357 (9)	0.0285 (9)	0.0109 (8)	0.0002 (7)	−0.0114 (7)
O3	0.0380 (9)	0.0379 (10)	0.0279 (9)	0.0104 (8)	0.0005 (7)	0.0102 (7)
N2	0.0231 (9)	0.0254 (10)	0.0212 (9)	−0.0017 (8)	0.0007 (7)	0.0001 (8)

Geometric parameters (Å, º) top

N1—C2	1.339 (3)	C4—H4	0.94 (2)
N1—C6	1.343 (3)	C5—C6	1.370 (3)
N1—H1	0.97 (3)	C5—H5	0.97 (2)
C2—C3	1.373 (3)	C6—H6	0.97 (2)
C2—H2	0.93 (2)	O1—N2	1.272 (2)
C3—C4	1.389 (3)	O2—N2	1.237 (2)
C3—H3	0.96 (2)	O3—N2	1.245 (2)
C4—C5	1.383 (3)

C2—N1—C6	122.2 (2)	C3—C4—H4	120.3 (13)
C2—N1—H1	117.5 (17)	C6—C5—C4	119.5 (2)
C6—N1—H1	120.3 (17)	C6—C5—H5	121.1 (15)
N1—C2—C3	120.3 (2)	C4—C5—H5	119.4 (15)
N1—C2—H2	117.2 (14)	N1—C6—C5	119.6 (2)
C3—C2—H2	122.5 (14)	N1—C6—H6	117.8 (14)
C2—C3—C4	118.7 (2)	C5—C6—H6	122.5 (14)
C2—C3—H3	119.8 (14)	O2—N2—O3	121.32 (18)
C4—C3—H3	121.6 (14)	O2—N2—O1	119.44 (18)
C5—C4—C3	119.8 (2)	O3—N2—O1	119.24 (17)
C5—C4—H4	119.8 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1	0.97 (3)	1.74 (3)	2.699 (2)	171 (3)
N1—H1···O3	0.97 (3)	2.47 (3)	3.160 (3)	128 (2)
C2—H2···O3	0.93 (2)	2.63 (2)	3.229 (3)	122.4 (18)
C2—H2···O2ⁱ	0.93 (2)	2.50 (2)	3.076 (3)	119.9 (18)
C3—H3···O2ⁱⁱ	0.96 (2)	2.62 (2)	3.272 (3)	125.3 (17)
C4—H4···O3ⁱⁱⁱ	0.94 (2)	2.65 (2)	3.244 (3)	121.5 (16)
C5—H5···O3ⁱⁱⁱ	0.97 (2)	2.61 (2)	3.240 (3)	122.8 (18)
C6—H6···O1^iv	0.97 (2)	2.38 (2)	3.215 (3)	143.1 (19)
C6—H6···O2^iv	0.97 (2)	2.60 (2)	3.384 (3)	137.8 (18)

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

Acknowledgements

The author thanks Dr I. F. Perepichka for providing single crystals of (I).

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