Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807028887/is2179sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807028887/is2179Isup2.hkl |
CCDC reference: 654997
Key indicators
- Single-crystal X-ray study
- T = 290 K
- Mean (C-C) = 0.003 Å
- R factor = 0.053
- wR factor = 0.133
- Data-to-parameter ratio = 15.0
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C1 - C2 ... 1.53 Ang. PLAT369_ALERT_2_C Long C(sp2)-C(sp2) Bond C1 - C2_a ... 1.53 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported HC5 .. O2 .. 2.64 Ang. PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 3
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 2 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
The title compound was synthesized according to Schmidt et al. (1984). Crystal suitable for X-ray diffraction has been obtained after slow evaporation from water/ethanol mixture (1:1) at room temperature.
Hydrogen atoms were located in a difference map. All H atoms were constrained to ride on their parent atoms, with Uiso(H) = 1.2Ueq(C).
The title compound, (I), has been synthesized as part of our synthetic and structural investigations of new organic materials with nonlinear and electro-optical properties (Chemla & Zyss, 1987; Wolff & Wortmann, 1999). We already analyzed the crystal structures of a number of pyridinium-betaines of squaric acid (Kolev et al., 2001, 2002, 2004; Kolev, Yancheva et al., 2005; Kolev, Wortmann et al., 2005), but without the essential member of the family, the unsubstituted compound, (I), their characterization remains incomplete. In order to provide relevant information on the changes observed upon substitution, we report its characteristic features.
The molecular features of (I) are similar to those in Kolev et al. (2001, 2002, 2004), Kolev, Yancheva et al. (2005), Kolev, Wortmann et al. (2005) and Uçar et al. (2005) with positive and negative charges situated on the pyridinium and squarate moiety, respectively (Scheme 1). The "semicarbonyl" C2—O1 bond length of 1.221 (2) Å shows the complete delocalization of the negative charge. In all reported structures the semi-carbonyl bond lengths, within the squarate fragment, are apparently unaffected by the substitution and their values vary around 1.22 Å. The C=O double bond length is also constant in reported structures with typical values around 1.201 Å. The pyridinium ring in (I) is planar with r.m.s deviation of 0.002 (2) Å and has partially quinoidal character reflected by the shorter C5—C6 and C8—C9 distances, most expressed in the 4-dimethylamino derivative (Kolev et al., 2002).
The C(Sq)—N(py) bond length bond length of 1.403 (4) Å is also unaffected by the presence of different substitutes. From the studied compounds only in 3-acetoxy-2-(acetylamino)pyridinium-1-squarate (Uçar et al., 2005) this value differs slightly and has a value of 1.422 (5) Å.
The dihedral angle between the squarate and pyridinium mean planes also show minor variations within the series of 3- and 4-substituted compounds, but differ significantly from the values for the 2-(3-benzoyl-1-pyridinio)-3,4-dioxocyclobutenolate derivative (Kolev, Yancheva et al., 2005), which is a sign that the conjugation between the molecular fragments is strongly decreased by the substitution at 2- and 3-position.
Similarly to the substituted pyridinium-betaines of squaric acid in the crystal structure of (I) molecules are connected through non-classical C—H···O hydrogen bonds (Table1) and π···π interactions between the oppositely charged squarate and pyridinium fragments [Cg1···O1iii 3.220 (3) Å; Cg1 is the controid of the pyridinium ring; symmetry code: (iii) x, 1 - y, 1/2 + z]. A side-to-side C4—HC4···O1i [symmetry code: (i) -x, 1 - y, -z] interaction of squarate and pyridinium fragments build up straight chains replicating along the c axis. A bifurcated head-to-tail C5—HC5···O2ii [symmetry code: (i) -1/2 + x, -1/2 + y, 1/2 - z] interaction connects three-dimensionally the chains.
Practically in all derivatives of (I) the squarate carbonyl O atom forms a bifurcated bond. The only observed exception is for 3-benzoylpyridinium betaine of squaric acid (Kolev, Yancheva et al., 2005) and could be explained by the steric effect of the phenyl substitute.
For related literature, see: Chemla & Zyss (1987); Kolev et al. (2001, 2002, 2004); Kolev, Wortmann et al. (2005); Kolev, Yancheva et al. (2005); Schmidt et al. (1984); Uçar et al. (2005); Wolff & Wortmann (1999).
Data collection: CAD-4 EXPRESS (Enraf–Nonius, 1994); cell refinement: CAD-4 EXPRESS; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Bruno et al., 2002); software used to prepare material for publication: WinGX (Farrugia, 1999).
C9H5NO3 | Dx = 1.497 Mg m−3 |
Mr = 175.14 | Melting point: not measured K |
Orthorhombic, Pbcn | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2n 2ab | Cell parameters from 22 reflections |
a = 5.0654 (2) Å | θ = 19.3–19.6° |
b = 18.8003 (17) Å | µ = 0.12 mm−1 |
c = 8.1609 (4) Å | T = 290 K |
V = 777.17 (9) Å3 | Prism, yellow |
Z = 4 | 0.40 × 0.36 × 0.36 mm |
F(000) = 360 |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.070 |
Radiation source: fine-focus sealed tube | θmax = 27.9°, θmin = 2.2° |
Graphite monochromator | h = 0→6 |
Non–profiled ω/2θ scans | k = −24→24 |
3425 measured reflections | l = −10→10 |
942 independent reflections | 3 standard reflections every 120 min |
559 reflections with I > 2σ(I) | intensity decay: −5% |
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)] = 0.053 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.134 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0456P)2 + 0.3645P] where P = (Fo2 + 2Fc2)/3 |
942 reflections | (Δ/σ)max < 0.001 |
63 parameters | Δρmax = 0.15 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C9H5NO3 | V = 777.17 (9) Å3 |
Mr = 175.14 | Z = 4 |
Orthorhombic, Pbcn | Mo Kα radiation |
a = 5.0654 (2) Å | µ = 0.12 mm−1 |
b = 18.8003 (17) Å | T = 290 K |
c = 8.1609 (4) Å | 0.40 × 0.36 × 0.36 mm |
Enraf–Nonius CAD-4 diffractometer | Rint = 0.070 |
3425 measured reflections | 3 standard reflections every 120 min |
942 independent reflections | intensity decay: −5% |
559 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.134 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.15 e Å−3 |
942 reflections | Δρmin = −0.20 e Å−3 |
63 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.5000 | 0.64018 (18) | 0.2500 | 0.0465 (8) | |
C2 | 0.3375 (4) | 0.58204 (12) | 0.1671 (3) | 0.0408 (5) | |
C3 | 0.5000 | 0.53134 (15) | 0.2500 | 0.0356 (6) | |
C4 | 0.3121 (4) | 0.42083 (12) | 0.1638 (3) | 0.0411 (5) | |
HC4 | 0.1779 | 0.4499 | 0.1194 | 0.061 (7)* | |
C5 | 0.3098 (5) | 0.34857 (13) | 0.1636 (3) | 0.0491 (6) | |
HC5 | 0.1706 | 0.3201 | 0.1032 | 0.059* | |
C6 | 0.5000 | 0.31182 (18) | 0.2500 | 0.0531 (9) | |
HC6 | 0.5000 | 0.2609 | 0.2500 | 0.064* | |
N1 | 0.5000 | 0.45673 (12) | 0.2500 | 0.0349 (6) | |
O1 | 0.1529 (3) | 0.58096 (9) | 0.0708 (2) | 0.0557 (5) | |
O2 | 0.5000 | 0.70389 (12) | 0.2500 | 0.0725 (9) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0433 (18) | 0.0490 (18) | 0.0471 (18) | 0.000 | −0.0043 (16) | 0.000 |
C2 | 0.0356 (11) | 0.0494 (13) | 0.0373 (11) | 0.0003 (10) | −0.0020 (10) | 0.0018 (10) |
C3 | 0.0325 (15) | 0.0415 (15) | 0.0330 (14) | 0.000 | −0.0009 (13) | 0.000 |
C4 | 0.0336 (10) | 0.0505 (13) | 0.0391 (11) | −0.0035 (11) | −0.0031 (10) | 0.0002 (10) |
C5 | 0.0430 (12) | 0.0530 (14) | 0.0512 (13) | −0.0102 (12) | 0.0009 (12) | −0.0054 (11) |
C6 | 0.051 (2) | 0.0440 (17) | 0.065 (2) | 0.000 | 0.007 (2) | 0.000 |
N1 | 0.0297 (12) | 0.0429 (14) | 0.0319 (12) | 0.000 | 0.0000 (11) | 0.000 |
O1 | 0.0484 (9) | 0.0637 (11) | 0.0549 (10) | 0.0019 (9) | −0.0204 (8) | 0.0061 (8) |
O2 | 0.080 (2) | 0.0418 (13) | 0.096 (2) | 0.000 | −0.0218 (18) | 0.000 |
C1—O2 | 1.198 (4) | C4—N1 | 1.363 (2) |
C1—C2 | 1.526 (3) | C4—HC4 | 0.9436 |
C2—O1 | 1.221 (2) | C5—C6 | 1.379 (3) |
C2—C3 | 1.430 (3) | C5—HC5 | 1.0133 |
C3—N1 | 1.403 (4) | C6—HC6 | 0.9571 |
C4—C5 | 1.359 (3) | ||
O2—C1—C2 | 135.73 (12) | N1—C4—HC4 | 114.5 |
O2—C1—C2i | 135.73 (12) | C4—C5—C6 | 119.6 (2) |
C2—C1—C2i | 88.5 (2) | C4—C5—HC5 | 122.3 |
O1—C2—C3 | 137.2 (2) | C6—C5—HC5 | 118.0 |
O1—C2—C1 | 135.2 (2) | C5i—C6—C5 | 119.9 (3) |
C3—C2—C1 | 87.55 (16) | C5i—C6—HC6 | 120.1 |
N1—C3—C2i | 131.82 (11) | C5—C6—HC6 | 120.1 |
N1—C3—C2 | 131.82 (11) | C4—N1—C4i | 120.6 (3) |
C2i—C3—C2 | 96.4 (2) | C4—N1—C3 | 119.69 (13) |
C5—C4—N1 | 120.1 (2) | C4i—N1—C3 | 119.69 (13) |
C5—C4—HC4 | 124.9 | ||
O2—C1—C2—O1 | 0.9 (3) | N1—C4—C5—C6 | −0.6 (3) |
C2i—C1—C2—O1 | −179.1 (3) | C4—C5—C6—C5i | 0.28 (15) |
O2—C1—C2—C3 | 180.0 | C5—C4—N1—C4i | 0.29 (16) |
C2i—C1—C2—C3 | 0.0 | C5—C4—N1—C3 | −179.71 (16) |
O1—C2—C3—N1 | −0.9 (3) | C2i—C3—N1—C4 | 177.06 (15) |
C1—C2—C3—N1 | 180.0 | C2—C3—N1—C4 | −2.94 (15) |
O1—C2—C3—C2i | 179.1 (3) | C2i—C3—N1—C4i | −2.94 (15) |
C1—C2—C3—C2i | 0.0 | C2—C3—N1—C4i | 177.06 (15) |
Symmetry code: (i) −x+1, y, −z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C4—HC4···O1ii | 0.94 | 2.36 | 3.036 (3) | 129 |
C5—HC5···O2iii | 1.01 | 2.64 | 3.218 (3) | 116 |
Symmetry codes: (ii) −x, −y+1, −z; (iii) x−1/2, y−1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C9H5NO3 |
Mr | 175.14 |
Crystal system, space group | Orthorhombic, Pbcn |
Temperature (K) | 290 |
a, b, c (Å) | 5.0654 (2), 18.8003 (17), 8.1609 (4) |
V (Å3) | 777.17 (9) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.40 × 0.36 × 0.36 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3425, 942, 559 |
Rint | 0.070 |
(sin θ/λ)max (Å−1) | 0.659 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.134, 1.04 |
No. of reflections | 942 |
No. of parameters | 63 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.15, −0.20 |
Computer programs: CAD-4 EXPRESS (Enraf–Nonius, 1994), CAD-4 EXPRESS, XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Bruno et al., 2002), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
C4—HC4···O1i | 0.94 | 2.36 | 3.036 (3) | 128.5 |
C5—HC5···O2ii | 1.01 | 2.64 | 3.218 (3) | 116.4 |
Symmetry codes: (i) −x, −y+1, −z; (ii) x−1/2, y−1/2, −z+1/2. |
The title compound, (I), has been synthesized as part of our synthetic and structural investigations of new organic materials with nonlinear and electro-optical properties (Chemla & Zyss, 1987; Wolff & Wortmann, 1999). We already analyzed the crystal structures of a number of pyridinium-betaines of squaric acid (Kolev et al., 2001, 2002, 2004; Kolev, Yancheva et al., 2005; Kolev, Wortmann et al., 2005), but without the essential member of the family, the unsubstituted compound, (I), their characterization remains incomplete. In order to provide relevant information on the changes observed upon substitution, we report its characteristic features.
The molecular features of (I) are similar to those in Kolev et al. (2001, 2002, 2004), Kolev, Yancheva et al. (2005), Kolev, Wortmann et al. (2005) and Uçar et al. (2005) with positive and negative charges situated on the pyridinium and squarate moiety, respectively (Scheme 1). The "semicarbonyl" C2—O1 bond length of 1.221 (2) Å shows the complete delocalization of the negative charge. In all reported structures the semi-carbonyl bond lengths, within the squarate fragment, are apparently unaffected by the substitution and their values vary around 1.22 Å. The C=O double bond length is also constant in reported structures with typical values around 1.201 Å. The pyridinium ring in (I) is planar with r.m.s deviation of 0.002 (2) Å and has partially quinoidal character reflected by the shorter C5—C6 and C8—C9 distances, most expressed in the 4-dimethylamino derivative (Kolev et al., 2002).
The C(Sq)—N(py) bond length bond length of 1.403 (4) Å is also unaffected by the presence of different substitutes. From the studied compounds only in 3-acetoxy-2-(acetylamino)pyridinium-1-squarate (Uçar et al., 2005) this value differs slightly and has a value of 1.422 (5) Å.
The dihedral angle between the squarate and pyridinium mean planes also show minor variations within the series of 3- and 4-substituted compounds, but differ significantly from the values for the 2-(3-benzoyl-1-pyridinio)-3,4-dioxocyclobutenolate derivative (Kolev, Yancheva et al., 2005), which is a sign that the conjugation between the molecular fragments is strongly decreased by the substitution at 2- and 3-position.
Similarly to the substituted pyridinium-betaines of squaric acid in the crystal structure of (I) molecules are connected through non-classical C—H···O hydrogen bonds (Table1) and π···π interactions between the oppositely charged squarate and pyridinium fragments [Cg1···O1iii 3.220 (3) Å; Cg1 is the controid of the pyridinium ring; symmetry code: (iii) x, 1 - y, 1/2 + z]. A side-to-side C4—HC4···O1i [symmetry code: (i) -x, 1 - y, -z] interaction of squarate and pyridinium fragments build up straight chains replicating along the c axis. A bifurcated head-to-tail C5—HC5···O2ii [symmetry code: (i) -1/2 + x, -1/2 + y, 1/2 - z] interaction connects three-dimensionally the chains.
Practically in all derivatives of (I) the squarate carbonyl O atom forms a bifurcated bond. The only observed exception is for 3-benzoylpyridinium betaine of squaric acid (Kolev, Yancheva et al., 2005) and could be explained by the steric effect of the phenyl substitute.