Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270113013929/fa3317sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270113013929/fa3317Isup2.hkl | |
Chemical Markup Language (CML) file https://doi.org/10.1107/S0108270113013929/fa3317Isup3.cml |
CCDC reference: 957011
For related literature, see: Abram et al. (2000); Allen (2002); Belicchi-Ferrari, Bisceglie, Casoli, Durot, Morgenstern-Badarau, Pelosi, Pilotti, Pinelli & Tarasconi (2005); Belicchi-Ferrari, Bisceglie, Leporati, Pelosi & Tarasconi (2002); Belicchi-Ferrari, Bisceglie, Pelosi, Tarasconi, Albertini, Paolo Dall'Aglio, Pinelli, Bergamo & Savac (2004); Belicchi-Ferrari, Gasparri Fava, Pelizzi & Tarasconi (1992); Belicchi-Ferrari, Gasparri, Leporati, Pelizzi, Tarasconi & Tosi (1986); Beraldo & Gambino (2004); Casas et al. (2000, 2012); Du et al. (2002); Gómez Quiroga & Navarro Ranninger (2004); Hall et al. (2009); Kalinowski & Richardson (2005); Knežević et al. (2003); Leovac et al. (2005, 2007a, 2007b); Lobana et al. (2009); Vidović et al. (2011); Vrdoljak et al. (2009).
Pyridoxal semicarbazone dihydrate (PLSC.2H2O, 50 mg), which was prepared according to a known procedure (Knežević et al., 2003), was mixed with warm H2O (10 ml) and two drops of concentrated HNO3 were added to the mixture. The resulting clear solution was left at room temperature to evaporate to a small volume, from which yellow prismatic single crystals were filtered and washed with H2O (yield: 51 mg, 92%; m.p. 505 K). Analysis calculated for C9H13N5O6: C 37.63, H 4.56, N 24.38%; found: C 37.55, H 4.48, N 24.13%. Molar conductivity, ΛM (S cm2 mol-1): 138 (H2O), 60 (dimethylformamide). The compound is quite soluble in H2O, dimethylformamide and MeOH, less so in EtOH, and insoluble in Et2O.
H atoms bonded to C atoms were placed at calculated positions, with C—H distances fixed at 0.93 Å for aromatic Csp2 atoms and at 0.96 and 0.97 Å for methyl and methylene Csp3 atoms, respectively. The corresponding Uiso values of the H atoms were set at 1.2Ueq and 1.5Ueq of the parent Csp2 and Csp3 atoms, respectively. H atoms attached to N and O atoms were located in a difference Fourier map and refined isotropically.
Data collection: CrysAlis PRO (Agilent, 2013); cell refinement: CrysAlis PRO (Agilent, 2013); data reduction: CrysAlis PRO (Agilent, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012), PLATON (Spek, 2009) and PARST (Nardelli, 1995).
C9H13N4O3+·NO3− | Z = 2 |
Mr = 287.24 | F(000) = 300 |
Triclinic, P1 | Dx = 1.569 Mg m−3 Dm = 1.57 Mg m−3 Dm measured by flotation in bromoform – diethylether mixture |
Hall symbol: -P 1 | Melting point: 505 K |
a = 7.1093 (3) Å | Cu Kα radiation, λ = 1.54180 Å |
b = 8.1905 (4) Å | Cell parameters from 5840 reflections |
c = 11.6494 (6) Å | θ = 5.9–72.7° |
α = 110.117 (5)° | µ = 1.15 mm−1 |
β = 93.566 (4)° | T = 294 K |
γ = 104.589 (4)° | Block, translucent pale yellow |
V = 608.09 (5) Å3 | 0.49 × 0.33 × 0.18 mm |
Agilent Gemini S diffractometer | 2410 independent reflections |
Radiation source: fine-focus sealed tube | 2299 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.022 |
Detector resolution: 16.3280 pixels mm-1 | θmax = 72.7°, θmin = 4.1° |
ω scans | h = −8→8 |
Absorption correction: gaussian (CrysAlis PRO; Agilent, 2013) | k = −10→10 |
Tmin = 0.648, Tmax = 0.831 | l = −14→14 |
9478 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.042 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.123 | w = 1/[σ2(Fo2) + (0.0712P)2 + 0.1565P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
2410 reflections | Δρmax = 0.31 e Å−3 |
207 parameters | Δρmin = −0.20 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.034 (3) |
C9H13N4O3+·NO3− | γ = 104.589 (4)° |
Mr = 287.24 | V = 608.09 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.1093 (3) Å | Cu Kα radiation |
b = 8.1905 (4) Å | µ = 1.15 mm−1 |
c = 11.6494 (6) Å | T = 294 K |
α = 110.117 (5)° | 0.49 × 0.33 × 0.18 mm |
β = 93.566 (4)° |
Agilent Gemini S diffractometer | 2410 independent reflections |
Absorption correction: gaussian (CrysAlis PRO; Agilent, 2013) | 2299 reflections with I > 2σ(I) |
Tmin = 0.648, Tmax = 0.831 | Rint = 0.022 |
9478 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.123 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.31 e Å−3 |
2410 reflections | Δρmin = −0.20 e Å−3 |
207 parameters |
Experimental. Absorption correction: numerical absorption correction based on gaussian integration over a multifaceted crystal model CrysAlisPro, Agilent Technologies (2013). Selected FTIR data (KBr, ν, cm–1): 3331s, 3190vs, 3021–2655br, 1717vs, 1648m, 1551vs, 1428s, 1384vs, 1338s, 1305s, 1253m, 1181s, 1049s, 930m, 819w, 728m, 604m; |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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 | ||
O1 | 0.39375 (18) | −0.08434 (14) | 0.82584 (9) | 0.0458 (3) | |
O2 | 0.13596 (17) | −0.26177 (15) | 0.49673 (10) | 0.0452 (3) | |
O3 | 0.50461 (16) | 0.32306 (15) | 0.38814 (10) | 0.0453 (3) | |
N1 | 0.46254 (18) | 0.15784 (16) | 0.76394 (10) | 0.0367 (3) | |
N2 | 0.35489 (17) | 0.05302 (16) | 0.65103 (10) | 0.0331 (3) | |
N3 | 0.5881 (2) | 0.19177 (19) | 0.95758 (12) | 0.0479 (4) | |
N4 | 0.00310 (18) | −0.20154 (17) | 0.21980 (11) | 0.0369 (3) | |
C1 | 0.4760 (2) | 0.07714 (19) | 0.85024 (12) | 0.0353 (3) | |
C2 | 0.34297 (19) | 0.12480 (18) | 0.56968 (12) | 0.0324 (3) | |
H2A | 0.4082 | 0.2466 | 0.5878 | 0.039* | |
C3 | 0.22443 (18) | 0.01055 (18) | 0.44781 (11) | 0.0300 (3) | |
C4 | 0.12876 (19) | −0.17534 (18) | 0.41856 (12) | 0.0322 (3) | |
C5 | 0.01570 (19) | −0.28178 (19) | 0.30141 (13) | 0.0345 (3) | |
C6 | −0.0933 (2) | −0.4782 (2) | 0.26578 (15) | 0.0464 (4) | |
H6A | −0.0787 | −0.5449 | 0.1828 | 0.070* | |
H6B | −0.2305 | −0.4911 | 0.2699 | 0.070* | |
H6C | −0.0409 | −0.5248 | 0.3217 | 0.070* | |
C7 | 0.0897 (2) | −0.0249 (2) | 0.24367 (13) | 0.0368 (3) | |
H7 | 0.0743 | 0.0226 | 0.1829 | 0.044* | |
C8 | 0.20127 (19) | 0.08639 (18) | 0.35781 (12) | 0.0322 (3) | |
C9 | 0.2981 (2) | 0.28364 (19) | 0.38026 (13) | 0.0381 (3) | |
H9A | 0.2452 | 0.3124 | 0.3133 | 0.046* | |
H9B | 0.2671 | 0.3596 | 0.4567 | 0.046* | |
H1 | 0.518 (3) | 0.272 (3) | 0.7815 (16) | 0.035 (4)* | |
H3 | 0.526 (3) | 0.257 (3) | 0.320 (2) | 0.067 (6)* | |
H2 | 0.219 (4) | −0.192 (4) | 0.561 (3) | 0.085 (8)* | |
H4 | −0.065 (3) | −0.270 (3) | 0.147 (2) | 0.066 (6)* | |
H3A | 0.641 (3) | 0.307 (3) | 0.9725 (19) | 0.051 (5)* | |
H3B | 0.603 (3) | 0.161 (3) | 1.021 (2) | 0.054 (5)* | |
O4 | 0.6370 (2) | 0.53928 (18) | 0.82584 (12) | 0.0692 (4) | |
O5 | 0.7716 (3) | 0.56532 (18) | 1.00199 (13) | 0.0812 (6) | |
O6 | 0.8425 (3) | 0.79232 (18) | 0.94813 (14) | 0.0766 (5) | |
N5 | 0.7513 (2) | 0.63406 (18) | 0.92440 (11) | 0.0454 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0670 (7) | 0.0327 (5) | 0.0291 (5) | 0.0033 (5) | −0.0002 (4) | 0.0104 (4) |
O2 | 0.0520 (6) | 0.0396 (6) | 0.0396 (6) | 0.0012 (5) | −0.0066 (5) | 0.0204 (5) |
O3 | 0.0445 (6) | 0.0396 (6) | 0.0384 (6) | 0.0003 (4) | 0.0024 (4) | 0.0076 (5) |
N1 | 0.0470 (7) | 0.0304 (6) | 0.0248 (6) | 0.0034 (5) | −0.0035 (5) | 0.0080 (4) |
N2 | 0.0362 (6) | 0.0357 (6) | 0.0232 (5) | 0.0083 (5) | 0.0011 (4) | 0.0080 (4) |
N3 | 0.0693 (9) | 0.0360 (7) | 0.0271 (6) | −0.0007 (6) | −0.0089 (6) | 0.0125 (5) |
N4 | 0.0374 (6) | 0.0383 (6) | 0.0265 (6) | 0.0051 (5) | −0.0032 (4) | 0.0072 (5) |
C1 | 0.0432 (7) | 0.0344 (7) | 0.0250 (6) | 0.0087 (6) | 0.0028 (5) | 0.0095 (5) |
C2 | 0.0348 (6) | 0.0321 (6) | 0.0266 (6) | 0.0069 (5) | 0.0017 (5) | 0.0089 (5) |
C3 | 0.0284 (6) | 0.0342 (7) | 0.0256 (6) | 0.0083 (5) | 0.0035 (5) | 0.0095 (5) |
C4 | 0.0309 (6) | 0.0350 (7) | 0.0300 (6) | 0.0078 (5) | 0.0030 (5) | 0.0127 (5) |
C5 | 0.0320 (6) | 0.0342 (7) | 0.0324 (7) | 0.0070 (5) | 0.0026 (5) | 0.0087 (5) |
C6 | 0.0484 (8) | 0.0354 (7) | 0.0445 (8) | 0.0022 (6) | −0.0023 (6) | 0.0104 (6) |
C7 | 0.0402 (7) | 0.0395 (7) | 0.0289 (6) | 0.0076 (6) | 0.0000 (5) | 0.0145 (5) |
C8 | 0.0324 (6) | 0.0347 (7) | 0.0281 (6) | 0.0083 (5) | 0.0025 (5) | 0.0114 (5) |
C9 | 0.0451 (8) | 0.0344 (7) | 0.0330 (7) | 0.0076 (6) | 0.0003 (5) | 0.0144 (5) |
O4 | 0.0939 (10) | 0.0542 (7) | 0.0376 (6) | −0.0122 (7) | −0.0184 (6) | 0.0197 (6) |
O5 | 0.1186 (13) | 0.0452 (7) | 0.0539 (8) | −0.0165 (7) | −0.0412 (8) | 0.0252 (6) |
O6 | 0.1034 (12) | 0.0441 (7) | 0.0596 (8) | −0.0171 (7) | −0.0072 (7) | 0.0230 (6) |
N5 | 0.0552 (8) | 0.0384 (7) | 0.0328 (6) | 0.0000 (6) | 0.0005 (5) | 0.0122 (5) |
O1—C1 | 1.2261 (18) | C2—H2A | 0.9300 |
O2—C4 | 1.3375 (16) | C3—C4 | 1.4105 (19) |
O2—H2 | 0.85 (3) | C3—C8 | 1.4108 (17) |
O3—C9 | 1.4117 (18) | C4—C5 | 1.4002 (19) |
O3—H3 | 0.84 (3) | C5—C6 | 1.4948 (19) |
N1—N2 | 1.3491 (16) | C6—H6A | 0.9600 |
N1—C1 | 1.3906 (17) | C6—H6B | 0.9600 |
N1—H1 | 0.863 (19) | C6—H6C | 0.9600 |
N2—C2 | 1.2842 (17) | C7—C8 | 1.3779 (19) |
N3—C1 | 1.3311 (19) | C7—H7 | 0.9300 |
N3—H3A | 0.88 (2) | C8—C9 | 1.5096 (19) |
N3—H3B | 0.87 (2) | C9—H9A | 0.9700 |
N4—C5 | 1.3389 (18) | C9—H9B | 0.9700 |
N4—C7 | 1.3428 (19) | O4—N5 | 1.2386 (18) |
N4—H4 | 0.87 (3) | O5—N5 | 1.2369 (18) |
C2—C3 | 1.4634 (17) | O6—N5 | 1.2185 (18) |
C4—O2—H2 | 109.3 (18) | N4—C5—C4 | 117.93 (12) |
C9—O3—H3 | 106.6 (16) | N4—C5—C6 | 119.38 (13) |
N2—N1—C1 | 118.03 (12) | C4—C5—C6 | 122.68 (13) |
N2—N1—H1 | 120.0 (11) | C5—C6—H6A | 109.5 |
C1—N1—H1 | 122.0 (12) | C5—C6—H6B | 109.5 |
C2—N2—N1 | 118.84 (12) | H6A—C6—H6B | 109.5 |
C1—N3—H3A | 122.5 (13) | C5—C6—H6C | 109.5 |
C1—N3—H3B | 122.6 (14) | H6A—C6—H6C | 109.5 |
H3A—N3—H3B | 114.5 (19) | H6B—C6—H6C | 109.5 |
C5—N4—C7 | 124.19 (12) | N4—C7—C8 | 120.28 (13) |
C5—N4—H4 | 116.4 (15) | N4—C7—H7 | 119.9 |
C7—N4—H4 | 119.4 (15) | C8—C7—H7 | 119.9 |
O1—C1—N3 | 125.14 (13) | C7—C8—C3 | 118.74 (13) |
O1—C1—N1 | 121.78 (12) | C7—C8—C9 | 118.57 (12) |
N3—C1—N1 | 113.07 (13) | C3—C8—C9 | 122.67 (12) |
N2—C2—C3 | 118.49 (12) | O3—C9—C8 | 111.90 (11) |
N2—C2—H2A | 120.8 | O3—C9—H9A | 109.2 |
C3—C2—H2A | 120.8 | C8—C9—H9A | 109.2 |
C4—C3—C8 | 118.76 (12) | O3—C9—H9B | 109.2 |
C4—C3—C2 | 121.13 (12) | C8—C9—H9B | 109.2 |
C8—C3—C2 | 120.10 (12) | H9A—C9—H9B | 107.9 |
O2—C4—C5 | 115.57 (12) | O6—N5—O5 | 118.96 (14) |
O2—C4—C3 | 124.35 (12) | O6—N5—O4 | 122.57 (14) |
C5—C4—C3 | 120.08 (12) | O5—N5—O4 | 118.46 (13) |
C1—N1—N2—C2 | −179.11 (12) | C3—C4—C5—N4 | 0.25 (19) |
N2—N1—C1—O1 | 0.1 (2) | O2—C4—C5—C6 | 1.1 (2) |
N2—N1—C1—N3 | 178.94 (12) | C3—C4—C5—C6 | −178.43 (13) |
N1—N2—C2—C3 | −179.45 (11) | C5—N4—C7—C8 | 0.4 (2) |
N2—C2—C3—C4 | −1.49 (19) | N4—C7—C8—C3 | 0.8 (2) |
N2—C2—C3—C8 | 177.40 (11) | N4—C7—C8—C9 | 179.28 (12) |
C8—C3—C4—O2 | −178.53 (11) | C4—C3—C8—C7 | −1.46 (19) |
C2—C3—C4—O2 | 0.4 (2) | C2—C3—C8—C7 | 179.63 (12) |
C8—C3—C4—C5 | 0.93 (19) | C4—C3—C8—C9 | −179.84 (12) |
C2—C3—C4—C5 | 179.83 (11) | C2—C3—C8—C9 | 1.24 (19) |
C7—N4—C5—C4 | −1.0 (2) | C7—C8—C9—O3 | −109.53 (14) |
C7—N4—C5—C6 | 177.76 (14) | C3—C8—C9—O3 | 68.85 (16) |
O2—C4—C5—N4 | 179.76 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2···N2 | 0.85 (3) | 1.87 (3) | 2.5968 (16) | 143 (2) |
O3—H3···O1i | 0.84 (3) | 2.03 (3) | 2.8534 (16) | 170 (2) |
N1—H1···O4 | 0.863 (19) | 2.00 (2) | 2.8647 (18) | 177.8 (16) |
N3—H3A···O5 | 0.88 (2) | 1.98 (2) | 2.8542 (19) | 177.2 (19) |
N3—H3B···O1ii | 0.87 (2) | 2.09 (2) | 2.9497 (17) | 173.7 (18) |
N4—H4···O5iii | 0.87 (3) | 1.85 (3) | 2.7124 (18) | 173 (2) |
C9—H9A···O4iv | 0.97 | 2.41 | 3.206 (2) | 140 |
C7—H7···O6iv | 0.93 | 2.50 | 3.384 (3) | 160 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, −y, −z+2; (iii) x−1, y−1, z−1; (iv) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C9H13N4O3+·NO3− |
Mr | 287.24 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 294 |
a, b, c (Å) | 7.1093 (3), 8.1905 (4), 11.6494 (6) |
α, β, γ (°) | 110.117 (5), 93.566 (4), 104.589 (4) |
V (Å3) | 608.09 (5) |
Z | 2 |
Radiation type | Cu Kα |
µ (mm−1) | 1.15 |
Crystal size (mm) | 0.49 × 0.33 × 0.18 |
Data collection | |
Diffractometer | Agilent Gemini S diffractometer |
Absorption correction | Gaussian (CrysAlis PRO; Agilent, 2013) |
Tmin, Tmax | 0.648, 0.831 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9478, 2410, 2299 |
Rint | 0.022 |
(sin θ/λ)max (Å−1) | 0.619 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.123, 1.06 |
No. of reflections | 2410 |
No. of parameters | 207 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.31, −0.20 |
Computer programs: CrysAlis PRO (Agilent, 2013), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 2012), WinGX (Farrugia, 2012), PLATON (Spek, 2009) and PARST (Nardelli, 1995).
O1—C1 | 1.2261 (18) | N3—C1 | 1.3311 (19) |
O2—C4 | 1.3375 (16) | O4—N5 | 1.2386 (18) |
N1—N2 | 1.3491 (16) | O5—N5 | 1.2369 (18) |
N1—C1 | 1.3906 (17) | O6—N5 | 1.2185 (18) |
N2—C2 | 1.2842 (17) | ||
N2—N1—C1 | 118.03 (12) | O1—C1—N1 | 121.78 (12) |
C2—N2—N1 | 118.84 (12) | N3—C1—N1 | 113.07 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2···N2 | 0.85 (3) | 1.87 (3) | 2.5968 (16) | 143 (2) |
O3—H3···O1i | 0.84 (3) | 2.03 (3) | 2.8534 (16) | 170 (2) |
N1—H1···O4 | 0.863 (19) | 2.00 (2) | 2.8647 (18) | 177.8 (16) |
N3—H3A···O5 | 0.88 (2) | 1.98 (2) | 2.8542 (19) | 177.2 (19) |
N3—H3B···O1ii | 0.87 (2) | 2.09 (2) | 2.9497 (17) | 173.7 (18) |
N4—H4···O5iii | 0.87 (3) | 1.85 (3) | 2.7124 (18) | 173 (2) |
C9—H9A···O4iv | 0.97 | 2.41 | 3.206 (2) | 140 |
C7—H7···O6iv | 0.93 | 2.50 | 3.384 (3) | 160 |
Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x+1, −y, −z+2; (iii) x−1, y−1, z−1; (iv) −x+1, −y+1, −z+1. |
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Semicarbazones (SC) and the analogous thiosemicarbazones (TSC) are extensively investigated Schiff bases [see (I) and (II) in Scheme] with interesting structural, physicochemical and pharmacological properties (Lobana et al., 2009; Casas et al., 2000; Gómez Quiroga & Navarro Ranninger, 2004). The broad biological activity of SC (antiprotozoal and anticonvulsant) and TSC (antibacterial, antiviral and antitumor), as well as of their metal complexes, has been reviewed, together with proposed mechanisms of action (Beraldo & Gambino, 2004). The biological relevance of these compounds is usually related to their ability to form stable chelates with metal ions in vivo (Kalinowski & Richardson, 2005); there are, however, examples in which the structure and conformational flexibility of SC or TSC cores or the size of the attached substitituents can play an important role in their activity (Du et al., 2002; Hall et al., 2009).
The advantageous fact that SC and TSC Schiff bases can easily be modified by variation of the parent aldehyde or ketone has been used for the synthesis of derivatives incorporating biologically important substrates such as pyridoxal, which is one of the forms of vitamin B6 (Casas et al., 2012). In the last few decades, the pyridoxal thiosemicarbazone (PLTSC) complexes with a variety of metals have attracted particular interest due to their evident antitumor activity (Belicchi-Ferrari et al., 1992, 2004, 2005). Investigations into the structural and biological properties of the analogous pyridoxal semicarbazone (PLSC) complexes are also becoming more frequent than hitherto (Leovac et al., 2005, 2007a,b; Vidović et al., 2011; Jevtović, et al., 2011). Surprisingly, the Cambridge Structural Database (CSD, Release 5.33, August 2012; Allen, 2002) does not contain structural data for any corresponding PLSC ligands; by comparison, five crystal structures of the analogous sulfur-containing PLTSC ligands have been reported (Belicchi-Ferrari et al., 1986, 2002; Vrdoljak et al., 2009; Abram et al., 2000). The present work describes the synthesis and the first crystal structure of a Schiff base derived from semicarbazide and pyridoxal, namely (E)-4-[(2-carbamoylhydrazinylidene)methyl]-3-hydroxy-5-hydroxymethyl-2-methylpyridin-1-ium nitrate, (III).
The molecular structure of (III), together with the atom-labelling scheme and the hydrogen bonding within the asymmetric unit, is shown in Fig. 1. The asymmetric unit contains the PLSC fragment, protonated at the pyridine N atom, and a nitrate anion. In a review of the general structural properties of both SC and TSC (Casas et al., 2000), it was noted that the azomethine N and the O (or S) atom usually adopt relative trans positions, i.e. in an E configuration [see (I) in Scheme] with respect to the N1—C1 bond in the unsubstituted ligands. The present case is an exception to this rule, displaying a Z configuration [see (II) in Scheme], with an N2—N1—C1—O1 torsion angle of 0.1 (2)°. This is probably due to the complementary hydrogen bonding formed between what is thus a suitably oriented pair of N—H donors at atoms N1 and N3 of the PLSC cation and two of the nitrate O atoms (Fig. 1). It should be mentioned that in two crystal structures of unsubstitued PLTSC ligands [CSD refcodes FADBOB (Belicchi-Ferrari et al., 1986) and NUKFOP (Vrdoljak et al., 2009)], the molecules remain in the usual E configuration (average N2—N1—C1—O1 torsion angle is 179°), which is stabilized by the expected intramolecular hydrogen bond between the amine N3—H group and azomethine atom N2.
The structure of (III) is stabilized by an intramolecular O2—H2···N2 hydrogen bond (Table 1). The significance of this interaction can be appreciated by comparison with the two PLTSC analogues, viz. FADBOB and NUKFOP. These PLTSC are isolated as zwitterions, with the phenol atom O2 deprotonated, thus obviating the formation of the intramolecular O2—H2···N2 interaction. The orientation of the C2—N2—N1—C1(═S)—N3 fragment relative to the pyridoxal moiety can change by rotation around the C2—C3 bond; the N2—C2—C3—C4 torsion angle in the PLTSC analogues is 174° on average, while in (III) it is -1.49 (19)°. This comparison demonstrates the great flexibility of these Schiff bases and the importance of intra- and intermolecular interactions in establishing their configurations.
The bond lengths and angles listed in Table 2 are comparable to those found for similar semicarbazones derived from aromatic carbonyls (CSD; Allen, 2002). In PLSC, as in previous cases, the N2—N1, N1—C1, C1—N3 and C1—O1 bonds have partial double-bond character, which suggests that there is electron delocalization within the SC fragment. Closer inspection shows that N2—N1 [1.3491 (16) Å] is noticeably shorter than N1—C1 [1.3906 (17) Å], which is opposite to what is usually found in similar SC structures (average values for N2—N1 and N1—C1 are 1.38 and 1.36 Å, respectively). Another difference can be observed in the angle N1—C1—N3 [113.07 (13)°], which is considerably smaller than in previously reported structures (average value = 117.8°). The PLSC fragment as a whole is essentially planar with a near-zero dihedral angle [0.86 (5)°] between the best planes of the pyridine and SC moieties. Among the non-H atoms of the ligand the only significant deviation from planarity is observed for methoxy atom O3 whose orientation is apparently influenced by hydrogen bonding. Atom O3 deviates from the plane formed by all of the other non-H atoms of PLSC (r.m.s deviation = 0.01 Å) by 1.23 (1) Å.
The crystal packing in (III) is mediated by four N—H···O and one O—H···O hydrogen bonds (Table 1) with nearly linear geometries (all D—H···O > 170°). The strongest interaction is, as expected, formed between the charged parts of the molecules, the protonated pyridine N4 and nitrate O5iii [symmetry code: (iii) x-1, y-1, z-1]. In addition to this interaction, the inversion-related pair of hydrogen bonds based on N3—H3B···O1ii [symmetry code: (ii) -x+1, -y, -z+2], linking centrosymmetrically related molecules, together with the complementary hydrogen bonds, N1—H1···O4 and N3—H3A···O5, leads to the formation of discrete molecular ribbons, approximately 15 Å wide. Ribbons in the same plane are connected by two weak C—H···O interactions (Table 1) to form flat two-dimensional layers (Fig. 2). This structure therefore contains three types of hydrogen-bonded rings which can all be assigned with graph-set notation R22(8) (Etter, 1991). The nitrate anions which are lodged in these two-dimensional frameworks deviate only slightly from the plane of the cation [the dihedral angle between the best planes of the anion and the cation is 5.50 (9)°]. In agreement with the strengths of the nonbonded interactions, we observe that N5—O6, whose hydrogen-bond acceptor atom O6 is involved only in a weak C7—H7···O6iv contact [symmetry code: (iv) -x+1, -y+1, -z+1], is shorter than the other two N—O bonds (Table 2). The methoxy O3—H groups of the pyridoxal units are the only fragments that deviate significantly from the corresponding layers. They are oriented toward the O1 acceptors of neighbouring layers in order to form an O3—H3···O1i hydrogen bond [symmetry code: (i) -x+1, -y, -z+1] which connects the layers into a three-dimensional structure (Fig. 3). The average orthogonal separation between neighbouring layers is 3.3 Å.