Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768105040590/sn5027sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108768105040590/sn5027IIIsup2.hkl | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108768105040590/sn5027IVsup3.hkl |
CCDC references: 612190; 612191; 612192; 612193
1H NMR in liquid state was recorded at 500.13 MHz in dimethylsulfoxide-d6 (d6-DMSO) at room temperature. The 1H spectra were referenced to TMS by using dimethylsulfoxide-d6 (2.49 p.p.m.) signal as the internal reference; the proton recycle time was 2 s. Multiplicities are as follows: s, singlet; d, doublet; t, triplet and m, multiplet. The assignment of the NMR peaks of the free Schiff bases (I) was compared with the PL skeleton (Christen & Metzler, 1985; Harruff & Jenkins, 1976; Witherup & Abbott, 1975); compound (III) refer to van Genderen et al. (1989); the acid base adducts (II) and (IV) were compared with the free benzoic acid derivatives and Schiff bases spectra. The compounds synthesized were characterized by X-ray crystallography as reported above, but also by elemental analysis and NMR in solution.
2.1. X-ray Structure Determination.
Data were collected on a Bruker Apex diffractometer equipped with a CCD area detector and corrected for absorption using the SADABS program (Sheldrick, 2002). Data reduction was performed using Bruker SMART, Bruker SAINT and SHELXTL (Sheldrick, 2000) programs. For details, see Table 1 and 2. For (I): R: 0.0752, wR = 0.265, based on 2285 unique reflections collected at 295 (2) K and 190 model parameters; for (II): R: 0.0597, wR = 0.1808, based on 4399 unique reflections collected at 295 (2) K and 294 model parameters; for (III): R: 0.0508, wR = 0.1474, based on 1575 unique reflections collected at 295 (2) K and 118 model parameters; (IV): R1: 0.0371, wR2 = 0.0991, based on 2768 unique reflections collected at 100 (2) K and 226 model parameters.
2.2. Crystallization and Synthesis
In this paragraph the synthesis of (I) to (IV) as well as details to the preparations of the crystals are described.
Compound (I). N-(pyridoxylidene)-tolylamine, (I), was prepared after a method descried by Iwanami (1968), pyridoxal hydrochloride was condensed in aqueous solution at pH 7.5 with p-toluidine to the Schiff base (I). Compound (I) was crystallized by solving it in excess of dichloromethane and slowly evaporating it at room temperature. The crystals were filtrated, washed with diethyl ether and dried over potassium hydroxide. m. p. 190–193 °C, 1H NMR (500 MHz, d6-DMSO, 300 K, only in open form) ? (p.p.m., TMS) = 2.35 (s, 3H, 1???-CH3), 2.42 (s, 3H, 2?-CH3), 4.76 (d, 2H, 3 J(H,H) = 5.4 Hz, 5?-CH2-), 5.42 (t, 1H, 3 J(H,H) = 5.4 Hz, 5??-OH), 7.25–7.45 (m, 4H, H2??,3??,5??,6??), 7.97 (s, 1H, H6), 9.17 (s, 1H, H4?), 14.04 (s, 1H, H3?) p.p.m., Analysis calculated for C15 H 16 N2 O2: C 68.49, H 2.39, N 10.93%, found: C 70.18, H 6.36, N 10.98%.
Compound (II). The N-(pyridoxylidene)-tolylamine (I)–2-nitrobenzoic acid complex, (II), was prepared by adding (I) (1 g, 3.9 mmol) to a solution of 4-nitrobenzoic acid (0.63 g, 3.8 mmol) in dichloromethane. Complex (IV) can be crystallized by diluting the solution with dichloromethane slowly evaporating the solvent under reduced pressure. The crystals were filtrated of, washed with diethyl ether and dried over potassium hydroxide. m. p. decomposition <170 °C, 1H NMR (500 MHz, d6-DMSO, 300 K, only in open form) ? (p.p.m., TMS) = 2.35 (s, 3H, 1???-CH3), 2.42 (s, 3H, 2?-CH3), 4.76 (s, 2H, 5?-CH2- broad), 5.40 (s, 1H, 5??-OH broad), 7.25–7.45 (m, 4H, H2??,3??,5??,6??), 7.98 (s, 1H, H6), 9.17 (s, 1H, H4?), 14.04 (s, 1H, H3? broad) p.p.m. (compound (I)), 7.7–8.0 (m, 4H, H3A,4 A,5 A,H6A), 9.46 (s, 1H, OH broad) p.p.m. (2-nitrobenzoic acid).
Compound (III). N-(pyridoxylidene)-methylamine, (III), was prepared after a method described in the literature (Heyl et al., 1948; Heyl et al., 1952; Metzler, 1957; van Genderen et al., 1989), pyridoxal hydrochloride was condensed in methanolic solution with methylamine hydrochloride to the Schiff base (III). Compound (III) was crystallized from dioxane / hexane (1 / 4) at room temperature. The crystals were filtrated of, washed with hexane and dried over potassium hydroxide. m. p. 145–146 °C, 1H NMR (500.13 MHz, d6-DMSO, 300 K, only in open form) ? (p.p.m., TMS): 2.35 (s, 3H, 2?-CH3), 3.50 (s, 3H, 4??-CH3), 4.63 (s, 2H, 5?-CH2-), 5.32 (s, 1H, broad 5?-CH2—OH), 7.85 (s, 1H, H6), 8.86 (s,1H, H4?), 14.32 (s, 1H, H3?), Analysis calculated for C9 H12 N2 O2: C 59.98, H 6.72, N 15.55%, found: C 60.55, H 6.57, N 15.15%.
Compound (IV). The N-(pyridoxylidene)-methylamine (III)-4-nitrobenzoic acid complex, (IV), was prepared by adding (III) (1 g, 5.55 mmol) to a solution of 4-nitrobenzoic acid (0.89 g, 5.32 mmol) in ABS. THF. Complex (IV) can be crystallized by two procedures, slowly evaporating the solvent under reduced pressure or stepwise cooling the mixture to −4 °C. The crystals were filtrated of, washed with diethyl ether and dried over potassium hydroxide. m. p. 145–149 °C, 1H NMR (500.13 MHz, d6-DMSO, 300 K) ? (p.p.m., TMS): 2.34 (s, 3H, 2?-CH3), 3.50 (s, 3H, 4??-CH3), 4.67 (s, 2H, 5?-CH2-), 7.84 (s, 1H, H6), 8.86 (s,1H, H4?) p.p.m. of open form and 6.18 (s, 1H, H4?), 2.37 (s, 3H, 2?-CH3), 2.27 (s, 1H, –NH) of cyclic aminal form (compound (III)), 8.15–8-35 (m, 4H, H2,3,5,6), 7.69 (OH, broad) p.p.m. (4-nitrobenzoic acid), Analysis calculated for C16 H 17 N3 O6: C 55.33, H 4.93, N 12.10%, found: C 55.44, H 4.70, N 11.99%.
Data collection: Bruker SMART for compound_III_, compound_IV_. Cell refinement: Bruker SMART for compound_III_, compound_IV_. Data reduction: Bruker SAINT for compound_III_, compound_IV_. For all compounds, program(s) used to solve structure: SHELXTL (Sheldrick, 2000); program(s) used to refine structure: SHELXTL (Sheldrick, 2000); molecular graphics: SHELXTL (Sheldrick, 2000); software used to prepare material for publication: SHELXTL (Sheldrick, 2000).
C15H16N2O2 | F(000) = 544 |
Mr = 256.30 | Dx = 1.313 Mg m−3 |
Monoclinic, P21/n | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yn | Cell parameters from 25 reflections |
a = 4.001 (4) Å | θ = 8.0–15.0° |
b = 25.09 (3) Å | µ = 0.09 mm−1 |
c = 12.940 (11) Å | T = 295 K |
β = 93.65 (8)° | Plate, yellow |
V = 1296 (2) Å3 | 0.40 × 0.20 × 0.10 mm |
Z = 4 |
Stoe four-circle diffractometer | Rint = 0.150 |
Radiation source: fine-focus sealed tube | θmax = 25.0°, θmin = 2.3° |
Graphite monochromator | h = 0→4 |
ω scans | k = −29→29 |
2631 measured reflections | l = −15→14 |
2287 independent reflections | 3 standard reflections every 30 min |
874 reflections with I > 2σ(I) | intensity decay: 3% |
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)] = 0.076 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.214 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | w = 1/[σ2(Fo2) + (0.054P)2] where P = (Fo2 + 2Fc2)/3 |
2287 reflections | (Δ/σ)max < 0.001 |
178 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.27 e Å−3 |
C15H16N2O2 | V = 1296 (2) Å3 |
Mr = 256.30 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 4.001 (4) Å | µ = 0.09 mm−1 |
b = 25.09 (3) Å | T = 295 K |
c = 12.940 (11) Å | 0.40 × 0.20 × 0.10 mm |
β = 93.65 (8)° |
Stoe four-circle diffractometer | Rint = 0.150 |
2631 measured reflections | 3 standard reflections every 30 min |
2287 independent reflections | intensity decay: 3% |
874 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.076 | 0 restraints |
wR(F2) = 0.214 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.19 e Å−3 |
2287 reflections | Δρmin = −0.27 e Å−3 |
178 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 | ||
N1 | −0.4329 (12) | 0.2020 (2) | 0.1845 (4) | 0.0472 (13) | |
N2 | 0.2070 (11) | 0.1148 (2) | 0.4823 (3) | 0.0491 (13) | |
C2 | −0.3236 (14) | 0.1527 (2) | 0.2012 (4) | 0.0473 (16) | |
C3 | −0.1383 (15) | 0.1392 (2) | 0.2934 (4) | 0.0432 (15) | |
C4 | −0.0726 (13) | 0.1764 (2) | 0.3694 (4) | 0.0354 (13) | |
C5 | −0.1906 (13) | 0.2285 (2) | 0.3503 (4) | 0.0400 (14) | |
C6 | −0.3649 (14) | 0.2390 (3) | 0.2588 (4) | 0.0488 (16) | |
H6 | −0.4414 | 0.2736 | 0.2466 | 0.059* | |
C2' | −0.3996 (19) | 0.1123 (3) | 0.1181 (5) | 0.075 (2) | |
H2'A | −0.4960 | 0.1298 | 0.0573 | 0.112* | |
H2'B | −0.5550 | 0.0865 | 0.1417 | 0.112* | |
H2'C | −0.1965 | 0.0947 | 0.1020 | 0.112* | |
O3' | −0.0387 (12) | 0.08775 (16) | 0.3035 (3) | 0.0628 (14) | |
H3' | 0.040 (15) | 0.080 (2) | 0.378 (5) | 0.075* | |
C4' | 0.1052 (14) | 0.1627 (3) | 0.4658 (4) | 0.0454 (16) | |
H4' | 0.1465 | 0.1887 | 0.5164 | 0.054* | |
O5' | −0.3204 (10) | 0.26215 (18) | 0.5155 (3) | 0.0577 (12) | |
H5' | −0.226 (15) | 0.280 (2) | 0.572 (5) | 0.069* | |
C5' | −0.1378 (15) | 0.2727 (2) | 0.4281 (4) | 0.0513 (17) | |
H5'A | 0.0987 | 0.2756 | 0.4490 | 0.062* | |
H5'B | −0.2108 | 0.3062 | 0.3970 | 0.062* | |
C1" | 0.6789 (14) | 0.0616 (3) | 0.7640 (4) | 0.0508 (17) | |
C2" | 0.5209 (15) | 0.0269 (2) | 0.6938 (5) | 0.0555 (17) | |
H2" | 0.5130 | −0.0093 | 0.7088 | 0.067* | |
C3" | 0.3751 (15) | 0.0458 (2) | 0.6017 (4) | 0.0519 (17) | |
H3" | 0.2759 | 0.0219 | 0.5541 | 0.062* | |
C4" | 0.3736 (13) | 0.0992 (2) | 0.5788 (4) | 0.0419 (15) | |
C5" | 0.5323 (14) | 0.1340 (2) | 0.6482 (5) | 0.0481 (16) | |
H5" | 0.5380 | 0.1702 | 0.6331 | 0.058* | |
C6" | 0.6818 (13) | 0.1153 (3) | 0.7394 (4) | 0.0494 (16) | |
H6" | 0.7874 | 0.1392 | 0.7857 | 0.059* | |
C1"' | 0.8431 (17) | 0.0411 (3) | 0.8643 (5) | 0.073 (2) | |
H1"A | 0.6737 | 0.0321 | 0.9106 | 0.110* | |
H1"B | 0.9860 | 0.0683 | 0.8952 | 0.110* | |
H1"C | 0.9737 | 0.0101 | 0.8510 | 0.110* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.044 (3) | 0.048 (3) | 0.049 (3) | 0.011 (3) | −0.005 (2) | 0.004 (3) |
N2 | 0.045 (3) | 0.053 (3) | 0.048 (3) | 0.002 (3) | −0.006 (3) | 0.005 (3) |
C2 | 0.038 (4) | 0.064 (5) | 0.039 (4) | −0.001 (3) | −0.001 (3) | −0.001 (3) |
C3 | 0.046 (4) | 0.043 (4) | 0.040 (4) | 0.005 (3) | −0.001 (3) | 0.000 (3) |
C4 | 0.029 (3) | 0.037 (3) | 0.040 (3) | 0.000 (3) | −0.001 (3) | 0.005 (3) |
C5 | 0.025 (3) | 0.051 (4) | 0.044 (3) | 0.000 (3) | −0.002 (3) | 0.002 (3) |
C6 | 0.044 (4) | 0.056 (4) | 0.047 (4) | 0.009 (3) | 0.001 (3) | 0.000 (3) |
C2' | 0.083 (5) | 0.075 (5) | 0.063 (5) | 0.001 (4) | −0.017 (4) | −0.013 (4) |
O3' | 0.077 (3) | 0.051 (3) | 0.058 (3) | 0.008 (2) | −0.014 (3) | −0.002 (2) |
C4' | 0.034 (3) | 0.057 (4) | 0.044 (4) | −0.005 (3) | 0.001 (3) | −0.001 (3) |
O5' | 0.044 (2) | 0.078 (3) | 0.050 (2) | −0.008 (2) | −0.005 (2) | −0.016 (2) |
C5' | 0.040 (3) | 0.062 (4) | 0.051 (4) | −0.002 (3) | −0.008 (3) | 0.001 (3) |
C1" | 0.041 (4) | 0.068 (5) | 0.043 (4) | 0.016 (3) | −0.003 (3) | 0.003 (4) |
C2" | 0.057 (4) | 0.054 (4) | 0.055 (4) | 0.005 (3) | −0.005 (3) | 0.005 (3) |
C3" | 0.051 (4) | 0.053 (4) | 0.050 (4) | 0.001 (3) | −0.009 (3) | −0.003 (3) |
C4" | 0.033 (3) | 0.045 (4) | 0.047 (3) | 0.003 (3) | 0.001 (3) | 0.006 (3) |
C5" | 0.046 (4) | 0.039 (3) | 0.059 (4) | −0.006 (3) | −0.008 (3) | 0.004 (3) |
C6" | 0.039 (4) | 0.054 (4) | 0.054 (4) | −0.005 (3) | −0.009 (3) | 0.003 (3) |
C1"' | 0.065 (5) | 0.084 (5) | 0.069 (4) | 0.008 (4) | −0.014 (4) | 0.015 (4) |
N1—C2 | 1.325 (7) | O5'—C5' | 1.410 (7) |
N1—C6 | 1.353 (7) | O5'—H5' | 0.92 (6) |
N2—C4' | 1.283 (7) | C5'—H5'A | 0.9700 |
N2—C4" | 1.433 (7) | C5'—H5'B | 0.9700 |
C2—C3 | 1.404 (7) | C1"—C2" | 1.383 (8) |
C2—C2' | 1.494 (8) | C1"—C6" | 1.384 (8) |
C3—O3' | 1.356 (7) | C1"—C1"' | 1.507 (8) |
C3—C4 | 1.369 (7) | C2"—C3" | 1.377 (7) |
C4—C5 | 1.405 (7) | C2"—H2" | 0.9300 |
C4—C4' | 1.438 (7) | C3"—C4" | 1.372 (8) |
C5—C6 | 1.362 (7) | C3"—H3" | 0.9300 |
C5—C5' | 1.502 (7) | C4"—C5" | 1.378 (7) |
C6—H6 | 0.9300 | C5"—C6" | 1.371 (7) |
C2'—H2'A | 0.9600 | C5"—H5" | 0.9300 |
C2'—H2'B | 0.9600 | C6"—H6" | 0.9300 |
C2'—H2'C | 0.9600 | C1"'—H1"A | 0.9600 |
O3'—H3' | 1.01 (6) | C1"'—H1"B | 0.9600 |
C4'—H4' | 0.9300 | C1"'—H1"C | 0.9600 |
C2—N1—C6 | 118.4 (5) | O5'—C5'—H5'A | 109.7 |
C4'—N2—C4" | 121.7 (5) | C5—C5'—H5'A | 109.7 |
N1—C2—C3 | 120.9 (5) | O5'—C5'—H5'B | 109.7 |
N1—C2—C2' | 117.7 (5) | C5—C5'—H5'B | 109.7 |
C3—C2—C2' | 121.4 (6) | H5'A—C5'—H5'B | 108.2 |
O3'—C3—C4 | 122.6 (5) | C2"—C1"—C6" | 118.2 (5) |
O3'—C3—C2 | 116.5 (5) | C2"—C1"—C1"' | 120.5 (6) |
C4—C3—C2 | 120.9 (5) | C6"—C1"—C1"' | 121.4 (6) |
C3—C4—C5 | 117.4 (5) | C3"—C2"—C1" | 120.2 (6) |
C3—C4—C4' | 121.4 (5) | C3"—C2"—H2" | 119.9 |
C5—C4—C4' | 121.1 (5) | C1"—C2"—H2" | 119.9 |
C6—C5—C4 | 118.8 (5) | C4"—C3"—C2" | 121.2 (6) |
C6—C5—C5' | 118.8 (5) | C4"—C3"—H3" | 119.4 |
C4—C5—C5' | 122.4 (5) | C2"—C3"—H3" | 119.4 |
N1—C6—C5 | 123.6 (6) | C3"—C4"—C5" | 118.9 (5) |
N1—C6—H6 | 118.2 | C3"—C4"—N2 | 116.8 (5) |
C5—C6—H6 | 118.2 | C5"—C4"—N2 | 124.3 (5) |
C2—C2'—H2'A | 109.5 | C6"—C5"—C4" | 120.0 (5) |
C2—C2'—H2'B | 109.5 | C6"—C5"—H5" | 120.0 |
H2'A—C2'—H2'B | 109.5 | C4"—C5"—H5" | 120.0 |
C2—C2'—H2'C | 109.4 | C5"—C6"—C1" | 121.5 (5) |
H2'A—C2'—H2'C | 109.5 | C5"—C6"—H6" | 119.3 |
H2'B—C2'—H2'C | 109.5 | C1"—C6"—H6" | 119.3 |
C3—O3'—H3' | 110 (3) | C1"—C1"'—H1"A | 109.4 |
N2—C4'—C4 | 120.2 (6) | C1"—C1"'—H1"B | 109.5 |
N2—C4'—H4' | 119.9 | H1"A—C1"'—H1"B | 109.5 |
C4—C4'—H4' | 119.9 | C1"—C1"'—H1"C | 109.5 |
C5'—O5'—H5' | 110 (4) | H1"A—C1"'—H1"C | 109.5 |
O5'—C5'—C5 | 110.0 (5) | H1"B—C1"'—H1"C | 109.5 |
C6—N1—C2—C3 | −0.7 (9) | C4"—N2—C4'—C4 | −177.6 (5) |
C6—N1—C2—C2' | −179.7 (5) | C3—C4—C4'—N2 | 0.1 (8) |
N1—C2—C3—O3' | 179.8 (6) | C5—C4—C4'—N2 | 179.1 (5) |
C2'—C2—C3—O3' | −1.2 (8) | C6—C5—C5'—O5' | 111.9 (6) |
N1—C2—C3—C4 | 1.6 (9) | C4—C5—C5'—O5' | −66.8 (7) |
C2'—C2—C3—C4 | −179.4 (6) | C6"—C1"—C2"—C3" | 0.8 (9) |
O3'—C3—C4—C5 | −179.6 (5) | C1"'—C1"—C2"—C3" | −179.2 (6) |
C2—C3—C4—C5 | −1.5 (8) | C1"—C2"—C3"—C4" | −2.1 (10) |
O3'—C3—C4—C4' | −0.6 (9) | C2"—C3"—C4"—C5" | 2.4 (9) |
C2—C3—C4—C4' | 177.5 (6) | C2"—C3"—C4"—N2 | −178.3 (6) |
C3—C4—C5—C6 | 0.6 (8) | C4'—N2—C4"—C3" | 159.5 (6) |
C4'—C4—C5—C6 | −178.4 (5) | C4'—N2—C4"—C5" | −21.2 (9) |
C3—C4—C5—C5' | 179.3 (5) | C3"—C4"—C5"—C6" | −1.5 (9) |
C4'—C4—C5—C5' | 0.3 (8) | N2—C4"—C5"—C6" | 179.2 (5) |
C2—N1—C6—C5 | −0.2 (9) | C4"—C5"—C6"—C1" | 0.2 (9) |
C4—C5—C6—N1 | 0.2 (9) | C2"—C1"—C6"—C5" | 0.1 (9) |
C5'—C5—C6—N1 | −178.5 (5) | C1"'—C1"—C6"—C5" | −179.9 (6) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3′—H3′···N2 | 1.01 (6) | 1.71 (6) | 2.547 (6) | 138 (5) |
O5′—H5′···N1i | 0.92 (6) | 1.86 (6) | 2.751 (6) | 162 (5) |
Symmetry code: (i) x+1/2, −y+1/2, z+1/2. |
C15H17N2O2·C7H4NO4 | Z = 2 |
Mr = 423.42 | F(000) = 444 |
Triclinic, P1 | Dx = 1.363 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.683 (5) Å | Cell parameters from 25 reflections |
b = 12.188 (6) Å | θ = 7.0–15.0° |
c = 12.562 (6) Å | µ = 0.10 mm−1 |
α = 114.88 (4)° | T = 295 K |
β = 99.61 (5)° | Plate, yellow |
γ = 96.03 (5)° | 0.40 × 0.20 × 0.10 mm |
V = 1031.8 (10) Å3 |
Stoe four-circle diffractometer | Rint = 0.018 |
Radiation source: fine-focus sealed tube | θmax = 25.0°, θmin = 2.7° |
Graphite monochromator | h = −9→8 |
ω scans | k = −10→14 |
3866 measured reflections | l = −14→14 |
3591 independent reflections | 3 standard reflections every 30 min |
2383 reflections with I > 2σ(I) | intensity decay: 3% |
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: inferred from neighbouring sites |
wR(F2) = 0.153 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | w = 1/[σ2(Fo2) + (0.078P)2 + 0.250P] where P = (Fo2 + 2Fc2)/3 |
3591 reflections | (Δ/σ)max < 0.001 |
289 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
C15H17N2O2·C7H4NO4 | γ = 96.03 (5)° |
Mr = 423.42 | V = 1031.8 (10) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.683 (5) Å | Mo Kα radiation |
b = 12.188 (6) Å | µ = 0.10 mm−1 |
c = 12.562 (6) Å | T = 295 K |
α = 114.88 (4)° | 0.40 × 0.20 × 0.10 mm |
β = 99.61 (5)° |
Stoe four-circle diffractometer | Rint = 0.018 |
3866 measured reflections | 3 standard reflections every 30 min |
3591 independent reflections | intensity decay: 3% |
2383 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.153 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.20 e Å−3 |
3591 reflections | Δρmin = −0.21 e Å−3 |
289 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 | ||
N1 | 0.3837 (3) | 0.39957 (19) | 0.61412 (18) | 0.0491 (5) | |
H1 | 0.436 (3) | 0.490 (3) | 0.661 (2) | 0.059* | |
N2 | 0.1882 (3) | −0.05211 (18) | 0.43292 (19) | 0.0543 (5) | |
C2 | 0.4127 (3) | 0.3212 (2) | 0.6597 (2) | 0.0505 (6) | |
C3 | 0.3362 (3) | 0.1967 (2) | 0.5884 (2) | 0.0508 (6) | |
C4 | 0.2308 (3) | 0.1581 (2) | 0.4724 (2) | 0.0455 (6) | |
C5 | 0.2015 (3) | 0.2461 (2) | 0.4302 (2) | 0.0448 (6) | |
C6 | 0.2821 (3) | 0.3653 (2) | 0.5036 (2) | 0.0498 (6) | |
H6 | 0.2665 | 0.4247 | 0.4766 | 0.060* | |
C2' | 0.5234 (4) | 0.3678 (2) | 0.7851 (2) | 0.0652 (8) | |
H2'A | 0.5569 | 0.4560 | 0.8211 | 0.098* | |
H2'B | 0.6299 | 0.3329 | 0.7829 | 0.098* | |
H2'C | 0.4546 | 0.3444 | 0.8320 | 0.098* | |
O3' | 0.3704 (3) | 0.11905 (18) | 0.63546 (17) | 0.0718 (6) | |
H3' | 0.314 (4) | 0.040 (3) | 0.574 (3) | 0.086* | |
C4' | 0.1539 (3) | 0.0284 (2) | 0.3975 (2) | 0.0487 (6) | |
H4' | 0.0782 | 0.0037 | 0.3221 | 0.058* | |
O5' | −0.0915 (2) | 0.15341 (17) | 0.29060 (16) | 0.0599 (5) | |
H5' | −0.161 (4) | 0.217 (3) | 0.313 (3) | 0.072* | |
C5' | 0.0863 (3) | 0.2116 (2) | 0.3073 (2) | 0.0539 (6) | |
H5'A | 0.0832 | 0.2855 | 0.2961 | 0.065* | |
H5'B | 0.1404 | 0.1568 | 0.2463 | 0.065* | |
C1" | −0.0151 (4) | −0.4320 (2) | 0.2301 (3) | 0.0601 (7) | |
C2" | 0.0859 (4) | −0.3819 (3) | 0.3470 (3) | 0.0668 (8) | |
H2" | 0.1094 | −0.4331 | 0.3833 | 0.080* | |
C3" | 0.1523 (4) | −0.2573 (2) | 0.4106 (2) | 0.0585 (7) | |
H3" | 0.2216 | −0.2253 | 0.4891 | 0.070* | |
C4" | 0.1175 (3) | −0.1796 (2) | 0.3598 (2) | 0.0500 (6) | |
C5" | 0.0193 (4) | −0.2286 (2) | 0.2422 (3) | 0.0660 (8) | |
H5" | −0.0025 | −0.1776 | 0.2055 | 0.079* | |
C6" | −0.0461 (4) | −0.3535 (2) | 0.1798 (3) | 0.0667 (8) | |
H6" | −0.1135 | −0.3859 | 0.1008 | 0.080* | |
C1"' | −0.0881 (5) | −0.5683 (3) | 0.1590 (3) | 0.0893 (10) | |
H1"A | −0.1705 | −0.5843 | 0.0854 | 0.134* | |
H1"B | −0.1497 | −0.5969 | 0.2058 | 0.134* | |
H1"C | 0.0095 | −0.6108 | 0.1405 | 0.134* | |
O1A | 0.3064 (2) | 0.67846 (15) | 0.65137 (16) | 0.0641 (5) | |
O2A | 0.5470 (2) | 0.62426 (15) | 0.72514 (16) | 0.0579 (5) | |
O3A | 0.8271 (4) | 0.7693 (2) | 0.9965 (3) | 0.1141 (10) | |
O4A | 0.5413 (4) | 0.7212 (2) | 0.9720 (2) | 0.0875 (7) | |
N1A | 0.6726 (4) | 0.7791 (2) | 0.9651 (2) | 0.0654 (6) | |
C1A | 0.5391 (3) | 0.8338 (2) | 0.8060 (2) | 0.0418 (5) | |
C2A | 0.6496 (3) | 0.8689 (2) | 0.9179 (2) | 0.0467 (6) | |
C3A | 0.7410 (3) | 0.9875 (2) | 0.9901 (2) | 0.0600 (7) | |
H3A | 0.8153 | 1.0084 | 1.0650 | 0.072* | |
C4A | 0.7209 (4) | 1.0747 (2) | 0.9496 (3) | 0.0670 (8) | |
H4A | 0.7822 | 1.1556 | 0.9976 | 0.080* | |
C5A | 0.6120 (4) | 1.0443 (2) | 0.8398 (3) | 0.0602 (7) | |
H5A | 0.5995 | 1.1041 | 0.8130 | 0.072* | |
C6A | 0.5209 (3) | 0.9252 (2) | 0.7690 (2) | 0.0493 (6) | |
H6A | 0.4454 | 0.9053 | 0.6948 | 0.059* | |
C7A | 0.4535 (3) | 0.7015 (2) | 0.7206 (2) | 0.0447 (6) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0503 (12) | 0.0378 (11) | 0.0483 (12) | 0.0038 (9) | 0.0024 (9) | 0.0135 (9) |
N2 | 0.0649 (13) | 0.0409 (11) | 0.0467 (12) | 0.0016 (10) | 0.0014 (10) | 0.0163 (10) |
C2 | 0.0528 (14) | 0.0448 (14) | 0.0441 (14) | 0.0059 (11) | 0.0030 (11) | 0.0146 (11) |
C3 | 0.0572 (15) | 0.0432 (14) | 0.0464 (14) | 0.0048 (11) | 0.0013 (12) | 0.0201 (11) |
C4 | 0.0470 (13) | 0.0408 (13) | 0.0414 (13) | 0.0048 (10) | 0.0050 (10) | 0.0145 (10) |
C5 | 0.0423 (13) | 0.0450 (13) | 0.0429 (13) | 0.0037 (10) | 0.0055 (10) | 0.0185 (11) |
C6 | 0.0512 (14) | 0.0454 (14) | 0.0502 (15) | 0.0044 (11) | 0.0031 (12) | 0.0232 (12) |
C2' | 0.0732 (18) | 0.0538 (16) | 0.0482 (15) | 0.0019 (13) | −0.0078 (13) | 0.0143 (13) |
O3' | 0.1005 (15) | 0.0470 (11) | 0.0522 (11) | 0.0032 (10) | −0.0166 (10) | 0.0225 (9) |
C4' | 0.0516 (14) | 0.0443 (14) | 0.0412 (13) | 0.0036 (11) | 0.0036 (11) | 0.0146 (11) |
O5' | 0.0507 (11) | 0.0534 (11) | 0.0563 (11) | 0.0033 (8) | −0.0026 (8) | 0.0137 (9) |
C5' | 0.0503 (15) | 0.0565 (15) | 0.0506 (15) | 0.0049 (12) | 0.0019 (12) | 0.0247 (12) |
C1" | 0.0660 (17) | 0.0449 (15) | 0.0658 (18) | 0.0002 (12) | 0.0148 (14) | 0.0240 (13) |
C2" | 0.092 (2) | 0.0536 (16) | 0.0615 (18) | 0.0112 (15) | 0.0146 (16) | 0.0341 (14) |
C3" | 0.0751 (18) | 0.0520 (15) | 0.0442 (14) | 0.0068 (13) | 0.0022 (13) | 0.0232 (12) |
C4" | 0.0574 (15) | 0.0417 (13) | 0.0446 (14) | 0.0031 (11) | 0.0061 (11) | 0.0173 (11) |
C5" | 0.085 (2) | 0.0454 (15) | 0.0560 (16) | −0.0035 (14) | −0.0111 (14) | 0.0259 (13) |
C6" | 0.0773 (19) | 0.0489 (16) | 0.0563 (16) | −0.0071 (13) | −0.0092 (14) | 0.0206 (13) |
C1"' | 0.116 (3) | 0.0474 (17) | 0.092 (2) | −0.0062 (17) | 0.011 (2) | 0.0287 (17) |
O1A | 0.0567 (11) | 0.0497 (10) | 0.0574 (11) | −0.0006 (8) | −0.0171 (9) | 0.0110 (8) |
O2A | 0.0573 (10) | 0.0389 (9) | 0.0595 (11) | 0.0051 (8) | −0.0059 (8) | 0.0132 (8) |
O3A | 0.1031 (19) | 0.113 (2) | 0.118 (2) | 0.0220 (16) | −0.0329 (16) | 0.0648 (17) |
O4A | 0.1167 (19) | 0.0785 (15) | 0.0878 (17) | 0.0207 (14) | 0.0367 (15) | 0.0512 (13) |
N1A | 0.0807 (18) | 0.0622 (15) | 0.0434 (12) | 0.0130 (13) | −0.0045 (12) | 0.0215 (11) |
C1A | 0.0400 (12) | 0.0396 (12) | 0.0385 (12) | 0.0044 (10) | 0.0040 (10) | 0.0132 (10) |
C2A | 0.0498 (14) | 0.0448 (13) | 0.0387 (13) | 0.0079 (11) | 0.0040 (11) | 0.0150 (11) |
C3A | 0.0531 (15) | 0.0548 (16) | 0.0437 (14) | 0.0014 (12) | −0.0040 (12) | 0.0031 (12) |
C4A | 0.0655 (18) | 0.0369 (14) | 0.0710 (19) | −0.0052 (12) | 0.0054 (15) | 0.0057 (13) |
C5A | 0.0643 (17) | 0.0418 (14) | 0.0691 (18) | 0.0044 (12) | 0.0109 (14) | 0.0230 (13) |
C6A | 0.0495 (14) | 0.0474 (14) | 0.0455 (14) | 0.0064 (11) | 0.0036 (11) | 0.0191 (11) |
C7A | 0.0456 (13) | 0.0417 (13) | 0.0373 (12) | −0.0004 (11) | 0.0012 (11) | 0.0140 (10) |
N1—C2 | 1.324 (3) | C2"—H2" | 0.9300 |
N1—C6 | 1.339 (3) | C3"—C4" | 1.372 (3) |
N1—H1 | 1.01 (3) | C3"—H3" | 0.9300 |
N2—C4' | 1.270 (3) | C4"—C5" | 1.378 (4) |
N2—C4" | 1.417 (3) | C5"—C6" | 1.375 (4) |
C2—C3 | 1.394 (3) | C5"—H5" | 0.9300 |
C2—C2' | 1.492 (4) | C6"—H6" | 0.9300 |
C3—O3' | 1.336 (3) | C1"'—H1"A | 0.9600 |
C3—C4 | 1.396 (3) | C1"'—H1"B | 0.9600 |
C4—C5 | 1.405 (3) | C1"'—H1"C | 0.9600 |
C4—C4' | 1.449 (3) | O1A—C7A | 1.230 (3) |
C5—C6 | 1.356 (3) | O2A—C7A | 1.256 (3) |
C5—C5' | 1.504 (3) | O3A—N1A | 1.221 (3) |
C6—H6 | 0.9300 | O4A—N1A | 1.206 (3) |
C2'—H2'A | 0.9600 | N1A—C2A | 1.460 (3) |
C2'—H2'B | 0.9600 | C1A—C2A | 1.378 (3) |
C2'—H2'C | 0.9600 | C1A—C6A | 1.387 (3) |
O3'—H3' | 0.95 (3) | C1A—C7A | 1.507 (3) |
C4'—H4' | 0.9300 | C2A—C3A | 1.370 (4) |
O5'—C5' | 1.410 (3) | C3A—C4A | 1.369 (4) |
O5'—H5' | 0.96 (3) | C3A—H3A | 0.9300 |
C5'—H5'A | 0.9700 | C4A—C5A | 1.364 (4) |
C5'—H5'B | 0.9700 | C4A—H4A | 0.9300 |
C1"—C6" | 1.369 (4) | C5A—C6A | 1.371 (4) |
C1"—C2" | 1.378 (4) | C5A—H5A | 0.9300 |
C1"—C1"' | 1.504 (4) | C6A—H6A | 0.9300 |
C2"—C3" | 1.373 (4) | ||
C2—N1—C6 | 123.2 (2) | C4"—C3"—C2" | 120.8 (2) |
C2—N1—H1 | 122.1 (14) | C4"—C3"—H3" | 119.6 |
C6—N1—H1 | 114.8 (14) | C2"—C3"—H3" | 119.6 |
C4'—N2—C4" | 122.0 (2) | C3"—C4"—C5" | 119.1 (2) |
N1—C2—C3 | 118.4 (2) | C3"—C4"—N2 | 116.9 (2) |
N1—C2—C2' | 119.7 (2) | C5"—C4"—N2 | 124.0 (2) |
C3—C2—C2' | 122.0 (2) | C6"—C5"—C4" | 119.4 (2) |
O3'—C3—C2 | 117.3 (2) | C6"—C5"—H5" | 120.3 |
O3'—C3—C4 | 123.0 (2) | C4"—C5"—H5" | 120.3 |
C2—C3—C4 | 119.8 (2) | C1"—C6"—C5" | 122.2 (3) |
C3—C4—C5 | 119.2 (2) | C1"—C6"—H6" | 118.9 |
C3—C4—C4' | 119.8 (2) | C5"—C6"—H6" | 118.9 |
C5—C4—C4' | 121.0 (2) | C1"—C1"'—H1"A | 109.5 |
C6—C5—C4 | 117.9 (2) | C1"—C1"'—H1"B | 109.5 |
C6—C5—C5' | 119.9 (2) | H1"A—C1"'—H1"B | 109.5 |
C4—C5—C5' | 122.2 (2) | C1"—C1"'—H1"C | 109.5 |
N1—C6—C5 | 121.6 (2) | H1"A—C1"'—H1"C | 109.5 |
N1—C6—H6 | 119.2 | H1"B—C1"'—H1"C | 109.5 |
C5—C6—H6 | 119.2 | O4A—N1A—O3A | 124.4 (3) |
C2—C2'—H2'A | 109.5 | O4A—N1A—C2A | 119.1 (2) |
C2—C2'—H2'B | 109.5 | O3A—N1A—C2A | 116.5 (3) |
H2'A—C2'—H2'B | 109.5 | C2A—C1A—C6A | 116.9 (2) |
C2—C2'—H2'C | 109.5 | C2A—C1A—C7A | 122.9 (2) |
H2'A—C2'—H2'C | 109.5 | C6A—C1A—C7A | 119.9 (2) |
H2'B—C2'—H2'C | 109.5 | C3A—C2A—C1A | 122.6 (2) |
C3—O3'—H3' | 105.3 (19) | C3A—C2A—N1A | 116.9 (2) |
N2—C4'—C4 | 121.1 (2) | C1A—C2A—N1A | 120.5 (2) |
N2—C4'—H4' | 119.4 | C4A—C3A—C2A | 118.6 (2) |
C4—C4'—H4' | 119.4 | C4A—C3A—H3A | 120.7 |
C5'—O5'—H5' | 107.0 (17) | C2A—C3A—H3A | 120.7 |
O5'—C5'—C5 | 112.9 (2) | C5A—C4A—C3A | 120.7 (2) |
O5'—C5'—H5'A | 109.0 | C5A—C4A—H4A | 119.6 |
C5—C5'—H5'A | 109.0 | C3A—C4A—H4A | 119.6 |
O5'—C5'—H5'B | 109.0 | C4A—C5A—C6A | 119.8 (3) |
C5—C5'—H5'B | 109.0 | C4A—C5A—H5A | 120.1 |
H5'A—C5'—H5'B | 107.8 | C6A—C5A—H5A | 120.1 |
C6"—C1"—C2" | 117.8 (2) | C5A—C6A—C1A | 121.3 (2) |
C6"—C1"—C1"' | 120.8 (3) | C5A—C6A—H6A | 119.4 |
C2"—C1"—C1"' | 121.4 (3) | C1A—C6A—H6A | 119.4 |
C3"—C2"—C1" | 120.8 (3) | O1A—C7A—O2A | 126.1 (2) |
C3"—C2"—H2" | 119.6 | O1A—C7A—C1A | 119.2 (2) |
C1"—C2"—H2" | 119.6 | O2A—C7A—C1A | 114.7 (2) |
C6—N1—C2—C3 | 1.1 (4) | C4'—N2—C4"—C3" | −175.3 (2) |
C6—N1—C2—C2' | −178.2 (2) | C4'—N2—C4"—C5" | 5.5 (4) |
N1—C2—C3—O3' | 178.7 (2) | C3"—C4"—C5"—C6" | 1.9 (5) |
C2'—C2—C3—O3' | −2.0 (4) | N2—C4"—C5"—C6" | −178.9 (3) |
N1—C2—C3—C4 | −0.5 (4) | C2"—C1"—C6"—C5" | −0.3 (5) |
C2'—C2—C3—C4 | 178.7 (2) | C1"'—C1"—C6"—C5" | −179.8 (3) |
O3'—C3—C4—C5 | 179.9 (2) | C4"—C5"—C6"—C1" | −0.8 (5) |
C2—C3—C4—C5 | −0.9 (4) | C6A—C1A—C2A—C3A | −1.1 (4) |
O3'—C3—C4—C4' | −0.3 (4) | C7A—C1A—C2A—C3A | 173.4 (2) |
C2—C3—C4—C4' | 178.9 (2) | C6A—C1A—C2A—N1A | 178.4 (2) |
C3—C4—C5—C6 | 1.8 (4) | C7A—C1A—C2A—N1A | −7.1 (4) |
C4'—C4—C5—C6 | −178.0 (2) | O4A—N1A—C2A—C3A | 124.2 (3) |
C3—C4—C5—C5' | −178.7 (2) | O3A—N1A—C2A—C3A | −55.0 (3) |
C4'—C4—C5—C5' | 1.5 (4) | O4A—N1A—C2A—C1A | −55.4 (4) |
C2—N1—C6—C5 | −0.1 (4) | O3A—N1A—C2A—C1A | 125.4 (3) |
C4—C5—C6—N1 | −1.4 (4) | C1A—C2A—C3A—C4A | 0.4 (4) |
C5'—C5—C6—N1 | 179.1 (2) | N1A—C2A—C3A—C4A | −179.1 (2) |
C4"—N2—C4'—C4 | −178.6 (2) | C2A—C3A—C4A—C5A | 0.0 (4) |
C3—C4—C4'—N2 | −3.7 (4) | C3A—C4A—C5A—C6A | 0.2 (4) |
C5—C4—C4'—N2 | 176.1 (2) | C4A—C5A—C6A—C1A | −1.0 (4) |
C6—C5—C5'—O5' | −122.0 (3) | C2A—C1A—C6A—C5A | 1.4 (4) |
C4—C5—C5'—O5' | 58.5 (3) | C7A—C1A—C6A—C5A | −173.3 (2) |
C6"—C1"—C2"—C3" | 0.3 (4) | C2A—C1A—C7A—O1A | 149.2 (2) |
C1"'—C1"—C2"—C3" | 179.7 (3) | C6A—C1A—C7A—O1A | −36.5 (3) |
C1"—C2"—C3"—C4" | 0.9 (5) | C2A—C1A—C7A—O2A | −33.5 (3) |
C2"—C3"—C4"—C5" | −2.0 (4) | C6A—C1A—C7A—O2A | 140.9 (2) |
C2"—C3"—C4"—N2 | 178.7 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2A | 1.01 (3) | 1.55 (3) | 2.549 (3) | 170 (2) |
N1—H1···O1A | 1.01 (3) | 2.63 (3) | 3.362 (3) | 129.4 (18) |
O3′—H3′···N2 | 0.95 (3) | 1.69 (3) | 2.553 (3) | 150 (3) |
O5′—H5′···O1Ai | 0.96 (3) | 1.75 (3) | 2.704 (3) | 175 (3) |
Symmetry code: (i) −x, −y+1, −z+1. |
C9H12N2O2 | F(000) = 384 |
Mr = 180.21 | Dx = 1.288 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 2559 reflections |
a = 11.046 (2) Å | θ = 2.3–26.0° |
b = 4.8739 (8) Å | µ = 0.09 mm−1 |
c = 18.027 (3) Å | T = 295 K |
β = 106.728 (5)° | Prism, yellow |
V = 929.5 (3) Å3 | 0.45 × 0.23 × 0.04 mm |
Z = 4 |
Bruker APEX diffractometer | 1814 independent reflections |
Radiation source: fine-focus sealed tube | 1575 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
ω scans | θmax = 26.0°, θmin = 2.4° |
Absorption correction: multi-scan SADABS (Sheldrick, 2002) | h = −13→13 |
Tmin = 0.942, Tmax = 0.996 | k = −5→6 |
7547 measured reflections | l = −22→22 |
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)] = 0.051 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.147 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.081P)2 + 0.210P] where P = (Fo2 + 2Fc2)/3 |
1814 reflections | (Δ/σ)max < 0.001 |
124 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.15 e Å−3 |
C9H12N2O2 | V = 929.5 (3) Å3 |
Mr = 180.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.046 (2) Å | µ = 0.09 mm−1 |
b = 4.8739 (8) Å | T = 295 K |
c = 18.027 (3) Å | 0.45 × 0.23 × 0.04 mm |
β = 106.728 (5)° |
Bruker APEX diffractometer | 1814 independent reflections |
Absorption correction: multi-scan SADABS (Sheldrick, 2002) | 1575 reflections with I > 2σ(I) |
Tmin = 0.942, Tmax = 0.996 | Rint = 0.018 |
7547 measured reflections |
R[F2 > 2σ(F2)] = 0.051 | 0 restraints |
wR(F2) = 0.147 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.20 e Å−3 |
1814 reflections | Δρmin = −0.15 e Å−3 |
124 parameters |
Experimental. An attempt was made to collect the data at low temperatures, 100 K, but the crystals appeared to bend and the diffraction pattern was "smeared" out. Because the sample appeared stable at room temperature, the data for this model were collected under ambient conditions. |
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 | ||
N1 | 0.33158 (14) | 0.9353 (3) | 0.73842 (8) | 0.0563 (4) | |
C2 | 0.23292 (16) | 0.7683 (4) | 0.72121 (10) | 0.0569 (5) | |
N2 | 0.16429 (14) | 0.2641 (3) | 0.52244 (8) | 0.0644 (4) | |
C3 | 0.20633 (15) | 0.5964 (3) | 0.65605 (10) | 0.0526 (4) | |
C4 | 0.28744 (15) | 0.5949 (3) | 0.60903 (9) | 0.0483 (4) | |
C5 | 0.39162 (15) | 0.7735 (3) | 0.62841 (8) | 0.0494 (4) | |
C6 | 0.40727 (17) | 0.9379 (3) | 0.69197 (9) | 0.0542 (4) | |
H6 | 0.4749 | 1.0597 | 0.7038 | 0.065* | |
C2' | 0.1494 (2) | 0.7638 (6) | 0.77358 (13) | 0.0902 (8) | |
H2'A | 0.1846 | 0.8802 | 0.8175 | 0.135* | |
H2'B | 0.0667 | 0.8288 | 0.7458 | 0.135* | |
H2'C | 0.1433 | 0.5795 | 0.7910 | 0.135* | |
O3' | 0.10295 (12) | 0.4366 (3) | 0.64144 (9) | 0.0731 (4) | |
H3' | 0.101 (2) | 0.344 (5) | 0.5970 (15) | 0.088* | |
C4' | 0.26173 (17) | 0.4136 (3) | 0.54162 (10) | 0.0546 (4) | |
H4' | 0.3184 | 0.4084 | 0.5122 | 0.066* | |
C5' | 0.48884 (18) | 0.7821 (4) | 0.58448 (10) | 0.0613 (5) | |
H5'A | 0.4460 | 0.7916 | 0.5294 | 0.074* | |
H5'B | 0.5395 | 0.9468 | 0.5988 | 0.074* | |
O5' | 0.56938 (13) | 0.5497 (3) | 0.59947 (8) | 0.0697 (4) | |
H5' | 0.604 (2) | 0.533 (5) | 0.6523 (15) | 0.084* | |
C4" | 0.1432 (2) | 0.0936 (4) | 0.45376 (13) | 0.0821 (7) | |
H4"A | 0.1288 | −0.0924 | 0.4666 | 0.123* | |
H4"B | 0.0706 | 0.1596 | 0.4144 | 0.123* | |
H4"C | 0.2161 | 0.1009 | 0.4350 | 0.123* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0627 (8) | 0.0584 (9) | 0.0465 (7) | 0.0063 (7) | 0.0137 (6) | −0.0009 (6) |
C2 | 0.0555 (9) | 0.0655 (11) | 0.0502 (9) | 0.0120 (8) | 0.0162 (7) | 0.0051 (8) |
N2 | 0.0666 (9) | 0.0588 (9) | 0.0595 (9) | −0.0012 (7) | 0.0050 (7) | −0.0049 (7) |
C3 | 0.0483 (8) | 0.0554 (10) | 0.0523 (9) | 0.0047 (7) | 0.0118 (7) | 0.0073 (7) |
C4 | 0.0555 (9) | 0.0444 (8) | 0.0426 (8) | 0.0053 (7) | 0.0102 (7) | 0.0068 (6) |
C5 | 0.0605 (9) | 0.0465 (9) | 0.0408 (8) | 0.0009 (7) | 0.0138 (7) | 0.0088 (6) |
C6 | 0.0643 (10) | 0.0499 (9) | 0.0472 (8) | −0.0053 (7) | 0.0142 (7) | 0.0008 (7) |
C2' | 0.0741 (13) | 0.132 (2) | 0.0751 (14) | 0.0003 (14) | 0.0378 (11) | −0.0137 (14) |
O3' | 0.0574 (7) | 0.0879 (10) | 0.0764 (9) | −0.0132 (7) | 0.0229 (6) | −0.0080 (7) |
C4' | 0.0619 (10) | 0.0515 (9) | 0.0475 (9) | 0.0052 (8) | 0.0111 (7) | 0.0031 (7) |
C5' | 0.0735 (11) | 0.0687 (11) | 0.0446 (9) | −0.0141 (9) | 0.0214 (8) | 0.0042 (8) |
O5' | 0.0723 (8) | 0.0950 (11) | 0.0466 (7) | 0.0061 (7) | 0.0249 (6) | −0.0006 (7) |
C4" | 0.0899 (15) | 0.0714 (13) | 0.0697 (13) | −0.0027 (11) | −0.0013 (11) | −0.0182 (10) |
N1—C2 | 1.323 (2) | C2'—H2'A | 0.9600 |
N1—C6 | 1.343 (2) | C2'—H2'B | 0.9601 |
C2—C3 | 1.403 (3) | C2'—H2'C | 0.9600 |
C2—C2' | 1.498 (3) | O3'—H3' | 0.92 (3) |
N2—C4' | 1.263 (2) | C4'—H4' | 0.9300 |
N2—C4" | 1.453 (3) | C5'—O5' | 1.417 (2) |
C3—O3' | 1.344 (2) | C5'—H5'A | 0.9700 |
C3—C4 | 1.399 (2) | C5'—H5'B | 0.9700 |
C4—C5 | 1.405 (2) | O5'—H5' | 0.92 (3) |
C4—C4' | 1.463 (2) | C4"—H4"A | 0.9600 |
C5—C6 | 1.368 (2) | C4"—H4"B | 0.9601 |
C5—C5' | 1.507 (2) | C4"—H4"C | 0.9600 |
C6—H6 | 0.9300 | ||
C2—N1—C6 | 118.57 (14) | C2—C2'—H2'C | 109.5 |
N1—C2—C3 | 121.54 (15) | H2'A—C2'—H2'C | 109.5 |
N1—C2—C2' | 118.44 (17) | H2'B—C2'—H2'C | 109.5 |
C3—C2—C2' | 120.02 (18) | C3—O3'—H3' | 105.0 (16) |
C4'—N2—C4" | 118.58 (18) | N2—C4'—C4 | 121.49 (17) |
O3'—C3—C4 | 122.27 (16) | N2—C4'—H4' | 119.3 |
O3'—C3—C2 | 118.12 (15) | C4—C4'—H4' | 119.3 |
C4—C3—C2 | 119.61 (15) | O5'—C5'—C5 | 112.37 (14) |
C3—C4—C5 | 117.87 (15) | O5'—C5'—H5'A | 109.1 |
C3—C4—C4' | 120.10 (15) | C5—C5'—H5'A | 109.1 |
C5—C4—C4' | 122.03 (15) | O5'—C5'—H5'B | 109.1 |
C6—C5—C4 | 117.93 (15) | C5—C5'—H5'B | 109.1 |
C6—C5—C5' | 119.12 (15) | H5'A—C5'—H5'B | 107.9 |
C4—C5—C5' | 122.90 (15) | C5'—O5'—H5' | 108.4 (15) |
N1—C6—C5 | 124.44 (16) | N2—C4"—H4"A | 109.4 |
N1—C6—H6 | 117.8 | N2—C4"—H4"B | 109.5 |
C5—C6—H6 | 117.8 | H4"A—C4"—H4"B | 109.5 |
C2—C2'—H2'A | 109.5 | N2—C4"—H4"C | 109.5 |
C2—C2'—H2'B | 109.4 | H4"A—C4"—H4"C | 109.5 |
H2'A—C2'—H2'B | 109.5 | H4"B—C4"—H4"C | 109.5 |
C6—N1—C2—C3 | −0.1 (2) | C4'—C4—C5—C6 | 179.23 (14) |
C6—N1—C2—C2' | 179.39 (17) | C3—C4—C5—C5' | 177.23 (15) |
N1—C2—C3—O3' | −178.66 (15) | C4'—C4—C5—C5' | −3.5 (2) |
C2'—C2—C3—O3' | 1.9 (3) | C2—N1—C6—C5 | −1.8 (3) |
N1—C2—C3—C4 | 1.7 (2) | C4—C5—C6—N1 | 1.8 (2) |
C2'—C2—C3—C4 | −177.71 (17) | C5'—C5—C6—N1 | −175.57 (16) |
O3'—C3—C4—C5 | 178.79 (14) | C4"—N2—C4'—C4 | 178.61 (15) |
C2—C3—C4—C5 | −1.6 (2) | C3—C4—C4'—N2 | 2.9 (2) |
O3'—C3—C4—C4' | −0.5 (2) | C5—C4—C4'—N2 | −176.32 (15) |
C2—C3—C4—C4' | 179.09 (14) | C6—C5—C5'—O5' | 104.48 (18) |
C3—C4—C5—C6 | 0.0 (2) | C4—C5—C5'—O5' | −72.7 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3′—H3′···N2 | 0.92 (3) | 1.73 (3) | 2.570 (2) | 152 (2) |
O5′—H5′···N1i | 0.92 (3) | 1.95 (3) | 2.865 (2) | 171 (2) |
Symmetry code: (i) −x+1, y−1/2, −z+3/2. |
C9H13N2O2·C7H4NO4 | F(000) = 728 |
Mr = 347.33 | Dx = 1.506 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5759 reflections |
a = 7.113 (2) Å | θ = 2.2–26.0° |
b = 11.797 (3) Å | µ = 0.12 mm−1 |
c = 18.314 (5) Å | T = 100 K |
β = 94.644 (7)° | Plate, yellow |
V = 1531.7 (7) Å3 | 0.38 × 0.34 × 0.10 mm |
Z = 4 |
Bruker APEX diffractometer | 3005 independent reflections |
Radiation source: fine-focus sealed tube | 2768 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.027 |
ω scans | θmax = 26.0°, θmin = 2.1° |
Absorption correction: multi-scan SADABS (Sheldrick, 2002) | h = −8→8 |
Tmin = 0.954, Tmax = 0.989 | k = −14→14 |
13011 measured reflections | l = −22→22 |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | w = 1/[σ2(Fo2) + (0.051P)2 + 0.840P] where P = (Fo2 + 2Fc2)/3 |
3005 reflections | (Δ/σ)max = 0.001 |
235 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
C9H13N2O2·C7H4NO4 | V = 1531.7 (7) Å3 |
Mr = 347.33 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 7.113 (2) Å | µ = 0.12 mm−1 |
b = 11.797 (3) Å | T = 100 K |
c = 18.314 (5) Å | 0.38 × 0.34 × 0.10 mm |
β = 94.644 (7)° |
Bruker APEX diffractometer | 3005 independent reflections |
Absorption correction: multi-scan SADABS (Sheldrick, 2002) | 2768 reflections with I > 2σ(I) |
Tmin = 0.954, Tmax = 0.989 | Rint = 0.027 |
13011 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | Δρmax = 0.27 e Å−3 |
3005 reflections | Δρmin = −0.24 e Å−3 |
235 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 | ||
N1 | 0.71589 (15) | 0.27114 (10) | 0.77076 (6) | 0.0155 (2) | |
H1 | 0.663 (2) | 0.2713 (13) | 0.7216 (9) | 0.019* | |
N2 | 0.96460 (16) | 0.31311 (10) | 1.03172 (6) | 0.0161 (2) | |
H2 | 0.925 (2) | 0.3824 (14) | 1.0116 (9) | 0.019* | |
C2 | 0.72986 (18) | 0.36344 (11) | 0.81193 (7) | 0.0158 (3) | |
C3 | 0.81124 (18) | 0.35547 (11) | 0.88710 (7) | 0.0147 (3) | |
C4 | 0.87066 (17) | 0.24484 (11) | 0.91174 (7) | 0.0143 (3) | |
C5 | 0.85457 (18) | 0.15034 (11) | 0.86361 (7) | 0.0151 (3) | |
C6 | 0.77561 (18) | 0.16637 (11) | 0.79410 (7) | 0.0163 (3) | |
H6 | 0.7620 | 0.1038 | 0.7615 | 0.020* | |
C2' | 0.6658 (2) | 0.47474 (12) | 0.78045 (7) | 0.0203 (3) | |
H2'A | 0.5980 | 0.4627 | 0.7323 | 0.030* | |
H2'B | 0.7754 | 0.5234 | 0.7751 | 0.030* | |
H2'C | 0.5816 | 0.5112 | 0.8132 | 0.030* | |
O3' | 0.82704 (13) | 0.44392 (8) | 0.92668 (5) | 0.0188 (2) | |
C4' | 0.94601 (17) | 0.22953 (11) | 0.98611 (7) | 0.0149 (3) | |
H4' | 0.9833 | 0.1558 | 1.0023 | 0.018* | |
C5' | 0.92272 (19) | 0.03307 (11) | 0.88697 (7) | 0.0173 (3) | |
H5'A | 0.9067 | −0.0187 | 0.8444 | 0.021* | |
H5'B | 1.0589 | 0.0367 | 0.9029 | 0.021* | |
O5' | 0.82394 (14) | −0.01176 (8) | 0.94497 (5) | 0.0191 (2) | |
H5' | 0.715 (3) | −0.0354 (14) | 0.9274 (9) | 0.023* | |
C4" | 1.0390 (2) | 0.30165 (12) | 1.10783 (7) | 0.0192 (3) | |
H4"A | 1.1521 | 0.3488 | 1.1166 | 0.029* | |
H4"B | 1.0715 | 0.2222 | 1.1180 | 0.029* | |
H4"C | 0.9434 | 0.3262 | 1.1401 | 0.029* | |
O1A | 0.51104 (14) | 0.40141 (8) | 0.60777 (5) | 0.0230 (2) | |
O2A | 0.59342 (14) | 0.22296 (9) | 0.63592 (5) | 0.0221 (2) | |
O3A | 0.23102 (19) | 0.22864 (11) | 0.25580 (6) | 0.0402 (3) | |
O4A | 0.16524 (16) | 0.06417 (9) | 0.29863 (6) | 0.0309 (3) | |
N1A | 0.23218 (17) | 0.15998 (11) | 0.30576 (6) | 0.0221 (3) | |
C1A | 0.45656 (17) | 0.25993 (11) | 0.51603 (7) | 0.0149 (3) | |
C2A | 0.43198 (18) | 0.33935 (11) | 0.45944 (7) | 0.0161 (3) | |
H2A | 0.4626 | 0.4166 | 0.4689 | 0.019* | |
C3A | 0.36357 (18) | 0.30673 (12) | 0.38985 (7) | 0.0174 (3) | |
H3A | 0.3498 | 0.3601 | 0.3510 | 0.021* | |
C4A | 0.31560 (18) | 0.19387 (12) | 0.37837 (7) | 0.0168 (3) | |
C5A | 0.33738 (18) | 0.11278 (11) | 0.43312 (7) | 0.0176 (3) | |
H5A | 0.3023 | 0.0361 | 0.4237 | 0.021* | |
C6A | 0.41167 (18) | 0.14643 (11) | 0.50202 (7) | 0.0165 (3) | |
H6A | 0.4322 | 0.0918 | 0.5400 | 0.020* | |
C7A | 0.52625 (18) | 0.29850 (12) | 0.59268 (7) | 0.0166 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0190 (5) | 0.0168 (6) | 0.0105 (5) | −0.0004 (4) | −0.0010 (4) | 0.0007 (4) |
N2 | 0.0198 (6) | 0.0149 (6) | 0.0132 (5) | −0.0001 (4) | −0.0007 (4) | 0.0010 (4) |
C2 | 0.0163 (6) | 0.0158 (6) | 0.0153 (6) | −0.0006 (5) | 0.0010 (5) | 0.0014 (5) |
C3 | 0.0157 (6) | 0.0153 (6) | 0.0133 (6) | −0.0007 (5) | 0.0013 (5) | 0.0003 (5) |
C4 | 0.0143 (6) | 0.0150 (6) | 0.0136 (6) | −0.0012 (5) | 0.0018 (5) | 0.0002 (5) |
C5 | 0.0154 (6) | 0.0145 (6) | 0.0155 (6) | −0.0015 (5) | 0.0020 (5) | 0.0003 (5) |
C6 | 0.0199 (6) | 0.0141 (6) | 0.0150 (6) | −0.0006 (5) | 0.0023 (5) | −0.0016 (5) |
C2' | 0.0276 (7) | 0.0170 (7) | 0.0155 (7) | 0.0020 (5) | −0.0032 (5) | 0.0020 (5) |
O3' | 0.0264 (5) | 0.0143 (5) | 0.0153 (5) | 0.0016 (4) | −0.0017 (4) | −0.0020 (4) |
C4' | 0.0145 (6) | 0.0143 (6) | 0.0159 (6) | −0.0014 (5) | 0.0017 (5) | 0.0011 (5) |
C5' | 0.0226 (7) | 0.0141 (6) | 0.0150 (6) | 0.0004 (5) | 0.0004 (5) | 0.0000 (5) |
O5' | 0.0227 (5) | 0.0171 (5) | 0.0170 (5) | −0.0037 (4) | −0.0020 (4) | 0.0036 (4) |
C4" | 0.0250 (7) | 0.0202 (7) | 0.0118 (6) | −0.0017 (5) | −0.0015 (5) | −0.0007 (5) |
O1A | 0.0293 (5) | 0.0203 (5) | 0.0183 (5) | 0.0024 (4) | −0.0047 (4) | −0.0041 (4) |
O2A | 0.0284 (5) | 0.0236 (5) | 0.0135 (5) | 0.0054 (4) | −0.0034 (4) | 0.0003 (4) |
O3A | 0.0620 (8) | 0.0401 (7) | 0.0162 (6) | 0.0005 (6) | −0.0119 (5) | 0.0020 (5) |
O4A | 0.0343 (6) | 0.0294 (6) | 0.0279 (6) | −0.0010 (5) | −0.0033 (5) | −0.0144 (5) |
N1A | 0.0222 (6) | 0.0268 (7) | 0.0167 (6) | 0.0059 (5) | −0.0022 (5) | −0.0069 (5) |
C1A | 0.0129 (6) | 0.0173 (6) | 0.0145 (6) | 0.0015 (5) | 0.0015 (5) | 0.0000 (5) |
C2A | 0.0175 (6) | 0.0148 (6) | 0.0162 (6) | −0.0006 (5) | 0.0018 (5) | −0.0002 (5) |
C3A | 0.0186 (6) | 0.0191 (7) | 0.0147 (6) | 0.0030 (5) | 0.0023 (5) | 0.0024 (5) |
C4A | 0.0155 (6) | 0.0219 (7) | 0.0128 (6) | 0.0029 (5) | −0.0006 (5) | −0.0040 (5) |
C5A | 0.0177 (6) | 0.0149 (6) | 0.0202 (7) | 0.0008 (5) | 0.0025 (5) | −0.0018 (5) |
C6A | 0.0179 (6) | 0.0165 (6) | 0.0154 (6) | 0.0030 (5) | 0.0021 (5) | 0.0025 (5) |
C7A | 0.0140 (6) | 0.0211 (7) | 0.0145 (6) | 0.0007 (5) | 0.0012 (5) | −0.0004 (5) |
N1—C2 | 1.3236 (18) | C5'—H5'B | 0.9900 |
N1—C6 | 1.3643 (18) | O5'—H5' | 0.862 (18) |
N1—H1 | 0.946 (17) | C4"—H4"A | 0.9800 |
N2—C4' | 1.2922 (17) | C4"—H4"B | 0.9800 |
N2—C4" | 1.4566 (17) | C4"—H4"C | 0.9800 |
N2—H2 | 0.930 (17) | O1A—C7A | 1.2517 (17) |
C2—C3 | 1.4526 (18) | O2A—C7A | 1.2603 (17) |
C2—C2' | 1.4905 (18) | O3A—N1A | 1.2217 (17) |
C3—O3' | 1.2702 (16) | O4A—N1A | 1.2293 (17) |
C3—C4 | 1.4334 (18) | N1A—C4A | 1.4670 (17) |
C4—C5 | 1.4202 (18) | C1A—C6A | 1.3955 (19) |
C4—C4' | 1.4340 (19) | C1A—C2A | 1.3975 (18) |
C5—C6 | 1.3623 (19) | C1A—C7A | 1.5201 (18) |
C5—C5' | 1.5160 (18) | C2A—C3A | 1.3817 (19) |
C6—H6 | 0.9500 | C2A—H2A | 0.9500 |
C2'—H2'A | 0.9800 | C3A—C4A | 1.386 (2) |
C2'—H2'B | 0.9800 | C3A—H3A | 0.9500 |
C2'—H2'C | 0.9800 | C4A—C5A | 1.3854 (19) |
C4'—H4' | 0.9500 | C5A—C6A | 1.3862 (19) |
C5'—O5' | 1.4222 (16) | C5A—H5A | 0.9500 |
C5'—H5'A | 0.9900 | C6A—H6A | 0.9500 |
C2—N1—C6 | 124.04 (11) | C5—C5'—H5'B | 109.1 |
C2—N1—H1 | 123.1 (10) | H5'A—C5'—H5'B | 107.8 |
C6—N1—H1 | 112.8 (10) | C5'—O5'—H5' | 109.0 (11) |
C4'—N2—C4" | 123.93 (12) | N2—C4"—H4"A | 109.5 |
C4'—N2—H2 | 113.8 (10) | N2—C4"—H4"B | 109.4 |
C4"—N2—H2 | 122.3 (10) | H4"A—C4"—H4"B | 109.5 |
N1—C2—C3 | 119.50 (12) | N2—C4"—H4"C | 109.5 |
N1—C2—C2' | 119.86 (12) | H4"A—C4"—H4"C | 109.5 |
C3—C2—C2' | 120.63 (11) | H4"B—C4"—H4"C | 109.5 |
O3'—C3—C4 | 123.92 (12) | O3A—N1A—O4A | 123.44 (12) |
O3'—C3—C2 | 119.85 (12) | O3A—N1A—C4A | 118.42 (12) |
C4—C3—C2 | 116.23 (11) | O4A—N1A—C4A | 118.14 (12) |
C5—C4—C3 | 120.83 (12) | C6A—C1A—C2A | 119.61 (12) |
C5—C4—C4' | 119.72 (12) | C6A—C1A—C7A | 120.63 (12) |
C3—C4—C4' | 119.45 (11) | C2A—C1A—C7A | 119.74 (12) |
C6—C5—C4 | 118.52 (12) | C3A—C2A—C1A | 120.72 (13) |
C6—C5—C5' | 119.25 (12) | C3A—C2A—H2A | 119.6 |
C4—C5—C5' | 122.23 (12) | C1A—C2A—H2A | 119.6 |
C5—C6—N1 | 120.85 (12) | C2A—C3A—C4A | 118.13 (12) |
C5—C6—H6 | 119.6 | C2A—C3A—H3A | 120.9 |
N1—C6—H6 | 119.6 | C4A—C3A—H3A | 120.9 |
C2—C2'—H2'A | 109.4 | C5A—C4A—C3A | 122.80 (12) |
C2—C2'—H2'B | 109.5 | C5A—C4A—N1A | 118.76 (12) |
H2'A—C2'—H2'B | 109.5 | C3A—C4A—N1A | 118.41 (12) |
C2—C2'—H2'C | 109.5 | C4A—C5A—C6A | 118.24 (12) |
H2'A—C2'—H2'C | 109.5 | C4A—C5A—H5A | 120.9 |
H2'B—C2'—H2'C | 109.5 | C6A—C5A—H5A | 120.9 |
N2—C4'—C4 | 121.92 (12) | C5A—C6A—C1A | 120.45 (12) |
N2—C4'—H4' | 119.0 | C5A—C6A—H6A | 119.8 |
C4—C4'—H4' | 119.0 | C1A—C6A—H6A | 119.8 |
O5'—C5'—C5 | 112.59 (11) | O1A—C7A—O2A | 125.60 (12) |
O5'—C5'—H5'A | 109.1 | O1A—C7A—C1A | 117.82 (12) |
C5—C5'—H5'A | 109.1 | O2A—C7A—C1A | 116.58 (12) |
O5'—C5'—H5'B | 109.1 | ||
C6—N1—C2—C3 | −0.70 (19) | C6—C5—C5'—O5' | −117.39 (13) |
C6—N1—C2—C2' | 178.08 (12) | C4—C5—C5'—O5' | 62.83 (16) |
N1—C2—C3—O3' | 179.21 (12) | C6A—C1A—C2A—C3A | 0.07 (19) |
C2'—C2—C3—O3' | 0.44 (19) | C7A—C1A—C2A—C3A | −178.10 (11) |
N1—C2—C3—C4 | −0.43 (18) | C1A—C2A—C3A—C4A | 1.65 (19) |
C2'—C2—C3—C4 | −179.20 (12) | C2A—C3A—C4A—C5A | −1.5 (2) |
O3'—C3—C4—C5 | −177.80 (12) | C2A—C3A—C4A—N1A | 176.35 (11) |
C2—C3—C4—C5 | 1.82 (18) | O3A—N1A—C4A—C5A | −172.61 (13) |
O3'—C3—C4—C4' | 2.6 (2) | O4A—N1A—C4A—C5A | 8.14 (18) |
C2—C3—C4—C4' | −177.73 (11) | O3A—N1A—C4A—C3A | 9.49 (19) |
C3—C4—C5—C6 | −2.13 (19) | O4A—N1A—C4A—C3A | −169.76 (12) |
C4'—C4—C5—C6 | 177.42 (12) | C3A—C4A—C5A—C6A | −0.5 (2) |
C3—C4—C5—C5' | 177.65 (12) | N1A—C4A—C5A—C6A | −178.30 (11) |
C4'—C4—C5—C5' | −2.79 (19) | C4A—C5A—C6A—C1A | 2.27 (19) |
C4—C5—C6—N1 | 1.01 (19) | C2A—C1A—C6A—C5A | −2.08 (19) |
C5'—C5—C6—N1 | −178.79 (11) | C7A—C1A—C6A—C5A | 176.07 (12) |
C2—N1—C6—C5 | 0.4 (2) | C6A—C1A—C7A—O1A | −159.08 (12) |
C4"—N2—C4'—C4 | 179.53 (12) | C2A—C1A—C7A—O1A | 19.07 (18) |
C5—C4—C4'—N2 | 179.48 (12) | C6A—C1A—C7A—O2A | 20.35 (18) |
C3—C4—C4'—N2 | −0.96 (19) | C2A—C1A—C7A—O2A | −161.50 (12) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2A | 0.946 (17) | 1.706 (17) | 2.6137 (15) | 159.8 (15) |
N2—H2···O3′ | 0.930 (17) | 1.806 (17) | 2.5952 (15) | 141.0 (14) |
O5′—H5′···O1Ai | 0.862 (18) | 1.840 (18) | 2.6995 (15) | 175.0 (17) |
Symmetry code: (i) −x+1, y−1/2, −z+3/2. |
Experimental details
(compound_I_) | (compound_II_) | (compound_III_) | (compound_IV_) | |
Crystal data | ||||
Chemical formula | C15H16N2O2 | C15H17N2O2·C7H4NO4 | C9H12N2O2 | C9H13N2O2·C7H4NO4 |
Mr | 256.30 | 423.42 | 180.21 | 347.33 |
Crystal system, space group | Monoclinic, P21/n | Triclinic, P1 | Monoclinic, P21/c | Monoclinic, P21/c |
Temperature (K) | 295 | 295 | 295 | 100 |
a, b, c (Å) | 4.001 (4), 25.09 (3), 12.940 (11) | 7.683 (5), 12.188 (6), 12.562 (6) | 11.046 (2), 4.8739 (8), 18.027 (3) | 7.113 (2), 11.797 (3), 18.314 (5) |
α, β, γ (°) | 90, 93.65 (8), 90 | 114.88 (4), 99.61 (5), 96.03 (5) | 90, 106.728 (5), 90 | 90, 94.644 (7), 90 |
V (Å3) | 1296 (2) | 1031.8 (10) | 929.5 (3) | 1531.7 (7) |
Z | 4 | 2 | 4 | 4 |
Radiation type | Mo Kα | Mo Kα | Mo Kα | Mo Kα |
µ (mm−1) | 0.09 | 0.10 | 0.09 | 0.12 |
Crystal size (mm) | 0.40 × 0.20 × 0.10 | 0.40 × 0.20 × 0.10 | 0.45 × 0.23 × 0.04 | 0.38 × 0.34 × 0.10 |
Data collection | ||||
Diffractometer | Stoe four-circle diffractometer | Stoe four-circle diffractometer | Bruker APEX diffractometer | Bruker APEX diffractometer |
Absorption correction | – | – | Multi-scan SADABS (Sheldrick, 2002) | Multi-scan SADABS (Sheldrick, 2002) |
Tmin, Tmax | – | – | 0.942, 0.996 | 0.954, 0.989 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2631, 2287, 874 | 3866, 3591, 2383 | 7547, 1814, 1575 | 13011, 3005, 2768 |
Rint | 0.150 | 0.018 | 0.018 | 0.027 |
(sin θ/λ)max (Å−1) | 0.595 | 0.595 | 0.617 | 0.617 |
Refinement | ||||
R[F2 > 2σ(F2)], wR(F2), S | 0.076, 0.214, 1.00 | 0.049, 0.153, 1.00 | 0.051, 0.147, 1.02 | 0.036, 0.098, 1.00 |
No. of reflections | 2287 | 3591 | 1814 | 3005 |
No. of parameters | 178 | 289 | 124 | 235 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.27 | 0.20, −0.21 | 0.20, −0.15 | 0.27, −0.24 |
Computer programs: Bruker SMART, Bruker SAINT, SHELXTL (Sheldrick, 2000).
N1—C2 | 1.325 (7) | C3—C4 | 1.369 (7) |
N1—C6 | 1.353 (7) | C4—C4' | 1.438 (7) |
N2—C4' | 1.283 (7) | C5—C5' | 1.502 (7) |
C3—O3' | 1.356 (7) | O5'—C5' | 1.410 (7) |
C2—N1—C6 | 118.4 (5) | C6—C5—C5' | 118.8 (5) |
O3'—C3—C4 | 122.6 (5) | N2—C4'—C4 | 120.2 (6) |
C3—C4—C4' | 121.4 (5) | O5'—C5'—C5 | 110.0 (5) |
C3—C4—C4'—N2 | 0.1 (8) | C6—C5—C5'—O5' | 111.9 (6) |
D—H···A | D—H | H···A | D···A | D—H···A |
O3'—H3'···N2 | 1.01 (6) | 1.71 (6) | 2.547 (6) | 138 (5) |
O5'—H5'···N1i | 0.92 (6) | 1.86 (6) | 2.751 (6) | 162 (5) |
Symmetry code: (i) x+1/2, −y+1/2, z+1/2. |
N1—C2 | 1.324 (3) | C5—C5' | 1.504 (3) |
N1—C6 | 1.339 (3) | O5'—C5' | 1.410 (3) |
N2—C4' | 1.270 (3) | O1A—C7A | 1.230 (3) |
C3—O3' | 1.336 (3) | O2A—C7A | 1.256 (3) |
C3—C4 | 1.396 (3) | C1A—C7A | 1.507 (3) |
C4—C4' | 1.449 (3) | ||
C2—N1—C6 | 123.2 (2) | O5'—C5'—C5 | 112.9 (2) |
O3'—C3—C4 | 123.0 (2) | O1A—C7A—O2A | 126.1 (2) |
C3—C4—C4' | 119.8 (2) | O1A—C7A—C1A | 119.2 (2) |
C6—C5—C5' | 119.9 (2) | O2A—C7A—C1A | 114.7 (2) |
N2—C4'—C4 | 121.1 (2) | ||
C6—C5—C5'—O5' | −122.0 (3) | C6A—C1A—C7A—O2A | 140.9 (2) |
C6A—C1A—C7A—O1A | −36.5 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2A | 1.01 (3) | 1.55 (3) | 2.549 (3) | 170 (2) |
N1—H1···O1A | 1.01 (3) | 2.63 (3) | 3.362 (3) | 129.4 (18) |
O3'—H3'···N2 | 0.95 (3) | 1.69 (3) | 2.553 (3) | 150 (3) |
O5'—H5'···O1Ai | 0.96 (3) | 1.75 (3) | 2.704 (3) | 175 (3) |
Symmetry code: (i) −x, −y+1, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
O3'—H3'···N2 | 0.92 (3) | 1.73 (3) | 2.570 (2) | 152 (2) |
O5'—H5'···N1i | 0.92 (3) | 1.95 (3) | 2.865 (2) | 171 (2) |
Symmetry code: (i) −x+1, y−1/2, −z+3/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2A | 0.946 (17) | 1.706 (17) | 2.6137 (15) | 159.8 (15) |
N2—H2···O3' | 0.930 (17) | 1.806 (17) | 2.5952 (15) | 141.0 (14) |
O5'—H5'···O1Ai | 0.862 (18) | 1.840 (18) | 2.6995 (15) | 175.0 (17) |
Symmetry code: (i) −x+1, y−1/2, −z+3/2. |
In various enzymatic transformations of amino acids (e.g., racemization, decarboxylation and transamination), the cofactor (vitamin B6) pyridoxal-5?-phosphate (PLP) (Christen & Metzler, 1985; Fujiwara, 1973) plays an important role (Malashkevich et al.; 1993, Spies & Toney, 2003; Zhou & Toney, 1999). According to the crystal structures of PLP-dependent enzymes (Jansonius 1998; Jager et al., 1994; Shaw et al., 1997; Smith et al., 1989; Stamper et al., 1998), the cofactor is located in the active site of the enzyme. The ring nitrogen is involved in an intermolecular OHN hydrogen bond with an aspartic acid side chain, and the phosphate group forms three hydrogen bonds with other amino acid residues. Whereas in aqueous solution the aldehyde function of PLP is easily hydrated (Harruff & Jenkins, 1976; van Genderen et al., 1989; Witherup & Abbott, 1975), PLP forms in the enzymic environment in the absence of the substrate generally a so called "internal aldimine", consisting of a Schiff base with the ε-amino group of a lysine residue of the enzyme. "External aldimines" are formed with the amino acid substrates and their reaction products. The aldehyde and all aldimines contain an additional intramolecular hydrogen bond, which is essential for the enzymatic function (Christen & Metzler, 1985).
Of special importance are two functional OHN-hydrogen bonds as illustrated below. In the first step of the catalytic cycle, it is assumed that the bridging proton of the intramolecular OHN-hydrogen bond has to be transferred from the hydroxyl oxygen to the imino nitrogen, a process which is assisted by protonation of the pyridine ring. The role of the intermolecular OHN hydrogen bond is not clear: it could first serve as attachment point of the cofactor with the protein, as the phosphate group, but it could also assist the proton transfer in the intramolecular OHN hydrogen bond.
In order to elucidate the role of the intramolecular hydrogen bond, model studies have been reported for several model Schiff bases of aromatic ortho-hydroxylaldehydes, dissolved in organic liquids or embedded in the organic solid state (Benedict et al., 1998; Dziembowska et al., 2001; Hansen et al., 1998; Limbach et al., 2004; Rozwadowski et al., 1999). In these studies, tautomeric equilibria between enolimine forms (OH-forms) and ketoamine forms (NH-forms) have been established which interconvert very rapidly via proton transfers. As these models did not contain the pyridine ring function nor the phosphate chain, the influence of these substitutents on the intramolecular hydrogen bond was not studied.
Therefore, we have been interested in the question of the coupling of the intra- and the intermolecular OHN hydrogen bonds, a problem that we wanted to study by a combination of crystallographic and liquid state NMR techniques. However, for this task it was necessary to design and crystallize model Schiff bases that mimic the PLP cofactor in its natural environment.
As the phosphate group is not directly involved in the chemical function of PLP, we prepared several novel acid base 1: 1 complexes of benzoic acid derivatives with Schiff bases of pyridoxal (PL, R? = H), with R = tolyl and methyl in order to vary the basicity of the Schiff base nitrogen atom. We were able to crystallize compounds (I) to (IV) depicted above, whose X-ray crystallographic structures are reported in this paper.
As the phosphate group is not directly involved in the chemical function of PLP, we prepared several novel acid base 1: 1 complexes of benzoic acid derivatives with Schiff bases of pyridoxal (PL, R? = H), with R = tolyl and methyl in order to vary the basicity of the Schiff base nitrogen atom. We were able to crystallize compounds (I) to (IV) depicted above, whose X-ray crystallographic structures are reported in this paper.
3. Results and discussion
To our knowledge, the X-ray crystal structures of the known compounds (I) and (III) have not yet been reported. Unfortunately it was not possible to crystallize the adducts of (I) and of (III) with the same benzoic acid derivative. However, we thought that this would not constitute a major problem as the acidity of 2-nitrobenzoic acid and of 4-nitrobenzoic acid, with the pKa = 2.17 and 3.44 respectively (Polanski & Bak, 2003), are not very different.
The structures, crystal packing and the hydrogen bond network of (I) to (IV) are depicted in Figs. 1 4, selected structural and hydrogen bond data are assembled in Tables 3 and 4. In the following, we will first discuss the hydrogen bonded networks and the packing diagrams of these crystals as well as the problem of the location of the protons in the intra- and the intermolecular hydrogen bonds.
The aldenamine Schiff base (I) (Fig. 1) forms OHN hydrogen bonded chains involving the hydroxyl side groups and the pyridine rings of adjacent molecules, exhibiting an N····O distance of the intermolecular hydrogen bond of 2.752 (7) Å (I). In the intramolecular OHN hydrogen bridge the proton is located near the oxygen atom that is supported by the single bond character of the C3?-O3? distance of 1.358 (3) Å (I) and the double bond character of the N2—C4? distance of 1.2919 (18) Å (I), expected for an enolimine form of the Schiff base.
In the aldenamine Schiff base-2-nitrobenzoic acid adduct (II) (Fig. 2) the bonding situation in the intramolecular OHN hydrogen bond is not altered as compared to (I). However, the pyridine ring is now involved in an intermolecular OHN hydrogen bond with the carboxylic group of the acid added. The crystal packing shows that the hydroxyl group of the Schiff base is involved in an intermolecular OHO hydrogen bond to the carboxyl group of the acid, in particular to the free oxygen atom O1A with the corresponding O····O heavy atom distance of 2.699 (3) Å. The benzene ring in (II) is not located in the plane of the carboxyl group. The ortho nitro group attached to C2A is twisted because of steric hindrance with the neighboring carboxyl group. The bond angles of the benzene ring shows significant deviations 120°, probably because of the presence of the electron-withdrawing nitro and carboxylic groups.
The O····N distance of the intermolecular OHN hydrogen bond in (II) is only 2.550 (3) Å. This represents a substantial compression of the heavy atom distance as compared to the weaker intermolecular OHN hydrogen bonds of (I). The proton seems to be located near nitrogen leading to a zwitterionic structure. This conclusion is corroborated by the observation that the C2—N1—C6 angle of the pyridine ring increases substantially by protonation of the nitrogen atom, and that the two C····O bond lengths of the carboxylic acid groups become equal upon ionization, in agreement with earlier NMR and X-ray crystallographic studies on complexes of 2,4,6-trimethylpyridine (collidine) with derivatives of benzoic acids (Foces-Foces et al., 1999; Lorente et al., 2001).
The crystal structure of the aldimine Schiff base (III) is depicted in Fig. 3. Although the basicity of the CH3—N group is expected to be larger than of the corresponding tolyl-N group in (I), the proton in the intramolecular OHN hydrogen bond remains on the oxygen atom: the C3?-O3? distance of 1.342 (2) Å (III) and the N2—C4? distance of 1.263 (2) Å (III) suggest again an enolimine form. (III) is packed as cyclic dimers, involving intermolecular OHN hydrogen bonds between the hydroxylic side group and the pyridine rings. The N····O distance is 2.868 (2) Å, substantially larger than in the corresponding chains of (I).
The crystal structure of the aldimine Schiff base-4-nitrobenzoic acid adduct (IV) is depicted in Fig. 4. As in (II), an acid-base complex exhibiting an intermolecular OHN hydrogen bond between the carboxylic group and the pyridine ring is formed. These complexes are also linked again by intermolecular OHO hydrogen bonds as in (II), exhibiting an O····O distance of 2.6996 (15) Å. The benzene ring in (IV) is almost coplanar with the carboxyl groups, because the nitro group in the para-position does not induce steric hindrance.
The two C····O distances of the carboxylic group of (IV) indicate a transfer of the proton in the intermolecular OHN hydrogen bond to nitrogen similar to that seen in (II). Again, the N····O distance is quite short (2.6122 (16) Å). However, a big difference occurs in the intramolecular OHN hydrogen bond. The protonation of the pyridine ring leads also to a shift of the proton in the intramolecular OHN hydrogen bond from oxygen to nitrogen. In other words, the tautomeric equilibrium is shifted to the ketoamine form. This is manifest by a shortening of the C3?-O3? distance of 1.2699 (17) Å and the increase N2—C4? distance of 1.2919 (18) Å, that corresponds to an increased double bond character of the first and an increased single bond character of the second bond.
Additionally, we have studied the Schiff bases and their adducts (I) to (IV) with 1H NMR in liquid state. We note, however, that the NMR spectra of (I) to (IV) are complicated by the fact that in addition to the open form also a cyclic aminal form can be formed, depending on the solvent and of the acid added. For DMSO we find that the Schiff bases (I) and (III) are present in the open form.
This is in good agreement with earlier studies on pyridoximines (Harruff & Jenkins, 1976; van Genderen et al., 1989). Furthermore, we observed that protonation of the ring nitrogen atom by dissolving the 1: 1 adduct (IV) in DMSO resulted in the formation of the pyridinium salt of the cyclic aminal form; the H4? resonance shifts upfield to 6.18 p.p.m. and the N-methyl signal was found at 2.37 p.p.m., as expected for an amine. A similar result was reported by van Genderen et al. (1989) who protonated (I) in DMSO with hydrochloride gas. By contrast, when the aldenamine adduct (II) was dissolved in DMSO, only the open form was observed. In all crystallographic structures only open forms were observed.
4. Conclusion
Whenever the Schiff base nitrogen atoms of PLP carry an aliphatic substituent such as in the internal and external aldimines of PLP in the enzyme environment, protonation of the ring nitrogen will have also shift the proton in the intramolecular hydrogen bond from oxygen to the Schiff base nitrogen, a circumstance that increases its positive electric charge. This charge seems to be pre-requisite for the reactivity of the enzyme. Finally, we note that if the Schiff base nitrogen atom would carry an aromatic substituent this effect does not occur. In contrast, that all crystallographic structures were only observed in the open form, the protonation of the ring nitrogen atom of the acid base adduct of the aldimine Schiff base in liquid state leads to the formation of the pyridinium salt of the cyclic aminal form.