| Literature DB >> 28217335 |
Jecika Maciel Velasques1, Vanessa Carratu Gervini1, Adaílton João Bortoluzzi2, Renan Lira de Farias3, Adriano Bof de Oliveira4.
Abstract
The reaction between 5-nitro-isatin and phenyl-hydrazine in acidic ethanol yields the title compound, C14H10N4O3, whose mol-ecular structure deviates slightly from a planar geometry (r.m.s. deviation = 0.065 Å for the mean plane through all non-H atoms). An intra-molecular N-H⋯O hydrogen bond is present, forming a ring of graph-set motif S(6). In the crystal, mol-ecules are linked by N-H⋯O and C-H⋯O hydrogen-bonding inter-actions into a two-dimensional network along (120), and rings of graph-set motif R22(8), R22(26) and R44(32) are observed. Additionally, a Hirshfeld surface analysis suggests that the mol-ecules are stacked along [100] through C=O⋯Cg inter-actions and indicates that the most important contributions for the crystal structure are O⋯H (28.5%) and H⋯H (26.7%) inter-actions. An in silico evaluation of the title compound with the DHFR enzyme (di-hydro-folate reductase) was performed. The isatin-hydrazone derivative and the active site of the selected enzyme show N-H⋯O(ASP29), N-H⋯O(ILE96) and Cg⋯Cg(PHE33) inter-actions.Entities:
Keywords: Hirshfeld surface calculation; crystal structure; in silico evaluation; isatin–hydrazone derivative; two-dimensional hydrogen-bonded network
Year: 2017 PMID: 28217335 PMCID: PMC5290558 DOI: 10.1107/S2056989016020375
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The molecular structure of the title compound, showing displacement ellipsoids drawn at the 50% probability level. The intramolecular hydrogen bond is shown as a dashed line.
Hydrogen-bond geometry (Å, °)
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| N4—H5⋯O1 | 0.88 | 2.03 | 2.7479 (10) | 137 |
| N1—H1⋯O1i | 0.88 | 1.96 | 2.8310 (10) | 171 |
| C10—H6⋯O3ii | 0.95 | 2.63 | 3.5542 (13) | 166 |
| C12—H8⋯O2iii | 0.95 | 2.47 | 3.3943 (13) | 163 |
Symmetry codes: (i) ; (ii) ; (iii) .
Figure 2A packing diagram of the title compound, showing the N—H⋯O and C—H⋯O interactions (dashed lines) connecting the molecules into a two-dimensional network in the (120) plane. The graph-set motifs for the crystal packing are: R1 = (8), R2 = (26) and R3 = (32).
Figure 3A packing diagram of the title compound showning the C⋯Cg interactions (as dashed lines) building a chain along [100]. [Symmetry codes: (iv) x − 1, y, z; (v) x + 1, y, z.]
Figure 4A Hirshfeld surface graphical representation (d norm) for the title compound. The surface is drawn with transparency and all atoms are labelled. The surface regions with strongest intermolecular interactions for atoms H1, O1 and C14 are shown in magenta.
Figure 5A Hirshfeld surface graphical representation (d norm) for the title compound. The surface is drawn with transparency and all atoms are labelled. The surface regions with strongest intermolecular interactions for atoms H8, O2 and C1 are shown in magenta.
Figure 6Hirshfeld surface fingerprint two-dimensional plot for the 5-nitroisatin-3-phenylhydrazone crystal structure showing the O⋯H contacts in detail (cyan dots). The O⋯H contribution for the crystal packing amounts to 28.5%, being the most important intermolecular connection. The d e (y axis) and d i (x axis) values are the closest external and internal distances [in Å] from given points on the Hirshfeld surface.
Figure 7Intermolecular interactions between the title compound and the dihydrofolate reductase enzyme. The interactions are shown as dashed lines and the figure is simplified for clarity.
Experimental details
| Crystal data | |
| Chemical formula | C14H10N4O3 |
|
| 282.26 |
| Crystal system, space group | Triclinic, |
| Temperature (K) | 200 |
|
| 5.7504 (4), 9.7190 (6), 12.1976 (7) |
| α, β, γ (°) | 111.196 (2), 96.759 (2), 98.497 (2) |
|
| 617.69 (7) |
|
| 2 |
| Radiation type | Mo |
| μ (mm−1) | 0.11 |
| Crystal size (mm) | 0.48 × 0.16 × 0.10 |
| Data collection | |
| Diffractometer | Bruker APEXII CCD area detector |
| Absorption correction | Multi-scan ( |
|
| 0.949, 0.989 |
| No. of measured, independent and observed [ | 11325, 3971, 3281 |
|
| 0.017 |
| (sin θ/λ)max (Å−1) | 0.726 |
| Refinement | |
|
| 0.039, 0.117, 1.03 |
| No. of reflections | 3971 |
| No. of parameters | 190 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.37, −0.26 |
Computer programs: APEX2 and SAINT (Bruker, 2013 ▸), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▸), DIAMOND (Brandenburg, 2006 ▸), GOLD (Verdonk et al., 2003 ▸), Crystal Explorer (Wolff, et al., 2012 ▸), publCIF (Westrip, 2010 ▸) and enCIFer (Allen et al., 2004 ▸).
| C14H10N4O3 | |
| Triclinic, | |
| Mo | |
| Cell parameters from 2154 reflections | |
| θ = 2.3–31.0° | |
| α = 111.196 (2)° | µ = 0.11 mm−1 |
| β = 96.759 (2)° | |
| γ = 98.497 (2)° | Prism, yellow |
| 0.48 × 0.16 × 0.10 mm |
| Bruker APEXII CCD area detector diffractometer | 3971 independent reflections |
| Radiation source: fine-focus sealed tube, Bruker APEX2 CCD | 3281 reflections with |
| Graphite monochromator | |
| φ and ω scans | θmax = 31.1°, θmin = 1.8° |
| Absorption correction: multi-scan (SADABS; Bruker, 2013) | |
| 11325 measured reflections |
| Refinement on | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: inferred from neighbouring sites | |
| H-atom parameters constrained | |
| 3971 reflections | (Δ/σ)max < 0.001 |
| 190 parameters | Δρmax = 0.37 e Å−3 |
| 0 restraints | Δρmin = −0.26 e Å−3 |
| 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. |
| C1 | 0.74444 (16) | 0.10997 (10) | 0.47144 (8) | 0.01734 (17) | |
| C2 | 0.58388 (16) | 0.19030 (10) | 0.42434 (8) | 0.01692 (17) | |
| C3 | 0.63293 (16) | 0.17378 (10) | 0.30690 (8) | 0.01701 (17) | |
| C4 | 0.53990 (17) | 0.22036 (10) | 0.21904 (8) | 0.01863 (18) | |
| H2 | 0.4130 | 0.2737 | 0.2283 | 0.022* | |
| C5 | 0.64117 (17) | 0.18525 (11) | 0.11683 (8) | 0.02053 (19) | |
| C6 | 0.8299 (2) | 0.10968 (12) | 0.10014 (9) | 0.0255 (2) | |
| H3 | 0.8968 | 0.0921 | 0.0299 | 0.031* | |
| C7 | 0.92000 (19) | 0.06009 (12) | 0.18685 (9) | 0.0240 (2) | |
| H4 | 1.0462 | 0.0062 | 0.1767 | 0.029* | |
| C8 | 0.81885 (16) | 0.09218 (10) | 0.28844 (8) | 0.01844 (17) | |
| C9 | 0.26077 (16) | 0.34671 (10) | 0.65458 (8) | 0.01776 (17) | |
| C10 | 0.25473 (19) | 0.34151 (12) | 0.76695 (9) | 0.0244 (2) | |
| H6 | 0.3603 | 0.2920 | 0.7976 | 0.029* | |
| C11 | 0.0939 (2) | 0.40895 (13) | 0.83359 (9) | 0.0296 (2) | |
| H7 | 0.0883 | 0.4047 | 0.9099 | 0.036* | |
| C12 | −0.0597 (2) | 0.48282 (13) | 0.78973 (10) | 0.0284 (2) | |
| H8 | −0.1711 | 0.5280 | 0.8354 | 0.034* | |
| C13 | −0.04899 (19) | 0.49000 (11) | 0.67893 (9) | 0.0248 (2) | |
| H9 | −0.1521 | 0.5418 | 0.6494 | 0.030* | |
| C14 | 0.11070 (18) | 0.42243 (11) | 0.61027 (9) | 0.02091 (19) | |
| H10 | 0.1173 | 0.4278 | 0.5344 | 0.025* | |
| N1 | 0.87794 (14) | 0.05403 (9) | 0.38620 (7) | 0.01994 (17) | |
| H1 | 0.9867 | 0.0010 | 0.3923 | 0.024* | |
| N2 | 0.54638 (17) | 0.23011 (10) | 0.02105 (8) | 0.02622 (19) | |
| N3 | 0.43091 (14) | 0.26487 (9) | 0.47905 (7) | 0.01813 (16) | |
| N4 | 0.41836 (15) | 0.27045 (9) | 0.58791 (7) | 0.01990 (17) | |
| H5 | 0.5115 | 0.2250 | 0.6195 | 0.024* | |
| O1 | 0.75650 (12) | 0.09474 (8) | 0.56864 (6) | 0.02078 (15) | |
| O2 | 0.36881 (18) | 0.28657 (11) | 0.03076 (8) | 0.0393 (2) | |
| O3 | 0.64526 (18) | 0.20633 (12) | −0.06636 (8) | 0.0416 (2) |
| C1 | 0.0163 (4) | 0.0189 (4) | 0.0187 (4) | 0.0066 (3) | 0.0039 (3) | 0.0081 (3) |
| C2 | 0.0171 (4) | 0.0202 (4) | 0.0165 (4) | 0.0077 (3) | 0.0050 (3) | 0.0084 (3) |
| C3 | 0.0160 (4) | 0.0198 (4) | 0.0176 (4) | 0.0072 (3) | 0.0050 (3) | 0.0081 (3) |
| C4 | 0.0187 (4) | 0.0222 (4) | 0.0182 (4) | 0.0089 (3) | 0.0055 (3) | 0.0091 (3) |
| C5 | 0.0229 (5) | 0.0257 (4) | 0.0165 (4) | 0.0093 (4) | 0.0049 (3) | 0.0103 (3) |
| C6 | 0.0278 (5) | 0.0344 (5) | 0.0206 (4) | 0.0158 (4) | 0.0107 (4) | 0.0125 (4) |
| C7 | 0.0242 (5) | 0.0326 (5) | 0.0217 (4) | 0.0162 (4) | 0.0100 (4) | 0.0121 (4) |
| C8 | 0.0183 (4) | 0.0217 (4) | 0.0179 (4) | 0.0084 (3) | 0.0047 (3) | 0.0085 (3) |
| C9 | 0.0181 (4) | 0.0201 (4) | 0.0169 (4) | 0.0075 (3) | 0.0053 (3) | 0.0071 (3) |
| C10 | 0.0269 (5) | 0.0326 (5) | 0.0187 (4) | 0.0138 (4) | 0.0066 (4) | 0.0120 (4) |
| C11 | 0.0357 (6) | 0.0389 (6) | 0.0195 (4) | 0.0163 (5) | 0.0127 (4) | 0.0117 (4) |
| C12 | 0.0293 (5) | 0.0329 (5) | 0.0256 (5) | 0.0152 (4) | 0.0133 (4) | 0.0085 (4) |
| C13 | 0.0250 (5) | 0.0260 (4) | 0.0274 (5) | 0.0138 (4) | 0.0085 (4) | 0.0107 (4) |
| C14 | 0.0235 (5) | 0.0236 (4) | 0.0208 (4) | 0.0112 (3) | 0.0076 (3) | 0.0111 (3) |
| N1 | 0.0203 (4) | 0.0257 (4) | 0.0196 (4) | 0.0133 (3) | 0.0068 (3) | 0.0111 (3) |
| N2 | 0.0310 (5) | 0.0332 (4) | 0.0206 (4) | 0.0144 (4) | 0.0074 (3) | 0.0136 (3) |
| N3 | 0.0184 (4) | 0.0215 (3) | 0.0171 (3) | 0.0076 (3) | 0.0056 (3) | 0.0085 (3) |
| N4 | 0.0216 (4) | 0.0265 (4) | 0.0172 (3) | 0.0130 (3) | 0.0069 (3) | 0.0108 (3) |
| O1 | 0.0218 (3) | 0.0259 (3) | 0.0201 (3) | 0.0108 (3) | 0.0059 (3) | 0.0122 (3) |
| O2 | 0.0468 (5) | 0.0577 (6) | 0.0299 (4) | 0.0370 (5) | 0.0134 (4) | 0.0241 (4) |
| O3 | 0.0475 (5) | 0.0687 (6) | 0.0280 (4) | 0.0299 (5) | 0.0198 (4) | 0.0305 (4) |
| C1—O1 | 1.2421 (11) | C9—C14 | 1.3942 (12) |
| C1—N1 | 1.3669 (11) | C9—N4 | 1.4029 (11) |
| C1—C2 | 1.4848 (12) | C10—C11 | 1.3845 (14) |
| C2—N3 | 1.3119 (11) | C10—H6 | 0.9500 |
| C2—C3 | 1.4490 (12) | C11—C12 | 1.3913 (16) |
| C3—C4 | 1.3882 (12) | C11—H7 | 0.9500 |
| C3—C8 | 1.4144 (12) | C12—C13 | 1.3863 (15) |
| C4—C5 | 1.3900 (13) | C12—H8 | 0.9500 |
| C4—H2 | 0.9500 | C13—C14 | 1.3919 (13) |
| C5—C6 | 1.3923 (13) | C13—H9 | 0.9500 |
| C5—N2 | 1.4631 (12) | C14—H10 | 0.9500 |
| C6—C7 | 1.3902 (13) | N1—H1 | 0.8800 |
| C6—H3 | 0.9500 | N2—O2 | 1.2267 (12) |
| C7—C8 | 1.3838 (13) | N2—O3 | 1.2316 (12) |
| C7—H4 | 0.9500 | N3—N4 | 1.3202 (11) |
| C8—N1 | 1.3915 (11) | N4—H5 | 0.8800 |
| C9—C10 | 1.3939 (13) | ||
| O1—C1—N1 | 126.00 (8) | C14—C9—N4 | 121.93 (8) |
| O1—C1—C2 | 127.42 (8) | C11—C10—C9 | 119.56 (9) |
| N1—C1—C2 | 106.58 (7) | C11—C10—H6 | 120.2 |
| N3—C2—C3 | 126.40 (8) | C9—C10—H6 | 120.2 |
| N3—C2—C1 | 126.92 (8) | C10—C11—C12 | 120.53 (9) |
| C3—C2—C1 | 106.67 (7) | C10—C11—H7 | 119.7 |
| C4—C3—C8 | 119.72 (8) | C12—C11—H7 | 119.7 |
| C4—C3—C2 | 134.01 (8) | C13—C12—C11 | 119.47 (9) |
| C8—C3—C2 | 106.26 (7) | C13—C12—H8 | 120.3 |
| C3—C4—C5 | 116.83 (8) | C11—C12—H8 | 120.3 |
| C3—C4—H2 | 121.6 | C12—C13—C14 | 120.93 (9) |
| C5—C4—H2 | 121.6 | C12—C13—H9 | 119.5 |
| C4—C5—C6 | 123.62 (9) | C14—C13—H9 | 119.5 |
| C4—C5—N2 | 118.74 (8) | C13—C14—C9 | 118.93 (9) |
| C6—C5—N2 | 117.64 (8) | C13—C14—H10 | 120.5 |
| C7—C6—C5 | 119.64 (9) | C9—C14—H10 | 120.5 |
| C7—C6—H3 | 120.2 | C1—N1—C8 | 110.92 (7) |
| C5—C6—H3 | 120.2 | C1—N1—H1 | 124.5 |
| C8—C7—C6 | 117.46 (9) | C8—N1—H1 | 124.5 |
| C8—C7—H4 | 121.3 | O2—N2—O3 | 123.29 (9) |
| C6—C7—H4 | 121.3 | O2—N2—C5 | 118.18 (8) |
| C7—C8—N1 | 127.81 (8) | O3—N2—C5 | 118.50 (9) |
| C7—C8—C3 | 122.66 (8) | C2—N3—N4 | 116.98 (8) |
| N1—C8—C3 | 109.53 (8) | N3—N4—C9 | 121.85 (8) |
| C10—C9—C14 | 120.56 (9) | N3—N4—H5 | 119.1 |
| C10—C9—N4 | 117.49 (8) | C9—N4—H5 | 119.1 |
| O1—C1—C2—N3 | 2.70 (16) | C14—C9—C10—C11 | 1.64 (16) |
| N1—C1—C2—N3 | −177.67 (9) | N4—C9—C10—C11 | −176.92 (9) |
| O1—C1—C2—C3 | −178.71 (9) | C9—C10—C11—C12 | −0.59 (17) |
| N1—C1—C2—C3 | 0.91 (10) | C10—C11—C12—C13 | −0.70 (18) |
| N3—C2—C3—C4 | −2.73 (17) | C11—C12—C13—C14 | 0.97 (17) |
| C1—C2—C3—C4 | 178.67 (10) | C12—C13—C14—C9 | 0.06 (16) |
| N3—C2—C3—C8 | 176.72 (9) | C10—C9—C14—C13 | −1.37 (15) |
| C1—C2—C3—C8 | −1.87 (10) | N4—C9—C14—C13 | 177.12 (9) |
| C8—C3—C4—C5 | −1.17 (14) | O1—C1—N1—C8 | −179.93 (9) |
| C2—C3—C4—C5 | 178.23 (10) | C2—C1—N1—C8 | 0.44 (10) |
| C3—C4—C5—C6 | −1.17 (15) | C7—C8—N1—C1 | 177.81 (10) |
| C3—C4—C5—N2 | 179.09 (8) | C3—C8—N1—C1 | −1.68 (11) |
| C4—C5—C6—C7 | 2.57 (17) | C4—C5—N2—O2 | −5.61 (15) |
| N2—C5—C6—C7 | −177.69 (9) | C6—C5—N2—O2 | 174.63 (10) |
| C5—C6—C7—C8 | −1.48 (16) | C4—C5—N2—O3 | 175.99 (10) |
| C6—C7—C8—N1 | 179.74 (10) | C6—C5—N2—O3 | −3.77 (15) |
| C6—C7—C8—C3 | −0.83 (16) | C3—C2—N3—N4 | −177.84 (8) |
| C4—C3—C8—C7 | 2.21 (15) | C1—C2—N3—N4 | 0.47 (14) |
| C2—C3—C8—C7 | −177.34 (9) | C2—N3—N4—C9 | −179.85 (8) |
| C4—C3—C8—N1 | −178.26 (8) | C10—C9—N4—N3 | 177.74 (9) |
| C2—C3—C8—N1 | 2.18 (10) | C14—C9—N4—N3 | −0.80 (15) |
| H··· | ||||
| N4—H5···O1 | 0.88 | 2.03 | 2.7479 (10) | 137 |
| N1—H1···O1i | 0.88 | 1.96 | 2.8310 (10) | 171 |
| C10—H6···O3ii | 0.95 | 2.63 | 3.5542 (13) | 166 |
| C12—H8···O2iii | 0.95 | 2.47 | 3.3943 (13) | 163 |