organic compounds
4-Fluorobenzyl (Z)-2-(2-oxoindolin-3-ylidene)hydrazine-1-carbodithioate
aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia, and bEaStCHEM School of Chemistry, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
*Correspondence e-mail: abdfatah@uitm.edu.my
The title compound, C16H12FN3OS, a fluorinated dithiocarbazate imine derivative, was synthesized by the one-pot, multi-component condensation reaction of hydrazine hydrate, carbon disulfide, 4-fluorobenzyl chloride and isatin. The compound demonstrates near-planarity across much of the molecule in the solid state and a Z configuration for the azomethine C=N bond. The Z form is further stabilized by the presence of an intramolecular N—H⋯O hydrogen bond. In the extended structure, molecules are linked into dimers by N—H⋯O hydrogen bonds and further connected into chains along either [20] or [100] by weak C—H⋯S and C—H⋯F hydrogen bonds, which further link into corrugated sheets and in combination form the overall three-dimensional network.
Keywords: crystal structure; dithiocarbazate; fluorine; isatin; z configuration; hydrogen bond.
CCDC reference: 2339543
Structure description
Various sulfur-containing molecules isolated from natural sources have been reported to exhibit a broad spectrum of biological activities (Wang et al., 2020; Chen & Li, 2023). Some synthetic sulfur-containing drugs inspired by natural products include the antibiotics dalfopristin and quinupristin, and the anticancer agents phthalascidin and ixabepilone (Mustafa & Winum, 2022; Hai et al., 2021). The ubiquitous role of fluorine in the design of bioactive molecules is expending rapidly, as a better understanding of the unique properties of this element is gained. The introduction of a fluorinated substituent atom can influence pKa, basicity, conformation, intrinsic potency, membrane permeability, metabolic stability and pharmacokinetic properties (Richardson, 2021; Ali & Zhou, 2023). The literature reveals that various fluorine- and sulfur-containing drugs have been approved by the US Food and Drug Administration to combat diseases. Some examples are the recently reported lenacapavir for the treatment of HIV-1 infection (Paik, 2022; Han & Lu, 2023) and belzutifan for the treatment of kidney cancer (Deeks, 2021; Fallah et al., 2022). As part of our ongoing studies in this area, we now describe the synthesis and structure of the title compound.
The title compound crystallizes in the triclinic P with one molecule in (Fig. 1). Its conformation and geometric details are similar to those in three closely related compounds; namely (Z)-benzyl 2-(5-methyl-2-oxoindolin-3-ylidene)hydrazinecarbodithioate, benzyl 2-(5-chloro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)hydrazinecarbodithioate and benzyl 2-(5-bromo-2-oxo-1,2-dihydro-3H-indol-3-yldene)hydrazinecarbodithioate (Abdul Manan et al., 2011, 2023), the main difference being the dihedral angles between the aromatic rings and isatin moieties; 70.9° in the first, 72.6° in the second and 74.5° in the third compound, while in the title compound this dihedral angle is 82.6 (4)°.
In the crystal of the title compound, individual molecules form inversion dimers through pairwise N1—H1⋯O2 [H⋯O = 1.93 (6) Å, N⋯O = 2.844 (10) Å] hydrogen bonds (Table 1) in the common R22(8) motif. A second set of dimers is formed through weak C6—H6⋯S11 [H⋯S = 2.944 (3) Å, C⋯S = 3.819 (11) Å] hydrogen bonds in an R22(18) motif, and the combination of the two dimeric interactions forms chains propagating along [20] (Fig. 2). A second set of chains is formed by two pairs of weak hydrogen bonds: two donors, C11—H11A and C17—H17, interact simultaneously with S10 [H⋯S 2.918 (2) and 3.028 (3) Å, C⋯S = 3.876 (10) and 3.908 (11) Å] and the donors C14—H14 and C16—H16 interact in an alternating fashion with F15 [H⋯F = 2.523 (6) and 2.685 (7) Å, C⋯F = 3.347 (11) and 3.540 (12) Å], forming R21(6) and R22(8) motifs, respectively. This results in flat, tape-like chains running along [100] (Fig. 3), which can combine with either the N—H⋯O hydrogen-bonded dimers, or the weakly hydrogen-bonded dimer, giving corrugated sheets in both cases, lying in the (02) or (01) planes, respectively. The combination of these weaker interactions forms the overall three-dimensional structure.
Synthesis and crystallization
30 ml of an ethanolic solution of KOH (1.68 g, 0.03 mol, 1.0 eq) was mixed with hydrazine hydrate (1.50 g, 0.03 mol, 99%, 1.0 eq) and stirred at 0°C. Carbon disulfide (2.28 g, 0.03 mol, 1.0 eq) followed by 4-fluorobenzyl chloride (4.34 g, 0.03 mol, 1.0 eq) were added to the initial mixture with constant stirring. After 1 h, 40 ml of an ethanolic solution of isatin (4.42 g, 0.03 mol, 1.0 eq) were added and the resulting mixture was heated under reflux for 3 h. A yellow solid product was formed, which was then filtered and dried over silica gel, yielding yellow crystals on recystallization from ethanol solution (yield: 8.1 g, 78%). m.p. 214–215°C; 1H (400 MHz, d6-DMSO) δ: (p.p.m.): 4.51 (s, 2H), 6.90 (d, J = 7.89 Hz, 1H) 7.03 (t, J = 7.21 Hz, 1H), 7.13 (t, J = 17.69 Hz, 2H), 7.36 (td, J = 14.25, 8.19 Hz, 1H), 7.44–7.49 (m, 3H), 11.32 (s, 1H), 13.92 (s, 1H); 19F{1H} (376 MHz, d6-DMSO) δ: (p.p.m): −114.82; HRMS m/z (ESI+), found: [M + H]+ 346.0480, C16H12FN3OS2 requires [M + H]+ 346.0484.
Refinement
Crystal data, data collection and structure . The structure was refined as a two component twin with component 2 rotated by −179.99° around [−0.00 − 0.00 1.00] (reciprocal) or [−0.31 0.02 0.95] (direct), and a refined twin fraction of 0.451 (3).
details are summarized in Table 2
|
Structural data
CCDC reference: 2339543
https://doi.org/10.1107/S2414314624002359/hb4466sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624002359/hb4466Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2414314624002359/hb4466Isup3.cml
C16H12FN3OS2 | Z = 2 |
Mr = 345.41 | F(000) = 356 |
Triclinic, P1 | Dx = 1.480 Mg m−3 |
a = 6.7949 (2) Å | Cu Kα radiation, λ = 1.54184 Å |
b = 6.9491 (2) Å | Cell parameters from 4435 reflections |
c = 16.7080 (8) Å | θ = 6.6–75.3° |
α = 89.525 (3)° | µ = 3.28 mm−1 |
β = 82.547 (3)° | T = 125 K |
γ = 82.347 (3)° | Needle, yellow |
V = 775.25 (5) Å3 | 0.13 × 0.03 × 0.01 mm |
Rigaku XtaLAB P200K diffractometer | 7828 independent reflections |
Radiation source: Rotating Anode, Rigaku MM-007HF | 6291 reflections with I > 2σ(I) |
Rigaku Osmic Confocal Optical System monochromator | Rint = 0.072 |
Detector resolution: 5.8140 pixels mm-1 | θmax = 76.0°, θmin = 2.7° |
shutterless scans | h = −8→8 |
Absorption correction: multi-scan (CrysAlisPro; Rigaku OD, 2023) | k = −8→8 |
Tmin = 0.651, Tmax = 1.000 | l = −20→20 |
21967 measured reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Hydrogen site location: mixed |
R[F2 > 2σ(F2)] = 0.106 | H-atom parameters constrained |
wR(F2) = 0.268 | w = 1/[σ2(Fo2) + (0.020P)2 + 9.4P] where P = (Fo2 + 2Fc2)/3 |
S = 1.00 | (Δ/σ)max < 0.001 |
7828 reflections | Δρmax = 0.89 e Å−3 |
215 parameters | Δρmin = −0.94 e Å−3 |
2 restraints |
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. Refined as a 2-component twin. |
x | y | z | Uiso*/Ueq | ||
S10 | 0.9380 (4) | 0.0909 (4) | 0.82867 (14) | 0.0439 (6) | |
S11 | 0.5880 (4) | 0.2351 (4) | 0.73604 (14) | 0.0429 (6) | |
F15 | 0.2547 (9) | 0.9804 (10) | 0.9766 (3) | 0.0562 (16) | |
O2 | 1.3272 (9) | 0.0761 (10) | 0.5848 (4) | 0.0400 (15) | |
N1 | 1.2988 (12) | 0.1631 (13) | 0.4524 (5) | 0.0385 (18) | |
H1 | 1.430 (7) | 0.105 (13) | 0.430 (5) | 0.046* | |
N3 | 0.8885 (11) | 0.2295 (11) | 0.6073 (5) | 0.0373 (18) | |
N4 | 0.9629 (12) | 0.1679 (13) | 0.6748 (5) | 0.0405 (19) | |
H4 | 1.103 (6) | 0.123 (14) | 0.677 (6) | 0.049* | |
C2 | 1.2330 (14) | 0.1453 (14) | 0.5322 (6) | 0.038 (2) | |
C3 | 1.0120 (13) | 0.2237 (14) | 0.5419 (6) | 0.037 (2) | |
C4 | 0.9678 (15) | 0.2821 (14) | 0.4622 (6) | 0.042 (2) | |
C5 | 0.7917 (16) | 0.3639 (15) | 0.4326 (6) | 0.045 (2) | |
H5 | 0.670188 | 0.393144 | 0.467968 | 0.053* | |
C6 | 0.7985 (17) | 0.4011 (15) | 0.3513 (6) | 0.048 (3) | |
H6 | 0.679127 | 0.452949 | 0.330486 | 0.058* | |
C7 | 0.9757 (17) | 0.3643 (15) | 0.2992 (6) | 0.049 (3) | |
H7 | 0.976563 | 0.392205 | 0.243434 | 0.059* | |
C8 | 1.1512 (17) | 0.2875 (15) | 0.3280 (6) | 0.048 (3) | |
H8 | 1.273295 | 0.263580 | 0.292639 | 0.057* | |
C9 | 1.1449 (15) | 0.2465 (15) | 0.4086 (6) | 0.041 (2) | |
C10 | 0.8446 (14) | 0.1609 (15) | 0.7460 (6) | 0.042 (2) | |
C11 | 0.4666 (14) | 0.2322 (15) | 0.8402 (5) | 0.043 (2) | |
H11A | 0.344241 | 0.168552 | 0.841732 | 0.051* | |
H11B | 0.558102 | 0.154445 | 0.873365 | 0.051* | |
C12 | 0.4107 (14) | 0.4338 (15) | 0.8764 (5) | 0.041 (2) | |
C13 | 0.5556 (15) | 0.5522 (16) | 0.8848 (6) | 0.046 (3) | |
H13 | 0.692085 | 0.506535 | 0.866780 | 0.055* | |
C14 | 0.5052 (16) | 0.7368 (16) | 0.9192 (6) | 0.047 (2) | |
H14 | 0.604631 | 0.817543 | 0.925452 | 0.056* | |
C15 | 0.3072 (16) | 0.7973 (17) | 0.9436 (6) | 0.047 (3) | |
C16 | 0.1582 (15) | 0.6873 (16) | 0.9379 (5) | 0.042 (2) | |
H16 | 0.022436 | 0.734970 | 0.956436 | 0.051* | |
C17 | 0.2117 (15) | 0.5020 (17) | 0.9037 (6) | 0.046 (3) | |
H17 | 0.111006 | 0.421622 | 0.899065 | 0.055* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S10 | 0.0359 (12) | 0.0552 (17) | 0.0425 (12) | −0.0080 (12) | −0.0098 (10) | 0.0027 (11) |
S11 | 0.0303 (11) | 0.0540 (16) | 0.0450 (12) | −0.0058 (11) | −0.0070 (10) | −0.0004 (11) |
F15 | 0.060 (4) | 0.058 (4) | 0.051 (3) | −0.015 (3) | −0.002 (3) | −0.008 (3) |
O2 | 0.032 (3) | 0.047 (4) | 0.042 (3) | −0.003 (3) | −0.009 (3) | −0.002 (3) |
N1 | 0.032 (4) | 0.042 (5) | 0.041 (4) | −0.004 (4) | −0.006 (3) | −0.001 (3) |
N3 | 0.029 (4) | 0.032 (5) | 0.052 (4) | −0.005 (3) | −0.007 (3) | −0.005 (4) |
N4 | 0.039 (5) | 0.043 (5) | 0.043 (4) | −0.014 (4) | −0.007 (3) | 0.000 (4) |
C2 | 0.040 (5) | 0.030 (5) | 0.045 (5) | −0.011 (4) | −0.007 (4) | −0.007 (4) |
C3 | 0.032 (5) | 0.032 (5) | 0.049 (5) | −0.008 (4) | −0.010 (4) | −0.004 (4) |
C4 | 0.045 (6) | 0.032 (5) | 0.054 (5) | −0.017 (5) | −0.016 (4) | −0.001 (4) |
C5 | 0.043 (6) | 0.044 (6) | 0.050 (5) | −0.008 (5) | −0.017 (4) | −0.003 (5) |
C6 | 0.056 (7) | 0.038 (6) | 0.056 (6) | −0.007 (5) | −0.030 (5) | 0.007 (5) |
C7 | 0.072 (8) | 0.037 (6) | 0.043 (5) | −0.009 (5) | −0.021 (5) | 0.003 (4) |
C8 | 0.062 (7) | 0.041 (6) | 0.044 (5) | −0.012 (5) | −0.014 (5) | −0.002 (4) |
C9 | 0.045 (6) | 0.037 (6) | 0.046 (5) | −0.017 (5) | −0.014 (4) | 0.000 (4) |
C10 | 0.033 (5) | 0.043 (6) | 0.051 (5) | −0.007 (4) | −0.007 (4) | −0.009 (4) |
C11 | 0.038 (5) | 0.047 (6) | 0.044 (5) | −0.013 (5) | −0.002 (4) | 0.006 (4) |
C12 | 0.040 (5) | 0.047 (6) | 0.035 (5) | −0.008 (5) | −0.005 (4) | 0.005 (4) |
C13 | 0.032 (5) | 0.050 (7) | 0.057 (6) | −0.005 (5) | −0.008 (4) | 0.006 (5) |
C14 | 0.050 (6) | 0.046 (7) | 0.047 (5) | −0.015 (5) | −0.010 (5) | 0.001 (5) |
C15 | 0.049 (6) | 0.055 (7) | 0.037 (5) | −0.006 (5) | −0.008 (4) | 0.001 (5) |
C16 | 0.041 (5) | 0.051 (7) | 0.034 (5) | −0.005 (5) | −0.001 (4) | 0.000 (4) |
C17 | 0.038 (5) | 0.063 (8) | 0.039 (5) | −0.015 (5) | −0.008 (4) | 0.006 (5) |
S10—C10 | 1.637 (10) | C6—C7 | 1.387 (15) |
S11—C10 | 1.780 (10) | C7—H7 | 0.9500 |
S11—C11 | 1.828 (9) | C7—C8 | 1.383 (14) |
F15—C15 | 1.375 (12) | C8—H8 | 0.9500 |
O2—C2 | 1.213 (11) | C8—C9 | 1.371 (13) |
N1—H1 | 0.96 (3) | C11—H11A | 0.9900 |
N1—C2 | 1.360 (12) | C11—H11B | 0.9900 |
N1—C9 | 1.412 (12) | C11—C12 | 1.512 (14) |
N3—N4 | 1.339 (10) | C12—C13 | 1.386 (13) |
N3—C3 | 1.286 (11) | C12—C17 | 1.391 (13) |
N4—H4 | 0.96 (3) | C13—H13 | 0.9500 |
N4—C10 | 1.351 (12) | C13—C14 | 1.392 (15) |
C2—C3 | 1.516 (13) | C14—H14 | 0.9500 |
C3—C4 | 1.445 (13) | C14—C15 | 1.365 (14) |
C4—C5 | 1.403 (13) | C15—C16 | 1.360 (14) |
C4—C9 | 1.399 (13) | C16—H16 | 0.9500 |
C5—H5 | 0.9500 | C16—C17 | 1.396 (15) |
C5—C6 | 1.376 (13) | C17—H17 | 0.9500 |
C6—H6 | 0.9500 | ||
C10—S11—C11 | 102.7 (5) | C8—C9—N1 | 129.8 (10) |
C2—N1—H1 | 121 (6) | C8—C9—C4 | 122.1 (10) |
C2—N1—C9 | 112.3 (8) | S10—C10—S11 | 126.9 (6) |
C9—N1—H1 | 126 (6) | N4—C10—S10 | 121.4 (7) |
C3—N3—N4 | 117.2 (8) | N4—C10—S11 | 111.6 (7) |
N3—N4—H4 | 124 (6) | S11—C11—H11A | 109.1 |
N3—N4—C10 | 121.9 (8) | S11—C11—H11B | 109.1 |
C10—N4—H4 | 114 (6) | H11A—C11—H11B | 107.9 |
O2—C2—N1 | 128.1 (9) | C12—C11—S11 | 112.4 (7) |
O2—C2—C3 | 126.4 (9) | C12—C11—H11A | 109.1 |
N1—C2—C3 | 105.5 (8) | C12—C11—H11B | 109.1 |
N3—C3—C2 | 126.7 (9) | C13—C12—C11 | 121.1 (9) |
N3—C3—C4 | 127.3 (9) | C13—C12—C17 | 118.7 (10) |
C4—C3—C2 | 105.9 (8) | C17—C12—C11 | 120.2 (9) |
C5—C4—C3 | 132.9 (10) | C12—C13—H13 | 119.3 |
C9—C4—C3 | 108.3 (9) | C12—C13—C14 | 121.3 (10) |
C9—C4—C5 | 118.9 (9) | C14—C13—H13 | 119.3 |
C4—C5—H5 | 120.7 | C13—C14—H14 | 121.3 |
C6—C5—C4 | 118.7 (10) | C15—C14—C13 | 117.4 (10) |
C6—C5—H5 | 120.7 | C15—C14—H14 | 121.3 |
C5—C6—H6 | 119.3 | C14—C15—F15 | 118.1 (9) |
C5—C6—C7 | 121.4 (10) | C16—C15—F15 | 117.8 (9) |
C7—C6—H6 | 119.3 | C16—C15—C14 | 124.2 (11) |
C6—C7—H7 | 119.8 | C15—C16—H16 | 121.2 |
C8—C7—C6 | 120.4 (9) | C15—C16—C17 | 117.7 (10) |
C8—C7—H7 | 119.8 | C17—C16—H16 | 121.2 |
C7—C8—H8 | 120.8 | C12—C17—C16 | 120.8 (10) |
C9—C8—C7 | 118.5 (10) | C12—C17—H17 | 119.6 |
C9—C8—H8 | 120.8 | C16—C17—H17 | 119.6 |
C4—C9—N1 | 108.1 (8) | ||
S11—C11—C12—C13 | −61.5 (11) | C5—C4—C9—N1 | −179.5 (8) |
S11—C11—C12—C17 | 120.0 (8) | C5—C4—C9—C8 | −0.6 (14) |
F15—C15—C16—C17 | 179.4 (8) | C5—C6—C7—C8 | 0.5 (16) |
O2—C2—C3—N3 | −0.1 (15) | C6—C7—C8—C9 | 0.8 (15) |
O2—C2—C3—C4 | −177.7 (9) | C7—C8—C9—N1 | 177.9 (10) |
N1—C2—C3—N3 | 177.8 (9) | C7—C8—C9—C4 | −0.7 (15) |
N1—C2—C3—C4 | 0.3 (10) | C9—N1—C2—O2 | 178.4 (9) |
N3—N4—C10—S10 | −178.3 (7) | C9—N1—C2—C3 | 0.5 (10) |
N3—N4—C10—S11 | 1.7 (12) | C9—C4—C5—C6 | 1.8 (14) |
N3—C3—C4—C5 | 2.4 (17) | C10—S11—C11—C12 | 103.8 (7) |
N3—C3—C4—C9 | −178.4 (9) | C11—S11—C10—S10 | 4.6 (8) |
N4—N3—C3—C2 | 3.1 (13) | C11—S11—C10—N4 | −175.4 (7) |
N4—N3—C3—C4 | −179.9 (9) | C11—C12—C13—C14 | −179.0 (9) |
C2—N1—C9—C4 | −1.1 (11) | C11—C12—C17—C16 | 179.5 (9) |
C2—N1—C9—C8 | −179.9 (10) | C12—C13—C14—C15 | −0.6 (15) |
C2—C3—C4—C5 | 179.9 (10) | C13—C12—C17—C16 | 1.0 (14) |
C2—C3—C4—C9 | −0.9 (10) | C13—C14—C15—F15 | −179.0 (9) |
C3—N3—N4—C10 | −177.4 (9) | C13—C14—C15—C16 | 1.4 (15) |
C3—C4—C5—C6 | −179.1 (10) | C14—C15—C16—C17 | −0.9 (15) |
C3—C4—C9—N1 | 1.2 (10) | C15—C16—C17—C12 | −0.3 (14) |
C3—C4—C9—C8 | −179.9 (9) | C17—C12—C13—C14 | −0.5 (15) |
C4—C5—C6—C7 | −1.8 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.96 (3) | 1.92 (5) | 2.845 (10) | 159 (9) |
N4—H4···O2 | 0.96 (3) | 2.02 (8) | 2.725 (10) | 128 (8) |
C6—H6···S11ii | 0.95 | 2.94 | 3.819 (11) | 154 |
C11—H11A···S10iii | 0.99 | 2.92 | 3.876 (10) | 163 |
C14—H14···F15iv | 0.95 | 2.52 | 3.347 (11) | 145 |
C16—H16···F15v | 0.95 | 2.68 | 3.540 (12) | 150 |
C17—H17···S10iii | 0.95 | 3.03 | 3.908 (11) | 155 |
Symmetry codes: (i) −x+3, −y, −z+1; (ii) −x+1, −y+1, −z+1; (iii) x−1, y, z; (iv) −x+1, −y+2, −z+2; (v) −x, −y+2, −z+2. |
Funding information
The authors acknowledge Universiti Teknologi MARA for financial support.
References
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