Regiospecific substitution of the β-vinylic sp2 carbon of cyclohexenones bearing the α-chloro- and β-tosylate-groups: Single crystal XRD/Hirshfeld surface/in-silico studies of three representative compounds European Journal of Chemistry 11 (4) (2020) 261-275 European Journal of Chemistry ISSN 2153-2249 (Print) / ISSN 2153-2257 (Online) – Copyright © 2020 The Authors – Atlanta Publishing House LLC – Printed in the USA. This work is published and licensed by Atlanta Publishing House LLC – CC BY NC – Some Rights Reserved. http://dx.doi.org/10.5155/eurjchem.11.4.261-275.2020 European Journal of Chemistry View Journal Online View Article Online Regiospecific substitution of the β-vinylic sp2 carbon of cyclohexenones bearing the α-chloro- and β-tosylate-groups: Single crystal XRD/Hirshfeld surface/in-silico studies of three representative compounds Arkalgud Satyanarayana Jeevan Chakravarthy 1,2 and Suresh Hari Prasad 2,* 1 Department of Studies in Chemistry, Jnana Bharathi Campus, Bangalore University, Bengaluru, 560056, India jeechakravarthy@gmail.com (A.S.J.C.) 2 Department of Studies in Chemistry, Central College Campus, Bengaluru City University, Bengaluru, 560001, Karnataka, India hariprasad@bub.ernet.in (S.H.P.) * Corresponding author at: Department of Studies in Chemistry, Central College Campus, Bengaluru City University, Bengaluru, 560001, Karnataka, India. e-mail: hariprasad@bub.ernet.in (S.H. Prasad). 10.5155/eurjchem.11.4.261-275.2020 Received: 11 August 2020 Received in revised form: 14 September 2020 Accepted: 15 September 2020 Published online: 31 December 2020 Printed: 31 December 2020 2-Chloro-3-tosyl-5,5-dimethyl-2-cyclohexenone was subjected to a series of regiospecific Suzuki-Miyaura cross-coupling reactions in suspensions of nine different substituted boronic acids, Pd(OAc)2, P(Ph3)3, K3PO4 and 1,4-dioxane solvent, under sealed tube conditions. The regiospecific substitution of the tosyl-group by the aryl group in preference over the chloride- group was observed. A comparison between the bromo- and tosylate group’s reactivities is highlighted. Using the methodology, the products: 2-chloro-3-aryl-5,5- dimethyl-2-cyclohexenones were isolated in greater than 85% yields. Good quality crystals of three representative compounds were obtained by slow evaporation technique and subjected to single crystal XRD studies, Hirshfeld surface analysis, 3-D energy framework, and molecular docking studies. Crystal data for compound 3; C15H17ClO4S: monoclinic, space group P21/c (no. 14), a = 8.8687(3) Å, b = 10.5537(4) Å, c = 16.6862(7) Å, β = 89.807(3)°, V = 1561.78(10) Å3, Z = 4, T = 290 K, μ(MoKα) = 0.390 mm-1, Dcalc = 1.398 g/cm3, 13623 reflections measured (6.716° ≤ 2Θ ≤ 54.962°), 3570 unique (Rint = 0.0467, Rsigma = 0.0512) which were used in all calculations. The final R1 was 0.0452 (I > 2σ(I)) and wR2 was 0.1019 (all data). Crystal data for compound 5e; C20H18O2FCl: monoclinic, space group P21/c (no. 14), a = 6.4900(5) Å, b = 18.6070(13) Å, c = 14.2146(11) Å, β = 102.324(2)°, V = 1677.0(2) Å3, Z = 4, T = 296(2) K, μ(MoKα) = 0.239 mm-1, Dcalc = 1.309 g/cm3, 25575 reflections measured (6.262° ≤ 2Θ ≤ 52.224°), 3283 unique (Rint = 0.0494, Rsigma = 0.0307) which were used in all calculations. The final R1 was 0.0875 (I > 2σ(I)) and wR2 was 0.2056 (all data). Crystal data for compound 5h; C12H13OSCl: triclinic, space group P-1 (no. 2), a = 6.7517(6) Å, b = 8.8376(9) Å, c = 12.6049(12) Å, α = 109.538(3)°, β = 98.597(3)°, γ = 90.417(3)°, V = 699.52(12) Å3, Z = 2, T = 290 K, μ(MoKα) = 0.410 mm-1, Dcalc = 1.376 g/cm3, 28754 reflections measured (6.114° ≤ 2Θ ≤ 59.288°), 3898 unique (Rint = 0.0544, Rsigma = 0.0349) which were used in all calculations. The final R1 was 0.1101 (I > 2σ(I)) and wR2 was 0.2481 (all data). Vinyl-chloride Single crystal XRD Molecular docking Competing coupling sites Hirshfeld surface analysis Cyclic α,β-unsaturated ketones Cite this: Eur. J. Chem. 2020, 11(4), 261-275 Journal website: www.eurjchem.com 1. Introduction In recent years, the pseudohalides (Organomesylates, nonaflates, tosylates, and triflates) have proved as useful substitutes thereby replacing organic halides in cross-coupling reactions [1,2]. There exists interest among scientists world- wide to study the regiospecific control over multiple competing coupling sites [3]. In particular, organotosylates are emerging as new coupling partners in the Suzuki-Miyaura cross-coupling reactions. They form suitable economical pseudohalide alternatives to halides, due to their high stability and easy handling. Literature reports are available for the coupling of aryl- /alkyl-tosylates with aryl boronic acid [4]. However, no reports exist for the regiospecific substitution of the cyclic vinylic tosylate group preferentially over the vinylic chloride, in α,β- unsaturated cyclicketone systems. Earlier, we had reported the synthesis of some chloro-/aryl- substituted-5,5-dimethyl-2-cyclohexenones from their pre- cursor dihalocyclohexenones. We had found the regiospecific substitution of the bromo-group when subjected to the Suzuki- Miyaura cross-coupling reaction [5]. In further continuation of our investigations of coupling reactions of compounds with differential bond strengths [6,7], we now report for the first instance of time, an alternative method for the synthesis of nine chloro- and aryl-substituted 5,5-dimethyl-2-cyclohexenones: the 2-chloro-3-aryl-5,5-dimet- hyl-2-cyclohexenones (5a-i) from the corresponding tosylate- precursor: 2-chloro-3-tosyl-5,5-dimethyl-2-cyclohexenone (3) in greater than 85% yields (Scheme 1). ABSTRACT RESEARCH ARTICLE KEYWORDS http://dx.doi.org/10.5155/eurjchem.11.4.261-275.2020 http://www.eurjchem.com/ http://dx.doi.org/10.5155/eurjchem.11.4.261-275.2020 mailto:jeechakravarthy@gmail.com mailto:hariprasad@bub.ernet.in mailto:hariprasad@bub.ernet.in http://www.eurjchem.com/ https://crossmark.crossref.org/dialog/?doi=10.5155/eurjchem.11.4.261-275.2020&domain=pdf&date_stamp=2020-12-31 262 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 1. Crystal structure and refinement statistics. Properties / Compound 3 5e 5h CCDC 1875712 1940404 1940405 Empirical formula C15H17ClO4S C20H18ClFO C12H13OSCl Formula weight 328.80 328.79 289.78 Temperature (K) 290 296(2) 290 Crystal system Monoclinic Monoclinic Triclinic Space group P21/c P21/c P-1 a (Å) 8.8687(3) 6.4900(5) 6.7517(6) b (Å) 10.5537(4) 18.6070(13) 8.8376(9) c (Å) 16.6862(7) 14.2146(11) 12.6049(12) α (°) 90 90 109.538(3) β (°) 89.807(3) 102.324(2) 98.597(3) γ (°) 90 90 90.417(3) Volume (Å3) 1561.78(10) 1677.0(2) 699.52(12) Z 4 4 2 ρcalc (g/cm3) 1.398 1.309 1.376 μ (mm-1) 0.390 0.239 0.410 F(000) 688.0 688.0 302.0 Crystal size (mm3) 0.35 × 0.33 × 0.30 0.34 × 0.29 × 0.25 0.39 × 0.35 × 0.30 Radiation MoKα (λ = 0.71073 Å) MoKα (λ = 0.71073 Å) MoKα (λ = 0.71073 Å) 2Θ range for data collection (°) 6.716 to 54.962 6.262 to 52.224 6.114 to 59.288 Index ranges -11 ≤ h ≤ 11 -12 ≤ k ≤ 13 -21 ≤ l ≤ 18 -8 ≤ h ≤ 8 -22 ≤ k ≤ 22 -17 ≤ l ≤ 17 -9 ≤ h ≤ 9 -12 ≤ k ≤ 12 -17 ≤ l ≤ 17 Reflections collected 13623 25575 28754 Independent reflections 3570 [Rint = 0.0467, Rsigma = 0.0512] 3283 [Rint = 0.0494, Rsigma = 0.0307] 3898 [Rint = 0.0544, Rsigma = 0.0349] Data/restraints/parameters 3570/0/193 3283/0/211 3898/0/176 Goodness-of-fit on F2 1.041 1.055 1.060 Final R indexes [I≥2σ (I)] R1 = 0.0452, wR2 = 0.0906 R1 = 0.0875, wR2 = 0.1968 R1 = 0.1101, wR2 = 0.2374 Final R indexes [all data] R1 = 0.0612, wR2 = 0.1019 R1 = 0.1060, wR2 = 0.2056 R1 = 0.1374, wR2 = 0.2481 Largest diff. peak/hole (e Å-3) 0.29/-0.33 0.29/-0.37 0.50/-0.50 Scheme 1. Regiospecific synthesis of 2-chloro-3-aryl-5,5-dimethyl-2-cyclohexenones (5a-i). The newly synthesized compounds were purified by column chromatography and recrystallized using petroleum benzine (60-74 °C). Good quality crystals of three represent- tative compounds which include the substrate tosylate 3 and two products: 2-chloro-3-(3'-fluoro-4'-phenyl)-phenyl-5,5- dimethyl-2-cyclohexenone (5e) and 2-chloro-3-(2'-benzothio phenyl)-5,5-dimethyl-2-cyclohexenone (5h) were obtained by slow evaporation technique and subjected to single crystal X- ray diffraction study. Their evaluation unambiguously confirms the formation of the tosylate and its regiospecific conversion into 2-chloro-3-aryl-5,5-dimethyl-2-cyclohexenones, by ipso- substitution of tosyl group. The Hirshfeld 3-D energy frame- work and in silico docking studies are reported. 2. Experimental 2.1. Materials and characterization All reactions were performed using oven-dried glass apparatus. Analytical Reagent grade solvents were purchased from SD Fine Chemicals Limited and Merck; Bangalore and used without further purification. The progress of the reactions was periodically monitored by Thin Layer Chromatography analysis of aliquots (Merck 60F254 precoated silica plates) at a regular interval of time. The purification of the crude compounds was done by column chromatography using silica gel (Merck, 60- 120 mesh) as the stationary phase and 2:8 ethyl acetate and petroleum benzine (60-74 °C) as the mobile phase. IR spectra of the compounds were recorded using Bruker ALPHA-P instru- ment. GC-MS were recorded on Agilent instrument equipped with Ascentis Express C18 (50 mm × 2.1 mm × 2.7 µm) column. 1H NMR and 13C NMR of the novel compounds were obtained on Bruker AC 400 spectrometer using CDCl3 as solvent and tetra- methylsilane as internal standard. Chemical shifts are reported in δ (ppm downfield) with reference to tetramethyl silane. Elemental analyses were carried out with a VarioMicro Cube V1.9.7 CHNS mode elemental analyzer. Melting point of the compounds isolated as solids was recorded using VEEGO melting point apparatus model: VMP-DS and remain uncorrected. Single-crystal X-ray diffraction (XRD) data were collected at 290 K on Bruker Apex II diffractometer. The complete intensity data set was processed using SAINT software [8]. Direct method was employed to solve the structure of the compounds using SHELXS program, followed by refinement by full matrix least squares based on F2 using SHELXL [9]. All non-hydrogen atoms were refined anisotropically, while hydrogen atoms were fixed at chemically allowed positions. After several cycles of refinement, the structures of molecules 3, 5e and 5h were finally reduced to the Goodness-of-Fit to 1.04, 1.055, and 1.06, respectively (Table 1). All geometrical data were calculated using PLATON [10], ORTEP and packing diagrams were generated using MERCURY [11]. The bond length and bond angle values are summarized in Tables 2 and 3, which are in agreement with reported structures [12,13]. The Hirshfeld surfaces were mapped on dnorm and electrostatic potential using a STO-3G basis set at the Hartree-Fock (HF) level of theory. The associated two-dimensional fingerprint plots were used to calculate the percentage contribution of various interatomic contacts towards the formation of three-dimensional Hirshfeld surface, using CrystalExplorer 17.5 software [14-16]. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 263 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 2. Bond lengths of compounds 3, 5e and 5h (AÅ ). Compound 3 Compound 5e Compound 5h Atoms Distance Atoms Distance Atoms Distance S1-O3 1.4240 (16) Cl1-C6 1.733 (5) C6-C1 1.341 (3) S1-O4 1.4248 (16) F1-C13 1.363 (5) C6-C5 1.497 (4) S1-O1 1.6152 (14) C5-C6 1.340 (6) C16-C11 1.393 (3) S1-C9 1.749 (2) C5-C9 1.479 (6) C2-C3 1.517 (3) Cl1-C5 1.724 (2) C5-C4 1.507 (6) C2-C1 1.520 (3) O1-C6 1.401 (2) C13-C14 1.380 (6) C3-C4 1.531 (4) O2-C4 1.213 (2) C13-C12 1.390 (6) C3-C7 1.527 (4) C1-C6 1.495 (3) C12-C11 1.392 (6) S1-C16 1.729 (2) C1-C2 1.535 (3) C2-C3 1.521 (7) S1-C9 1.742 (2) C2-C8 1.530 (3) C20-C19 1.380 (8) Cl1-C6 1.734 (2) C2-C3 1.532 (3) C7-C3 1.537 (7) C10-C9 1.375 (3) C3-C4 1.502 (3) C12-C15 1.489 (6) C10-C11 1.425 (3) C4-C5 1.485 (3) C6-C1 1.484 (7) C3-C8 1.511 (4) C2-C7 1.537 (3) C14-C9 1.396 (6) C5-O1 1.222 (3) C5-C6 1.334 (3) C10-C11 1.380 (7) C5-C4 1.491 (4) C9-C14 1.377 (3) C10-C9 1.392 (6) C9-C1 1.465 (3) C9-C10 1.383 (3) C1-O1 1.208 (6) C6-C1 1.341 (3) C10-C11 1.381 (3) C1-C2 1.498 (7) C6-C5 1.497 (4) C11-C12 1.383 (3) C15-C16 1.374 (7) C2-C3 1.517 (3) C12-C13 1.386 (3) C15-C20 1.410 (7) C2-C1 1.520 (3) C12-C15 1.503 (3) C3-C8 1.531 (7) C3-C4 1.531 (4) C13-C14 1.386 (3) C4-C3 1.517 (6) C3-C7 1.527 (4) Table 3. Bond angles of compounds 3, 5e and 5h (°). Compound 3 Compound 5e Compound 5h Atoms Angle Atoms Angle Atoms Angle O3-S1-O4 120.14 (10) C6-C5-C9 125.1 (4) C16-S1-C9 91.94 (11) O3-S1-O1 109.55 (9) C6-C5-C4 120.0 (4) C9-C10-C11 113.5 (2) O4-S1-O1 102.02 (9) C9-C5-C4 114.9 (4) C13-C14-C15 121.5 (2) O3-S1-C9 109.77 (10) F1-C13-C14 116.9 (4) C5-C4-C3 112.27 (19) O4-S1-C9 110.19 (10) F1-C13-C12 119.0 (4) C10-C9-C1 123.9 (2) O1-S1-C9 103.69 (9) C14-C13-C12 124.1 (4) C10-C9-S1 110.99 (16) C6-O1-S1 121.56 (12) C13-C12-C11 115.0 (4) C1-C9-S1 125.07 (17) C6-C1-C2 112.63 (16) C13-C12-C15 125.2 (4) C1-C6-C5 123.7 (2) C8-C2-C3 109.54 (17) C11-C12-C15 119.8 (4) C1-C6-Cl1 122.68 (19) C8-C2-C1 109.25 (17) C5-C6-C1 123.3 (4) C5-C6-Cl1 113.61 (18) C3-C2-C1 107.80 (17) C5-C6-Cl1 122.3 (4) C11-C16-C15 121.0 (2) C8-C2-C7 108.81 (18) C1-C6-Cl1 114.4 (4) C11-C16-S1 111.57 (16) C3-C2-C7 110.46 (17) C13-C14-C9 119.5 (4) C15-C16-S1 127.41 (19) C1-C2-C7 110.96 (17) C19-C20-C15 119.4 (5) C3-C2-C1 116.16 (19) C4-C3-C2 112.57 (17) C11-C10-C9 121.0 (4) C16-C11-C12 120.1 (2) O2-C4-C5 121.8 (2) O1-C1-C6 122.0 (5) C16-C11-C10 112.0 (2) O2-C4-C3 123.39 (19) O1-C1-C2 122.6 (5) C12-C11-C10 127.9 (2) C5-C4-C3 114.83 (18) C6-C1-C2 115.4 (4) C2-C3-C4 107.5 (2) C6-C5-C4 121.3 (2) C16-C15-C20 118.4 (5) C2-C3-C7 111.53 (19) C6-C5-Cl1 122.03 (17) C16-C15-C12 119.9 (5) C4-C3-C7 110.1 (2) C4-C5-Cl1 116.66 (15) C20-C15-C12 121.7 (4) C2-C3-C8 108.4 (2) C5-C6-O1 117.68 (19) C10-C9-C14 117.8 (4) C4-C3-C8 110.0 (2) C5-C6-C1 123.88 (19) C10-C9-C5 120.2 (4) C7-C3-C8 109.4 (2) O1-C6-C1 118.12 (17) C14-C9-C5 122.0 (4) O1-C5-C4 122.9 (2) C14-C9-C10 121.6 (2) C5-C4-C3 115.2 (4) O1-C5-C6 120.6 (2) C14-C9-S1 118.81 (17) C1-C2-C3 113.4 (4) C4-C5-C6 116.5 (2) C10-C9-S1 119.57 (17) C2-C3-C4 108.2 (4) C6-C1-C9 127.4 (2) C11-C10-C9 118.3 (2) C2-C3-C8 109.6 (4) C16-C15-C14 118.8 (2) C11-C12-C15 120.4 (2) C4-C3-C8 109.6 (4) C14-C13-C12 121.1 (2) C13-C12-C15 120.9 (2) C2-C3-C7 109.0 (4) C6-C1-C2 117.7 (2) C14-C13-C12 120.8 (2) C4-C3-C7 111.4 (4) C9-C1-C2 114.95 (18) C9-C14-C13 119.0 (2) C8-C3-C7 109.1 (5) C13-C12-C11 117.5 (2) The interaction energies in a molecule, resulting in the formation of three-dimensional architecture of a crystal, were calculated using CrystalExplorer17.5 software [17,18]. The software was also used to calculate interaction energies in the representative crystals of compounds 3, 5e and 5h. Crystallographic structure of 121p (H-ras) protein with a resolution of 1.54 Å was obtained from protein data bank (PDB). The heteroatom and ligand data were removed from the protein pdb file and used for further docking studies. The novel molecules 5e and 5h were taken as ligands. Ligand and protein molecules were converted into pdbqt format in PyRx 0.8 docking tool, with a built-in Vina wizard [19]. The protein and ligand were docked with a grid box size of 42.1, 39.87, 43.82 Å and grid centre 5.86, 25.15 and 11.93 Å. The atomic interactions and electrostatic maps of the ligands were calculated using the autogrid module. Out of several possible interactions, the complex with lowest binding energy was considered for ligand- protein docking studies. Molecular graphics laboratory (MGL) tools were used to analyze the results from Vina Wizard and the best conformation with lowest binding energy was exported for 2D plot generation using Ligplot+ [20]. The docking confor- mation of the best complex was represented using PyMOL [5]. 2.2. Synthesis and analytical data 2.2.1. Synthesis of 2-chloro-3-tosyl-5,5-dimethyl-2- cyclohexenone (3) To a solution of 2-chloro-5,5-dimethyl-1,3-cyclohexane- dione (2, 11.49 mmole) and triethylamine (2.32 g, 22.988 mmole) in 30 mL THF, stirred at room temperature, was added p-toluenesulfonylchloride (p-TsCl, 2.5 g, 13.157 mmole) over a period of 1 hour. After completion of addition, the reaction mixture was heated to reflux and the progress of the reaction 264 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 was periodically monitored by TLC analysis of small aliquots at regular intervals of time. After the complete conversion was indicated by disappearance of starting material on TLC, the reaction mixture was diluted with water and extracted with ethylacetate (3 × 20 mL).The organic layer was separated, washed with water (3 × 20 mL), brine solution (3 × 20 mL) and purified by column chromatography using 2:8 ethyl acetate: petroleum benzine (60-74 °C) as mobile phase and silica gel (100-200 mesh) as stationary phase to isolate 3.6 g of 2-chloro- 3-tosyl-5,5-dimethyl-2-cyclohexenone (3) (Scheme 1). 2-Chloro-3-tosyl-5,5-dimethyl-2-cyclohexenone (3): Color: White. Yield: 96%. M.p.: 196-198 °C. FT-IR (KBr, ν, cm-1): 2959, 2931, 2877, 1698, 1613, 1369, 1341, 1266, 1177, 1141, 1089, 1018, 988, 947, 915, 809, 737, 668, 637, 597, 565, 547. 1H NMR (400 MHz, CDCl3, δ, ppm): 1.12 (s, 6H, 2CH3), 2.44 (s, 2H, CH2- C=C), 2.51 (s, 3H, Ar-CH3), 2.83 (s, 2H, CH2-CO), 7.38 (d, 2H, J = 8 Hz, Ar), 7.88 (d, 2H, J = 8 Hz, Ar). 13C NMR (100 MHz, CDCl3, δ, ppm): 21.7 (2CH3), 27.8 (CCH3), 27.9 (ArCH3), 32.7 (CH2-C=C), 51.0 (CH2-CO), 122.1 (Ar), 128.3 (Ar), 130.0 (Ar), 132.9 (Ar), 146.3 (C-O), 160.6 (CCl), 191.2 (CO). MS (EI, m/z (%)): 329 (M+, 100). Anal. calcd. for C15H17ClO4S: C, 54.79; H, 5.21; S, 9.75. Found: C, 54.68; H, 5.18; S, 9.72%. CCDC number: 1875712. 2-Chloro-3-(3'-fluoro-4'-phenyl)-phenyl-5, 5-dimethyl-2-cyclo hexenone (5e): Color: White. Yield: 94%. M.p.: 82-84 °C. FT-IR (KBr, ν, cm-1): 2962, 2925, 2870, 1677, 1613, 1554, 1482, 1402, 1343, 1306, 1242, 1129, 998, 966, 839, 771, 722, 701, 647, 578, 559, 481, 455. 1H NMR (400 MHz, CDCl3, δ, ppm): 1.19 (s, 6H, 2CH3), 2.49 (s, 2H, CH2-C=C), 2.82 (s, 2H, CH2-CO), 7.01 (d, 2H, J = 7.6 Hz, Ar-H), 7.38 (d, 1H, J = 7.2 Hz, Ar-H), 7.42-7.46 (m, 3H, Ar-H), 7.58 (d, 2H, J = 7.6 Hz, Ar-H). 13C NMR (100 MHz, CDCl3, δ, ppm): 28.0 (CH3), 33.3 (C), 49.1 (CH2-C=C), 51.2 (CH2-CO), 117.6 (Ar), 117.9 (Ar), 125.9 (Ar), 127.7 (Ar), 128.4 (Ar), 128.6 (Ar), 129.1 (Ar), 130.3 (Ar), 134.4 (Ar), 134.5 (Ar), 135.6 (Ar), 136.5 (C-O), 153.2 (CCl), 195.3 (CO). MS (EI, m/z (%)): 329 (M+, 100). Anal. calcd. for C20H18ClFO: C, 73.06; H, 5.52. Found: C, 72.96; H, 5.41%. CCDC number: 1940404. 2-Chloro-3-(2’-benzothiophenyl)-5, 5-dimethyl-2-cyclohexenone (5h): Color: White solid. Yield: 91%. M.p.: 101-103 °C. FT-IR (KBr, ν, cm-1): 3015, 2961, 2929, 1679, 1412, 1344, 1271, 1215, 1155, 1115, 854, 833, 743, 666, 587, 508, 430. 1H NMR (400 MHz, CDCl3, δ, ppm): 1.18 (s, 6H, 2CH3), 2.51 (s, 2H, CH2-C=C), 2.85 (s, 2H, CH2-CO), 7.33-7.34 (m, 3H, Ar-H), 7.77-7.81 (m, 2H, Ar-H). 13C NMR (100 MHz, CDCl3, δ, ppm): 28.1 (CH3), 33.2 (CH3), 49.7 (C), 51.2 (CH2-C=C), 53.4 (CH2-CO), 122.0 (Ar), 123.9 (Ar), 124.1 (Ar), 124.5 (Ar), 126.3 (Ar), 131.5 (Ar), 133.5 (Ar), 139.1 (C-O), 154.8 (CCl), 194.7 (CO). MS (EI, m/z (%)): 291 (M+, 100). Anal. calcd. for C16H15ClOS: C, 66.08; H, 5.20; S, 11.03%. Found: C, 65.87; H, 5.13; S, 10.89%. CCDC number: 1940405. 2.2.2. General procedure for the preparation of 2-chloro-3- aryl-5,5-dimethyl-2-cyclohexenones (5a-i) A suspension of 2-chloro-3-tosyl-5,5-dimethyl-2-cyclo- hexenone (3, 0.5 g, 2.11 mmole), aryl boronic acid (4a-i, 1.1 mmolar equivalent), Pd(OAc)2 catalyst (10 mg, 0.044 mmoles, 0.21 mol%), PPh3(50 mg, 0.19 mmoles) and K3PO4 (0.87 g, 4.09 mmoles) in 5 mL of 1,4-dioxanewere taken in a 15 mL Sigma- Aldrich Ace pressure tube along with a magnetic pellet, purged with N2 gas and sealed. The pressure tube was introduced into a preheated oil bath at 110 °C and magnetically stirred for a period of 4-8 hours. After complete conversion of reactants as indicated by TLC analysis, the reaction was allowed to attain ambient temperature, transferred to a beaker, and diluted with ethyl acetate (20 mL). The extract was filtered over a bed of Celite® and washed with ethyl acetate (20 mL). The combined filtrate was concentrated on a rotary evaporator and the crude product was purified by column chromatography using silica gel (Merck, 60-120 mesh) as the stationary phase and ethyl acetate: petroleum benzine (60-74 °C) in the ratio 2:8 as mobile phase to isolate the compounds 2-chloro-3-aryl-5,5-dimethyl- 2-cyclohexenones 5a-i in greater than 80% yield (Scheme 1). 3. Results and discussions 5,5-Dimethyl-1,3-cyclohexanedione (1) was sequentially converted to 2-chloro-5,5-dimethyl-2,3-cyclohexanedione (2) by reaction with N-chlorosuccinimide (NCS) in CHCl3 [5]. Compound 2 on heating with p-toluenesulfonylchloride (p- TsCl) with triethylamine (TEA) in THF furnished the novel organotosylate:2-chloro-3-tosyl-5, 5-dimethyl-2-cyclohexene one (3). The compound 3 is a suitable substrate for Suzuki-Miyaura cross-coupling reaction, with two possible reaction sites: the carbon bearing the chlorine and the carbon bearing the tosyl- group. Hence, as trial reaction 3 was subjected to Suzuki- Miyaura cross-coupling reaction with 2-methoxyphenyl boronic acid (4a), using different palladium catalysts: Pd(PPh3)4, Pd(OAc)2 and Pd(dppf)2Cl2, in the presence of differing bases: K2CO3/Na2CO3 and K3PO4 in DMF/1,4- dioxane/THF solvents.Out of several catalytic systems used, the best results with respect to reaction duration and isolated yields of mono-arylated product 2-chloro-3-(2’-methoxy) phenyl-5,5-dimethyl-2-cyclohexenone (5a) was obtained by employing Pd(OAc)2 (44 µmole), PPh3 (0.19 mmole), K3PO4 (4.09 mmole) in 5 mL 1,4-dioxane solvent at 110 °C under nitrogen atmosphere. The reaction conditions were further optimized and eight different aryl boronic acids (4b-i) were reacted with compound 3 under the same reaction conditions to obtain compounds 5b-i in greater than 85% isolated yields. Each reaction was carried for a minimum of three trails and the optimized yields and reaction durations are given in Table 4. Formation of products 5a-i confirms the regiospecific nature of the reaction due to differential carbon-chlorine and carbon- tosyl bond strengths. 3.1. Mechanism In general, α,β-unsaturated ketones are well recognized to be polarized with the separation of a discrete negative charge on the oxygen and corresponding positive charge on the β- vinylic carbon. In the reactant molecule 3, this renders the carbon-tosylate bond to cleave easily, rendering the tosylate group to become a good leaving group [21]. Further, the present study, in comparison to our earlier report [5] clearly indicates that between the bromo and the tosylate substituents, the reactivity of the tosylate group is slightly lesser when compared to the bromo substituent. The tosylate group, under the conditions employed by us takes a rather longer duration of time for completion of the reaction in comparison to the bromo- analogue, indicating that even though the tosyl group is a good leaving group, it has reactivity lesser than the bromo-group in terms of leaving group capacity. These results are in good concordance with the recent findings of other scientists. Therefore, all these studies indicate that the reactivity of leaving groups is bromo > triflate > tosylate > chloro [22]. The rest of the reaction mechanistic cycle for our reactions, we postulate that to traverse through accepted routes reported by other scientists for the Suzuki-Miyaura cross-coupling reaction [3,5,23]. 3.2. Crystal and molecular structure description Good quality crystals of three representative compounds: 2-chloro-3-tosyl-5,5-dimethyl-2-cyclohexenone (3), 2-chloro- 3-(3'-fluoro-4’-phenyl)-phenyl-5,5-dimethyl-2-cyclohexenone (5e) and 2-chloro-3-(2’-benzothiophenyl)-5, 5-dimethyl-2- cyclohexenone (5h) were obtained by slow evaporation method in AR grade petroleum benzene solvent and subjected to single-crystal XRD studies. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 265 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 4. 2-Chloro-3-aryl-5,5-dimethyl-2-cyclohexenones (5a-i). Entry Boronic acids 2-Chloro-3-aryl-5,5-dimethyl-2-cyclohexenones (Reaction duration and % yields) 1 B(OH)2 O 4a O Cl O 5a (4 hrs, 89%) 2 F B(OH)2 4b O Cl 5b (5 hrs, 90%) 3 F O B(OH)2 4c O Cl O F 5c (4 hrs, 87%) 4 F B(OH)2 4d O Cl F 5d (6 hrs, 88%) 5 B(OH)2 F C6H5 4e O Cl F 5e (7 hrs, 91%) 6 B(OH)2 4f O Cl 5f (4 hrs, 89%) 7 B(OH)2 S 4g O Cl S 5g (8 hrs, 86%) 8 B(OH)2 S 4h O Cl S 5h (6 hrs, 87%) 9 B(OH)2 4i O Cl 5i (5 hrs, 85%) The compounds 2-chloro-3-tosyl-5, 5-dimethyl-2-cyclo hexenone (3) and 2-chloro-3-(3'-fluoro-4'-phenyl)-phenyl-5,5- dimethyl-2-cyclohexenone (5e) crystallize in monoclinic system (P21/c). However, 2-chloro-3-(2'-benzothiophenyl)- 5,5-dimethyl-2-cyclohexenone (5h) crystallizes in triclinic system (P-1). The molecular view of compounds 3, 5e and 5h are given in Figure 1. The crystal structure and refinement details for the compounds 3, 5e and 5h are summarized in Table 1. In compound 3, the Cg1 [ring centroid of C1/C6] is puckered at C2 and exhibits nearly an envelope conformation of the type E2, with puckering amplitude Q = 0.490 Å, pseudo- rotation angle θ = 53.1(2)° and the relative phase angle φ = 78.8(3)°. In molecule 5e, the Cg1 phenyl ring is puckered at C3 displaying nearly an envelope conformation of the type 1E with total puckering amplitude Q = 0.462(6) Å, pseudo-rotation angle θ = 52.3(6)° and the relative phase angle φ = 105.5(9)°. However, in compound 5h, the Cg2 [ring centroid of C1/C6] is puckered at C3 and adopts half-chair conformation with the total puckering amplitude of Q = 0.473(3) Å, pseudo-rotation angle θ = 50.3(4)° and the relative phase angle of φ = 131.2(4)° [24, 25]. The puckering amplitudes are in agreement with the cyclohexenone ring of the compound C14H15ClO and C15H17ClO2 [26,27]. In compound 3, the Cg1 and Cg2 [ring centroid of C9/C14] planes are inclined to each other about the central -SO3 group with the dihedral angle of 62.38(9)°. The S1 atom in the central part of the structure exhibits distorted trigonal geometry, confirmed by the bond angle values of O4-S1-O3=120.14°, O3- S1-O1=109.54° and O4-S1-O1=102.02°. In molecule 5e, the Cg1 plane makes a dihedral angle of 57.82° and 24.03° with Cg2 [ring centroid of C9/C14] and Cg3 [ring centroid of C15/C20] planes, respectively. 266 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 5. Hydrogen bonding geometry (Å, °). Compound D-H···A D-H H···A D···A ∠ D-H···A Symmetry code 3 C10-H10···O4 0.93 2.58 3.433 154 1-x, -1/2+y, 1/2-z C11-H11···O2 0.93 2.58 3.371 143 -1+x, y, z C3-H3A···O1 0.93 2.62 3.437 143 2-x, 1/2+y, 1/2-z 5e C11-H11···Cl1# 0.93 2.84 3.634 144 1-x,1-y,1-z C20-H20···F1* 0.93 2.47 2.928 111 5h C8-H8A···O1 0.93 2.72 3.606 165 -1+x, y, z # Weak intermolecular interaction. * Intramolecular interaction. Compound 3 Compound 5e Compound 5h Figure 1. Labeled ORTEP drawn at 50% of probability for the molecules 3, 5e, and 5h. The plane of central fluorophenyl ring Cg2 makes the dihedral angle of 35.09° with Cg3 plane, indicating more twist between the planes of Cg1 and Cg2, due to electrostatic repulsion of hydrogen atoms on the ring systems. In molecule 5h, the Cg2 plane makes a dihedral angle of 22.90° with Cg4 [ring centroid of S1-C9/C16]. The packing diagrams for molecules 3, 5e, and 5h are depicted in Figure 2. The crystal structure of compound 3 is stabilized by intermolecular hydrogen bonding interactions of the type C3-H3A···O1, C10-H10···O4 and C11-H11...O2 connec- ting the molecules in the form of one-dimensional polymeric chains propagating infinitely along crystallographic b-axis (i), while these interactions generates the layer stacking appearance along crystallographic a-axis (ii).In the crystal structure of molecule 5e, the packing of molecules was established by a weak intermolecular interaction of the type C11-H11···Cl1 incorporating a graph set of R22(14) ring motif. Besides this, there is an intramolecular interaction between C20-H20···F1 (Table 5) incorporating an S(6) closed ring motif. In molecule 5h, the molecules are linked in the form of head-to- tail pattern through weak intermolecular interactions of the type C8-H8A···O1 to form one-dimensional independent polymeric chains propagating infinitely along crystallographic b-axis. The hydrogen bonding and interactions present in molecules 3, 5e, and 5h are given in Table 5. 3.3. Hirshfeld surfaces and two-dimensional fingerprint calculations The three-dimensional Hirshfeld surfaces were mapped on dnorm and electrostatic potential for the compounds 3, 5e and 5h, with the following area and volume: 335.11, 357.45, 304.41 Å2 and 383.93, 412.37, 343.47 Å3, respectively. The Hirshfeld surfaces for all the compounds were obtained in transparent mode to visualize atoms and functional groups involved in the molecular structures, as shown in Figure 3. The intermolecular interactions (Table 5) involved in the crystal packing of the compounds 3, 5e, and 5h were investigated. In the given orientations of Hirshfeld surfaces mapped on dnorm the reader can notice the donor parts of intermolecular interactions listed in Table 5. The bright red coloured circular spots labelled as 1, 2 and 3 on dnorm of compound 3 reveals the donor parts of intermolecular C10-H10···O4, C11-H11···O2 and C3-H3A···O1 interactions respectively. Fortunately, on the posture of dnorm surface of compound 5e, both, the donor and acceptor regions of weak intermolecular C11-H11···Cl1 interaction are seen at the bright red colored regions labelled as 1 and 2 respectively. Whereas, only the donor part (labelled as 1) of intermolecular C8-H8A···O1 interaction is visualized on the dnorm of compound 5h. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 267 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 (i) (ii) (a) (b) (c) Figure 2. (a) Packing of molecules in compound 3 (i) and (ii) viewed along b and a axes. The cyan-colored dotted lines are hydrogen bonding interactions. (b) Packing of molecules in compound 5e viewed along a axis. The cyan-colored dashed lines indicate intermolecular C11-H11···Cl1 and intra-molecular C20- H20···F1 interactions. (c) Packing of molecules in compound 5h viewed along the b axis. The cyan colored dashed lines indicate intermolecular C8-H8A···O1 interactions. Further, in the same way, the similar donor and acceptor regions of intermolecular interactions incurred in the crystal packing of the compounds 3, 5e and 5h are recognized as blue and red colored patches on the Hirshfeld surfaces mapped on electrostatic potentials. The presence of other blue and red colored patches on it demonstrates the positions of electro positive and negative elements of the molecules [28]. The two-dimensional fingerprint plots for molecules 3, 5e and 5h are given in Figure 4. The results of the compound 3 showed the inter-contacts H···O, H···H, H···C, and H···Cl have the following contribution 36.3, 33.9, 14.3 and 13.4%, respectively. This indicate, in compound 3, the H···O pairs of contacts have been recorded as the predominant contribution towards the formation of a three-dimensional Hirshfeld surface, which agrees with C-H···O interactions. In the compound 5e, the H...H, H...C, H···O, H···Cl and H···F inter contacts have contributed 42.4%, 22.6%, 10.5%, 10.3% and 9.3% respectively. The contribution of H···C and H···Cl to the Hirshfeld surface in compound 5e reflects the presence of weak intermolecular C11-H11···Cl1 interaction. Whereas, in compound 5h, the inter- contacts H···H, H···C, H···Cl, H···O and H...S have contributed 41.7, 14.5, 14.4, 11.8 and 9.7%, respectively, further the H···C and H···O contributions due to the presence of intermolecular C8-H8A···O1 interaction. In the compounds 5e and 5h the H···H pair of contacts is the major contribution. 3.4. Three-dimensional interaction energies The crystal packing with stabilized interactions is visualized and analysed using qualitative energy framework analysis. In this method, we calculated the interaction energy between the various molecular pairs and generated a three- dimensional topology of the dominant interactions in molecular crystal packing of the compounds 3, 5e and 5h. The total interaction energies of the compounds 3, 5e and 5h were resolved into Eele, Edis, Epol, and Erep components. 268 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Molecular orientation Hirshfeld surface mapped on dnorm Electrostatic potentials Compound 3 Compound 5e Compound 5h Figure 3. The Hirshfeld surfaces mapped on dnorm and electrostatic potentials for molecules 3, 5e, and 5h compounds. The bright red color spots on dnorm of each molecule indicates intermolecular interactions. The red and blue regions on electrostatic potentials represent the corresponding electrostatic negative acceptor and positive donor potentials involved in intermolecular interactions. Full contribution H-O 36.3% H-H 33.9% H-Cl 14.3% H-C 13.4% Compound 3 Full contribution H-H 42.4% H-C 22.6% H-O10.5% H-Cl10.3% H-F9.3% Compound 5e Full contribution H-H 41.7% H-C 14.5% H-Cl 14.4% H-O 11.8% H-S 9.7% Compound 5h Figure 4. The fingerprint plots compound 3, compound 5e, and compound 5h compounds. The grey-coloured pattern indicates the outline of the full fingerprint. The de and di along y and x axes are the closest nuclei external and internal to the three-dimensional Hirshfeld surface [29]. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 269 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 6. Interaction energies (kJ/mol), R is the distance between molecular centroids (mean atomic position) in AÅ . Total energies, only reported for two benchmarked energy models, are the sum of the four energy components, scaled appropriately (see the scale factor table below) for compound 3. Color code N Symmetry R Electron density Eele Epol Edis Erep Etot 1 -x, -y, -z 14.43 B3LYP/6-31G(d,p) 1.9 -0.2 -1.3 0.0 0.7 1 -x, -y, -z 8.20 B3LYP/6-31G(d,p) -10.9 -4.3 -46.6 32.1 -35.5 2 x, y, z 8.87 B3LYP/6-31G(d,p) -7.8 -2.4 -14.2 9.2 -16.7 2 -x, y+1/2, -z+1/2 6.77 B3LYP/6-31G(d,p) -11.1 -4.7 -34.0 23.8 -30.1 1 -x, -y, -z 12.87 B3LYP/6-31G(d,p) 0.9 -0.3 -7.2 1.9 -4.4 2 -x, y+1/2, -z+1/2 7.93 B3LYP/6-31G(d,p) -13.2 -4.8 -31.7 22.3 -31.4 2 x, -y+1/2, z+1/2 8.38 B3LYP/6-31G(d,p) -8.4 -2.5 -24.0 17.7 -20.7 1 -x, -y, -z 9.17 B3LYP/6-31G(d,p) -12.0 -2.6 -12.3 5.2 -22.1 2 x, -y+1/2, z+1/2 12.22 B3LYP/6-31G(d,p) -0.3 -0.3 -6.2 1.3 -5.2 Energy Model (30) kele kpol kdisp krep CE-HF ... HF/3-21G electron densities 1.019 0.651 0.901 0.811 CE-B3LYP ... B3LYP/6-31G(d,p) electron densities 1.057 0.740 0.871 0.618 Figure 5. The color-coding pattern of molecules surrounding the original molecule in a cluster of molecule 3 within the default radius of 3.8 Å, when it is viewed along crystallographic a, b and c axes. The color-coding scheme and their interaction energies in component form is given in Table 6. The three-dimensional interaction energy profiles of Coloumbic dispersion and total energy components were constructed for the title compounds using default red, green, and blue-colored tubes. The variation of thickness of solid cylinders mapping the molecules in each energy frame works to indicate the relative strength of interaction between the molecules, which are also confirmed by their noticeable higher negative energy values are given in Tables 6-8 and energy values are given in Figures 5, 6 and 7. In each profile of the title compounds 3, 5e and 5h, the tube size was maintained as 150 with 10kJ/mol cut-off energy values to avoid mapping of weak interactions and for clarity purpose they are depicted in Figure 8-10. In the cluster of 3 molecules, the maximum total interaction energy was Etot = -35.5 kJ/mol [Eele = -10. 9 kJ/mol; Epol = -4.3 kJ/mol; Edis = -46.69 kJ/mol and Erep = 32.1 kJ/mol] with the molecule interacting at the molecular centroid distance of R = 8.20 Å. The other higher total interaction energy Etot = -31.4 was observed for the molecules interacting at R = 7.93 Å [Eele = -13.2 kJ/mol; Epol = -4.8 kJ/mol; Edis = -31.7 kJ/mol and Erep = 22.3 kJ/mol]. The stabilization of 5e molecules, in which the highest total interaction energy Etot = -53.8 kJ/mol [Eele = -18.7 kJ/mol; Epol = -4.6 kJ/mol; Edis = -59.4 kJ/mol and Erep = 34.0 kJ/mol] was observed for the molecule interacting at R = 4.68 Å. The least total interaction energy Etot = -2.3 kJ/mol [Eele = -0.7 kJ/mol; Epol = -0.1 kJ/mol; Edis = -3.6 kJ/mol and Erep = 0.3 kJ/mol] in the cluster was found with the two molecules interacting at R = 14.31 Å. In the cluster of 5h molecules, the maximum total interaction energy was Etot = -27.5 kJ/mol [Eele=-2.9kJ/mol; Epol = -1.4 kJ/mol; Edis = -42.0 kJ/mol and Erep = 21.4 kJ/mol] interacting at R = 7.74 Å and it is observed as least Etot = -3.1 kJ/mol [Eele = 0.7 kJ/mol; Epol = -0.3 kJ/mol; Edis = -7.0 kJ/mol and Erep = 4.0 kJ/mol] with the molecule interacting at R = 14.68 Å. The above results show that the molecules with lesser distance have relatively strong interaction energy and vice versa, which also holds good with the laws of electrostatics. Further the interaction energy profile of each compound, in which the dispersion energies frame works dominates over the classical electrostatic energy frame works. 3.5. Molecular docking analysis One of the most vigorous ways to tackle cancer is chemotherapy. In order to treat cancer cells different approaches are employed. Newer drugs are being developed with main focus on targeted therapy. One of the important approaches is the in silico molecular docking studies. 270 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 7. Interaction energies (kJ/mol), R is the distance between molecular centroids (mean atomic position) in Å. Total energies, only reported for two benchmarked energy models, are the sum of the four energy components, scaled appropriately (see the scale factor table below) for compound 5e. Color code N Symmetry R Electron density Eele Epol Edis Erep Etot 1 -x, -y, -z 6.01 B3LYP/6-31G(d,p) -8.7 -5.1 -34.7 27.6 -26.2 1 -x, -y, -z 4.68 B3LYP/6-31G(d,p) -18.7 -4.6 -59.4 34.0 -53.8 2 x, -y+1/2, z+1/2 9.00 B3LYP/6-31G(d,p) -4.4 -1.3 -32.9 14.6 -25.3 2 x, y, z 14.21 B3LYP/6-31G(d,p) 0.3 -0.2 -7.8 3.3 -4.6 2 x, y, z 6.49 B3LYP/6-31G(d,p) -12.2 -2.7 -34.1 23.6 -30.1 1 -x, -y, -z 12.80 B3LYP/6-31G(d,p) -13.6 -4.5 -18.3 11.3 -26.6 1 -x, -y, -z 13.75 B3LYP/6-31G(d,p) -0.2 -0.4 -11.3 4.6 -7.6 2 x, -y+1/2, z+1/2 10.17 B3LYP/6-31G(d,p) -0.6 -0.4 -12.2 5.4 -8.3 2 x, y, z 14.31 B3LYP/6-31G(d,p) 0.7 -0.1 -3.6 “0.3 -2.3 Energy Model (30) kele kpol kdisp krep CE-HF ... HF/3-21G electron densities 1.019 0.651 0.901 0.811 CE-B3LYP ... B3LYP/6-31G(d,p) electron densities 1.057 0.740 0.871 0.618 Table 8. Interaction energies (kJ/mol), R is the distance between molecular centroids (mean atomic position) in Å. Total energies, only reported for two benchmarked energy models, are the sum of the four energy components, scaled appropriately (see the scale factor table below) for compound 5h. Color Code N Symmetry R Electron Density Eele Epol Edis Erep Etot 2 x, y, z 11.08 B3LYP/6-31G(d,p) -5.0 -2.2 -8.1 7.6 -9.3 1 -x, -y, -z 14.68 B3LYP/6-31G(d,p) 0.7 -0.3 -7.0 4.0 -3.1 2 x, y, z 6.75 B3LYP/6-31G(d,p) -10.3 -3.0 -23.9 16.6 -23.7 1 -x, -y, -z 7.74 B3LYP/6-31G(d,p) -2.9 -1.4 -42.0 21.4 -27.5 2 x, y, z 8.84 B3LYP/6-31G(d,p) -3.7 -2.1 -27.2 13.0 -21.1 1 -x, -y, -z 7.63 B3LYP/6-31G(d,p) -0.3 -1.8 -33.0 17.9 -19.4 1 -x, -y, -z 11.86 B3LYP/6-31G(d,p) -1.7 -0.5 -15.4 11.7 -8.3 1 -x, -y, -z 8.25 B3LYP/6-31G(d,p) -9.7 -1.0 -21.2 19.7 -17.3 1 -x, -y, -z 6.32 B3LYP/6-31G(d,p) -7.6 -1.1 -30.9 17.7 -24.9 1 -x, -y, -z 11.03 B3LYP/6-31G(d,p) -12.4 -3.9 -15.9 7.9 -24.9 Energy Model (30) kele kpol kdisp krep CE-HF ... HF/3-21G electron densities 1.019 0.651 0.901 0.811 CE-B3LYP ... B3LYP/6-31G(d,p) electron densities 1.057 0.740 0.871 0.618 Figure 6. The color-coding pattern of molecules surrounding the original molecule in a cluster of molecule 5e within the default radius of 3.8 Å, when it is viewed along crystallographic a, b and c axes. The color-coding scheme and their interaction energies in component form is given in Table 7. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 271 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Figure 7. The color-coding pattern of molecules surrounding the original molecule in a cluster of molecule 5h within the default radius of 3.8 Å, when it is viewed along crystallographic a, b and c axes. The color-coding scheme and their interaction energies in component form are given in Table 8. a-axis b-axis c-axis Eele Edis Etot Figure 8. Energy frameworks corresponding to Eele, Edis, and Etot for molecule 3 when viewed along crystallographic a, b and c axes. The tube size maintained was 150 and the energy cut-off was 10 kJ/mol. The thickness of solid cylinders represents the relative strength of interaction. In the present work, the molecules 5e and 5h were tested for its inhibitory action against h-ras (121p) by molecular docking studies. The free energy of binding for the compounds 5e and 5h with 121p was determined using PyRx 0.8 docking tool and nine different protein-ligand interactions were observed. Tables 11 and 12 represent the list of binding energies for each interaction and their respective root mean square deviation (RMSD) values. The interactions of the protein with ligands 5e and 5h exhibiting least binding energies (-8.6 and -8.0 kcal/mol) were selected for further analysis. PyMOL representations of the docked ligands and proteins are represented in Figure 11 and 12. The region of interaction between 5e and the protein is represented in Figure 11a, while Figure 12a represents the region of interaction between molecule 5h and the protein. Figures 11b, 11c, 12b, and 12c represent the 3D plot of the regions of interaction between the ligands and the amino acids of the protein. A 2D plot was also generated which represents the amino acids involved in hydrogen bonding and hydrophobic interactions with the ligand (Figures 11d and 12d). Ras genes belong to the class of oncogenes and the proteins they encode have been considered as potential targets for cancer therapy [31]. H-RAS genes encode H-ras protein, that is primarily a GTPase which converts GTP to GDP. This protein is involved in signal transduction from outside the cell to the nucleus to instruct the cell to grow and divide when bound to GTP. The enzyme is inactive or turned off when bound to GDP. Mutations in RAS genes result in H-ras proteins to remain in active state, thereby relaying the signal for cell division, leading to the growth of tumor. RAS mutations have been identified in more than 30% of the human tumors and 100% of the tumors in pancreatic cancer [32]. The docking results indicated molecule 5e showing hydrogen bonding with the amino acid Asp33 with a bond distance of 3.15 Å, while Ser17, Glu31, Val29, Asp119, Phe28, Lys117, Gly15, Gly13, Tyr32 and Thr35 showed hydrophobic interactions (Figure 11d). 272 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 Table 9. The list of binding affinities and RMSD values of molecule 5e interaction at different sites of H-ras. Ligand Binding affinity (kJ/mol) RMSD (ub) RMSD (lb) 121p_5e -8.6 0 0 121p_5e -8.6 2.188 1.281 121p_5e -8.5 2.269 1.660 121p_5e -8.5 8.053 2.809 121p_5e -8.1 1.281 1.175 121p_5e -7.7 7.620 2.584 121p_5e -7.6 18.650 16.903 121p_5e -7.0 8.028 3.079 121p_5e -7.0 22.764 20.101 Table 10. The list of binding affinities and RMSD values of molecule 5h interaction at different sites of H-ras. Ligand Binding affinity (kJ/mol) RMSD (ub) RMSD (lb) 121p_5h -8.0 0 0 121p_5h -8.0 2.944 1.505 121p_5h -7.8 6.856 2.605 121p_5h -7.0 7.848 4.680 121p_5h -7.0 3.258 1.563 121p_5h -6.9 1.729 1.353 121p_5h -6.8 8.512 4.605 121p_5h -6.7 5.854 3.658 121p_5h -6.5 4.252 3.400 a-axis b-axis c-axis Eele Edis Etot Figure 9. Energy frameworks corresponding to Eele, Edis, and Etot for molecule 5e when viewed along crystallographic a, b and c axes. The tube size maintained was 150 and the energy cut-off was 10 kJ/mol. The thickness of solid cylinders represents the relative strength of interaction. However, the ligand 5h showed only hydrophobic interactions with Glu31, Val29, Gly15, Ser17, Asp119, Asn116, Ala18, Phe28, Lys117 and Gly13 (Figure 10d). Janes et al. have reported the inhibitory action of ARS-1620 against KRAS [33]. Evidences show that GDP exhibits hydrogen bonding with various amino acids of H-ras such as Ser17, Gly13, Lys16, Gly15, Asp119, Ala146, Asn116, Val29, Asp30 and Ala18. Some of the key amino acids found in the interaction of molecules 5e and 5h with H-ras are the same amino acids which are involved in hydrogen bonding with GDP. Hence, the molecules 5e and 5h could be potential inhibitors against H-ras. Further experi- mental studies would prove its ability to act as an inhibitor in anticancer therapies. Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 273 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 a-axis b-axis c-axis Eele Edis Etot Figure 10. Energy frameworks corresponding to Eele, Edis, and Etot for molecule 5h when viewed along crystallographic a, b and c axes. The tube size maintained was 150 and the energy cut-off was 10 kJ/mol. The thickness of solid cylinders represents the relative strength of interaction. (a) (b) (c) (d) Figure 11. Molecular docking of molecule 5e with H-ras. (a) Surface model representing the interacting site of H-ras (121p) with molecule 5e (ligand). Blue color represents ligand and magenta color represents interacting amino acids of the protein. (b) Ribbon representation of the docked ligand with H-ras. (c) 3D representation of the ligand and the interacting amino acids. (d) 2D plot of interaction between ligand and amino acids of H-ras. Green line between the amino acids represents hydrogen bonding and other amino acids show hydrophobic interactions. 4. Conclusion In this article, we report an alternative route for the synthesis of 2-chloro-3-aryl-5,5-dimethylcyclohexenones. The successful regiospecific substitution of the vinylic tosylate group over the vinylic chloride group is highlighted. Single crystal XRD studies of three representative compounds are discussed. The Hirshfeld surface studies confirmed the presence of intermolecular interactions of the type C-H···O, C- H···Cl and C-H···O in the compounds 3, 5e and 5h, respectively. The two-dimensional fingerprint calculations showed that in the compounds 3 and 5e, the H···O and H···H; whereas in molecule 5h the H···H pairs of contacts have been served as major contributions towards crystal packing. 274 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 (a) (b) (c) (d) Figure 12. Molecular docking of molecule 5h with H-ras. (a) Surface model representing the interacting site of H-ras (121p) with molecule 5h (ligand). Red color represents the ligand and magenta color represents interacting amino acids of the protein. (b) Ribbon representation of the docked ligand with H-ras. (c) 3D representation of the ligand and the interacting amino acids. (d) 2D plot of interaction between ligand and amino acids of H-ras. Green line between the amino acids represents hydrogen bonding and other amino acids show hydrophobic interactions. The three-dimensional interaction energy frame works were studied in all the compounds and the dispersion energy frame works dominated over classical energy frame works. Molecular docking of the products shows good scope for the utilization of the compounds as ligands in anti-neoplastic activity. Acknowledgements The authors thank the parent universities: (1) Bangalore University; (2) Bengaluru Central University for all facilities provided; (3) Arkalgud Satyanarayana Jeevan Chakravarthy is thankful to the Council of Scientific and Industrial Research (CSIR), Government of India, New Delhi, India, for providing financial support in the form of a Senior Research Fellowship - Direct, videCSIR SRF – File no. 09/039(0119)/2018-EMR-1, dated April 16, 2018; (4) Grateful thanks is placed on record to the Sophisticated Analytical Instruments Facility (SAIF), Indian Institute of Technology, Madras, Chennai-600 036, Tamil Nadu, India, for XRD, data collection; (5) Mrs. Suchithra Bagepalli and Dr. Nagesh Babu, Department of Biochemistry, Maharani’s Science College for Women, Bengaluru, for extending DST-FIST lab facilities and docking studies; (6) Mr. N. Rangapa Sreenatha, Department of Physics, Government Engineering College, Hassan-573 201, Karnataka, for reducing the crystal structure; (7) Dr. B. S. Bandodkar, Dr. M. A. Venkatesha and Avinash, Raju, Bangalore for all the help rendered. Taken in part from the PhD thesis of Arkalgud Satyanarayana Jeevan Chakravarthy, submitted to Bangalore University, Bangalore, India - August 2020. Supporting information CCDC-1875712, CCDC-1940404 and CCDC-1940405 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via https://www.ccdc.cam.ac.uk/structures/, or by e-mailing data_request@ccdc.cam.ac.uk, or by contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44(0)1223-336033. Disclosure statement Conflict of interests: The authors declare that they have no conflict of interest. Author contributions: All authors contributed equally to this work. Ethical approval: All ethical guidelines have been adhered. Sample availability: Samples of the compounds are available from the author. Funding Council of Scientific and Industrial Research, India http://dx.doi.org/10.13039/501100001412 ORCID Arkalgud Satyanarayana Jeevan Chakravarthy http://orcid.org/0000-0003-3010-8402 HariPrasad Suresh http://orcid.org/0000-0001-7157-1538 References [1]. Li, Y.; Luo, Y.; Peng, L.; Li, Y.; Zhao, B.; Wang, W.; Lang, H.; Deng, Y.; Bai, R.; Lan, Y.; Yin, G. Nature Commun. 2020, 11, 417. [2]. Lee, H. W.; So, C. M.; Yuen, O. Y.; Wong, W. T.; Kwong, F. Y. Org. Chem. Front. 2020, 7, 926-932. [3]. Keaveney, S. T.; Kundu, G.; Schoenebeck, F. Angew. Chem. Int. Ed. Engl. 2018, 130, 12753-12757. [4]. Komeyama, K.; Tsunemitsu, R.; Michiyuki, T.; Yoshida, H.; Osaka, I. Molecules 2019, 24, 1458-1468. [5]. Chakravarthy, A. S. J.; Pavan, K. P.; Venkatesh, G. B.; Hariprasad, S. Synthetic Commun. 2020, 50(6), 849-857. [6]. Chakravarthy, A. S. J.; Madhura, M. J.; Gayathri, V.; Hariprasad, S. Tetrahedron Lett. 2020, 60(2), 151391. [7]. Chakravarthy, A. S. J.; Krishnamurthy, M. S.; Begum, N. S.; Hariprasad, S. Mol. Crys. Liq. Crys. 2019, 682(1), 65-76. [8]. APEX2 Bruker, SAINT-Plus and SADABS, Bruker AXS Inc., Wisconsin, Madison, USA, 2004. [9]. Sheldrick, G. M. Acta Cryst. C, 2015, 71, 3-8. [10]. Spek, A. L. Acta Cryst. C 2015, 71, 9-18. [11]. Macrae, C. F.; Bruno, I. J.; Chisholm, J. A.; Edgington, P. R.; McCabe, P.; Pidcock, E.; Rodriguez-Monge, L.; Taylor, R.; van de Streek, J.; Wood. P. A. J. Appl. Cryst. 2008, 41(2), 466-470. [12]. Sreenatha, N. R.; Lakshminarayana, B. N.; Ganesha, D. P.; Gnanendra, C. R. Acta Cryst. E 2018, 74, 1451-1454. [13]. Sreenatha, N. R.; Lakshminarayana, B. N.; Ganesha, D. P.; Vijayshankar, S.; Nagaraju, S. X-Ray Struc. Anal. Online 2018, 34, 24-25. [14]. Spackman, M. A.; Jayatilaka, D. Cryst. Eng. Comm. 2009, 11, 19-32. [15]. Spackman, M. A.; McKinnon, J. J.; Jayatilaka, D. Cryst. Eng. Comm. 2008, 10(4), 377-388. [16]. McKinnon, J. J.; Jayatilaka, D.; Spackman, M. A. Chem. Comm. 2017, 3814-3816. [17]. Turner, M. J.; McKinnon, J. J.; Wolff, S. K.; Grimwood, D. J.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer 17.5. The University of Western Australia, 2017. [18]. Turner, M. J.; Grabowsky, S.; Jayatilaka, D.; Spackman, M. A. J. Phys. Chem. Lett. 2014, 5, 4249-4255. [19]. Sanner, M. F. J. Mol. Grap. Mod. 1999, 17(1), 57-61. [20]. Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. Prot. Eng. 1995, 8(2), 127-134. [21]. McVeigh, M. S.; Kelleghan, A. V.; Yamano, M. M.; Knapp, R. R.; Garg, N. K. Org. Lett. 2020, 22(11), 4500-4504. [22]. Geenen, S. R.; Schumann, T.; Mueller, T. J. J. J. Org. Chem. 2020, 85(15), 9737-9750. [23]. Mpungose, P. P.; Vundla, Z. P.; Maguire, G. E. M.; Friedrich, H. B. Molecules 2018, 23(7), 1676-1699. https://www.ccdc.cam.ac.uk/structures/ mailto:data_request@ccdc.cam.ac.uk http://dx.doi.org/10.13039/501100001412 http://orcid.org/0000-0003-3010-8402 http://orcid.org/0000-0001-7157-1538 Chakravarthy and Prasad / European Journal of Chemistry 11 (4) (2020) 261-275 275 2020 – European Journal of Chemistry – CC BY NC – DOI: 10.5155/eurjchem.11.4.261-275.2020 [24]. Boeyens, J. C. A. J. Cryst. Mol. Struct. 1978, 8, 317-320. [25]. Cremer, D. Acta Cryst. B 1984, 40, 498-500. [26]. Sreenatha, N. R.; Chakravarthy, A. S. J.; Suchithra, B.; Lakshminarayana, B. N.; Hariprasad, S.; Ganesha, D. P. J. Mol. Struc. 2020, 1210, 127979. [27]. Sreenatha, N. R.; Chakravarthy, A. S. J.; Lakshminarayana, B. N.; Hariprasad, S. J. Mol. Struc. 2021, 1225, 129116. [28]. Sreenatha, N. R.; Lakshminarayana, B. N.; Ganesha, D. P.; Gnanendra, C. R.; Nagaraju, S.; Madan, S. K. Chem. Data Coll. 2018, 17-18, 394-403. [29]. Sreenatha, N. R.; Lakshminarayana, B. N.; Madan, S. K.; Mahadeva, T. N. P.; Kiran, K. S.; Vijayshankar, D, S.; Byrappa, K. Chem. Data Coll. 2017, 11-12, 131-138. [30]. Mackenzie, C. F.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. IUCrJ 2017, 4(5), 575-587. [31]. Gysin, S. Genes Cancer 2011, 2(3), 359-372. [32]. O’Bryan, J. P. Pharmacol Res. 2019, 139, 503-511. [33]. Janes, M. R.; Zhang, J.; Li, L. Cell 2018, 172(3), 578-589.e17. Copyright © 2020 by Authors. This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at http://www.eurjchem.com/index.php/eurjchem/pages/view/terms and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License (http://creativecommons.org/licenses/by-nc/4.0). By accessing the work, you hereby accept the Terms. This is an open access article distributed under the terms and conditions of the CC BY NC License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited without any further permission from Atlanta Publishing House LLC (European Journal of Chemistry). No use, distribution or reproduction is permitted which does not comply with these terms. Permissions for commercial use of this work beyond the scope of the License (http://www.eurjchem.com/index.php/eurjchem/pages/view/terms) are administered by Atlanta Publishing House LLC (European Journal of Chemistry). http://www.eurjchem.com/index.php/eurjchem/pages/view/terms http://creativecommons.org/licenses/by-nc/4.0 http://www.eurjchem.com/index.php/eurjchem/pages/view/terms 1. Introduction 2. Experimental 2.1. Materials and characterization 2.2. Synthesis and analytical data 2.2.1. Synthesis of 2-chloro-3-tosyl-5,5-dimethyl-2-cyclohexenone (3) 2.2.2. General procedure for the preparation of 2-chloro-3-aryl-5,5-dimethyl-2-cyclohexenones (5a-i) 3. Results and discussions 3.1. Mechanism 3.2. Crystal and molecular structure description 3.3. Hirshfeld surfaces and two-dimensional fingerprint calculations 3.4. Three-dimensional interaction energies 3.5. Molecular docking analysis 4. Conclusion Acknowledgements Supporting information Disclosure statement Funding ORCID References PrintField10: PrintField11: PrintField12: PrintField13: PrintField14: PrintField15: PrintField16: PrintField17: PrintField18: PrintField19: PrintField110: PrintField111: PrintField112: PrintField113: PrintField114: PrintField20: PrintField21: PrintField22: PrintField23: PrintField24: PrintField25: PrintField26: PrintField27: PrintField28: PrintField29: PrintField210: PrintField211: PrintField212: PrintField213: PrintField214: