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Al-Sanea MM, Hamdi A, Brogi S, S. Tawfik S, Othman DIA, Elshal M, Ur Rahman H, Parambi DGT, M. Elbargisy R, Selim S, Mostafa EM, Mohamed AAB. Design, synthesis, and biological investigation of oxadiazolyl, thiadiazolyl, and pyrimidinyl linked antipyrine derivatives as potential non-acidic anti-inflammatory agents. J Enzyme Inhib Med Chem 2023; 38:2162511. [PMID: 36633257 PMCID: PMC9848286 DOI: 10.1080/14756366.2022.2162511] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A novel series of 12 antipyrine derivatives containing 1,3,4-oxadiazoles (4a-d), 1,3,4-thiadiazoles (6a-d), and pyrimidines (8a-d), was preparedand assessed for its potential in vitro COX-2 inhibitors. Compared to Celecoxib, compounds 4b-d and 8d were the most potent derivatives c with a half-maximal inhibitory concentration range of 53-69 nM. Considering COX-2 selectivity index, compounds 4 b and 4c were chosen among these most potent derivatives for further investigation. The in vivo ability of compounds 4 b and 4c to counteract carrageenan-induced paw edoema has been assessed and their potential underlying mechanisms have been elucidated and the results have been further validated using molecular docking simulations.
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Affiliation(s)
- Mohammad M. Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia,CONTACT Mohammad M. Al-Sanea Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka72341, Saudi Arabia
| | - Abdelrahman Hamdi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Samar S. Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Dina I. A. Othman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mahmoud Elshal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Hidayat Ur Rahman
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Della G. T. Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Rehab M. Elbargisy
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Ehab M. Mostafa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Ahmed A. B. Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Ahmed A. B. Mohamed Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura35516, Egypt
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Shakil S, Rizvi SMD, Greig NH. In depth molecular interaction analyses of the complex of a proposed CTXM-inhibitor bound to the bacterial enzyme. J Biomol Struct Dyn 2023; 41:8362-8372. [PMID: 36224195 PMCID: PMC10481260 DOI: 10.1080/07391102.2022.2133009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/02/2022] [Indexed: 10/17/2022]
Abstract
A 'Thumb Rule for Antibiotic Design' against bacteria can be given as, 'The minimum pace of drug design ought to match the swiftness with which bacteria display cutting-edge resistance mechanisms; thereby outwitting the antibiotics and, in turn, the researchers'. Occurrence of drug resistance attributable to CXTM-variants in bacterial pathogens is widespread. In line with our above proposed thumb rule, the present article employed concatenation of virtual screening, docking and simulation to identify a potent in silico validated anti-CTXM-14 ligand. Specifically, this research used the 'MCULE' drug discovery platform to screen a total of 5 million candidate inhibitors to evaluate their binding efficacy with an antibiotic resistance enzyme, CTXM-14 found in bacterial pathogens. A new median approach between 'structure' and 'ligand'-based protocols was employed. Pharmacokinetic profiling was achieved by 'SWISS ADME'. Safety profile for humans was appraised by 'Toxicity Checker'. The complex consisting of the 'Top ligand' (obtained from the screen) harbored within the active pocket of the bacterial CTXM-14 was subjected to 60 ns molecular dynamics simulation with the aid of licensed YASARA STRUCTURE v.21.8.27. Complex tasks were performed by YANACONDA. Fine resolution figures (notably, plots generated from trajectory analyses) were constructed. Simulation snaps were acquired at every 250 picoseconds of the run. The ligand having the IUPAC name as 1-Amino-3-(4-hydroxyphenyl)pyrido[1,2-a]benzimidazole-2,4-dicarbonitrile demonstrated the overall best binding with CTXM-14. Fifteen amino acid residues were found to line the interacting pocket. Remarkably, all of these interacting residues were found to be present among the interacting residues displayed by the reference complex as well, i.e. CTXM-14:Vaborbactam complex (PDB ID 6V7H). A total of 240 simulation snaps were retrieved. The RMSD plot revealed that a plateau was achieved at 32 ns, after which the backbone RMSD fluctuations remained confined within 1.4-2 Å. Video recording of molecular actions was also achieved. In conclusion, this study provides a fresh lead molecule, 1-Amino-3-(4-hydroxyphenyl)pyrido[1,2-a]benzimidazole-2,4-dicarbonitrile against bacterial CTXM-14 protein. The study utilized a new median approach between 'structure' and 'ligand'-based drug design. The lead molecule passed ADMET conditions and an array of medicinal chemistry filters, and is further supported by a stable molecular dynamics. An acceptable skin permeation supports its probable use in antibiotic creams. Moreover, the study provides a clear 'Thumb Rule for Antibiotic Design' against bacteria, which although often assumed, can be clearly stated for the first time. Synthesis of the screening-proposed molecule followed by in-vitro and in-vivo validation is highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shazi Shakil
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed M Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - Nigel H Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches. Molecules 2022; 27:molecules27185930. [PMID: 36144666 PMCID: PMC9504514 DOI: 10.3390/molecules27185930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.
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Abdel-Aziz SA, Cirnski K, Herrmann J, Abdel-Aal MA, Youssif B, Salem O. Novel fluoroquinolone hybrids as dual DNA gyrase and urease inhibitors with potential antibacterial activity: Design, synthesis, and biological evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Chen X, Meng F, Zhang J, Zhang Z, Ye X, Zhang W, Tong Y, Ji X, Xu R, Xu XL, You QD, Jiang ZY. Discovery of 2-((2-methylbenzyl)thio)-6-oxo-4-(3,4,5-trimethoxyphenyl)-1,6-dihydropyrimidine-5-carbonitrile as a novel and effective bromodomain and extra-terminal (BET) inhibitor for the treatment of sepsis. Eur J Med Chem 2022; 238:114423. [DOI: 10.1016/j.ejmech.2022.114423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
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Structural Insights of Three 2,4-Disubstituted Dihydropyrimidine-5-carbonitriles as Potential Dihydrofolate Reductase Inhibitors. Molecules 2021; 26:molecules26113286. [PMID: 34072467 PMCID: PMC8198998 DOI: 10.3390/molecules26113286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
In this report, we describe the structural characterization of three 2,4-disubstituted-dihydropyrimidine-5-carbonitrile derivatives, namely 2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-4-propyl-1,6-dihydropyrimidine-5-carbonitrile 1, 4-(2-methylpropyl)-2-{[(4-nitrophenyl)methyl]sulfanyl}-6-oxo-1,6-dihydropyrimidine-5-carbonitrile 2, and 2-[(2-ethoxyethyl)sulfanyl]-6-oxo-4-phenyl-1,6-dihydropyrimidine-5-carbonitrile monohydrate 3. An X-ray diffraction analysis revealed that these compounds were crystallized in the centrosymmetric space groups and adopt an L-shaped conformation. One of the compounds (3) crystallized with a water molecule. A cyclic motif (R22(8)) mediated by N–H···O hydrogen bond was formed in compounds 1 and 2, whereas the corresponding motif was not favorable, due to the water molecule, in compound 3. The crystal packing of these compounds was analyzed based on energy frameworks performed at the B3LYP/6-31G(d,p) level of theory. Various inter-contacts were characterized using the Hirshfeld surface and its associated 2D-fingerprint plots. Furthermore, a molecular docking simulation was carried out to assess the inhibitory potential of the title compounds against the human dihydrofolate reductase (DHFR) enzyme.
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Shakil S, Rizvi SMD, Greig NH. High Throughput Virtual Screening and Molecular Dynamics Simulation for Identifying a Putative Inhibitor of Bacterial CTX-M-15. Antibiotics (Basel) 2021; 10:antibiotics10050474. [PMID: 33919115 PMCID: PMC8143117 DOI: 10.3390/antibiotics10050474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022] Open
Abstract
Background: Multidrug resistant bacteria are a major therapeutic challenge. CTX-M-type enzymes are an important group of class A extended-spectrum β-lactamases (ESBLs). ESBLs are the enzymes that arm bacterial pathogens with drug resistance to an array of antibiotics, notably the advanced-generation cephalosporins. The current need for an effective CTX-M-inhibitor is high. Objective: The aim of the current study was to identify a promising anti-CTX-M-15 ligand whose chemical skeleton could be used as a ‘seed-molecule’ for future drug design against resistant bacteria. Methods: Virtual screening of 5,000,000 test molecules was performed by ‘MCULE Drug Discovery Platform’. ‘ADME analyses’ was performed by ‘SWISS ADME’. TOXICITY CHECKER of MCULE was employed to predict the safety profile of the test molecules. The complex of the ‘Top inhibitor’ with the ‘bacterial CTX-M-15 enzyme’ was subjected to 102.25 ns molecular dynamics simulation. This simulation was run for 3 days on a HP ZR30w workstation. Trajectory analyses were performed by employing the macro ‘md_analyze.mcr’ of YASARA STRUCTURE version 20.12.24.W.64 using AMBER14 force field. YANACONDA macro language was used for complex tasks. Figures, including RMSD and RMSF plots, were generated. Snapshots were acquired after every 250 ps. Finally, two short videos of ‘41 s’ and ‘1 min and 22 s’ duration were recorded. Results: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile, denoted by the MCULE-1352214421-0-56, displayed the most efficient binding with bacterial CTX-M-15 enzyme. This screened molecule significantly interacted with CTX-M-15 via 13 amino acid residues. Notably, nine amino acid residues were found common to avibactam binding (the reference ligand). Trajectory analysis yielded 410 snapshots. The RMSD plot revealed that around 26 ns, equilibrium was achieved and, thereafter, the complex remained reasonably stable. After a duration of 26 ns and onwards until 102.25 ns, the backbone RMSD fluctuations were found to be confined within a range of 0.8–1.4 Å. Conclusion: 5-Amino-1-(2H-[1,2,4]triazino[5,6-b]indol-3-yl)-1H-pyrazole-4-carbonitrile could emerge as a promising seed molecule for CTX-M-15-inhibitor design. It satisfied ADMET features and displayed encouraging ‘simulation results’. Advanced plots obtained by trajectory analyses predicted the stability of the proposed protein-ligand complex. ‘Hands on’ wet laboratory validation is warranted.
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Affiliation(s)
- Shazi Shakil
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
| | - Syed M. Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81481, Saudi Arabia;
| | - Nigel H. Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA;
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Pyrimidines as block units in heterocycles: novel synthesis of pyrimidines and condensed pyrimidine derivatives. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01712-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Al-Wahaibi LH, Öztürk N, Hassan HM, Sert Y, El-Emam AA, Al-Tamimi AMS, Gökce H. Experimental (FT-IR, Laser-Raman and NMR) and theoretical comparative study on 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile, a potential bioactive agent. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the experimental and theoretical vibrational frequencies of a potential bioactive pyrimidine derivative molecule named 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile has been investigated. The experimental FT-IR and Laser-Raman spectra of the studied molecule are in the region (4000–400[Formula: see text]cm[Formula: see text] and (4000–100[Formula: see text]cm[Formula: see text], respectively, in gas phase. The vibrational modes and optimized ideal structure parameters(bond lengths, bond angles and selected dihedral angles) were calculated by using DFT/B3LYP, DFT/BHandHLYP and DFT/PBE1PBE methods with 6-311[Formula: see text]G(d,p) basis set. The theoretical mode assignments have been obtained by using potential energy distribution (PED) with the VEDA4 software program. Additionally, infrared and Raman intensities, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies and their clouds, and other related molecular properties were calculated and evaluated. The proton (1H) and carbon-13 ([Formula: see text]C) nuclear magnetic resonance (NMR) chemical shifts have been investigated for the title molecule, both experimentally (in DMSO-d[Formula: see text] and theoretically (in vacuum and DMSO). The thermodynamic properties of the tile compound have been investigated using the mentioned theoretical computational methods. The results revealed that there isgood agreement between experimental and theoretical results and these results have supported the related literature.
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Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Nuri Öztürk
- Dereli Vocational School, Giresun University, 28950 Giresun, Turkey
| | - Hanan M. Hassan
- Department of Pharmacology and Biochemistry, College of Pharmacy, Delta University for Science and Technology, Mansoura, Egypt
| | - Yusuf Sert
- Sorgun Vocational School, Bozok University, 66100 Yozgat, Turkey
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Abdul-Malek S. Al-Tamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Halil Gökce
- Vocational School of Health Services, Giresun University, 28200 Giresun, Turkey
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Synthesis and bioactivity evaluation of new pyrimidinone-5-carbonitriles as potential anticancer and antimicrobial agents. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-018-3254-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Al-Omary FA, Mary YS, Beegum S, Panicker CY, Al-Shehri MM, El-Emam AA, Armaković S, Armaković SJ, Van Alsenoy C. Molecular conformational analysis, reactivity, vibrational spectral analysis and molecular dynamics and docking studies of 6-chloro-5-isopropylpyrimidine-2,4(1H,3H)-dione, a potential precursor to bioactive agent. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Al-Tamimi AMS, Ghabbour HA, El-Emam AA. Crystal structure of 6-oxo-4-propyl-2-(propylthio)-1,6-dihydropyrimidine-5-carbonitrile, C 11H 15N 3OS. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C11H15N3OS, triclinic, P1̅ (no. 2), a = 4.6579(2) Å, b = 9.6316(5) Å, c = 13.6654(7) Å, α = 87.982(2)°, β = 87.330(2)°, γ = 78.403(2)°, V = 599.69(5) Å3, Z = 2, R
gt
(F) = 0.0450, wR
ref
(F
2
) = 0.128, T = 100 K.
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Affiliation(s)
- Abdul-Malek S. Al-Tamimi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | | | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
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Al-Wabli RI, Ghabbour HA, Lahsasni S, Al-Abdullah ES, El-Emam AA. Crystal structure of 5-ethyl-6-[(3-methylphenyl)sulfanyl]pyrimidine-2,4(1 H,3 H)-dione, C 13H 14N 2O 2S. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C13H14N2O2S, triclinic, P1̅ (no. 2), a = 4.8885(2) Å, b = 10.3414(5) Å, c = 12.6056(6) Å, α = 95.162(2)°, β = 97.487(1)°, γ = 101.494°, V = 614.73(5) Å3, Z = 2, R
gt
(F) = 0.0507, wR
ref
(F
2
) = 0.1149, T = 100 K.
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Affiliation(s)
- Reem I. Al-Wabli
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Siham Lahsasni
- Department of Chemistry, College of Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ebtehal S. Al-Abdullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riyadh 11451, Saudi Arabia
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El-Emam AA, Ghabbour HA, Al-Deeb OA, Abdelbaky MSM, García-Granda S. Crystal structure of 2-[(4-fluorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile, C 16H 16FN 3OS. Z KRIST-NEW CRYST ST 2016. [DOI: 10.1515/ncrs-2015-0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C16H16FN3OS, triclinic, P1̅ (no. 2), a = 5.6885(3) Å, b = 9.4378(4) Å, c = 15.0736(7) Å, α = 84.037(4)°, β = 81.442(4)°, γ = 74.271(4)°, V = 768.56(7) Å3, Z = 2, R
gt
(F) = 0.0518, wR
ref
(F
2
) = 0.1430, T = 100 K.
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Affiliation(s)
- Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Omar A. Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
| | - Mohammed S. M. Abdelbaky
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo – CINN, C/Julian Clavería, 8, 33006 Oviedo, (Asturias), Spain
| | - Santiago García-Granda
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O.Box 2457, Riaydh 11451, Saudi Arabia
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Spectroscopic and electronic structure calculation of a potential chemotherapeutic agent 5-propyl-6-(p-tolylsulfanyl)pyrimidine-2,4(1H,3H)-dione using first principles. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.07.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Senthilkumar N, Ravichandran YD, Kumar KM, Ramaiah S. Synthesis of a new series of pyrimidine derivatives: exploration of anti-proliferative activity on EAT cells and molecular docking. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-2086-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Alzoman NZ, Mary YS, Panicker CY, Al-Swaidan IA, El-Emam AA, Al-Deeb OA, Al-Saadi AA, Van Alsenoy C, War JA. Spectroscopic investigation (FT-IR and FT-Raman), vibrational assignments, HOMO-LUMO, NBO, MEP analysis and molecular docking study of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-(phenylsulfanyl)-pyrimidine-5-carbonitrile, a potential chemotherapeutic agent. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 139:413-24. [PMID: 25576938 DOI: 10.1016/j.saa.2014.12.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/16/2014] [Accepted: 12/15/2014] [Indexed: 11/29/2022]
Abstract
Vibrational spectral analysis of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-(phenylsulfanyl)-pyrimidine-5-carbonitrile was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry and vibrational wave numbers have been computed using density functional B3LYP method with 6-311++G(d,p)(5D,7F) as basis set. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using NBO analysis. The nonlinear optical behavior of the title compound is also theoretically predicted. From the MEP, it is evident that the negative charge covers the C≡N group and the positive region is over the phenyl and the pyrimidine rings. From the potential energy scan it is clear that the lone pairs of the sulfur atom prefer to point away from the pyrimidine ring and the C≡N group resulting with two possible minimum conformations at the N4C8S1C25 angle equal nearly 0° or 150°. Molecular docking results suggest that the compound might exhibit inhibitory activity against GPb and may act as potential anti-diabetic compound.
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Affiliation(s)
- Nourah Z Alzoman
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - C Yohannan Panicker
- Department of Physics, TKM College of Arts and Science, Kollam, Kerala, India.
| | - Ibrahim A Al-Swaidan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar A Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | | | - Javeed Ahmad War
- Department of Chemistry, Dr. H.S. Gour Central University, Sagar, M.P., India
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18
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Vibrational spectroscopic and molecular docking study of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile, a potential chemotherapeutic agent. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 137:569-80. [PMID: 25240829 DOI: 10.1016/j.saa.2014.08.112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/06/2014] [Accepted: 08/24/2014] [Indexed: 11/24/2022]
Abstract
FT-IR and FT-Raman spectra of 2-Benzylsulfanyl-4-[(4-methylphenyl)-sulfanyl]-6-pentylpyrimidine-5-carbonitrile were recorded and analyzed. The structure of the molecule has been optimized and the structural characteristics have been determined by density functional theory. The geometrical parameters (DFT) are in agreement with the XRD results. HOMO and LUMO and other chemical properties are reported. Nonlinear optical properties are reported. A detailed molecular picture of the title compound and its interactions were obtained from NBO analysis. The negative (red and yellow) regions of the MEP are related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity, as shown in the MEP plot and the title compound has several possible sites, CN, N atom of pyrimidine ring and sulfur atoms for electrophilic attack. From the molecular docking studies it is clear that the title compound binds at the catalytic site of the substrate by weak non-covalent interactions most prominent of which are H-bonding, π-π, alkyl-π, and amide-π interactions.
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19
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Al-Omary FAM, Raj A, Raju K, Panicker CY, Haress NG, El-Emam AA, El-Ashmawy MB, Al-Saadi AA, Van Alsenoy C, War JA. Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO analysis and molecular docking study of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-[3-trifluoromethyl)-anilino]pyrimidine-5-carbonitrile, a potential chemotherapeutic agent. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:520-33. [PMID: 25448953 DOI: 10.1016/j.saa.2014.09.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/28/2014] [Accepted: 09/18/2014] [Indexed: 11/30/2022]
Abstract
FT-IR and FT-Raman spectra of 2-[(4-chlorobenzyl)sulfanyl]-4-(2-methylpropyl)-6-[3-trifluoromethyl)-anilino]pyrimidine-5-carbonitrile were recorded and analyzed. The vibrational wave numbers were computed using DFT quantum chemical calculations. The data obtained from wave number calculations are used to assign vibrational bands obtained in infrared and Raman spectra. Potential energy distribution was done using GAR2PED program. The NH stretching wave number is red shifted by 102 cm(-1) in IR from the computed wave number, which indicates the weakening of the NH bond. The geometrical parameters (DFT) of the title compound are in agreement with the XRD results. NBO analysis, HOMO-LUMO, first hyperpolarizability and molecular electrostatic potential results are also reported. From the MEP map it is evident that the negative electrostatic potential regions are mainly localized over the CN and CF3 groups and are possible sites for electrophilic attack and positive regions are localized around NH group, indicating possible sites for nucleophilic attack. The preliminary docking results suggest that the title compound might exhibit inhibitory activity against GPb and may act as a potential anti-diabetic compound.
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Affiliation(s)
- Fatmah A M Al-Omary
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asha Raj
- Department of Physics, University College, Trivandrum, Kerala, India
| | - K Raju
- Department of Physics, University College, Trivandrum, Kerala, India
| | - C Yohannan Panicker
- Department of Physics, TKM College of Arts and Science, Kollam, Kerala, India.
| | - Nadia G Haress
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud B El-Ashmawy
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Abdulaziz A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Christian Van Alsenoy
- University of Antwerp, Chemistry Department, Universiteitsplein 1, B2610 Antwerp, Belgium
| | - Javeed Ahmad War
- Department of Chemistry, Dr. H.S. Gour Central University, Sagar, M.P., India
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20
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Synthesis of Novel 1-(3′-CHLORO-1′,4′-DIOXO-1′,4′-Dihydronaphthalen-2′-YL)-5-Substitued-1H-Pyrimidine-2,4-Dione as Potential Antibacterial Agents. Pharm Chem J 2014. [DOI: 10.1007/s11094-014-1072-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Attia MI, Kansoh AL, El-Brollosy NR. Antimicrobial pyrimidinones II: synthesis and antimicrobial evaluation of certain novel 5,6-disubstituted 2-(substituted amino)alkylthiopyrimidin-4(3H)-ones. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1253-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Haress NG, Ghabbour HA, El-Emam AA, Chidan Kumar CS, Fun HK. 6-[(2-Methyl-phen-yl)sulfan-yl]-5-propyl-pyrimidine-2,4(1H,3H)-dione. Acta Crystallogr Sect E Struct Rep Online 2014; 70:o768-9. [PMID: 25161558 PMCID: PMC4120546 DOI: 10.1107/s1600536814013269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 11/28/2022]
Abstract
In the title pyrimidine-2,4-dione derivative, C14H16N2O2S, the dihedral angle between the six-membered rings is 77.81 (10)°. The mol-ecule is twisted about the Cp-S (p = pyrimidine) bond, with a C-S-C-N torsion angle of -59.01 (17)°. An intramolecular C-H⋯S hydrogen bond generates an S(5) ring motif. In the crystal, bifurcated acceptor N-H⋯O and C-H⋯O hydrogen bonds generate inversion-related dimers incorporating R 2 (1)(9) and R 2 (2)(8) loops. These dimers are connected into a chain extending along the a-axis direction by a second pair of inversion-related N-H⋯O hydrogen bonds, forming another R 2 (2)(8) loop. The crystal structure is further stabilized by weak inter-molecular C-H⋯π inter-actions, generating a three-dimensional network.
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Affiliation(s)
- Nadia G. Haress
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
- King Abdullah Institute for Nanotechnology (KAIN), King Saud University, Riyadh 11451, Saudi Arabia
| | - C. S. Chidan Kumar
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Hoong-Kun Fun
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
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23
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Synthesis and in vitro antiproliferative evaluation of novel N-alkylated 6-isobutyl- and propyl pyrimidine derivatives. Bioorg Med Chem Lett 2014; 24:2913-7. [DOI: 10.1016/j.bmcl.2014.04.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/16/2014] [Accepted: 04/21/2014] [Indexed: 12/30/2022]
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24
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Zhou YJ, Lv J, Yu K, Ma JP, Guo DS. Supramolecular structures in three thiouracil derivatives: 5,6-trimethylene-2-sulfanylidene-1,2-dihydropyrimidin-4(3H)-one, 2-(4-fluorobenzylsulfanyl)-5,6-trimethylenepyrimidin-4(3H)-one and methyl 2-{[2-(4-fluorobenzylsulfanyl)-5,6-trimethylenepyrimidin-4-yl]oxy}acetate. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:416-20. [PMID: 24705060 DOI: 10.1107/s2053229614006111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/19/2014] [Indexed: 11/10/2022]
Abstract
The molecules of the title compounds, C7H8N2OS, (1), C14H13FN2OS, (2), and C17H17FN2O3S, (3), crystallize in the space groups C2/m, C2/c and Ia, respectively. Compounds (1) and (2), an S-alkylated derivative of (1), consist of only one symmetry-independent molecule, while (3), an O-alkylated derivative of (2), contains two independent molecules in the asymmetric unit. The molecules of (1) sit on crystallographic mirror planes. In the supramolecular structure of (1), a combination of N-H···O and N-H···S hydrogen bonds creates a molecular strap with C(6) and R2(2)(8) motifs, which is further stabilized by an S···S contact. In the packing of (2), a one-dimensional molecular column is made up of two kinds of dimers. One dimer, with an R2(2)(18) motif, is formed by a pair of C-H···O soft hydrogen bonds and the other, with an R2(2)(8) motif, is produced via a pair of N-H···O hard hydrogen bonds. In the packing of (3), molecules A and B form two different types of one-dimensional chain by intermolecular C-H···N hydrogen bonds, and by C···N and O···S contacts, respectively. Two such kinds of chain are connected alternately via interchain C-H···O hydrogen bonds, giving a two-dimensional sheet. Finally, a three-dimensional supramolecular structure is formed through weak intersheet C-H···F hydrogen bonds. The study of the molecular and supramolecular structures of thiouracil derivatives is significant in the development of lipoprotein-associated phospholipase A2 inhibitors.
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Affiliation(s)
- Yu-Jun Zhou
- Department of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Jing Lv
- Department of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Kai Yu
- Department of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Jian-Ping Ma
- Department of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Dian-Shun Guo
- Department of Chemistry, Shandong Normal University, Jinan 250014, People's Republic of China
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25
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Sert Y, El-Emam AA, Al-Deeb OA, Al-Turkistani AA, Ucun F, Cırak C. The biomolecule, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile: FT-IR, Laser-Raman spectra and DFT. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:86-97. [PMID: 24589995 DOI: 10.1016/j.saa.2014.01.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 11/25/2022]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey.
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar A Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Cağrı Cırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
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26
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Al-Omary FAM, Ghabbour HA, El-Emam AA, Chidan Kumar CS, Fun HK. 5-Propyl-6-(p-tolyl-sulfan-yl)pyrimidine-2,4(1H,3H)-dione. Acta Crystallogr Sect E Struct Rep Online 2014; 70:o179-80. [PMID: 24764894 PMCID: PMC3998333 DOI: 10.1107/s1600536814000749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/11/2014] [Indexed: 11/17/2022]
Abstract
In the title pymiridine-2,4-dione derivative, C14H16N2O2S, the dihedral angle between the six-membered rings is 66.69 (10)°. The molecule is twisted about the Cp—S (p = pyrimidine) bond, with a C—S—C—N torsion angle of −19.57 (16)°. In the crystal, adjacent molecules form inversion dimers through pairs of strong N—H⋯O hydrogen bonds, generating an R22(8) ring motif. The dimers are connected into chains extending along the c-axis direction through additional N—H⋯O hydrogen bonds.
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Affiliation(s)
- Fatmah A M Al-Omary
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
| | - Hazem A Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
| | - C S Chidan Kumar
- X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Hoong-Kun Fun
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, PO Box 2457, Riaydh 11451, Saudi Arabia
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27
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Attia MI, El-Emam AA, Al-Turkistani AA, Kansoh AL, El-Brollosy NR. Synthesis of novel 2-(substituted amino)alkylthiopyrimidin-4(3H)-ones as potential antimicrobial agents. Molecules 2013; 19:279-90. [PMID: 24378967 PMCID: PMC6271362 DOI: 10.3390/molecules19010279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 12/13/2013] [Accepted: 12/16/2013] [Indexed: 11/16/2022] Open
Abstract
5-Alkyl-6-(substituted benzyl)-2-thiouracils 3a,c were reacted with (2-chloroethyl) diethylamine hydrochloride to afford the corresponding 2-(2-diethylamino)ethylthiopyrimidin- 4(3H)-ones 4a,b. Reaction of 3a-c with N-(2-chloroethyl)pyrrolidine hydrochloride and/or N-(2-chloroethyl)piperidine hydrochloride gave the corresponding 2-[2-(pyrrolidin-1-yl)ethyl]-thiopyrimidin-4(3H)-ones 5a-c and 2-[2-(piperidin-1-yl)ethyl]thiopyrimidin-4(3H)-ones 6a,b, respectively. Treatment of 3a-d with N-(2-chloroethyl)morpholine hydrochloride under the same reaction conditions formed the corresponding 2-[2-(morpholin-4-yl)ethyl]thiopyrimidines 6c-f. On the other hand, 3a,b were reacted with N-(2-bromoethyl)phthalimide and/or N-(3-bromopropyl)phthalimide to furnish the corresponding 2-[2-(N-phthalimido)ethyl]-pyrimidines 7a,b and 2-[3-(N-phthalimido)-propyl]pyrimidines 7c,d, respectively. Compounds 3a-d, 4a,b, 5a-c, 6a-f and 7a-d were screened against Gram-positive bacteria (Staphylococcus aureus ATCC 29213, Bacillus subtilis NRRL 4219 and Bacillus cereus), yeast-like pathogenic fungus (Candida albicans ATCC 10231) and a fungus (Aspergillusniger NRRL 599). The best antibacterial activity was displayed by compounds 3a, 3b, 4a, 5a, 5b, 6d, 6f, 7b and 7d, whereas compounds 4b, 5b, 5c, 6a, 6b and 6f exhibited the best antifungal activity.
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Affiliation(s)
- Mohamed I Attia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Abdulghafoor A Al-Turkistani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Amany L Kansoh
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Nasser R El-Brollosy
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P. O. Box 2457, Riyadh 11451, Saudi Arabia.
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28
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Sert Y, Al-Turkistani AA, Al-Deeb OA, El-Emam AA, Ucun F, Çırak Ç. Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of a potential chemotherapeutic agent 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:97-105. [PMID: 24177876 DOI: 10.1016/j.saa.2013.09.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/07/2013] [Accepted: 09/29/2013] [Indexed: 11/27/2022]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09 W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art and Sciences, Bozok University, Yozgat 66100, Turkey.
| | | | - Omar A Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fatih Ucun
- Department of Physics, Faculty of Art and Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Çağrı Çırak
- Department of Physics, Faculty of Art and Sciences, Erzincan University, Yozgat 24100, Turkey
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29
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Shao YL, Zhang XH, Han JS, Zhong P. The Synthesis of 2-(Arylthio)arylcyanamides via Copper-Catalyzed Domino Intermolecular C-S Cross-Coupling Reaction of 2-Aminobenzothiazoles with Aryl Iodides. PHOSPHORUS SULFUR 2013. [DOI: 10.1080/10426507.2012.755973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Yin-Lin Shao
- a College of Chemistry and Materials Engineering , Wenzhou University , Wenzhou , 325035 , China
| | - Xiao-Hong Zhang
- a College of Chemistry and Materials Engineering , Wenzhou University , Wenzhou , 325035 , China
| | - Jiang-Sheng Han
- a College of Chemistry and Materials Engineering , Wenzhou University , Wenzhou , 325035 , China
| | - Ping Zhong
- a College of Chemistry and Materials Engineering , Wenzhou University , Wenzhou , 325035 , China
- b Oujiang College , Wenzhou University , Wenzhou , 325035 , China
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30
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Al-Deeb OA, Al-Turkistani AA, Al-Abdullah ES, El-Brollosy NR, Habib EE, El-Emam AA. Pyrimidine-5-carbonitriles – part III: synthesis and antimicrobial activity of novel 6-(2-substituted propyl)-2,4-disubstituted pyrimidine-5-carbonitriles. HETEROCYCL COMMUN 2013. [DOI: 10.1515/hc-2013-0139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Synthesis pharmacological evaluation and docking studies of pyrimidine derivatives. Eur J Med Chem 2012; 58:478-84. [DOI: 10.1016/j.ejmech.2012.09.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 12/11/2022]
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32
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Synthesis and bioactivity evaluation of new 6-aryl-5-cyano thiouracils as potential antimicrobial and anticancer agents. Molecules 2012; 17:9868-86. [PMID: 22902882 PMCID: PMC6268711 DOI: 10.3390/molecules17089868] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 07/25/2012] [Accepted: 08/10/2012] [Indexed: 11/23/2022] Open
Abstract
Several novel 6-aryl-5-cyano thiouracil derivatives were synthesized and explored for their activities as antibacterial, antifungal and anticancer agents. The antimicrobial evaluation revealed that compounds 7b and 7c possessed superior antibacterial activity against the Gram positive bacteria S. aureus and B. subtilis compared to the reference drug amoxicillin. Moreover, compound 4i was found to be a broad spectrum antimicrobial agent and it also exhibited the highest antifungal activity against C. albicans, even higher than the reference drug amphotericin B (MIC = 2.34, 3.00 μg/mL respectively). Selected compounds were tested for in vitro cytotoxicity at a single 10−5 M concentration in accordance to the NCI (USA) protocol. The preliminary screening results showed that most of the compounds had limited cytotoxic activity against renal cancer UO-31 and/or A498 cell lines. Nevertheless, compounds 6d and 6i displayed potent growth inhibitory effect toward non-small cell lung cancer HOP-92 and leukemia MOLT-4 cell lines, respectively.
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El-Emam AA, Al-Deeb OA, El-Brollosy NR, Ng SW, Tiekink ERT. 2-[(4-Chloro-benz-yl)sulfanyl]-4-(2-methyl-prop-yl)-6-[3-(trifluoro-meth-yl)anilino]-pyrimidine-5-carbonitrile. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2059-60. [PMID: 22807881 PMCID: PMC3393324 DOI: 10.1107/s1600536812025895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 06/07/2012] [Indexed: 11/26/2022]
Abstract
Three independent mol-ecules comprise the asymmetric unit of the title compound, C(23)H(20)ClF(3)N(4)S. The conformations of the mol-ecules are similar with the chloro-benzene and CF(3)-benzene rings almost perpendicular to, and almost co-planar with, the pyrimidinyl ring [range of dihedral angles = 80.36 (13)-88.07 (14) and 11.89 (14)-23.30 (14)°, respectively]; the benzene rings are roughly orthogonal to each other [64.81 (16)-72.16 (15)°]. In the crystal, two of the independent mol-ecules associate via weak N-H⋯N(cyano) hydrogen bonds and 12-membered {⋯HNC(3)N}(2) synthons; the third independent mol-ecule self-associates similarly but about a centre of inversion. The sample studied was found to be a non-merohedral twin and the minor twin component refined to 47.16 (7)%.
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El-Emam AA, Al-Deeb OA, El-Brollosy NR, Ng SW, Tiekink ERT. 2-Benzyl-sulfanyl-4-[(4-methyl-phen-yl)sulfan-yl]-6-pentyl-pyrimidine-5-carbonitrile. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2054. [PMID: 22807878 PMCID: PMC3393321 DOI: 10.1107/s1600536812025275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 06/03/2012] [Indexed: 11/10/2022]
Abstract
In the title compound, C(24)H(25)N(3)S(2), the S-bound benzene rings have orthogonal [dihedral angle = 85.31 (9)°] and splayed [67.92 (11)°] orientations with respect to the pyrimidine ring; the dihedral angle between the benzene rings is 48.18 (12)°. The pentyl group has an extended all-trans conformation and lies to one side of the pyrimidine ring [the N(py)-C(py)-C(p)-C(p) torsion angle = -85.7 (2)°; py = pyrimidine and p = pent-yl].
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Affiliation(s)
- Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar A. Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nasser R. El-Brollosy
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Seik Weng Ng
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Chemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203 Jeddah, Saudi Arabia
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El-Emam AA, Al-Deeb OA, Al-Turkistani AA, Ng SW, Tiekink ERT. 2-[(4-Chloro-benz-yl)sulfan-yl]-4-(2-methyl-prop-yl)-6-(phenyl-sulfan-yl)pyrimidine-5-carbonitrile. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o2055-6. [PMID: 22807879 PMCID: PMC3393322 DOI: 10.1107/s1600536812025810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/06/2012] [Indexed: 11/06/2023]
Abstract
In the title compound, C(22)H(20)ClN(3)S(2), the S-bound benzene rings are inclined [dihedral angles = 78.13 (10) and 36.70 (9)°] with respect to the pyrimidine ring. The methyl-propyl group occupies a position normal to the pyrimidine ring [N-C-C-C torsion angle = 92.3 (2)°]. In the crystal, supra-molecular layers are formed in the bc plane, being consolidated by C-H⋯π and π-π inter-actions, the latter between the pyrimidine and S-bound benzene rings [inter-centroid distance = 3.7683 (12) Å].
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Al-Deeb OA, El-Emam AA, Al-Turkistani AA, Ng SW, Tiekink ERT. 6-(2-Methyl-prop-yl)-4-oxo-2-sulfanyl-idene-1,2,3,4-tetra-hydro-pyrimidine-5-carbonitrile. Acta Crystallogr Sect E Struct Rep Online 2012; 68:o676-7. [PMID: 22412573 PMCID: PMC3295462 DOI: 10.1107/s1600536812005119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 02/06/2012] [Indexed: 11/11/2022]
Abstract
The title thio-uracil derivative, C(9)H(11)N(3)OS, exists in the thione form. The six atoms comprising the ring are almost coplanar [r.m.s. deviation = 0.015 Å] and the 2-methyl-propyl group lies approximately perpendicular to this plane [the N-C-C-C torsion angle is 72.88 (14)°]. Linear supra-molecular chains along [001] sustained by N-H⋯O and N-H⋯S hydrogen bonding feature in the crystal packing.
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Affiliation(s)
- Omar A. Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A. El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Seik Weng Ng
- Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Chemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203 Jeddah, Saudi Arabia
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Santra S, Ranjan P, Bera P, Ghosh P, Mandal SK. Anchored palladium nanoparticles onto single walled carbon nanotubes: Efficient recyclable catalyst for N-containing heterocycles. RSC Adv 2012. [DOI: 10.1039/c2ra20281f] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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El-Emam AA, Al-Deeb OA, Al-Turkistani AA, Ng SW, Tiekink ERT. 2-Benzyl-sulfanyl-4-pentyl-6-(phenyl-sulfan-yl)pyrimidine-5-carbonitrile. Acta Crystallogr Sect E Struct Rep Online 2011; 67:o3126. [PMID: 22220128 PMCID: PMC3247510 DOI: 10.1107/s1600536811044746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 10/26/2011] [Indexed: 11/10/2022]
Abstract
In the title pyrimidine derivative, C23H23N3S2, the phenylsulfanyl and benzylsulfanyl benzene rings are orientated away from the carbonitrile group and are twisted out of the plane of the central ring with dihedral angles of 77.66 (6) and 64.73 (5)°, respectively. The n-pentyl group has an extended trans conformation. In the crystal, supramolecular layers in the ab plane are sustained by C—H⋯π and π–π interactions [pyrimidine–phenylsulfanyl centroid–centroid distance = 3.8087 (7) Å].
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