1
|
Raimi MA, Rajee AO, Gber TE, Arikpo TO, Pembere AMS, Louis H. Cobalt group transition metals (TM: Co, Rh, Ir) coordination of S-doped porphyrins (TM_S@PPR) as sensors for molecular SO 2 gas adsorption: a DFT and QTAIM study. J Mol Model 2024; 30:85. [PMID: 38411800 DOI: 10.1007/s00894-024-05879-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024]
Abstract
CONTEXT The intricate challenges posed by SO2 gas underscore the imperative for meticulous monitoring and detection due to its adverse effects on health, the environment, and equipment integrity. Hence, this research endeavors to delve deeply into the intricate realm of transition-metals functionalized sulfur-doped porphyrins (S@PPR) surfaces through a comprehensive computational study. The electronic properties revealed that upon adsorption, Ir_S@PPR surface reflects the least energy gap of 0.109 eV at the O-site of adsorptions, indicating an increase in electrical conductivity which is a better adsorption trait. Owing to the negative adsorption energy observed, the adsorption behavior is described as chemisorption, with the greatest adsorption energy of - 10.306 eV for Ir_S@PPR surface at the S-site of adsorption. Based on the mechanistic attributes, iridium-functionalized S@PPR surface is a promising detecting material towards the sensing of SO2 gas. This report will provide useful insight for experimental researchers in selecting and engineering materials to be used as detectors for SO2 gas pollutant. METHOD All theoretical investigations were carried out using density functional theory (DFT), calculated at PW6B95-D3/GenECP/Def2svp/LanL2DZ computational method.
Collapse
Affiliation(s)
- Monsurat Alarape Raimi
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, University of Ilorin, Ilorin, Nigeria
| | | | - Terkumbur E Gber
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences Saveetha University, Chennai, India
| | - Temple Okah Arikpo
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | | | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria.
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| |
Collapse
|
2
|
Mookkan M, Kandasamy S, Al-Odayni AB, Abduh NAY, Srinivasan S, Revannasidappa BC, Kumar V, Chinnasamy K, Aravindhan S, Shankar MK. A Structural and In Silico Investigation of Potential CDC7 Kinase Enzyme Inhibitors. ACS OMEGA 2023; 8:47187-47200. [PMID: 38107948 PMCID: PMC10719926 DOI: 10.1021/acsomega.3c07059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
A crucial role in the regulation of DNA replication is played by the highly conserved CDC kinase. The CDC7 kinase could serve as a target for therapeutic intervention in cancer. The primary heterocyclic substance is pyrazole, and its derivatives offer great potential as treatments for cancer cell lines. Here, we synthesized the two pyrazole derivatives: 4-(2-(4-chlorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-1) and 4-(2-(2,4-difluorophenyl)hydrazinyl)-5-methyl-2-tosyl-1H-pyrazol-3(2H)-one (PYRA-2). The structural confirmation of both the compounds at the three-dimensional level is characterized using single crystal X-ray diffraction and density functional theory. Furthermore, the in silico chemical biological properties were derived using molecular docking and molecular dynamics (MD) simulations. PYRA-1 and PYRA-2 crystallize in the P-1 (a = 8.184(9), b = 14.251(13), c = 15.601(15), α = 91.57(8), β = 97.48(9), 92.67(9), V = 1801.1(3) 3, and Z = 2) and P21/n (a = 14.8648(8), b = 8.5998(4), c = 15.5586(8), β = 116.47(7), V = 1780.4(19) 3, and Z = 4), space groups, respectively. In both PYRA-1 and PYRA-2 compounds, C-H···O intermolecular connections are common to stabilize the crystal structure. In addition, short intermolecular interactions stabilizes with C-H···π and π-π stacking. Crystal packing analysis was quantified using Hirshfeld surface analysis resulting in C···H, O···H, and H···H contacts in PYRA-1 exhibiting more contribution than in PYRA-2. The conformational stabilities of the molecules are same in the gas and liquid phases (water and DMSO). The docking scores measured for PYRA-1 and PYRA-2 with CDC7 kinase complexes are -5.421 and -5.884 kcal/mol, respectively. The MD simulations show that PYRA-2 is a more potential inhibitor than PYRA-1 against CDC7 kinase.
Collapse
Affiliation(s)
- Mohanbabu Mookkan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Saravanan Kandasamy
- Faculty
of Chemistry, University of Warsaw, Ludwika Pasteura 1, Warsaw 02-093, Poland
| | - Abdel-Basit Al-Odayni
- Department
of Restorative Dental Science, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11545, Saudi Arabia
| | - Naaser Ahmed Yaseen Abduh
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Sugarthi Srinivasan
- Department
of Physics and Nanotechnology, SRM Institute
of Science and Technology, Kattankulathur 603203, India
| | - Bistuvalli Chandrashekara Revannasidappa
- Department
of Pharmaceutical Chemistry, NGSM Institute
of Pharmaceutical Sciences of Nitte - Deemed to be University, Paneer, Deralakatte, Mangalore 575018, Karnataka India
| | - Vasantha Kumar
- Department
of P.G. Chemistry, Sri Dharmasthala Manjunatheshwara
College (Autonomous), Ujire 574240, India
| | | | - Sanmargam Aravindhan
- Department
of Physics, Presidency College (Autonomous), University of Madras, Chennai 600 005, India
| | - Madan Kumar Shankar
- Department
of Chemistry-BMC, University of Uppsala, Husargatan 3, Uppsala 75237, Sweden
| |
Collapse
|