1
|
Majumdar D, Philip JE, Gassoumi B, Ayachi S, Abdelaziz B, Tüzün B, Roy S. Supramolecular clumps of μ 2-1,3-acetate bridges of Cd(II)-Salen complex: Synthesis, spectroscopic characterization, crystal structure, DFT quantization's, and antifungal photodynamic therapy. Heliyon 2024; 10:e29856. [PMID: 38707382 PMCID: PMC11066650 DOI: 10.1016/j.heliyon.2024.e29856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
The article divulges the crystal growth, synthesis, and X-ray structure characterization of one centrosymmetric cadmium complex, [Cd{CdL(μ2-1,3-acetate)}2] using Salen ligand (SL). The complex is further characterized using spectroscopic and analytical techniques, including DRS, SEM-EDX, PXRD, and ICP-MS. The crystallographic study showed that the complex has a monoclinic space P21/c. Addison parameters (Ʈ) show the hexagonal geometry of the central Cd(II) metal ion. Hirshfeld surface and 2-D fingerprint confirm supramolecular contacts despite weak C-H⋯O and C-H···π interactions. Energy frameworks, FMOs, global reactivity parameters, MEP, and energy bandgap explain the complex reactivity outlook. The complex inter- and intramolecular bonding interactions were explored through natural bond orbital (NBO), QTAIM, NCI-RDG, Electron Location Function (ELF), and Localized Orbital Locator (LOL) quantization methods. In addition, the complex and its synthetic components in vitro antibacterial efficacy were investigated using Gram-positive and Gram-negative microbial strains. SAR (structure-activity relationship) correlates with biological potency. Molecular docking assessed antimicrobial potency with proteins S. aureus (PDB ID: 1JIJ), C. albicans (PDB ID: 1M7A), E. coli (PDB ID: 1T9U), P. aeruginosa (PDB ID: 2UV0), and A. Niger (PDB ID: 3K4P). The findings are backed by the Protein-Ligand Interaction Profiler (PLIP). The antifungal potency and cell viability test of C. albicans were conducted using photodynamic therapy (APDT).
Collapse
Affiliation(s)
- Dhrubajyoti Majumdar
- Department of Chemistry, Tamralipta Mahavidyalaya, Tamluk, 721636, West Bengal, India
| | | | - Bouzid Gassoumi
- Laboratory of Advanced Materials and Interfaces (LIMA), University of Monastir, Faculty of Sciences of Monastir, Avenue of Environment, 5000, Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, Avenue of the Environment 5019 Monastir, University of Monastir, Tunisia
| | - Balkis Abdelaziz
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, Avenue of the Environment 5019 Monastir, University of Monastir, Tunisia
| | - Burak Tüzün
- Sivas Cumhuriyet University, Sivas Vocational School, Department of Plant and Animal Production, TR-58140, Sivas, Turkey
| | - Sourav Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560012, India
| |
Collapse
|
2
|
Gurbanov AV, Firoozbakht F, Pourshirband N, Sharafi-Badr P, Hayati P, Souri B, Eshghi F, Kaminsky W, Mahmoudi G, Verpoort F, Mehrabadi Z. A new 1D Mn(II) coordination polymer: Synthesis, crystal structure, hirshfeld surface analysis and molecular docking studies. Heliyon 2024; 10:e29565. [PMID: 38699722 PMCID: PMC11063412 DOI: 10.1016/j.heliyon.2024.e29565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024] Open
Abstract
The synthesis of novel metal-organic coordination polymers (MOCP) with the chemical formula [Mn2L (SCN)2(OH)2]3·CH3OH [L = 1,5-bis(pyridine-4-ylmethylene) carbonohydrazide] {1} was accomplished using two different techniques: solvothermal and sonochemical ultrasonic-assisted. An investigation was carried out to examine the impact of various factors such as reaction time, sonication power, temperature, and reactant concentration on the morphology and size of the crystals. Interestingly, it was found that sonication power and temperature did not affect the crystals' morphology and size. To further analyze the prepared microcrystals of MOCPs, SEM was utilized to examine their surface morphology, and XRD, elemental evaluation composition. The identification of the functional groups present in the prepared Mn-MOCPs was accomplished through the utilization of FT-IR spectroscopy. Subsequently, the calcination of 1 in an air atmosphere at 650 °C led to the formation of Mn3O4 nanoparticles. The geometric and electronic structure of the MOCPs was evaluated using density functional theory (DFT). The utilization of molecular docking methodologies demonstrated that the best cavity of the human androgen receptor possessed an interaction energy of -116.3 kJ mol-1. This energy encompassed a combination of both bonding and non-bonding interactions. The Results showed that steric interaction and electrostatic potential are the main interactions in AR polymer and Mn(II). These interactions in the defined cavity indicated that this polymer could be an effective anti-prostate candidate, because AR is involved in the growth of prostate cancer cells, and these interactions indicated the inhibition of prostate cancer cell growth.
Collapse
Affiliation(s)
- Atash V. Gurbanov
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- Excellence Center, Baku State University, Z. Khalilov Str. 23, AZ 1148 Baku, Azerbaijan
- Western Caspian University, Istiqlaliyyat Street 31, AZ 1001, Baku, Azerbaijan
| | - Fateme Firoozbakht
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran
| | - Nafiseh Pourshirband
- Department of Chemistry, Shahreza Branch, Islamic Azad University, P.O. Box 311-86145, Shahreza, Isfahan, Iran
| | - Paria Sharafi-Badr
- Department of Pharmacognosy and Pharmaceutical Biotechnology, School of Pharmacy, Iran University of Medical Sciences, Tehran, Iran
| | - Payam Hayati
- Organic and Nano Group (ONG), Department of Chemistry, Iran University of Science and Technology (IUST), PO Box 16846-13114, Tehran, Iran
| | - Bagher Souri
- Department of Chemistry, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran
| | - Fazlolah Eshghi
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz, Iran
| | - Werner Kaminsky
- X-ray Crystallography Laboratory, University of Washington, United States
| | - Ghodrat Mahmoudi
- Department of Chemistry, Faculty of Science, University of Maragheh, P.O. Box 55136-83111, Maragheh, Iran
- Chemistry Department, Faculty of Engineering and Natural Sciences, Istinye University, Sarıyer, Istanbul 34396, Turkey
| | - Francis Verpoort
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, China
| | - Zohreh Mehrabadi
- Department of Chemistry, Firoozabad Branch, Islamic Azad University, Firoozabad, Iran
| |
Collapse
|
3
|
Majumdar D, Frontera A, Roy S, Sutradhar D. Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN - Ions: A Holistic View in Crystal Engineering. ACS OMEGA 2024; 9:1786-1797. [PMID: 38222609 PMCID: PMC10785279 DOI: 10.1021/acsomega.3c08422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024]
Abstract
In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).
Collapse
Affiliation(s)
- Dhrubajyoti Majumdar
- Department
of Chemistry, Tamralipta Mahavidyalaya, Tamluk, West Bengal 721636, India
| | - Antonio Frontera
- Department
de Quimica, Universitat de les Illes Balears, Cra. de Valldemossa km 7.5, Palma de Mallorca (Baleares) 07122, Spain
| | - Sourav Roy
- Solid
State and Structural Chemistry Unit, Indian
Institute of Science, Bangalore 560012, India
| | - Dipankar Sutradhar
- School
of Advanced Sciences and Languages, VIT
Bhopal University, Kothrikalan, Sehore, Madhya Pradesh 466114, India
| |
Collapse
|
4
|
Chavez-Urias I, López-González LE, Plascencia-Martínez DF, García JJ, Flores-Alamo M, Sugich-Miranda R, Medrano F, Picos-Corrales LA, López-Gastélum KA, Velázquez-Contreras EF, Rocha-Alonzo F. l-Isoleucine-Schiff Base Copper(II) Coordination Polymers: Crystal Structure, Spectroscopic, Hirshfeld Surface, and DFT Analyses. ACS OMEGA 2023; 8:24601-24614. [PMID: 37457461 PMCID: PMC10339395 DOI: 10.1021/acsomega.3c02878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
A new copper(II) coordination polymer was synthesized from the l-isoleucine-Schiff base and characterized by elemental analysis, Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible (UV-vis) spectroscopy, single-crystal X-ray diffraction (XRD) analysis, electronic paramagnetic resonance, and thermogravimetric analysis. XRD analysis confirmed the square planar coordination geometry of metallic centers and a zipper-like polymer structure. Vibrational, electronic, and paramagnetic spectroscopies and thermal analysis were consistent with the crystal structure. A Hirshfeld surface (HS) and density functional theory (DFT) analyses were employed to gain additional insight into interactions responsible for complex packing. The quantitative examination of two-dimensional (2D) fingerprint plots revealed, among other van der Waals forces, the dominating participation of H···H and H···Cl interactions in the molecular packing. The use of computational methods provided great help in detailing the supramolecular interactions occurring in the crystal, which were mainly van der Waals attractions. The electronic transition analysis helped corroborate the electronic transitions observed experimentally in the absorption spectrum. The frequency and vibrational mode analysis gave a deeper insight into the characterization of the CuLCL complex.
Collapse
Affiliation(s)
- Iván
F. Chavez-Urias
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Luis E. López-González
- Centro
de Investigación Científica y de Educación Superior
de Ensenada, Carretera Tijuana-Ensenada 3918, Zona Playitas, Ensenada, Baja California 22860, México
| | - Damian F. Plascencia-Martínez
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Juventino J. García
- Facultad
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior Cd. Universitaria, Coyoacán,
Ciudad de México, Ciudad de México 04510, México
| | - Marcos Flores-Alamo
- Facultad
de Química, Universidad Nacional
Autónoma de México, Circuito Exterior Cd. Universitaria, Coyoacán,
Ciudad de México, Ciudad de México 04510, México
| | - Rocío Sugich-Miranda
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Felipe Medrano
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Lorenzo A. Picos-Corrales
- Facultad
de Ingeniería Culiacán, Universidad
Autónoma de Sinaloa, Ciudad Universitaria, Culiacán, Sinaloa 80013, México
| | - Karla-Alejandra López-Gastélum
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
- Centro de
Investigación en Alimentación y Desarrollo, Carretera a Ejido La Victoria Km
0.6, Hermosillo, Sonora 83304, México
| | - Enrique F. Velázquez-Contreras
- Departamento
de Investigación en Polímeros y Materiales, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| | - Fernando Rocha-Alonzo
- Departamento
de Ciencias Químico-Biológicas, Universidad de Sonora, Calle Rosales y Blvd. Luis Encinas s/n, Col. Centro, Hermosillo, Sonora 83000, México
| |
Collapse
|
5
|
Majumdar D, Philip JE, Dubey A, Tufail A, Roy S. Synthesis, spectroscopic findings, SEM/EDX, DFT, and single-crystal structure of Hg/Pb/Cu-SCN complexes: In silico ADME/T profiling and promising antibacterial activities. Heliyon 2023; 9:e16103. [PMID: 37251888 PMCID: PMC10213201 DOI: 10.1016/j.heliyon.2023.e16103] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
This work contemplates synthesizing M-SCN crystal compounds (M = Hg/Pb/Cu) in the presence of respective metal salts and exogenous ancillary SCN- ion by slowly evaporating the mixed solvent (CH3OH + ACN). The complexes were characterized by spectroscopy, SEM/EDX, and X-ray crystallography. The Hg-Complex, Pb-Complex, and Cu-Complex crystallize in the monoclinic space group (Z = 2/4). The crystal packing fascinatingly consists of weak covalent bonding and Pb⋯S contacts of tetrel type bond. Here are the incredible supramolecular topographies delineated by the Hirshfeld surface and 2D fingerprint plot. The B3LYP/6-311++G (d, p) level calculations in the gas phase optimized the compound's geometry. The energy difference (Δ) between HOMO-LUMO and global reactivity parameters investigates the complex's energetic activity. MESP highlights the electrophilic/nucleophilic sites and H-bonding interactions. Molecular docking was conceded with the Gram- + ve bacterium Bacillus Subtilis (PDB ID: 6UF6) and the Gram-ve bacterium Proteus Vulgaris (PDB ID: 5HXW) to authenticate the bactericidal activity. ADME/T explains the various pharmacological properties. In addition, we studied the antibacterial activity with MIC (μg/mL) values and time-kill kinetics against Staphylococcus aureus (ATCC 25923) and Bacillus subtilis (ATCC 6635) as Gram-positive, Pseudomonas aeruginosa (ATCC 27853) and Escherichia coli (ATCC 25922) as Gram-negative bacteria.
Collapse
Affiliation(s)
- Dhrubajyoti Majumdar
- Department of Chemistry, Tamralipta Mahavidyalaya, Tamluk-721636, West Bengal, India
| | | | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, 274203, India
- Department of Pharmacology, Saveetha Dental College, and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, 600077, India
| | - Aisha Tufail
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, 274203, India
| | - Sourav Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, India
| |
Collapse
|