1
|
Structural and optical properties of salicyl-N-methyl-4-stilbazolium tosylate: Thermal, DFT, MEP and Hirshfeld surface analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
2
|
A single-molecule with multiple investigations: Synthesis, characterization, computational methods, inhibitory activity against Alzheimer's disease, toxicity, and ADME studies. Comput Biol Med 2022; 146:105514. [DOI: 10.1016/j.compbiomed.2022.105514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/01/2022] [Accepted: 04/09/2022] [Indexed: 01/18/2023]
|
3
|
Synthesis, supramolecular structure, spectral properties and correlation between nonlinear optic, thermochemistry and thermal behavior of an α-Hydroxyphosphonate acid ester, dual experimental and DFT approaches. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
4
|
A new 1,2,3-triazole and its rhodamine B derivatives as a fluorescence probe for mercury ions. Anal Biochem 2020; 598:113690. [PMID: 32259511 DOI: 10.1016/j.ab.2020.113690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/02/2020] [Accepted: 03/12/2020] [Indexed: 02/08/2023]
Abstract
A newly synthesized compound, 5-methyl-1-phenyl-1H-1,2,3-triazole-4- carboxylic acid (MPC) was analyzed for its quantum chemical parameters and theoretical spectrum by computational chemistry. The calculated spectrum was in accord with the experimental measurements in a great degree. Then MPC was successfully designed and synthesized to a novel rhodamine B derivative RMPC. The RMPC exhibited about a 4000-fold increase in fluorescence intensity in the presence of Hg2+ ions over most other competitive metal ions. The triazole appended colorless chemodosimeter RMPC turns to pink upon the complex formation only with Hg2+ ions as a 1: 2 M ratio and enables naked-eye detection. The coordination mechanism of turning on/off fluorescence for Hg2+ ions were well proposed by explaining Hg2+ inducing the ring-opened rhodamine B moiety. The fluorescence imaging experiments of Hg2+ in HeLa cell demonstrated that the probe was labeled and it could be used in biological systems.
Collapse
|
5
|
The specific binding of a new 1,2,3-triazole to three blood proteins and it's appended rhodamine complex for selective detection of Hg 2. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117728. [PMID: 31748164 DOI: 10.1016/j.saa.2019.117728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
A synthesized compound, ethyl 2,5-diphenyl-2H-1,2,3-triazole-4- carboxylate (EDTC) was investigated on its physiochemical parameters and structural properties by using the quantum-chemical method. The results on the theoretical spectrum of EDTC were line with experimental fluorescence and absorption spectrum in large degree. Then EDTC was successfully synthesized to a novel rhodamine-based fluorescent probe (REDTC), which showed a distinct fluorescence enhancement upon the presence of Hg2+ in dimethyl formamide-water (DMF-H2O) buffer solution (pH 7.4). Meanwhile, the triazole appended colorless compound turns to pink upon complex formation with Hg2+ ions as 1:2 molar ratios and enables naked-eye detection. The chromogenic mechanism was determined by using spectroscopic measurements and TD DFT calculation. The fluorescence imaging experiments of Hg2+ in HeLa cell revealed that the probe REDTC could be labeled and it could be used in biological systems. Also, the intermediate EDTC was developed as a sensitive fluorescent probe for specific studies on the interactions to three kinds of blood proteins including human serum albumin (HSA), human immunoglobulin (HIg) and bovine hemoglobin (BHb) by using a series of spectroscopic methods and molecular docking under the simulative physiological conditions. The interactions between EDTC and these proteins led to the distinct fluorescence enhancement. The thermodynamic measured results further suggested that hydrophobic forces play a dominating role in stabilizing the complexes, which are in correspondence with the results from molecular docking. The UV-visible, synchronous, and three-dimensional (3D) fluorescence measurements demonstrated that EDTC influences the conformational of proteins and the microenvironment surrounding HSA, HIg, or BHb in aqueous solution.
Collapse
|
6
|
Structural studies of 3-[(E)-[(2E)-2-methyl-3-phenylprop-2-en-1-ylidene] amino]-1-phenylthiourea: Combined experimental and computational studies. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.04.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Density functional theory, molecular docking and bioassay studies on ( S)-2-hydroxy-N-(2 S,3 S,4 R, E)-1,3,4 trihydroxyicos-16-en-2-yl)tricosanamide. Heliyon 2019; 5:e02038. [PMID: 31417966 PMCID: PMC6690558 DOI: 10.1016/j.heliyon.2019.e02038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 02/24/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022] Open
Abstract
A novel indigoferamide-A, earlier isolated from the seeds of Indigofera heterantha Wall was characterized using density functional theory, molecular docking and bioassays studies. Density functional theory calculations were performed at B3LYP/6-31G(d,p) to gain geometric insight of the compound. Conformational analyses have been performed around three important dihedral angles to explore the lowest energy structure and conformer. The simulated vibrational spectrum of the compound at B3LYP/6-31G(d,p) was scaled with two scaling factors, and the scaled harmonic vibrations shows nice correlation with the experimental values. 1H and 13C NMR chemical shifts were calculated using Cramer's re-parameterized function W04 at 6- 31G(d,p) basis set. Several conformers lying within 2 kcal mol-1 of the minimum energy conformer were considered; however, the chemical shifts were not significantly different among these conformers. The Gaussian averaged theoretical 1H and 13C chemical shifts correlate nicely with the experimental data. Electronic properties such as band gap, ionization potential and electron affinities were also simulated for the first time, however, no comparison could be made with the experiment. The compound was also screened for urease, antiglycation activities and the theoretical explanation of the results is provided based on molecular docking simulations.
Collapse
|
8
|
The computational and experimental studies on a 1, 2, 3-triazole compound and its special binding to three kinds of blood proteins. J Biomol Struct Dyn 2019; 38:1185-1196. [PMID: 30909827 DOI: 10.1080/07391102.2019.1598498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A newly synthesized compound, ethyl 5-phenyl-2-(p-tolyl)-2H-1, 2, 3-triazole-4-carboxylate (EPPC) may be considered as a drug candidate and was exploited to study the structural and spectral properties by using quantum chemical calculation and multiple spectroscopic techniques. The results on theoretical spectrum of EPPC were consistent with experimental spectrum in great degree. In addition, EPPC has been as a special probe and investigated on the interactions with three kinds of blood proteins including human serum albumin (HSA), human immunoglobulin (HIgG) and bovine hemoglobin (BHb) by using UV-Vis, fluorescence spectroscopy and molecular modeling, respectively. Changes in various fluorescence and UV-Vis spectra were observed upon ligand binding along with a remarkable degree of fluorescence enhancement on complex formation under physiological condition with binding constant about 105 order of magnitudes, which caused the variations of conformation and microenvironment of these proteins in aqueous solution. The obtained results from the thermodynamic parameters calculated according to the van't Hoff equation indicated that the entropy change ΔS° and enthalpy change ΔH° were found to be 0.168 KJ/mol K and 22.154 KJ/mol for EPPC-HSA system, 0.284 KJ/mol K and 54.408 KJ/mol for EPPC-HIgG system, and 0.228 KJ/mol K and 37.548 KJ/mol for EPPC-BHb system, respectively, which demonstrated that the primary binding pattern is determined by hydrophobic interaction. The results of docking and molecular dynamics simulation using three proteins crystal models revealed that EPPC could bind to three proteins well into hydrophobic cavity, which showed good consistence with the spectroscopic measurements.Communicated by Ramaswamy H. Sarma.
Collapse
|
9
|
The B3 triangle faces of B6H62− as the preferred electron donor sites for successive interactions with HF in B6H6(HF)2– complexes (n = 1–8). Polyhedron 2019. [DOI: 10.1016/j.poly.2018.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
10
|
Studies of the Chemical Reactivity of a Series of Rhodanine Derivatives by Approaches to Quantum Chemistry. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/cmb.2019.93005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
11
|
New asymmetric and symmetric 2-((pyridin-4-yl)methylenamino)-3 aminomaleo nitrile and 2,3-bis((pyridin-4-yl)methylenamino)maleonitrile Schiff bases: Synthesis, experimental characterization along with theoretical studies. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
12
|
Improving the first hyperpolarizability of anthracene through interaction with HX molecules (XF, Cl, Br): A theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:353-365. [PMID: 29475184 DOI: 10.1016/j.saa.2018.02.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 01/28/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
The variations in nonlinear optical activity (NLO) of anthracene (C14H10) was investigated via intermolecular interactions between C14H10 and HX molecules (XF, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C14H10⋯HX complexes were computed. The adsorption of hydrogen halide through C14H10⋯HX complex formation, didn't change much the linear optical activities of C14H10 molecule, but the magnitude of the first hyperpolarizability of the C14H10⋯HX complexes to be as much as that of urea.
Collapse
|
13
|
Theoretical study of intermolecular interactions in FH⋯C 4 B 2 H 6 ⋯X clusters (X = H 2 O, CH 3 OH, NH 3 , O 2 , N 2 , HCN, CO, NO and CO 2 ). COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
14
|
Theoretical study of optical activity of 1:1 hydrogen bond complexes of water with S-warfarin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 168:180-189. [PMID: 27294546 DOI: 10.1016/j.saa.2016.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/02/2016] [Indexed: 06/06/2023]
Abstract
The molecular interaction between S-warfarin (SW) and a single water molecule was investigated using the B3LYP method at 6-311++G(d,p) basis set. The vibrational spectra of the optimized complexes have been investigated for stabilization checking. Quantum theories of atoms in molecules, natural bond orbitals, molecular electrostatic potentials and energy decomposition analysis methods have been applied to analyze the intermolecular interactions. The intermolecular charge transfer in the most stable complex is in the opposite direction from those in the other complexes. The optical spectra and the hyperpolarizabilities of SW-water hydrogen bond complexes have been computed.
Collapse
|
15
|
Neutral and cationic half-sandwich arene ruthenium, Cp*Rh and Cp*Ir oximato and oxime complexes: Synthesis, structural, DFT and biological studies. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
16
|
Spectroscopic (FT-IR, (1)H, (13)C NMR, UV), DOS and orbital overlap population analysis of copper complex of (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine by density functional theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1932-1940. [PMID: 25467688 DOI: 10.1016/j.saa.2014.10.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/14/2014] [Accepted: 10/23/2014] [Indexed: 06/04/2023]
Abstract
The geometric parameters, chemical shifts, FTIR, NMR and orbital overlap population along with DOS (density of states) to know different kinds of interactions for binding of copper atom with (E)-4-(2-(4-nitrophenyl) diazenyl)-N, N bis ((pyridin-2-yl) methyl) benzamine to form its copper complex has been reported by DFT methods. The theoretically predicted values for structural parameters are in agreement with the experimentally reported values. NMR chemical shifts calculated using B3LYP/DFT/GIAO level of theory gives information about binding of copper atom with three nitrogen atoms namely N (3, 8 and 11). Orbital overlap population analysis using DFT/B3LYP/SDD level of theory is used to study the kind of interactions involved in binding of copper with the three nitrogen atoms. DOS studies are done to know about the contribution of alpha, beta electrons to the valence and conduction band. IR spectroscopy investigations gave the absorption bands for the formation of title compound. Electronic spectrum along with HOMO-LUMO energies of the title compound has been investigated using Time-dependent (TD-DFT) approach.
Collapse
|
17
|
Molecular structure, IR spectra, and chemical reactivity of cisplatin and transplatin: DFT studies, basis set effect and solvent effect. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:902-8. [PMID: 26119356 DOI: 10.1016/j.saa.2015.06.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/24/2015] [Accepted: 06/04/2015] [Indexed: 05/10/2023]
Abstract
Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N-H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.
Collapse
|