ABSTRACT
Employing a synergistic combination of theoretical density functional theory (DFT) and experimental techniques, we conducted a comprehensive analysis elucidating the structural and pharmacological attributes of 5-(adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (5A4BT) as a potent COX inhibitor. The X-ray crystallographic data of 5A4BT showed the pivotal role played by weak interactions, notably π-π and C-H-π interactions, alongside hydrogen bonding, in orchestrating the intricate supramolecular architectures within the crystalline lattice. A quantitative analysis of the arrangement of the crystal structure, as well as both inter- and intramolecular interactions, was conducted using Hirshfeld surfaces and 2D fingerprint plots. Additionally, a comprehensive examination of the IR spectra was undertaken, employing both experimental methods and theoretical DFT techniques, to elucidate the vibrational characteristics of the compound. The strength of intermolecular N-H···S hydrogen bonding and charge transfer within the system was assessed through natural bonding orbital analysis. Moreover, Bader's atoms in molecules theory was employed to estimate the strength of intermolecular hydrogen bonds, revealing strong interactions within the 5A4BT dimer. The title compound exhibited binding affinities of -6.4 and -6.5 kcal/mol for COX1 (PDB 3KK6) and COX2 (1CX2) target proteins, respectively. For the first time, predictions regarding ADMET properties, drug-likeness, and toxicity, including favorable bioavailability, along with 100 ns molecular dynamics simulations, binding free energy, and energy decomposition per residue in the binding cavity of the protein from molecular mechanics generalized born surface area approach, collectively indicate the potential of 5A4BT as a nonselective COX inhibitor.
ABSTRACT
The present work encompasses a combined experimental and theoretical investigation of the molecular structure, vibrational wavenumbers, electronic structure at the ground and electronic excited states, molecular electrostatic potential surface of 7-(Trifluoromethyl)-1H-indole-2-carboxylic acid (TICA) and possibility of the title molecule as an aromatase inhibitor using molecular docking and molecular dynamic simulations. A stable conformer has been obtained using potential energy scans by varying appropriate dihedral angles. The obtained minimum energy conformer was further optimized at the 6-311++G (d, p) basis set by applying the most accepted B3LYP functional. A good agreement between experimental and calculated normal modes of vibration has been observed. The hydrogen-bonded interaction between two monomeric units of TICA has been investigated using NBO,QTAIM, and NCI (noncovalent interactions) analysis. Molecular docking of TICA with human placental aromatase (PDB ID: 3S79) reveals the formation of polar hydrogen bonds as well as hydrophobic interactions between the ligand and the protein, right in the binding cavity. TICA satisfies all pharmacokinetic filters (Lipinski rule of five, the Veber rule, Ghose rule, Egan rule, as well as the Muegge rule) and has a high bioavailability score of 0.85. Dynamic stability of the ligand within the binding pocket of the target protein has been confirmed by 100 ns molecular dynamics simulation results. The present study provides an excellent starting point for additional in vivo research, and TICA may eventually serve as a significant therapeutic candidate for the treatment of breast cancer.
Subject(s)
Aromatase Inhibitors , Molecular Dynamics Simulation , Carboxylic Acids , Electronics , Female , Humans , Indoles , Ligands , Molecular Docking Simulation , Molecular Structure , Placenta , Pregnancy , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Thermodynamics , VibrationABSTRACT
Extensive investigation on the molecular and electronic structure of 2-amino-5-trifluoromethyl-1,3,4-thiadiazole in the ground state and in the first excited state has been performed. The energy barrier corresponding to the conversion between imino and amino tautomers has been calculated, which indicates the existence of amino tautomer in solid state for the title compound. The FT-Raman and FT-IR spectra were recorded and compared with theoretical vibrational wavenumbers, and a good coherence has been observed. The MESP map, dipole moment, polarizability, and hyperpolarizability have been calculated to comprehend the properties of the title molecule. High polarizability value estimation of the title compound may enhance its bioactivity. Natural bonding orbital analysis has been done on monomer and dimer to investigate the charge delocalization and strength of hydrogen bonding, respectively. Strong hydrogen bonding interaction energies of 17.09/17.49 kcal mol-1 have been calculated at the B3LYP/M06-2X functional. The UV-vis spectrum was recorded and related to the theoretical spectrum. The title compound was biologically examined for anticancer activity by studying the cytotoxic performance against two human cancer cell lines (A549 and HeLa) along with the molecular docking simulation. Both molecular docking and cytotoxic performance against cancer cell lines show positive outcomes, and the title compound appears to be a promising anticancer agent.
ABSTRACT
Present work aims at identifying the conformational and spectroscopic profile of 2-acetamido-5-aminopyridine compound by means of experimental and computational methods. To achieve this, three-dimensional potential energy scan (PES) was performed by varying the selected dihedral angles at B3LYP/6-31+G(d,p) level of theory and thus stable conformers of the title compound were determined. The most stable conformer was further optimized at higher level and vibrational wavenumbers were calculated. Experimentally, vibrational features of title compound were determined by FT-IR and FT-Raman spectroscopic methods in the solid phase while the electronic absorption spectrum was recorded in methanol solution. On the basis of these investigations, the conformational and spectroscopic attributes of 2-acetamido-5-aminopyridine were interpreted.
Subject(s)
Acetamides/chemistry , Aminopyridines/chemistry , Pyridines/chemistry , Fourier Analysis , Models, Molecular , Molecular Conformation , Quantum Theory , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, RamanABSTRACT
Experimentally observed spectral data (FT-TR and FT-Raman) of 3-methylbezothiazole-2-thione (3MBT2T) were compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. UV-Vis spectrum of the title compound was recorded and the electronic properties, such as frontier molecular orbitals and band gap energies were calculated by TD-DFT approach. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better comprehension of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to investigate the stability of the molecule arising from charge delocalization. Global and local reactivity descriptors were also computed to predict reactivity and reactive sites on the molecule.
Subject(s)
Models, Chemical , Thiones/chemistry , Molecular Structure , Spectrophotometry, UltravioletABSTRACT
The reaction of N-(2-(hydrazinecarbonyl)aryl)benzamides 2a, b with indoline-2,3-diones 4ae in acidified ethanolic solution furnished the corresponding N-(2-(2-(2-oxoindolin-3-ylidene)hydrazinecarbonyl)phenyl)benzamides 5aj, respectively. Furthermore, 3-(2-oxoindolin-3-ylideneamino)-2-substituted quinazolin-4(3H)-ones 6aj were prepared by the reaction of 3-amino-2-arylquinazolin-4(3H)-one 3a, b with 4ae. Six derivatives of the twenty newly synthesized compounds showed remarkable antitumor activity against most of the tested cell lines, Daoy, UW228-2, Huh-7, Hela and MDA-MB231. Although these six compounds were more potent than the standard drug (CFM-1), indeed compounds 5b, 5d and 6b were the best candidates with IC50 values in the range 1.866.87, 4.4210.89 and 1.468.60 µg/ml and percentage inhibition in the range 77.188.7, 59.4184.8 and 75.488.0%, respectively. QSAR analyses on the current series of derivatives also have been performed for all five cancer cell lines and thus 10 statistically significant models were developed and internally cross validated.
Subject(s)
Antineoplastic Agents/pharmacology , Benzamides/pharmacology , Benzodiazepinones/pharmacology , Drug Design , Indoles/pharmacology , Quantitative Structure-Activity Relationship , Quinazolinones/pharmacology , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Benzamides/chemical synthesis , Benzamides/chemistry , Benzodiazepinones/chemical synthesis , Benzodiazepinones/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Dose-Response Relationship, Drug , HeLa Cells , Humans , Indoles/chemical synthesis , Indoles/chemistry , Molecular Structure , Quinazolinones/chemical synthesis , Quinazolinones/chemistry , Structure-Activity RelationshipABSTRACT
FT-Raman and FT-IR spectra of the title compound 2-{[5-(adamantan-1-yl)-4-methyl-4H-1,2,4-triazol-3-yl]sulfanyl}-N,N-dimethylethanamine were recorded and investigated. The DFT/B3LYP/6-311++G(d,p) method was used to compute the vibrational wavenumbers. A good coherence between experimental and theoretical wavenumbers shows the preciseness of the assignments. NLO properties like the dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface and contour map have been calculated to get a better cognizance of the properties of the title molecule. Natural bond orbital analysis has been applied to estimate the stability of the molecule arising from charge delocalization. The molecular docking studies concede that title compound may exhibit HIV-1 Protease 1N49 inhibitory activity.
Subject(s)
Adamantane/analogs & derivatives , HIV Protease Inhibitors/chemistry , HIV Protease/metabolism , HIV-1/enzymology , Triazoles/chemistry , Adamantane/chemistry , Adamantane/pharmacology , HIV Infections/drug therapy , HIV Infections/virology , HIV Protease Inhibitors/pharmacology , HIV-1/drug effects , Humans , Molecular Docking Simulation , Quantum Theory , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Triazoles/pharmacologyABSTRACT
Benzenesulfonamides incorporating cyanoacrylamide moieties with activity against tumour-associated human (h) isoforms hCA IX and XII (which are validated antitumor targets) were investigated for their quantitative structural activity relationships (QSAR). Multiple linear regression analysis was used to develop model relationships between molecular descriptors and inhibition constants (Ki). The molecular geometry optimization were performed on all molecules at DFT-B3LYP/6-311++G(d,p) level. Over 1250 molecular descriptors were calculated using Gaussian 09, Hyperchem and EDRAGON programs. Multiple linear regression equations have been developed and validated using leave-one-out cross-validated technique. The derived QSAR models are found to be statistically significant and show good predictive ability.
Subject(s)
Acrylamides/chemistry , Benzene/chemistry , Carbonic Anhydrase Inhibitors/chemistry , Carbonic Anhydrase Inhibitors/pharmacology , Sulfonamides/chemistry , Sulfonamides/pharmacology , Neoplasms/enzymology , Quantitative Structure-Activity RelationshipABSTRACT
Quantum chemical calculations of ground state energy, geometrical structure and vibrational wavenumbers of 1-acetylindole were carried out using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. The FT-IR and FT-Raman spectra were recorded in the condensed state. The fundamental vibrational wavenumbers were calculated and a good correlation between experimental and scaled calculated wavenumbers has been accomplished. Electric dipole moment, polarizability and first static hyperpolarizability values of 1-acetylindole have been calculated at the same level of theory and basis set. The results show that the 1-acetylindole molecule possesses nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-Visible spectrum of the molecule was recorded in the region 200-500nm and the electronic properties like HOMO and LUMO energies and composition were obtained using TD-DFT method. The calculated energies and oscillator strengths are in good correspondence with the experimental data. The thermodynamic properties of the compound under investigation were calculated at different temperatures.
Subject(s)
Indoles/chemistry , Models, Molecular , Molecular Conformation , Quantum Theory , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , ThermodynamicsABSTRACT
4-Phenyl-3H-1,3-thiazol-2-ol can exist in two tautomeric forms - keto and enol. Comprehensive investigation of molecular geometry and electronic structure in ground as well as in the first excited state of 4-Phenyl-3H-1,3-thiazol-2-ol (enol) has been carried out. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angles were varied in steps of 10° and molecular energy profile was calculated from -180° to +180°. Experimental FT-IR and FT-Raman spectra of title compound were compared with the spectral data obtained by DFT/B3LYP method. Dipole moment, polarizability, first static hyperpolarizability and molecular electrostatic potential surface map have been calculated to get a better insight of the properties of title molecule. Natural bond orbital (NBO) analysis has been done to study the stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and electronic properties such as frontier orbitals and band gap energies were calculated by TD-DFT approach. To compare the drug efficacy of enolic and keto forms, QSAR properties of both forms have also been computed and discussed.
Subject(s)
Electrons , Models, Molecular , Quantitative Structure-Activity Relationship , Quantum Theory , Thiazoles/chemistry , Triazoles/chemistry , Vibration , Molecular Conformation , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Static Electricity , Stereoisomerism , ThermodynamicsABSTRACT
A comprehensive investigation on the molecular structure, electronic properties and vibrational spectra of the 3-(adamantan-1-yl)-4-ethyl-1H-1,2,4-triazole-5(4H)thione, a novel potential anti-inflammatory agent has been done with the hope that the results of present study may be helpful in the prediction of its mechanism of biological activity. The experimentally observed spectral data (FT-IR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method. The (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge Including Atomic Orbital method and compared with experimental results. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, the molecular electrostatic potential surface, contour map have been calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were calculated by TD-DFT approach. Global and local reactivity descriptors have been computed to predict reactivity and reactive sites on the molecule.
Subject(s)
Adamantane/analogs & derivatives , Anti-Inflammatory Agents/chemistry , Models, Molecular , Quantum Theory , Triazoles/chemistry , Adamantane/chemistry , Dimerization , Electricity , Electrons , Hydrogen Bonding , Magnetic Resonance Spectroscopy , Molecular Conformation , Proton Magnetic Resonance Spectroscopy , Spectrophotometry, Ultraviolet , Spectrum Analysis, Raman , Static Electricity , Thermodynamics , VibrationABSTRACT
Extensive spectroscopic investigations along with theoretical quantum chemical studies on 3,5-dimethyl-4-methoxybenzoic acid (DMMBA) have been consummated. The fundamental vibrational transitions were addressed by experimental FT-IR (4000-400cm(-1)) and FT-Raman (4000-10cm(-1)) techniques and density functional calculations at B3LYP/6-311++G(d,p) and B3LYP/6-311++G(df,pd) levels of theory. The (1)H, (13)C and DEPT 135 NMR spectra of studied compound were recorded in deuterated dimethylsulfoxide (DMSO-d6), and compared with computed data obtained by using gauge including atomic orbital (GIAO) method. The electronic absorption spectra in methanol and ethanol solution were evaluated in the range of 200-400nm, and TD-DFT method was chosen for computational study. The spectroscopic and theoretical results were compared to the corresponding properties for monomer and dimer structures for the most stable conformer. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Moreover, the thermodynamic and nonlinear optical (NLO) properties were evaluated.
Subject(s)
Hydroxybenzoate Ethers/chemistry , Salicylates/chemistry , Dimerization , Magnetic Resonance Spectroscopy , Methylation , Models, Molecular , Quantum Theory , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, RamanABSTRACT
The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-Hâ¯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability ãßã, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.
Subject(s)
Acenaphthenes/chemistry , Electrons , Magnetic Resonance Spectroscopy , Models, Molecular , Nonlinear Dynamics , Optical Phenomena , Spectrum Analysis, Raman , Dimerization , Dimethyl Sulfoxide/chemistry , Hydrogen Bonding , Molecular Conformation , Solutions , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Thermodynamics , VibrationABSTRACT
Gabapentin (GP), structurally related to the neurotransmitter GABA (gamma-aminobutyric acid), mimics the activity of GABA and is also widely used in neurology for the treatment of peripheral neuropathic pain. It exists in zwitterionic form in solid state. The present communication deals with the quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of GP using density functional (DFT/B3LYP) method with 6-311++G(d,p) basis set. In view of the fact that amino acids exist as zwitterions as well as in the neutral form depending on the environment (solvent, pH, etc.), molecular properties of both the zwitterionic and neutral form of GP have been analyzed. The fundamental vibrational wavenumbers as well as their intensities were calculated and compared with experimental FT-IR and FT-Raman spectra. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The electric dipole moment, polarizability and the first hyperpolarizability values of the GP have been calculated at the same level of theory and basis set. The nonlinear optical (NLO) behavior of zwitterionic and neutral form has been compared. Stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV-Vis) spectrum of the title molecule has also been calculated using TD-DFT method. The thermodynamic properties of both the zwitterionic and neutral form of GP at different temperatures have been calculated.
Subject(s)
Amines/chemistry , Analgesics/chemistry , Cyclohexanecarboxylic Acids/chemistry , gamma-Aminobutyric Acid/chemistry , Gabapentin , Models, Molecular , Quantum Theory , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, RamanABSTRACT
Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of 4-chloro-3,5-dinitrobenzoic acid (CDNBA) were carried out by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. To determine lowest-energy molecular conformation of the title molecule, the selected torsion angle is varied every 10° and molecular energy profile is calculated from 0° to 360°. The optimized geometrical parameters obtained by DFT calculations are in good conformity with single crystal XRD data. The FT-IR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational wavenumbers as well as their intensities were calculated and a good agreement between observed and scaled calculated wavenumbers has been achieved. The electric dipole moment, polarizability and the first hyperpolarizability values of the CDNBA have been calculated at the same level of theory and basis set. The calculation results also show that the CDNBA molecule may has nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. Ultraviolet-visible (UV) spectrum of the title molecule has also been calculated using CIS and TD-DFT methods. The calculated energy and oscillator strength almost exactly reproduce the experimental data. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. The thermodynamic properties of the studied compound at different temperatures were calculated.
Subject(s)
Nitrobenzoates/chemistry , Halogenation , Magnetic Resonance Spectroscopy , Models, Molecular , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, RamanABSTRACT
A complete normal coordinate analysis of morphine using Wilson's GF matrix method and Urey Bradley force field has been carried out to understand the dynamical behaviour of morphine in relation to Leu5- and Met5-enkephalins. In addition, charge distribution on different atoms of morphine, along with that of Leu5- and Met5-enkephalins using CNDO/2 method is also reported. The similarity in charge distribution on some of the sites of these molecules is indicative of the possible interactions at the same receptor site. It is surmised that the recognition and interaction of active sites with the receptor must be dynamical in nature and for this the modes involving the active sites should play an important role. It is found that the binding to receptors is not static, but a dynamic process.