DFT and PCM-TD-DFT investigation of the electronic structures and spectra of 5-(3-phenyl-2-propenylidene)-2-thioxo-4-thiazolidinone derivatives

Designing of Thiazolidinones for COVID-19 and its Allied Diseases: An In silico Evaluation

In silico studies in terms of density functional theory (DFT), molecular docking, and ADMET (absorption, distribution, metabolism, excretion and toxicity) were performed for 55 thiazolidinones compounds derived from different amines and aldehydes. DFT is a computational quantum mechanical modeling method used to predict the various properties of the compounds. Different parameters such as Electronegativity (x), Chemical Hardness (ŋ), Chemical Potential (μ), Ionization potential (IP), and Electron Affinity (EA), etc. were calculated by Koopmans theorem. The compounds were docked with Molecular Operating Environment (MOE) software using already reported PDB files of BChE, AChE, and α-glucosidase. To analyze the Spike Glycoprotein of SARS-Cov-2 and heterocyclic compounds, molecular interactions study was carried out between Spike Glycoprotein of SARS-Cov-2 (6VXX) and 55 synthetic heterocyclic compounds. It was performed by the utilization of PyRx Virtual Screening Tool and AutoDock Vina based virtual environment was used in PyRx. Maximum binding affinity was observed with compound A7 which was -8.7 kcal/mol and then with A5 which was -8.5 respectively. In the case of the AChE enzyme, B5 has a maximum docking score of -12.9027 kcal/mol while C7 depicted the maximum score for the BChE enzyme with a value of -8.6971 kcal/mol. The docking studies revealed that C6 compound has maximum binding capacity toward glucosidase (-14.8735 kcal/mol). ADMET properties of under consideration compounds were determined by Swiss online-based software which concluded that these molecules have a drug-like properties and having no violation.

Introducing ortho-methoxyl group as a fluorescence-enhancing and bathochromic-shift bi-functional strategy for typical cysteine sensors

A practical strategy of introducing ortho-methoxyl group was explored to achieve the fluorescence-enhancing and bathochromic-shift bi-functional optimization. It was tested in the Cys sensing ISOPH-X series, thus the successful case, ISOPH-2, was obtained. It realized the optimization in a simple and compatible way. The corresponding strategy was basically established during the confirmation of checkpoints including applicable steadiness (over 24 h), wide pH range (7.0-9.0), rapid response (20 min), good biocompatibility, high sensitivity (LOD = 0.072 nm), high selectivity and biological monitoring of Cys in living cells as well as C. elegans. In this work, the o-methoxyl introduction strategy led to a 15 nm red shift and a near 4-fold fluorescence enhancement. This strategy could be combined with the double bond-introducing approach. Compared with reported strategies, by breaking the dilemma between red shift and strong fluorescent intensity, this strategy might offer beneficial information for exploiting better sensors with more fluorophores and mechanisms for their targets.

Solvent effects on excitation energies obtained using the state-specific TD-DFT method with a polarizable continuum model based on constrained equilibrium thermodynamics

Nonequilibrium solvation effects need to be treated properly in the study of electronic absorption processes of solutes since solvent polarization is not in equilibrium with the excited-state charge density of the solute. In this work, we developed a state specific (SS) method based on the novel nonequilibrium solvation model with constrained equilibrium manipulation to account for solvation effects in electronic absorption processes. Time-dependent density functional theory (TD-DFT) is adopted to calculate electronic excitation energies and a polarizable continuum model is employed in the treatment of bulk solvent effects on both the ground and excited electronic states. The equations based on this novel nonequilibrium solvation model in the framework of TDDFT to calculate vertical excitation energy are presented and implemented in the Q-Chem package. The implementation is validated by comparing reorganization energies for charge transfer excitations between two atoms obtained from Q-Chem and those obtained using a two-sphere model. Solvent effects on electronic transitions of coumarin 153 (C153), acetone, pyridine, (2E)-3-(3,4-dimethoxyphenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (DMHP), and uracil in different solvents are investigated using the newly developed code. Our results show that the obtained vertical excitation energies as well as spectral shifts generally agree better with the available experimental values than those obtained using the traditional nonequlibrium solvation model. This new model is thus appropriate to study nonequilibrium excitation processes in solution.