Stability and reactivity study of bio-molecules brucine and colchicine towards electrophile and nucleophile attacks: Insight from DFT and MD simulations

SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu3 metal cluster

The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV-Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range -17.08 to -58.52 kcal/mol in vacuum and -53.34 to -93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV-Vis of ABP is in agreement with theoretically predicted ones.

In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silico POM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones

In this work, Schiff bases and Thiazolidin-4-ones, were synthesized using Sonication and Microwave techniques, respectively. The Schiff base derivatives (3a-b) were synthesized via the reaction of Sulfathiazole (1) with benzaldehyde derivatives (2a-b), followed by the synthesis of 4-thiazoledinone (4a-b) derivatives by cyclizing the synthesized Schiff bases through thioglycholic acid. All the synthesized compounds were characterized by spectroscopic techniques such as FT IR, NMR and HRMS. The synthesized compounds were tested for their in vitro antimicrobial and antioxidant and in vivo cytotoxicity and hemolysis ability. The synthesized compounds displayed better antimicrobial and antioxidant activity and low toxicity in comparison to reference drugs and negative controls, respectively. The hemolysis test revealed the compounds exhibit lower hemolytic effects and hemolytic values are comparatively low and the safety of compounds is in comparison with standard drugs. Theoretical calculations were carried out by using the molecular operating environment (MOE) and Gaussian computing software and observations were in good agreement with the in vitro and in vivo biological activities. Petra/Osiris/Molinspiration (POM) results indicate the presence of three combined antibacterial, antiviral and antitumor pharmacophore sites. The molecular docking revealed the significant binding affinities and non-bonding interactions between the compounds and Erwinia Chrysanthemi (PDB ID: 1SHK). The molecular dynamics simulation under in silico physiological conditions revealed a stable conformation and binding pattern in a stimulating environment. HighlightsNew series of Thaiazolidin-4-one derivatives have been synthesized.Sonication and microwave techniques are used.Antimicrobial, Antioxidant, cytotoxicity, and hemolysis activities were observed for all synthesized compounds.Molecular Docking and DFT/POM analyses have been predicted.Communicated by Ramaswamy H. Sarma.

Study of the Mechanism of Hydrolysis of Hemicellulose from Lignocellulose during Alkali Thermal Pretreatment by Density Functional Theory and Experiment

The covalent bond fracture of hemicellulose leads to hemicellulose hydrolysis during lignocellulosic alkali thermal pretreatment, which has not previously been reported. Density functional theory was used to study the mechanism of hydrolysis of the hemicellulose model compounds under alkali conditions. There are four reaction paths for xylose formation, among which the reaction path with the lowest energy barrier is that in which the nucleophile captures H30 to generate water. The deprotonated hydroxyl group attacks the carbon on the glycoside bond, resulting in the cleavage of the glycoside bond and the formation of a new carbon-oxygen covalent bond, with an energy barrier of 154.2 kJ/mol. The nucleophile further attacks the glycosidic bond to form a new xylose residue with an energy barrier of 111.9 kJ/mol. When the glycosidic bond breaks, the orbital interaction with the largest proportion causes the transfer of ∼0.511 electron from the glycosidic bond oxygen to the deprotonated hydroxy oxygen. In situ Fourier transform infrared spectroscopy is used for the identification of functional groups during the alkali thermal pretreatment. As the temperature increases, the feasibility of the reaction increases. This study lays a theoretical foundation for the development of the alkali thermal pretreatment of lignocellulose.

TD-DFT, DFT, docking, MD simulations, and concentration-dependent SERS investigations of a bioactive trifluoromethyl derivative having human acetylcholinesterase and butyrylcholinesterase in silver colloids

CONTEXT

Various concentrations of (E)-4-methoxy-N'-(2-(trifluoromethyl)benzylidene) benzohydrazide (EMT) adsorbed on colloidal silver nanoparticles were studied using SERS and results were compared to the normal Raman spectrum. DFT calculations were used to validate experimental findings. Theoretically, the structures of the EMT and EMT-Ag6 systems were optimized. The UV-Vis spectral analysis's red shift and lower intensity behavior show that EMT has chemisorbed onto Ag nanoparticles. Charge transfer (CT) from Ag to EMT is highlighted by FMO analysis. The CT interaction in EMT and EMT-Ag6 was further verified by MEP and Mulliken charge analyses. The EMT was adsorbed on Ag nanoparticles with tilted orientation and orientation changes with colloidal concentration, according to SERS spectrum analysis. Docking EMT with 4PQE and 5DYW binding affinities are found to be -9.7 and -8.1 kcal/mol. MD simulations give the competence of 5DYW-EMT and 4PQE-EMT in their intended binding interactions and their ability to establish enduring associations with the protein of interest.

METHODS

DFT was used to optimize the molecular structures of EMT and EMT-Ag6 using B3LYP/6-311++G* (LANL2DZ basis set for Ag). A molecular dynamics simulation study was conducted on the 4PQE-EMT and 5DYW-EMT systems using the Desmond software for 100 ns.

Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions

CONTEXT

Theoretical investigation of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on spectral characteristics. When transitioning from plain drug to complexes, different modes of IND display a substantial shift in peak location. The 3561.26 cm^-1 band shows (~15.58 cm^-1) red shift upon dilution. The geometry in various solvents was calculated using quantum chemical calculation utilizing density functional theory (DFT). The highest ALIE values are located at the indole skeleton and on complexation with DC, and the ring atoms become more electron rich. The atom-centered density matrix propagation (ADMP) molecular dynamic (MD) calculation shows that the geometries optimized through the DFT calculation match the global minima effectively. MD simulations indicate that indole is more stable in water and methanol.

METHODS

DFT studies have been employed to study the interaction between indole and dichloromethane. CAM-B3LYP/6-311++G(d)(6D,7F) level of theory was employed using Gaussian 16 W suite. Quantum topological descriptors were discussed using quantum theory of atoms in molecules (QTAIM) with the help of Multiwfn software. Reduced density gradient (RDG) plot describes the nature of the interaction, while average local ionization energy (ALIE) explained the variation in local ionization energy of the molecular surface before and after complexation.

Adsorption of a thione derivative on carbon, AlN, and BN nanotubes: a detailed DFT and MD investigation

The performance of nanotubes (NT) of carbon (CC), aluminium-nitrogen (AlN), and boron-nitrogen (BN) as a sensor and nanocarrier for mercaptopurine (MCP) was investigated by means of a theoretical approach. The calculated negative values of adsorption energy showed the interaction and adsorption of MCP. Highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) distributions were only found on the NT counter portion of the drug-nanotube not on MCP for AlN-NT and BN-NT while HOMO is over MCP and LUMO is over NT for CC-NT. The polarizability of MCP-NTs is greater than that of MCP. Raman wavenumbers of MCP are enhanced in NTs, and hence, NTs can act as a sensor for the detection of MCP. Solvent dependency on adsorption behaviour is also presented in the manuscript, where we found that the AlN nanotube showed exceptionally high free energy of adsorption over other nanotubes in all solvent mediums. Solvation-free energies were also reported. Noncovalent interaction scattered plot also showed significant intermolecular interaction between AlN nanotubes and the mercaptopurine when compared to other nanotubes under study. To find the antiviral activity of MCP and MCP-NTs against antiviral activities, docking and molecular dynamics simulations were performed with 1HMP PDB. Recovery times show that MCP desorption occurs quickly. The MD simulations and docking results show that BN and CC-NTs with MCP show good activity as drug carriers.

In Silico study for acyclovir, ganciclovir and its derivatives to fight the COVID-19: Molecular docking, DFT calculations, ADME and td-Molecular dynamics simulations

In the present work, we have designed three molecules, acyclovir (A), ganciclovir (G) and derivative of hydroxymethyl derivative of ganciclovir (CH₂OH of G, that is D) and investigated their biological potential against the Mpro of nCoV via in silico studies. Further, density functional theory (DFT) calculations of A, G and D were performed using Gaussian 16 on applying B3LYP under default condition to collect the information for the delocalization of electron density in their optimized geometry. Authors have also calculated various energies including free energy of A, G and D in Hartree per particle. It can be seen that D has the least free energy. As mentioned, the molecular docking of the A, G and D against the Mpro of nCoV was performed using iGemdock, an acceptable computational tool and the interaction has been studied in the form of physical data, that is, binding energy for A, G and D were calculated in kcal/mol. It can be seen the D showed effective binding, that is, maximum inhibition that A and G. For a better understanding for the inhibition of the Mpro of nCoV by A, G and D, temperature dependent molecular dynamics simulations were performed. Different trajectories like RMSD, RMSF, Rg and hydrogen bond were extracted and analyzed. The results of molecular docking of A, G and D corroborate with the td-MD simulations and hypothesized that D could be a promising candidate to inhibit the activity of Mpro of nCoV.

Spectroscopic studies, quantum chemical investigations, and in silico and in vitro scrutiny of the diuretic drug trichlormethiazide adsorbed on AuNPs

Experimental and theoretical study was employed to study the adsorption of the diuretic drug, trichlormethiazide (TCM) molecule on AuNPs (TCMA). The stereoelectronic properties of the molecular structure of most stable conformers of TCM and TCMA were studied using DFT/B3LYP-6-311++G (d, p) together with LANL2DZ methodology. The Fourier transform Raman and Infrared spectra of TCM were recorded and analyzed. Quantum chemical calculations of TCM and TCMA molecules were used to evaluate the stability of the molecule, hyper-conjugative interactions, electron delocalization, and binding interactions. The calculated and experimentally observed vibrational frequencies of the molecule were assigned and compared. The shifting and intensity enhancement of the CCl₂ band manifests the back-donation and conjugation effect, which are the result of the presence of nitrogen atom adjoining the dichloromethyl groups and the oxygen in the sulfur dioxide group attached among the amino group and the chlorophenyl ring, respectively, which enhances bioactivity. Anticancer activity was examined based on molecular docking analysis, and it was identified that TCM and TCMA molecules act as good inhibitors against lung cancer. SERS analysis and MTT assay confirmed the molecular docking analysis results.