Density functional theory, spectroscopic and hydrogen bonding analysis of fenoxycarb–water complexes

Absorption wavelength (TD-DFT) and adsorption of metal chalcogen clusters with methyl nicotinate: Structural, electronic, IRI, SERS, pharmacological and antiviral studies (HIV and omicron)

The DFT B3LYP-LAND2DZ technique is used to examine interactions of Methyl nicotinate with copper selenide and zinc selenide clusters. The existence of reactive sites is determined using ESP maps and Fukui data. The energy variations between HOMO and LUMO are utilised to calculate various energy parameters. The Atoms in Molecules and ELF (Electron Localisation Function) maps are employed to investigate the topology of the molecule. The Interaction Region Indicator is used to determine the existence of non-covalent zones in the molecule. The UV-Vis spectrum using the TD-DFT method and DOS graphs are used to obtain the theoretical determination of electronic transition and properties. Structural analysis of the compound is obtained using theoretical IR spectra. To explore the adsorption of copper selenide and zinc selenide clusters on the Methyl nicotinate, the adsorption energy and theoretical SERS spectra are employed. Furthermore, pharmacological investigations are carried out to confirm the drug's non-toxicity. The compound's antiviral efficacy against HIV and Omicron is demonstrated via protein-ligand docking.

DFT and TD-DFT study of hydrogen bonded complexes of aspartic acid and n water (n = 1 and 2)

CONTEXT

Hydrogen bonds (HB) influence the conformational preferences of biomolecules and their optical and electronic properties. The directional interaction of molecules of water can be a prototype to understand the effects of HBs on biomolecules. Among the neurotransmitters (NT), L-aspartic acid (ASP) stands out due to its importance in health and as a precursor of several biomolecules. As it presents different functional groups and readily forms inter- and intramolecular HBs, ASP can be considered a prototype for understanding the behavior of NTs when interacting by HB with other substances. Although several theoretical studies have been performed in the past on isolated ASP and its formed complexes with water, both in gas and liquid phases, using DFT and TD-DFT formalisms, these works did not perform large basis set calculations or study electronic transitions of ASP-water complexes. We investigated the HB interactions in complexes of ASP and water molecules. The results show that the interactions between the carboxylic groups of ASP with water molecules, forming cyclic structures with two HBs, lead to more stable and less polar complexes than other conformers formed between water and the NH₂ group. It was observed that there is a relationship between the deviation in the UV-Vis absorption band of the ASP and the interactions of water with the HOMO and LUMO orbitals with the stabilization/destabilization of the S₁ state to the S₀ of the complexes. However, in some cases, such as 1:1 complex ASP-W2, this analysis may be inaccurate due to small changes in ΔE.

METHODS

We studied the landscapes of the ground state surface of different conformers of isolated L-ASP and the L-ASP-(H₂O)_n complexes (n = 1 and 2) using the DFT formalism, with the B3LYP functional, and six different basis sets: 6-31 +  + G(d,p), 6-311 +  + G(d,p), D95 +  + (d,p), D95V +  + (d,p), cc-pVDZ, and, cc-pVTZ basis sets. The cc-pVTZ basis set provides the minimum energy of all conformers, and therefore, we performed the analysis with this basis set. We evaluated the stabilization of the ASP and complexes using the minimum ground state energy, corrected by the zero point energy and the interaction energy between the ASP and the water molecules. We also calculated the vertical electronic transitions S₁ ← S₀, and their properties using the TD-DFT formalism at B3LYP/cc-pVTZ level with the optimized geometries for S₀ state with the same basis set. For the analysis of the vertical transitions of isolated ASP and the ASP-(H₂O)_n complexes, we calculated the electrostatic energy in the S₀ and S₁ states. We performed the calculations with the Gaussian 09 software package. We used the VMD software package to visualize the geometries and shapes of the molecule and complexes.

PES, molecular structure, spectroscopic (FT-IR, FT-Raman), electronic (UV-Vis, HOMO-LUMO), quantum chemical and biological (docking) studies on a potent membrane permeable inhibitor: dibenzoxepine derivative

The dibenzoxepines derivatives have found a broad application in biological and pharmaceutical fields as new prospective drugs. So, the molecule (3aS,12bS)-5-Chlor-2-methyl-2,3,3a,12b-tetrahydro-1H-dibenzo[2,3:6,7]oxepino[4,5-c]pyrrol has been characterized by DFT (Density Functional Theory) approach to predict the important properties of it. The minimum energy conformer has been found by PES (Potential Energy Surface) and then the structure is optimized. Further, the structure is characterized spectroscopically by FT-IR and FT-Raman techniques to know the functional group and chemically active atoms. The geometrical parameters, PED (Potential Energy Distribution) assignments have also been reported. The electronic properties of the title compound have been explained by UV-Vis and HOMO-LUMO analyses that describe the charge transfer between the atoms of the molecule. Molecular Electrostatic Potential (MEP), Electron Localization Function (ELF) and Localized Orbital Locator (LOL) have been depicted to know the chemically active regions. The electrophilic and nucleophilic regions have been shown by Fukui functions. The Non-Linear Optics (NLO) for non-linear optical effects and the Natural Bond Orbital (NBO) for charge delocalization were studied. To study the biological activity of the title compound, molecular docking has been performed which suggests that the title molecule may act as a membrane permeable inhibitor.