DFT investigation on the structural and vibrational behaviours of the non-protein amino acids in hybrid explicit/continuum solvent: a case of the zwitterions γ-aminobutyric and α - aminoisobutyric acids.

BACKGROUND: The influence of hybrid solvation models on the molecular structures and vibrational characteristics of g-aminobutyric acid (GABA) and a-aminoisobutyric acid (AIB) zwitterions was assessed by employing a variety of Density Functional Theory (DFT). The quantum chemical methods included the B3LYP and B3PW91 hybrid functionals and the 6­311++G(d,p) basis set. METHODS: The most stable conformation derived from the potential energy surface (PES) scans using the B3LYP/6-311++G(d,p) model chemistry for each studied molecule was predicted within a continuum environment represented by the COSMO and SMD solvation models. The stable structures were subsequently immersed in explicit/COSMO and explicit/SMD hybrid solvation models, where 10 and 8 water molecules were explicitly positioned around the functional groups of the GABA and AIB zwitterions, respectively. The number of water molecules chosen was sufficient to prevent proton transfer among the carboxylate group (COO-) and the ammonium group (NH3+) within each molecule under investigation. After optimizing the geometry of each hydrated complex, the normal vibrational modes were determined. The scaled theoretical frequencies obtained from the various model chemistries were then compared to available experimental data from infrared (IR) and Raman spectroscopy. RESULTS: In the case of GABA and AIB molecules, the comparisons revealed that the B3LYP/6-311++G(d,p) model chemistry yielded wavenumber values that closely matched the experimental IR and Raman data, particularly when the explicit/SMD solvent was employed. The computed results indicate deviations of less than 4% when compared to the experimental data for the two molecules under investigation.

Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer's drug.

In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid ß-protein (Aß) enzyme, which causes the Alzheimer's disease. The molecular dynamics analysis confirms the reliability of the docking results.Communicated by Ramaswamy H. Sarma.

SERS and DFT studies of 2-(trichloroacetyl)pyrrole chemisorbed on the surface of silver and gold coated thin films: In perspective of biosensor applications.

The adsorption and orientations of 2-(trichloroacetyl)pyrrole (TCAP) adsorbed on a fabricated silver-coated thin film (SCF), and gold-coated thin film (GCF) were investigated using surface-enhanced Raman scattering (SERS) studies and compared with the normal Raman scattering (nRs) spectrum of TCAP. The observed nRs and SERS spectra of TCAP were validated theoretically using DFT quantum chemical calculations. Initially, the molecular structure of TCAP, TCAP-Ag3 , and TCAP-Au4 molecular systems were optimized and analyzed. The fabricated SCF and GCF are characterized using FESEM analysis, which confirms that the silver and gold nanoparticles of the corresponding films are spherical in shape. The obtained significant red-shift in UV-visible spectra of TCAP added on SCF and GCF surfaces reveal that the TCAP strongly adsorbed on SCF and GCF surfaces. The frontier molecular orbitals analysis authenticates the charge-transfer interaction from Ag3 and Au4 metal clusters to the TCAP molecule, leading to the adsorption of TCAP molecule on Ag3 and Au4 metal clusters, which validates the UV-vis results. SERS spectral analysis confirms that the TCAP chemisorbed on SCF and GCF surfaces with tilted orientation and the corresponding results were validated theoretically. The calculated SERS enhancement factor values illustrate that the GCF surface exhibits a higher SERS signal enhancement than the SCF surface. Therefore, the present investigation will be useful for the development of active SERS substrates and pyrrole-related biosensors.

Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP).

The effects of the interaction of the monovalent (Li+, Na+, K+) and divalent (Mg2+) counterions hexahydrated (6H2O), with the PO2- group, on the geometrical and vibrational characteristics of 3', 5'-dDCMP, were studied using the DFT/B3LYP/6-31++G(d) method. These calculations were performed using the explicit (6H2O) and hybrid (6H2O/Continuum) solvation models. The optimizations reveal that in the conformation g-g- and in the explicit model of solvation, the small ions (Li+, Na+) deviate from the bisector plane of the angle O1-P-O2 and the large ions (K+ and Mg2+) remain in this plane, whereas in the hybrid model of solvation, the counterions deviate from this plane. However, when the conformer is g+g+, the monovalent counterions deviate and divide the remainder of the plane regardless of the type of solvation model. In addition, the g-g- conformer is the most stable in the presence of the explicit solvent, while the g+g+ conformer is the most stable in the presence of the hybrid solvent. Finally, the normal modes of the conformers g-g- and g+g+ in the presence of the counterions in the hybrid model show a better agreement with the available experimental data of the DNA forms A, B (g-g-), and Z (g+g+) relatively to the explicit model. This very good agreement is illustrated by the very small deviations ≤ 0.08% (g-g-) and ≤ 0.41% (g+g+) observed between the calculated and experimental data for the PO2- (asymmetric) stretching mode in the presence of the counterion K+ in the hybrid model. Graphical abstract.

Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method.

Solvent effects on the structural and vibrational features of l-glycylvaline (L-GV) and l-glycylvalylglycine (L-GVG) in zwitterionic forms have been performed by means of DFT method. Relaxed potential energy surface scans (RPES) performed at B3LYP/6-31++G(d) level were used to map the reaction coordinate surfaces and to identify the geometries corresponding to the minima energy. Explicit solvation model, where L-GV and L-GVG are respectively surrounded by 9 and 11 water molecules interacting with H-donor and H-acceptor sites, as well as the different hybrid solvation models of solvation (explicit/COSMO, explicit/PCM and explicit/CPCM) allowed to analyze the hydration effects. Those number of water molecules are sufficient to fully hydrate carboxyl(CtOO-), amine (NtH3+) and amide (NH, C=O) groups. Harmonic vibrational modes calculated after geometry optimization on each solvated complex are performed at B3LYP/6-31++g(d) and PBE0/6-31++g(d) methods and a post-processing treatment enable us to assign the vibrational modes of LGV and L-GVG. The frequencies of the assigned modes obtained using B3LYP in explicit/COSMO are in good agreement with available IR and Raman values than those found in both explicit/PCM and explicit/CPCM which proved to be very close.

Solvent effects on the structures and vibrational features of zwitterionic dipeptides: L-diglycine and L-dialanine.

Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic L-diglycine and L-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N t H[Formula: see text], COO (-)) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of L-diglycine and L-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for L-diglycine and 2 % for L-dialanine, and they appear more accurate than those found using the explicit model (12W). Graphical Abstract DFT/6-31++G∗ Optimized structures of L-diglycine (top) and L-dialanine (bottom) surrounded by 12 water molecules all embedded in a continuum.