Antagonistic properties of a natural product-Bicuculline with the gamma-aminobutyric acid receptor: studied through electrostatic potential mapping, electronic and vibrational spectra using ab initio and density functional theory

Heme Protein Binding of Sulfonamide Compounds: A Correlation Study by Spectroscopic, Calorimetric, and Computational Methods

Protein-ligand interaction studies are useful to determine the molecular mechanism of the binding phenomenon, leading to the establishment of the structure-function relationship. Here, we report the binding of well-known antibiotic sulfonamide drugs (sulfamethazine, SMZ; and sulfadiazine, SDZ) with heme protein myoglobin (Mb) using spectroscopic, calorimetric, ζ potential, and computational methods. Formation of a 1:1 complex between the ligand and Mb through well-defined equilibrium was observed. The binding constants obtained between Mb and SMZ/SDZ drugs were on the order of 10⁴ M^-1. SMZ with two additional methyl (-CH₃) substitutions has higher affinity than SDZ. Upon drug binding, a notable loss in the helicity (via circular dichroism) and perturbation of the three-dimensional (3D) protein structure (via infrared and synchronous fluorescence experiments) were observed. The binding also indicated the dominance of non-polyelectrolytic forces between the amino acid residues of the protein and the drugs. The ligand-protein binding distance signified high probability of energy transfer between them. Destabilization of the protein structure upon binding was evident from differential scanning calorimetry results and ζ potential analyses. Molecular docking presented the best probable binding sites of the drugs inside protein pockets. Thus, the present study explores the potential binding characteristics of two sulfonamide drugs (with different substitutions) with myoglobin, correlating the structural and energetic aspects.

Effects of antibiotics on enhanced biological phosphorus removal and its mechanisms

Many kinds of antibiotics are continuously discharged into wastewater and typically cause a great decrease in sewage treatment performance, whereas mechanisms of differences in the impacts of commonly used antibiotics on phosphate removal are still elusive. Thus, an enhanced biological phosphorus removal (EBPR) system, as an effective method of phosphate removal, was developed, and its performance in the treatment of artificial wastewater containing antibiotics at short- (8 h) and long-term (15 days) exposure was investigated. The results show that phosphorus removal was consistently inhibited by the addition of antibiotics with a significant difference (P < 0.05). To interpret the phenomena, mechanistic equations were developed, and the results indicate that for short-term tests, the difference was mainly caused by the suppression of polyhydroxyalkanoate (PHA) degradation and the activity of polyphosphate kinase (PPK), resulting in the different inhibition of the soluble orthophosphorus (SOP) uptake process. For long-term tests, the difference in SOP uptake was principally caused by the inhibition of PHA degradation and the activity of PPK, whereas the difference in SOP release resulted from the inhibition of activities of exopolyphosphatase (PPX) and adenylate kinase (ADK). Moreover, micro-mechanisms of such inhibition were identified from molecular docking and electrostatic potential.

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of (1)H and (13)C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

Synthesis, structural and spectral analysis of 1-(pyrazin-2-yl) piperidin-2-ol by density functional theory

The organic compound 1-(pyrazin-2-yl) piperidin-2-ol (abbreviated as PPOL) has been synthesized and characterized by IR, Raman, (1)H NMR and UV-Vis spectroscopy. The Fourier-transform Raman (3500-50cm(-1)) and infrared spectra (4000-400cm(-1)) were recorded in the solid state and interpreted by comparison with theoretical spectra derived from density functional theory (DFT) calculations. The optimized geometry, frequency and intensity of the vibrational bands of the compound was obtained by the density functional theory using 6-31G(d,p) basis set. In the optimized geometry results shows that geometry parameters are good agreement with XRD values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. In calculation of electronic absorption spectra, TD-DFT calculations were carried out in the both gas and solution phases. (1)H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. (1)H NMR analysis is evident for O-H⋯O intermolecular interaction of the title molecule. The thermodynamic properties of the title compound have been calculated at different temperatures and the results reveal that the standard heat capacities (Cp,m), standard entropies (Sm) and standard enthalpy changes (Hm) increase with rise in temperature. In addition, HOMO and LUMO energies and the first-order hyperpolarizability have been computed.

Quantum chemical and spectroscopic (FT-IR and FT-Raman) investigations of 3-methyl-3h-imidazole-4-carbaldehyde

FT-IR and FT-Raman spectra of 3-methyl-3h-imidazole-4-carbaldehyde (3M3HI4C) were recorded in the region 4000-400cm(-1) and 3500-50cm(-1), respectively. Optimized geometric parameters, conformational equilibria, normal mode frequencies, and corresponding vibrational assignments of 3M3HI4C were theoretically examined by quantum chemical methods for the first time. All vibrational frequencies were assigned in detail with the help of total energy distribution (TEDs). The experimental wavenumbers were compared with the scaled vibrational frequencies determined by DFT/B3LYP method. The results showed that the B3LYP/6-311++G(d,p) method predicts vibrational frequencies and the structural parameters effectively. The most stable conformer of the title compound was determined. The total electron density and molecular electrostatic potential surfaces of the molecule were constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron+nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. The lower energy band was assigned to the HOMO→LUMO transition. Natural bond orbital analysis of title molecule has been performed to indicate the presence of intramolecular charge transfer. Energies, relative stabilities, and dipole moments of title molecule were also compared and analyzed in the gas phase and in solvents. Furthermore, solvent effects on the geometry and vibrational frequency of 3M3HI4C were studied theoretically at the DFT/B3LYP level in combination with the conductor polarizable continuum model (C-PCM).

Comparative vibrational spectroscopic studies, HOMO-LUMO, NBO analyses and thermodynamic functions of p-cresol and 2-methyl-p-cresol based on DFT calculations

In the present study structural properties of p-cresol, and 2-methoxy-p-cresol have been studied by using B3LYP/cc-pvdz and B3PW91/cc-pvdz of Density Functional Theory (DFT) utilizing Becke three exchange functional and Lee Yang Paar correlation functional. The Fourier transform infrared and Fourier transform Raman spectra of title molecules were recorded (solid phase). Optimized geometry, harmonic vibrational frequencies and various thermodynamic parameters of the title compounds were calculated with B3LYP/cc-pvdz, and B3PW91/cc-pvdz basis sets. Non-linear optical (NLO) behavior of the p-cresol and 2-methoxy-p-cresol were investigated by determining of electric dipole moment, polarizability α, and hyperpolarizability β using the above mentioned basis sets. The molecular properties such as ionization potential, electronegativity, chemical potential, electrophilicity have been deduced from HOMO-LUMO analysis employing the same basis sets. A detailed interpretation of the infrared and Raman spectra of title molecules were reported. UV spectrum was measured in different solvent. The energy and oscillator strength are calculated by Time Dependant Density Functional Theory (TD-DFT) results. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The complete assignments were performed on the basis of the potential energy distribution (PED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method. Finally the theoretical FT-IR, FT-Raman, and UV spectra of the title molecules have also been constructed.

Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid--Corlumine

The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

Vibrational (FT-IR and FT-Raman) spectra, NBO, HOMO-LUMO, Molecular electrostatic potential surface and computational analysis of 4-(trifluoromethyl)benzylbromide

In this work, the vibrational characteristics of 4-(trifluoromethyl) benzylbromide (TFMBB) have been investigated and both the experimental and theoretical vibrational data indicate the presence of functional groups in the title molecule. The density functional theoretical (DFT) computations were performed at the B3LYP/6-311+G (d,p) levels to derive the optimized geometry, vibrational wavenumbers with IR and Raman intensities. Furthermore, the molecular orbital calculations such as natural bond orbitals (NBOs), HOMO-LUMO energy gap and Mapped molecular electrostatic potential (MEP) surfaces were also performed with the same level of DFT. The thermal flexibility of molecule in associated with vibrational temperature was also illustrated on the basis of correlation graphs. The detailed interpretation of the vibrational spectra has been carried out with the aid of potential energy distribution (PED) results obtained from MOLVIB program. The delocalization of electron density of various constituents of the molecule has been discussed with the aid of NBO analysis.

Spectroscopic and quantum chemical study of an alkaloid aristolochic acid I

Aristolochic acids (AAs) (Aristolochiaceae) are used in the traditional Chinese herb medicine. We have presented the geometry optimization, electrostatic potential surface, frontier orbital energy gap and vibrational wavenumbers of aristolochic acid I (AA I) using ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method employing 6-311G(d,p) basis set. A complete vibrational assignment has been done on the basis of calculations on monomer and dimer of AA I. The UV-vis absorption spectrum has been recorded in ethanol solvent and compared with the calculated one in the gas phase as well as in solvent environment (integral-equation formalism polarizable continuum model; IEF-PCM) using TD-DFT/6-31G basis set. A short outline of the NBO analysis segment with their structural meaning has been presented. The variation of thermodynamic properties with temperature was calculated theoretically and the thermal response of the compound has been recorded with the help of differential scanning calorimetry (DSC) in N2 environment.

FT-IR, FT-Raman and DFT quantum chemical study on the molecular conformation, vibrational and electronic transitions of 1-(m-(trifluoromethyl)phenyl)piperazine

The FTIR and FT-Raman spectra of 1-(m-(trifluoromethyl)phenyl)piperazine [TFMPP] have been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of the compound was obtained by the density functional theory using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. A detailed interpretation of the infrared and Raman spectra were also reported based on potential energy distribution (PED). UV-Vis spectrum of the compound was recorded and the electronic properties HOMO and LUMO energies were measured by TD-DFT approach. Furthermore, molecular electrostatic potential is performed and also the calculated HOMO and LUMO energies show that charge transfer occurs within the molecule.

Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as "pau branco". Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The (13)C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d,p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

Vibrational (FT-IR and FT-Raman) spectra and quantum chemical studies on the molecular orbital calculations, chemical reactivity and thermodynamic parameters of 2-chloro-5-(trifluoromethyl) aniline

In this work, the vibrational characteristics of 2-chloro-5-(trifluoromethyl) aniline have been investigated and both the experimental and theoretical vibrational data indicate the presence of various functional groups within the title molecule. The influence of chlorine substituent on the vibrational wavenumbers of a molecule in comparison with aniline and trifluoromethyl aniline has been discussed in detail. The density functional theoretical (DFT) computations were performed at the B3LYP/6-31++G(3df,3pd)/6-31G(3df,3pd) levels to derive the optimized geometry, vibrational wavenumbers with IR and Raman intensities. Furthermore, the molecular orbital calculations such as; natural bond orbitals (NBOs) and HOMO-LUMO energy gap and mapped molecular electrostatic potential (MEP) surfaces were also performed with the same level of DFT. The temperature dependence thermodynamic parameters of a molecule were illustrated on the basis of their correlation graphs. The detailed interpretation of the vibrational spectra has been carried out with the aid of potential energy distribution (PED) results obtained from MOLVIB program. The delocalization of electron density in various constituents of the molecule has been discussed with the aid of NBO and HOMO-LUMO energy gap analysis.