Shedding light into the biological activity of aminopterin, via molecular structural, docking, and molecular dynamics analyses.

In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, αIIBß3 and α5ß1integrins, human dihydrofolate reductase, main protease (Mpro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), αIIBß3 and α5ß1 integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), Mpro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.Communicated by Ramaswamy H. Sarma.

Iron affects localization of Ght5 in fission yeast.

Iron is an essential cofactor for eukaryotic cells, as well as a toxic metal under certain conditions. On the other hand, glucose is the preferred energy and carbon source by most organisms and is an important signaling molecule in the regulation of biological processes. In Schizosaccharomyces pombe, the Ght5 hexose transporter, known as a high affinity glucose transporter, is required for cell proliferation in low glucose concentrations. Herein, we aimed to investigate the effects of iron stress on the Ght5 hexose transporter under glucose repression and derepression conditions. The effect of iron stress on the expression profile of the ght5 gene was analyzed by RT-qPCR and western blot. The localization of the Ght5-mNeonGreen fusion protein examined with confocal microscopy. Our results revealed that iron stress had an inhibitory effect on ght5 expression, and it altered Ght5 localization on the cell surface, causing it to accumulate in the cytoplasm.

Molecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases.

The cationic pentapeptide Glu-Gln-Arg-Pro-Arg (EQRPR) belongs to the family of anti-cancer peptides with significant anti-cancer activity. However, the mechanism by which the peptide performs this activity is unknown. In this study, we explored the pharmaceutical profile of Glu-Gln-Arg-Pro-Arg pentapeptide and revealed its anticancer properties by in silico docking studies. Moreover, the effect of EQRPR behavior of the DPPC membrane was investigated by means of Langmuir monolayer technique and the results were discussed in terms of mutual interactions. To evaluate the binding mechanisms, the pentapeptide and its various D-amino acid substituted analogs were docked to both epidermal growth factor receptor (EGFR) tyrosine kinase and proto-oncogene tyrosine-protein kinase, Fyn. Simultaneous binding of the pentapeptides to both EGFR and Fyn proteins, which are receptor- and non-receptor-kinases, respectively, suggest that these peptides can be an effective agent for cancer treatment. Moreover, to show the potential of the investigated pentapeptides to overcome the generated mutation-related drug resistance to EGFR targeted therapies, molecular docking investigations of EQRPR and all its D-analogs were performed against the prospective targets: Wild type EGFRWT and mutant EGFRT790M. Erlotinib and TAK-285 were used as reference molecules. The strong interaction of the peptide with EGFRWT (from -9.24 to -9.75 kcal/mol) and the secondary mutant EGFRT790M (from -9.28 to -9.64 kcal/mol) observed in most cancer recurrence cases indicates its good potential to overcome drug resistance in cancer therapy. In addition, the pharmacological properties of the investigated pentapeptides were revealed by in silico ADME (Absorption, Distribution, Metabolism, Excretion) and toxicity analysis.Communicated by Ramaswamy H. Sarma.

Structural and vibrational investigations and molecular docking studies of a vinca alkoloid, vinorelbine.

Vinorelbine, a vinca alkaloid, is an antimitotic drug that inhibits polymerisation process of tubulins to microtubules, and is widely used in cancer chemotherapy. Due to the importance of the structure-activity relationship, in this work the conformational preferences of the vinorelbine molecule were surched by PM3 method. The obtained lowest energy conformer was then optimized at DFT/B3LYP/6-31G(d,p) level of theory and the structural characteristics were determined. Frontier orbital (HOMO, LUMO) and molecular electrostatic potential (MEP) analyses were performed for the optimized structure. The experimental FT-IR, Raman and UV-VIS spectral data of vinorelbine along with the theoretical DFT/B3LYP/6-31G(d,p) calculations were investigated in detail. The vibrational wavenumbers were assigned based on the calculated potential energy distribution (PED) of the vibrational modes. To shed light into the anticancer property of vinorelbine as microtubule destabilizer, the most favourable binding mode and the interaction details between vinorelbine and tubulin were revealed by molecular docking studies of vinorelbine into the α,ß-tubulin (PDB IDs: 4O2B; 1SA0; 7CNN) and binding free energies were calculated by the combination of Molecular Mechanics/Generalized Born Surface Area (MMGBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods {MM/PB(GB)SA}. The calculated vinorelbine-7CNN binding free energy, using by MM/PB(GB)SA approach, was found to be the best (-50.39 kcal/mol), and followed by vinorelbine-4O2B (-28.5 kcal/mol) and vinorelbine-1SA0 (-17.59 kcal/mol) systems. Moreover, the interaction of vinorelbine with the cytochrome P450 enzymes (CYP), which are known to help in the metabolism of many drugs in the body, was investigated by docking studies against CYP2D6 and CYP3A4 targets.Communicated by Ramaswamy H. Sarma.

Evolution and ontogeny of bacteriocytes in insects.

The ontogenetic origins of the bacteriocytes, which are cells that harbour bacterial intracellular endosymbionts in multicellular animals, are unknown. During embryonic development, a series of morphological and transcriptional changes determine the fate of distinct cell types. The ontogeny of bacteriocytes is intimately linked with the evolutionary transition of endosymbionts from an extracellular to an intracellular environment, which in turn is linked to the diet of the host insect. Here we review the evolution and development of bacteriocytes in insects. We first classify the endosymbiotic occupants of bacteriocytes, highlighting the complex challenges they pose to the host. Then, we recall the historical account of the discovery of bacteriocytes. We then summarize the molecular interactions between the endosymbiont and the host. In addition, we illustrate the genetic contexts in which the bacteriocytes develop, with examples of the genetic changes in the hosts and endosymbionts, during specific endosymbiotic associations. We finally address the evolutionary origin as well as the putative ontogenetic or developmental source of bacteriocytes in insects.

Mitochondrial Spermidine Synthase is Essential for Blood-stage growth of the Malaria Parasite.

Positively-charged polyamines are essential molecules for the replication of eukaryotic cells and are particularly important for the rapid proliferation of parasitic protozoa and cancer cells. Unlike in Trypanosoma brucei, the inhibition of the synthesis of intermediate polyamine Putrescine caused only partial defect in malaria parasite blood-stage growth. In contrast, reducing the intracellular concentrations of Spermidine and Spermine by polyamine analogs caused significant defects in blood-stage growth in Plasmodium yoelii and P. falciparum. However, little is known about the synthesizing enzyme of Spermidine and Spermine in the malaria parasite. Herein, malaria parasite conserved Spermidine Synthase (SpdS) gene was targeted for deletion/complementation analyses by knockout/knock-in constructs in P. yoelii. SpdS was found to be essential for blood-stage growth. Live fluorescence imaging in blood-stages and sporozoites confirmed a specific mitochondrial localization, which is not known for any polyamine-synthesizing enzyme so far. This study identifies SpdS as an excellent drug targeting candidate against the malaria parasite, which is localized to the parasite mitochondrion.

Structural and spectral analysis of anticancer active cyclo(Ala-His) dipeptide.

The theoretically possible most stable conformation of the cyclic dipeptide, which has a significant anticancer activity, was examined by conformational analysis method and then by DFT calculations. With DFT calculations, cyclo(Ala-His) dipeptide was found to be more stable in boat form than in planar conformation. Moreover, conformations of the dimeric forms of the title molecule were investigated. The dimeric forms of the cyclo(Ala-His) dipeptide were created by combining two identical cyclo(Ala-His) monomers, in lowest energy configuration and as a result three energetically possible dimeric structures were obtained. The solid phase FTIR and Raman spectra of cyclo(Ala-His) have been recorded. The spectra were interpreted with the aid of quantum chemical calculations based on density functional theory, using B3LYP and wb97xd methods with 6-311++G(d,p) basis set, in order to elucidate structural and spectral properties of the investigated molecule. Experimental vibrational spectra are found to be in accord with the simulated vibrational spectra. The assignment of the vibrational modes was performed depending on the calculated potential energy distribution (PED). In slico molecular docking of cyclo(Ala-His) was also carried out with DNA. The drug likeness and ADMET properties were analyzed for the prediction of pharmacokinetic profiles. The results revealed that the compound has the potential to be the leading molecule in the drug discovery process.

Evaluation of anti-cancer and anti-covid-19 properties of cationic pentapeptide Glu-Gln-Arg-Pro-Arg, from rice bran protein and its d-isomer analogs through molecular docking simulations.

Bioactive peptides derived from food proteins are becoming increasingly popular due to the growing awareness of their health-promoting properties. The structure and mechanism of anti-cancer action of pentapeptide Glu-Gln-Arg-Pro-Arg (EQRPR) derived from a rice bran protein are not known. Theoretical and experimental methods were employed to fill this gap. The conformation analysis of the EQRPR pentapeptide was performed first and the obtained lowest energy conformer was optimized. The experimental structural data obtained by FTIR and CD spectroscopies agree well with the theoretical results. d-isomer introduced one-by-one to each position and all D-isomers of the peptide were also examined for its possible anti-proteolytic and activity enhancement properties. The molecular docking revealed avid binding of the pentapeptide to the integrins α5ß1 and αIIbß3, with Kd values of 90 nM and 180 nM, respectively. Moreover, the EQRPR and its D-isomers showed strong binding affinities to apo- and holo-forms of Mpro, spike glycoprotein, ACE2, and dACE2. The predicted results indicate that the pentapeptide may significantly inhibit SARS-CoV-2 infection. Thus, the peptide has the potential to be the leading molecule in the drug discovery process as having multifunctional with diverse biological activities.

Synthesis, molecular modelling, FT-IR, Raman and NMR characterization, molecular docking and ADMET study of new nickel(II) complex with an N4-tetradentate thiosemicarbazone.

A new nickel(II) complex was synthesized by using S-propyl-thiosemicarbazide and 2-amino-3,5-dibromobenzaldehyde. The complex, obtained by the template effect of nickel ions, was structurally analysed by experimental and theoretical vibrational spectroscopy, NMR and density functional theory (DFT) calculations. By using DFT/B3LYP method with 6-311++G(d, p) basis set, the most stable molecular structure of the title molecule was calculated. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the molecule under investigation were determined and compared with the experimental vibrational spectra. The vibrational assignment was achieved using the calculated potential energy distributions of the vibrational modes. Moreover, the molecular electrostatic potential (MEP), the highest occupied molecular orbital (HOMO) and the lowest occupied molecular orbital (LUMO) energies were calculated, Molecular docking of the molecule was carried out against DNA in order to identify the potential inhibitory action of the title compound. The findings suggested that the aforementioned compound has a strong binding affinity to interact with DNA residues DT8, DC9, DG12, DG16, DA17, and DA18 through the intermolecular hydrogen bonds. Also the performed in silico ADMET analysis was the prediction of the synthesized molecule's pharmacokinetic and toxicity profile expressing good oral drug like actions and non-toxic nature. The complex has been shown to have the possibility to become a model molecule for drug development processes.Communicated by Ramaswamy H. Sarma.

Synthesis, antimicrobial activity, molecular docking and ADMET study of a caprolactam-glycine cluster.

Density functional theory calculations were performed with DFT method using both b3lyp/6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gram-negative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process.Communicated by Ramaswamy H. Sarma.

In Silico design of AVP (4-5) peptide and synthesis, characterization and in vitro activity of chitosan nanoparticles.

BACKGROUND: Arginine-vasopressin (AVP) is a neuropeptide and provides learning and memory modulation. The AVP (4-5) dipeptide corresponds to the N-terminal fragment of the major vasopressin metabolite AVP (4-9), has a neuroprotective effect and used in the treatment of Alzheimer's and Parkinson's disease. METHODS: The main objective of the present study is to evaluate the molecular mechanism of AVP (4-5) dipeptide and to develop and synthesize chitosan nanoparticle formulation using modified version of ionic gelation method, to increase drug effectiveness. For peptide loaded chitosan nanoparticles, the synthesized experiment medium was simulated for the first time by molecular dynamics method and used to determine the stability of the peptide, and the binding mechanism to protein (HSP70) was also investigated by molecular docking calculations. A potential pharmacologically features of the peptide was also characterized by ADME (Absorption, Distribution, Metabolism and Excretion) analysis. The characterization, in vitro release study, encapsulation efficiency and loading capacity of the peptide loaded chitosan nanoparticles (CS NPs) were performed by Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques. Additionally, in vitro cytotoxicity of the peptide on human neuroblastoma cells (SH-SY5Y) was examined with XTT assay and the statistical analysis was evaluated. RESULTS: The results showed that; hydrodynamic size, zeta potential and polydispersity index (PdI) of the peptide-loaded CS NPs were 167.6 nm, +13.2 mV, and 0.211, respectively. In vitro release study of the peptide-loaded CS NPs showed that 17.23% of the AVP (4-5)-NH2 peptide was released in the first day, while 61.13% of AVP (4-5)-NH2 peptide was released in the end of the 10th day. The encapsulation efficiency and loading capacity were 99% and 10%, respectively. According to the obtained results from XTT assay, toxicity on SHSY-5Y cells in the concentration from 0.01 µg/µL to 30 µg/µL were evaluated and no toxicity was observed. Also, neuroprotective effect was showed against H2O2 treatment. CONCLUSION: The experimental medium of peptide-loaded chitosan nanoparticles was created for the first time with in silico system and the stability of the peptide in this medium was carried out by molecular dynamics studies. The binding sites of the peptide with the HSP70 protein were determined by molecular docking analysis. The size and morphology of the prepared NPs capable of crossing the blood-brain barrier (BBB) were monitored using DLS and SEM analyses, and the encapsulation efficiency and loading capacity were successfully performed with UV Analysis. In vitro release studies and in vitro cytotoxicity analysis on SHSY-5Y cell lines of the peptide were conducted for the first time. Grapical abstract.

Synthesis, FT-IR and NMR characterization, antimicrobial activity, cytotoxicity and DNA docking analysis of a new anthraquinone derivate compound.

A new anthraquinone [1-(2-Aminoethyl)piperazinyl-9,10-dioxo-anthraquinone] derivative was synthesized and characterized by density functional theory (DFT) calculations, experimental and theoretical vibrational spectroscopy and NMR techniques. The most stable molecular structure of the title molecule was determined by DFT B3LYP method with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The fundamental vibrational wavenumbers, IR and Raman intensities for the optimized structure of the investigated molecule were calculated and compared with the experimental vibrational spectra. The vibrational assignment of the molecule was done using the potential energy distribution analysis. The molecular electrostatic potential (MEP), highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital (LUMO) were also calculated. The antibacterial activities of the new anthraquinone derivative against Gram-positive and Gram-negative bacteria were determined, and it was shown that the highest effectiveness was against Staphylococcus aureus and S. epidermidis while no activity was against Gram-negative bacteria. Moreover, the antimycotic activity of the title compound was examined and the cytotoxicity of anthraquinone derivate was determined. In order to find the possible inhibitory activity of the title compound, molecular docking of the molecule was carried out against DNA. The results indicated that the mentioned compound has a good binding affinity to interact with the DC3, DG4, DA5, DC21 and DC23 residues of DNA via the intermolecular hydrogen bonds. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Synthesis, molecular docking and ADMET study of ionic liquid as anticancer inhibitors of DNA and COX-2, TOPII enzymes.

A new ionic liquid was synthesized by the reaction of caprolactam with salicylic acid (CL-SA) and characterized by analysis of spectroscopic and DSC data. The optimized geometry and the electrostatic potential map of CL-SA were calculated with DFT method using the wb97xd/6-31++G(d,p) level of theory. Molecular docking study of the CL-SA was carried out to clarify the probable binding modes between the title compound and DNA and COX-2 and TOPII enzymes. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized ionic liquid which expressed good oral drug-like behavior and non-toxic nature. It was revealed that the compound has a potential to become a lead molecule in drug discovery process.Communicated by Ramaswamy H. Sarma.

In silico Analysis of Sulpiride, Synthesis, Characterization and In vitro Studies of its Nanoparticle for the Treatment of Schizophrenia.

BACKGROUND: Sulpiride, which has selective dopaminergic blocking activity, is a substituted benzamide antipsychotic drug playing a prominent role in the treatment of schizophrenia, which more selective and primarily blocks dopamine D2 and D3 receptor. OBJECTIVE: This study has two main objectives, firstly; the molecular modeling studies (MD and Docking, ADME) were conducted to define the molecular profile of sulpiride and sulpiridereceptor interactions, another to synthesize polymeric nanoparticles with chitosan, having the advantage of slow/controlled drug release, to improve drug solubility and stability, to enhance utility and reduce toxicity. METHODS: Molecular dynamic simulation was carried out to determine the conformational change and stability (in water) of the drug and the binding profile of D3 dopamine receptor was determined by molecular docking calculations. The pharmacological properties of the drug were revealed by ADME analysis. The ionic gelation method was used to prepare sulpiride loaded chitosan nanoparticles (CS NPs). The Dynamic Light Scattering (DLS), UV-vis absorption (UV), Scanning Electron Microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy techniques were carried out to characterize the nanoparticles. In vitro cell cytotoxicity experiments examined with MTT assay on mouse fibroblast (L929), human neuroblastoma (SH-SY5Y) and glioblastoma cells (U-87). The statistical evaluations were produced by ANOVA. RESULTS: The residues (ASP-119, PHE-417) of D3 receptor provided a stable docking with the drug, and the important pharmacological values (blood brain barrier, Caco-2 permeability and human oral absorption) were also determined. The average particle size, PdI and zeta potential value of sulpiride- loaded chitosan NPs having a spherical morphology were calculated as 96.93 nm, 0.202 and +7.91 mV. The NPs with 92.8% encapsulation and 28% loading efficiency were found as a slow release profile with 38.49% at the end of the 10th day. Due to the formation of encapsulation, the prominent shifted wave numbers for C-O, S-O, S-N stretching, S-N-H bending of Sulpiride were also identified. Mitochondrial activity of U87, SHSY-5Y and L929 cell line were assayed and evaluated using the SPSS program. CONCLUSION: To provide more efficient use of Sulpiride having a low bioavailability of the gastrointestinal tract, the nanoparticle formulation with high solubility and bioavailability was designed and synthesized for the first time in this study for the treatment of schizophrenia. In addition to all pharmacological properties of drug, the dopamine blocking activity was also revealed. The toxic effect on different cell lines have also been interpreted.

Molecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB).

CLTOAB is an ammonium-based ionic liquid composed of ε-Caprolactam (CL) C6H11NO and tetraoctylammonium bromide (TOAB) (C32H68BrN). In this study, experimental IR and Raman spectra of CLTOAB ionic liquid together with the computational results of the compound have been reported. The optimized geometry, vibrational frequencies, IR intensities and Raman activities of the CLTOAB were calculated using the wb97xd and B3LYP density functional methods combined with the 6-31G(d,p) basis set using Gaussian 03 program. The complete assignment of the bands was performed based on the potential energy distributions (PED%). The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The Gauge-including atomic orbital 1H-NMR and 13C-NMR chemical shifts calculations were carried out and compared with the experimental data. Furthermore to evaluate interaction between CLTOAB and DNA, molecular docking study was carried out. Communicated by Ramaswamy H. Sarma.

Structural analysis, spectroscopic characterization and molecular docking studies of the cyclic heptapeptide.

The theoretically possible stable conformer of the cyclic heptapeptide, that has significant anti-metastatic activity, was examined by conformational analysis followed by DFT calculations. Experimental infrared and Raman spectroscopy, together with theoretical DFT (6-31G (d,p) basis set)-based quantum chemical calculations, have been used to understand the structural and spectral characteristics of cyclo(Gly-Arg-Gly-Asp-Ser-Pro-Ala) {cyclo(GRGDSPA)}. A complete analysis of the vibrational spectrum has been reported on the basis of potential energy distribution (PED%) data of the vibrational modes. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound. The simulated spectra satisfactorily coincide with the experimental spectra. In addition, molecular electrostatic potential and frontier molecular orbital analysis were investigated using theoretical calculations. The stability of the molecule, arising from hyperconjugative interaction and charge delocalization, has been analyzed using natural bond orbital analysis and a high E(2) value reveals the presence of strong interaction between donors and acceptors. Molecular docking studies with fibronectin were performed on cyclo(GRGDSPA) in order to understand its inhibitory nature. The results indicate that the docked ligand {cyclo(GRGDSPA)} forms a stable complex with human fibronectin and gives a binding affinity value of -7.7 kcal/mol, which points out that cyclo(GRGDSPA) might exhibit inhibitory activity against the attachment of melanoma cells to human fibronectin.

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin.

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of ß-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with -.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO-LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.

Elemental and spectroscopic characterization of plasters from Fatih Mosque-Istanbul (Turkey) by combined micro-Raman, FTIR and EDXRF techniques.

The characterization of the plasters and coloring agents of the wall paintings of Fatih Mosque have been performed using combined micro-Raman, FTIR and EDXRF techniques. The investigations show that the plaster used on the walls has mixed gypsum-lime binders. Cinnabar {HgS}, lead red {Pb3O4} and hematite {α-Fe2O3} were identified in the red surfaces. Blue color is attributed to ultramarine blue {Na8-10Al6Si6O24S2-4}. Green color is assigned to mixtures of green earth, copper phthalocyanine {Cu(C32Cl16N8)} and brochantite {CuSO4·3Cu(OH)2}. Strontium yellow {SrCrO4} and zinc white {ZnO} were also used to ensure the color tone. The results provide a basis for future restoration of wall paints.

A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations.

In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted.

Structural and vibrational study of primidone based on monomer and dimer calculations.

Primidone (Mysoline), with the chemical formula 5-ethyl-5-phenyl-hexahydropyrimidine- 4,6-dione (C12H14N2O2), has been a valuable drug in the treatment of epilepsy. In the present work, the experimental IR and Raman spectra of solid phase primidone were recorded, and the results were compared with theoretical wavenumber values of monomer and dimer forms of the title molecule. Vibrational spectral simulations in the dimer form were carried out to improve the assignment of the bands in the solid phase experimental spectra. The possible stable conformers of free molecule were searched by means of torsion potential energy surfaces scan studies through two dihedral angles. The molecular geometries of the monomer and dimer forms of title molecule were optimized using DFT method at B3LYP/6-31++G(d,p) level of theory. Using PEDs determined the contributions of internal (stretching, bending, etc.) coordinates to each normal mode of vibration. Further, HOMO-LUMO energy gap and NBO properties of the investigated molecule in monomer and dimer forms were also calculated.