Co-, Fe-, Ni-doped and co-doped rutile GeO2: insights from ab-initio calculations

Rutile germanium oxide (rutile GeO₂), a semiconductor, can act as a half-metallic compound and is a promising material for spintronic and optoelectronic applications. Calculations were performed using the Korringa–Kohn–Rostoker (KKR) approach and the coherent potential approximation (CPA), which were further combined with two approximations, the local density approximation (LDA) and the self-interaction corrected LDA approximation (LDA-SIC), to study the electronic structure of bulk rutile GeO₂ doped and co-doped with three transition-metal impurities: Fe, Co, and Ni. The doping value was set to 10%, while the co-doping level was set to 5% for each impurity. The main findings of this work are: (1) a direct ultrawide bandgap of 4.80 eV is observed and the rutile GeO₂ exhibits an N-type semiconducting property. (2) Doped and co-doped GeO₂ acquire a magnetic behavior and exhibit half-metallicity. (3) The mechanism responsible for these properties is also studied. (4) The critical temperature can reach 334 K when GeO₂ is doped with Fe, while it rises to 398 K when it is co-doped with Fe and Co. (5) The spin polarization can be improved by co-doping. It can be inferred that rutile GeO₂ doped or co-doped with (Co, Fe) transition metals can be considered to be potential candidates for spintronic and optoelectronic applications.     

Quantum chemical insight into molecular structure,density functional theory calculations,vibrational dynamics,natural population analysis,Hirshfeld analysis,and molecular docking approach to chalcone 1-4-bromophenyl-3-(2-methoxyphenyl)prop-2-en-1-one

The structure of the novel chalcone 1-4-bromophenyl-3-(2-methoxyphenyl)prop-2-en-1-one has been characterized by Fourier transform infrared and Fourier transform Raman. Density functional theory with Becke, 3-parameter, Lee-Yang-Parr functional was used for the optimization of geometry. The comprehensive assignments of the vibrational spectra have been performed with the aid of normal coordinate analysis. Stability of the molecule and intra/intermolecular charge transfer have been analyzed using natural bond orbital analysis. The existence of intermolecular C-H?O, blueshifted hydrogen bond was investigated by bond length variation. Hirshfeld and two-dimensional fingerprint plot analyses have been performed to study the nature of interactions present in the molecule. The docked complex gives a constancy of ?8.2?kcal/mol toward the androgen receptor.     

The molecular structures, vibrational spectroscopies (FT-IR and Raman) and quantum chemical calculations of n-alkyltrimethylammonium bromides

The FT-IR and micro-Raman spectra of three n-alkyltrimethylammonium bromides (dodecyltrimethylammonium bromide (DTAB), tetradecyltrimethylammonium bromide (TTAB) and hexadecyl(cetyl)trimethylammonium bromide (CTAB)) in powder form were recorded in the regions 4000–550 cm^?1 and 3200–300 cm^?1, respectively. The optimized geometries and vibrational frequencies of DTAB, TTAB and CTAB have been carried out with ab initio Hartree-Fock (HF) and density functional theory method B3LYP calculations with the 6–31 G (d, p) basis set in the ground state. The comparison of the observed fundamental vibrational frequencies and calculated results for the fundamental vibrational frequencies of DTAB, TTAB and CTAB indicate that the scaled B3LYP method is superior compared to the scaled HF method.     

Thermal isomerization and cyclization of 1-naphthylacetylene: Experimental results, quantum chemical and transition state theory calculations

The isomerization of 1-naphthylacetylene diluted in argon was studied behind reflected shock waves in a 2 in i.d. single pulse shock tube over the temperature range 1000-1250 K and overall densities of ∼3 × 10⁻⁵ mol/cm³. The only reaction product found in the post shock mixtures was acenaphthylene. The first order rate constant of the isomerization was found to be k = 2.08 × 10¹² exp(−54.2 × 10³/RT) s⁻¹, where R is expressed in units of cal/K mol. Potential energy surfaces of the cyclization reaction 1-naphthylacetylene → acenaphthylene and the isomerization 1-naphthylacetylene → 2-naphthylacetylene were calculated using the Becke three-parameter hybrid method with Lee-Yang-Parr correlation functional approximation (B3LYP). Structure, energy and frequency calculations were carried out with the Dunning correlation consistent polarized double ζ (cc-pVDZ) basis set. The rate constant (k_∞) for the 1-naphthylacetylene → acenaphthylene cyclization was calculated using transition state theory, the value obtained is k_∞ = 3.52 × 10¹² exp(−55.9 × 10³/RT) s⁻¹, where R is expressed in units of cal/K mol. The agreement between the experiment and the calculations is very good. RRKM calculations were done to transfer k_∞ to the pressure of the single pulse shock tube experiments. In view of high temperature and the large molecule involved the deviation from k_∞ is very small. The isomerization 1-naphthylacetylene → 2-naphthylacetylene proceeds via the formation of an unstable intermediate 1,2-naphthalenocyclobutene and has a high barrier of ∼83.5 kcal/mol. In view of this high barrier, the isomerization cannot compete with the cyclization that proceeds with a barrier of ∼56 kcal/mol.     

Structural studies on banana oil,isoamyl acetate,by means of microwave spectroscopy and quantum chemical calculations

The rotational spectrum of isoamyl acetate, H₃C–COO–(CH₂)₂–CH(CH₃)₂, has been recorded and assigned using a molecular beam Fourier transform microwave (MB-FTMW) spectrometer in the frequency range of 3–26.5?GHz. One conformer has been observed. By comparing the spectroscopic data with the quantum chemical data, it was found that the conformer observed does not have C_s symmetry. The rotational and centrifugal distortion constants were determined. The barrier to internal rotation of the acetate methyl group was found to be 93.98?cm^?1. Due to the high number of the conformers, a systematic nomenclature will be presented.     

XRD studies,vibrational spectra,and molecular structure of 1H‐imidazo [4,5‐b]pyridine based on DFT quantum chemical calculations

The molecular structures and vibrational properties of 1H‐imidazo[4,5‐b]pyridine in its monomeric and dimeric forms are analyzed and compared to the experimental results derived from the X‐ray diffraction (XRD), infrared (IR), and Raman studies. The theoretical data are discussed on the basis of density functional theory (DFT) quantum chemical calculations using Lee–Yang–Parr correlation functional (B3LYP) and 6‐31G(d,p) basis. This compound crystallizes in orthorhombic structure, space group Pna2₁(C_2v⁹) and Z = 4. The planar conformation of the skeleton and presence of the N H···N hydrogen bond was found to be characteristic for the studied system. The temperature dependence of IR and Raman modes was studied in the range 4–294 K and 8–295 K, respectively. The normal modes, which are unique for the imidazopyridine derivatives are identified. Copyright © 2009 John Wiley & Sons, Ltd.     

Identification of dual Acetyl-CoA carboxylases 1 and 2 inhibitors by pharmacophore based virtual screening and molecular docking approach

Acetyl-CoA carboxylase (ACC) is a crucial metabolic enzyme that plays a vital role in obesity-induced type 2 diabetes and fatty acid metabolism. To identify dual inhibitors of Acetyl-CoA carboxylase1 and Acetyl-CoA carboxylase2, a pharmacophore modelling approach has been employed. The best HypoGen pharmacophore model for ACC2 inhibitors (Hypo1_ACC2) consists of one hydrogen bond acceptor, one hydrophobic aliphatic and one hydrophobic aromatic feature, whereas the best pharmacophore (Hypo1_ACC1) for ACC1 consists of one additional hydrogen-bond donor (HBD) features. The best pharmacophore hypotheses were validated by various methods such as test set, decoy set and Cat-Scramble methodology. The validated pharmacophore models were used to screen several small-molecule databases, including Specs, NCI, ChemDiv and Natural product databases to identify the potential dual ACC inhibitors. The virtual hits were then subjected to several filters such as estimated $\text{ IC}_{50}$ value, quantitative estimation of drug-likeness and molecular docking analysis. Finally, three novel compounds with diverse scaffolds were selected as potential starting points for the design of novel dual ACC inhibitors.     

Selenium dioxide: Rotational analysis and Franck-Condon calculations for the 3130 Å 1B2-X̃1A1 absorption system

Band contour analyses of the absorption bands of ⁷⁸Se¹⁶O₂ and ⁸⁰Se¹⁶O₂ at 2949 Å, assigned to the 1₀³ transition (King and McLean, in press), show that they are type A, with transition moment directed in-plane and parallel to the line joining the oxygen nuclei. The electronic transition responsible for the B absorption system of the molecule is therefore ${}^1\text{B}{}_2\text{-}\text{X}\text{?}{}^1\text{A}{}_1$ under the C_2v point group. The contour analysis gives the excited state bond angle as 101.0°, and the bond length as 1.74 Å. The latter value is confirmed by Franck-Condon calculations. There is therefore an increase in bond length and a decrease in bond angle upon electronic excitation. This agrees with the predictions of molecular orbital theory.     

A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling,docking, de novo drug design and molecular dynamics analysis

When X-ray structure of a ligand-bound receptor is not available, homology models of the protein of interest can be used to obtain the ligand-binding cavities. The steroelectronic properties of these cavities are directly related to the performed molecular model coordinates. Thus, the use of different template structures for homology may result in variation of ligand-binding modes. We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377–7387, 2008). In this present study, a homology modeling study based on the β2-adrenergic receptor for both CB1 and CB2 receptors was performed, and the results were compared with rhodopsin-based models. In addition, the role of membrane bilayers to the adopted conformations of potent AMG3 CB ligand has been analyzed for receptor-free and membrane-associated receptor systems. The performed MD trajectory analysis results have shown that gauche conformations at the terminal segment of the alkyl side chain of AMG3 are not favored in solution. Different adopting dihedral angles defined between aromatic and dithiolane rings at the active sites of the CB1 and CB2 receptors, which are adapted lead to different alkyl side chain orientations and thus, may give clues to the medicinal chemists to synthesize more selective CB ligands. The binding sites of receptors derived by rhodopsin-based models have been regenerated using the β2-adrenergic based template receptors. The re-obtained models confirmed the ligand-binding pockets that were derived based on rhodopsin.     

Novel B,C-ring truncated deguelin derivatives reveals as potential inhibitors of cyclin D1 and cyclin E using molecular docking and molecular dynamic simulation

The overexpression of cyclin D1 and cyclin E due to their oncogenic potential and amplification has been associated with a higher mortality rate in many cancers. The deguelin is a natural compound, has shown promising anti-cancer activity by directly binding cyclin D1 and cyclin E and thus suppressing its function. The C7a atomic position of deguelin structure contains a proton that generates stabilized radical, as a result, decomposed deguelin reduces its structural stability and significantly decreases its biological activity. To design deguelin derivatives with the reduced potential side effect, series of B, C-ring truncated derivatives were investigated as cyclin D1 and cyclin E inhibitors. R-group-based enumeration was implemented in the deguelin scaffold using the R-group enumeration module of Schrödinger. Drug-Like filters like, REOS and PAINs series were applied to the enumerated compound library to remove compounds containing reactive functional groups. Further, screened compounds were docked within the ligand-binding cavity of cyclin D1 and cyclin E crystal structure, using Glide SP and XP protocol to obtain docking poses. Enrichment calculations were done using SchrÖdinger software, with 1000 decoy compounds (from DUD.E database) and 60 compounds (XP best poses) along with deguelin, to validate the docking protocol. The receiver operating characteristic (ROC) curve indicates R²?=?0.94 for cyclin D1 and R²?=?0.79 for cyclin E, suggesting that the docking protocol is valid. Besides, we explored molecular dynamics simulation to probe the binding stability of deguelin and its derivatives within the binding cavity of cyclin D1 and cyclin E structures which are associated with the cyclin D1 and cyclin E inhibitory mechanism.

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Conformational landscape of small organosilicon compounds from the combined use of gas electron diffraction,IR and Raman spectroscopies and quantum chemical calculations: diethyldichlorosilane

A conformational study of diethyldichlorosilane and the elucidation of the gas‐phase molecular structures of its four conformers have been performed using the combined approach of gas‐phase electron diffraction and computational techniques. Moreover, the Raman spectrum of the liquid and the IR spectra of the gas and liquid phases have been recorded and thoroughly analyzed on the basis of the scaled quantum‐mechanical force field methodology. The results of the vibrational assignment have given spectroscopic evidence of the presence of the different conformers in the samples. Copyright © 2009 John Wiley & Sons, Ltd.     

Adsorption and dissociation of molecular hydrogen on Pt/CeO2 catalyst in the hydrogen spillover process: A quantum chemical molecular dynamics study

Ultra accelerated quantum chemical molecular dynamics method (UA-QCMD) was used to study the dynamics of the hydrogen spillover process on Pt/CeO₂ catalyst surface for the first time. The direct observation of dissociative adsorption of hydrogen on Pt/CeO₂ catalyst surface as well as the diffusion of dissociative hydrogen from the Pt/CeO₂ catalyst surface was simulated. The diffusion of the hydrogen atom in the gas phase explains the high reactivity observed in the hydrogen spillover process. Chemical changes, change of adsorption states and structural changes were investigated. It was observed that parallel adsorption of hydrogen facilitates the dissociative adsorption leading to hydrogen desorption. Impact with perpendicular adsorption of hydrogen causes the molecular adsorption on the surface, which decelerates the hydrogen spillover. The present study also indicates that the CeO₂ support has strong interaction with Pt catalyst, which may cause an increase in Pt activity as well as enhancement of the metal catalyst dispersions and hence increasing the rate of hydrogen spillover reaction.     

DFT and MP2 based quantum mechanical calculations and a theoretical vibrational spectroscopic investigation on roscovitine,a potential drug to treat cancers

Theoretically possible stable conformers of free roscovitine molecule in its electronic ground state were searched by means of molecular dynamics and energy minimization calculations performed using the MM2 force field. Afterwards, geometry optimization and thermochemistry calculations were carried out at room temperature for each of the found minimum‐energy conformers using the MP2 and DFT based electronic structure methods and different Pople‐style basis sets. The results obtained from these calculations confirmed that the strong intramolecular hydrogen bonding between the purine‐nitrogen and hydroxyl‐hydrogen atoms plays an important role on the rigidity of roscovitine molecule and causes a dramatic reduction in the number of the possible stable conformers of this molecule at room temperature. Furthermore, the same calculation results also revealed that two of the found seven stable conformers are considerably more favorable in energy than the others and thus dominate the experimental room‐temperature spectra of the molecule. In the light of the theoretical vibrational spectral data obtained for these two conformers, a successful assignment of the fundamental bands observed in the experimental IR and Raman spectra recorded at room temperature for solid roscovitine and for its ethanol solution is given, and the effects of the substitution and intramolecular hydrogen bonding on the fundamental bands associated with purine and phenyl group vibrations are discussed in detail. In the fitting of the calculated harmonic wavenumbers to the corresponding experimental wavenumbers, two different scaling procedures, called ‘dual scale factors’ and ‘Scaled Quantum Mechanical Force Field (SQM FF) methodology’, were applied independently. Both procedures yielded results generally in good agreement with the experiment; however, the SQM FF methodology proved its superiority over the other. Copyright © 2010 John Wiley & Sons, Ltd.     

Design,synthesis, and molecular docking studies of new [1,2,4]triazolo[4,3-a]quinoxaline derivatives as potential A2B receptor antagonists

Molecular Diversity - Many shreds of evidence have recently correlated A2B receptor antagonism with anticancer activity. Hence, the search for an efficient A2B antagonist may help in the...     

Design,antihuman immunodeficiency activity and molecular docking studies of synthesized 2-aryl and 2-pyrimidinyl pyrrolidines

Molecular Diversity - A series of thirty-one new compounds were synthesized and evaluated for their anti-HIV-1 and cytotoxicity activity. Of these, twelve were found to be inhibitors of HIV...