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Larbi T.,Tunis el Manar University | Doll K.,University of Ulm | Doll K.,Institute of Theoretical Chemistry | Manoubi T.,Tunis el Manar University
Journal of Alloys and Compounds | Year: 2016

We present a combined theoretical and experimental investigation concerning the magnetic semiconductor Mn3O4. We measured the absorbance spectra with ultraviolet-visible spectrophotometry in the near infrared region (UV-Vis-NIR) using a spectrophotometry technique, and deduced this way the band gap. Electron paramagnetic resonance (EPR) spectroscopy is performed to study the paramagnetic properties of the Mn2+ center. Fourier transform infrared spectroscopy (FTIR) of the film displays the characteristic absorption bands of Mn3O4 located at around 553 cm−1 and 673 cm−1. Morphological properties are studied using the scanning electron microscopy (SEM) technique which revealed a smooth and rough surface. In order to interpret our experimental data obtained, we explored the ferromagnetic and ferrimagnetic order of Mn3O4 in a spinel structure by employing density functional theory (DFT) on the level of the PBE0 hybrid functional as implemented in the CRYSTAL14 code. Our results include the optimized geometries, the density of states, the infrared and Raman spectra and infrared dielectric properties. The theoretical results show an excellent agreement with the experimental ones. Correlations between infrared (IR) phonon modes and dielectric properties are also established. © 2016 Elsevier B.V.

Cao H.,CAS Beijing National Laboratory for Molecular | Huang Y.,Institute of Theoretical Chemistry | Liu Z.,CAS Beijing National Laboratory for Molecular
Proteins: Structure, Function and Bioinformatics | Year: 2016

To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12-33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R=0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. © 2016 Wiley Periodicals, Inc.

Zheng Y.,Northeast Normal University | Xiong T.,Northeast Normal University | Lv Y.,Northeast Normal University | Zhang J.,Northeast Normal University | And 2 more authors.
Organic and Biomolecular Chemistry | Year: 2013

A combination of computational and experimental methods was carried out to elucidate the mechanism of palladium-catalyzed water-assisted benzylic C-H amination with N-fluorobenzenesulfonimide (NFSI), which involved the oxidative addition of PdII to PdIV-species as a rate-limiting step, followed by water-assisted concerted metalation-deprotonation (CMD) of the PdIV complex and water-assisted reductive elimination (RE) processes, and then a nucleophilic addition process to generate the final product and complete the catalytic cycle. The stability of the PdIV complex could be ascribed to the suitable ligands with strong σ-donors and resistance to decomposition, as well as being sufficiently bulky because the water-clusters assembled the ligands through hydrogen bonds to act as one multidentate ligand. Calculation results suggested that water also plays a crucial role as a proton transferring bridge in water-assisted CMD and RE processes. The corresponding experimental findings substantiate the expectation. Additionally, NFSI was found to act as both the oxidant and the nitrogen source to facilitate the reaction, while the steric effect of the bulky -N(SO2Ph)2 group contributed to circumventing the o-C-H amination. In this reaction, we investigated a novel spiro-cyclopalladation intermediate, formed by the reaction of the PdIV centre with pristine-carbon instead of ortho-carbon, which might be valuable for our understanding and further development of transition metal catalyzed C-H functionalization. © 2013 The Royal Society of Chemistry.

Zhang J.-P.,Jilin Institute of Chemical Technology | Jin L.,Jilin Institute of Chemical Technology | Zhang H.-X.,Institute of Theoretical Chemistry
Wuli Huaxue Xuebao/ Acta Physico - Chimica Sinica | Year: 2011

The geometries of ground and excited states of a series of ruthenium complexes [Ru(iph)(L)2]2+ (L=cpy (1), mpy (2), npy (3); iph=2,9-di(1-methyl-2-imidazole)-1,10-phenanthroline, cpy=4-cyano pyridine, mpy=4-methyl pyridine, npy=4-N-methyl pyridine) were optimized by the Becke's three-parameter functional and the Lee-Yang-Parr (B3LYP) functional and unrestricted B3LYP methods, respectively. Timedependent density functional theory (TD-DFT) method at the B3LYP level together with the polarized continuum model (PCM) were used to obtain their absorption and phosphorescent emission spectra in acetone media based on their optimized ground and excited-state geometries. The results revealed that the optimized structural parameters agreed well with the corresponding experimental results. The highest occupied molecular orbitals were localized mainly on the d orbital of the metal and the π orbital of the iph ligand for 1 and 2, and the npy ligand for 3, while the lowest unoccupied molecular orbitals were mainly composed of π* orbital of the iph ligand. Therefore, the lowest-lying absorptions and emissions were assigned to the metal to ligand charge transfer (MLCT)/intra-ligand charge transfer (ILCT) transition for 1 and 2, and the ligand to ligand charge transfer (LLCT) transition for 3. The lowest-lying absorptions are at 509 nm (1), 527 nm (2), and 563 nm (3) and the phosphorescence emissions at 683 nm (1), 852 nm (2), and 757 nm (3). The calculation results show that the absorption and emission transition characteristics and the phosphorescence color can be changed by altering the π electron-donating ability of the L ligand. © Editorial office of Acta Physico-Chimica Sinica.

Fan J.-R.,Institute of Theoretical Chemistry | Zheng Q.-C.,Institute of Theoretical Chemistry | Zheng Q.-C.,Jilin University | Cui Y.-L.,Institute of Theoretical Chemistry | And 2 more authors.
Journal of Biomolecular Structure and Dynamics | Year: 2015

Cytochrome P450 (CYP) 3A7 plays a crucial role in the biotransformation of the metabolized endogenous and exogenous steroids. To compare the metabolic capabilities of CYP3A7-ligands complexes, three endogenous ligands were selected, namely dehydroepiandrosterone (DHEA), estrone, and estradiol. In this study, a three-dimensional model of CYP3A7 was constructed by homology modeling using the crystal structure of CYP3A4 as the template and refined by molecular dynamics simulation (MD). The docking method was adopted, combined with MD simulation and the molecular mechanics generalized born surface area method, to probe the ligand selectivity of CYP3A7. These results demonstrate that DHEA has the highest binding affinity, and the results of the binding free energy were in accordance with the experimental conclusion that estrone is better than estradiol. Moreover, several key residues responsible for substrate specificity were identified on the enzyme. Arg372 may be the most important residue due to the low interaction energies and the existence of hydrogen bond with DHEA throughout simulation. In addition, a cluster of Phe residues provides a hydrophobic environment to stabilize ligands. This study provides insights into the structural features of CYP3A7, which could contribute to further understanding of related protein structures and dynamics. © 2015 © 2015 Taylor & Francis.

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