Tailoring and functionalizing the graphitic-like GaN and GaP nanostructures as selective sensors for NO, NO, and NH adsorbing: a DFT study.

Context: Langmuir adsorption of gas molecules of NO, NO, and NH on the graphitic GaN and GaP sheets has been accomplished using density functional theory. The changes of charge density have shown a more important charge transfer for GaN compared to GaP which acts both as the electron donor while gas molecules act as the stronger electron acceptors through adsorption on the graphitic-like GaN surface. The adsorption of NO and NO molecules introduced spin polarization in the PL-GaN sheet, indicating that it can be employed as a magnetic gas sensor for NO and NO sensing.

Transition metal (X = Mn, Fe, Co, Ni, Cu, Zn)-doped graphene as gas sensor for CO and NO detection: a molecular modeling framework by DFT perspective.

Context: In this research, CO and NO adsorption on doped nanographene (NG) sheets with transition metals (Fe, Ni, Zn) and (Mn, Co, Cu), respectively, have been applied for scavenging of these toxic gases as the environmental pollutants. The values of changes of atomic charge density have illustrated a more significant charge transfer for Ni-doped C-NG through CO adsorption and a more remarkable charge transfer for Co-doped C-NG through NO adsorption. The data of NMR spectroscopy has depicted several fluctuations around the graph of Zn-doped on the nanographene surface.

Increasing the Performance of {[(1-x-y) LiCoCu] (Al and Mg doped)] O}, xLiMnO, yLiCoO Composites as Cathode Material in Lithium-Ion Battery: Synthesis and Characterization.

Twenty-eight samples of {[(1-x-y) LiCoCu](Al and Mg doped)]O}, xLiMnO, and yLiCoO composites were synthesized using the sol-gel method. Stoichiometric weights of LiNO, Mn(Ac)⋅4HO, Co(Ac)⋅4HO, Al(NO).Ho, Mg(NO)⋅6HO, and Cu(NO).

Fabrication and characterization of the FeO@SiO-rGO nanocomposite: a catalyst for multi-component reactions.

A novel nanocomposite is synthesized by covalently modifying reduced graphene oxide (rGO) with FeO@SiO nanoparticles. FeO was synthesized using a co-precipitation method, and SiO was then coated onto the FeO a sol-gel method. Graphene oxide was synthesized using the Hummers' method.

A Novel Cathode Material Synthesis and Thermal Characterization of (1-x-y) LiCoTiFePO, xLiMnPO, yLiFePO Composites for Lithium-Ion Batteries (LIBs).

Lithium-ion batteries are known for their high efficiency for storing electrical energy, especially for hybrid vehicles. In this research, the development of mixture composites in the cathode electrode of LIBs has been discussed and designed based on ternary solid solutions. We have given a novel synthesis and method preparation of cathode electrode materials to reduce costs while increasing the efficiency and simultaneity for the future of these technologies.

Carbazochrome carbon nanotube as drug delivery nanocarrier for anti-bleeding drug: quantum chemical study.

The interaction between drugs and single-walled carbon nanotubes is proving to be of fundamental interest for drug system of delivery and nano-bio-sensing. In this study, the interaction of pristine CNT with carbazochrome, an anti-hemorrhagic or hemostatic agent, was investigated with M06-2X functional and 6-31G basis set. All probable positions of related adsorption for these kind drugs were thought-out to find out which one is energetically suitable.

Synthesis and antithrombotic activity of 1-benzyl-N'-benzylidenepiperidine-3-carbohydrazide derivatives.

: Platelet aggregation inhibition and interfering with clot formation are essential tools for antithrombotic therapy and there is a need for discovering new antithrombotic agents. In this study, we synthesized a series of benzylidenepiperidine-3-carbohydrazide derivatives (1f-11f), bearing various selected substituents on both the piperidine ring nitrogen and the hydrazide nitrogen. The synthesized compounds were characterized by FTIR, HNMR spectroscopic techniques, CHN/O elemental analysis and electrospray ionization mass spectra.

Symmetry Breaking of B2N((-, 0, +)): An Aspect of the Electric Potential and Atomic Charges.

In this study, the three forms of B2N((-, 0, +))-radical, anion and cation-have been compared in terms of electric potential and atomic charges, ESP, rather than the well-known cut of the potential energy surface (PES). We have realized that the double minimum of the BNB radical is related to the lack of the correct permutational symmetry of the wave function and charge distribution. The symmetry breaking (SB) for B2N((0, +)) exhibits energy barrier in the region of (5-150) cm(-1).

Cell membrane causes the lipid bilayers to behave as variable capacitors: A resonance with self-induction of helical proteins.

Cell membrane has a unique feature of storing biological energies in a physiologically relevant environment. This study illustrates a capacitor model of biological cell membrane including DPPC structures. The electron density profile models, electron localization function (ELF) and local information entropy have been applied to study the interaction of proteins with lipid bilayers in the cell membrane.

Metal-doped graphene layers composed with boron nitride-graphene as an insulator: a nano-capacitor.

A model of a nanoscale dielectric capacitor composed of a few dopants has been investigated in this study. This capacitor includes metallic graphene layers which are separated by an insulating medium containing a few h-BN layers. It has been observed that the elements from group IIIA of the periodic table are more suitable as dopants for hetero-structures of the {metallic graphene/hBN/metallic graphene} capacitors compared to those from groups IA or IIA.

A Computational Study of Cytotoxicity of Substituted Amides of Pyrazine- 2-carboxylic acids Using QSAR and DFT Based Molecular Surface Electrostatic Potential.

Pyrazine derivatives are important class of compounds with diverse biological and cytotoxic activities and clinical applications. In this study, B3 p 86 / 6 - 31 (+ +) G * was used to compute and map the molecular surface electrostatic potentials of a group of substituted amides of pyrazine-2-carboxylic acids to identify common features related to their subsequent cytotoxicities. Several statistical properties including potentials extrema (Vs ,min,Vs ,max), the average of positive electrostatic potential on the surface (Vs (+)), the average of V(r) over the surface (Vs) and the Lowest Unoccupied Molecular Orbital (LUMO) and system cytotoxicities were computed.

In silico study of effects of polymorphisms on biophysical chemical properties of oxidized N-terminal domain of X-ray cross-complementing group 1 protein.

Base excision repair (BER) is the major pathway involved in removal of endogenous and mutagen-induced DNA damage. The X-ray cross-complementing group 1 protein (XRCC1), which participates in BER, is a scaffolding protein. The oxidized XRCC1 N-terminal domain (NTD) forms additional interactions with DNA polymerase β (Pol β).

Comparison of 4-chloro-2-nitrophenol adsorption on single-walled and multi-walled carbon nanotubes.

The adsorption characteristics of 4-chloro-2-nitrophenol (4C2NP) onto single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) from aqueous solution were investigated with respect to the changes in the contact time, pH of solution, carbon nanotubes dosage and initial 4C2NP concentration. Experimental results showed that the adsorption efficiency of 4C2NP by carbon nanotubes (both of SWCNTs and MWCNTs) increased with increasing the initial 4C2NP concentration. The maximum adsorption took place in the pH range of 2-6.

A new generation of B(n)N(n) rings as a supplement to boron nitride tubes and cages.

In B(n)N(n) cages or tubes, when the quasi-borazine rings are attached to each other through a pair of common atoms of B and N, the bonding structure is named class A. On the other hand, there are some B(n)N(n) rings including a covalent bond between two atoms of B and N, which are named class B. In all previous studies, both reports of synthesis and theoretical calculation of boron nitride tubes and cages, the quasi-borazine units are attached together like class A.

Role of the salt bridge between Arg176 and Glu126 in the thermal stability of the Bacillus amyloliquefaciens α-amylase (BAA).

In the Bacillus amyloliquefaciens α-amylase (BAA), the loop (residues 176-185; region I) that is the part of the calcium-binding site (CaI, II) has two more amino acid residues than the α-amylase from Bacillus licheniformis (BLA). Arg176 in this region makes an ionic interaction with Glu126 from region II (residues 118-130), but this interaction is lost in BLA owing to substitution of R176Q and E126V. The goal of the present work was to quantitatively estimate the effect of ionic interaction on the overall stability of the enzyme.

Molecular dynamic study of human prion protein upon D178N mutation: new perspective to H-bonds, salt bridges and the critical amino acids.

The molecular dynamics simulation method was used to investigate the structural details for human prion protein (PrPN) and its D178N mutant (PrPM). Root-mean-square fluctuations (RMSFs) and the root-mean-square deviations (RMSDs) showed an increase in the flexibility and high dynamic plasticity of PrPM. Average Total energy for PrPM and PrPN sequentially was -2.

Combined 3D-QSAR modeling and molecular docking study on multi-acting quinazoline derivatives as HER2 kinase inhibitors.

A series of new quinazoline derivatives has been recently reported as potent multi-acting histone deacetylase (HDAC), epidermal growth factor receptor (EGFR), and human epidermal growth factor receptor 2 (HER2) inhibitors. HER2 is one of the major targets for the treatment of breast cancer and other carcinomas. Three-dimensional structure-activity relationship (3D-QSAR) is a well-known technique, which is used to drug design and development.

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant.

Investigation of solvent effect and NMR shielding tensors of p53 tumor-suppressor gene in drug design.

The p53 tumor-suppressor gene encodes a nuclear phosphoprotein with cancer- inhibiting properties. The most probable cancerous mutations occur as point mutations in exons 5 up to 8 of p53, as a base pair substitution that encompasses CUA and GAT sequences. As DNA drug design represents a direct genetic treatment of cancer, in the research reported computational drug design was carried out to explore, at the Hartree-Fock level, effects of solvents on the thermochemical properties and nuclear magnetic resonance (NMR) shielding tensors of some atoms of CUA involved in the hydrogen-bonding network.

Design of fMet-tRNA and calculation of its bonding properties by quantum mechanics.

It is generally accepted that initiation of protein synthesis in Escherichia coli starts with formyl-methionine, directed by the codons of AUG or GUG. In one case, reinitiating on the mRNA of amber mutants of UUG is used as the initiation codon. Early studies indeed showed that the triplets AUG, GUG, and UUG are the most effective in stimulating fMet-tRNA binding to ribosomes in vitro.

The study of adsorption characteristics Cu2+ and Pb2+ ions onto PHEMA and P(MMA-HEMA) surfaces from aqueous single solution.

The adsorption characteristics of Cu2+ and Pb2+ ions onto poly2-hydroxyethyl methacrylate (PHEMA) and copolymer 2-hydroxyethyl methacrylate with monomer methyl methacrylate P(MMA-HEMA) adsorbent surfaces from aqueous single solution were investigated with respect to the changes in the pH of solution, adsorbent composition (changes in the weight percentage of MMA copolymerized with HEMA monomer), contact time and the temperature in the individual aqueous solutions. The linear correlation coefficients of Langmuir and Freundlich isotherms were obtained. The results revealed that the Langmuir isotherm fitted the experimental results better than the Freundlich isotherm.

Thermodynamic study of interaction of TSPP, CoTsPc, and FeTsPc with calf thymus DNA.

The interaction of two water soluble phthalocyanines, cobalt(II) 4,4 ,4 ,4 -tetrasulfo-phthalocyanine (CoTsPc) and iron(II) 4,4 ,4 ,4 -tetrasulfo-phthalocyanine (FeTsPc), and one water soluble porphyrin, tetra sodium meso-tetrakis(p-sulfophenyl)porphyrin (TSPP), with calf thymus DNA has been studied by UV-Vis spectroscopy at five different temperatures (20, 25, 30, 35, and 40 degrees C). The optical absorption spectra of these materials were analyzed to obtain binding constants and stoichiometries using SQUAD software. The results show that the best fitting corresponds to a 1 : 1 complex model between a base pair of DNA and these materials.

A kinetic Monte Carlo simulation study of inositol 1,4,5-trisphosphate receptor (IP3R) calcium release channel.

Most of the previously theoretical studies about the stochastic nature of the IP3R calcium release channel gating use the chemical master equation (CME) approach. Because of the limitations of this approach we have used a stochastic simulation algorithm (SSA) presented by Gillespie. A single subunit of De Young-Keizer (DYK) model was simulated using Gillespie algorithm.

QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift.

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results.

Simulation of DNA bases in water: Comparison of the Monte Carlo algorithm with molecular mechanics force fields.

The interaction between the nucleic acid bases and solvent molecules has an important effect in various biochemical processes. We have calculated total energy and free energy of the solvation of DNA bases in water by Monte Carlo simulation. Adenine, guanine, cytosine, and thymine were first optimized in the gas phase and then placed in a cubic box of water.