Weakened Mn-O bond in Mn-Ce catalysts through K doping induced oxygen activation for boosting benzene oxidation at low temperatures

K-doped Mn-Ce solid solution catalysts were synthesized using a combination of coprecipitation and hydrothermal methods, demonstrating excellent performance in benzene oxidation. The catalyst K1Ce5Mn5 exhibited comparable activity to noble metal catalysts, achieving a 90 % benzene conversion at approximately 194 ℃. Durable tests under dry and moist conditions revealed that the catalyst could maintain its activity for 50 h at 218 ℃ and 236 ℃, respectively. Characterization results indicated that the catalyst's enhanced activity resulted from the weakened Mn-O bonding caused by the introduction of K+, facilitating the activation of oxygen and its involvement in the reaction. CeOx, the main crystalline phase of Mn-Ce solid solutions, provided abundant oxygen vacancies for capturing and activating oxygen molecules for the weakened Mn-O structures. This conclusion was further supported by partial density of state analysis from density functional theory computations, revealing that the introduction of K+ weakened the orbital hybridization of Mn3d and O2p. Finally, in situ diffuse reflectance infrared Fourier-transform spectroscopy (in situ DRIFTS) studies on Ce5Mn5 and K1Ce5Mn5 catalysts suggested that the introduction of K+ promoted the conversion of adsorbed benzene. Furthermore, intermediate products were transformed more rapidly for K1Ce5Mn5 compared to Ce5Mn5.

A literature review of the increased intracellular free calcium concentration by biofield therapy or laser exposure. An explanation by using a theoretical study of hydrated calcium ions

INTRODUCTION

A revision of several experimental results on cells shows that electromagnetic radiation, either produced by biofield therapy (BFT) or laser, induced an increase in intracellular free calcium concentration. An explanation of this phenomenon is proposed.

METHODS

Quantum chemistry calculations were performed on Ca2+ with different degrees of hydration with the DFT/r2SCAN-3c method together with the implicit solvation model SMD.

RESULTS

Ca2+ dehydration energy by quantum calculations, in an aqueous medium, coincides with the experimental results of the energy of the photon emitted in biofield therapies and lasers. This strongly suggests that the increased intracellular free calcium concentration is because of calcium ion dehydration upon the application of radiation. The Ca2+ dehydration increases the membrane potential due to an augment of the net charge on Ca2+ and it moves near the membrane by the attraction of its negative ions. The voltage-dependent channels are also activated by this membrane potential.

CONCLUSION

The increased intracellular Ca2+ concentration occurs with biofield therapy (BFT) or laser. A novel explanation is given based on resonance-induced Ca2+ dehydration with applied radiation, supported by experimental data and theoretical calculations.

Innovatively feasible wet incipient method for preparing Cu doped TiO2 nanocomposite: Electro-optical measurement supported by quantitative quantum and classical calculations

The Cu-doped titanium oxide (Cu/TiO2) nanocomposite was systematically prepared using the innovatively feasible incipient wet impregnation method. Notably, the samples were derived from the raw materials through water dilution only. The successful formation of the host anatase TiO2 phase was confirmed by the characteristic peaks observed in the acquired X-ray powder diffraction (XRD) spectrum, which displayed intense peaks attributed to Cu2+ scattering sites, indicating the formation of crystallite Cu/TiO2 nanostructures. Dielectric measurements revealed that Cu/TiO2 possesses a higher dielectric permittivity compared to undoped TiO2. The conductivity for both structures exhibited a decreasing trend with increasing temperature. Interestingly, the measured optical properties indicated that Cu/TiO2 exhibited the minimum energy gap and maximum refractive index. This was further validated by qualitative time-dependent density functional calculation on a stable structural model, which was confirmed through semi-empirical molecular dynamic calculations. Thus, we have demonstrated the capability of our innovatively feasible synthesis method to produce the industrially important Cu-doped TiO2.

Biosorption of zinc (II) from synthetic wastewater by using Inula Viscosa leaves as a low-cost biosorbent: Experimental and molecular modeling studies

The use of biosorption as a strategy for lowering the amount of pollution caused by heavy metals is particularly encouraging. In this investigation, a low-cost and efficient biosorbent, Inula Viscosa leaves were used to remove zinc ions (Zn²⁺) from synthetic wastewater. A Fourier transform infrared spectroscopy experiment, a scanning electron microscopy experiment, and an energy dispersive X-ray spectroscopy experiment were used to describe the support. Several different physicochemical factors, such as the beginning pH value, contact duration, initial zinc concentration, biosorbent dose, and temperature, were investigated in this study. When the Langmuir, Freundlich, Temkin, Toth, and Redlich-Peterson models were used to match the data from the Inula Viscosa leaves biosorption isotherms, it was found that the biosorption isotherms correspond most closely with the Langmuir isotherm. On the other hand, the kinetic biosorption process was investigated using pseudo-first-order, pseudo-second-order (PS2), and Elovich models. The PS2 model was the one that provided the most accurate description of the biosorption kinetics. The thermodynamics process shows the spontaneous and endothermic character of Zn²⁺ sorption on Inula Viscosa leaves, which also entails the participation of physical interactions. In addition, the atom-in-molecule analysis, density functional theory, and the conductor like screening model for real solvents, were used to investigate the relationship that exists between quantum calculations and experimental outcomes.

Theoretical and experimental study of the photodegradation of methyl orange in the presence of different morphologies of Au-ZnO using Monte Carlo dynamic simulation

Herein, a simple approach was formed based on synthesizing different morphologies of ZnO and Au-ZnO as photocatalyst. In this study, ZnO and Au-ZnO were synthesized via a co-precipitation method and fully characterized via scanning electron microscopy (SEM), X-ray diffraction (XRD), and energy-dispersive X-ray spectroscopy (EDX). Three different ratios of Zn2+:OH- (1:2, 1:3, and 1:5) controlled the morphology of samples, which were made into spindle, star, and flower structures, respectively. Then, the photocatalytic activity was studied and compared. Their comparison showed that the flower morphology for ZnO and Au-ZnO was more effective in photocatalytic degradation and decolorization of methyl orange dye. Also, quantum and Monte Carlo (MC) calculations were carried out to investigate the adsorption of methyl orange (MO) molecules on ZnO(111) surface in the presence of Au or without Au in aqueous conditions by Monte Carlo adsorption locator simulations in the Materials Studio 2017 software. Au created a tendency to form a relatively strong interaction of MO with the ZnO(111) surface. The adsorption of MO on Au-ZnO(111) in the presence of Au was more significant than that of MO on ZnO(111), suggesting Au could significantly improve the reactivity of the methyl orange toward the ZnO(111).

Hydrazone-based Materials; DFT, TD-DFT, NBO Analysis, Fukui Function, MESP Analysis, and Solar Cell Applications

Due to numerous pharmaceutical and biological activities hydrazone (TC) based materials, it was important to investigate quantum chemical studies such as Density functional theory (DFT) calculations, natural bond orbital (NBO) analysis, molecular electrostatic potential (MESP), and local reactivity usage Fukui function for six TC derivatives compounds. DFT, NBO, MESP, and local reactivity calculations were obtained via utilizing CAM-Becke's three-parameter functional and Leee Yange Parr (CAM-B3LYP) functional and 6-311G +  + (2d, 2p) basis set. Optimized molecular structures for all studied compounds were obtained usage the DFT/CAM-B3LYP/6-311G +  + (2d, 2p) method. In addition, the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), energy gap (E_g), light harvest efficiency (LHE), and open-circuit voltage (Voc) of all studied MSs are calculated and illustrated. These properties indicate that these molecular modeling structures as good candidates for utilization in organic DSSCs. The calculated spectroscopic investigations of hydrazine derivatives have been obtained by applying the TD/CAM-B3LYP/6-311G +  + (2d, 2p) method. the calculated UV-Vis absorption spectra for molecular structures under study show nice correlations with experimental spectra.

Structural insight into locked nucleic acid based novel antisense modifications: A DFT calculations at monomer and MD simulations at oligomer level

In the present study, five novel LNA based antisense modifications have been proposed. A conformational search was carried out using TANGO, followed by geometry optimization using MOPAC. Based on their electronic energies the most stable conformation for each modification was identified. Further, DFT based full geometry optimization on the most stable conformations at the gas phase B3LYP/6-31G(d,p) using a Gaussian03 and single point energy calculations on the optimized structures at the solvent phase B3LYP/6-311G(d,p) level of theory were done to derive their quantum chemical descriptors using the Gaussian09. A comparison of global reactivity descriptors confirmed that the LNA based modifications were the most reactive. Base-pair stability was recorded by observing the binding energies and base-pairing conformations of modified GC base pairs at the B3LYP/6-311G(d,p) level of theory. Molecular dynamics simulations have been performed at the oligomer duplex level by incorporating individual modifications on 20-mer RNA-RNA duplexes using AMBER16. Free energy calculations of duplex structures suggested that incorporation of A2 modification into the RNA-RNA duplex increased the duplex binding affinity similar to LNA. Whereas, the A3 modification showed less binding compared to LNA but improved binding compared to MOE. This computational approach using quantum chemical methods may be very useful to propose better modifications than the existing ones before performing the experiments in the area of antisense technology.

Hydrogen bonding catalysis by water in epoxide ring opening reaction

Water can act as catalyst is perhaps the most intriguing property reported of this molecule in the last decade. However, despite being an integral part of many enzyme structures, the role of water in catalyzing enzymatic reactions remains sparsely studied. In a recent study, we have shown that the epoxide ring opening in aspartate proteases follows a two-step process involving water. In this work, we attempt to unravel the electronic basis of the co-catalytic role of water in the epoxide ring opening reaction by employing high-level quantum mechanical calculations at M06-2X/6-31+G(d,p) level of accuracy. Our computed electron density and its reduced gradient show that water anchor the reactant molecules through strong H-bond bridges. In addition, the strong ionizing power of water allows better charge delocalization to stabilize the transition states and oxyanion intermediate. Electrostatic analyses suggest greater charge transfer from the aspartates to the epoxide in the transition state, which is found to be exergonic in nature rendering a low-barrier reaction compared to a control system where water was omitted in the reaction field. This elucidated mechanism at electronic level could promote further research to search for the co-catalytic role of water in other enzymes.

Membrane organization and intracellular transport of a fluorescent analogue of 27-hydroxycholesterol

Oxysterols are cholesterol metabolites with multiple functions in controlling cellular homeostasis. In particular, 27-hydroxycholesterol (27-OH-Chol) has been shown to regulate a variety of physiological functions, but little is known about its uptake, intracellular trafficking, and efflux from cells. This is largely due to a lack of suitable analogs of 27-OH-Chol, which mimic this oxysterol closely. Here, we present the intrinsically fluorescent 27-hydroxy-cholestatrienol (27-OH-CTL), which differs from 27-OH-Chol only by having two additional double bonds in the steroid ring system. Based on molecular dynamics (MD) simulations, we show that 27-OH-CTL possesses almost identical membrane properties compared to 27-OH-Chol. By comparative imaging of 27-OH-CTL and of the cholesterol analogue cholestatrienol (CTL) in living cells, we assess the impact of a single hydroxy group on sterol trafficking. We find that human fibroblasts take up more CTL than 27-OH-CTL, but efflux the oxysterol analogue more efficiently. For both sterols, efflux includes shedding of vesicles from the plasma membrane. Intracellular, 27-OH-CTL accumulates primarily in lipid droplets (LDs), while CTL is mostly found in endosomes and lysosomes. Using fluorescence recovery after photobleaching (FRAP), we find for both sterols a rapidly exchanging pool, which moves orders of magnitude faster than sterol containing vesicles and LDs. In summary, by applying a new fluorescent derivative of 27-OH-Chol we demonstrate that human cells can distinguish sterols based on a single hydroxy group in the side chain, resulting in different transport itineraries, dynamics, and efflux kinetics. Both intrinsically fluorescent cholesterol and oxysterol analogues show rapid non-vesicular transport in human fibroblasts.

The effect of functionalization on solubility and plasmonic features of gold nanoparticles

Effect of functionalization on stability, solubility, and plasmonic features of gold nanoparticle with the general formula of Au₁₈(SR)₁₄ in water solvent has been studied in this work. Thiol functional groups including 1,1-mercapto-ethyl alcohol, s-cysteamine, thioglycolic acid, and beta-mercaptoethanol have been used. Electronic band-gap, excitation energies, dipole moment, and hardness for all gold nanoparticles in water solvent were investigated using the quantum mechanical approach. Intermolecular forces, radial distribution function (RDF), mean square displacement (MSD), and solvation free energy were calculated by using simulation methods. Electronic band-gap, and excitation energy analysis show that surface modification of gold nanoparticles can change their electronic and plasmonic properties. The analysis of dipole moments indicates that ligands affect the nanoparticle's solubility. An increase of hardness and therefore chemical stability can be observed for functionalized nanoparticles compared to the bare structure. Intermolecular energies analyses suggest that structure with 1,1-mercapto ethyl alcohol ligand has the strongest interaction with the solvent. The analysis of RDF diagrams also indicates that the molecule with 1,1-mercapto ethyl alcohol ligand has the sharpest pick. The slope of the linear part of MSD diagrams that is the criterion of solute's lateral diffusion is the highest value for nanoparticle with 1,1-mercapto ethyl alcohol ligand. Furthermore, functionalization also affects solvation free energy contributions. According to obtained data of quantum mechanical calculations and molecular dynamics simulations, it may be concluded that particle with 1,1-mercapto ethyl alcohol is the best ligand for increasing solubility, stability, and plasmonic functions of Au₁₈(SR)₁₄ structures among the examined ones.

The rotational spectrum of acetophenone-CO2: Preferred non-covalent interactions

The rotational spectrum of the acetophenone-CO₂ complex was investigated by pulsed jet-expansion Fourier transform microwave spectroscopy combined with ab initio calculations. In the supersonically cooled jet, only one isomer has been observed which is characterized by a dominant (CO₂)C···O tetrel bond and a secondary (C-H)_methyl∙∙∙O weak hydrogen bond. Johnson's non-covalent interaction, Bader's quantum theory of atoms in molecules and Symmetry-Adapted Perturbation Theory analyses have been applied to understand better the nature of non-covalent interactions in the acetophenone-CO₂ complex.

DFT study of electron absorption and emission spectra of pyramidal LnPc(OAc) complexes of some lanthanide ions in the solid state

The electron absorption and emission spectra were measured for the pyramidal LnPc(OAc) complexes in the solid state and co-doped in silica glass, where Ln=Er, Eu and Ho. The theoretical electron spectra were determined from the quantum chemical DFT calculation using four approximations CAM-B3LYP/LANL2DZ, CAM-B3LYP/CC-PVDZ, B3LYP/LANL2DZ and B3LYP/CC-PVDZ. It was shown that the best agreement between the calculated and experimental structural parameters and spectroscopic data was reached for the CAM-B3LYP/LANL2DZ model. The emission spectra were measured using the excitations both in the ligand and lanthanide absorption ranges. The possibility of energy transfer between the phthalocyanine ligand and excited states of lanthanide ions was discussed. It was shown that the back energy transfer from metal states to phthalocyanine state is responsible for the observed emission of the studied complexes both in the polycrystalline state and silica glass.

Supercell program: a combinatorial structure-generation approach for the local-level modeling of atomic substitutions and partial occupancies in crystals

Background

Disordered compounds are crucially important for fundamental science and industrial applications. Yet most available methods to explore solid-state material properties require ideal periodicity, which, strictly speaking, does not exist in this type of materials. The supercell approximation is a way to imply periodicity to disordered systems while preserving “disordered” properties at the local level. Although this approach is very common, most of the reported research still uses supercells that are constructed “by hand” and ad-hoc.

Results

This paper describes a software named supercell, which has been designed to facilitate the construction of structural models for the description of vacancy or substitution defects in otherwise periodically-ordered (crystalline) materials. The presented software allows to apply the supercell approximation systematically with an all-in-one implementation of algorithms for structure manipulation, supercell generation, permutations of atoms and vacancies, charge balancing, detecting symmetry-equivalent structures, Coulomb energy calculations and sampling output configurations. The mathematical and physical backgrounds of the program are presented, along with an explanation of the main algorithms and relevant technical details of their implementation. Practical applications of the program to different types of solid-state materials are given to illustrate some of its potential fields of application. Comparisons of the various algorithms implemented within supercell with similar solutions are presented where possible.

Conclusions

The all-in-one approach to process point disordered structures, powerful command line interface, excellent performance, flexibility and GNU GPL license make the supercell program a versatile set of tools for disordered structures manipulations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13321-016-0129-3) contains supplementary material, which is available to authorized users.

Evaluation of adsorption and desorption steps in the solid-phase extraction of explosives using carbon/silica gel nanocomposites

New series of carbon/silica gel nanocomposites, carbosils, prepared by the carbonization of starch bound to silica gel, and carbosils additionally silylated with octadecyldimethylchlorosilane were synthesized. These materials were applied as adsorbents in the solid-phase extraction of explosive nitrate esters and nitroaromatics from aqueous solutions. The adsorption and desorption steps were evaluated separately. It was found that both the molecular properties of explosives (dipole moments, orbital energies, solvation effects) and textural properties influenced by carbon deposits or octadecyl moieties have a large impact on the recovery rates. It was shown that the composites with moderate content of carbon deposits or with the highest amounts of carbon deposits and additionally silylated can be used as materials tailored for extraction of explosives from the aqueous solutions.

New structures of hydronium cation clusters

Four new hydronium ion structures are investigated by means of quantum mechanical calculations at the DFT/B3LYP6-311+G(2d,2p) level of theory. There exist experimental crystallographic hydronium cations (H₁₁O₅ ⁺) of two different geometrical structures, one BEXFEQ (acyclic) and one IYEPEH (cyclic). Molecular calculations reveal their relative stability. Another hydronium cation NEBDII (H₁₅O₇ ⁺) when optimized reveals a totally new and unexpected structure. All three optimized structures are shown to be quite stable as judged by their binding energies, and therefore may possibly be found in solution. A main result of this article is the discovery of three new optimized structures of hydronium ions, all of which are preferentially ring structures. The optimized structure of H₁₅O₇ ⁺ is a cube lacking a vertex. Putting a water molecule at the "empty" vertex leads by energy optimization to a structure of H₁₇O₈ ⁺ which has the approximate symmetry of a cube. This cubic structure, as judged by its fragments, is one of the most interesting of the hydronium ions studied in this paper. The addition of H₃O⁺ to a group of seven neutral molecules in the hypothetical reaction H₃O⁺ + 7 H₂O → H₁₇O₈ ⁺ induces two water molecules to each capture a proton at the expense of two other water molecules (converting them into hydroxyl anions) leading to a cluster with the formula [ H 3 O + 0.7 ] 3 [ H 2 O ] 3 + 0.1 [ OH - 0.6 ] 2 , where the superscripts are the integrated QTAIM atomic charges (in atomic units) on the respective species (inside the bracket) or on groups of a given species (outside the bracket). The cubic arrangement of 3H₃O⁺.3H₂O.2OH^- is accompanied with a significant redistribution of charge: Each hydronium cation carries ca. +0.7 au, the hydroxyl anions only around -0.6 au each, while the water molecules remain quasi-neutral with a slight positive charge.