Semiempirical Calculations Research Articles

Trigonal distortion in zigzag-antiferromagnet iron phosphorus trisulfide

The electronic structure of ${\mathrm{FePS}}_{3}$ was resolved using x-ray absorption spectroscopy with linear dichroism of x ray between in-plane and out-of-plane geometries. By integrating the measurements with semiempirical calculations, the observed nonvanishing feature in the dichroism spectra demands a site symmetry lower than cubic to be taken into account. These effects cause an energy splitting between ${a}_{1g}$ and ${e}_{g}^{\ensuremath{\pi}}$ orbitals of around 0.350 eV, contrary to previous reports purporting a smaller and insignificant energy splitting. Furthermore, reduction in the Slater integral was needed to establish agreement with experiment and theory suggesting metal-ligand covalency in the system. These findings shed light on how the local crystalline environment affects the electronic structure and the anisotropy in ${\mathrm{FePS}}_{3}$ and will prove imperative in its potential spintronic applications.

Regioselective Synthesis, Structural Characterization, and Antiproliferative Activity of Novel Tetra-Substituted Phenylaminopyrazole Derivatives.

A small library of highly functionalized phenylaminopyrazoles, bearing different substituents at position 1, 3, and 4 of the pyrazole ring, was prepared by the one-pot condensation of active methylene reagents, phenylisothiocyanate, and substituted hydrazine (namely, methyl- and benzyl-hydrazine). The identified reaction conditions proved to be versatile and efficient. Furthermore, the evaluation of alternative stepwise protocols affected the chemo- and regio-selectivity outcome of the one-pot procedure. The chemical identities of two N-methyl pyrazole isomers, selected as prototypes of the whole series, were unambiguously identified by means of NMR and mass spectrometry studies. Additionally, semiempirical calculations provided a structural rationale for the different chromatographic behavior of the two isomers. The prepared tetra-substituted phenylaminopyrazoles were tested in cell-based assays on a panel of cancer and normal cell lines. The tested compounds did not show any cytotoxic effect on the selected cell lines, thus supporting their pharmaceutical potentials.

Development of cigarette filter with biomass-based activated carbon for naphthalene removal from mainstream smoke

Naphthalene is one of the concentrated polycyclic aromatic hydrocarbons (PAHs) in cigarette mainstream smoke. Accumulated exposure to naphthalene causes various health problems such as irritation, gastrointestinal problems, neurological symptoms, renal problems, hematological disorders, and cancer. This study aimed to develop a biomass-based activated carbon from dried hemp (Cannabis sativa) stem for the removal of naphthalene from cigarette mainstream smoke. Activated carbon was prepared at an activation temperature of 350 to 550 °C using phosphoric acid as the activating agent. The elemental composition, porous texture, and surface functional groups of the activated carbon were determined by elemental analysis, nitrogen adsorption measurements, and temperature-programmed desorption (TPD). We found that the specific surface area and oxygen-containing functional groups of the carbon facilitate naphthalene adsorption where 77–96% of the naphthalene was removed from cigarette mainstream smoke. In addition, a computational investigation with a semiempirical PM7 calculation has provided the adsorption energies of naphthalene on oxygen-containing functional groups. As expected, the carboxyl group showed high efficiency in naphthalene adsorption, which is consistent with the experimental results.

Nonlinear polarization effect of functionalized graphene quantum dots

Graphene quantum dots (GQDs) are nanoscale structures of graphene with quantum properties and edge effects that give photoluminescence properties. The effect of quantum confinement and differences in the nature of GQD structure makes its optical characteristics highly dependent on the size of the structure. This study explains a few exploratory semi-empirical calculations of nonlinear polarization properties of functionalized GQD (fGQD) three-dimensionally. Based on this, the calculation of the linear polarization and first hyperpolarization was performed by the finite field method, which is based on the expansion of the energy and dipole moment. As a result, the fGQD molecule dominantly has high optical nonlinear properties as indicated by the high β values (71 to 4488 a.u.). In general, the first hyperpolarizabilities have a linear relationship with the dipole moments. It was potentially used for the second harmonic imaging microscopy (SHIM) application.

Vibrational relaxation and triggering of the non-equilibrium vibrational decomposition of CO2 in gas discharges

Non-equilibrium vibrational dissociation CO2 → CO + O at translational–rotational temperatures T ⩽ 1200 K is investigated with semi-empiric and computational models. The governing parameter has been introduced, where Q is the specific volumetric power coupled into vibrational states and n 0 is the initial number density of CO2. It has been shown that the non-equilibrium vibrational process can only be triggered when exceeds some critical value determined by the speed of vibrational relaxation. Simple semi-empiric calculations are backed by the state-to-state simulations of the CO2 vibrational kinetics in two-modes approximation performed for conditions of microwave sustained gas discharges. The vibrational kinetics model is benchmarked against the experimental vibrational relaxation times as well as the shock tube data on the rate of the process CO2 + M → CO + O + M for M = Ar and literature data for M = CO2. At T = 300 K the estimated W m3 or 35 W (m− 3 Pa− 2) (p is the gas pressure). is found to always increase with increased T.

Theoretical Analysis of the Adsorption of Pentachlorophenol and 6-OH-BDE-47 (6-Hydroxy-2,2’,4,4’-Tetrabromodiphenyl Ether) by Boron Nitride Nanotubes Decorated with Double-Decker Lanthanide(III) Phthalocyanine Complexes

Environmental issues have become an urgent concern, and low-cost, high-efficiency environmental remediation and energy utilization are currently high priorities. In this work, zigzag (9,0) and (18,0) boron nitride nanotubes modified by double-decker lanthanide(III) phthalocyanine complexes (BN90-LnPc2, BN180-LnPc2) were investigated by semi-empirical quantum chemistry calculations. The shorter the bond length between the nitrogen atom in the complex and the hydroxyl group of the contaminant, the greater the change in the C-O-H bond angle, implying stronger adsorption. In view of the neutral and deprotonated forms of pentachlorophenol and 6-OH-BDE-47 (6-Hydroxy-2,2’,4,4’-tetrabromodiphenyl ether), the effects of the hydrogen bond on the contaminants were significantly different. The analytical results of the HSAB reactivity descriptors and frontier molecular orbitals showed that BN180-YbPc2 performed best of all the composite systems, and the interaction with pentachlorophenol was stronger than with 6-OH-BDE-47. Furthermore, BN180-YbPc2 is beneficial as a solar-energy material, according to its electronic excitation spectrum. Ultimately, the calculated results were as expected due to the materials’ multifunctional characteristics, and the exploration of material development for specific properties will be the direction for future work.

Semi-empirical studies on odd parity levels system of manganese atom in multiconfiguration approximation

We present the results of semi-empirical calculations of the fine structure (fs) and the hyperfine structure (hfs) for the odd-parity level system of the manganese atom in a large multiconfiguration basis. Recently, new measurements applying laser induced fluorescence on an atomic beam and in a hollow cathode discharge lamp provided the hyperfine structure constants A and B for altogether 50 odd-parity levels. Therefore, a hyperfine structure many-body parameterization method was successfully used for such complicated system, composed of 71 configurations. In general, a good agreement between the experimental and the calculated values for the fs and hfs fits was obtained.

The origin for hydrocarbons fast transport and photoswitching permeation behavior in grafted laminar CdTe membranes

Thin laminar CdTe nanoflake membranes grafted by oleic acid were investigated for sorption characteristics and permeation of permanent gases and hydrocarbons depending on the process temperature. A huge influence of temperature was revealed, enabling enhancement of the ideal selectivity for butane-methane separation from 28 to over 100 with the change of process conditions from 25 °C to 10 °C. The separation factor attains 26 in mixed-gas CH4/C4H10 separation experiments. Both sorption enthalpy and activation energy of diffusion were evaluated for penetrants, exhibiting the role of low activation barriers in fast transport of condensable hydrocarbons. The experimental results were proved by a semi-empirical calculation, illustrating swelling of grafted layer with heavy hydrocarbons. The effect was proved experimentally with in situ diffraction experiment. The low activation energy for the transport of condensable hydrocarbons, strong temperature dependence of permeance, and huge extinction coefficient of CdTe nanoflakes enable modulating the membrane permeance with laser irradiation, demonstrated with permeance photoswitching.

ULYSSES: An Efficient and Easy to Use Semiempirical Library for C+.

We introduce ULYSSES, a user-friendly and robust C++ library for semiempirical quantum chemical calculations. In its current version, ULYSSES is equipped with a large set of different semiempirical models, most of which are based on the Neglect of Diatomic Differential Overlap (NDDO) approximation. Empirical corrections for dispersion and hydrogen bonding are available for most methods, so that higher quality is achieved in the calculation of energies of nonbonded complexes. The library is furthermore equipped with geometry optimization, as well as modules for calculating molecular properties of general interest. Ideal gas thermodynamics is available and allows single structure as well as conformer (multistructure) averaged properties to be calculated. We offer the possibility to use several vibrational partition functions according to the nature of interactions being studied: for covalent systems, the traditional harmonic oscillator approximation is available; for nonbonded complexes, we systematically extended the partition function proposed by Grimme for all thermodynamic functions. The library is also capable of running Born-Oppenheimer molecular dynamics.

Pulsed EPR Study of the Initial Steps of Radical-Scavenging Reactions of C70 with Diphenylphosphine Oxide, Hydroxycyclohexyl, and 2-Hydroxypropyl Radicals

The radical scavenging reactions of C70 were investigated using time-resolved (TR-) and pulsed electron paramagnetic resonance (EPR) methods. In the diphenylphosphine oxide (DPPO) radical and C70 system, structural isomers of the adduct radicals of C70 appeared in the TR-EPR spectrum with clear hyperfine structures due to the phosphorus atom. Four isomers were identified through the analysis of the hyperfine coupling constants. The assignment of the adduct radicals was confirmed by the semiempirical calculation of the relative addition reaction rate constants that produce each isomer. The radical scavenging rate constants, ksca, of C70 in toluene were determined for DPPO, hydroxylcyclohexyl, and 2-hydroxypropyl radicals through electron spin echo observations using the pulsed-EPR method. The ksca values were nearly 109 mol-1 dm3 s-1 and were almost equal to the diffusion-controlled rate constant in toluene. This proves that C70 acts as an excellent radical scavenger. In addition, the radical addition rate constants, kadd, of C70 for varying carbon atoms in C70 were obtained by considering the peak intensity ratio of the adduct radicals in the TR-EPR spectrum. In this study, we demonstrated that the large number of carbon atoms in pentagons (five-membered rings) is responsible for the high reactivity of fullerenes.

Desorption of organic molecules from interstellar ices, combining experiments and computer simulations: Acetaldehyde as a case study

Context. Explaining the presence of complex organic molecules (COMs) in interstellar environments requires a thorough understanding of the physics and chemistry occurring in the interplay between the gas phase and interstellar surfaces. Experiments and computer simulations are pivotal in building a comprehensive catalogue of processes of relevance for the build up of organic molecules in those environments. Aims. We combine experiments with tailored computer simulations to study the desorption dynamics of acetaldehyde CH3CHO – an important organic precursor in cold interstellar environments - on amorphous solid water for the first time. Our goals with this paper are twofold. Firstly, we want to contextualise the role of this molecule in the evolution of organic molecules in space. Secondly, we want to suggest a joint scheme to produce quantitative information on desorption magnitudes based on the combination of computations and experiments. This scheme can be adopted to refine measurements of other molecules. Methods. We determined desorption energies and pre-exponential factors of desorption theoretically using molecular dynamics simulations that combine semi-empirical and density functional calculations. We also performed temperature-programmed desorption experiments with acetaldehyde on top of non-porous amorphous solid water. The combination of theoretical and experimental results allows us to derive reliable quantities, which are required for understanding the desorption dynamics of interstellar COMs (iCOMs) atop interstellar ices. Results. The average theoretical and experimental desorption energies found for CH3CHO desorbing from non-porous amorphous solid water (np-ASW) surfaces are 3624 K and 3774 K, respectively. The pre-exponential factor determined theoretically is vtheo = 2.4 × 1012 s−1 while from the experiments it was possible to constrain this magnitude to 1012±1 s−1. Conclusions. The comparison of the desorption energies of CH3CHO with other COMs, such as CH3NH2 or CH3NO, shows that CH3CHO is more volatile. Therefore, we suggest that, in consideration of the average binding energy, CH3CHO should undergo preferential desorption during the ice-sublimation phase in hot cores enriching the gas-phase in this particular component. In addition, the overall low binding energy suggests a possible early return to the gas phase of pre-stellar cores due to non-thermal effects (i.e. reactive desorption or cosmic-ray-induced desorption). This could explain the prevalence of CH3CHO in the gas phase of pre-stellar cores. Dedicated laboratory and theoretical efforts are required to confirm this last point.

Measurement of nuclide production cross sections for proton-induced reactions on [formula omitted]Ni and [formula omitted]Zr at 0.4, 1.3, 2.2, and 3.0 GeV

Nuclide production cross sections for proton-induced reactions on natNi and natZr at incident energies of 0.4, 1.3, 2.2, and 3.0 GeV were measured by the activation method at Japan Proton Accelerator Research Complex (J-PARC). In total, 24 and 43 residual nuclides were measured for the natNi and natZr targets, respectively. Among them, the cross sections of the following reactions were measured for the first time: natZr(p,x)28Mg, natZr(p,x)42K, natZr(p,x)43K, natZr(p,x)44gSc, natZr(p,x)55Co, natZr(p,x)69mZn, and natZr(p,x)93Y reactions. To examine the prediction capabilities, the measured data were compared with the spallation reaction models in PHITS (INCL4.6, Bertini, and JAM as intranuclear cascade models, and GEM as an evaporation model), INCL++/ABLA07, semi-empirical calculation code SPACS, and the JENDL/HE-2007 library. From the evaluation introducing the mean square deviation factor, the best reproducibility was exhibited by the JENDL/HE-2007 library for natNi and INCL++/ABLA07 for natZr.

Adsorptive removal of toxic malachite green from its aqueous solution by Bambusa vulgaris leaves and its acid-treated form: DFT, MPR and GA modeling

In the current investigation, bamboo leaves (BL), H2SO4 treated bamboo leaves (SBL), and H3PO4 treated bamboo leaves (PBL) were utilized as biosorbents for the elimination of Malachite Green (MG) from the synthetic medium. The adsorption study was executed under the variation of different experimental conditions like pH, biosorbent dosage, contact time, and the temperature on the MG. Langmuir isotherm fit the adsorption data with maximum monolayer adsorption capacity, 151.735 mg/g at 298 K − 168.339 mg/g at 318 K for PBL. The data fitted the pseudo-2nd -order kinetic model for all three adsorbents with a correlation coefficient greater than 0.99, indicating that chemisorption controls adsorption. The Dubinin-Radushkevich isotherm indicated that the mean sorption energy (E) is a physisorption mechanism. So, the process involves physical sorption as well as chemical sorption processes with negligible sorption energy. The FTIR, Raman Spectra, and 13C NMR results show that different functional groups of cellulose, hemicellulose and lignin are involved in MG elimination. The theoretical studies were applied for a deeper understanding of the adsorption mechanism of MG using semi-empirical quantum chemical calculations. The DFT Calculations yielded valuable information about quantum chemical properties, like EHOMO, ELUMO, electrophilicity, chemical reactivity, dipole moment, and hardness for adsorbent/adsorbate components and the binding energy from adsorbent/adsorbate interactions. Multiple polynomial regression and genetic algorithm also have been successfully applied to predict the removal percentage of malachite green.

Endohedrally Functionalized Metal–Organic Cage-Cross-Linked Polymer Gels as Modular Heterogeneous Catalysts

The immobilization of homogeneous catalysts onto supports to improve recyclability while maintaining catalytic efficiency is often a trial-and-error process limited by poor control of the local catalyst environment and few strategies to append catalysts to support materials. Here, we introduce a modular heterogenous catalysis platform that addresses these challenges. Our approach leverages the well-defined interiors of self-assembled Pd12L24 metal-organic cages/polyhedra (MOCs): simple mixing of a catalyst-ligand of choice with a polymeric ligand, spacer ligands, and a Pd salt induces self-assembly of Pd12L24-cross-linked polymer gels featuring endohedrally catalyst-functionalized junctions. Semi-empirical calculations show that catalyst incorporation into the MOC junctions of these materials has minimal affect on the MOC geometry, giving rise to well-defined nanoconfined catalyst domains as confirmed experimentally using several techniques. Given the unique network topology of these freestanding gels, they are mechanically robust regardless of their endohedral catalyst composition, allowing them to be physically manipulated and transferred from one reaction to another to achieve multiple rounds of catalysis. Moreover, by decoupling the catalyst environment (interior of MOC junctions) from the physical properties of the support (the polymer matrix), this strategy enables catalysis in environments where homogeneous catalyst analogues are not viable, as demonstrated for the Au(I)-catalyzed cyclization of 4-pentynoic acid in aqueous media.

Mechanistic insights into ion-beam induced reduction of graphene oxide: An experimental and theoretical study

Interest in graphene oxide (GO) due to its controllable and adjustable properties has been increasing, especially in the field of electronic and electrochemical charge storage devices. Hence, the modification of surface chemistry and structure of GO can be outlined as crucial for achieving the preferable properties. In this study, we have investigated the influence of 15 keV proton-beam irradiation on GO structure and surface chemistry. The results obtained by Raman spectroscopy, Fourier-transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS) were complemented with theoretical ones, obtained by using density functional theory (DFT), semi-empirical (SE) calculations and inelastic thermal spike (iTS) model. The FTIR and XPS results showed that proton irradiation partially reduces the GO with the preferential removal of the alkoxy and epoxy groups. Also, we identified a clear linear relation between the decresase of oxygen content and the decrease of ID/IG ratio i.e. increasing disorder of GO structure. The SE and DFT calculations highlighted a reduction of GO as a single- or multi-step process depending on the type of basal-plane or edge oxygen group. Dynamic SE calculations revealed that for kinetic energy of hydrogen below 1.5 eV the reduction is chemically driven, while at energies higher than 20 eV, the reduction of GO is a result of physical processes. iTS results showed that increase of temperature might contribute to reduction of GO via desorption of epoxy and alcoxy groups, as the least thermally stable groups (T ∼200 °C). The results of this work emphasize the capabilities ion beam irradiation for gradual modification of surface chemistry and structural properties of GO by providing more information about the mechanisms of hydrogen interaction with individual groups, interplay between defect creation, oxygen content and accompaning effects of ion energy loss processes.

NON-LINEAR OPTICAL PROPERTIES STUDY OF TWO HETEROCYCLIC COMPOUNDS

In an attempt towards understanding the relation between molecular structure-nonlinear optic activity (NLO) among heterocycles, with special reference to the identity, number and position of the heteroatom, semiempirical calculations were carried out. This paper reports the Non-linear optical properties of two heterocyclic compounds namely 3-[2-Oxo-2-(2-oxo-2H-chromen-3-yl)-ethylidene]-1,3-dihydro-indol-2-one (3OCEDI) and Quinolin-8-ol (QL). To understand the Non-Linear Optical properties of coumarin dyes we computed dipole moment (μ), electronic polarizability (α), and the mean was first hyperpolarizability (βo) using B3LYP density functional theory method in conjunction with 6-31G(d, p) basis set.All the calculations were carried out in gas phase and in acetonitrile medium. The optimized geometry of both compounds shows a 3D helical structure. The results indicate that given the same number and type of atoms and double bonds in a molecule, linear conjugation excels over cyclic or crossed conjugation in enhancing hyperpolarizabilities and it seems to be far more critical than a chiral centre.

Modeling and Optimisation of Comlexity by the β-Cyclodextrin of an Organic Pollutant Model: m-Methyl Red

Studies of cyclodextrin chemistry using quantum chemical methods are mainly adopted to investigate the formation of the inclusion complex causing changes in the physicochemical properties of the cyclodextrin guest. In this paper, we conducted a computational modeling study of the inclusion complexes of β-cyclodextrin (β-CD) with m-Methyl Red (m-MR) by using parametric method 6 (PM6), the semi empirical molecular orbital calculations and the natural bond orbital method (NBO). The inclusion process is carried out by maintaining the coordinates of the β-CD fixed and by displacing the guest molecule. The different relative positions between m-MR and β-CD are measured with respect to the distance between the reference atom (N) in the guest molecule and the origin of the coordinates from the equatorial plane of β-CD. The m-MR/β-CD (B) inclusion complex has a lower negative value of ΔG compared to another m-MR/β-CD (A) complex, highlighting the spontaneous behavior of the inclusion process. In addition, during the process of inclusion, the complexation energy is negative, which allows us to affirm that the complexation of m-MR in the β-CD is thermodynamically favorable. Among two directions A and B, the minimum energy generated from the PM6 was obtained in the orientation B and the guest molecule is partially encapsulated in the cavity of β-CD. In the NBO analysis, the stabilization energy is also usually used to characterize the hydrogen bond interaction between a lone pair (LP(Y)) of an atom Y and an anti-bonding orbital (BD٭(X-H)).

Surface potential and local conductivity measurements of micropatterned aromatic monolayers covalently attached to n-Si(111) via Si–C and Si–O bonds

The surface potentials and local conductivity of self-assembled monolayers (SAMs) formed using aromatic molecules covalently bonded to n-type silicon (111) via Si–C and Si–O bonds were measured using Kelvin probe force microscopy (KPFM) and conductive AFM (CAFM). Surface potential measurements were done using micropatterned SAMs with hexadecyl SAM as a reference to eliminate surface potential variations due to the cantilever tips. Micropatterning was conducted via vacuum ultraviolet photolithography at λ = 172 nm. Ellipsometry, X-ray photoelectron spectroscopy, static water contact angle and atomic force microscopy tests show that the aromatic SAMs were well-organized despite the short molecular lengths of the precursors. KPFM results show that Si–C bonded SAMs have higher surface potentials compared to Si–O SAMs, which is in agreement with dipole moments estimated by Molecular Orbital Package semi-empirical computations. CAFM scans showed conductive domains for the aromatic SAM regions, and Si–O SAMs exhibited a higher current than Si–C SAMs.

Friction sensitivity of nitramine energetic materials: a prediction based on genetic function approximation

In this paper, we report a quantitative structure-property relationship (QSPR) model development for friction sensitivity prediction of nitramine energetic materials. The model is obtained by means of a sophisticated method, namely, genetic function approximation and consists of 10 descriptors. As a training set, we have applied 80 nitramine energetic materials of a few families, both molecular and salt-like. The corresponding test set included 30 compounds. As a result, we have obtained a good correlation with R2 = 0.90. Only two descriptors, the heat of formation and quadrupole components, need semi-empirical quantum-chemical calculations, while the rest ones are so-called “fast descriptors” meaning the relatively short time of the prediction. Using the obtained QSPR model along with our recent method for fast crude estimation of the detonation properties based on empirical formulas we have modified a few energetic salts in order to obtain materials with better friction sensitivity and detonation performance. This was mainly done by changing the constituting ions: thus, 10 nitramine energetic materials with improved characteristics were proposed.

A theoretical insight to understand the structures and dynamics of thiazole derivatives

Quantum chemical analysis of some Thiazole derivatives, namely (2-Chlorobenzothiazole; 5-acetyl-2,4dimethylthiazole; 2-Chlorobenzothiazole; Phthalylsulfathaizole; 2,4,5 Trimethyl thiazole) was performed by using Gaussian 9 software with semi-empirical calculation method such as density functional theory (DFT) and the basis sets used were the DFT/B3LYP methods using 6-311G (d, p). Various quantum chemical parameters such as electronic density, highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO) energy levels, and the energy difference between highest and lowest unoccupied molecular orbitals (ELUMO-EHOMO), etc. were calculated. High EHOMO values suggests that the molecule can contribute the electrons towards bond formation; however, the lower values of ELUMO indicate that the molecule can easily accept the electrons. Besides that, the low value of the energy bandgap (ΔE) confirms the excellent inhibition efficiencies of the derivatives. Furthermore, by using these frontier orbital energies, different parameters like ionization energy, electron affinity, global hardness, electronegativity were also calculated. In this article, a theoretical study was performed only to determine the correlation between various parameters related to the electronic structure of Thiazole derivatives and their competence to mitigate the corrosion process.