Semiempirical Theory Research Articles

Nonadiabatic Photodynamics of Amantadine and 1-Cyanoadamantane Cations.

Cations of diamondoids and derivatives thereof have recently become the subject of experimental, spectroscopic studies due to their potential role in astrochemistry. In particular, their electronic spectra and photoinduced dynamics trigger great interest. Here, we report on computational investigations of two nitrogen-containing derivatives of the adamantane cation (Ada+, ), the amantadine cation (Ama+, ) and the 1-cyanoadamantane cation (Ada-CN+, C10H15CN+). Specifically, we study electronic (vibrationally resolved) spectra and nonadiabatic molecular dynamics (modeled using the surface hopping approach based on semiempirical electronic structure theory) of these radical cations. The internal conversion time constants as well as reactive relaxation outcomes (cage-opening and hydrogen loss) are compared for the two derivatives and also with the case of Ada+.[29] Remarkably, we find a longer ground-state recovery time for Ada-CN+ than for Ama+ (for the same excitation energy window), despite a smaller excitation energy for the former. Thus, a static energy gap law cannot be used to rationalize nonadiabatic dynamics and excited state lifetimes in this case: Dynamics and details of the couplings between several states play a decisive role.

A Variant of the Local Similarity Theory and Approximations of Vertical Profiles of Turbulent Moments of the Atmospheric Convective Boundary Layer

The approximation of the turbulent moments of the atmospheric convective layer is based on a variant of the local similarity theory using the concepts of the semi-empirical theory of Prandtl turbulence. In the proposed variant of the local similarity theory, the second moment of vertical velocity and the “spectral” Prandtl mixing length are used as basic parameters. This approach allows us to extend Prandtl’s theory to turbulent moments of vertical velocity and buoyancy and additionally offer more than ten new approximations. The comparison of the proposed approximation with other variants of the theory of local similarity is considered. It is shown that the selected basic parameters significantly improve the agreement between the local similarity approximations and experimental data. The approximations are consistent with observations in the turbulent convective layer of the atmosphere, the upper boundary of which nearly corresponds to the lower boundary of the temperature inversion. Analytical approximations of local similarity can find applications in the construction of high-order moment closures in the vortex of resolving numerical turbulence models, as well as in the construction of “mass-flux” parametrization.

Enhancing hydrogen sulphide removal efficiency: A DFT study on selected functionalized graphene-based materials

In response to the escalating demand for cleaner energy sources, this study investigates the potential of carefully selected functionalized graphene-based materials for enhancing hydrogen sulphide (H2S) removal in fuel streams, utilizing semi-empirical and density functional theory (DFT) calculations for molecular-level insights. A particular focus is placed on aliphatic methyl (-CH), alcohol (-COH), carboxylate (-COO), carbonyl (-CO), and acid (-COOH) -functionalized graphene, aiming to bridge gaps between desulphurization methods and graphene applications, specifically targeting H2S removal. Through extensive computational analyses, the research unravels the intricate interactions between chosen functionalized graphene materials and sulfur compounds like H2S, emphasizing mechanisms contributing to improved desulphurization efficiency. Our study's analysis highlights the superior performance of carboxylate (-COO)-functionalized graphene, mainly through dissociative adsorption mechanisms. The study systematically evaluates the influence of selected functional groups on adsorption activity, emphasizing the significance of dissociation. Overall, this research advances desulphurization strategies and underscores the potential of functionalized graphene in sustainable energy solutions.

Automatic Determination of the Non-Covalent Stable Conformations of the NO2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach.

We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.

МОДЕЛИ ТУРБУЛЕНТНОСТИ В РАСЧЕТАХ АЭРОДИНАМИЧЕСКИХ ХАРАКТЕРИСТИК ГАЗОВЫХ ПОТОКОВ

Abstract. The review of the most common turbulence models in engineering calculations, which allow approximate description of turbulent flows using the Reynolds equations of motion, is carried out, and their areas of application are shown. To calculate turbulent flows by solving the Reynolds equations, a closure hypothesis is adopted for apparent turbulent stresses and other variables included in the equations.
 It is noted that Businex is considered one of the main ones, which is confirmed by experimental studies of turbulence, which show that the turbulent flow is characterized by the presence of an energy cascade from large to smaller scales.
 In addition, the authors considered: the semi-empirical Prandtl theory based on the assumption that turbulent motion consists of an infinite number of vortices of various scales that interact with each other and transfer energy from large scales to smaller ones, models specially adapted to a specific type of problem, for example, LES for modeling the interaction of turbulent flows, a generalized theory of developed turbulence (GDT, Generalized Theory of Turbulence), which is a theory, developed for the description and simulation of turbulent flows in various technical devices.
 It is proved that one of the most common approaches is to use models with different levels of detail, starting with simpler models and moving on to more complex ones, if necessary to achieve the required accuracy. This approach is called the "ladder of models" or RANS/LES method. 
 Subject of research: turbulence models for calculating aerodynamic characteristics of gas flows.
 Materials and methods: the basis of the performed research is a number of scientific works of domestic and foreign researchers in this field and the results obtained by the authors in the course of the work.
 A systematic approach is used, meaning consideration and study of the object of research as an integrated system consisting of many interrelated elements.
 Results: The authors note that one of the most common approaches is to use models with different levels of detail, starting with simpler models and moving on to more complex ones if necessary to achieve the required accuracy. This approach is called the "ladder of models" or RANS/LES method. 
 Conclusions: The choice of a turbulence model for specific cases depends on a number of factors, including flow characteristics, available data, accuracy requirements and computational capabilities. The selection criteria include: physical properties and flow mode; the degree of accuracy of calculations and calculation capabilities.

Multicomponent steady-state modeling, performance optimization and prediction of cleaning frequency for treatment of cellulosic manmade fibre industry stream using polysodium 4- styrenesulfonate (PSS) incorporated nanofiltration membrane

Effect of polysodium 4-styrenesulfonate (PSS) in the skin layer on performance of nanofiltration (NF) membrane was analyzed for treatment of saline stream from manmade fiber industry. The NF membrane with 0.05 % (w/w) PSS concentration in aqueous phase had better hydrophilicity (contact angle: 330) and water flux of 27 L.m−2.h−1 along with significant salt rejection (Na2SO4: 90 %, CaSO4: 85 % and NaCl: 80 %) at transmembrane pressure 8.3 bar and crossflow rate 100 L.h−1. A long-term study with the wastewater showed that the intermittent cleaning of the membrane every 6 h led to 16 L.m−2.h−1 average permeate flux and sulfate rejection above 95 %.A two-component, steady-state model was used to quantify the performance of the selected membrane. Based on the fouling study, a semi-empirical theory was proposed to identify the cleaning frequency. The theory developed is useful for the operation, maintenance and recovery of the divalent salts from reject stream of such industry.

Classical and local similarity in problems of turbulent convection: Extension of Prandtl semi-empirical theory for horizontal layers of water and air mediums

A variant of the local similarity theory is considered, assuming a priori specification of two basic dimensional parameters: the second moment of vertical velocity and the “spectral” Prandtl mixing length. Such selection of basic parameters lets us interpret the algebraic formulas of Prandtl's semiempirical turbulence theory for the coefficients of turbulent heat transfer and kinetic energy dissipation as relationships of the local similarity theory. A priori approximations of the basic parameters are based on known relationships and consider the upper boundary of the convective layer as a solid wall. Within the framework of local similarity theory, approximations for the turbulent moments of buoyancy and vertical velocity of arbitrary order are also proposed. The correspondence of these approximations to experimental data has been established in both air and water mediums, as well as in the results of numerical modeling. Such correspondence allows us to conclude that a wide class of vertical profiles of turbulent moments in a windless convective layer depends only on two basic parameters: the second moment of vertical velocity and the “spectral” Prandtl mixing length. The obtained result indicates the universal nature of the theory of local similarity and is a significant addition to the semiempirical Prandtl theory.

Electrochemical and theoretical studies of the interaction between anticancer drug ponatinib and dsDNA

In this study, electrochemical and theoretical studies were performed to explain the interaction mechanism between ponatinib (PNT), a third generation tyrosine kinase inhibitor, and dsDNA. The electrochemical part was conducted in phosphate-buffered saline (PBS) at physiological pH of 7.4 and in acetate buffer with a pH of 4.7, using square wave voltammetry. A boron-doped diamond electrode was used in a bulk-incubated solution. The theoretical part was investigated using computational methods, such as the semiempirical method PM7 and density functional theory (DFT). Significant differences in the electrochemical behavior of PNT in the presence of DNA confirmed the occurrence of interactions. The results obtained in the acetate buffer strongly suggested the preferential interaction of PNT with guanine residues. However, at physiological pH, it can be concluded that PNT interacts with dGua and dAdo in the dsDNA molecule. These results are consistent with outcomes from the theoretical studies, where quantum-chemical calculations showed that both electrochemically detectable nucleobases form hydrogen bonds with the drug. These bonds appeared to be stronger with guanine than with adenine. According to the computational studies, the dsDNA major groove is the energetically preferred site for the complexation of PNT.

Investigating interactions between derivatives of graphene nanosheets and articaine for prolonged dental anesthetic effects: A multiscale modeling study

The controlled release of anesthetic molecules for extended local anesthesia has emerged as a promising strategy in pain management. In this context, we focus on the interactions between graphene nanosheet derivatives (GND) and the anesthetic molecule articaine (ART). Our motivation for studying ART adsorption stems from our previous extensive computational study, which demonstrated that among local anesthetic molecules, ART shows the strongest binding to pristine graphene. To understand the binding of articaine to graphene nanosheets, we conducted an extensive multiscale modeling study using modern levels of theory. We employed a combination of semiempirical (GFN-xTB) and density functional theory calculations (DFT and TD-DFT) to obtain reliable geometrical parameters, binding energies, and quantum-molecular descriptors, crucial for understanding the binding mechanism of articaine. Detailed electron density analysis within the considered systems provided important insights into the noncovalent binding between graphene derivatives and articaine. Additionally, to observe the dynamics and behavior of the system in a biologically relevant environment, we conducted molecular dynamics (MD) simulations based on the GFN-FF method. This study aims to advance the development of effective drug-carrier systems for sustained pain relief. We intend to identify the graphene modifications that could lead to stronger binding of articaine, thereby enabling slower release and prolonged anesthetic effect.

Причины возникновения усталостных трещин в подкрановых балках мостовых кранов тяжелого режима работы

This article discusses the causes of fatigue cracks in the crane girders of overhead cranes that work with heavy loads, high speeds, and a large number of inclusions within an hour. The main defects and damages of crane beams are shown. As a result of repeated exposure to loads on crane beams, fatigue failures and stress redistribution occur, which can lead to complete destruction. The article focuses on determining the regularity of fatigue crack growth under various material properties and loads, as well as the possibility of using semi-empirical theory. At the end of the article, the ways of changing the fastening of the rail to the crane beam are given as an additional measure when strengthening structures with a reduced resource.

A general approach for predicting convective heat transfer coefficients in turbulent systems

A generalized approach for predicting turbulent convective heat transfer coefficients using large eddy simulation is presented. This model is based on semi-empirical transport theory, which links the local convective heat transfer rate to the local energy dissipation rate within the near-wall boundary layer. We apply these approaches to agitated tanks, pipe flow systems, cylinders in crossflow, and tube bundles. We validate the generality and reliability of the theoretical model against expectations from experimentally derived empirical design correlations.

Solvent and Substituent Size Influence on the Cyclochiral Rigidity of Aminomethylene Derivatives of Resorcin[4]arene.

Resorcin[4]arenes (R[4]A) are a group of macrocyclic compounds whose peculiar feature is the presence of eight hydroxyl groups in their structure. The directional formation of intramolecular hydrogen bonds with their participation leads to the formation of a cyclochiral racemic mixture of these compounds. Their stability strongly depends on the substituent and especially the environment in which they are located. The paper discusses the cyclochiral nature of aminomethylene derivatives of R[4]A (AMD-R[4]A). Their cyclochiral rigidity in non-polar solvents has been shown. The influence of the size of the alkyl groups in the amino substituents of AMD-R[4]A on their cyclochiral nature was noted. To calculate the reaction paths for their racemization, the nudged elastic band (NEB) method was employed using the semi-empirical DFT (GFN1-xTB) approach. The calculated activation barrier energies for their racemization in chloroform, obtained through various semi-empirical quantum chemical methods (SE), Hartree-Fock (HF), and density functionals theory (DFT), show good correlation with experimental observations. Among the tested methods, the B38LYP-D4 method is highly recommended due to its fast computational speed and accuracy, which is comparable to the time-consuming double-hybrid DH-revDSD-PBEP86 approach.

Wyprowadzenie fenomenologicznych równań hydromechaniki przepływów wielofazowych

In the article, a multi-phase (non-homogeneous, heterogeneous) medium is considered as a macrosystem (continuum) composed of several (at least two) phases, such as a carrier phase (liquid, vapor or gas) and a carried phase (solid particles, bubbles or drops).The masses and mixtures of these phases undergo continuous changes over time due to the addition or separation of new masses to or from both phases. The model takes into account interphase transitions, discontinuities inside the mixture, and the possibility of phases being either continuous or discrete, depending on their location. A method for preliminary smoothing of discontinuities has been developed, leveraging the fact that the location in space, as well as the shape and size of the discrete phase are random. A function, denoted as φi (x, y, z, t), has been introduced, which indicates the probability of the presence of the i-th phase in the vicinity of a given point in space at time t, or that the given point of space x, y, z at time t belongs to the set of points of the i-th phase. On the other hand, this probability can be interpreted as the volumetric concentration of the i-th phase at a given point in space (i.e., the ratio of the measure of the set of points belonging to the i-th phase in the vicinity of the point under consideration at time t to the measure of the entire set of points in the surrounding area). This hypothetical medium, being equivalent to the original one, serves as a model for a multi-phase (inhomogeneous, heterogeneous, two-phase) medium. The uniqueness of the model arises from its construction. In addition, this paper considers several main areas of theoretical and experimental research concerning the hydrodynamics of a multi-phase (two-phase suspension-carrying) flow of a continuous medium. It also discusses the most important results achieved in existing works. A critical analysis of known theories for mathematically describing the motion of multi-phase (two-phase) systems and methods for averaging the hydrodynamic characteristics of a turbulent flow are given. The procedure for closing the equations systems of hydromechanics of multi-phase flows proposed in existing works is carried out within the framework of semi-empirical theories of turbulence. In nature, the vast majority of multi-phase (two-phase, inhomogeneous) mixtures exhibit turbulent behavior, making its study a crucial practical task. The mathematical description of the motion of a turbulent multi-phase flow relies on stylized laws of mechanics. The methods of operational analysis proposed at various times by different researchers for the mathematical description of the motion of a multi-phase (two-phase) flow have varying degrees of approximation and certain limited areas of application. One of the main challenges in formulating differential equations for the motion of a turbulent multi-phase (two-phase, suspension-carrying) flow is the fact that in a turbulent flow of a mixture, where the characteristics of the flow change chaotically and randomly over time and at each point in space, both in magnitude and in direction, there are surfaces with weak and strong discontinuities. Consequently, the actual values of velocity and pressure of a multi-phase flow, strictly speaking, cannot be considered continuous functions of the coordinates of space and time throughout the entire region occupied by the mixture.

Proposed modification to a muscle-like acid-base switchable [2](2)rotaxane for improved force delivery

ABSTRACTSwitchable rotaxanes are good candidates for molecular machines because of their ability to undergo reversible and repeatable co-conformational isomerism in response to an external stimulus. An acid-base switchable [2](2)rotaxane reported by Li et al. [J Org Chem. 79(15): [6996–7004] has been reported to exhibit a 48% change in length upon a stimulus-induced change in protonation state, suggesting that it could serve as the fundamental element of a ‘molecular muscle’. In the present work, the mechanical behaviour of this topologically complex system is explored with calculations based on semiempirical electronic structure theory. Our calculations predict that the original system will not work as envisioned. Although the calculations confirm a 48% change in length, they also reveal an energy barrier to ring shuttling upon deprotonation, preventing the immediate delivery of force. Therefore, a modification to the system is proposed. Similar semiempirical calculations were carried out on the modified system and the force calculated. The average force generated from the modified system is predicted to be approximately −86 pN. The results demonstrate that the proposed modification reduces the force generated by ring shuttling by 11% but largely eliminates the energy barrier to ring shuttling so that the force is immediately available.

2D-QSAR, Docking, Molecular Dynamics Simulations with the MM/GBSA Approaches against Graves' Disease and PTPN22

Graves' disease (GD) is an autoimmune condition that frequently causes hyperthyroidism and thyrotoxicosis. Protein tyrosine phosphatase, non-receptor type 22 (lymphoid) isoform 1 (PTPN22), is a promising therapeutic candidate for treating GD, rheumatoid arthritis, type 1 diabetes, and other autoimmune disorders. In this dataset, 31 molecular compounds and two standard drugs were optimized using the semi-empirical PM7 theory method via MOPAC v22.0.4 to reveal the key influencing factors contributing to their grave's disease inhibition activity and selectivity. Using QSARIN software, the acquired properties/descriptors were used to create a quantitative structural activities relationship (QSAR) model, and the similarities between the observed and predicted pIC50 values were examined. A molecular docking simulation study also uncovers non-covalent interactions between the investigated compounds and the receptors. The observed ligand-protein interactions with GD proteins (PDB ID 2XPG and 4QT5) and PTPN22 (PDB ID 3BRH) were investigated. The pharmacokinetics (ADMET) properties were also investigated. Finally, molecular dynamics (MD) simulation and MM/GBSA studies that demonstrated stable trajectory and molecular properties with a consistent interaction profile were used to validate the stability of the compounds in the complex with PTPN22.

Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands.

The determination of minimum free energy pathways (MFEP) is one of the most widely used strategies to study reactive processes. For chemical reactions in complex environments, the combination of quantum mechanics (QM) with a molecular mechanics (MM) representation is usually necessary in a hybrid QM/MM framework. However, even within the QM/MM approximation, the affordable sampling of the phase space is, in general, quite restricted. To reduce drastically the computational cost of the simulations, several methods such as umbrella sampling require performing a priori a selection of a reaction coordinate. The quality of the computed results, in an affordable computational time, is intimately related to the reaction coordinate election which is, in general, a nontrivial task. In this work, we provide an approach to model reactive processes in complex environments that does not require the a priori selection of a reaction coordinate. The proposed methodology combines QM/MM simulations with an extrapolation of the nudged elastic bands (NEB) method to the free energy surface (FENEB). We present and apply our own FENEB scheme to optimize MFEP in different reactive processes, using QM/MM frameworks at semiempirical and density functional theory levels. Our implementation is based on performing the FENEB optimization by uncoupling the optimization of the band in a perpendicular and tangential direction. In each step, a full optimization with the spring force is performed, which guarantees that the images remain evenly distributed. The robustness of the method and the influence of sampling on the quality of the optimized MFEP and its associated free energy barrier are studied. We show that the FENEB method provides a good estimation of the reaction barrier even with relatively short simulation times, supporting that its combination with QM/MM frameworks provides an adequate tool to study chemical processes in complex environments.

Topology Molecular Indices Relationship of Electronic Properties of N-Alkanes and Branched Alkanes

Eight electronic properties; HUMO, LUMO, HOMO-LUMO energy gap, dipole moment point-charge, dipole moment hybrid, molecular weight, heat of formation and zero-point energy of 60 normal and branched alkanes were examined using topology molecular indices. All the electronic properties were calculated using semi-empirical self-consistent molecular orbital theory. The relationship of electronic calculation properties with seven models of topology indices based on degree and/or distance were obtained in terms of their correlation, regression and principal component analysis. Most of the properties were well-modelled (r2 > 0.82) by topology molecular indices except the dipole moment point-charge and hybrid. The PCA resulted in 7 properties and 60 structures of alkanes that produced two principal components with eigenvalues of greater than 1. The first principal component explained 60.388%, while the second principal component explained 26.457%, bringing a cumulative value of 86.845% to the data variation.

Oscillations of the Helium II – Vapor Interface during Motion in a Channel of a Relatively Large Diameter

The article considers the motion of superfluid helium in a U-shaped cylindrical channel with a diameter significantly larger than the helium capillary constant in the approximation of an inviscid incompressible fluid. When a heat flux is applied near the end-face section of one of the channel elbows, a vapor layer emerges near the heater, and the helium II – vapor interface begins to move. The purpose of the calculation is to determine the interface position as a function of time. The heat transfer in a liquid is described using the semi-empirical Gorter-Mellink theory. The processes in the vapor are analyzed based on the methods of molecular kinetic theory. The influence of the gravity field is studied. The system of equations is reduced to an ordinary second-order differential equation, which is solved numerically. Various process development scenarios depending on the heat flux are obtained. The occurrence of oscillations is described, and the influence of parameters on the oscillation amplitude and frequency is analyzed. In this way, the previously obtained experimental data have been interpreted.

Theoretical investigation of the performance of benzimidazole derivatives as mild steel organic corrosion inhibitors in acidic environments.

The efficiency of various benzimidazole derivatives as mild steel corrosion inhibitors in HCl and H2SO4 medium was evaluated using quantum chemical methods. The AM1 semi-empirical method and Density Functional Theory (DFT) at the B3LYP/6-31G* level were used. The orbital energies (EHOMO and ELUMO), Separation Energy (ELUMO-EHOMO), Dipole moment (µ), Log P, Polarizability, molecular volume, molecular weight, Hardness (η) and Softness (S) are the computed quantum chemical characteristics linked to inhibitory efficiency. There was a strong link between quantum chemical parameters and experimental inhibition efficiency. The findings revealed that the Inhibition Efficiency was linked to a number of quantum chemical factors. The 2-mercaptobenzimidazole derivative had a higher Inhibition Efficiency (IE) than the other benzimidazole derivatives, according to the results.

To the development of hydraulic regulations of turbulent flows in pipelines

The results of the theoretical analysis of the turbulent movement of water in pipelines are given. It is proposed to evaluate the parameters of turbulent flows based on the indicators of molecular and turbulent viscosity with the introduction of the conditional relative thickness of the boundary layer into the calculations. The dependencies of the logarithmic law of the distribution of averaged velocities in the cross-sections of pipelines have been clarified. Unlike similar formulas of the semi-empirical theory of turbulent motion, they correspond to the boundary conditions on the pipeline wall. New theoretical dependencies between the main parameters of turbulent flows in pipelines were obtained. It is proved that the magnitude of the coefficients of hydraulic friction is determined by two parameters: the conditional relative thickness of the boundary layer and the proportionality factor, which takes into account the change in tangential stresses in the turbulent flow. The adequacy of the obtained dependencies is confirmed by their correspondence to the experimental data of the hydraulic dependencies of turbulent flows, on the basis of which the current standards for hydraulic calculations of water pipes were developed. For hydraulically smooth pipes, an explicit dependence was obtained for hydraulic friction coefficients in a wide range of Reynolds numbers (from 7 10³ to 10⁷). It almost completely corresponds to the well-known Prandtl-Colebrook’s formula, which has an implicit form. Numerical values and analytical dependencies between parameters of turbulent flow in hydraulically smooth pipelines are determined. It was established that with an increase in the Reynolds number, the values of both the conditional and absolute thicknesses of the boundary layer decrease, and with the increasing of the pipe diameters, they grow. It is shown that the thickness of the boundary layer depends on the type and magnitude of the roughness of the inner surface of the pipes and it is decisive when other parameters of turbulent flows in pipelines are evaluating.