Semi-empirical Research Articles

Installation performance of torpedo anchor at different installation heights under the action of currents: The example of T98 torpedo anchor

The deep-sea torpedo anchor is an innovative and cost-effective anchorage foundation. However, marine environmental loads such as currents have a significant impact on the free-fall installation of torpedo anchors in water, often leading to the failure of installation due to excessive inclination or large deviations from the installation location. Therefore, taking the T98 torpedo anchor commonly used in practical engineering as an example, this paper systematically investigates its installation characteristics under the action of currents. First, based on OpenFOAM®, a 3D numerical model is established to simulate the underwater falling process of torpedo anchors via dynamic model analysis method. Using the validated model, the influence of currents on the installation performance of torpedo anchors is then explored. Based on the findings, the installation conditions of T98 anchors at different installation heights are recommended. Finally, a semi-empirical method for estimating the anchor inclination and deviation of torpedo anchors under current action is proposed, which may facilitate the assessment of installation inclination and determine the installation release point of torpedo anchors.

A Combined Approach for Predicting Binding Affinity of Zika Virus NS2B-NS3 Protease Inhibitors Using Semi-Empirical Methods and Molecular Docking Algorithms

Zika virus (ZIKV) is a mosquito-borne virus that has emerged as a major public health concern due to its association with severe neurological disorders. In recent years, there has been increasing interest in exploring natural products as potential therapeutics for ZIKV infection. This study aimed to predict the binding affinity of natural compounds to the ZIKV NS2B-NS3 protease (NS2B-NS3pro) using multiple molecular docking algorithms and semiempirical quantum mechanical methods. Our results demonstrate that semiempirical methods can improve the accuracy of molecular docking studies for natural compounds. In this particular case, the PM7 (Parametric Method Number 7) method showed a significant improvement in the coefficient of determination (R2 = 0.85). We expect this combined approach to aid in the development of natural product-based therapies for ZIKV infection and to highlight the importance of continued research in this field.

Quantitative analysis of charge transfer plasmons in silver nanocluster dimers using semiempirical methods.

Plasmonic metal nanoclusters are widely used in chemistry, nanotechnology, and biomedicine. In metal nanocluster dimers, coupling of the plasmons leads to the emergence of two distinct types of modes: (1) bonding dipole plasmons (BDP), which occurs when charge oscillates synchronously within each nanocluster, and (2) charge transfer plasmons (CTP), which occurs when charge oscillates between two conductively linked nanoclusters. Although TDDFT-based modeling has uncovered some trends in these modes, it is computationally expensive for large dimers, and quantitative analysis is challenging. Here, we demonstrate that the semiempirical quantum mechanical method INDO/CIS enables us to quantify the CTP character of each excited state efficiently. In end-to-end Ag nanowire dimers, the longitudinal states have CTP character that decreases with increasing gap distance and nanowire length. In side-by-side dimers, the transverse states have CTP character and generally larger than in the end-to-end dimers, particularly for the longer nanowires. In side-by-side dimers where one nanowire is shifted along the length of the other, the CTP character of the longitudinal states peaks when the dimer is shifted by two Ag-Ag bond lengths, while the transverse states show decreasing CTP character as displacement increases. In the larger Ag31+ nanorod dimers, CTP character follow a similar distance dependence to that seen in the small nanowire but have smaller overall CTP character than the nanowires. Our study demonstrates that INDO/CIS is capable of modeling metal nanocluster dimers at a low computational cost, making it possible to study larger dimers that are difficult to analyze using TDDFT.

Monitoramento e previsão de recalques visando uma melhor caracterização da estratigrafia do solo: um estudo de caso de um edifício de 23 andares

Abstract The settlement is a critical factor in foundation selection. To ensure the safety and stability of a structure, engineers must accurately predict settlement and design the foundation accordingly. However, in cases where the soil stratigraphy is complex, a more detailed analysis is necessary to determine safe and cost-effective solutions for a building's foundation. This paper presents a case study in which settlement monitoring was performed on a 23-story building with spread footings laid on a stiff rock layer of limited thickness overlying more compressible layers of clay and sand. The building was monitored through four construction stages, during which data on vertical displacements and stress distribution on the soil were obtained. To improve the accuracy of the results, a methodology for calibrating the thicknesses of the soil strata was applied, based on the measured settlements, soil-structure interaction, and estimates from semi-empirical methods. Furthermore, a numerical analysis was performed using the finite element method, where more conservative displacements were observed. Finally, the safety of the building was evaluated by verifying angular distortions.

Sorting drug conformers in enzyme active sites: the XTB way.

In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.

A first-principles exploration of the conformational space of sodiated di-saccharides assisted by semi-empirical methods and neural network potentials.

Previous exploration of the conformational space of sodiated mono-saccharides using a random search algorithm leads to ∼103 structurally distinct conformers covering an energy range of ∼150 kJ mol-1. Thus, it is reasonable to expect that the number of distinct conformers for a given disaccharide would be on the order of 106. Efficient identification of distinct conformers at the first-principles level has been demonstrated with the assistance of neural network potential (NNP) with an accuracy of ∼1 kJ mol-1 compared to DFT. Leveraging a local minima database of neutral and sodiated glucose (Glc), we develop algorithms to systematically explore the conformation landscape of 19 Glc-based sodiated disaccharides. To accelerate the exploration, the NNP method is implemented. The NNP achieves an accuracy of ∼2.3 kJ mol-1 compared to DFT, offering a comparable quality to that of DFT. Through a multi-model approach integrating DFTB3, NNP and DFT, we can rapidly locate low-energy disaccharide conformers at the first-principles level. The methodology we show here can be used to efficiently explore the potential energy landscape of any di-saccharides when first-principles accuracy is required.

Review of source models for reproducing and predicting strong motions by empirical Green's function method

AbstractShort‐period ground motions from earthquakes are calculated by semiempirical methods such as the empirical Green's function method or the stochastic Green's function method. In this review paper, I summarized source models developed for reproducing and predicting ground motions in the theoretical methods at first, and then reviewed the source models applied to reproducing and predicting ground motions in the empirical Green's function method in these about 40 years. Finally, I showed some issues to be solved about source modeling in order to predict accurate short‐period motions in the near‐fault regions.

Tenability on schiff base Hydrazone derivatives and Frontier molecular orbital

Context hydrazine compounds based on 1,3,5-triazine were synthesised and their molecular structures were characterised by elemental analysis, Electronic, IR and 1H NMR spectra. The spectral behaviour of the newly prepared compounds in organic solvents of different polarities was extensively studied and correlated to the molecular structure. In this study, 1,3,5-Triazine derivatives (L1, L6, L7, L8) have been subjected to theoretical studies using the Semi-empirical PM3 quantum chemical method. The physical-chemical properties of some Hydrazone derivatives are determined theoretically. The molecular geometry, the Highest Occupied Molecular Orbital (HOMO) - Lowest Unoccupied Molecular Orbital (LUMO) energy gap, molecular hardness (η), ionisation energy (IE), Electron affinity and total energy were analysed, and applications as biological effects were done.

Photoisomerization pathways of trans-resveratrol.

Resveratrol is well-known for promoting health benefits due to its antioxidant, anti-aging, anti-carcinogenic, and other beneficial activities. Understanding the photophysics of resveratrol is essential for determining its applicability to pharmaceutical innovations. In the present work, we used an explore-then-assess strategy to map the internal conversion pathways of trans-resveratrol. This strategy consists of exploring the multidimensional configurational space with nonadiabatic dynamics simulations based on a semiempirical multireference method, followed by a feasibility assessment of reduced-dimensionality pathways at a high ab initio theoretical level. The exploration step revealed that internal conversion to the ground state may occur near five distinct conical intersections. The assessment step showed that the main photoisomerization pathway involves a twisted-pyramidalized S1/S0 conical intersection, yielding either trans or cis isomers. However, a secondary path was identified, where cis-trans isomerization happens in the excited state and internal conversion occurs at a cyclic conical intersection, yielding a closed-ring resveratrol derivative. This derivative, which can be formed through this direct path or an indirect photoexcitation, may be connected to the production of oxygen-reactive species previously reported and have implications in photodynamic therapy.

КОМПЬЮТЕРНОЕ МОДЕЛИРОВАНИЕ ОРГАНИЧЕСКИХ ФОРМ ЦИНКА И СЕЛЕНА НА ОСНОВЕ БЕЛКА КОЛЛАГЕНА

This article presents the results of research aimed at developing a theoretical computer model of organic forms of zinc, selenium and their interaction with collagen matrix. Collagen was chosen as an organic carrier. Quantum chemical, semiempirical and molecular dynamic methods were used to study changes in molecular properties and to perform quantum mechanical modeling of atomic structures using HyperChem v8.0 software. Molecular structures of organic forms of trace elements with amino acids were designed and optimized geometrically. The present study considers different variants and combinations of zinc and selenium compounds with four amino acids most commonly found in collagen. The correctness of geometric optimization, potential energy minimization and balanced energy properties of the system were evaluated based on the total energy of the components. The results obtained indicate potential interaction of trace elements with collagen amino acids.

Phase Fraction Estimation Using Measured Dilation, a Lattice Parameter Model, and a Curve-Fitting Method

Dilatometry is a measurement frequently used to analyze phase transformations in steels during austenite decomposition. Such analyses are essential for the design of heat treatments and for determining the final phase fractions. This paper presents a simple and systematic method to estimate the evolution of the non-measurable phase fraction of ferrite, pearlite, bainite, and martensite during Continuous Cooling Transformation (CCT) experiments. The optimization-based method uses the measured dilation curve, a lattice parameter model, and a semi-empirical curve-fitting method. The latter assumes specific shapes of the transformation rates. The proposed approach can reconstruct the dilation curve and estimate the phase fractions with high accuracy.

The p-block challenge: assessing quantum chemistry methods for inorganic heterocycle dimerizations.

The elements of the p-block of the periodic table are of high interest in various chemical and technical applications like frustrated Lewis-pairs (FLP) or opto-electronics. However, high-quality benchmark data to assess approximate density functional theory (DFT) for their theoretical description are sparse. In this work, we present a benchmark set of 604 dimerization energies of 302 "inorganic benzenes" composed of all non-carbon p-block elements of main groups III to VI up to polonium. This so-called IHD302 test set comprises two classes of structures formed by covalent bonding and by weaker donor-acceptor (WDA) interactions, respectively. Generating reliable reference data with ab initio methods is challenging due to large electron correlation contributions, core-valence correlation effects, and especially the slow basis set convergence. To compute reference values for these dimerization reactions, after thorough testing, we applied a computational protocol using state-of-the-art explicitly correlated local coupled cluster theory termed PNO-LCCSD(T)-F12/cc-VTZ-PP-F12(corr.). It includes a basis set correction at the PNO-LMP2-F12/aug-cc-pwCVTZ level. Based on these reference data, we assess 26 DFT methods in combination with three different dispersion corrections and the def2-QZVPP basis set, five composite DFT approaches, and five semi-empirical quantum mechanical methods. For the covalent dimerizations, the r2SCAN-D4 meta-GGA, the r2SCAN0-D4 and ωB97M-V hybrids, and the revDSD-PBEP86-D4 double-hybrid functional are found to be the best-performing methods among the evaluated functionals of the respective class. However, since def2 basis sets for the 4th period are not associated to relativistic pseudo-potentials, we obtained significant errors in the covalent dimerization energies (up to 6 kcal mol-1) for molecules containing p-block elements of the 4th period. Significant improvements were achieved for systems containing 4th row elements by using ECP10MDF pseudopotentials along with re-contracted aug-cc-pVQZ-PP-KS basis sets introduced in this work with the contraction coefficients taken from atomic DFT (PBE0) calculations. Overall, the IHD302 set represents a challenge to contemporary quantum chemical methods. This is due to a large number of spatially close p-element bonds which are underrepresented in other benchmark sets, and the partial covalent bonding character for the WDA interactions. The IHD302 set may be helpful to develop more robust and transferable approximate quantum chemical methods in the future.

Discovery of molybdenum based nitrogen fixation catalysts with genetic algorithms.

Computational discovery of organometallic catalysts that effectively catalyze nitrogen fixation is a difficult task. The complexity of the chemical reactions involved and the lack of understanding of natures enzyme catalysts raises the need for intricate computational models. In this study, we use a dataset of 91 experimentally verified ligands as starting population for a Genetic Algorithm (GA) and use this to discover molybdenum based nitrogen fixation catalyst in trigonal bipyramidal and octahedral configurations. Through evolutionary discovery with a semi-empirical quantum method driven GA and a density functional theory (DFT) based screening process, we find 3 promising catalyst candidates that are shown to effectively catalyze the first protonation step of the Schrock cycle. Synthetic accessibility (SA) scores are used to guide the GA towards reasonable ligands and the work features a description of the GA framework, including pre-screening of catalyst candidates that involves assignment of metal coordination atoms and catalyst stereoisomers. This research thus not only offers insights into the specific field of molybdenum-based catalysts for nitrogen fixation but also demonstrates the broader applicability and potential of genetic algorithms in the field of catalyst discovery and materials science.

Excited state properties of an A-D-A non-fullerene electron acceptor: a LC-TD-DFTB study.

Understanding charge transfer processes is essential to estimate the performance of organic photovoltaic technologies. Although experimental production is on the rise, predictability strongly relies on theoretical modeling, which is limited to the size of semiconductors. As a computationally favorable approach, we benchmarked the long-range corrected (LC) time-dependent (TD) formulation of the semi-empirical density functional-based tight-binding method (DFTB) for three polycyclic aromatic hydrocarbons (PAHs) and studied the DTP-IC-4Ph molecule, a PAH-based non-fullerene electron acceptor (NFA) with an A-D-A backbone structure. After a thorough investigation into the long-range parameter (ω) tuning for naphthalene, anthracene and pyrene, the excitation energies, oscillator strengths and Natural Transition Orbitals (NTOs) were compared with the standard ωB97X-D/6-31G(d,p) level of theory and the ADC2/6-31G(d,p) multiconfigurational method. We estimated mobility-related properties of the NFA and considered 1000 thermally accessible configurations to qualitatively reproduce the experimental absorption profile and investigate the energetic disorder. Finally, we conducted a fragment-based analysis using the one-electron transition density matrix (1TDM) to determine the character of the excited states and investigate the effect of side chains on exciton formation. Our results are sensitive to the level of theory and highly dependent on the long-range parameter but suggest that the presence of alkyl chains promotes a higher average charge delocalization and allows for additional hopping mechanisms, favoring the charge transfer dynamics.

Phase-dependent polymerization isomerism in the coordination complexes of a flexible bis(β-diketonato) ligand.

First prepared in the late 70s, the pro-ligand 1,3-bis(3,5-dioxo-1-hexyl)benzene (H2bdhb) contains two acetoacetyl terminations linked to a central 1,3-phenylene unit through dimethylene bridges. Since each termination can be either in diketonic or keto-enolic form, in organic solution it exists as a mixture of three spectroscopically resolvable tautomers. In the presence of pyridine, Co2+ and the bdhb2- anion form a crystalline dimeric compound with formula [Co2(bdhb)2(py)4] (2) and a Co⋯Co separation of more than 11 Å. Complex 2 contains two pseudo-octahedrally coordinated and non-interacting high-spin cobalt(II) ions (S = 3/2) displaying a large easy-plane anisotropy (D ∼ 70 cm-1), as consistently indicated by magnetic measurements, X-band EPR spectra, and complete active space self-consistent field/N-electron valence state perturbation theory (CASSCF/NEVPT2) calculations. At cryogenic temperatures (T < 7 K) and in an applied static magnetic field, the compound shows detectably slow magnetic relaxation, which occurs through direct and Raman mechanisms. Combined mass spectrometry, UV-Vis, and 1H/2H NMR data, including an isotopic labelling experiment and a determination of molecular weight by diffusion ordered spectroscopy (DOSY), show that 2 rearranges to monomeric high-spin [Co(bdhb)(py)x] species (x = 0, 1, or 2) in organic solution (CH2Cl2, THF) with concomitant partial dissociation of the py ligands. The X-band EPR spectra in a frozen CH2Cl2/toluene matrix concurrently suggest a significant alteration of the coordination environment upon dissolution. These observations are fairly well reproduced by density functional theory (DFT) and CASSCF/NEVPT2 calculations on the lowest Gibbs free energy conformers of each species, as provided by an extensive conformational search based on meta-dynamics simulations and semiempirical tight-binding methods. After the vanadyl analogue, compound 2 provides the second example of polymerization isomerism in the 1 : 1 adducts of bdhb2- with divalent metal ions.

Reversible hydrogen storage and release mechanism of a B2N monolayer: a first-principles insight.

It was found the physical adsorption could be an efficient strategy for high capacity, high efficiency and high safety in hydrogen storage. In this research, a systematic investigation into the potential of the B2N monolayer as an excellent physical adsorption hydrogen storage material is conducted by utilizing the first-principles calculation method. The findings of the investigation demonstrate that the B2N monolayer has a planar lattice and excellent structural stability. It is possible for H2 molecules to adsorb onto the B2N monolayer spontaneously. Both the individual adsorption and saturation adsorption corresponded to average adsorption energies ranging from -0.221 to -0.194 eV, fulfilling the physical adsorption criteria. In the case of saturation adsorption, a 1 × 2 × 1 B2N supercell can store a total of 24 H2 molecules, with the hydrogen gravimetric density up to 14.511 wt% and volumetric density up to 138 g L-1. A semi-empirical calculation method is used to research the performance of the system in terms of adsorption and desorption with actual temperature and pressure conditions. Under the actual conditions with adsorption carried out at 30 atm/233 K and desorption carried out at 3 atm/358 K, the maximal reversible hydrogen storage capacity of the hydrogen storage system based on the B2N monolayer can still reach 12.157 wt%, which is superior to that of many other boron-nitrogen compounds and metal-free functionalized hydrogen storage materials. The findings of this work indicate that the pristine B2N monolayer is one of the promising physical adsorption materials which could achieve excellent reversible hydrogen storage under defined conditions.

Electron-driven molecular processes for cyanopolyacetylenes HC2n+1N (n = 3, 4, and 5).

Linear carbon series cyanopolyacetylenes (HC2n+1N) (n = 3, 4, and 5) are astromolecules found in the atmosphere of Titan and interstellar media such as TMC-1 (Taurus molecular cloud-1). All these compounds are also detected in IRC + 10 216. In the present work, we comprehensively investigate electron interaction with important cyanopolyacetylene compounds, viz. HC7N (cyano-tri-acetylene), HC9N (cyano-tetra-acetylene), and HC11N (cyano-penta-acetylene). The study covers incident electron energies ranging from the ionization threshold to 5 keV. Various electron-driven molecular processes are quantified in terms of total cross-sections. The quantum spherical complex optical potential (SCOP) is used to determine elastic (Qel) and inelastic (Qinel) cross-sections. Ionization is the most important inelastic effect that opens various chemical pathways for the generation of different molecular species; we computed the ionization cross-section (Qion) and discrete electronic excitation cross-section (ΣQexc) using the complex scattering potential-ionization contribution (CSP-ic) method. The cyanopolyacetylene compounds are difficult to handle experimentally owing to the health risks involved. Therefore, there are no prior experimental data available for these molecules; only Qion have been reported theoretically. Thus, the present work is the maiden report on computing Qel, Qinel, ΣQexc, and QT. In order to provide an alternative approach and further validation of the present work, we employed our recently developed two-parameter semi-empirical method (2p-SEM) to compute Qel and QT. Additionally, we predict the polarizability of the HC11N molecule, which has not been reported in the existing literature. This prediction is based on a correlation study of polarizabilities of molecules with Qion values from the same series of molecules.

Developing semi-empirical water model for efficiently simulating temperature-dependent chemisorption of CO2 in amine solvents.

Classical molecular dynamics (MD) simulations without bond forming/breaking cannot be used to model chemical reactions (CRs) among small molecules. Although the first-principle MD simulation can adequately describe CRs with explicit water molecules, such simulation is normally too costly for most researchers to afford. Generally, water molecules in a solvent can exert hydrophobic forces on reacting molecules, which yields a so-called caging effect that cannot be ignored when constructing a free energy landscape for reacting molecules. Many recently developed semi-empirical methods (such as DFTB, PM6 and xTB) are highly efficient for modeling CRs, however none of them can be directly used to model bulk water properly. Here, we developed a modified xTB approach that enables the simulation of CRs in explicit water. Using the chemisorption of CO2 by amines in water as an example application, we demonstrate that our approach yielded results comparable with the first-principle ones, while only using a limited computing resource. Potentially, our proposed semi-empirical water model can be utilized for the computational study of any CR in water.

Dynamics of the activated state of NAD-dependent dehydrogenase investigated by a weighted histogram analysis semi-empirical method

Dynamics and catalytic activities of the redox enzyme's active site. Elucidation of the molecular dynamics of alcohol dehydrogenase by using weighted histogram analysis semi-empirical method (WHA-SEM) and umbrella sampling.

Window air permeability calculation methodology with regard to temperature loading

Air permeability is an important characteristic of windows, which significantly affects the energy consumption of a building and the quality of indoor climate in winter. Existing experimental studies confirm that the air permeability of windows can increase significantly when the outside temperature decreases. This phenomenon is associated with temperature deformations. Nevertheless, currently in the practice of window design the dependence of air permeability on temperature effects is not taken into account. There are methods of windows air permeability experimental determination that take into account temperature loads, but they require unique equipment and are large labor inputs. In view of this, this paper proposes a semi-empirical method for calculating the air permeability of windows with regard to temperature loads, which uses data from standard laboratory tests. This method is based on identifying the system of infiltration channels, which is formed by the window structure, with an elementary system for which the analytical solution of the infiltration equation is known. It can be used for more accurate calculations of the building's energy consumption in the cold period of time, as well as for obtaining a scientifically justified limitation of window structure deflections under the combined action of wind and temperature loads.