Semi-empirical Research Articles

Synthesis, Hemolytic Activity, and In Silico Studies of New Bile Acid Dimers Connected with a 1,2,3-Triazole Ring.

The synthesis of bile acid conjugates plays a significant role in pharmacology and organic chemistry. These complex compounds are widely studied due to their potential therapeutic applications (e.g., drug carriers or antibacterial agents) and their impact on interactions with biological target systems. It is important to determine the biological activity of the obtained conjugates with potential pharmacological applications. The research aimed to synthesize acyl conjugates of bile acids, determine the influence of acyl groups on potential antibacterial activity and evaluate the impact of conjugation on hemolytic activity. New acetyl bile acid acetyl dimers were synthesized using the "Click Chemistry" reaction, aiming to investigate their hemolytic and antibacterial activity. The structures of all compounds were confirmed through spectral analysis techniques, including 1H and 13C nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FT-IR), and electrospray ionization-mass spectrometry (ESI-MS). The PM5 semiempirical method was also used to estimate the heat of formation of individual conjugates, and the prediction of activity spectra for substances (PASS) technique was used to determine the pharmacokinetic potential of compounds. Docking studies indicate that obtained conjugates have the potential ability to inhibit the biosynthesis of Lipid II and block DNA gyrase. These compounds can therefore be treated as potential candidates for antibacterial compounds. Research findings suggest that conjugating bile acids and their derivatives through 1,2,3-triazole ring, results in final products with reduced hemolytic activity.

Impact of Future Low-Emissions Combustor Technology on Acoustic Scaling Laws

A first-of-its-kind examination of broadband noise associated with a far-term advanced low-emission aerocombustor concept is presented. Because of design trends and expected cycle changes for future aircraft propulsion systems, noise generated by sources in the combustor are expected to become of increasing significance for airport-community noise. The paper assesses the impact on legacy semi-empirical noise-prediction methods from the expected radical departures from current combustor operating conditions and designs, such as fuel/air distribution and flame anchoring techniques. Such methods are essential in system-level noise assessments at the preliminary design stage for advanced air transports to assure that overall environmental goals are met. Detailed unsteady pressure measurements, obtained in a fundamental combustion noise experiment using a combustor rig at relevant pressures and temperatures are analyzed. In addition to an advanced far-term low-emissions concept, a reference configuration with the test section arranged to model a modern combustor sector was also studied. For the test rig in the current-generation configuration, the measured broadband acoustic data are reasonably well described by the acoustic-power scaling laws used in legacy semi-empirical noise-prediction methods. For the future-advanced configuration, the legacy scaling laws, with some notable exceptions, provide correct trends, but with much less accuracy.

Semi-empirical determination of radiative parameters for atomic cobalt

The values of the radiative parameters for atomic cobalt were determined using a semi-empirical method. The eigenvector amplitudes determined in our previously published research were adopted. In most cases, the calculated values of the oscillator strengths and radiative lifetimes agree well with the experimental data. Predictions of the values of the radiative parameters are also provided.

Assessment of settlement prediction by theoretical and semi-empirical methods in a granular soil profile in the Brazilian Northeast

The direct study investigates settlements from a circular load test with a diameter of 50 cm, conducted at the Experimental Field of Geotechnics and Foundations of the Federal University of Ceará. The study utilizes data from laboratory and field tests to determine parameters, employing both the classical methodology of Elasticity Theory and semi-empirical methods such as those by Décourt (1992), Schmertmann (1978), Barata (1984), Burland & Burbidge (1985), Meyerhof (1965), and Sandroni (1991). Laboratory tests included physical characterization, direct shear tests, triaxial tests, and Standard Penetration Tests (SPT). The direct load test conducted according to NBR 6489/19 standard served as a reference for comparing calculation methods. Comparative analysis using the least squares method indicates that the methods of Schmertmann (1978) and Sandroni (1991) yielded results closer to the direct load test, whereas the methods of Burland & Burbidge (1985), Barata (1984), and Meyerhof (1965) showed greater variation.

A Wave Drift Force Model for Semi-Submersible Types of Floating Wind Turbines in Large Waves and Current

The correct prediction of slowly varying wave drift loads is important for the mooring analysis of floating wind turbines (FWTs). However, present design analysis tools fail to correctly predict these loads in conditions with current and moderate and large waves. This paper presents a semi-empirical method to correct zero-current potential-flow quadratic transfer functions (QTFs) of horizontal wave drift loads in conditions with current and moderate and large waves. The method is applicable to column-stabilized types of substructures or semi-submersibles. In the first step, the potential-flow QTF is corrected for potential-flow wave–current effects by applying a heuristic method. Second, the generalized Exwave formula corrects for viscous drift effects. Viscous drift effects become important for moderate and large waves. Conditions with current in the same direction as the waves increase the viscous drift contribution further. The method is validated by comparing QTF predictions with empirical QTFs identified from model test data for the INO Windmoor semi. While potential-flow QTFs agree well with the empirical data for small seastates without current, they underestimate the wave drift loads for moderate and large seastates. Conditions with current increase the underestimation. The semi-empirical correction method significantly improves predictions.

Dxtb-An efficient and fully differentiable framework for extended tight-binding.

Automatic differentiation (AD) emerged as an integral part of machine learning, accelerating model development by enabling gradient-based optimization without explicit analytical derivatives. Recently, the benefits of AD and computing arbitrary-order derivatives with respect to any variable were also recognized in the field of quantum chemistry. In this work, we present dxtb-an open-source, fully differentiable framework for semiempirical extended tight-binding (xTB) methods. Developed entirely in Python and leveraging PyTorch for array operations, dxtb facilitates extensibility and rapid prototyping while maintaining computational efficiency. Through comprehensive code vectorization and optimization, we essentially reach the speed of compiled xTB programs for high-throughput calculations of small molecules. The excellent performance also scales to large systems, and batch operability yields additional benefits for execution on parallel hardware. In particular, energy evaluations are on par with existing programs, whereas the speed of automatically differentiated nuclear derivatives is only 2 to 5 times slower compared to their analytical counterparts. We showcase the utility of AD in dxtb by calculating various molecular and spectroscopic properties, highlighting its capacity to enhance and simplify such evaluations. Furthermore, the framework streamlines optimization tasks and offers seamless integration of semiempirical quantum chemistry in machine learning, paving the way for physics-inspired end-to-end differentiable models. Ultimately, dxtb aims to further advance the capabilities of semiempirical methods, providing an extensible foundation for future developments and hybrid machine learning applications. The framework is accessible at https://github.com/grimme-lab/dxtb.

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d-Block.

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

The Unmanned Aerial Vehicle-Based Estimation of Turbulent Heat Fluxes in the Sub-Surface of Urban Forests Using an Improved Semi-Empirical Triangle Method

The Unmanned Aerial Vehicle-Based Estimation of Turbulent Heat Fluxes in the Sub-Surface of Urban Forests Using an Improved Semi-Empirical Triangle Method

Exploring the potential of boron-nitride nanobelts in environmental applications: Greenhouse gases capture

This study examines boron-nitride nanobelts, including Möbius-type, for capturing and detecting nine greenhouse gases (ammonia, carbon dioxide, carbon monoxide, hydrogen sulfide, methane, methanol, nitric dioxide, nitric oxide, and phosgene). Negative adsorption energies indicate favorable adsorption on both nanobelt types. The systems show recovery times ranging between 2 h to few nanoseconds. Only nitric oxide forms covalent bonds; other gases interact non-covalently. Molecular dynamics simulations reveal consistent single-molecule interactions and attractive forces with multiple molecules. Semi-empirical tight-binding methods, as implemented in the xTB software were used for computational efficiency. Results demonstrate the potential of boron-nitride nanobelts for environmental monitoring and remediation of industrial toxic gas emissions, addressing concerns about human health and environmental impact.

Machine Learning Approach to Vertical Energy Gap in Redox Processes.

A straightforward approach to calculating the free energy change (ΔG) and reorganization energy of a redox process is linear response approximation (LRA). However, accurate prediction of redox properties is still challenging due to difficulties in conformational sampling and vertical energy-gap sampling. Expensive hybrid quantum mechanical/molecular mechanical (QM/MM) calculations are typically employed in sampling energy gaps using conformations from simulations. To alleviate the computational cost associated with the expensive QM method in the QM/MM calculation, we propose machine learning (ML) methods to predict the vertical energy gaps (VEGs). We tested several ML models to predict the VEGs and observed that simple models like linear regression show excellent performance (mean absolute error ∼0.1 eV) in predicting VEGs in all test systems, even when using features extracted from cheaper semiempirical methods. Our best ML model (extra trees regressor) shows a mean absolute error of around 0.1 eV while using features from the cheapest QM method. We anticipate our approach can be generalized to larger macromolecular systems with more complex redox centers.

Droplet Microfluidic Method for Estimating the Dynamic Interfacial Tension of Ion-Crosslinked Sodium Alginate Microspheres.

The research focuses on optimizing the production of hydrogel microspheres using droplet microfluidics for pharmaceutical and bioengineering applications. A semiempirical method has been developed to predict the dynamic interfacial tension at the interface of ion-cross-linked sodium alginate microsphere-sunflower oil modified with glacial acetic acid and Tween 80 surfactant. These microspheres are produced in a small-scale coaxial device that is manufactured using affordable DLP/LCD 3D printing technology with a transparent photopolymer. The method was tested to design the minireactor in the device, which allows for the production of fully cross-linked microspheres that are ready for use at the output of the reactor without additional cross-linking steps in the microsphere collector. The mathematical expression for estimating the interfacial tension at the moment of formation of a hydrogel microsphere includes the Reynolds number for a two-phase liquid, the Ohnesorge number, and the surface tension at the liquid-air interface for continuous medium flow (modified oil). The reliability of the prediction is confirmed for continuous medium and dispersed phase flow rates of 0.8-3.2 and 0.01-0.08 mL/min, respectively. The evolution of the interfacial tension from the moment the microspheres formed and the estimated ultimate interfacial tension in a cross-linked hydrogel-modified oil system contributed to the reliable determination of the linear size of a minireactor. The ultimate interfacial tension of 76.5 ± 0.3 mN/m was determined using the Young-Laplace equation, which is based on measuring the surface free energy of the hydrogel as soft matter using the Owens-Wendt method. Additionally, the equilibrium static contact angle of the fully cross-linked hydrogel surface wetted with oil is measured using the sessile drop method. From a practical perspective, a method for optimizing and streamlining the high-tech manufacturing of cross-linked polymer microspheres and mini- and microchannel devices for use in bioengineering and pharmaceutical applications is suggested.

Theoretical Modeling of Sr(q+) He (q = 0, 1, 2) van der Waals Systems Including Spin-Orbit Coupling.

Using an ab initio methodology that incorporates pseudopotential technique in conjunction with pair potential approaches, core polarization potentials (CPP), large basis sets of Gaussian type, and full configuration interaction calculations, we investigate interaction of neutral and charged Srq+(q = 0,1,2) with helium atom. In this context, the core-core interaction of Sr2+-He is included using an accurately performed potential for the ground state at CCSD(T) level of calculation. Also, the potential energy curves and permanent and transition dipole moments of the ground state and numerous excited states have been performed respectively for Sr+He and SrHe systems. Subsequently, the spin-orbit effect is considered by utilizing a semiempirical method for states dissociating into Sr+(5p) + He, Sr+(6p) + He, Sr+(4d) + He, Sr+(5d) + He, Sr(5s5p) + He, and Sr(5s4d) + He. The spectroscopic constants of the Srq+(q = 0, 1, 2) He states, with and without spin-orbit interaction, are derived and assessed in comparison to the existing theoretical and experimental studies. Such comparison has revealed good agreement, especially, for the Sr+He ionic system. Additionally, the spin-orbit effect is considered for the X2Σ+ → 22Π1/2,3/2 and X2Σ+ → 32Σ1/2 + transition dipole moments for Sr+He.

Electron interaction with NFx (x = 1–3)

In this theoretical study on electron scattering with NFx (x = 1–3) targets in the energy range spanning from the ionisation threshold (I) to 2000 eV, we quantify various electron-driven molecular processes and report corresponding cross-sections. This study is prompted by the discrepancy between theoretical and experimental ionisation cross-sections ( Q ion ) for NFx (x = 1–3), containing highly electronegative fluorine, and the paucity of elastic and total ( Q tot ) cross-sections for these significant plasma relevant molecules. The quantum spherical complex optical potential method is used to derive elastic ( Q el ) and total ( Q tot ) cross-sections. To compute the Q ion , we employed a semi-empirical method, Complex Scattering Potential – ionisation contribution (CSP-ic). Present findings are compared with existing results available in the literature. This work is the first study to report Q el and Q tot for the two radicals NF and NF2.

Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies.

The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.

Amesp: Atomic and molecular electronic structure program

The atomic and molecular electronic structure program (Amesp) is a general-purpose electronic structure program designed for the study of molecular electronic structures. It incorporates a series of modern electronic structure methods, including Hartree–Fock, density functional theory, Multiconfigurational self-consistent field, Møller–Plesset, configuration-interaction, coupled-cluster, semiempirical methods, and molecular force fields. Amesp strives to offer an efficient and user-friendly tool specifically designed for computing for molecules ranging from small to complex biomolecules. In this paper, we highlight the features of Amesp and offer an overview.

Exploring Bacillus species xylanases for industrial applications: screening via thermostability and reaction modelling.

Xylanases derived from Bacillus species hold significant importance in various large-scale production sectors, with increasing demand driven by biofuel production. However, despite their potential, the extreme environmental conditions often encountered in production settings have led to their underutilisation. To address this issue and enhance their efficacy under adverse conditions, we conducted a theoretical investigation on a group of five Bacillus species xylanases belonging to the glycoside hydrolase GH11 family. Bacillus sp. NCL 87-6-10 (sp_NCL 87-6-10) emerged as a potent candidate among the selected biocatalysts; this Bacillus strain exhibited high thermal stability and achieved a transition state with minimal energy requirements, thereby accelerating the biocatalytic reaction process. Our approach aims to provide support for experimentalists in the industrial sector, encouraging them to employ structural-based reaction modelling scrutinisation to predict the ability of targeted xylanases. Utilising crystal structure data available in the Carbohydrate-Active enzymes database, we aimed to analyse their structural capabilities in terms of thermal-stability and activity. Our investigation into identifying the most prominent Bacillus species xylanases unfolds with the help of the semi-empirical quantum mechanics MOPAC method integrated with the DRIVER program is used in calculations of reaction pathways to understand the activation energy. Additionally, we scrutinised the selected xylanases using various analyses, including constrained network analyses, intermolecular interactions of the enzyme-substrate complex and molecular orbital assessments calculated using the AM1 method with the MO-G model (MO-G AM1) to validate their reactivity.

Retraction Note: Two Semi-Empirical Methods for Determination of Shafranov Shift in IR-T1 Tokamak

Retraction Note: Two Semi-Empirical Methods for Determination of Shafranov Shift in IR-T1 Tokamak

An enhanced stability evaluation system for entry-type excavations: Utilizing a hybrid bagging-SVM model, GP and kriging techniques

In underground mining, especially in entry-type excavations, the instability of surrounding rock structures can lead to incalculable losses. As a crucial tool for stability analysis in entry-type excavations, the critical span graph must be updated to meet more stringent engineering requirements. Given this, this study introduces the support vector machine (SVM), along with multiple ensemble (bagging, adaptive boosting, and stacking) and optimization (Harris hawks optimization (HHO), cuckoo search (CS)) techniques, to overcome the limitations of the traditional methods. The analysis indicates that the hybrid model combining SVM, bagging, and CS strategies has a good prediction performance, and its test accuracy reaches 0.86. Furthermore, the partition scheme of the critical span graph is adjusted based on the CS-BSVM model and 399 cases. Compared with previous empirical or semi-empirical methods, the new model overcomes the interference of subjective factors and possesses higher interpretability. Since relying solely on one technology cannot ensure prediction credibility, this study further introduces genetic programming (GP) and kriging interpolation techniques. The explicit expressions derived through GP can offer the stability probability value, and the kriging technique can provide interpolated definitions for two new subclasses. Finally, a prediction platform is developed based on the above three approaches, which can rapidly provide engineering feedback.

Critical current in a two-dimensional non-magnetically insulated crossed-field gap with monoenergetic emission

Prior studies have developed theories for the maximum permissible current, or critical current, for one-dimensional planar and cylindrical crossed-field diodes where the magnetic field is below the Hull cutoff, meaning that an electron emitted from the cathode reaches the anode. Here, we develop semi-empirical and analytical models to predict the critical current for a two-dimensional (2D) planar diode with nonzero monoenergetic initial velocity. The semi-empirical method considers the geometry, nonzero initial velocity, and magnetic field as multiplicative corrections to the Child–Langmuir law for space-charge limited current in a one-dimensional planar diode with an initial velocity of zero. These results agree well with 2D particle-in-cell (PIC) simulations using the over-injection method to assess virtual cathode formation for different emission widths, magnetic field strengths, and initial velocities. The analytical solution agrees better with PIC results because it accounts for the coupling of the magnetic field, geometry, and initial velocity that the semi-empirical approach does not.

Absolute dimensions of solar-type eclipsing binaries

Context. The binary star NY Hya is a bright, detached, double-lined eclipsing system with an orbital period of just under five days with two components each nearly identical to the Sun and located in the solar neighbourhood. Aims. The objective of this study is to test and confront various stellar evolution models for solar-type stars based on accurate measurements of stellar mass and radius. Methods. We present new ground-based spectroscopic and photometric as well as high-precision space-based photometric and astrometric data from which we derive orbital as well as physical properties of the components via the method of least-squares minimisation based on a standard binary model valid for two detached components. Classic statistical techniques were invoked to test the significance of model parameters. Additional empirical evidence was compiled from the public domain; the derived system properties were compared with archival broad-band photometry data enabling a measurement of the system’s spectral energy distribution that allowed an independent estimate of stellar properties. We also utilised semi-empirical calibration methods to derive atmospheric properties from Strömgren photometry and related colour indices. Results. We measured (percentages are fractional uncertainties) masses, radii, and effective temperatures of the two stars in NY Hya and found them to be MA = 1.1605 ± 0.0090 M⊙ (0.78%), RA = 1.407 ± 0.015 R⊙ (1.1%), Teff, A = 5595 ± 61 K (1.09%), MB = 1.1678 ± 0.0096 M⊙ (0.82%), RB = 1.406 ± 0.017 R⊙ (1.2%), and Teff, B = 5607 ± 61 K (1.09%). The atmospheric properties from Strömgren photometry agree well with spectroscopic results. No evidence was found for nearby companions from high-resolution imaging. A detailed analysis of space-based data revealed a small but significant eccentricity (e cos ω) of the orbit. The spectroscopic and frequency analysis on photometric time series data reveal evidence of clear photospheric activity on both components likely in the form of star spots caused by magnetic activity. Conclusions. We confronted the observed physical properties with classic and magnetic stellar evolution models. Classic models yielded both young pre-main-sequence and old main-sequence turn-off solutions with the two components at super-solar metallicities, in disagreement with observations. Based on chromospheric activity and X-ray observations, we invoke magnetic models. While magnetic fields are likely to play an important role, we still encounter problems in explaining adequately the observed properties. To reconcile the observed tensions we also considered the effects of star spots known to mimic magnetic inhibition of convection. Encouraging results were obtained, although unrealistically large spots were required on each component. Overall we conclude that NY Hya proves to be complex in nature, and requires additional follow-up work aiming at a more accurate determination of stellar effective temperature and metallicity.