Semiempirical Program Research Articles

Optimized parametric hydrodynamic databases provide accurate response predictions and describe the physics of vortex-induced vibrations

We address the problem of obtaining accurate predictions of the vortex-induced vibrations (VIV) of flexible structures placed in cross-flow by reconstructing fluid force databases in parametric form. The forces are expressed in terms of hydrodynamic coefficients, which depend on several variables and parameters, including the structural properties and geometry, frequency and amplitude of vibration, and the flow conditions, so that a comprehensive database obtained with systematic experiments would require an intractably large number of tests. Therefore, we develop a method for determining optimal parametric hydrodynamic databases directly from a variety of free- and forced-vibration experiments on both rigid and flexible cylinders, by minimizing the error between the predicted responses using a software driven by the force database, and the measured data. We first describe the process of selecting an appropriate parametrization of the fluid forces as function of reduced frequency and non-dimensional amplitude of vibration, informed by Gaussian-Process-Regression-guided automated experiments. Several examples are selected to demonstrate the method’s ability to acquire optimal hydrodynamic databases, including data sets highlighting the effect of Reynolds number and the addition of in-line motion to cross-flow rigid cylinder VIV. The proposed methodology is further demonstrated to be effective when used with the semi-empirical program VIVA for flexible cylinder VIV, yielding significant improvements in prediction accuracy compared to baseline results. It therefore serves as a potential solution for the development of a digital twin for marine risers, an in-situ, real-time riser response prediction and structural health monitoring system.

A Multidisciplinary Possibilistic Approach to Size the Empennage of Multi-Engine Propeller-Driven Light Aircraft

In considering aircraft design, it is very important to effectively size the tail configuration for stability and control. Multidisciplinary design optimization (MDO) focuses on the use of numerical optimization in the design of systems with multiple subsystems or disciplines of consideration. However, MDO uses deterministic calculations, and does not consider the uncertainties that arise from the employed analyses, including errors due to linearization and simplification. For problems with inadequate input data, the possibility-based design optimization (PBDO) scheme can be implemented in its stead to achieve reliable designs using membership functions for epistemic uncertainties. A multidisciplinary, possibilistic approach is presented to define the sizing of the empennage configuration of a twin-engine propeller-driven aircraft by changing shape parameters while satisfying the design requirements given the tailless aircraft configuration, the flight conditions, and various uncertainties. The corresponding disciplines are aerodynamics, stability and control, propulsion and weight and balance. Herein, different design requirements are considered including longitudinal/lateral/directional trim and stability characteristics, manufacturing and controllability criteria, handling qualities, operational requirements, airworthiness and survivability. The resulting aerodynamic characteristics and flight dynamic stability outcomes show that the optimized tail configuration for the proposed aircraft fully complied with airworthiness requirements and predefined constraints while considering several uncertainties due to the use of early-stage statistical estimations. The proposed approach can be used to enhance the preliminary design of multi-engine propeller-driven light aircraft where only low-fidelity, statistical estimations are available. The resulting output is not only an optimized aircraft configuration, but one where the stability of the design has been ensured. In this work, the aerodynamic characteristics have been determined using a validated semi-empirical program called MAPLA, developed for light aircraft designs and development in the preliminary design phase. Furthermore, the optimization framework consists of a deterministic optimizer that runs sequentially with a possibility assessment algorithm.

Calculate the Thermal Properties of (S2F2) Using Semi-empirical Quantum Mechanics (MNDO / PM3)

In this paper, thermal properties were performed by using semi-empirical theoretical calculations to study the molecular structure of a nonlinear molecular system, the (S2F2) molecule in the infrared region, by using semi-empirical quantum programs in the (MNDO / PM3) method. This study is under the condition of obtaining the stable structure of the molecule in which the molecule obtains the minimum value of the total energy. The thermodynamic properties were also calculated, including the heat of formation, whose value was (-61.002kcal / mol), the entropy and its value (78.2916 cal / mol.k), as well as the heat capacity (15.9454 cal / mol.k) and the enthalpy (3763.434 cal /mol), Gibbs Free Energy, it was valued at (-19567.5 cal / mol), these values ​​were taken at the standard temperature 298 k, withdrawing these relationships in graphs and showing the changes in the state That the molecule passes through, and comparing these values with the experimental results.

Stopping cross section of vanadium for H + and He + ions in a large energy interval deduced from backscattering spectra

Abstract We have experimentally determined electronic stopping cross sections of vanadium for 50–2750 keV protons and for 250–6000 keV He ions by relative measurements in backscattering geometry. To check the consistency of the employed procedure we investigate how to define adequate reference stopping cross section data and chose different reference materials. To proof consistency of different reference data sets, an intercomparison is performed to test the reliability of the evaluation procedure for a wide range of energies. This process yielded consistent results. The resulting stopping cross section data for V are compared to values from the IAEA database, to the most commonly employed semi-empirical program SRIM, and to calculations according to CasP. For helium, our results show a significant deviation of up to 10% with respect to literature and to SRIM, but are in very good agreement with the CasP predictions, in particular when charge-exchange processes are included in the model.

New experimental stopping power data of 4He, 16O, 40Ar, 48Ca and 84Kr projectiles in different solid materials

Abstract New experimental data on energy loss of 4 He, 16 O, 40 Ar, 48 Ca and 84 Kr ions in thin, self-supporting foils of C, Al, Ni, Ag, Lu, Au, Pb and Th are presented. The measurements, using the TOF-E method, were done in a very broad energy range around the stopping power maximum; typically from 0.1 to 11 MeV/u. When available, the extracted stopping power values are compared with the previously published data. The overall agreement is good although a fair comparison is difficult as the covered energy range is much larger than in previous measurements. The small error bars and a broad coverage allowed us to test the predictions of theoretical codes: PASS, CasP, and semi-empirical programs: SRIM, LET, MSTAR, and the Hubert table predictions. The deviations of PASS predictions from the experimental data do not exceed 20% for all the measured combinations. CasP predictions are within 15% from the data for heavier ions but diverge up to 40% for lighter ions. Semi-empirical approaches, including SRIM, deviate from the experimental data by less than 5% for the regions already covered by previous experiments but err by about 10–20% for the ion/target combinations that were not measured before: Ca in Lu as well as Kr in Lu, Pb, and Th.

The electronic structure properties of 20 L-amino acids in neutral and zwitterion forms: Quantum-chemical calculations

The conformational diversity of the 20 DNA-encoded proteinogenic amino acids and their zwitterions in the gaseous state and in the state with the first hydration shell was analyzed using the PM3 and PM7 semi-empirical quantum-chemistry programs.

The quantum-chemical approach to calculations of thermodynamic and structural parameters of formation of fatty acid monolayers with hexagonal packing at the air/water interface

The structural parameters of fatty acid (with formula CnH2n+1COOH, n = 7-16) monolayers at the air/water interface were modeled within quantum-chemical semiempirical program complex Mopac 2012 (PM3 method). On the basis of quantum-chemical calculations it was shown that molecules in the highly ordered monolayer can be oriented at the angle ∼16° (tilted monolayer), or at the angle ∼0° to the normal to the air/water interface (untilted monolayer). The structural parameters of both tilted and untilted monolayers correspond well to the experimental data. The parameters of the unit cell of the modelled tilted monolayer are: a = 8.0-8.2 Å and b = 4.2-4.5 Å (with the corresponding experimental data 8.4-8.7 Å and 4.9-5.0 Å). For the modelled untilted monolayer these parameters are: a = 7.7-8.0 Å; b = 4.6 Å (with the corresponding experimental data 8.4 Å and 4.8-4.9 Å). Enthalpy, entropy and Gibbs' energy of clusterization were calculated for both structures. The correlation dependencies of the calculated parameters on the number of pair intermolecular CHHC interactions in the clusters and the pair interactions between functional groups were obtained. It was shown that the spontaneous clusterization of the fatty carboxylic acids at the air/water interface under standard conditions is energetically preferable for molecules which have 13 or more carbon atoms in the alkyl chain and this result also agrees with the corresponding experimental parameters.

Interrelation of sorption properties and nanostructure of carbon molecular sieves from anthracites of Kuzbass

Main regularities in the formation of nanotexture and structure of carbon porous materials and development of pores in Kuzbass anthracites were considered. Basic principles of the production of carbon sorbents for efficient separation of gases such as methane and helium, hydrogen and carbon monoxide, were studied. Sorbents produced from Kuzbass coals were analyzed with the help of gas chromatography, SEM with element analyzer, sorpometry, and gas porometry. The literature data on the size of pores and associates of nanofragments were compared to the width of pores andsize of entrance windows in models of CMS (carbon molecular sieve) nanofragments, which were estimated with the help of quantum chemical modeling in MOPAC/PM-3 semiempirical program. The work resulted in the production of carbon molecular sieves for extraction of hydrogen from gas mixtures and in obtaining the data on the main characteristics of sorbents produced.

Development of a semi-empirical program for predicting the braking performance of a passenger vehicle

Since the invention of automobiles, the need to know the braking performance of vehicles has been acknowledged. However, because there are numerous design variables as well as nonlinearities in the braking system, it is difficult to predict the performance accurately. In this paper, a computational program is developed to estimate the braking performance numerically. This synthetic braking performance program accounts for pedal force, pedal travel and deceleration of braking parts, such as master cylinder, booster, valve, brake pad, rotor, and hoses. To improve the accuracy of program, a semi-empirical model of a braking system is introduced by using the empirical test data of pad compression, hose expansion and the friction coefficient between the pad and rotor. The accuracy of the estimation is evaluated by comparing it to the actual vehicle test results. The developed program is easy for the brake system engineers to manipulate and it can be used in the development of new vehicles by incorporating the graphical presentations.

X-ray diffraction and quantum-chemical analysis of a single crystal of 2,5-dimethyl-3,4-dihydro-2h-pyran-2-carboxylic acid

The structure of synthesized 2,5-dimethyl-3,4-dihydro-2H-pyran-2-carboxylic acid was investigated by the single crystal X-ray diffraction analysis method. It was established that the molecule of the acid exists in the form of the endo isomer while the single crystal exists as a racemate of the two enantiomeric endo stereomers. Quantum-chemical calculations of a model of the macrocell of the acid by means of the semiempirical MOPAC2009 program agree well with the X-ray diffraction data.

Stability studies of double-base propellants with centralite and malonanilide stabilizers using MO calculations in comparison to thermal studies

Propellants containing nitrate esters need stabilizers to avoid early decomposition or even explosion during storage. Newly prepared malonanilides M1– M5 were tested in stabilizing double-base propellants (DBPs). Their stabilization was compared with the effect of classical stabilizer N,N′-diethyldiphenyl urea ( C1) using both practical thermal stability tests (qualitative and quantitative tests) and theoretical molecular orbital calculations. This research shows that the new stabilizers (malonanilides) have good stabilizing effects. Some of malonanilides e.g. ( M5) and ( M2) have higher stability effects. Different mechanisms were suggested to explain the role of different stabilizers. Molecular orbital calculations using the semi-empirical program AM1 are performed on the new and classical stabilizers. Correlation was made between the volume (ml) of NO x , weight loss (wt%), other thermal analyses data, calculated thermodynamic parameters like activation energy ( E a, kJ mol −1) of the decomposed propellant samples containing different stabilizers and some of their calculated properties such as HOMO, LUMO energies, the charge distribution and the π-bond order. The stabilization effect decreases with the increase in HOMO energy. The correlation between the net charge and parameters measured for the stabilization effect shows good accordance. Comparison of the results obtained show that the high electron charge on N atom of the stabilizers and on its benzene ring is the most important factor, but not the only factor governing the stabilization effect of the stabilizers.

Energy loss of 132Xe-ions in thin foils

The energy loss of 132Xe-ions in C, Al, Ni, Ag, Lu, Au, Pb and Th foils was measured in the energy range from 0.1 to 5 MeV/u using the TOF-E method. The results are compared with previously published data and with the predictions of several computer codes. They include theoretical codes: PASS, CASP, semi-empirical programs: SRIM, LET and the Hubert table predictions.

Combining a genetic algorithm with a linear scaling semiempirical method for protein–ligand docking

In the search for more energetically precise docking methods and to avoid the problem of defining suitable ligand force fields, we have built a software to perform rigid molecular docking by combining a genetic algorithm with a linear scaling semiempirical program. The resulting AlgoGen-DivCon software uses the Divide and Conquer linear scaling methodology to evaluate protein–ligand interaction energies using quantum semiempirical hamiltonians while conformational search is performed by a genetic algorithm which optimizes the position of a mobile ligand relative to a fixed protein system. Tests have been performed to assess the performance of AlgoGen-DivCon. Our results on the docking of 8-azaxanthine, oxonic acid and uric acid in a 700 atom Urate Oxidase model are structurally very similar to known crystallographic structures and prove that it is now possible to perform in a reasonable amount of time molecular dockings of relatively large protein–ligand complexes using a quantum description of the interaction energy.

Geometrical effect on the first hyperpolarizability of thiophene-substituted stilbene derivatives

This paper presents dipole moment ( μ), static mean polarizability ( α) and mean first hyperpolarizability ( β) of thiophene-substituted stilbene derivatives calculated in the framework of density functional theory. The calculations were performed using a finite field approach implemented in the density functional program allchem. All-electron type basis sets optimized for the calculation of the polarizabilities and hyperpolarizabilities using a local exchange-correlation functional were employed. The molecular structures have been fully optimized using the semiempirical program MSINDO. The calculated mean first hyperpolarizability trends are in agreement with the experimental trends obtained from hyper-Rayleigh scattering technique. This work shows that the increased of hyperpolarizability of the studied thiophene-substituted stilbene derivatives is due to a geometrical effect of their trans and cis isomers.

A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs.

An exploratory semiempirical Hamiltonian (PM3BP) is developed to model hydrogen bonding in nucleic acid base pairs. The PM3BP Hamiltonian is a novel reparametrization of the PM3 Hamiltonian designed to reproduce experimental base pair dimer enthalpies and high-level density-functional results. The parametrization utilized a suite of integrated nonlinear optimization algorithms interfaced with a d-orbital semiempirical program. Results are compared with experimental values and with benchmark density-functional (mPWPW91/MIDI!) calculations for hydrogen-bonded nucleic acid dimers and trimers. The PM3BP Hamiltonian is demonstrated to outperform the AM1, PM3, MNDO, and MNDO/H Hamiltonians for dimer and trimer structures and interaction enthalpies and is shown to reproduce experimental dimer interaction enthalpies that rival density-functional results for an over 3 orders of magnitude reduction in computational cost. The tradeoff between a high accuracy gain for hydrogen bonding at the expense of sacrificing some generality is discussed. These results provide insight into the limits of conventional semiempirical forms for accurate modeling of biological interactions.

Mechanism for large first hyperpolarizabilities of phosphonic acid stilbene derivatives.

This paper presents calculations of dipole moments (mu), static polarizabilities (alpha), and first hyperpolarizabilities (beta) of phosphonic acid stilbene derivatives calculated in the framework of density functional theory. These calculations were performed using a finite field approach implemented in the density functional program ALLCHEM and were of an all-electron type using local exchange-correlation functional and specially designed basis sets. The molecular structures have been fully optimized using the semiempirical program MSINDO. Some of the investigated stilbenes have been synthesized very recently while others are described for the first time. Donor and acceptor groups of these analogues have been modified and the influence of these changes on the first hyperpolarizabilities has been investigated. This work demonstrates that the nonlinear optical response beta of these compounds increases dramatically when the acceptor moiety is displaced by analogues containing alkali metal groups. A general mechanism for the design of novel nonlinear optical materials with large first hyperpolarizabilities is described.

Quantum mechanical quantitative structure activity relationships to avoid mutagenicity in dental monomers

The objective of this study was to identify through quantum mechanical quantitative structure activity relationships (Q-QSARs) chemical structures in dental monomers that influence their mutagenicity. AMPAC, a semiempirical computer program that provides quantum mechanical information for chemical structures, was applied to three series of reference chemicals: a set of methacrylates, a set of aromatic and a set of aliphatic epoxy compounds. QSAR models were developed using this chemical information together with mutagenicity data (Salmonella TA100, Ames Test). CODESSA, a QSAR program that calculates quantum chemical descriptors from information generated by AMPAC and statistically matches these descriptors with observed biological properties was used. QSARs were developed which had r 2 values exceeding 0.90 for each study series. These QSARs were used to accurately predict the mutagenicity of BISGMA, a monomer commonly used in dentistry, and two epoxy monomers with developing use in dentistry, GY-281 and UVR-6105. The Q-QSAR quantum mechanical descriptors correctly predicted the level of mutagenicity for all three compounds. The descriptors in the correlation equation pointed to components of structure that may contribute to mutagenesis. The QSARs also provided 'dose windows' for testing mutagenicity, circumventing the need for extensive dose exploration in the laboratory. The Q-QSAR method promises an approach for biomaterials scientists to predict and avoid mutagenicity from the chemicals used in new biomaterial designs.

The Ideal Gas Thermodynamics of Diesel Fuel Ingredients. I. Naphthalene Derivatives and Their Radicals

The molecular fundamentals of 21 naphthalene derivatives were investigated, calculated and evaluated, and their ideal gas thermodynamic properties were calculated, for the sake of simulating the combustion properties of diesel fuel. Ten of these species are stable molecules and 11 are radicals. The molecular fundamentals are calculated using Gaussian 94 ab initio and MOPAC 6 semiempirical programs. The results can be used to estimate the MOPAC performance with polyaromatic species.

Trans-cis isomerisation of azobenzene amphiphiles containing a sulfonyl group

Trans-cis isomerisation of the azo amphiphilic derivatives 4-(N-methyl-N-n-dodecyl)amino-4′-(N-thiazol-2-yl) sulfonamidoazobenzene (1) and 4-(N-methyl-N-n-dodecyl)amino-4′-(N-pyrimidin-2-yl)sulfonamidoazobenzene (2), each containing a sulfonyl group and a heterocyclic ring, was observed during irradiation of the amphiphile solutions at the absorption band maximum (ca. 450 nm). The reverse cis-trans transition occurred at room temperature as a thermal relaxation. Quantum chemical calculations yielded the optimum geometry of the trans, cis and transition forms. The trans-cis potential energy difference obtained by the DFT B3LYP method is in the range of 67.5–70.7 kJ mol-1 and the activation energy is ca. 129.7–132.5 kJ mol-1, depending on the basis set. The UV-Vis spectra of the cis and trans form of 1 and 2 were calculated using the INDO1/S semiempirical program. The calculated spectra of the cis-trans mixtures and those obtained experimentally were very close in shape. For the alcanoyl derivative 4-(n-undecyl)carbonamido-4′- (N-thiazol-2-yl)sulfonamidoazobenzene (3) the illumination with low intensity monochromatic light (365 nm) caused isomerisation but the system needed up to 72 h to recover the trans form by thermal relaxation.

Modeling of the interconversion between Z and E isomeric forms of pyridine-2-formyl thiosemicarbazone

The isomeric interconversion between Z and E forms of a thiosemicarbazone derivative, namely, pyridine-2-formyl thiosemicarbazone (PATS-2) has been modeled in this work with the semi-empirical program GEOMOP. PATS-2 is an electrode surface modifier, relevant in the context of metalloproteins electrochemistry. The strategy of modeling included the definition and geometry optimization of eight starting conformations for each of the two PATS-2 isomers (Z and E). Rotations over PATS-2 CN double bond, a supposedly prohibited conversion, were imposed to the molecule in order to monitor the Z–E transition, since that is the most likely route for the experimentally observed interconversion. Results indicated that PATS-2 CN bond order has a significantly lower value than that expected for a conventional double bond of the same kind, suggesting that a rotation at that point in the molecule, a condition for the observed isomerization, is feasible. The greater stability of the E isomer, experimentally observed, could be accounted for by energetic and entropic considerations based on results from the modeling work. We found that the Z↔E trajectories proceed through small shifts in energy and imply intermediate conformational rearrangements during interconversion. Most stable transient conformers along a 180° rotation, including the most likely transition state geometry, were identified.