Journal of Molecular Modeling最新文献

Context

This work presents analytical expressions for ro-vibrational energy models of diatomic molecules by introducing fractional parameters to improve molecular interaction analysis. Thermodynamic models, including Helmholtz free energy, mean thermal energy, entropy, and isochoric heat capacity, are formulated for diatomic molecules such as CO (X ¹∑⁺), Cs₂ (3 ³∑_g⁺), K₂ (X ¹∑_g⁺), ⁷Li₂ (6 ¹Π_u), ⁷Li₂ (1 ³Δ_g), Na₂ (5 ¹Δ_g), Na₂ (C(2) ¹Π_u), and NaK (c ³∑⁺). The incorporation of fractional parameters improves predictive accuracy for vibrational energies, as shown by reductions in percentage average absolute deviations from 0.5511 to 0.2185% for CO. Findings indicate a linear decrease in Helmholtz free energy and an initial increase in heat capacity with rising temperature, providing valuable insights for characterizing materials and optimizing molecular processes in chemistry, material science, and chemical engineering. The results obtained show strong agreement with established theoretical predictions and experimental data, validating the robustness and applicability of the proposed models.

Methods

The energy equations are derived by solving the radial Schrödinger equation for a variant of the Tietz potential using the generalized fractional Nikiforov-Uvarov (GFNU) method in addition to a Pekeris-type approximation for the centrifugal term. The canonical partition function is derived using the modified Poisson series formula, which serves as a basis for calculating other thermodynamic functions. All computations are carried out using MATLAB programming software.

Context

Oxirene, surmised to exist in the interstellar medium, was synthesized in the laboratory only recently. The present study investigates theoretically to what extent the two exotic molecules, oxirene and its thia-analogue thiirene, are capable of forming molecular self-aggregates and undergo micro-hydration under cooperative hydrogen bonding as the tour de force. Cogent molecular descriptors, such as binding energies for cluster formation, molecular electrostatic potential (MESP), effective atomic charges, infrared spectroscopic response, criticality profiles from the quantum theory of atoms in molecules (QTAIM), hydrogen bond energies, and reduced density gradient (RDG) maps identifying non-covalent interactions (NCI), all in unison confirm theoretically the existence and characterize the aggregates. In particular, infrared spectra display frequency down-shifts for the hydrogen bonded C–H vibrations in aggregates and for O–H in hydrated complexes. This work carried out in silico, should furnish credible tenets toward identification of oxirene and thiirene self-aggregates and their micro-hydrated complexes that potentially exist in the interstellar medium.

Method

By means of a molecular modeling program AVOGADRO, a multitude of initial-guess clusters under universal force field (UFF) were generated, which were subsequently optimized employing the GAUSSIAN16 suite of programs with the tightest convergence criterion, at the ωB97xD level of density functional theory embodying long-range dispersion effects, in conjunction with a reliable basis set 6–311 ++ G(2d,2p). The versatile package GAUSSVIEW yields the structures, vibrational frequencies, and criticality information, respectively.

Context

The reaction of NO₂ with pristine and Pt-doped SnS₂ surfaces is investigated theoretically and compared with the experiment. Transition state theory formalism for gas sensors is adopted to present NO₂ gas sensing. The dissociation temperature at approximately 150 °C is found to be of great importance in NO₂ reactions. The adsorption and transition states of NO₂ with pristine and Pt-doped SnS₂ are calculated. Pt doping includes 0.5, 1, and 1.5% in accordance with available experimental results. The variation of thermodynamic quantities such as Gibbs free energy with Pt concentration and temperature is calculated. Transition state theory parameters that are suitable for the present sensor are determined. The results include the variation in response time with temperature, Pt concentration, and NO₂ concentration. Response and response time as a function of temperature are rarely investigated in theoretical calculations, which is one of the advantages of the present study. Optimum response temperature and Pt concentration are found. The results agree with available experimental results.

Methods

Density functional theory at the B3LYP level optimize molecular structures. 6-311G** basis set is used for all elements except Sn and Pt treated using SDD basis set. Gaussian 09 program and its facilities are used to perform present optimizations.

Context

Drilling fluids must reduce the coefficient of friction between the drilling equipment and the drilled rock or well casing. Friction forces become particularly relevant in drilling with a high angle gain, in which cases oil-based fluids are generally used. The latter are highly lubricating, but harmful to the environment. For environmental and economic reasons, there is great interest in the development of new additives that enable the use of water-based drilling fluids in all phases of well drilling. Preliminary experimental results show that there is a synergistic effect between glyceryl monooleate (GMO), normally used as lubricant additive, and carboxymethyl cellulose (CMC), a polysaccharide normally used in water-based drilling fluids as a rheological modifier, resulting in extremely low friction coefficients. This work aimed to clarify, through theoretical calculations, the interaction between CMC and GMO, as well as their role in reducing the coefficient of friction between the drilling equipment and the drilled rock when added to water-based fluids.

Methods

Calculations based on density functional theory (DFT) were used to predict which, CMC or GMO, preferentially binds to the metal surface. The interactions between the polysaccharide and the surfactant were studied through a combination of classical molecular dynamics and DFT calculations. Finally, dynamic calculations were carried out involving fragments of the polysaccharide, the surfactant and hematite (Fe₂O₃) representing the metal surface, since in the experimental conditions the metal surface will be covered by a primary oxide layer. The results pointed to the preferential binding of CMC to hematite. Regarding the interaction between polymer and surfactant, it was found that the polar part of the GMO interacts with the CMC through hydrogen bonds while the nonpolar carbon chain remains close to the polymer due to hydrophobic interactions. Molecular dynamics calculations showed that GMO increases the binding energy of CMC to hematite and also that this increase in the binding energy is highly influenced by electrostatic interactions.

Context

In order to obtain environmentally friendly emulsion explosives formulations with higher power, based on zero oxygen balance, formulations of titanium hydride (TiH₂)—high-power emulsion explosives were optimally designed. The results show that the zero oxygen balance formulation produces almost no toxic and harmful gases. The detonation temperature and detonation heat are increased. And the detonation volume decreases along with the increase in the content of TiH₂. Zero oxygen balance formulation can effectively enhance the explosive power of TiH₂-type high-power emulsion explosives compared to traditional formulations while improving its environmental friendliness and safety. This paper provides a basis for further development of the optimal brisance and environmentally friendly explosive formulations.

Methods

The principle of zero oxygen balance was applied to theoretically design the formulations of titanium hydride (TiH₂)—high-power emulsion explosives. To find a zero-oxygen balanced formulation with the best detonation performance, Hess’s Law and Cast’s Law were used to calculate the detonation parameters such as detonation heat and detonation temperature. Also, the B-W method was used to anticipate the detonation products

Graphical Abstract

Context

To improve the prediction model of insulation strength for gaseous medium, it is needed to investigate the effect of external electric field on molecular microscopic descriptors. In this study, the global and local descriptors in the present of the external electric field are analyzed for non-polar gases and polar gases. According to the correlation analysis between molecular microscopic descriptors and insulation strength, both traditional regression and machine learning models can be used to predict the insulation strength of gaseous medium. The accuracy of insulation strength prediction models is effectively improved after considering the impact of external electric field on microscopic descriptors. The model based on the random forest achieves the highest accuracy. Furthermore after 1,000 rounds of training, the average R², MSE, MAE and NMBE of the test sets in the random forest model are 0.9239, 0.0346, 0.1581 and 0.1750, respectively. The average cross-validation score is 0.160, which is based on MSE as the evaluation criterion.

Methods

The Gaussian 16 software is utilized to optimize the 71 gas molecules using the M06-2X method and the 6–311 + + G(d, p) basis set. Molecular local descriptors are obtained using the wavefunction analysis software Multiwfn.

Context

Rare earth elements (REE) are indispensable in numerous green technologies owing to their exceptional physical and chemical attributes. Separating REE is a pivotal process to meet the increasing demands of the high-tech industry. Understanding the hydrolysis of REE in aqueous environments marks the initial stride in comprehending their separation mechanisms. Sulfate commonly coexists in high-concentration solutions alongside REE, stemming from mineral processing. We analyzed the hydrolysis of REE and their complexes with sulfate using DFT methods. We present and discuss on the structural characteristics of hydrolysis species and sulfate complexes in alignment with existing experimental data. Estimates of Gibbs free energies for hydrolysis and sulfate complex formation were compared against literature values. REE pose challenges owing to the labile nature of aqua complexes and the pivotal role of system dynamics. We showed that hydrolysis reactions could be suitably modeled, yielding an error margin of approximately 5 kcal mol⁻¹ concerning experimental values, employing the M06 exchange–correlation functional with the SMD implicit solvation model. However, sulfate chemical species proved to be more challenging, exhibiting larger error margins with substantial variations across the REE series. The Raman spectrum analysis of lanthanum sulfate complexes demonstrated excellent agreement with experimental values.

Method

We applied the M06, PBE, and PBE0 exchange–correlation functionals combined with def2-TZVP basis sets and SMD to obtain the Gibbs free energies of hydrolysis and sulfate complexation with lanthanides in aqueous solution. The calculations were performed using the ORCA program.

Graphical Abstract

Context

While the pure Au₁₆ cluster tends to exist in a 3D cage shape, the doubly doped W₂@Au₁₆ is found to prefer a tubular form containing three five-membered Au rings stabilized by the W₂ dimer vertically placed inside a tube-like Au₁₆ framework. Formation of self-assembled nanotubes containing five-membered Au rings from the tube-like W₂@Au₁₆ cluster is also feasible, and such a tubular structure constitutes an ideal building block for generating gold-assembled nanotubes, providing us with a useful approach for designing some novel tailor-made materials with interesting optoelectronic properties.

Methods

Density functional theory (DFT) calculations using the TPSS functional and the cc-pVDZ-PP basis set are employed to determine some noticeable effects of the doping of the W₂ dimer on the structure, stability, and optical properties of pure Au16 gold clusters.

Graphical Abstract