Journal of Molecular Modeling最新文献

Context

Sulfur dichloride (SCl₂) molecules form a harmful substance; however, it is widely used in the industry as insecticide and in organic synthesis. In contact with water, these molecules produce other toxic and corrosive gases. Therefore, it is important to remove them from the environment. In this work, we have studied the boron phosphide (BP) monolayer (ML) doped with metal atoms to be considered as a sensor material for the detection of sulfur dichloride (SCl₂) molecules. Studies are done by applying the density functional theory (DFT) according to the PWscf code of the Quantum ESPRESSO, using the projector-augmented-wave (PAW) method within the framework of the generalized gradient approximation (GGA) with the PBE parameterization. The results obtained indicate weak interactions between the SCl₂ molecule and the pristine BP monolayer. However, after metal-doping (with atoms of: Ga, In, N and As) the interactions between the SCl₂ molecule and the ML was increased, as expected. Parameters such as the adsorption energy (E_ad), work function (Ф), Bandgaps (E_g), recovery time (τ), electronegativity (χ) and chemical potential (μ) have been analyzed. The results suggest that the metal-doped BP monolayer may be a promising sensing material for gas sensor devices to detect SCl₂ molecules.

Methods

The SCl₂-metal-doped BP ML has been investigated using DFT calculations as implemented in the PWscf code of the Quantum ESPRESSO, and using PAW pseudopotential within the framework of the GGA-PBE and energy cutoff of 40Ry. The force components were smaller than 0.05 eV/Å and the Grimme-D2 scheme was considered. The Brillouin zone was sampled using a Monkhorst–Pack grid of 5 × 5 × 1 and 17 × 17 × 1 k-points for structural relaxations and electronic-properties calculations.

Context

The H₂CCCH radical plays a crucial role in combustion chemistry, astrophysical processes, and the formation of complex organic molecules, serving as a key intermediate in the synthesis of polycyclic aromatic hydrocarbons and soot precursors. The reactions of H₂CCCH with small species are significant for understanding the mechanisms of hydrocarbon transformation in combustion, atmospheric chemistry, and interstellar environments. In the present study, the mechanism and kinetics of the H + H₂CCCH have been thoroughly characterized. The calculated results indicate that the reaction can proceed via H-addition to the H₂CCCH carbon chain without an energy barrier, forming the adducts (C₃H₄). These intermediates can then undergo H₂-abstraction or carbon-chain cleavage to create various products, in which PR₁ (¹HCCCH + H₂) and PR₄ (H₂CCC + H₂) are the main products of the reaction system. Furthermore, the triplet potential surface shows the dominant channel forming the product PR₁₁ (³HCCCH + H₂). In the low-temperature region, PR₄ is dominant, exhibiting a 70% branching ratio at 400 K; at higher temperatures, the PR₁₁ product prevails, with a 65.7% branching ratio at 2000 K. The bimolecular rate constants of the reaction are positively dependent on temperatures but negatively dependent on pressures. The calculated rate constants in this study agree well with the available literature data. The computational results of the H + H₂CCCH reaction provide profound insights into the theoretical aspects and offer valuable applications for modeling reaction systems involving the propargyl radicals.

Methods

The B3LYP and CCSD(T) methods, combined with the aug-cc-pVnZ (n = T, Q, 5) basis sets, were employed to optimize structures and calculate single-point energies for all species involved in the reaction. The temperature range (200 – 2000 K) and pressure range (0 – 7600 Torr) were used to calculate the bimolecular rate constants for the dominant reaction pathways. The TST, VRC-TST, and RRKM models, with the small curvature tunneling correction, were employed for the kinetic calculations.

Context

In order to estimate the mechanical behavior of the propellant under working pressures, the effect of pressure on the mechanical properties of hydroxyl-terminated polybutadiene (HTPB) propellants was studied by analyzing the uniaxial tensile strength and maximum strain master curves under the test conditions of – 20 ~ 70 °C, 0.5 mm/min ~ 500 mm/min with different pressures from 0 to 10 MPa. The results show that the master curves for tensile strength are obviously affected by the pressure in the range of 0.15 ~ 3 MPa, while the master curves for tensile strength are insensitive to pressures below 0.15 MPa or above 3 MPa. The master curves for maximum strain are unaffected in the whole concerned pressure range. A power function can be used to study the relationship between tensile strength and temperature or strain rate and to predict the change trend of the temperature and strain rate sensitive indexes with the pressure, which may be useful in the formulation designing of HTPB solid propellants.

Methods

The uniaxial tensile propellant test was used to obtain the tensile strength and maximum strain master curves under different pressures, which were plotted at a reference temperature of 20 °C under different pressures by means of the overlap joints method. A power function method was developed to study the relationship between tensile strength and temperature or strain rate.

Context

In this study, a series of carefully designed oxygen-rich bicyclic ozonides, derived from 2,3-dihydrofuran (2,6,7,8-tetraoxabicyclo[3.2.1]octane), have been studied with meticulous attention to the incorporation of nitro and/or trinitromethyl (TNM) substituents. These compounds exhibit significant promise as high-energy–density materials (HEDMs), thus representing a pioneering avenue in the realm of advanced energetic materials. Evaluating the energetic performances and impact sensitivity is the focus of our theoretical calculations. The majority of the designed compounds exhibit elevated density, complemented by outstanding detonation properties. Each of these compounds demonstrates a high positive heat of formation, with many of them displaying impact sensitivities well suited for applications in high-energy density materials (HEDMs). Due to their significant oxygen content, all 45 designed compounds maintain a high positive oxygen balance. This unique combination of high-performance characteristics and low sensitivities positions them as promising candidates for high-energy explosives. Notably, among the compounds, FOZ23 (3-nitro-5-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane), FOZ19 (3-nitro-4-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane), and FOZ24 (1-nitro-5-(trinitromethyl)-2,6,7,8-tetraoxabicyclo[3.2.1]octane) exhibit exceptional performance and sensitivities, warranting further investigation and consideration. From the analysis of BDE of C-NO₂ and O–O linkages, it was found that the peroxide bond is stronger than C-NO₂ bond. Therefore, peroxides can be used for various applications in the nearby future by incorporating proper substitutions.

Methods

Gaussian 09 program was used for geometry optimization and vibrational frequency analysis of the selected compounds. The method employed for the study was density functional theory at the B3LYP level of approximation using aug-cc-pVDZ as the basis set. Multiwfn program was employed for Electrostatic potential analysis.

Graphical abstract

Context

Anacardic acid (AA), a key compound in cashew nut shell liquid, is used in medicines and food preservation because of its antimicrobial and antioxidant properties. AA has four forms: saturated, monoene, diene, and triene. Extracting these forms using different solvents is difficult through experiments. To solve this, molecular dynamics (MD) simulations are used to study how AA behaves in three solvents: hexane, ethanol, and carbon tetrachloride. The results show that ethanol forms stronger hydrogen bonds with AA and allows higher movement of AA molecules, making it a better solvent for extraction. These findings help in selecting efficient and sustainable solvents for AA extraction.

Methods

MD simulations utilize the Optimized Potential for Liquid Simulations force field to describe the interactions of AA with hexane, ethanol, and carbon tetrachloride. MD simulations are performed using GROMACS open-source package. Structural properties, such as radial distribution functions and hydrogen bonding, and transport properties, like mean square displacement (MSD), are studied to understand how AA behaves in each solvent. These simulations reveal detailed interactions between AA and the solvents, showing why ethanol works better for extraction.

Context

Molecular docking is vital for structure-based virtual screening and heavily depends on accurate and robust scoring functions. Scoring functions often inadequately account for the breakage of solvent hydrogen bonds, hindering the accuracy of predicting binding energy. Here, we introduce LeScore, a novel scoring function that specifically incorporates the hydrogen bonding penalty (HBP) in an aqueous environment, aiming to penalize unfavorable polar interactions when hydrogen bonds with water are broken but the energy loss is not fully compensated by newly formed protein–ligand interactions. LeScore was optimized for descriptor combinations and subsequently validated using a testing data set, achieving a Pearson correlation coefficient (rp) of 0.53 in the training set and 0.52 in the testing set. To evaluate its screening capability, a subset of the Directory of Useful Decoys: Enhanced (DUD-E) was used. And LeScore achieved an AUC of 0.71 for specific targets, outperforming models without HBP and enhancing the ranking and classification of active compounds. Overall, LeScore provides a robust tool for improving virtual screening, especially in cases where hydrogen bonding is crucial for ligand binding.

Method

LeScore is formulated as a linear combination of descriptors, including van der Waals interactions, hydrogen bond energy, ligand strain energy, and newly integrated HBP. The function was optimized using multiple linear regression (MLR) on the PDBbind 2019 dataset. Evaluation metrics, such as Pearson and Spearman correlation coefficients were utilized to assess the performance of 12 descriptor combinations. Additionally, the study employed datasets from the DUD-E to evaluate LeScore’s ability to distinguish active ligands from decoys across multiple target proteins.

Context

Anthracycline anticancer antibiotics from Streptomyces peucetius show high affinity for nucleobases. This study uses quantum mechanical density functional theory (DFT) to investigate interactions between doxorubicin (DOX) tautomers and the guanine-cytosine (GC) base pair. Intermolecular distances and interaction energies reveal structural relationships and stabilization. Interaction energy studies show that DOX-GC has greater binding affinity and greater stability in the aqueous phase as compared to that in gaseous phase. Interestingly, the tautomer which show greater affinity for GC in the gas phase is different from the one in the aqueous phase. Reduced density gradient (RDG) scatter plots and quantum theory of atoms in molecules (QTAIM) confirm the presence of hydrogen bonds and its strength. Natural bond orbital (NBO) analysis elucidates donor–acceptor orbital interactions. These findings provide an understanding of the intermolecular interactions between DOX tautomers and the GC base pair, which is likely to provide insight into the molecular basis for DOX’s anticancer activity and therapeutic efficacy.

Methods

DFT calculations were performed using the B3LYP functional with a 6-31G(d,p) basis set in the Gaussian 09 package, including solvent effects through the integral equation formalism polarizable continuum model (IEF-PCM). Topological analysis and quantum theory of atoms in molecules (QTAIM) studies were conducted using the Multiwfn program, while non-covalent interactions were analysed using visual molecular dynamics (VMD) software.

Graphical Abstract

Context

This research focuses on the theoretical study of six push–pull molecules composed of conjugated bridges based on porphyrin and metalloporphyrins where the metals used are Fe(II), Co(II), Ni(II), Cu(II), and Zn(II); these bridges are linked at their ends by acceptor groups (–NO₂) and donors (–N(CH₃)₂) at the meso positions of the cycles mentioned before. The CAM–B3LYP, M08HX, and MN15 functionals tend to describe well the systems studied in non-linear optics NLO in addition to the use of the basis set 6–31 +  + G(d,p) which is considered to be the adequate and least expensive basis set. The highest values of the first static hyperpolarizabilities (β_tot) are assigned to the two molecules 2A and 3A; the corresponding values are as follows: β_tot (2A) = 46.43 * 10⁻³⁰ esu and β_tot (3A) = 46.30 * 10⁻³⁰ esu. The highest value of the second static hyperpolarizability (γ_av) is assigned to the molecule 1A5 with a value of 9.49 * 10⁻³⁵ esu. The highest values of the first dynamic hyperpolarizabilities (({beta }_||^{lambda }(-2omega ;omega ,omega ))) and second dynamics hyperpolarizabilities (({gamma }_||^{lambda }(-2omega ;omega ,omega ,0))) are attributed to the molecule 2A; the corresponding values are as follows:({beta }_||^{lambda }(-2omega ;omega ,omega ))) (2A) = 8229.88 * 10⁻³⁰ esu and ({gamma }_||^{lambda }(-2omega ;omega ,omega ,0)) (2A) =  − 10,943.10 * 10⁻³⁵ esu. The molecules 1A2 and 1A5 based on the metals Co(II) and Zn(II), respectively, are the most profitable in second- and third-order dynamic NLOs. The specific solvents for the six molecules are acetone, acetonitrile, and dichloromethane. The maximum wavelengths recorded for all molecules in vacuum and in combination with all solvents are in the range 355.75 to 397.15 nm and absorb in the UV transparency.

Method

All calculations were performed with the Gaussian 16 program. The dispersion functional B3LYP–D3 is used for optimizations. Electronic parameters were calculated using the following functionals: CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, M08-HX, M06-2X, MN12SX, and MN15. The basis set studied for the whole manuscript is 6–31 +  + G(d,p) for non-metallic atoms and LanL2DZ for transition metals. Other basis sets studied include 6–31G(d,p), 6–31 +  + G(d,p), cc–pVDZ, AUG–cc–pVDZ, 6–311G(d,p), 6–311 +  + G(d,p), cc–pVTZ, and AUG–cc–pVTZ. The natural bond orbital (NBO) method was also considered. The implicit solvation models studied are solvation models based on density (SMD) and conductor polarizable continuum model (C–PCM). The time-dependent density functional (TD-DFT) approach was also studied.

Graphical Abstract

Context

This article suggests that the olfaction process can be simplified to an adsorption mechanism by utilizing the Machilis hrabei olfactory receptor MhOR5 as a biological adsorbent. The odorant molecules such as geosmin, linalool, and o-cresol were used as adsorbates. The aim of the present study is to provide new insights into the docking process of the tested odorants on MhOR5 using numerical simulation via an advanced statistical physics model to fit the corresponding response curves.

Methods

In the present work, an advanced theory based on statistical physics formalism is applied to understand and analyze the experimental dose-olfactory response curves of three odorant molecules on the Machilis hrabei olfactory receptor. Indeed, a monolayer model with four energy levels developed using the grand canonical ensemble was successfully applied to analyze the adsorption mechanism of geosmin, linalool, and o-cresol on MhOR5 through the interpretation of the different fitted parameters. Stereographically, it was found that geosmin, linalool, and o-cresol molecules were docked on MhOR5 binding pockets with nonparallel orientations (multi-molecular process) since all the numbers of the studied odorants adsorbed on one binding pocket were superior to 1. Energetically, the values of the molar adsorption energies ΔE_i (i = 1, 2, 3, and 4) related to the four types of binding pockets (varied between 6.18 and 18.43 kJ/mol) demonstrated that the three odorants were exothermically and physically docked on MhOR5 since all values of ΔE_i were positive and inferior to 40 kJ/mol. The proposed model may also be applied to calculate and interpret two thermodynamic potentials: the internal energy E_int and adsorption entropy S_a. Additionally, the physicochemical parameters may be used to stereographically and energetically characterize the heterogeneity of the insect MhOR5 surface. The docking simulation results demonstrated that the estimated binding affinities or energy score values (varied between 6.27 and 18.40 kJ/mol) were slightly similar to molar adsorption energy values and were included in the adsorption energy bands of the three adsorption energy distributions (AEDs).

Context

Zinc sulfide (ZnS) and (zinc telluride (ZnTe) are binary semiconductor compounds that exhibit excellent optical and electrical properties, and the mechanical behavior at the nanoscale level is crucial for their potential application. Nevertheless, experimental data are scarce regarding the mechanical characteristics of ZnS and ZnTe. For better applications of ZnS and ZnTe-based devices, it is crucial to understand, design, and control their mechanical properties. In this work, we have examined the indentation on (001), (110), and (111) planes of ZnS and ZnTe at the nanometric scale, along with an exploration of the associated plastic deformation utilizing molecular dynamics techniques. We compared and analyzed the loading curves, dislocation distribution evolutions, atomic displacement vectors, and stress distributions of the two materials under indentation.

Method

The indentation simulations were performed in molecular dynamics software LAMMPS, using the Stillinger–Weber potential model. Visual analysis is done using OVITO software. A spherical indenter with a diameter of 12.0 nm moves down to the substrates for a depth of 5.0 nm at a steady speed of 0.01 nm/ps. Distinct anisotropic characteristics can be detected from the loading forces, dislocation distributions, atomic displacement vectors, and stress distributions. The dislocation distributions exhibit fourfold, twofold, and threefold symmetries in the case of (001), (110), and (111) planes. Results indicate that stress underneath the indenter should prompt the atoms to move, subsequently leading to the formation, propagation, and distribution of the dislocations. Another notable characteristic is the emergence of prismatic loops in ZnS. The findings offering valuable data for future utilization considerations.