Journal of Molecular Modeling最新文献

Context

This article mainly studies three isomers of C₅H₃N₇O₁₀, namely 5-methyl-3,4-dinitro-1- (trinitromethyl) -1H pyrazole (1), 4-methyl-3,5-dinitro-1- (trinitromethyl) -1H pyrazole (2), and 3,5-bis (dinitromethyl) -4-nitro-1H-pyrazole (3). These three substances are excellent candidates for energetic materials, but their properties under external electric fields (EEF) have not been studied. Therefore, this article studied the properties of three isomers under EEF using density functional theory (DFT), and conducted statistical analysis on the obtained data, including the molecular structure, frontier molecular orbitals, surface electrostatic potential, and nitrate charge of the three isomers. The results showed that applying EEF to the trigger bonds of 1 and 2 increased bond length, leading to a decrease in material stability. The change in bond length induced by 3 was relatively stable, and the results obtained from calculating the nitro charge were consistent with the bond length results. When an EEF is applied to three substances, the polarization degree of the molecules of the three substances increases. It is worth mentioning that the polarization degree of the molecules under the influence of a negative EEF is greater than that of a positive EEF.

Methods

Using density functional theory, the B3LYP/6–311 + G (d, p) method was employed for structural optimization. After optimizing convergence, ensure that there are no imaginary frequencies to obtain a stable structure. Wave function analysis was performed using Multiwfn 3.8 and VMD 1.9.3. The EEF strength ranged from − 0.02 a.u. to 0.02 a.u., with a growth gradient of 0.005 a.u.

Context

Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions. Density functional theory (DFT) served as the computation framework for all calculations, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvation effects were incorporated through the implementation of the polarizable continuum model (PCM) simulating an aqueous solvent environment. The geometries of the five most stable complexes show exclusively p-p interactions among the aromatic moieties in a displaced parallel plane stacking arrangement with interplanar heights and displacements in the range of 3.22–3.62 Å and 0.50–0.63 Å, respectively, at ωB97XD level. The calculated total energies and binding energies indicate two stabilizing p-p interactions: lumiflavin-tyrosine and lumiflavin-tryptophan, with the later stronger for the more stable complexes by 2 kcal mol⁻¹. The complexes are less entropically favored than the independent molecules as verified by the positive association free Gibbs energies with LC-ωPBE and nearly zero with ωB97XD. Orbital analysis indicates a smaller HOMO–LUMO gap for complexes compared to the individual compounds suggesting a charge transfer component to the interaction. Moreover, the HOMO is localized on tryptophan and HOMO-1 on tyrosine, consistent with the strength of the respective interactions with lumiflavin.

Methods

The initial geometry was based on the atom coordinates of the bonding tryptophan-riboflavin-tyrosine region in the protein crystallographic data with the ribityl tail being discarded, leading to a model complex: tryptophan-lumiflavin-tyrosine. The initial conformational search using the Amber force field within the Gabedit led to 30 unique conformations. The subsequent calculations, energy optimization and orbital analysis, were performed in Guassian16 at density functional theory (DFT) level, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6–311+ +g** basis set. The solvent, water, was accounted for using the polarized continuum model (PCM).

Context

Based on the transition state theory, a molecular diffusion model in the narrow channels of Brewsterite zeolite was established. In this model, the molecular interaction at the potential barrier was simplified to only consider the repulsive potential, so that the analytical relationship between the diffusion coefficient and the temperature and the Lennard–Jones interaction parameter was derived. We used the molecular dynamics method to simulate the diffusion of four molecules, CF₄, CH₄, Ar, and Ne, in Brewsterite zeolite and evaluated the rationality of the model. The results show that the three molecules CF₄, CH₄, and Ar meet the predictions of the model, while the Ne molecule does not. At the same time, by analyzing the trend of the diffusion coefficient with the load, we further explain the reason for this difference. In short, this study reveals the diffusion mechanism of molecules in the narrow pores of Brewsterite zeolite. This provides new ideas for optimizing the performance of zeolite materials and applying them to catalysis and separation processes.

Methods

The simulations were carried out with Refson’s MOLDY code in the NVT ensemble. The short-range Lennard–Jones forces were calculated with the link cell method. A Nose–Hoover thermostat was used to realize the thermal equilibrium state of the samples. In the simulation, the time steps were 1 fs and the total simulation time was 51 ns. The initial temperature was set to 300 K.

Context

Protein secondary structure prediction is essential for understanding protein function and characteristics and can also facilitate drug discovery. Traditional methods for experimentally determining protein structures are both time-consuming and costly. Computational biology offers a viable alternative by predicting protein structures from their sequences. Protein secondary structure is defined by the local spatial arrangement of the protein backbone, resulting from hydrogen bonds between amino acids.

Methods

In this study, we introduce TransConv, a model that combines transformer models with convolutional blocks to predict protein secondary structures from amino acid sequences. Transformer models are effective at capturing long-range dependencies through self-attention mechanisms. We integrate convolutional blocks into the transformer architecture to improve the detection of important local features. This hybrid model captures both long-range interactions and local features, leading to more accurate predictions of protein secondary structures, thus offering an efficient solution for this critical task. The experimental outcomes on the benchmark datasets depict the superiority of the proposed approach over the state-of-the-art (SOTA) models in the literature.

Context

There has been growing interest in amino acid ionic liquids because of their low-cost synthesis and superior biodegradability and biocompatibility compared to traditional ionic liquids. In this study, we have investigated the structure and dynamics of three ionic liquids consisting of N-butyl N-methyl piperidinium [Pip] cation with amino acid (lysine [Lys], histidine [His], and arginine [Arg]) anions. The radial distribution functions, the spatial distribution functions, and the coordination numbers have been used to analyze the structure in the bulk phase. The time-correlation functions for hydrogen bonds, ion pairs, and ion cage formation have been calculated to analyze the dynamic properties. The hydrogen bonds found between the ion pairs are mostly electrostatically dominant with moderate to weaker strengths. The [Pip][His] system showed the strongest interaction energy between the ion pairs, while the [Pip][Lys] system demonstrated faster dynamics consistent with its higher diffusion and ion conductivity.

Method

The density functional theory at M06-2X/6–311 + + G(d,p) level was employed for geometry optimization and wave function calculations. The theory of atoms-in-molecule was used for the topological analysis of electron density. The classical molecular dynamics simulations with OPLS-AA force field were employed to study the dynamics of the systems.

Graphical Abstract

Context

Exploration for renewable and environmentally friendly energy sources has become a major challenge to overcome the depletion of fossil fuels and their environmental hazards. Therefore, solar cell technology, as an alternative solution, has attracted the interest of many researchers. In the present work, the Cs₂XInBr₆ (X = Cu or Ag) compounds as lead-free halide perovskites have been studied due to their direct energy gap in the range of solar energy, thermodynamic stability, low effective mass of electrons, and high absorption coefficient. The calculated optical gap and static refractive index about 1.35 (1.51) eV and 1.47 (1.41), respectively using BS (GW) approach for the Cs₂AgInBr₆ compound were in good agreement with experimental data. The threshold absorption was estimated about 1.03 (1.22) using BS (GW) approach (which correspond to the optical gap) for the Cs₂CuInBr₆ compound. Both compounds have small (< 0.35) reflection coefficient in the infrared, visible and UV regions and high absorption coefficient (10⁵ cm⁻¹). In the infrared and visible regions, the absorption coefficient of the Cu-based compound is much larger than the other, therefore this material can be more useful as an absorbent layer in solar cells (SC). Due to the fact that the spectrum of sunlight that reaches the earth includes 47% infrared, 46% visible and 7% ultraviolet, the Cu-based compound is more efficient for the SCs and the Cs₂AgInBr₆ compound is more suitable in the design of detectors.

Methods

The electronic, structural and optical properties of Cs₂XInBr₆ (X = Cu or Ag) compounds have been calculated and analyzed using the Abinit computational package based on density functional theory (DFT). The ultrasoft pseudopotentials within the framework of the generalized gradient approximation (GGA) are adopted for the electron exchange–correlation potential and are employed for the calculations of the electronic, and optical properties as well. The wave functions have expanded on a plane-wave basis set to cutoff energy of 950 eV and 64 k-points with a k-mesh of 4 × 4 × 4 are considered for the integrations over the Brillouin zone. The behavior of the real and imaginary parts of the dielectric function and other optical quantities have been simulated using both RPA-GW (random phase approximation with GW energies) and Bethe–Salpeter formalisms.

Context

Nitrocellulose, widely used in energetic materials, is prone to thermal and chemical degradation, compromising safety and performance. Stabilizers are molecules used in the composition of nitrocellulose-based propellants to inhibit the autocatalytic degradation process that produces nitrous gases and free nitric acids. Curcumin, (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione, known for its antioxidant properties and a potential green stabilizer, was investigated using Density Functional Theory (DFT) focusing on its interaction with nitrogen dioxide. Two mechanisms were analyzed: aromatic ring nitration and free radical formation. The results indicate that nitration of the aromatic ring of curcumin and the formation of a curcumin-based free radical are viable. The computed Gibbs free activation energy (∆^‡G°) and the activation enthalpy (∆^‡H°) for two different temperatures, 298.15 K (room temperature) and 363.15 K (typical temperature in aging tests), are respectively 43.64 kcal/mol and 44.78 kcal/mol for the first reaction, and 31.54 kcal/mol and 35.31 kcal/mol for the second. The radical-based mechanism favors improved kinetics. These findings demonstrate curcumin’s potential as an effective stabilizer, providing comparable performance to traditional compounds with lower environmental impact.

Methods

DFT calculations were carried out using Gaussian 09 and Orca 5.0.1 packages. The ωB97M-V, B3LYP, and M062X functionals were employed with the 6–311 + G(d) and 6-311G(d) basis sets. Solvent effects were modeled using the Conductor-like Polarizable Continuum Model (CPCM) and Solvation Model based on Density (SMD) continuum solvent models. Thermochemical data were computed using the same levels of calculation.

Context

In this work, a comparative study on the catalytic conversion of 5-hydroxymethyl furfural (HMF) to 2,5-bis(hydroxymethyl)furan (BHMF) on precious Pd(111) and nonprecious Cu(111) was systematically performed. On the basis of the calculated activation energy (E_a) and reaction energy (E_r), the optimal energy path for the hydrogenation of HMF (F-CHO) into BHMF (F-CH₂OH) on Pd(111) is as follows: F-CHO + 2H → F-CHOH + H → F-CH₂OH; the minimum reaction path on Cu(111) is F-CHO + 2H → F-CH₂O + H → F-CH₂OH. On Cu(111), the formation of F-CH₂OH from F-CH₂O hydrogenation is the rate-determining step because it has the highest reaction energy barrier and the smallest rate constant. The comparison of HMF hydrogenation on Pd(111) and Cu(111) reveals their inherent differences in selectivity, mainly due to the different adsorption configurations of HMF and BHMF, and it was concluded that the nonprecious Cu(111) is a promising hydrogenation catalyst for the production of BHMF from the hydrogenation of HMF.

Methods

All plane-wave DFT calculations were performed via the Vienna ab initio simulation package (VASP). The exchange and correlation energies were computed via the generalized gradient approximation (GGA) of the Perdew, Burke, and Ernzerhof (PBE) functional with the projector augmented wave (PAW) method.

Context

Dopamine (beta )-monooxygenase (D(beta )M) is an essential enzyme in the organism that regioselectively converts dopamine into R-norepinephrine, the key step of the reaction, studied in this paper, is a hydrogen atom transfer (HAT) from dopamine to a superoxo complex on D(beta )M, forming a hydroperoxo intermediate and dopamine radical. It was found that the formation of a hydrogen bond between dopamine and the D(beta )M catalyst strengthens the substrate-enzyme interaction and facilitates the HAT which takes place selectively to give the desired enantiomeric form of the product. Six reactions leading to the hydroperoxo intermediate were analyzed in detail using theoretical and computational tools in order to identify the most probable reaction mechanism. The reaction force analysis has been used to demonstrate that the nature of the activation energy is mostly structural and largely due to the initial approach of species in order to get closer to each other to facilitate the hydrogen abstraction. On the other hand, the reaction electronic flux revealed that electronic activity driving the reactions is triggered by polarization effects and, in the most probable reaction among the six studied, it takes place in a concerted and non-spontaneous way. Chemical events driving the reaction have been identified and the energy absorbed or delivered by each one was quantified in detail.

Methods

The dopamine and a computational model of the copper superoxo complex on D(beta )M were optimized at B3LYP-D3(BJ)/6-311 G(d,p) level theory in the Gaussian 16 software package. Optimization and IRC calculations were performed in the gas phase and through the PCM solvation model to mimic the protein medium. Non-covalent interactions were plotted using the NCI-plot software.

Graphical abstract

The interaction of dopamine with copper superoxo complex on D(beta )M is studied in order to characterize the mechanism of the hydrogen atom transfer step in the conversion of dopamine into norepinephrine.

Context

The analysis of the changes in the electronic structure along intrinsic reaction coordinate (IRC) paths for model reactions: (i) ethylene + butadiene cycloaddition, (ii) prototype SN2 reaction Cl⁻ + CH3Cl, (iii) HCN/CNH isomerization assisted by water, (iv) CO + HF → C(O)HF was performed, in terms of changes in the deformation density (Δr) and the deformation of MEP (ΔMEP). The main goal was to further examine the utility of the ΔMEP as a descriptor of chemical bonding, and to compare the pictures resulting from Δr and ΔMEP. Both approaches clearly show that the main changes in the electronic structure occur in the TS region. The ΔMEP picture is fully consistent with that based on Δρ for the reactions of the neutral species leading to the neutral products without large charge transfer between the fragments. In the case of reactions with large electron density displacements, the ΔMEP picture is dominated by charge transfer leading to more clear indication of charge shifts than the analysis of Δr.

Methods

All the calculations were performed using the ADF package. The Becke–Perdew exchange–correlation functional was used with the Grimme’s dispersion correction (D3 version) with Becke-Johnson damping. The Slater TZP basis sets defined within the ADF program were applied. For the analysed reactions, the stationary points were determined and verified by frequency calculations, and the IRC was determined. Further analysis was performed for the structures of reactants, TS, products, and the points corresponding to the minimum and maximum of the reaction force. For each point, two fragments, A and B, corresponding to the reactants were considered. The deformation density was calculated as the difference between the electron density of the system AB and the sum of densities of A and B, (Delta rho left(rright)= {rho }^{AB}left(rright)-{rho }^{A}left(rright){-rho }^{B}left(rright),) with the same fragment definition as in the ETS-NOCV method. Correspondingly, deformation in MEP was determined as (Delta Vleft(rright)={V}^{AB}left(rright)- {V}^{A}left(rright)- {V}^{B}left(rright)).