Journal of Molecular Modeling最新文献

Context

Alzheimer’s disease (AD) is the leading cause of dementia around the world, totaling about 55 million cases, with an estimated growth to 74.7 million cases in 2030, which makes its treatment widely desired. Several studies and strategies are being developed considering the main theories regarding its origin since it is not yet fully understood. Among these strategies, the 5-HT₆ receptor antagonism emerges as an auspicious and viable symptomatic treatment approach for AD. The 5-HT₆ receptor belongs to the G protein-coupled receptor (GPCR) family and is closely implicated in memory loss processes. As a serotonin receptor, it plays an important role in cognitive function. Consequently, targeting this receptor presents a compelling therapeutic opportunity. By employing antagonists to block its activity, the 5-HT₆ receptor’s functions can be effectively modulated, leading to potential improvements in cognition and memory.

Methods

Addressing this challenge, our research explored a promising avenue in drug discovery for AD, employing Artificial Neural Networks–Quantitative Structure-Activity Relationship (ANN-QSAR) models. These models have demonstrated great potential in predicting the biological activity of compounds based on their molecular structures. By harnessing the capabilities of machine learning and computational chemistry, we aimed to create a systematic approach for analyzing and forecasting the activity of potential drug candidates, thus streamlining the drug discovery process. We assembled a diverse set of compounds targeting this receptor and utilized density functional theory (DFT) calculations to extract essential molecular descriptors, effectively representing the structural features of the compounds. Subsequently, these molecular descriptors served as input for training the ANN-QSAR models alongside corresponding biological activity data, enabling us to predict the potential efficacy of novel compounds as 5-hydroxytryptamine receptor 6 (5-HT₆) antagonists. Through extensive analysis and validation of ANN-QSAR models, we identified eight new promising compounds with therapeutic potential against AD.

Context

The intermolecular interactions of ethyl acetate (EtOAc)-water (H₂O)/ethanol (EtOH) mixtures were investigated using a combination of Raman spectroscopy and quantum chemical calculations. The computational approach was used to analyze the structure of hydrogen-bonded complexes of ethyl acetate with water/ethanol molecules, based on density functional theory (DFT). The calculated frequencies closely matched the experimental Raman values, with differences being under 4%. Experimental data show that when the concentrations of ethyl acetate in the ethyl acetate/water/ethanol solutions were reduced, almost all Raman spectral bands are blue-shifted. The AIM analysis reveals that all the given complexes possess a positive energy density, indicating that the molecules interact electrostatically. The energy and bond length indicate that the methyl group forms relatively weak hydrogen bonds. Analysis indicates that EtOAc forms weak H-bonding C = O∙∙∙H and C-H∙∙∙O, which are recognized as van der Waals interactions. As the amount of ethyl acetate decreases in the complex, the interaction forces also decrease. This could also explain why the bands are blue-shifted. It was discovered that the title complexes’ hydrogen bond energy decreased exponentially as bond length increased.

Methods

The geometries of the molecular complexes were optimized using the Gaussian 09W program and the B3LYP/6–311 +  + G(d,p) set of functions. The potential energy distribution (PED) analysis was performed using VEDA 4.0 software. Raman spectra were drawn using the Origin 8.5 software. The Multiwfn 3.8 software was used to calculate topological parameters of electron density in molecular systems. GaussView 6.0 and Visual Molecular Dynamics (VMD) 1.9.3 tools were used to visualize all computational results.

Graphical Abstract

Context

1,1- and 1,2-ethenedithiol are elusive systems that could potentially exist in interstellar space, similar to analogous diols. In this paper, we investigate the structure, stability, and bonding characteristics of these compounds as well as the ions produced by protonation, deprotonation, or simple ionization processes. 1,2-ethenedithiol has two isomers, Z and E, with the most stable conformer being syn-anti for the Z isomer and anti-anti for the E isomer. However, the energy gaps between the different conformers are never larger than 6 kJ·mol⁻¹. For 1,1-ethenedithiol, the global minimum is the syn-anti conformer. The vertical and adiabatic ionization processes as well as the intrinsic basicities and acidities of these families of compounds were analyzed and compared with those of the corresponding diols previously reported in the literature. This comparison revealed not only the numerical differences in these thermodynamic properties but also distinct trends between the two families of compounds.

Methods

State-of-the-art G4 ab initio calculations were employed to calculate the structures and total energies of the systems under investigation. The QTAIM, ELF, and NBO approaches were used to analyze the electron density of all the neutral and charged systems included in our study. Van der Waals contributions, when relevant, were analyzed by locating regions of low reduced density gradient(s) using the NCIPLOT approach.

Graphical Abstract

Context

The exploration of CL-20 eutectic has been a subject of fervent interest within the realm of high-energy material modification. Through the utilization of density functional and molecular dynamics methods, an investigation into the characteristics of hexanitrohexaazaisowurtzitane (CL-20)/4,4′,5,5′-tetranitro-2H,2′H-3,3′-bipyrazole (TNBP)within the molar ratio range of 4:1–1:4 was conducted. This inquiry encompassed the scrutiny of molecular interaction pathways, attachment force, initiating molecular distance, unified energy concentration, and physical characteristics. Furthermore, the EXPLO-5 was harnessed to prognosticate the explosion features and byproducts of unadulterated CL-20, TNBP, and CL-20/TNBP frameworks. The findings delineate a substantial differentiation in the electrostatic charge distribution on the surface between CL-20 and TNBP particles, signifying the preeminence of intermolecular interactions between disparate entities over those within similar entities, thus intimating the plausibility of the eutectic constitution. Remarkably, the identification of maximal attachment force at a molar ratio of 1:1 suggests the heightened likelihood of eutectic formation, propelled primarily by electrostatic and van der Waals forces. The resultant eutectic explosive evinces intermediate reactivity and exemplary mechanical attributes. Moreover, the detonation achievement of the eutectic with a molar proportion of 1:1 straddles that of CL-20 and TNBP, representing a new type of insensitive high-energy material.

Methods

The testing method employs the Materials Studio software and utilizes the molecular dynamics (MD) method to predict the properties of CL-20/TNBP cocrystals with different ratios and crystal faces. The MD simulation time step is set to 1 fs, and the total MD simulation time is 2 ns. An isothermal-isobaric (NPT) ensemble is used for the 2 ns MD simulation. The COMPASS force field is employed, with the temperature set to 295 K. The prediction of detonation characteristics and products is conducted using the EXPLO-5 software.

Context

We explore the influence of strongly hydrophilic confinement on various properties of water, such as density, enthalpy, potential energy, radial distribution function, entropy, specific heat capacity, structural dynamics, and transition temperatures (freezing and melting temperatures), using monatomic water (mW) model. The properties of water are found to be dependent on confinement and the wall-fluid surface interaction. Hysteresis loops are observed for density, enthalpy, potential energy, and entropy around the transition temperatures, while the size of hysteresis loops varies with confinement and surface interaction. In smaller pore sizes (H ≤ 20), the solid phase displays a higher density compared to the liquid phase, which is unconventional behavior compared to bulk water systems due to the pronounced hydrophilic properties of the confinement surface. Specific heat capacity exhibits more oscillations in the confined system compared to bulk water, stemming from uneven enthalpy differences across equal temperature intervals. During phase transformation in both heating and quenching processes, there is an abrupt change observed in specific heat capacity. Confinement exerts a notable impact on entropy in the solid phase, but its influence is negligible in the liquid phase. At lower pore sizes (H < 25 Å), there is more fluctuation in freezing temperature for all wall-fluid interactions, which diminishes beyond pore sizes of H > 25 Å. Similarly, more oscillatory behavior is observed in melting temperatures at lower pore sizes (H < 40 Å), which diminishes at higher pore sizes (H > 40 Å). During the quenching process, a sudden jump in the in-plane orientational and tetrahedral order parameters indicates the formation of an ordered phase, specifically a diamond crystalline structure. The percentages of different crystalline structures (cubic diamond, hexagonal diamond, and 2D hexagonal) vary with both the confinement size and the wall-fluid interaction strength.

Methods

Cooling and heating simulations are conducted with the mW water model using LAMMPS for different nanoscale confinement separation sizes ranging from 8.5 to 70 Å within the temperature range of 100–350 K. The water is modeled using two-body and three-body interaction potential (Stillinger–Weber potential) and the confinement is introduced using LJ 9–3 water-wall interaction potential. Entropy is calculated using RDF data obtained from the simulation experiments for each temperature point with increments or decrements of 2.5 K. The transition temperatures are estimated using the specific heat capacity analysis.

Context

Currently, Chagas disease represents an important public health problem affecting more than 8 million people worldwide. The vector of this disease is the Trypanosoma cruzi (Tc) parasite. Our research specifically focuses on the structure and aggregation states of the enzyme aldo-keto reductase of Tc (TcAKR) reported in this parasite. TcAKR belongs to the aldo-keto reductase (AKR) superfamily, enzymes that catalyze redox reactions involved in crucial biological processes. While most AKRs are found in monomeric forms, some have been reported to form dimeric and tetrameric structures. This is the case for some TcAKR. To better understand how TcAKR multimers form and remain stable, we conducted a comprehensive computational analysis using molecular dynamics (MD) simulations. Our approach to elucidating the aggregation states of TcAKR involved two strategies. Initially, we explored the dynamic behaviour of pre-assembled TcAKR dimers. Subsequently, we examined the self-aggregation of eight monomers. This investigation led to the identification of crucial residues that contribute to the stabilization of protein-protein interactions. It was also found that TcAKRs can form stable supramolecular assemblies, with each monomer typically surrounded by three first neighbours. These findings align with experimental reports of tetrameric or more complex supramolecular structures. Our computational studies could guide further experimental investigations aiming at drug development and assist in designing strategies to modulate aggregation.

Method

Atomistic molecular dynamics simulations were carried out. The TcAKR 3D model structure was obtained by homology modelling using the Swiss Model for the TcAKR sequence (GenBank accession no. EU558869). Further, we checked the model with Alphafold2 and found a high degree of similarity between models. Several tools were used to build the dimers including CLUSPRO, GRAMM-Docking, Hdock, and Py-dock. Protein superstructures were built using the PACKMOL package. CHARMM-GUI was used to set up the simulation systems. GROMACS version 2020.5 was used to perform the simulations with the CHARMM36 force field for the protein and ions and the TIP3P model for water. Further analyses were performed using VMD, GROMACS, AMBER tools, MDLovoFit, bio3d, and in-house programs.

Context

The theory of reactivity based on cDFT has been supplemented with the new method of calculating the atomic and local indices. With the use of previously derived relationship of the electron density gradient to the softness kernel and to the linear response function, we deliver theoretical analysis to obtain significant reactivity indices—the electron density derivatives: local softness and local hypersoftness together with the global hyperhardness index and the derivative of the global softness with respect to the number of electrons. The local derivatives have been applied in the calculation of responses of atoms to perturbation by an external potential by the alchemical approach. The vital role of the local softness has been confirmed; the potential role of the hypersoftness has been indicated.

Method

Our original theoretical scheme has been numerically illustrated with the results obtained with electron density calculations with B3LYP method implemented in Gaussian 16 package. The aug-cc-pvqz basis set has been routinely applied, except for the Ca atom (cc-pvqz). Using the pVTZ basis set recommended by Sadlej was necessary for the potassium atom.

Graphical Abstract

Context

The production of bioethanol from renewable raw materials is a decisive factor in the economic development of many countries. However, the complexity of the processes and the numerous experimental variables involved require a deeper understanding of the chemical reactions that take place during bioethanol production to define optimal parameters. Here, we have employed density functional theory–based calculations to investigate the local reactivity of oligomeric systems by considering crystalline and amorphous cellulose models to better understand some details regarding pulp pretreatment processes. Our results evidence a higher chemical susceptibility of amorphous portions of cellulose to chemicals typically employed in acid hydrolysis. Additionally, we observed that glucose monomers coming from cellulose hydrolysis may undergo oxidation, leading to the formation of byproducts such as hydroxymethylfurfural (HMF), acetic acid, formic acid, and levulinic acid. The analysis of local chemical softness indexes indicated that cellulose hydrolysis may be associated with intermediate chemical steps. Finally, we investigated the influence of distinct solvents (dielectric constants) on the local reactivity of the systems, evidencing a relevant role of the solvent dielectric constant for cellulose degradation in glucose.

Methods

Initial three-dimensional structures were constructed. Pre-optimizations were performed in a Hartree–Fock (HF) approach employing the PM7 semi-empirical hamiltonian. The structures were then re-optimized via density functional theory (DFT). The local reactivity study of the systems was conducted through the condensed-to-atoms Fukui indexes (CAFI). Systematic changes of the dielectric constants were also considered in geometry optimization and CAFI calculations to estimate the influence of solvents on the reactivity of the systems.

Context

Looking for novel outstanding performance materials suitable for organic solar cells, we constructed a range of non-fullerene acceptors (NFAs) evolved from the recently synthesized acceptor molecule identified as DICTIF, structured around fluorene core where 2-(2,3-dihydro-3-oxo-1H-inden-1-ylidene) propanedinitrile presented the terminals end-groups. Employing density functional theory (DFT) and time dependent-DFT (TD-DFT) simulations, we have simulated the impact of altering the end groups of DICTIF molecule by five assorted acceptors molecules, for the purpose of exploring their opto-electronic properties and their performance in organic solar cell (OSC) applications. We proved that the designed non-fullerene acceptors provide enhanced efficiency compared to the synthesized molecule, such as planar geometries and narrower energy gap ranging from 1.51 to 1.95 eV. A red shift in absorption was observed for all tailored molecules (λ_max = 583.5–711.4 nm) as compared to the reference molecule (λ_max = 578 nm).Various decisive factors such as frontier molecular orbitals (FMOs), exciton binding energy (EB), absorption maximum (λ_max), open circuit voltage (V_OC), reorganization energies (RE), transition density matrix (TDM), reduced density gradient (RDG), and electron-hole overlap have also been computed for analyzing the performance of NFAs. Low reorganizational energy values facilitate charge mobility which improves the conductivity of all the designed molecules. This study showed that our novel tailored molecules might be suitable candidates for the fabrication of highly efficient photovoltaic materials.

Methods

After testing various hybrid functionals, optimized geometries were assigned using DFT HSEH1PBE/6-31G(d) level of theory. Electronic excitations and absorption spectra were investigated using the TD-DFT MPW1PW91/6-31G(d) level of theory. We ascertained that HSEH1PBE/6-31G(d) level of theory yield the closest calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of the DICTIF to the corresponding experimental ones and that TD-MPW1PW91//6-31G(d) was the most suitable level of theory for exploring electronic excitations and finding the maximum of absorption (λ_max).

Context

The diatomic molecules of potassium (^{varvec{39}}varvec{K}_{varvec{2}}left( varvec{a}^{varvec{3}}varvec{sum }_{varvec{u}}^{varvec{+}}right) ) is widely used in industrial chemicals and alternative energy. Besides that, (^{varvec{39}}varvec{K}_{varvec{2}}left( varvec{a}^{varvec{3}}varvec{sum }_{varvec{u}}^{varvec{+}}right) ) is very useful for researching molecular interactions and energy states, especially in the context of quantum chemistry and spectroscopy. In the present work, a newly proposed diatomic potential model within relativistic and non-relativistic quantum mechanics has been considered, to obtain corresponding energy eigenvalues and related normalized eigenfunctions.

Methods

The Dirac equation has been solved for an arbitrary spin-orbit quantum number (varvec{kappa }) using the path integral technique with the (varvec{q})-deformed generalized Pöschl-Teller potential (varvec{(DGPT)}). By including a Pekeris-type approximation to handle the centrifugal factor, it was possible to obtain the spin and pseudospin-symmetric solution of the relativistic energy eigenvalues and wave equation. To assess the correctness of this work, Maple software was used to present some numerical findings for various values of (varvec{n}) and (varvec{kappa }). With the constraint (varvec{tilde{lambda }}varvec{>}varvec{tilde{eta }+1}), it was shown that in the situation of pseudospin symmetry, only bound states exist with negative energy. In the non-relativistic limits, the non-relativistic ro-vibrational energy expression of the diatomic molecule is derived from the relativistic energy equation under spin symmetry. Under Varshni conditions, both vibrational and ro-vibrational energies of the (^{varvec{39}}varvec{K}_{varvec{2}}left( varvec{a}^{varvec{3}}varvec{sum }_{varvec{u}}^{varvec{+}}right) ) molecule were computed and compared with the (varvec{RKR}) data. The average absolute percentage deviations from the (varvec{RKR}) data obtained for the potassium molecule are (varvec{0.5018%}). This demonstrates that the (varvec{(DGPT)}) model is a very consistent model to study and characterize diatomic molecules.