Journal of Molecular Modeling最新文献

Context: Flaviviruses cause severe encephalitic or hemorrhagic diseases in humans. Its members, Kyasanur forest disease virus (KFDV) and Alkhumra hemorrhagic fever virus (ALKV), cause hemorrhagic fever and are prevalent in India and Saudi Arabia, respectively, while the tick-borne encephalitis virus (TBEV) causes a dangerous encephalitic infection in Europe and Asia. However, little information is available about the targets of immune responses for these deadly viruses. Here, we predict potential antigenic peptide epitopes of viral envelope protein for inducing a cell-mediated and humoral immune response.

Methods: Using the Immune Epitope Database and Analysis Resource (IEDB-AR), we identified 13 MHC-I and two MHC-II dominant conserved epitopes in KFDV and ALKV and six MHC-I and three MHC-II epitopes in TBEV envelope proteins. Parallelly, we also predicted B-cell linear and discontinuous envelope protein epitopes for these viruses. Interestingly, the epitopes are conserved in all three viral envelope proteins. Further, the discontinuous epitopes are structurally compared with the available DENV, ZIKV, WNV, TBEV, and LIV envelope protein antibody structures. Overall structural comparison analyses highlight (i) lateral ridge epitope in the ED-III domain of E protein, and (ii) envelope dimer epitope (EDE) could be targeted for developing potent vaccine candidates as well as therapeutic antibody production. Moreover, existing structural and biochemical functions of the same epitopes in homologous viruses are predicted to have a reduced antibody-dependent enhancement (ADE) effect on flaviviral infection.

Context: Hydrazones have been studied for a myriad of chemical and physiochemical properties, such as sensors, chelators and numerous biological activities. Experimental data indicates that hydrazones are unstable under cathodic potentials irrespective of the solvent. The single electron reduction of hydrazones to produce radical anions result in unstable species that cleaves at the N-N bond in a heterolytic manner. The literature has proposed a mechanism favouring the radical on the imine moiety, however in this study DFT calculations suggest the radical on the amine product is more likely upon bond cleavage. This has implications on electrochemical mechanisms, and the active molecule in biological studies viz the method of delivery to target areas.

Methods: Density functional theory calculations were carried out using the GAMESS software package. The structures were optimized in the gas phase (B3LYP/6-31G(d,p)) as indicated by the absence of imaginary frequencies in the Hessian, and in CH₃CN (B3LYP/6-31G(d,p)/SMD) with the Pople polarization functions. As a comparison, selected pathways were fully optimized using PBE0/6-31G(d,p) and PBE0/6-31G(d,p)/SMD for gas phase and CH₃CN, respectively with the Pople polarization functions. The values were not significantly different (< 5% difference). As such only the B3LYP is evaluation is discussed.

Context: Computational drug repurposing methods have been continuously developed in recent years to alleviate the high costs associated with drug development. As drug targets or the products of disease-related genes, proteins play an important role in drug repurposing. Although the potential has been demonstrated, heterogeneous graphs with proteins as independent nodes have yet to be studied, where extracting high-quality protein features from heterogeneous graphs poses a significant challenge. A novel drug repurposing model based on the feature construction of multi-layer ensemble (DRML-Ensemble) is proposed in this study. The performance of DRML-Ensemble, as evaluated on publicly available datasets, achieves an AUPR value of 0.93 and an AUROC value of 0.92, surpassing those of existing state-of-the-art methods. Additionally, DRML-Ensemble demonstrates its notable ability for drug repurposing in Alzheimer's disease.

Methods: DRML-Ensemble is primarily composed of multiple layers of heterogeneous graph feature construction (HGFC). Each HGFC can extract protein features by leveraging the relationships between drugs, diseases, and proteins. These protein features are then utilized in subsequent layers to build drug and disease features, facilitating drug repurposing. By stacking multiple layers, optimal protein features can be obtained from the heterogeneous graph, consequently improving the accuracy of drug repurposing. However, an excessive· stacking of layers usually affect the model's training process, for example, causing problems such as overfitting; a multi-layer ensemble prediction module is designed to further improve the model's performance.

Context: Thermoplastic elastomer styrene-ethylene-butylene-styrene block copolymer (SEBS) has excellent mechanical properties and aging resistance, so it has good application prospects in thermoplastic solid propellants. The selection of plasticizer is one of the keys to the formulation design of thermoplastic solid propellant. The compatibility of the plasticizer with the polymer determines the plasticizer's ability to plasticize the polymer's molecular chain segments. Herein, the compatibility of four plasticizers with SEBS was investigated, and the results declared that the order of compatibility between SEBS and the four plasticizers is SEBS/WO > SEBS/DOS > SEBS/DEP > SEBS/TA.

Methods: Physical compatibility of SEBS binder with plasticizer triacetin (TA), diethyl phthalate (DEP), dioctyl sebacate (DOS), and 26# industrial white oil (WO) was simulated using molecular dynamics (MD) method via Materials Studio 8.0, and the simulation results were verified experimentally. The results showed that the compatibility of SEBS with these plasticizers can be comprehensively evaluated by analyzing solubility parameters, radial distribution functions, and blend miscibility simulations.

Context: To investigate the influence of two typical nitro explosives, 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) and nitroguanidine (NQ), on the thermal decomposition mechanism of 3,4-Bis (3-nitrofurazan-4-yl) furoxan (DNTF). The study simulates the dynamical behavior of the DNTF/DNTF, DNTF/NQ, and DNTF/LLM-105 systems at different temperatures. We analyzed their thermal decomposition mechanisms through decomposition processes, reaction paths, and product evolution. Building on our analysis of thermal decomposition mechanisms, we found that introducing these two components (NQ and LLM-105) significantly alters the decomposition mechanism of DNTF. This introduction promotes the breakdown of DNTF molecules, modifies the thermal decomposition processes, and consequently changes the reaction pathways. In the DNTF/DNTF system, the product C₃N₄O₄ remains stable, while the N-O bond in NO₂ undergoes repeated breaking and formation, ultimately converting into NO. Conversely, in the mixed system, NO₂ persists throughout the simulation, while the reaction product C₃N₄O₄ undergoes additional reactions and eventually disappears at higher temperatures. This behavioral disparity determines distinct decomposition mechanisms between the mixed and pure DNTF systems.

Methods: To investigate the thermal decomposition mechanisms of DNTF/LLM-105 and DNTF/NQ composite energetic materials, the first-principles calculation software CP2K is used. The GFNI-xTB (Geometry, Frequency, and Noncovalent, eXtended Tight Binding) program within CP2K is employed. This method provides a powerful tool for performing calculations with arbitrary accuracy on complex systems.

Context: Corrosion, the degradation of materials due to chemical reactions with their environment presents significant challenges both economically and environmentally. It affects various industries, including construction, transportation, and manufacturing, leading to equipment failures, safety hazards, and increased maintenance costs. Coumarin derivatives have shown promise due to their inherent chemical properties and potential for biodegradability. In this study, a series of the coumarin derivatives were examined in silico to reveal their potential corrosion inhibition properties toward the Fe(110) and Cu(111) surfaces. The compounds investigated include coumarin (2H-chromen-2-one, 1), furanocoumarin (7H-furo[3,2-g]chromen-7-one, 2), dihydrofurano coumarin (2,3-dihydro-7H-furo[3,2-g]chromen-7-one, 3), pyrano coumarin-linear type (8,8-dimethyl-2H,8H-pyrano[3,2-g]chromen-2-one, 4), pyrano coumarin-angular type (8,8-dimethyl-2H,8H-pyrano[2,3-f]chromen-2-one, 5), bicoumarin (3,3'-methylenebis(2H-chromen-2-one), 6), and phenyl coumarin (4-phenyl-2H-chromen-2-one, 7). The findings suggest that the bicoumarin derivative 6 exhibits the lowest adsorption energy with the Fe(110) surface, while the same energy absolute value is about two times lower for the Cu(111) surface. This is due to the formation of a planar configuration of a molecule of 6 on the metal surfaces with the participation of both coumarin fragments upon interacting with the Fe(110) surface, while one coumarin fragment interacts with the Cu(111) surface.

Methods: Density functional theory (DFT) calculations were employed to study the electronic properties of the coumarin derivatives. The specific computational method used was B3LYP, a hybrid functional that combines with the 6-311 +  + G(d,p) basis set. Each coumarin derivative was first subjected to a geometry optimization to find the most stable molecular structure. Electronic properties, dipole moments, and molecular electrostatic potential surfaces were calculated. The Monte Carlo simulations were used to model the adsorption behavior of the coumarin derivatives on metal surfaces, namely, Fe(110) and Cu(111). These simulations allowed to visualize interaction of the studied molecules with the metal surfaces, which is crucial for their function as corrosion inhibitors. The present study provides a comprehensive understanding of the corrosion inhibition potential of the applied coumarin derivatives. The insights gained from these methods can inform the development of effective, sustainable corrosion inhibitors that are both environmentally friendly and highly efficient.

Context: Amino acids are a highly effective and environmentally friendly adsorbent for SO₂. However, there has been no comprehensive study of the binding modes between amino acids and SO₂ at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO₂ are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06 kcal/mol for Asp, - 12.43 to - 1.63 kcal/mol for Lys, and - 7.42 to - 0.60 kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode.

Methods: Amino acids and complexes of amino acids with SO₂ were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO₂.

Context: The electron localization is a concept that allows scientists to better understand the physical and chemical properties of electronic systems. It is associated with the propensity of electron pairs with opposite spins to accumulate as well as with their response to external perturbations. This paper contains a detailed description of the design and implementation of the program KLD, which was primarily developed in our research group to elucidate electron localization in molecular systems by evaluating the information content of electron-pair density functions. KLD employs two information-based functions as a real space measure of the Fermi and Coulomb holes for same-spin electrons and shows a better resolution as compared to other methods (i.e., ELF). Information about the acceleration of the code is also included in the present work, being noticeable the reduction of wall-time calculation and the error calculation between versions.

Methods: KLD was designed to be easy to use, extend, and maintain; thus, many principles of modern software development, extensive testing, and package management were adopted. The latest version of the KLD program was created utilizing the Compute Unified Device Architecture (CUDA) version, which allows it to use the computational capacity of NVIDIA Graphics Processing Units (GPUs) for processing purposes. The electron-pair conditional density was calculated from the canonical molecular orbitals obtained at the HF/6-31G(2df,p) level, or alternatively the natural orbitals in the case of explicit correlated wavefunctions computed at the MP2/6-31G(2df,p)//HF/6-31G(2df,p) level.

Context: To explore the influence of the external electric field (EEF) on ε-CL-20. The molecular structure, frontier molecular orbitals (FMOs), global reactivity parameters (GRP), surface electrostatic potential, nitro charge, and UV-Vis spectra of ε-CL-20 under EEF were studied using density functional theory (DFT). The calculation results show that the electric field applied along N16-N24 has a significant effect on the structure of ε-CL-20. With an increase in the positive EEF, the bond length of the initiating bond decreases, and the bond order and bond dissociation energy increase, which increases the thermal stability of ε-CL-20 to a certain extent. In addition, with an increase in the positive EEF intensity, the LUMO migrates from both sides of the positive electric field to one side of the nitro group, and the HOMO migrates from the skeleton to the nitro group. It is worth noting that in the negative EEF, when the electric field strength changed from 0 to 0.016 a.u., the negative charge of the total nitro group gradually decreased. When the electric field strength becomes 0.02 a.u., the negative charge of the total nitro group suddenly increases, and ε-CL-20 is significantly polarized. When the electric field strength is sufficiently strong, the occupied and unoccupied orbitals of the ε-CL-20 molecule change, resulting in a change in the energy level difference between the occupied and unoccupied orbitals, which further excites the corresponding excited state, resulting in a new UV-Vis absorption peak.

Methods: Based on the density functional theory (DFT), the structural optimization and energy calculation were carried out by using B3LYP/6-311 + G(d, p) and B3LYP/def2-TZVPP methods, respectively. After optimization convergence, vibration analysis was performed without imaginary frequencies to obtain stable configurations. Then the molecular structure, frontier molecular orbitals (FMOs), global reactivity parameters (GRP), surface electrostatic potential, nitro charge, and UV-Vis spectra were analyzed.

Context

Single-wall carbon nanotubes (SWCNT) dispersed in water with the help of sodium dodecyl sulfate (SDS) surfactants exhibit a temperature dependent near infrared (NIR) exciton spectrum. Due to their biocompatibility and NIR spectrum falling within the transparent window for biological tissue, SWCNTs hold potential for sensing temperature inside cells. Here, we seek to elucidate the mechanism responsible for this temperature dependence, focusing on changes in the water coverage of the SWCNT as the surfactant structure changes with temperature. We compare optical absorption spectra in the UV–Vis-IR range and fully atomistic molecular dynamics (MD) simulations. The observed temperature dependence of the spectra for various SWCNTs may be attributed to changes in the dielectric environment and its impact on excitons. MD simulations reveal that the adsorbed SDS molecules effectively shield the SWCNT, with ~ 70% of water molecules removed from the first two adlayers; this coverage shows a modest temperature dependence. Although we are not able to directly demonstrate how this influences the NIR spectrum, this represents a potential pathway given the strong influence of the water environment on the excitons in SWCNTs.

Methods

Optical absorption measurements were carried out in the UV–Vis-NIR range using a Varian Cary 5000 spectrophotometer in a temperature-controlled environment. PeakFit™ v. 4.06 was used as peak-fitting program in the spectral range 900–1400 nm (890–1380 meV) as a function of the temperature. Fully atomistic molecular dynamics simulations were conducted using the NAMD2 package. The CHARMM force field comprising two-body bond stretching, three-body angle deformation, four-body dihedral angle deformation, and nonbonded interactions (electrostatic and Lennard–Jones 6–16 potentials) was employed.