Theoretical study of potential energetic material PETN/DNTF eutectic explosive based on molecular dynamics method.

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. 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 1fs, and the total MD simulation time is 2ns. An isothermal-isobaric (NPT) ensemble is used for the 2ns MD simulation. The COMPASS force field is employed, with the temperature set to 295K. The prediction of detonation characteristics and products is conducted using the EXPLO-5 software.

HighlightsAccording to the design of the experiment (DoE), multivariate analysis models were used to optimize the critical process parameters combined with multi-objective optimization.Based on the optimized operating conditions, the MILT-HD method not only enhances the extraction efficiency from Amomi fructus but also reduces energy demands and CO2 emissions.Based on the density functional theoretical (DFT) and molecular dynamics (MD) simulations, the mechanisms for ionic liquids (ILs) to improve the extraction efficiency of essential oil was comprehensively revealed.In this paper, Amomi fructus (Latin) was used to explore the mechanism of ionic liquids (ILs) in improving the extraction efficiency of essential oils. Microwave assisted ionic liquid treatment followed by a hydro-distillation (MILT-HD) process for isolating Amomi fructus essential oil was optimized by multi-objective optimization. Under optimum operating conditions, the IL-assisted extraction method not only enhances extraction efficiency but also reduces energy demands and CO2 emissions. Since the hydrogen bond structure network of cellulose in the cell wall is an important reason for hindering diffusion of essential oils, the mechanism of ILs was explored by density functional theoretical (DFT) and molecular dynamics (MD) simulations. According to DFT calculations, ILs can facilitate the cleavage of cellulose chains and have strong non-covalent interactions with cellulose. Based on the MD simulations, the degree of destruction of the cellulose hydrogen bond structure was explored. According to the DFT and MD simulations, the ILs can significantly destroy cellulose structure, thereby promoting essential oil release from the plant. These results were confirmed by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). This work is conducive to better understand the MILT-HD process for isolating essential oil and comprehensively understand the mechanism of ILs in the extraction process.

Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces

This study explores the corrosion inhibition potential of two expired pharmaceutical compounds Abrocitinib (ABR) and Abemaciclib (ABM) as sustainable alternatives to conventional steel corrosion inhibitors in acidic environments. Using a synergistic approach that combines density functional theory (DFT) and molecular dynamics (MD) simulations, the electronic, structural, and adsorption behaviours of the inhibitors were comprehensively examined. The computed energy gaps ( ΔE ) between 0.911 and 0.950 eV, alongside high electrophilicity indices ( ω = 3.468–3.560 eV), indicate strong electron‐donating capabilities and reactivity toward metal surfaces. ABM demonstrated a superior adsorption energy of −183.322 kcal/mol, suggesting stronger surface interaction and better inhibition performance. Mulliken charge analysis revealed key adsorption centers around nitrogen and oxygen atoms, while radial distribution functions from MD simulations confirmed robust metal‐inhibitor interactions and the formation of a stable protective layer. These findings not only demonstrate the feasibility of reusing pharmaceutical waste for corrosion protection but also introduce an environmentally responsible strategy for sustainable corrosion control in acidic industrial applications.

This study investigates the structure and evolution of lanthanum acetate hydrated clusters using density functional theory (DFT) and molecular dynamics (MD) simulations to explore the influence of organic ammonium leaching...

The efforts of this thesis are directed towards understanding the physical driving forces that mediate membrane protein self-assembly processes within the native environment of membrane proteins, the bilayer milieu. While many defined determinants contribute to the energetics of membrane protein self-assembly, such as electrostatics, non-polar side-chain packing, hydrogen bonding, and solvophobic effects, the roles that these driving forces play have not been well characterized. The inability to describe the role of these physical driving forces in processes involving membrane proteins comes from the lack of quantitative thermodynamic measurements concerning membrane protein self-assembly equilibria within the lipid bilayer environment. These thermodynamic measurements would describe the free energy of self-assembly (∆G°) and the breakdown of this term into enthalpic (∆H°) and entropic components (∆S°). The studies within this thesis bridge the gaps in our knowledge of membrane protein self-assembly by quantifying the contributions of non-polar side-chain packing in the dimerization reaction of the large poly-topic membrane protein CLC-ec1 within lipid bilayers. An emphasis on describing non-polar side-chain packing was chosen due to membrane proteins commonly exhibiting the packing of transmembrane helices and surfaces lined with non-polar residues within lipid bilayers. Furthermore, non-polar side-chain packing is thought to be a significant contributor to membrane protein self-assembly, but its quantification has been limited. An emphasis is placed within the thesis on quantifying non-polar side-chain packing interactions in terms of van der Waals (VDW) interaction energies. Chapter 1 of this thesis describes the pertinent background of the driving forces thought to be involved in membrane protein self-assembly and provides an extensive review of the membrane protein CLC-ec1. The studies within this thesis employed a novel method, called the subunit capture method, to measure CLC-ec1 dimerization within membranes. Chapter 2 describes the subunit capture method and other methods commonly used throughout the thesis. Chapter 3 describes the first study, which characterizes the impact of removing non-polar side-chain contacts on the stoichiometry of the CLC-ec1 homodimer. Computational analysis of the dimerization interface of CLC-ec1 characterized non-polar side-chain packing by measuring the VDW interaction energies of side-chains within a structure of CLC-ec1 determined by x-ray crystallography. Subsequent experiments targeted non-polar side-chains exhibiting favorable VDW interaction energies by substituting 4-5 of the native residues at a time to the smaller residue alanine, depleting the favorable VDW interactions at the dimerization interface. The CLC-ec1 multiple alanine constructs revealed that the stoichiometry of CLC-ec1 is dependent upon the non-polar side-chains at the dimerization interface, as each construct becomes entirely monomeric in lipid bilayers. The studies also found that changes in CLC-ec1 stoichiometry occur in a solvent-dependent manner as three of the four CLC-ec1 multiple alanine constructs remain stable dimers in detergent micelles. Lastly, the study exposes a molecular hot-spot at residue 194, characterizing the substitution to alanine at that position as important for dimer stoichiometry in both detergents and lipids. The contents of Chapter 4 present the findings from a second study that sought answers to two questions. The study begins by posing the first question: Are protein-protein interactions driving the dimerization of CLC-ec1? To answer this question, we performed long all-atom molecular dynamics (MD) simulations to quantify the interactions of CLC-ec1 in a dimeric and monomeric state while embedded in a lipid bilayer. Through the quantification of VDW interaction energies, the measurements revealed that the interactions within each state are similar in magnitude. The findings from the MD simulations present VDW interactions as important to CLC-ec1 dimerization but not as a determinant that excessively stabilizes the CLC-ec1 dimer complex. The results from the analysis of the MD simulations allowed us to form the second question of the study: Will removing side-chain packing interactions at the dimerization interface destabilize the CLC-ec1 homodimer? The second question was thoroughly investigated by measuring the changes in dimerization free energy of CLC-ec1 constructs that contained single substitutions to alanine that generate cavities at the dimerization interface. The various changes in CLC-ec1 dimer stability due to the alanine substitutions were compared to the MD computational analysis to find no correlation between the two datasets. We conclude that while the CLC-ec1 single alanine substitutions destabilize the dimer complex, the removal of non-polar packing interactions from the dimer state of CLC-ec1 does not explain the measured changes in stability. The final chapter in this thesis, Chapter 5, presents a discussion of how the results obtained within this thesis fit into our current understanding of membrane protein self-assembly. Included in the discussion, we reason that CLC-ec1 may not have excessively favorable non-polar packing interactions at the CLC-ec1 dimerization interface in order to retain a flexible interface for function -related activities. Finally, Chapter 5 will conclude by posing a few future directions of study to answer new questions we have encountered while performing the work presented in this thesis.

The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained models, with a bond-angle potential to control chain stiffness, for chain lengths comparable to the persistence length of the chains. We varied both the density of the monomeric units and the effective temperature that controls the quality of the implicit solvent. For very stiff chains, only a single transition from an isotropic fluid to a nematic is found, with a phase diagram of "swan-neck" topology. For less stiff chains, however, also unmixing between isotropic fluids of different concentration, ending in a critical point, occurs for temperatures above a triple point. The associated critical behavior is examined in the MD simulations and found compatible with Ising universality. Apart from this critical behavior, DFT calculations agree qualitatively with the MD simulations.

The aim of the present study was to reveal the mechanisms underlying the formation of ternary complexes with a model system of amylose (AM), lauric acid (LA), and β-lactoglobulin (βLG) using experimental studies and molecular dynamics (MD) simulations. Experimental analyses showed that hydrophobic interactions and hydrogen bonds contributed more than electrostatic forces to the formation of the AM-LA-βLG complex. MD simulations indicated that interactions between AM and βLG through electrostatic forces and hydrogen bonds, and to a less extent van der Waals forces, and interactions between AM and LA through van der Waals forces, were mostly responsible for complex formation. The combination of experimental results and MD simulations has provided new mechanistic insights and led us to conclude that hydrophobic interactions, van der Waals forces between AM and LA, and van der Waals forces and hydrogen bonds between AM and βLG were the main driving forces for the formation of the AM-LA-βLG complex.

The dependence of the reaction initiation mechanism of pentaerythritol tetranitrate (PETN) on shock orientation and shock strength is investigated with molecular dynamics simulations using a reactive force field and the multiscale shock technique. In the simulations, a single crystal of PETN is shocked along the [110], [001], and [100] orientations with shock velocities in the range 3-10 km/s. Reactions occur with shock velocities of 6 km/s or stronger, and reactions initiate through the dissociation of nitro and nitrate groups from the PETN molecules. The most sensitive orientation is [110], while [100] is the most insensitive. For the [001] orientation, PETN decomposition via nitro group dissociation is the dominant reaction initiation mechanism, while for the [110] and [100] orientations the decomposition is via mixed nitro and nitrate group dissociation. For shock along the [001] orientation, we find that CO-NO(2) bonds initially acquire more kinetic energy, facilitating nitro dissociation. For the other two orientations, C-ONO(2) bonds acquire more kinetic energy, facilitating nitrate group dissociation.

The initial response of PETN under the coupling of preheating, impact and defects was simulated by Multiscale Shock Technique (MSST) method and molecular dynamics. The temperature change of PETN during impact compression can be divided into three stages: (1) the elastoplastic change of the system caused by initial compression; (2) part of PETN decomposes and releases energy to raise temperature; (3) a secondary chemical reaction occurs, resulting in rapid temperature rise. Under the given conditions, a higher initial preheating temperature will lead to faster decomposition of PETN; The existence of defects will accelerate the decomposition of PETN molecules; Coupling the highest preheating temperature with defects will lead to the fastest decomposition of PETN molecules, while in the defect-free PETN system with a preheating temperature of 300 K, the decomposition of PETN molecules is the slowest. For the case of Us = 8 km·s−1, the effect of defects on the initial PETN reaction is greater than the initial preheating temperature; When the impact velocity is greater than 9 km·s−1, the impact velocity is an important factor affecting the decomposition of PETN molecules. For Us = 10 km·s−1, NO2 is the main initial product in the defective PETN crystal, while in the perfect PETN crystal, it is the combination of NO2 and HONO. The chemical reaction kinetics analysis shows that the preheating temperature and defects will accelerate the decomposition of PETN. The higher the preheating temperature, the faster the decomposition of PETN. For the case of Us = 7 km·s−1, 8 km·s−1 and 9 km·s−1, the existence of defects will increase the decomposition rate by more than 50% regardless of the initial preheating temperature. In the case of Us = 10 km·s−1, the improvement of decomposition rate by defects is not as significant as the initial preheating temperature.

Based on molecular dynamics (MD) simulation, the binding energy, cohesive energy density (CED), bond length, and mechanical parameters were calculated for 2,6-diamino-3,5-dinitropyrazine-l-oxide (LLM-105) crystal, octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) crystal, and their co-crystals under different temperatures. Three LLM-105/HMX patterns were constructed to investigate the influence of component proportion on structures and properties of co-crystals, in which the mole ratios of LLM-105 and HMX are 1:1, 1:2, and 2:1. The effect of temperature and components on the stability and sensitivity were investigated as well. The results show that the binding energies, CED and mechanical parameters of all the co-crystals, decrease when the temperature increases from 248 to 398K, while their maximum N-NO2 bond length (Lmax) increases with rising temperature, indicating that the sensitivities increase and stabilities decrease when temperature rises. At all temperatures, co-crystals exhibit larger CED and shorter bond length than that of single explosive, demonstrating that they are more stable and less sensitive than single crystal, where the stability of co-crystals was ordered as 2:1>1:1>1:2. Moreover, the bulk modulus (K) and shear modulus (G) of co-crystals are lower than that of HMX, conversely, the Cauchy pressure and K/G are higher than that of HMX, implying co-crystals have better ductility. Finally, the 2:1 ratio of LLM-105/HMX co-crystal was identified as the excellent one, owning to the highest binding energy, highest CED, shortest Lmax, and greatest ductility. Graphical Abstract Models of LLM-105/HMX and one of the properties.

Background(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters or suppressors, depending on the cancer type. In particular, PKCε is frequently implicated in cancer promotion, making it a potential target for anticancer drugs. To improve isozyme selectivity of balanol, exhaustive structural and activity relationship (SAR) studies have been performed in the last two decades, but with limited success. More recently, fluorination on balanol has shown improved selectivity for PKCε, although the fluorine effect is not yet clearly understood. Understanding the origin to this fluorine-based selectivity will be valuable for designing better balanol-based ATP mimicking inhibitors. Computational approaches such as molecular dynamics (MD) simulations can decipher the fluorine effect, provided that correct charges have been assigned to a ligand. Balanol analogues have multiple ionisable functional groups and the effect of fluorine substitutions on the exact charge state of each analogue bound to PKA and to PKCε needs to be thoroughly investigated in order to design highly selective inhibitors for therapeutic applications.ResultsWe explored the charge states of novel fluorinated balanol analogues using MD simulations. For different potential charge states of these analogues, Molecular Mechanics Generalized Born Surface Area (MMGBSA) binding energy values were computed. This study suggests that balanol and the most potent fluorinated analogue (5S fluorine substitution on the azepane ring), have charges on the azepane ring (N1), and the phenolic (C6′′OH) and the carboxylate (C15′′O2H) groups on the benzophenone moiety, when bound to PKCε as well as PKA.ConclusionsTo the best our knowledge, this is the first study showing that the phenolate group is charged in balanol and its analogues binding to the ATP site of PKCε. Correct charge assignments of ligands are important to obtain predicted binding energy values from MD simulations that reflect experimental values. Both fluorination and the local enzymatic environment of the ATP site can influence the exact charge states of balanol analogues. Overall, this study is highly valuable for further rational design of potent balanol analogues selective to PKCε.

The objectives of this study were as follows: (i) To develop an in silico technique, based on molecular dynamics (MD) simulations, to predict glass transition temperatures (Tg) of amorphous pharmaceuticals. (ii) To computationally study the effect of plasticizer on Tg. (iii) To investigate the intermolecular interactions using radial distribution function (RDF). Amorphous sucrose and water were selected as the model compound and plasticizer, respectively. MD simulations were performed using COMPASS force field and isothermal-isobaric ensembles. The specific volumes of amorphous cells were computed in the temperature range of 440-265 K. The characteristic "kink" observed in volume-temperature curves, in conjunction with regression analysis, defined the Tg. The MD computed Tg values were 367 K, 352 K and 343 K for amorphous sucrose containing 0%, 3% and 5% w/w water, respectively. The MD technique thus effectively simulated the plasticization effect of water; and the corresponding Tg values were in reasonable agreement with theoretical models and literature reports. The RDF measurements revealed strong hydrogen bond interactions between sucrose hydroxyl oxygens and water oxygen. Steric effects led to weak interactions between sucrose acetal oxygens and water oxygen. MD is thus a powerful predictive tool for probing temperature and water effects on the stability of amorphous systems during drug development.

Photocatalytic activity of ZnMn2O4/TiO2 heterostructure under solar light irradiation: Experimental and theoretical study

High-capacity hydrogen storage in zirconium decorated psi-graphene: acumen from density functional theory and molecular dynamics simulations