Computational insights of noncovalent interactions in xylan hydrate crystal.

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.

A detailed computational study covering density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations of some spirocyclic compounds interacting with a B-DNA has been performed. DFT calculations were performed using the B3LYP functional with 6-311++G(d,p) basis set and were used to identify the electrophilic and nucleophilic centers in electrostatic forces. NMR results were in agreement with previous experimental data and approved the reliability of the used method and basis set. The in silico screening results showed that spirocyclic compounds fulfill the Lipinski's rule of five and can be developed as potential oral bioavailable drug candidates. Based on molecular docking results, the binding affinities follow the 4c < 4d < 4a = 4b < 4e < 4g < 4f order and ranged from −8.6 to −9.7 kcal/mol indicating a reasonably favorable interaction between DNA and investigated compounds. The adducts were stabilized by hydrophobic and hydrogen bonding interactions. The MD simulations performed for 100 ns and the results are reported in terms of variables such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), center of mass (COM) separation distance between DNA and ligands, intermolecular hydrogen bonds, and radial distribution functions (RDF). The MD simulations demonstrated that compounds 4a and 4d bind into the minor groove of 1BNA and may act as potential biological probes for B-DNA. Communicated by Ramaswamy H. Sarma

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...

This study presents a comprehensive multiscale computational investigation into the effect of alkyl chain length on the CO2 capture performance of ammonium-based deep eutectic solvents (DESs). Density functional theory (DFT), COSMO-RS calculations, and molecular dynamics (MD) simulations were employed to probe the molecular interactions as well as the structural and dynamical characteristics between CO2 and three DESs containing lactic acid (LA) as the hydrogen bond donor. Interaction energy analysis and vibrational spectra revealed that, in all studied DESs, CO2 preferentially interacts with the LA rather than with the anion or cation. COSMO-RS predictions confirmed that longer chains improve CO2 solubility by increasing hydrophobicity and free volume. Furthermore, MD analysis showed that CO2-LA interactions dominate, and longer chains reduce cation-CO2 proximity due to steric effects. Structural and dynamic analyses, including RDF, SDF, Voronoi, and van Hove correlation functions, confirmed stronger CO2 interactions, reduced ion mobility, and more extensive hydrogen bonding networks in longer-chain DESs. Spectral shifts further indicated physical absorption and increased cation involvement in CO2 capture for longer chains. Finally, the findings demonstrate that extending the cation alkyl chain enhances overall CO2 uptake through stronger dispersion forces, increased free volume, and more diverse hydrogen bonding. Increasing the alkyl chain length of the cation appears to reduce its interaction with CO2, likely due to enhanced steric hindrance. However, as the alkyl chain length increases from DES(1) to DES(3), the overall CO2 uptake improves. This enhancement is attributed to reduced cation-anion and cation-LA interactions caused by steric effects, which in turn increases the availability of the anion and LA to interact more effectively with CO2.

Mechanism research on surface hydration of kaolinite, insights from DFT and MD simulations

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 employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

DFT, MD simulations and experimental analysis of adsorptive complexation and isotope separation of gadolinium ion with macrocyclic crown ether embedded polymeric resin

Exploring boron nitride nanotubes as potential drug delivery vehicles using density functional theory and molecular dynamics – An overview

Understanding the adsorption behavior of molecular hydrogen (H2) on solid surfaces is essential for a variety of technological applications, including hydrogen storage and catalysis. We examined the adsorption of H2 (∼2800 configurations) molecules on the surface of fullerene (C60) using a combined approach of density functional theory (DFT) and molecular dynamics (MD) simulations with an improved Lennard-Jones (ILJ) potential force field. First, we determined the adsorption energies and geometries of H2 on the C60 surface using DFT calculations. Calculations of the electronic structure help elucidate underlying mechanisms administrating the adsorption process by revealing how H2 molecules interact with the C60 surface. In addition, molecular dynamics simulations were performed to examine the dynamic behavior of H2 molecules on the C60 surface. We accurately depicted the intermolecular interactions between H2 and C60, as well as the collective behavior of adsorbed H2 molecules, using an ILJ potential force field. Our findings indicate that H2 molecules exhibit robust physisorption on the C60 surface, forming stable adsorption structures with favorable adsorption energies. Calculated adsorption energies and binding sites are useful for designing efficient hydrogen storage materials and comprehending the nature of hydrogen's interactions with carbon-based nanostructures. This research provides a comprehensive understanding of H2 adsorption on the C60 surface by combining the theoretical framework of DFT calculations with the dynamical perspective of MD simulations. The outcomes of the present research provide new insights into the fields of hydrogen storage and carbon-based nanomaterials, facilitating the development of efficient hydrogen storage systems and advancing the use of molecular hydrogen in a variety of applications.

This study comprehensively investigates Al2O3's mechanical properties, focusing on fracture toughness, surface energy, Young's modulus, and crack propagation. The density functional theory (DFT) is employed to model the vacancies in Al2O3, providing essential insights into this material's structural stability and defect formation. The DFT simulations reveal a deep understanding of vacancy-related properties and their impact on mechanical behavior. In conjunction with molecular dynamics (MD) simulations, the fracture toughness and crack propagation in Al2O3 are explored, offering valuable information on material strength and durability. The surface energy of Al2O3 is also assessed using DFT, shedding light on its interactions with the surrounding environment. The results of this investigation highlight the significant impact of oxygen vacancies on mechanical characteristics such as ultimate strength and fracture toughness, drawing comparisons with the effects observed in the presence of aluminum vacancies. Additionally, the research underscores the validation of fracture toughness outcomes derived from both DFT and MD simulations, which align well with findings from established experimental studies. Additionally, the research underscores the validation of fracture toughness outcomes derived from DFT and MD simulations, aligning well with findings from established experimental studies. The combination of DFT and MD simulations provides a robust framework for a comprehensive understanding of Al2O3's mechanical properties, with implications for material science and engineering applications.

The inhibitor activity of some azo compound derivatives using density functional theory and molecular dynamics simulations

Probing the adsorption and release mechanisms of cytarabine anticancer drug on/from dopamine functionalized graphene oxide as a highly efficient drug delivery system

We report a detailed density functional theory and molecular dynamics study of hydrogen bonding between trehalose and water, with a special emphasis on interactions in the amorphous solid state. For comparison, water-water interactions in water dimers and tetramers are evaluated using quantum calculations. The results show that the hydrogen bonding energy is dependent not only on the geometry (bond length and angle) but also on the local environment of the hydrogen bond. This is seen in quantum calculations of complexes in vacuum as well as in amorphous solid states with periodic boundary conditions. The temperature-induced glass transition in the trehalose-water system was studied using molecular dynamics simulations with varying cooling and heating rates. The obtained parameters of the glass transition are in good agreement with the experiments. Moreover, the dehydration of trehalose in the glassy state was investigated through a gradual dehydration with multiple small steps under isothermal conditions. From these simulations, the values of water sorption energy at different temperatures were obtained. The partial molar enthalpy of mixing of water value of -18 kJ/mol found in calorimetric experiments was accurately reproduced in these simulations. These findings are discussed in light of the hydrogen bonding data in the system. We conclude that the observed exothermic effect is due to different responses of liquid and glassy matrices to perturbations associated with the addition or removal of water molecules.

Recent experiments on proton conducting ionic liquids point to half-neutralized diamine-triflate salts as promising candidates for applications in power generation and energy conversion electrochemical devices. Structural and dynamical properties of the simplest among these compounds are investigated by a combination of density functional theory (DFT) and molecular dynamics (MD) simulations based on an empirical force field. Three different cations have been considered, consisting of a pair of amine-ammonium terminations joined by a short aliphatic segment -(CH2) n- with n = 2, 3, and 4. First, the ground state structure, vibrational eigenstates, and hydrogen-bonding properties of single ions, neutral ion pairs, small neutral aggregates of up to eight ions, and molecularly thin hydrogen bonded wires have been investigated by DFT computations. Second, structural and dynamical properties of homogeneous liquid and amorphous phases are investigated by MD simulations over the temperature range of 200 ≤ T ≤ 440 K. Structure factors, radial distribution functions, diffusion coefficient, and electrical conductivity are computed and discussed, highlighting the inherent structural heterogeneity of these compounds. The core investigation, however, is the characterization of connected paths consisting of cation chains that could support proton transport via a Grotthuss-type mechanism. Since simulations are carried out using a force field of fixed bonding topology, this analysis is based on the equilibrium structure only, using geometrical criteria to identify potential paths for proton conduction. Paths of connected cations can reach a length of 80 cations and 30 Å, provided that bridging oxygen atoms from triflate anions are taken into account. The effects of water contamination at 1% weight concentration on the structure, dynamics, and paths for proton transport are discussed.