Unlocking the Full Potential of Heteroatom-Doped Graphene-Based Supercapacitors through Stacking Models and SHAP-Guided Optimization.

Graphene-based supercapacitors have emerged as a promising candidate for energy storage due to their superior capacitive properties. Heteroatom-doping is a method of improving the capacitive properties of graphene-based electrodes, but the optimal doping conditions and electrochemical properties are not yet fully understood due to the synergistic effects that occur. Many parameters, such as doping content, defects, specific surface area (SA), electrolyte, and more, could affect the capacitance (CAP).

Structural Investigation of Beta-Cyclodextrin Complexes with Cannabidiol and Delta-9-Tetrahydrocannabinol in 1:1 and 2:1 Host-Guest Stoichiometry: Molecular Docking and Density Functional Calculations.

The complexation of β-cyclodextrin (β-CD) with cannabidiol (CBD) and Δ-tetrahydrocannabinol (THC) was investigated using molecular docking and M062X/6-31G(d,p) calculations. The calculations suggested two possible complex formations of 1:1 and 2:1 host-guest molecular ratio of β-CD with CBD and THC. The preferred orientation of all complexes in this study exhibited the hydrogen bonding between hydroxy-substituted benzene ring of CBD and THC with the β-CD's secondary hydroxy groups at the wide rim.

Rotations of F-ATPase and V-ATPase analyzed by a torque approach.

F-type ATP synthase (F-ATPase) and vacuolar ATP hydrolase (V-ATPase) are well-known biomolecular motors, which play significant catalytic roles in ATP synthesis and ATP hydrolysis reactions. Their rotational torques are important factors involved in their rotational behavior that can be measured experimentally but with considerable difficulty. To overcome this difficulty and thereby provide an in-depth understanding of their operation mechanism, we herein carry out simple and fast computer modelling to study the two proteins, using our torque approach that relies on interatomic forces and coordinates of unequilibrated configurations taken from brief molecular dynamics (MD) simulations.

Molecular Dynamic Simulation Analysis on the Inclusion Complexation of Plumbagin with β-Cyclodextrin Derivatives in Aqueous Solution.

Stable encapsulation of medically active compounds can lead to longer storage life and facilitate the slow-release mechanism. In this work, the dynamic and molecular interactions between plumbagin molecule with β-cyclodextrin (BCD) and its two derivatives, which are dimethyl-β-cyclodextrin (MBCD), and 2--monohydroxypropyl-β-cyclodextrin (HPBCD) were investigated. Molecular dynamics simulations (MD) with GLYCAM-06 and AMBER force fields were used to simulate the inclusion complex systems under storage temperature (4 °C) in an aqueous solution.

Theoretical Investigation of the Enantioselective Complexations between pfDHFR and Cycloguanil Derivatives.

Point mutations in dihydrofolate reductase (DHFR), especially the double mutant variant (A16V + S108T), led to ineffective inhibiting by cycloguanil (Cyc). Cycloguanil derivatives showed good inhibiting properties against wild-type and mutant DHFR with an inhibition constant as low as the nanomolar level. However, there have been no reports on the stereochemistry of the compounds, and this is important because the pure enantiomeric form of a chiral drug can exert desirable, as well as non-desirable responses on the body or both.

Simulation Study of Interactions Between Two Bioactive Components from and 5-Lipoxygenase.

Introduction: Compound D and DMPBD are compounds extracted from Plai or Roxb., which have antiasthmatic properties. Thai herbal pharmacopoeia have indicated that approximate 50% of Thai prescriptions for asthma contain Plai.

Structural and Dynamics Perspectives on the Binding of Substrate and Inhibitors in Mycobacterium tuberculosis DHFR.

Dihydrofolate reductase (DHFR), an essential enzyme in the folate pathway, is a potential target for new anti-tuberculosis drugs. Fifteen crystal structures of DHFR complexed with NADPH and various inhibitors are available in the RCSB Protein Data Bank, but none of them is a substrate binding structure. Therefore, we performed molecular dynamics simulations on ternary complexes of DHFR:NADPH with a substrate (dihydrofolate) and each of three competitive inhibitors the in 2,4-diaminopyrimidine series (P1, P157, and P169), in order to gain insight into the inhibition-mechanism of DHFR in the folate pathway.

A novel prediction approach for antimalarial activities of Trimethoprim, Pyrimethamine, and Cycloguanil analogues using extremely randomized trees.

Malaria is still one of the most serious diseases in tropical regions. This is due in part to the high resistance against available drugs for the inhibition of parasites, Plasmodium, the cause of the disease. New potent compounds with high clinical utility are urgently needed.

Influence of Ethanol as a Co-Solvent in Cyclodextrin Inclusion Complexation: A Molecular Dynamics Study.

Molecular dynamics (MD) simulations were used to investigate the dynamics and host-guest interactions of the inclusion complexes between a potent anti-HIV agent, UC781, and three different types of cyclodextrins (CDs) including βCD, 2,6-dimethyl-βCD (MβCD), and 2-hydroxypropyl-βCD (HPβCD) in aqueous solution with ethanol (EtOH) as a co-solvent. The MD simulation results revealed that EtOH as the co-solvent and the type of cyclodextrin affected the inclusion complex formation. From this study, UC781/MβCD provided the most stable inclusion complex.

Molecular dynamics simulations of UC781-cyclodextrins inclusion complexes in aqueous solution.

The inclusion complexes of highly potent anti-HIV agent, UC781, with β-cyclodextrin (βCD), 2,6-dimethyl-β-cyclodextrin (MβCD), and 2-hydroxypropyl-β-cyclodextrin (HPβCD) in aqueous solution were investigated by molecular dynamics simulations. Simulations show that the phenyl ring of UC781 is trapped inside CD cavities, while the NH group of UC781 interacts with secondary hydroxyl groups at the wider rim of CDs. The different types of CDs directly affect the binding energy and the stability of the inclusion complexes.

Predicting complexation thermodynamic parameters of β-cyclodextrin with chiral guests by using swarm intelligence and support vector machines.

The Particle Swarm Optimization (PSO) and Support Vector Machines (SVMs) approaches are used for predicting the thermodynamic parameters for the 1:1 inclusion complexation of chiral guests with beta-cyclodextrin. A PSO is adopted for descriptor selection in the quantitative structure-property relationships (QSPR) of a dataset of 74 chiral guests due to its simplicity, speed, and consistency. The modified PSO is then combined with SVMs for its good approximating properties, to generate a QSPR model with the selected features.

Molecular dynamics simulations of beta-cyclodextrin in aqueous solution.

Molecular dynamics (MD) simulations of beta-cyclodextrin (beta-CD) have been carried out in aqueous solution at 300 K over a period of about 200 ps using Tripos force field. The atomic trajectories obtained by these simulations have been analysed by means of the occurrence of hydrogen bonds. The MD simulations lead to an association of seven water molecules into the beta-CD cavity which is in a good agreement with X-ray crystallography experiments.