Constant charge method or constant potential method:Which is better for molecular modeling of electrical double layers?

In molecular modeling of electrical double layers(EDLs),the constant charge method(CCM)is prized for its computational efficiency but cannot maintain electrode equipotentiality like the more resourceintensive constant potential method(CPM),potentially leading to inaccuracies.In certain scenarios,CCM can yield results identical to CPM.However,there are no clear guidelines to determine when CCM is sufficient and when CPM is required.Here,we conduct a series of molecular simulations across various electrodes and electrolytes to present a comprehensive comparison between CCM and CPM under different charging modes.Results reveal that CCM approximates CPM effectively in capturing equilibrium EDL and current-driven dynamics in open electrode systems featuring ionic liquids or regular concentration aqueous electrolytes,while CPM is indispensable in scenarios involving organic and highly concentrated aqueous electrolytes,nanoconfinement effects,and voltage-driven dynamics.This work helps to select appropriate methods for modeling EDL systems,prioritizing accuracy while considering computationalefficiency.

Decoding molecular mechanisms:brain aging and Alzheimer's disease

The complex morphological,anatomical,physiological,and chemical mechanisms within the aging brain have been the hot topic of research for centuries.The aging process alters the brain structure that affects functions and cognitions,but the worsening of such processes contributes to the pathogenesis of neurodegenerative disorders,such as Alzheimer's disease.Beyond these observable,mild morphological shifts,significant functional modifications in neurotransmission and neuronal activity critically influence the aging brain.Understanding these changes is important for maintaining cognitive health,especially given the increasing prevalence of age-related conditions that affect cognition.This review aims to explore the age-induced changes in brain plasticity and molecular processes,differentiating normal aging from the pathogenesis of Alzheimer's disease,thereby providing insights into predicting the risk of dementia,particularly Alzheimer's disease.

Molecular simulation study of the microstructures and properties of pyridinium ionic liquid[HPy][BF_(4)]mixed with acetonitrile

The microstructures and thermodynamic properties of mixed systems comprising pyridinium ionic liquid[HPy][BF_(4)]and acetonitrile at different mole fractions were studied using molecular dynamics simulation in this work.The following properties were determined:density,self-diffusion coefficient,excess molar volume,and radial distribution function.The results show that with an increase in the mole fraction of[HPy][BF_(4)],the self-diffusion coefficient decreases.Additionally,the excess molar volume initially decreases,reaches a minimum,and then increases.The rules of radial distribution functions(RDFs)of characteristic atoms are different.With increasing the mole fraction of[HPy][BF_(4)],the first peak of the RDFs of HA1-F decreases,while that of CT6-CT6 rises at first and then decreases.This indicates that the solvent molecules affect the polar and non-polar regions of[HPy][BF_(4)]differently.

A promising approach for quantifying focal stroke modeling and assessing stroke progression:optical resolution photoacoustic microscopy photothrombosis

To investigate the mechanisms underlying the onset and progression of ischemic stroke,some methods have been proposed that can simultaneously monitor and create embolisms in the animal cerebral cortex.However,these methods often require complex systems and the effect of age on cerebral embolism has not been adequately studied,although ischemic stroke is strongly age-related.In this study,we propose an optical-resolution photoacoustic microscopy-based visualized photothrombosis methodology to create and monitor ischemic stroke in mice simultaneously using a 532 nm pulsed laser.We observed the molding process in mice of different ages and presented age-dependent vascular embolism differentiation.Moreover,we integrated optical coherence tomography angiography to investigate age-associated trends in cerebrovascular variability following a stroke.Our imaging data and quantitative analyses underscore the differential cerebrovascular responses to stroke in mice of different ages,thereby highlighting the technique's potential for evaluating cerebrovascular health and unraveling age-related mechanisms involved in ischemic strokes.

MODELING AND NUMERICAL SIMULATION OF ONBOARD MOLECULAR SIEVE OXYGEN GENERATION SYSTEM

A mathematical model for simulating concentric-bed and other components of molecular sieve oxygen concentrator is established. In the model, the binary Langmuir equilibrium adsorption equation is adopted to describe the adsorption performance of the adsorbent, the linear driving force (LDF) model is used to describe the mass transfer rate, and the thermal effect during adsorption is considered. The finite difference method is used in simulation and comparison. Numerical results have a reasonable agreement with the experimental research.

Characterization of Gallic Acid Interaction with Human Serum Albumin by Spectral and Molecular Modeling Methods

The binding of drugs with human serum albumin（HSA） is a crucial factor influencing the distribution and bioactivity of drugs in the body.To understand the action mechanisms between gallic acid（GA,3,4,5-trihydroxybenzoic acid） and HSA,the binding of GA with HSA was investigated by a combined experimental and computational approach.The fluorescence properties of HSA and the binding parameters of GA collectively indicate that the binding is characterized by static quenching mechanism at one high affinity binding site.According to the estimated molecular distance between the donor（HSA） and the acceptor（GA）,the binding is related to the fluorescence resonance energy transfer.As indicated by the thermodynamic parameters,hydrophobic interaction plays a major role in the GA-HSA complex.Further,the experimental results reveal that GA is bound in the large hydrophobic cavity of subdomain IIA in the site I of HSA,which is well approved by molecular docking.

Host-guest interaction of β-cyclodextrin with isomeric ursolic acid and oleanolic acid:physicochemical characterization and molecular modeling study

Ursolic acid(UA) and oleanolic acid(OA) are insoluble drugs. The objective of this study was to encapsulate them into β-cyclodextrin(β-CD) and compare the solubility and intermolecular force of β-CD with the two isomeric triterpenic acids. The host-guest interaction was explored in liquid and solid state by ultraviolet-visible absorption,1H NMR, phase solubility analysis, and differential scanning calorimetry, X-ray powder diffractometry, and molecular modeling studies. Both experimental and theoretical studies revealed that β-CD formed 1: 1 water soluble inclusion complexes and the complexation process was naturally favorable. In addition, the overall results suggested that ring E with a carboxyl group of the drug was encapsulated into the hydrophobic CD nanocavity. Therefore, a clear different inclusion behavior was observed, and UA exhibited better affinity to β-CD compared with OA in various media due to little steric interference, which was beneficial to form stable inclusion complex with β-CD and increase its water solubility effectively.

Diesel molecular composition and blending modeling based on SUBEM framework

Diesel molecular compositional model has important application for diesel quality prediction,blending,and molecular-level process model development.In this paper,different types of diesel molecular compositional and blending models were constructed based on the SU-BEM framework.More than 1500 representative molecules were selected to form the molecular structure library.The probability density functions(PDFs)combination was determined by experimental data and experience.A quadratic optimization strategy combining genetic algorithm with local optimization algorithm was adopted to improve the accuracy of the compositional model.The model results show good agreement with the experimental data.The diesel blending model was constructed at the molecular-level based on the above diesel compositional models.The properties of the blending model accord with the experimental regulations.It is proved that the compositional models and blending model constructed have high accuracy and strong prediction capability,and are applicable to the industrial process.

Inclusion complexes of cefuroxime axetil with β-cyclodextrin:Physicochemical characterization, molecular modeling and effect of Larginine on complexation

The inclusion complexes of poorly water-soluble cephalosporin, cefuroxime axetil(CFA), were prepared with β-cyclodextrin(βCD) with or without addition of L-arginine(ARG) to improve its physicochemical properties. We also investigated the effect of ARG on complexation efficiency(CE) of βCD towards CFA in an aqueous medium through phase solubility behaviour according to Higuchi and Connors. Although phase solubility studies showed AL(linear) type of solubility curve in presence and absence of ARG, the CE and association constant(Ks) of βCD towards CFA were significantly promoted in presence of ARG,justifying its use as a ternary component. The solid systems of CFA with βCD were obtained by spray drying technique with or without incorporation of ARG and characterized by differential scanning calorimetry(DSC), X-ray powder diffractometry(XRPD), scanning electron microscopy(SEM), and saturation solubility and dissolution studies. The molecular modeling studies provided a better insight into geometry and inclusion mode of CFA inside βCD cavity. The solubility and dissolution rate of CFA were significantly improved upon complexation with βCD as compared to CFA alone. However, ternary system incorporated with ARG performed better than binary system in physicochemical evaluation. In conclusion, ARG could be exploited as a ternary component to improve the physicochemical properties of CFA via βCD complexation.

Homology Modeling of Mosquitocidal Cry30Ca2 of Bacillus thuringiensis and Its Molecular Docking with N-acetylgalactosamine

Abstract Objective To investigate the theoretical model of the three-dimensional structure of mosquitocida Cry3OCa2 and its molecular docking with N-acetylgalactosamine. Methods The theoretical model of Cry30Ca2 was the Cry4Ba. Docking studies were performed N-acetylgalactosamine on the putative receptor. predicted by homology modeling on the structure of to investigate the interaction of Cry3OCa2 with Results Cry3OCa2 toxin is a rather compact molecule composed of three distinct domains and has approximate overall dimensions of 95 by 75 by 60A. Domain I is a helix bundle, Domain Ⅱ consists of three antiparallel β-sheets, Domain Ⅲ is composed of two β-sheets that adopt a 13-sandwich fold. Residue 32111e in loop1, residues 342Gin 343Thr and 345Gin in loop2, residue 393Tyr in loop3 of Cry3OCa2 are responsible for the interactions with GalNAc via 7 hydrogen bonds, 6 of them were related to the oxygen atoms of hydroxyls of the ligand, and one to the nitrogen of the ligand. Conclusion The 3D structure of Cry3OCa2 resembles the previously reported Cry toxin structures but shows still some distinctions. Several residues in the loops of the apex of domain Ⅱ are responsible for the interactions with N-acetylgalactosamine.

Molecular Modeling of the Chain Structures of Polybenzoxazines

The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

Investigation of molecular aggregation mechanism of glipizide/cyclodextrin complexation by combined experimental and molecular modeling approaches

Cyclodextrin complexation is a wise strategy to enhance aqueous solubility of waterinsoluble drugs.However,the aggregation mechanism of drug-cyclodextrin complexes is still unclear.This research aimed to investigate the molecular aggregation mechanism of glipizide/cyclodextrin complexation by the combination of experimental and modeling methods.Binding free energies between glipizide and cyclodextrins from modeling calculations were higher than those by the phase solubility diagram method.Both experimental and modeling results showed that methylated-β-cyclodextrin exhibited the best solubilizing capability to glipizide.Size-measurement results confirmed the aggregation between glipizide and all four cyclodextrins in high concentrations.Glipizide/γ-cyclodextrin and glipizide/β-cyclodextrin complexes showed stronger aggregation trend than HP-β-cyclodextrin and methylated-β-cyclodextrin.The substituted groups in the rim of HP-β-cyclodextrin and methylated-β-cyclodextrin lead to weak aggregation.This research provided us a clear molecular mechanism of glipizide/cyclodextrin complexation and aggregation.This research will also benefit the formulation development of cyclodextrin solubilization.

Characterization of Amino Acid Based Molecular Micelles with Molecular Modeling

The enantiomers of chiral drugs often have different potencies, toxicities, and biochemical properties. Therefore, the FDA and other worldwide regulatory agencies require manufactures to test and prove the enantiomeric purity of chiral drugs. Amino acid based molecular micelles (AABMM) have been used in chiral CE separations since the 1990’s because of their low environmental impact and because their properties can easily be tuned by changing the amino acids in the chiral surfactant head groups. Using molecular dynamics simulations to investigate the structures and properties of AABMM is part of an ongoing study focusing on investigating and elucidating the factors responsible for chiral recognition with AABMM. The results will be useful for the proper design and selection of more efficient chiral selectors. The micelles investigated contained approximately twenty covalently linked surfactant monomers. Each monomer was in turn composed of an undecyl hydrocarbon chain bound to a dipeptide headgroup containing of all combinations of L-Alanine, L-Valine, and L-Leucine. These materials are of interest because they are effective chiral selectors in capillary electrophoresis separations. Molecular dynamics simulation analyses were used to investigate how the sizes and positions of the headgroup amino acid R-groups affected the solvent accessible surface areas of each AABMM chiral center. In addition, headgroup dihedral angle analyses were used to investigate how amino acid R-group size and position affected the overall headgroup conformations. Finally, distance measurements were used to study the structural and conformational flexibilities of each AABMM headgroup. All analyses were performed in the context of a broader study focused on developing structure-based predictive tools to identify the factors responsible for a) self-assembly, b) function, c) higher ordered structure and d) molecular recognition of these amino acid based molecular micelles.

Molecular Modeling Studies of Vascular Endothelial Growth Factor Receptor Tyrosine Kinase Inhibitors Combining Molecular Docking and 3D-QSAR Methods

The vascular endothelial growth factor （VEGF） and its receptor tyrosine kinases VEGFR-2 or kinase insertdomain receptor （KDR） have emerged as attractive targets for the design of novel anticancer agents. In the present work, molecular docking method combined with three dimensional quantitative structure-activity relationships （comparative molecular field analysis （CoMFA） and comparative molecular similarity indice analysis （CoMSIA）） to analyze the possible interactions between KDR and those derivatives which acted as selective inhibitors. The CoMFA and CoMSIA models gave a cross-validated coefficient Q2 of 0.713 and 0.549, non-cross-validated R2 values of 0.974 and 0.878, and predicted R2 values of 0.966 and 0.823, respectively. The 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. The information obtained from 3D-QSAR and docking studies were very helpful to design novel selective inhibitors of KDR with desired activity and good chemical property.

Synthesis, Spectroscopic, Molecular Modeling and Anti-Fungal Studies of Some Divalent Metal Complexes of 4-Hydroxyacetophenone Isonicotinoyl Hydrazone

A novel ligand N-4-hydroxyacetophenone isonicotinoyl hydrazone and its manganese(II) and nickel(II) metal complexes have been synthesized. The synthesized Schiff base and its metal complexes have been characterized by physical state determination, melting point and solubility measurements in different solvents, infrared, proton nuclear magnetic resonance, mass spectrometric and powder X-ray spectroscopic techniques. The thermal properties of the prepared compounds were obtained from TG/DTG measurements. On the basis of the analytical techniques, the ligand was found to be bidentate in nature coordinating to the metal ions through the azomethine nitrogen and carbonyl oxygen atoms leading to distorted octahedral geometries of the metal complexes which were modeled using MM2 force field. The ligand and its metal(II) complexes were evaluated for antifungal activity against Aspergillus fumigatus, Aspergillus niger, Candida albicans and Rhizopus stolonifera. The antifungal evaluation results revealed an enhanced activity upon coordination of the ligand with the metal(II) ions. The activity of the metal complex to the tested fungal strains was in the order Ni(II) > Mn(II).

From molecular dynamics to lattice Boltzmann:a new approach for pore-scale modeling of multi-phase flow

Most current lattice Boltzmann （LBM） models suffer from the deficiency that their parameters have to be obtained by fitting experimental results. In this paper, we propose a new method that integrates the molecular dynamics （MD） simulation and LBM to avoid such defect. The basic idea is to first construct a molecular model based on the actual components of the rock-fluid system, then to compute the interaction force between the rock and the fluid of different densities through the MD simulation. This calculated rock-fluid interaction force, combined with the fluid-fluid force determined from the equation of state, is then used in LBM modeling. Without parameter fitting, this study presents a new systematic approach for pore-scale modeling of multi-phase flow. We have validated this ap- proach by simulating a two-phase separation process and gas-liquid-solid three-phase contact angle. Based on an actual X-ray CT image of a reservoir core, we applied our workflow to calculate the absolute permeability of the core, vapor-liquid H20 relative permeability, and capillary pressure curves.

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

Structural analysis and molecular modeling of twoantitrichosanthin IgE clones from phage antibody library

Recently we constructed a murine IgE phage surfacedisplay library and screened out two IgE (Fab) cloneswith specific binding activity to Trichosanthin (TCS). Inthis work, the Vε and Vκ genes of the two clones weresequenced and their putative germline gene usages werestudied. On the basis of the known 3D structure of Trichosanthin and antibody, molecular modeling was carriedout to study the antigen-antibody interaction. The possible antigenic determinant sites on the surface of TCSrecognized by both the clones were analyzed, and the reaction forces between TCS and two Fab fragments werealso analyzed respectively.

Inclusion Property and Molecular Modeling of Calix[4]arene Derivatives

The inclusion properties of two calix[4]arene derivatives 5,11,17,23 tetra tert butyl 25, 27 bis (isopropyl carbamoyl methoxy) 26,28 diundecenyloxy calix[4]arene (C[4]A) and 25,27 dibutoxy 5,11,17,23 tetra tert butyl 26,28 diundecenyloxy calix[4]arene (C[4]B) were studied by gas chromatographic method. It was found that C[4]A could form inclusion complexes with benzene, toluene, methanol and ethanol while C[4]B could only form inclusion complex with methanol, which might be due to the different conformations of C[4]A and C[4]B. Molecular modeling showed that CH/π and OH/π interactions played important roles in the forming of inclusion complexes.

Predicting liposome formulations by the integrated machine learning and molecular modeling approaches

Liposome is one of the most widely used carriers for drug delivery because of the great biocompatibility and biodegradability.Due to the complex formulation components and preparation process,formulation screening mostly relies on trial-and-error process with low efficiency.Here liposome formulation prediction models have been built by machine learning(ML)approaches.The important parameters of liposomes,including size,polydispersity index(PDI),zeta potential and encapsulation,are predicted individually by optimal ML algorithm,while the formulation features are also ranked to provide important guidance for formulation design.The analysis of key parameter reveals that drug molecules with logS[-3,-6],molecular complexity[500,1000]and XLogP3(≥2)are priority for preparing liposome with higher encapsulation.In addition,naproxen(NAP)and palmatine HCl(PAL)represented the insoluble and water-soluble molecules are prepared as liposome formulations to validate prediction ability.The consistency between predicted and experimental value verifies the satisfied accuracy of ML models.As the drug properties are critical for liposome particles,the molecular interactions and dynamics of NAP and PAL liposome are further investigated by coarse-grained molecular dynamics simulations.The modeling structure reveals that NAP molecules could distribute into lipid layer,while most PAL molecules aggregate in the inner aqueous phase of liposome.The completely different physical state of NAP and PAL confirms the importance of drug properties for liposome formulations.In summary,the general prediction models are built to predict liposome formulations,and the impacts of key factors are analyzed by combing ML with molecular modeling.The availability and rationality of these intelligent prediction systems have been proved in this study,which could be applied for liposome formulation development in the future.