Molecular mechanics and dynamics simulation of hydrogen diffusion in aluminum melt

The main impurities in aluminum melt are hydrogen and Al_2O_3,which can deteriorate melt quality and materials performance.However,the diffusion process of H atoms in aluminum melt and the interactions among Al atoms,Al_2O_3 and hydrogen have been studied rarely.Molecular mechanics and dynamics simulations are employed to study the diffusion behaviors of different types of hydrogen,such as free H atoms,H atoms in H_2 and H^+ions in H_2O using COMPASS force field.Correspondingly,force field types h,h1h and h1o are used to describe different types of hydrogen which are labeled as H_h,H_(h1h) and H_(h1o).The results show that the adsorption areas are maximum for H_(h1o),followed by H_(h1h) and H_h.The diffusion ability of H_(h1o) is the strongest whereas H_h is hard to diffuse in aluminum melt because of the differences in radius and potential well depth of various types of hydrogen.Al_2O_3 cluster makes the Al atoms array disordered,creating the energy conditions for hydrogen diffusion in aluminum melt.Al_2O_3 improves the diffusion of H_h and H_(h1o),and constrains H_(h1h) which accumulates around it and forms gas porosities in aluminum.H_(h1o) is the most dispersive in aluminum melt,moreover,the distance of Al-H_(h1o) is shorter than that of Al-H_(h1h),both of which are detrimental to the removal of H_(h1o).The simulation results indicate that the gas porosities can be eliminated by the removal of Al_2O_3 inclusions,and the dispersive hydrogen can be removed by adsorption function of gas bubbles or molten fluxes.

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes （SWCNT＇s） is established to describe the nonlinear stress-strain curve of SWCNT＇s and to predict both the elastic properties and breaking strain of SWCNT＇s during tensile deformation. An analysis based on the virtual internal bond （VIB） model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT＇s.

Molecular Mechanics Study on Asymmetry Catalysis

A ground state model about an asymmetry hydrogenation of methyl pyruvate over Pt-nanocluster catalyst with a modifier cinconidine has been built. The role of the modifier in the catalytic process is explained.

THE INFLUENCE OF SUBSTITUENT ELECTRONIC EFFECT ON ETHYLENE OLIGOMERIZATION ACTIVITIES OF BIS(IMINO)PYRIDYL Fe(Ⅱ) CATALYSTS:A COMBINED MOLECULAR MECHANICS AND CHARGE EQUILIBRATION METHOD

Bis(imino)pyridyl Fe(Ⅱ) complexes are important catalysts in ethylene oligomerization for preparingα-olefins. The metal net charge-activity relationship of bis(imino)pyridyl Fe(Ⅱ) complexes was investigated by molecular mechanics (MM) and net charge equilibration(QEq) method with modified Dreiding force field.It was found that metal net charge was in reverse ratio to ethylene oligomerization activity.Electron-donor substituents with less steric hindrance to the central metal were favorable to Fe complex act...

Determination of Three-Dimensional Structures of Oridonin in Solution by NOESY Spectrum and Molecular Mechanics Calculation

The phase sensitive NOESY spectrum of oridonin was treated using Full Relaxation Matrix Analysis(FRMA) approach, and the cross relaxation rates of proton pairs were obtained by diagonalizing the NOE matrix of oridonin. The inter proton distances were calculated according to 1/r6 ij ∝σij. The three-dimensional structure of oridonin in solution was calculated by the combination of WUPH, WUPH-S method with molecular mechanics minimization on the basis of NMR experiment.

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phcnylamidc) Dimethyl (tetra-methylecyclopenta- dienyl)Silane Titanium Dichloride

Crystal and molecular structure of (2.6-dipropylphenylamidc) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained tyom a mixture of ether/hexane as orthorhombic, with a = 12.658 (3 ) A. b = 16.62 (3) A. c = 11 .760 (2) A. V = 2474,2 (9) A. Z = 4. space group Pnma. R = 0.0399. Compound I compose of the R -bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.

A Study of a Molecular Mechanics Field Used in Simulating Enantiorecognition

A molecular mechanics field, Alchemy II, was utilized to model the chiral recognition between S-N-acetyl-alpha-methyl-alpha-naphthylamine and (R, S)-N-(3, 5-dinitrophrnyl)-alpha-methyl-benzeneacetamide and between beta-cyclodextrin and (R, S)-fenoprofen. Some preliminary results have: been obtained to sustain the three-point action models and the induce-fit action in enantiorecognition.

FULLERENE GEOMETRY PREDICTION WITH MOLECULAR MECHANICS CALCULATIONS

A serial of fullerenes had been built and the optimized geome- tries had been obtained with the energy minimization of molecular mechanics calculations according to the fact that the pentagonal number is exactly 12 in the fullerenes which consist of pentagons and hexagons.The fullerene geometry prediction could facilitate further theoretical and synthetical studies in the near future.

Fluid-Solid Interaction Analysis of Drug Delivery Mechanism to Damaged Cancer Cellules in the Shape of Single-Walled Carbon Nanocone by Molecular Mechanics Approach

Drug delivery systems able to deliver the required dose of the drug to the target level use active or passive nano metric designed systems. In the earlier researches, carbon nanocones are used for transferring the serum to damaged proteins and damaged cancer cellules. In this lecture, stability analysis of drug delivery to damaged cancer cellutes is studied in the shape of single-walled carbon nanocone. In this method, each atom is considered as node and interactions between them are supposed as 3D-beam elements. By supposing that potential energy in macro relations is equal to the nano relations, nano-drug characteristics can be calculated. Then shape functions can be extracted to use in blood＇s FEM model and using reduced-order method, divergence velocities of carbon nanocone can be found. In this lecture, carbon nanocones are modeled with different dimensions and boundary conditions and stability of them in blood flow is studied and optimized carbon nanocone is selected in blood flow. Results show that conical nano-drug structures have more efficiency in blood flow rather than tube nano-drug structures and by increasing length of carbon nanocones, dimensionless stability parameter decreased and by increasing declination angle of carbon nanocones, dimensionless stability parameter increased.

Comparative Molecular Mechanics and Quantum Mechanics Study of Monohydration of Nucleic Acid Bases

DNA is the most important biological molecule and its hydration contributes essentially to the structure and functions of the double helix. We analyze the monohydration of the individual bases of nucleic acids and their methyl derivatives using methods of Molecular Mechanics (MM) with the Poltev-Malenkov (PM), AMBER and OPLS force fields, as well as ab initio Quantum Mechanics (QM) calculations at MP2/6-31G(d,p) level of theory. A comparison is made between the calculated interaction energies and the experimental enthalpies of microhydration of bases, obtained from mass spectrometry at low temperatures. Each local water-base interaction energy minimum obtained with MM corresponds to the minimum obtained with QM. General qualitative agreement was observed in the geometrical characteristics of the local minima obtained via the two groups of methods. MM minima correspond to slightly more coplanar structures than those obtained via QM methods, and the absolute MM energy values overestimate corresponding values obtained with QM. For Adenine and Thymine the QM local minima energy values are closer to those obtained by the PM potential (average of 0.72 kcal/mol) than by the AMBER force field (1.86 kcal/mol). The differences in energy between MM and QM results are more pronounced for Guanine and Cytosine, especially for minima with the water molecule forming H-bonds with two proton-acceptor centers of the base. Such minima are the deepest ones obtained via MM methods while QM calculations result in the global minima corresponding to water molecule H-bonded to one acceptor and one donor site of the base. Calculations for trimethylated bases with a water molecule corroborate the MM results. The energy profiles were obtained with some degrees of freedom of the water molecule being frozen. This data will contribute to the improvement of the molecular mechanics force fields.

Molecular Mechanism and Molecular Design of Lubricating Oil Antioxidants

To overcome the limitations of traditional experimental“trial and error”methods in lubricant additive design,a new molecular design method based on molecular structure parameters is established here.The molecular mechanism of the antioxidant reaction of hindered phenol,diphenylamine,and alkyl sulfide are studied via molecular simulations.Calculation results show that the strong electron-donating ability and high hydrogen-donating activity of the antioxidant molecule and the low hydrogen-abstracting activity of free radicals formed after dehydrogenation are the internal molecular causes of the shielding of phenol and diphenylamine from scavenging peroxy free radicals,and the strong electron-donating ability is the internal molecular cause of the high activity of thioether in decomposing alkyl hydrogen peroxide.Based on this antioxidant molecular mechanism,a molecular design rule of antioxidant is proposed,namely“high EHOMO,large Q(S),low bond dissociation energy BDE(O—H)and BDE(N—H)”.Two new antioxidants,PAS-I and PAS-II,are designed and prepared by chemical bonding of hindered phenol,diphenylamine,and sulfur atoms.Experimental results show that these antioxidants both have excellent antioxidant effects in lubricating oil,and that PAS-II is the superior antioxidant,consistent with theoretical predictions.

Absorption characteristics,model,and molecular mechanism of hydrogen sulfide in morpholine acetate aqueous solution

The solubility of H_(2)S was measured in solutions of N-butyl-N-methylmorpholine acetate([Bmmorp][Ac])containing 20%-40%(mass)water at experimental temperatures ranged from 298.15 to 328.15 K and pressures up to 320 k Pa.The total solubility of H_(2)S increased with higher temperatures,lower pressures,and reduced water content.The reaction equilibrium thermodynamic model was used to correlate the solubility data.The results indicate that the chemical reaction equilibrium constant decrease with increasing water content and temperature,whereas Henry constant increase with increasing water content and temperature.Compared with other ionic liquids,H_(2)S exhibits a higher physical absorption enthalpy and a lower chemical absorption enthalpy in[Bmmorp][Ac]aqueous solution.This suggests that[Bmmorp][Ac]has a strong physical affinity for H_(2)S and low energy requirement for desorption.Quantum chemical methods were used to investigate the molecular mechanism of H_(2)S absorption in ionic liquids.The interaction energy analysis revealed that the binding of H_(2)S with the ionic liquid in a1:2 ratio is more stable.Detailed analyses by the methods of the interaction region indicator and the atoms in molecules were conducted to the interactions between H_(2)S and the ionic liquid.

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.

Seed Storability in Rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

Transcriptome profiling and RXR gene family identification reveals the molecular mechanism of rapid aging after spawning of cuttlefish Sepiella japonica

Sepiella japonica is a worldwide marine cuttlefish species of high economic value.S.japonica routinely modifying behaviors in reproductive life,such as rapid aging until death after spawning,has been recognized in artificial breeding.However,reproductive behavior at the level of genes is rarely reported,thus,the research on the genetic basis of behavior,reproduction,and artificial breeding was limited.We applied RNA-seq in different stages of reproduction to investigate the reason of rapid aging after spawning,pre-maturity,pre-spawning after maturity,and post-spawning.The retinoid X receptor(RXR)gene family in S.japonica was identified,and 1343–1452 differentially expressed genes(DEGs)in all 3 stages of reproductive life were identified from pairwise m RNA comparisons.Furthermore,through the GO term and KEGG analysis,S.japonica could handle neuronal development and network formation before maturity and have a functional degradation of neural communication,signal transduction,vision,and gene expression after spawning.Eight Sj RXRαs have been identified and they played different roles in growth development or reproduction.Therefore,the regulation of several channels and receptors is the intrinsic molecular mechanism of rapid aging after spawning in S.japonica.This study revealed the survival strategy and provided fundamental data on the level of genes for understanding the reproductive behavior and the reproduction of S.japonica.

Molecular mechanisms of aflatoxin neurotoxicity and potential neuroprotective agents

Aflatoxins(AFTs)represent one of the most notorious classes of deadly mycotoxins produced by certain fungi that are found on agricultural crops.Aflatoxins are highly toxic to mammals and are known to cause a series of detrimental effects,including neuro-,hepato-,nephron-,and immuno-toxicity.In this original review we summarize the mechanisms of aflatoxin-induced neurotoxicity and the clinical potential of novel neuroprotective agents.Aflatoxin B1(AFB1)is the most toxic congener among the 21 identified AFTs.Recent studies have shown that food borne exposure to AFB1 and/or its metabolites often leads to fatal neurotoxicity in animals and humans.Animal studies indicated that AFB1 exposure could induce abnormal behavioral changes,including anxiety,lethargy disorders,depression-like behavior,cognitive,learning and memory defects,and decreased feeding behavior.Mechanistically,AFB1 exposure has been associated with lipid peroxidation,ablation of non-enzymatic and enzymatic antioxidant defense systems and decreased neurotransmitter levels.AFB1 exposure has also been shown to induce DNA damage,apoptosis,pyroptosis,and mitochondrial dysfunction in the brain tissue.Several signaling pathways,including gasdermin D,toll like receptor 2(TLR2),TLR4,Akt,NF-κB,ERK/MAPK,protein kinase C(PKC),and mitochondrial apoptotic pathways have been shown to participate in AFB1-induced neuronal or astrocyte cell death.Targeting these pathways by small molecules(e.g.,quercetin,curcumin,and gallic acid,and dimethyl fumarate),Chinese herbal extracts(e.g.,Artichoke leaf extract,Chelidonium majus ethanolic extract,pumpkin extract,and Crocus sativus L.tea),and probiotic supplements could effectively improve AFB1-induced neurobehavioral abnormalities and neurotoxicity.To date,the precise molecular mechanisms of AFB1-induced neurotoxicity and potential neuroprotective agents remain unclear.In the present review,the clinical manifestations,molecular mechanisms,and potential neuroprotective agents of AFB1-induced neurotoxicity are summarized in the broadest overview.It is most hopeful that this broad reaching review provides valuable insights and stimulates broader discussion to develop the effective neuroprotective agents against aflatoxins.

Boswellic acids: a review on its pharmacological properties, molecular mechanism and bioavailability

Boswellic acids is a general term for a series of pentacyclic triterpenoid compounds that are isolated from the oleogin resin of the Boswellia genus and serve as the main active ingredient.It exhibits a wide range of biological activities,such as anti-inflammatory,anti-cancer,antibacterial,antiviral,hepatoprotective,neuroprotective,anti-diabetic,and anti-thrombotic properties.As a result,it has gained significant recognition among practitioners of traditional Chinese and Indian medicine.These biological effects may be associated with multiple molecular targets and signal transduction pathways.However,the poor pharmacokinetic properties of the substance lead to lower bioavailability,which affects its effectiveness.To address this issue,scientists have proposed a number of strategies,such as solid dispersions,phytosome®technologies,and novel drug delivery systems.This article aims to provide a comprehensive overview for boswellic acids on the phytochemistry,molecular mechanisms,potential therapeutic applications,and strategies to improve bioavailability.

Dysregulated microRNAs in type 2 diabetes and breast cancer:Potential associated molecular mechanisms

Type 2 diabetes(T2D)is a multifaceted and heterogeneous syndrome associated with complications such as hypertension,coronary artery disease,and notably,breast cancer(BC).The connection between T2D and BC is established through processes that involve insulin resistance,inflammation and other factors.Despite this comprehension the specific cellular and molecular mechanisms linking T2D to BC,especially through microRNAs(miRNAs),remain elusive.miRNAs are regulators of gene expression at the post-transcriptional level and have the function of regulating target genes by modulating various signaling pathways and biological processes.However,the signaling pathways and biological processes regulated by miRNAs that are associated with T2D and BC have not yet been elucidated.This review aims to identify dysregulated miRNAs in both T2D and BC,exploring potential signaling pathways and biological processes that collectively contribute to the development of BC.

Classification of musical hallucinations and the characters along with neural-molecular mechanisms of musical hallucinations associated with psychiatric disorders

BACKGROUND Musical hallucinations(MH)involve the false perception of music in the absence of external stimuli which links with different etiologies.The pathomechanisms of MH encompass various conditions.The etiological classification of MH is of particular importance and offers valuable insights to understand MH,and further to develop the effective treatment of MH.Over the recent decades,more MH cases have been reported,revealing newly identified medical and psychiatric causes of MH.Functional imaging studies reveal that MH activates a wide array of brain regions.An up-to-date analysis on MH,especially on MH comorbid psychiatric conditions is warranted.AIM To propose a new classification of MH;to study the age and gender differences of MH in mental disorders;and neuropathology of MH.METHODS Literatures searches were conducted using keywords such as“music hallucination,”“music hallucination and mental illness,”“music hallucination and gender difference,”and“music hallucination and psychiatric disease”in the databases of PubMed,Google Scholar,and Web of Science.MH cases were collected and categorized based on their etiologies.The t-test and ANOVA were employed(P<0.05)to compare the age differences of MH different etiological groups.Function neuroimaging studies of neural networks regulating MH and their possible molecular mechanisms were discussed.RESULTS Among the 357 yielded publications,294 MH cases were collected.The average age of MH cases was 67.9 years,with a predominance of females(66.8%females vs 33.2%males).MH was classified into eight groups based on their etiological mechanisms.Statistical analysis of MH cases indicates varying associations with psychiatric diagnoses.CONCLUSION We carried out a more comprehensive review of MH studies.For the first time according to our knowledge,we demonstrated the psychiatric conditions linked and/or associated with MH from statistical,biological and molecular point of view.

Advances in Molecular Regulatory Mechanisms of Fruit Trees under Low Temperature Stress

The most recent research findings on the tolerance of fruit trees to cold stress are reviewed from a molecular perspective,including the perception and transduction of low temperature calcium signaling,CBF-dependent molecular regulatory mechanisms,non-CBF-dependent molecular regulatory mechanisms,and so forth.The objective is to provide a reference basis for further improving the cold resistance of fruit trees and cultivating new varieties of hardy plants.