The chemical environment and structural ordering in liquid Mg-Y-Zn system:An ab-initio molecular dynamics investigation of melt for the formation mechanism of LPSO structure

In an effort to clarify the formation mechanism of LPSO structure in Mg-Y-Zn alloy,the chemical environment and structural ordering in liquid Mg-rich Mg-Y-Zn system are investigated with the aid of ab-initio molecular dynamics simulation.In liquid Mg-rich Mg-Y alloys,the strong Mg-Y interaction is determined,which promotes the formation of fivefold symmetric local structure.For Mg-Zn alloys,the weak Mg-Zn interaction results in the fivefold symmetry weakening in the liquid structure.Due to the coexistence of Y and Zn,the strong attractive interaction is introduced in liquid Mg-Y-Zn ternary alloy,and contributes to the clustering of Mg,Y,Zn launched from Zn.What is more,the distribution of local structures becomes closer to that in pure Mg compared with that in binary Mg-Y and Mg-Zn alloys.These results should relate to the origins of the Y/Zn segregation zone and close-packed stacking mode in LPSO structure,which provides a new insight into the formation mechanism of LPSO structure at atomic level.

Molecular simulation study on the evolution process of hydrate residual structures into hydrate

The clathrate hydrate memory effect is a fascinating phenomenon with potential applications in carbon capture,utilization and storage(CCUS),gas separation,and gas storage as it can accelerate the secondary formation of clathrate hydrate.However,the underlying mechanism of this effect remains unclear.To gain a better understanding of the mechanism,we conducted molecular dynamic simulations to simulate the initial formation and reformation processes of methane hydrate.In this work,we showed the evolution process of hydrate residual structures into hydrate cages.The simulation results indicate that the residual structures are closely related to the existence of hydrate memory effect,and the higher the contribution of hydrate dissociated water to the hydrate nucleation process,the faster the hydrate nucleation.After hydrate dissociation,the locally ordered structures still exist after hydrate dissociation and can promote the formation of cluster structures,thus accelerating hydrate nucleation.Additionally,the nucleation process of hydrate and the formation process of clusters are inseparable.The size of clusters composed of cup-cage structures is critical for hydrate nucleation.The residence time at high temperature after hydrate decomposition will affect the strength of the hydrate memory effect.Our simulation results provide microscopic insights into the occurrence of the hydrate memory effect and shed light on the hydrate reformation process at the molecular scale.

Structural characterizations andα-glucosidase inhibitory activities of four Lepidium meyenii polysaccharides with different molecular weights

Four polysaccharides(MCPa,MCPb,MCPc,MCPd)were obtained from Lepidium meyenii Walp.Their structures were characterized by chemical and instrumental methods including total sugar,uronic acid and protein content determi-nation,UV,IR and NMR spectroscopy,as well as monosaccharide composition determination and methylation analy-ses.Four polysaccharides were a group of glucans with different molecular weights ranging from 3.12 to 14.4 kDa,and shared a similar backbone chain consisting of(1→4)-glucose linkages with branches attached to C-3 and C-6.Furthermore,bioactivity assay showed that MCPs had concentration-dependent inhibitory activity onα-glucosidase.MCPb(Mw=10.1 kDa)and MCPc(Mw=5.62 kDa)with moderate molecular weights exhibited higher inhibitory activ-ity compared with MCPa and MCPd.

Molecular Dynamics Simulations of Silica Nanotube： Structural and Vibrational Properties Under Different Temperatures

Four-, six-, and eight-membered ring silica nanotubes at temperatures from 300 K to 1600 K are relaxed by classical molecular dynamics simulations with three potential models. The simulation results indicate that the stability of the end rings of the three silica nanotubes gradually decreases with increase in temperature. The validity of the vibrational features of silica nanotubes is shown by the vibrational density of states. Infrared spectra on the silica nanotubes under different temperatures are investigated. A detailed assignment of each spectral peak to the corresponding vibrational mode of the three nanotubes has been addressed. The results are in good agreement with the other theoretical and experimental

Structural origin for composition-dependent nearest atomic distance in Cu–Zr metallic glass

We systematically investigate the structures of Cu–Zr metallic glass(MG) by varying the Cu concentration in classic molecular-dynamics simulation. From the pair distribution functions(PDFs), it is found that the nearest atomic distance between Zr atom and Zr atom increases significantly after adding Cu, which is related to the composition-dependent coordination behavior between Cu atom and Zr atom in the nearest neighbors. The portion of PDF related to the nearest connection is decomposed into the contributions from quadrilateral structure, pentagonal structure, hexagonal structure,and heptagonal bipyramid structure. Although the population of denser structures, i.e. 5-, 6-, and 7-number sharing ones,increases with Cu addition increasing, the connection distances between the central atoms in all these bipyramids increase for Zr–Zr pairs, leading to the expansion of Zr–Zr nearest atomic distance. These results unveil the effect of the interplay between chemical interaction and geometric packing on the atomic-level structure in Cu–Zr metallic glasses.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame(Sesamum indicum L.) plays a crucial role in Ethiopian agriculture,serving both subsistence and commercial purposes.However,our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited.To address this knowledge gap,we genotyped 368 Ethiopian sesame germplasms,categorizing into four distinct breeding groups:Accessions,landraces,improved varieties,and wild types,using a comprehensive set of 28 polymorphic markers,including 23 simple sequence repeat(SSR) and five Insertion-Deletion(InDel) markers.These markers ensured robust genomic representation,with at least two markers per linkage group.Our results unveiled substantial genetic diversity,identifying a total of 535 alleles across all accessions.On average,each locus displayed 8.83 alleles,with observed and expected heterozygosity values of 0.30 and 0.36,respectively.Gene Diversity and Polymorphic Information Content(PIC) were recorded at 0.37 and 0.35.The percentage of polymorphic loci varied significantly among breeding groups,ranging from8.00% to 82.40%,indicating high diversity in accessions(82.4%),moderate diversity in improved varieties(31.20%) and landraces(29.60%),and limited diversity in wild types(8.00).Analysis of Molecular Variance(AMOVA) results emphasized significant genetic differentiation among populations,with substantial diversity(P<0.001) within each population.Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations,while the larger proportion of genetic diversity(92%) resided within each individual sesame population,showcasing heightened diversity within each group.Our study’s findings received support from both Bayesian clustering and Neighbor-joining(NJ) analysis,reaffirming the credibility of our genetic structure insights.Notably,Population structure analysis at its highest Δk value(k=2) revealed the existence of two primary genetic clusters,further subdivided into four sub-populations at k=4.Similarly,NJ analysis identified two prominent clusters,each displaying additional sub-clustering.In conclusion,our research provides a comprehensive understanding of genetic groups,subpopulations,and overall diversity within Ethiopian sesame populations.These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections.This genetic richness holds promise for breeding and conservation efforts,highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Structural Properties and Energy Analysis of Zr_(x)Cu_(90-x)Al_(10)Ternary Metallic Glasses

Classical molecular dynamics(MD)were conducted to study the structure and energy distribution of Zr_(x)Cu_(90-x)Al_(10)(x=20,30,40,50,60,70)ternary alloys.When the Zr composition is 30%,the glass transition temperature reaches the maximum value and the Zr_(30)Cu_(60)Al_(10)owns high glass forming ability(GFA).Analysis of the short⁃range structure shows that there are more low⁃energy Zr⁃centered polyhedron with high coordination number(CN)and Cu and Al⁃centered coordination polyhedron with CN=12 in Zr_(30)Cu_(60_Al_(10)alloy.As the medium⁃range structure is concerned,Zr_(30)Cu_(60_Al_(10)alloy has the largest number of coordination polyhedron connection sharing three atoms and connection in this way presenting the lowest energy.These low⁃energy and stable short and medium⁃range structures contribute to the high GFA of Zr_(30)Cu_(60_Al_(10).

A Modified Molecular Structural Mechanics Method for Analysis of Carbon Nanotubes

A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.

Computational investigation on the molecular structure and chemical reactivity of a traditional Chinese medicine extract MK-1 molecule

MK-1 molecule(C_(16)H_(16)O_(2)),the simplest structure of vitamin K(VK)compound family,is an extract from traditional Chinese medicine Cymbopogon distans(Nees ex Steud.)Wats(Chinese name YunXiangCao),which has attracted a great deal of attention in recent years due to its antiasthmatic,antitussives and expectorant effects.To investigate the molecular structure and chemical reactivity of MK-1 molecule,computational investigations on six conformational minima structures were carried out at the MP2/6-311++G(2d,2p)level of theory.Several local reactivity descriptors including condensed Fukui function,average local ionization energy,and molecular electrostatic potential on each individual atom were determined to predict the intrinsic reactivity of MK-1 molecule.

Structure and Vibrational Spectroscopy of 2-Methylallyl Alcohol

The intramolecular O−H…πhydrogen bond has garnered significant research interest in recent decades.In this work,we utilized the infrared(IR)-vacuum-ultraviolet(VUV)nonresonant ionization detected IR spectroscopy(NRID-IR)method to study the molecular structure of neutral and cationic 2-methylallyl alcohol(MAA,CH_(2)=C(CH_(3))−CH_(2)−OH).Density functional theory calculations revealed five stable neutral and three stable cationic MAA conformers,respectively.Two neutral MAA conformers are expected to have an O−H…πintramolecular hydrogen bond interaction,based on the structural characterization that the OH group is directed toward the C=C double bond.The IR spectra of both neutral(2700−3700 cm^(−1))and cationic MAA(2500−7200 cm^(−1))were measured,and the anharmonic IR spectra were calculated at the B3LYP-D3(BJ)/def2-TZVPP level.The OH stretching vibration frequency of neutral MAA was observed at 3656 cm−1,slightly lower than those of methanol and ethanol.In contrast,the OH stretching vibration of cationic MAA was red-shifted by about 140 cm^(−1)compared to neutral MAA.The interaction region indicator and natural bond orbital analysis suggest that the O−H…πinteraction in neutral MAA is weak,and may not play a major role in stabilizing the neutral MAA.

Emerging structures and dynamic mechanisms ofγ-secretase for Alzheimer’s disease

γ-Secretase,called“the proteasome of the membrane,”is a membrane-embedded protease complex that cleaves 150+peptide substrates with central roles in biology and medicine,including amyloid precursor protein and the Notch family of cell-surface receptors.Mutations inγ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer’s disease.γ-Secretase has thus served as a critical drug target for treating familial Alzheimer’s disease and the more common late-onset Alzheimer’s disease as well.However,critical gaps remain in understanding the mechanisms of processive proteolysis of substrates,the effects of familial Alzheimer’s disease mutations,and allosteric modulation of substrate cleavage byγ-secretase.In this review,we focus on recent studies of structural dynamic mechanisms ofγ-secretase.Different mechanisms,including the“Fit-Stay-Trim,”“Sliding-Unwinding,”and“Tilting-Unwinding,”have been proposed for substrate proteolysis of amyloid precursor protein byγ-secretase based on all-atom molecular dynamics simulations.While an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-boundγ-secretase,molecular dynamics simulations on a resolved model of Notch1-boundγ-secretase that was reconstructed using the amyloid precursor protein-boundγ-secretase as a template successfully capturedγ-secretase activation for proper cleavages of both wildtype and mutant Notch,being consistent with biochemical experimental findings.The approach could be potentially applied to decipher the processing mechanisms of various substrates byγ-secretase.In addition,controversy over the effects of familial Alzheimer’s disease mutations,particularly the issue of whether they stabilize or destabilizeγ-secretase-substrate complexes,is discussed.Finally,an outlook is provided for future studies ofγ-secretase,including pathways of substrate binding and product release,effects of modulators on familial Alzheimer’s disease mutations of theγ-secretase-substrate complexes.Comprehensive understanding of the functional mechanisms ofγ-secretase will greatly facilitate the rational design of effective drug molecules for treating familial Alzheimer’s disease and perhaps Alzheimer’s disease in general.

Effects of N_2 Pressure on the Structural and Electrical Properties of TiN Films Deposited by Laser Molecular Beam Epitaxy

Titanium nitride （TiN） films were deposited on Si（100） substrates by laser molecular beam epitaxy（LMBE）,and their properties of structure and resistivity with varying N2 pressure were investigated.The results showed that atomically flat TiN films with layer-by-layer growth mode were successfully grown on Si（100） substrates,and （200） was the preferred orientation.With the increasing of N2 pressure,the N/Ti ratio gradually increased and the diffraction peak progressively shifted towards lower diffraction angle.At pressure of 0.1 Pa,stoichiometric TiN film was formed which exhibited the characteristic diffraction angle of （200） plane.All films showed high reflectance to infrared spectrum and the films with overstoichiometry and understoichiometry had a higher resistivity owing to the surface particles and lattice distortion,while the stoichiometric TiN film depicted the minimum resistivity,around 19 μΩ·cm.

Simulation of Tensile Behaviors of Bamboo-like Carbon Nanotubes Based on Molecular Structural Mechanics Approach Combining with Finite Element Analysis

A molecular structural mechanics approach combining with finite element analysis(MSM/FEA) was applied to study the microstructure and tensile behaviors of bamboo-like carbon nanotubes(BCNTs). The mathematical model of tensile behaviors of BCNTs was established based on molecular structural mechanics theory. The deformations of BCNTs, with different diameters and compartments set based on the experimental investigation on BCNT structures synthesized by chemical vapor depositon, under tensile load, were analyzed with ANSYS programmed. Results show that the BCNTs have good tensile properties, and those Young's modulus can reach 0.84 Tpa. Through the analysis, it can be found that the Young's modulus of BCNTs depends on the diameters and the length of compartment, which is in good agreement with our experimental tests for the tensile performances of individual BCNT.

Study of structural and magnetic properties of Fe(80)P-9B(11) amorphous alloy by ab initio molecular dynamic simulation

The structural and magnetic properties of Fe80P9B11 amorphous alloy are investigated through ab initio molecular dynamic simulation. The structure evolution of Fe（80）P9B（11） amorphous alloy can be described in the framework of topological fluctuation theory, and the fluctuation of atomic hydrostatic stress gradually decreases upon cooling. The left sub peak of the second peak of Fe–B partial pair distribution functions（PDFs） becomes pronounced below the glass transition temperature, which may be the major reason why B promotes the glass formation ability significantly. The magnetization mainly originates from Fe 3d states, while small contribution results from metalloid elements P and B. This work may be helpful for developing Fe-based metallic glasses with both high saturation flux density and glass formation ability.

Optical and Structural Properties of In_(0.52)Al_(0.48)As/InP Structures Grown at Very High Arsenic Overpressures by Molecular Beam Epitaxy

Growth of ln0.52Al0.48As epitaxial layers on lnP(100) substrates by molecular beam epitaxy at a wide range of arsenic overpressures (V/III flux ratios from 30 to 300) has been carried out. Analysis performed using low-temperature photoluminescence (PL) and double-axis X-ray diffraction (XRD) shows a strong and prominent dependence of the PL and XRD linewidths on the V/III flux ratio. Under our growth conditions, both the PL and XRD linewidths exhibit a minimum point at a V/III flux ratio of 150 which corresponds to a maximum in the PL intensity and XRD intensity ratio. Flux ratios exceeding 150 result in an increase in both the PL and XRD linewidths corresponding to a reduction in their associated intensities. Room temperature Raman scattering measurements show a narrowing in the lnAs-like and AlAs-like longitudinal-optic (LO)phonon linewidths which broaden at high flux ratios, while the LO phonon frequencies exhibit a gradual reduction as the flux ratio is increased. PL spectra taken at increasing temperatures show a quenching of the main emission peak followed by the evolution of a broad lower energy emission which is possibly associated with deep lying centres. This effect is more prominent in samples grown at lower V/III flux ratios. Hall effect measurements show a gradual reduction in the mobility in correspondence to an increase in the electron concentration as the flux ratio is increased.

Water Photomolecular Evaporation Due to Light-Mediated Ortho-Para Spin Transitions

Recent discoveries have revealed a groundbreaking phenomenon where light alone, without any thermal input, can induce water evaporation, termed the “photomolecular effect”. This study explores a novel hypothesis that this effect can be explained by ortho-para magnetic spin interactions in water molecules within the water-air interface layer. Water molecules, consisting of hydrogen and oxygen, exhibit different nuclear spin states: ortho-(triplet) and para-(singlet). The interaction of polarized light with these spin states may induce transitions between the rotational levels of ortho- and para-forms due to catalysts like triplet oxygen (O2) in its inhomogeneous magnetic field. Resonance pumping at 532 nm (~18,797 cm−1) due to the transition v1-v2-v3 ~ 0-8-2 (~18,796 cm−1) results in an increase in molecular energy sufficient to overcome intermolecular forces at the water surface, thereby causing evaporation. The proposed ortho-para conversion mechanism involves spin-orbit coupling and specific resonance conditions. This theory provides a quantum mechanical perspective on the photomolecular effect, potentially offering insights into natural processes such as cloud formation and climate modeling, as well as practical applications in solar desalination and industrial drying. Further experimental validation is required to confirm the role of spin interactions in light-induced water evaporation.

Molecular Structural Characterization and Quantitative Prediction of Reduced Ion Mobility Constants for Diversified Organic Compounds

Based on two-dimensional topological structures, a novel molecular electronegativity interaction vector with hybridization （MEHIV） was developed to describe atomic hybridization state in different molecular environments. Five quantitative models by MEHIV characterization and multiple linear regression modeling were successfully established to predict reduced ion mobility constants （Ko） of alkanes, aromatic hydrocarbons, fatty alcohols, fatty aldehydes and ketones and carboxylic esters. The correlation coefficients Roy by leave-one-out cross-validation are 0.792, 0.787, 0,949, 0.972 and 0.981, respectively, and the standard deviations SDcv are 0.067, 0.086, 0.064, 0.043 and 0.042, respectively. These results suggested that MEHIV is an excellent topological index descriptor with many advantages such as straightforward physicochemical meaning, high characterization competence, convenient expansibility and easy manipulation.

Preparation and Fluorescence Properties of Co-doped Nanocomposite Film Based on Supra Molecular Structure

A novel materials design procedure based on the co-doping of metal nanoparticle and azo dye compound （MNPADC） is developed to improve the properties of functional molecules. The synthesized materials were characterized by transmission electron micrograph （TEM）, ultraviolet-visible absorption spectra （UV-Vis） and fluorescence spectra （FS）. It was found that the fluorescence intensity of methyl orange （MO） was enhanced by 5 times in the aqueous composite system doped with silver nanoparticles whereas it was reduced by 15% and 20% in composite films with co-mixing and coating structures, respectively. The results indicate that the properties of functional molecules can be greatly improved in composite film with supra molecular structure and that the procedure presented here is effective.

Molecular dynamics simulation of relationship between local structure and dynamics during glass transition of Mg_7Zn_3 alloy

The rapid solidification process of Mg7Zn3 alloy was simulated by the molecular dynamics method. The relationship between the local structure and the dynamics during the liquid-glass transition was deeply investigated. It was found that the Mg-centered FK polyhedron and the Zn-centered icosahedron play a critical role in the formation of Mg7Zn3 metallic glass. The self-diffusion coefficients of Mg and Zn atoms deviate from the Arrhenius law near the melting temperature and then satisfy the power law. According to the time correlation functions of mean-square displacement, incoherent intermediate scattering function and non-Gaussian parameter, it was found that the β-relaxation in Mg7Zn3 supercooled liquid becomes more and more evident with decreasing temperature, and the α-relaxation time rapidly increases in the VFT law. Moreover, the smaller Zn atom has a faster relaxation behavior than the Mg atom. Some local atomic structures with short-range order have lower mobility, and they play a critical role in the appearance of cage effect in theβ-relaxation regime. The dynamics deviates from the Arrhenius law just at the temperature as the number of local atomic structures begins to rapidly increase. The dynamic glass transition temperature （Tc） is close to the glass transition point in structure （TgStr）.

Molecular Design and Electronic Structure Investigation of Novel Nitrogen Heteroatom 2-β-Naphthylbenzoxazoles

For the aim of finding new available functional materials, a series of nitrogen heteroatom 2 β naphthylbenzoxazole molecules were designed based on the experiment and theoretical studies of 2 β naphthylbenzoxazole molecule. Geometry optimization of the 2 β naphthylbenzoxazole was carried out by using Hyperchem Molecular Mechanics plus MM+. The planar molecular structure was obtained. The quantum chemistry calculating method PPP SCF CI, which is specially available to treat electron spectrum, was applied to investigate each novel designed molecules. Their electronic structures were analyzed in detail, it shows that total π electron energy decreased linearly with the number of replaced nitrogen. Single nitrogen atom located in benzoxazole ring or naphthalene ring results in contrary changes of level difference of FMO; multiple nitrogen atoms located in different molecular positions will lead to polarization of extremum in the level difference of FMO; and 5 nitrogen heteroatoms reach the culmination. Considering other electronic structure information, some favorable designed molecules were identified.