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.

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.

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.

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.

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.

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.

DFT Study on Molecular Structures and ROS Scavenging Mechanisms of Novel Antioxidants from Lespedeza Virgata

The molecular structure and radical scavenging activity of three novel antioxidants from Lespedeza Virgata, lespedezavirgatol, lespedezavirgatal, and lespedezacoumestan, have been studied using density functional theory with the B3LYP and BhandHLYP methods. The optimized geometries of neutral, radical cation, radical and anion forms were obtained at the B3LYP/6-31G（d） level, in which it was found that all the most stable conformations contain intramolecular hydrogen bonds. The same results were obtained from the MP2 method. The homolytic O-H bond dissociation enthalpy and the adiabatic ionization potential of neutral and anion forms for the three new antioxidants and adiabatic electron affinity and H-atom affinity for hydroxyl radical, superoxide anion radical, and hydrogen peroxide radical were determined both in gas phase and in aqueous solution using IEF-PCM and CPCM model with UAHF or Bondi cavity. The antioxidant activities and reactive oxygen species scavenging mechanisms were then discussed, and the results obtained from different methods are consistent. Furthermore, the antioxidant activities are consistent with the experimental findings of the compounds under investigation.

Regulating the Solvation Structure of Li^(+) Enables Chemical Prelithiation of Silicon-Based Anodes Toward High-Energy Lithium-Ion Batteries

The solvation structure of Li^(+) in chemical prelithiation reagent plays a key role in improving the low initial Coulombic efficiency(ICE) and poor cycle performance of silicon-based materials. Never theless, the chemical prelithiation agent is difficult to dope active Li^(+) in silicon-based anodes because of their low working voltage and sluggish Li^(+) diffusion rate. By selecting the lithium–arene complex reagent with 4-methylbiphenyl as an anion ligand and 2-methyltetrahydrofuran as a solvent, the as-prepared micro-sized Si O/C anode can achieve an ICE of nearly 100%. Interestingly, the best prelithium efficiency does not correspond to the lowest redox half-potential(E_(1/2)), and the prelithiation efficiency is determined by the specific influencing factors(E_(1/2), Li^(+) concentration, desolvation energy, and ion diffusion path). In addition, molecular dynamics simulations demonstrate that the ideal prelithiation efficiency can be achieved by choosing appropriate anion ligand and solvent to regulate the solvation structure of Li^(+). Furthermore, the positive effect of prelithiation on cycle performance has been verified by using an in-situ electrochemical dilatometry and solid electrolyte interphase film characterizations.

Unraveling structure and performance of protein a ligands at liquid–solid interfaces: A multi-techniques analysis

Oriented ligand immobilization is one of the most effective strategies used in the design and construction of a high-capacity protein A chromatography. In this work, cysteine was introduced as anchoring sites by substituting a specific residue on Helix Ⅰ, Ⅱ, and at C-terminus of antibody binding domain Z from protein A, respectively, to investigate structural evolution and binding behavior of protein A ligands at liquid-solid interfaces. Among the three affinity dextran-coated Fe_(3)O_(4) magnetic nanoparticles(Fe_(3)O_(4)@Dx MNPs), affinity MNPs with the immobilized ligand via N11C on Helix Ⅰ(Fe_(3)O_(4)@Dx-Z_(1) MNPs) had the highest helical content, and MNPs with the immobilized ligand via G29C on Helix Ⅱ(Fe_(3)O_(4)@Dx-Z_(2) MNPs) had the lowest helical content at the same pHs. It was attributed to less electrostatic attraction of ligand to negatively charged surface on Fe_(3)O_(4)@Dx-Z_(1) MNPs because of less positive charged residues on Helix Ⅰ(K6) than Helix Ⅱ(R27/K35). Among the three affinity MNPs, moreover, the highest affinity to immunoglobulin G(IgG) binding was observed on Fe_(3)O_(4)@Dx-Z_(1) MNPs in isothermal titration calorimetry measurement, further validating greater structural integrity of the ligand on Fe_(3)O_(4)@Dx-Z_(1) MNPs. Finally,the study of IgG binding on MNPs and 96-well plates showed that anchoring sites for ligand immobilization had distinct influences on IgG binding and IgG-mediated antigen binding. This work illustrated that anchoring sites of the ligands had a striking significance for the molecular structure of the ligand at liquid-solid interfaces and raised an important implication for the design and optimization of protein A chromatography and protein A-based immunoassay analysis.

SEMI-EMPIRICAL CALCULATION FOR ELECTRONIC STRUCTURE OF C60 CLUSTER BY MOLECULAR DYNAMICS AND MNDO APPROACH

The electronic structure for C 60 was semi empirically investigated by using MD (molecular dynamics) and MNDO (modified neglect of diatomic overlap) approach of quantum chemistry.Especially,taking both σ and π orbitals into account,one electron energy levels,those symmetries and π orbital occupancies as well as electron excitation energies for different select rules,cohesive energy,ionization energies and electronic affinity forces were calculated.The obtained molecular orbital ratio shows a wide separation of σ and π types,and near HOMO and LUMO levels there are π orbitals mainly.The calculated semi empirical calculation results are in good agreement with experimental and ab initio calculation data.

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.

Interactive association between processing induced molecular structure changes and nutrient delivery on a molecular basis,revealed by cutting-edge vibrational biomolecular spectroscopy

Background:This study was conducted to determine protein molecular structure profiles and quantify the relationship between protein structural features and protein metabolism and bioavailability of blend pel eted products(BPP)based on co-products(canola or carinata)from processing with different proportions of pulse pea screenings and lignosulfonate chemical compound.Method:The protein molecular structures were determined using the non-invasive advanced vibrational molecular spectroscopy(ATR-FT/IR)in terms of chemical structure and biofunctional groups of amides(ⅠandⅡ),α-helix andβ-sheet.Results:The results showed that increasing the level of the co-products in BPP significantly increased the spectral intensity of the amide area and amide height.The products exhibited similar protein secondaryα-helix toβ-sheet ratio.The protein molecular structure profiles(amidesⅠandⅡ,α-helix toβ-sheet)were highly associated with protein degradation kinetics and intestinal digestion.In conclusion,the non-invasive vibrational molecular spectroscopy(ATR-FT/IR)could be used to detect inherent structural make-up characteristics in BPP.Conclusion:The molecular structural features related to protein biopolymer were highly associated with protein utilization and metabolism.

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics （MD） simulations are performed to study the stability of structure H clathrate-hydrates of methane＋large-molecule guest substance （LMGS） at temperatures of 270, 273, 278 and 280 K under canonical （NVT-） ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane （2-MB）, 2,3-dimethylbutane （2,3-DMB）, neohexane （NH）, methylcyclohexane （MCH）, adamantane and tert-butyl methyl ether （TBME）. In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions （RDFs） of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.

Molecular characteristics and structure–activity relationships of food-derived bioactive peptides

Peptides are functional active fragments of proteins which can provide nutrients needed for human growth and development,and they also have unique physiological activity characteristics relative to proteins.Bioactive peptides contain a great deal of development potential.More specifically,food-derived bioactive peptides have the advantages of a wide variety of sources,unique structures,high efficiency and safety,so they have broad development prospects.This review provides an overview of the current advances regarding the preparation,functional characteristics,and structure–activity relationships of food-derived bioactive peptides.Moreover,the prospects for the future development and application of food-derived bioactive peptides are discussed.This review may provide a better understanding of foodderived bioactive peptides,and some constructive inspirations for further research and applications in the food industry.

Molecular Structure of Kerogen in the Longmaxi Shale: Insights from Solid State NMR, FT-IR, XRD and HRTEM

Kerogen plays an important role in shale gas adsorption,desorption and diffusion.Therefore,it is necessary to characterize the molecular structure of kerogen.In this study,four kerogen samples were isolated from the organic-rich shale of the Longmaxi Formation.Raman spectroscopy was used to determine the maturity of these kerogen samples.Highresolution transmission electron microscopy(HRTEM),13 C nuclear magnetic resonance(13 C NMR),X-ray diffraction(XRD)and Fourier transform infrared(FT-IR)spectroscopy were conducted to characterize the molecular structure of the shale samples.The results demonstrate that VReqv of these kerogen samples vary from 2.3%to 2.8%,suggesting that all the kerogen samples are in the dry gas window.The macromolecular carbon skeleton of the Longmaxi Formation kerogen is mainly aromatic(fa’=0.56).In addition,the aromatic structural units are mainly composed of naphthalene(23%),anthracene(23%)and phenanthrene(29%).However,the aliphatic structure of the kerogen macromolecules is relatively low(fal*+falH=0.08),which is presumed to be distributed in the form of methyl and short aliphatic chains at the edge of the aromatic units.The oxygen-containing functional groups in the macromolecules are mainly present in the form of carbonyl groups(fac=0.23)and hydroxyl groups or ether groups(falO=0.13).The crystallite structural parameters of kerogen,including the stacking height(Lc=22.84?),average lateral size(La=29.29?)and interlayer spacing(d002=3.43?),are close to the aromatic structural parameters of anthracite or overmature kerogen.High-resolution transmission electron microscopy reveals that the aromatic structure is well oriented,and more than 65%of the diffractive aromatic layers are concentrated in the main direction.Due to the continuous deep burial,the longer aliphatic chains and oxygen-containing functional groups in the kerogen are substantially depleted.However,the ductility and stacking degree of the aromatic structure increases during thermal evolution.This study provides quantitative information on the molecular structure of kerogen samples based on multiple research methods,which may contribute to an improved understanding of the organic pores in black shale.

Synthesis and X-ray Crystal Structure of a New Molecular Clip

The synthesis and X-ray crystal structure of a new molecular clip 2 was reported. It （C24H24N4O2, Mr = 400.47） crystallizes in the space group C2/c with a = 15.587（2）, b = 8.5805（12）, c = 15.259（2） A, β = 102.448（3）°, V= 1992.9 （5）A63, Z = 4, Dc = 1.335 g/cm63,μ = 0.087 mm^-1 and F（000） = 848. It remains monomeric in the crystal and a tape-like structure is formed in the crystal structure of molecular clip. The most unusual structural feature of 2 is the boat conformation of its cyclohexyl ring imposed by the ring fusion at C（9）-C（9a）.

Structure and Properties of Self-reinforced Material Made from Ultra-high Molecular Weight Polyethylene-montmorillonite Nanocomposite

High-strength and high-modulus ultra-high molecular weight polyethylene(UHMWPE), named self-reinforced material, was obtained by the elongation of UHMWPE-montmorillonite nanocomposite at melting temperature. According to the scanning electron microscope(SEM) analysis, a great deal of fibrillar texture formed in the direction of elongation, and the tensile fractured surface was similar to that of highly oriented fiber. The transmission electron microscope(TEM) and selective area electron diffraction(SAED) analyses reveal that the reinforced phase of the self-reinforced material is an extended chain crystal and its size is about 50_200 nm wide and several microns long, and the montmorillonite layers are broken up to pieces in the size from 100 to 10 nm. The broken layers which have a huge surface area interacting strongly with macromolecules reduces the entanglement density of UHMWPE and induces the chain orientation in flow field. It is supposed that the astriction of montmorillonite layers to polyethylene chains is not only end-tethered but also side-tethered. The differential scan calorimetry(DSC) analysis shows that there are two endothermal peaks for the self-reinforced material, of which the peak at a higher temperature(136.4 ℃) is ascribed to the melting of the reinforced phase.