Synthesis and Ion-Binding Properties of Polymeric Pseudocrown Ethers: A Molecular Dynamics Study

Abstract

A novel method for producing inexpensive polymeric pseudocrown ethers in situ during free-radical polymerizations was investigated using molecular dynamics simulations. This scheme is based upon a template ion and exploits the tendency of oligomeric ethylene glycol diacrylates to form intramolecular cycles during polymerization. In the scheme, a template ion is used to induce the poly(ethylene glycol) diacrylates (PEGDA) to assume cyclic structures before polymerization with a comonomer. Experimental studies demonstrated that certain salts that were insoluble in nonpolar solvents were solubilized upon the addition of oligomeric poly(ethylene glycol) (PEG) due to complexation. Further evidence of cation binding by oligomeric PEG was obtained by ¹H NMR studies of PEG and its complexes with metal salts. To optimize the template ion synthesis approach, molecular dynamics simulations were performed on PEGDA containing between two and ten ethylene glycol repeating units, with and without the presence of cations. Simulation results indicated that the presence of the templating cation significantly decreased the mean end-to-end distance, thereby bringing the unsaturated endgroups into close proximity. The PEGDA ligand that resulted in the most effective templatization for Na⁺ contained four ethylene glycol repeating units. Simulation times greater than 50 ps had little effect on the results for ligands containing 7 or fewer ethylene glycol repeating units.     

不对称周环取代酞菁配合物的分子结构特征

文章综合分析了迄今国内外合成的不对称周环取代酞菁配合物的研究成果,总结了不对称周环取代酞菁配合物一般具有的ABBB、AABB和ABAB三种类型的分子结构特征。不对称取代酞菁配合物所具有的这些特殊结构特征使得它们在化学、物理学、生物学上呈现出特异的性能。     

Orientation of the OmpF Porin in Planar Lipid Bilayers

The outer‐membrane protein OmpF is an abundant trimeric general diffusion porin that plays a central role in the transport of antibiotics and colicins across the outer membrane of E. coli. Individual OmpF trimers in planar lipid bilayers (PLBs) show one of two current–voltage asymmetries, thus implying that insertion occurs with either the periplasmic or the extracellular end first. A method for establishing the orientation of OmpF in PLB was developed, based on targeted covalent modification with membrane‐impermeant reagents of peripheral cysteine residues introduced near the periplasmic or the extracellular entrance. By correlating the results of the modification experiments with measurements of current asymmetry or the sidedness of binding of the antibiotic enrofloxacin, OmpF orientation could be quickly determined in subsequent experiments under a variety of conditions. Our work will allow the precise interpretation of past and future studies of antibiotic permeation and protein translocation through OmpF and related porins.     

Properties of Nafion Under Uniaxial Loading at Different Temperatures: A Molecular Dynamics Study

Nafion membrane encounters many different thermal conditions and mechanical loadings because of its wide range of applications as a proton exchange membrane (PEM). Molecular dynamics simulation of hydrated Nafion at different temperatures is carried out to investigate the alteration of the physical properties of Nafion under uniaxial loading over a wide range of temperatures. According to the simulation results, increase of the temperature reduces the yield stress. The results also show that the polymer chains ordering increases the glass transition temperature and enhances the self-diffusion coefficient of water in hydrated Nafion. Comparisons show that the elastic modulus and viscosity coefficient obtained from the simulations at different temperatures are qualitatively in agreement with the measured values from experiments.     

多孔硅支撑磷脂双层膜的制备与表征

制备了一种以多孔硅为基底的新型支撑磷脂双层膜,多孔硅具有良好的光反射干涉性能,在多孔硅表面构筑磷脂双分子层膜有望形成一类新型的生物传感器.通过电化学刻蚀法制备了孔径为35～45 nm,孔道深度约为15μm的多孔硅,并用电子显微镜观测了其孔道结构,经原子力显微镜检测,其表面均方根粗糙度(RMSR)仅为0.64nm.用挤出...     

Orientation of the Monomeric Porin OmpG in Planar Lipid Bilayers

Outer membrane protein G (OmpG) is a non‐selective porin from Escherichia coli. OmpG is a monomer, which makes it unusual among porins, and suggests that it may be useful in biotechnology. In planar lipid bilayers, individual OmpG pores reconstituted by insertion from detergent exhibit pronounced asymmetry in current‐voltage relationships and voltage‐dependent gating. Here, this asymmetry is used to deduce the orientation of OmpG in the bilayers. We introduced two cysteines into the extracellular loops of OmpG. Cleavage of the disulfide bond formed by these residues significantly increases spontaneous gating of the pore. By adding DTT to one side of the bilayer or the other, we demonstrated that pores showing a quiet trace at negative potentials have a “trans” conformation (extracellular loops on the trans side of the bilayer), while pores showing a quiet trace at positive potentials have a “cis” conformation (extracellular loops on the cis side). With this knowledge, we examined the binding of a cyclodextrin to OmpG. When the cyclodextrin was presented to the extracellular face of the pore, transient multisite interactions were observed. In contrast, when the cyclodextrin was presented to the periplasmic face, a more stable single‐site interaction occurred. Because the cyclodextrin can act as a molecular adapter by binding analytes, this information serves to advance the use of OmpG as a biosensor.     

DNTF对NC塑化特性的分子动力学模拟及实验研究

为研究DNTF对CMDB推进剂力学性能的作用机理,通过分子动力学模拟方法建立了NC纯物质和NC/DNTF共混物分子模型,研究了DNTF对NC塑化过程中微观结构的影响,采用拉伸试验研究了DNTF对CMDB推进剂力学性能的影响。结果表明,DNTF与NC分子形成氢键,使NC内分子的氢键减弱,NC分子的刚性降低;加入DNTF后,DNTF-CMDB推进剂的抗拉强度降低、延伸率增加;20℃时延伸率由8.69%增加到33.6%,50℃时延伸率由14.86%增加到45.6%。分子动力学模拟计算结果与拉伸试验结果一致。     

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.     

Probing and Manipulating the Lateral Pressure Profile in Lipid Bilayers Using Membrane-Active Peptides—A Solid-State 19F NMR Study

The lateral pressure profile constitutes an important physical property of lipid bilayers, influencing the binding, insertion, and function of membrane-active peptides, such as antimicrobial peptides. In this study, we demonstrate that the lateral pressure profile can be manipulated using the peptides residing in different regions of the bilayer. A ¹⁹F-labeled analogue of the amphiphilic peptide PGLa was used to probe the lateral pressure at different depths in the membrane. To evaluate the lateral pressure profile, we measured the orientation of this helical peptide with respect to the membrane using solid-state ¹⁹F-NMR, which is indicative of its degree of insertion into the bilayer. Using this experimental approach, we observed that the depth of insertion of the probe peptide changed in the presence of additional peptides and, furthermore, correlated with their location in the membrane. In this way, we obtained a tool to manipulate, as well as to probe, the lateral pressure profile in membranes.     

Effect of Acetyl Group on Mechanical Properties of Chitin/Chitosan Nanocrystal: A Molecular Dynamics Study

Chitin fiber is the load-bearing component in natural chitin-based materials. In these materials, chitin is always partially deacetylated to different levels, leading to diverse material properties. In order to understand how the acetyl group enhances the fracture resistance capability of chitin fiber, we constructed atomistic models of chitin with varied acetylation degree and analyzed the hydrogen bonding pattern, fracture, and stress-strain behavior of these models. We notice that the acetyl group can contribute to the formation of hydrogen bonds that can stabilize the crystalline structure. In addition, it is found that the specimen with a higher acetylation degree presents a greater resistance against fracture. This study describes the role of the functional group, acetyl groups, in crystalline chitin. Such information could provide preliminary understanding of nanomaterials when similar functional groups are encountered.     

Structural and Molecular Properties of Residual Birch Kraft Lignins

The residual lignins from unbleached and oxygen-bleached birch kraft pulps were isolated by acid hydrolysis and characterized by elemental analysis, methoxyl content, permanganate degradation, size exclusion chromatography and quantitative 13-C NMR. Calculations based on the reduction in kappa number after the acid hydrolysis revealed that only about one third or less of the material assumed to be lignin could be isolated as polymeric lignin. This was shown to be a syringyl-guajacyl type of lignin with a syringyl-to-guaiacyl ratio of approximately 1:1. The rest of the material found in the acid solution after hydrolysis and identified by GC-MS and by pyrolysis-GC-MS was to a large extent low molecular weight furanoid structures probably originating from polysaccharide degradation products, with only traces of lignin-derived compounds present.     

聚环氧乙烷、聚四氢呋喃及其共聚醚力学性能的MD模拟

为寻求预示复合材料力学性能的理论方法,对优选NEPE推进剂的黏合剂预聚物提供基础信息,在COMPASS力场下,取NVT系综,对聚环氧乙烷、聚四氢呋喃和它们的无规共聚醚进行了分子动力学(MD)模拟,并计算出弹性系数、模量、泊松比和柯西压等力学参数.经比较发现,聚环氧乙烷的刚性和延展性最优,共聚醚次之,聚四氢呋喃最差.     

钴取代的锑钨酸盐的电化学性质研究

合成了一例过渡金属钴取代型锑钨酸盐化合物,并对该化合物进行了X-射线单晶衍射实验以及红外表征,结构分析表明,该化合物为八个钴取代的三聚锑钨酸盐化合物,该化合物的电化学曲线显示其对H2O2的还原反应具有一定催化效果。     

用分子动力学模拟研究碳纳米管对顺丁橡胶摩擦性能的影响

采用分子动力学模拟方法研究碳纳米管（CNTs）对顺丁橡胶（BR）摩擦性能的影响。模拟结果表明,与纯BR相比,CNTs/BR复合材料的橡胶分子间作用力和橡胶分子运动空间更小,橡胶分子更加稳定,玻璃化温度和刚性更高,摩擦界面温度和摩擦界面橡胶分子运动速度更低,摩擦因数较小,耐磨性能提高。     

Molecular Dynamics of DHHC20 Acyltransferase Suggests Principles of Lipid and Protein Substrate Selectivity

Lipid modification of viral proteins with fatty acids of different lengths (S-acylation) is crucial for virus pathogenesis. The reaction is catalyzed by members of the DHHC family and proceeds in two steps: the autoacylation is followed by the acyl chain transfer onto protein substrates. The crystal structure of human DHHC20 (hDHHC20), an enzyme involved in the acylation of S-protein of SARS-CoV-2, revealed that the acyl chain may be inserted into a hydrophobic cavity formed by four transmembrane (TM) α-helices. To test this model, we used molecular dynamics of membrane-embedded hDHHC20 and its mutants either in the absence or presence of various acyl-CoAs. We found that among a range of acyl chain lengths probed only C16 adopts a conformation suitable for hDHHC20 autoacylation. This specificity is altered if the small or bulky residues at the cavity’s ceiling are exchanged, e.g., the V185G mutant obtains strong preferences for binding C18. Surprisingly, an unusual hydrophilic ridge was found in TM helix 4 of hDHHC20, and the responsive hydrophilic patch supposedly involved in association was found in the 3D model of the S-protein TM-domain trimer. Finally, the exchange of critical Thr and Ser residues in the spike led to a significant decrease in its S-acylation. Our data allow further development of peptide/lipid-based inhibitors of hDHHC20 that might impede replication of Corona- and other enveloped viruses.     

电解质对卵磷脂双分子层电化学行为的影响

实验利用自组装技术在铂电极上制备支撑的卵磷脂双层膜（s-BLM）作为生物膜的模型,利用循环伏安法（cV）和电化学阻抗谱（EIS）对由电解质KCI引起的s-BLM通透性的变化进行了研究。结果表明,KCI可与s-BLM发生较强的相互作用,导致s—BLM表面磷脂分子的有序排列受到影响,产生一些离子通道,增加了对探针分子电流响应,同时降低了s—BLM的电阻。     

Mass Spectrometry,Ion Mobility Separation and Molecular Modelling: A Powerful Combination for the Structural Characterisation of Substituted Cyclodextrins Mixtures

When working on the synthesis of substituted cyclodextrins (CDs), the main challenge remains the analysis of the reaction media content. Our objective in this study was to fully characterise a complex isomers mixture of Lipidyl-βCDs (LipβCD) obtained with a degree of substitution 1 (DS = 1) from a one-step synthesis pathway. The benefit of tandem mass spectrometry (MS/MS) and ion mobility separation hyphenated with mass spectrometry (IM-MS) was investigated. The MS/MS fragment ion‘s relative intensities were analysed by principal component analysis (PCA) to discriminate isomers. The arrival time distribution (ATD) of each isomer was recorded using a travelling wave ion mobility (TWIM) cell allowing the determination of their respective experimental collision cross section (CCS_exp). The comparison with the predicted theoretical CCS (CCS_th) obtained from theoretical calculations propose a regioisomer assignment according to the βCD hydroxyl position (2, 3, or 6) involved in the reaction. These results were validated by extensive NMR structural analyses of pure isomers combined with molecular dynamics simulations. This innovative approach seems to be a promising tool to elucidate complex isomer mixtures such as substituted cyclodextrin derivatives.     

黑梯炸药力学性能与感度的分子动力学研究

为了研究黑梯炸药配方对其力学性能与感度的影响,用Materials Studio软件建立了黑梯炸药的晶胞模型。采用分子动力学方法,计算了不同配方的黑梯炸药的力学性能、引发键键长分布、键连双原子作用能与内聚能密度,并对其变化情况并进行了比较。结果表明,在黑梯炸药中,随着RDX的质量分数从30%增加到80%,黑梯炸药的力学性能参数在一定范围内波动,其中拉伸模量变化范围为1.772 3~2.825 1GPa,剪切模量变化范围为0.636 6~1.042 8GPa,体积模量变化范围为2.734 1~3.747 9GPa,柯西压变化范围为1.203 2~2.181 6GPa,泊松比变化范围为0.354 6~0.397 0,而最大键长从0.155 4nm增至0.162 6nm,键连双原子作用能从167.6kJ/mol减至152.3kJ/mol,内聚能密度从0.899kJ/cm~3减至0.678kJ/cm~3,表明炸药的感度增大。