环形高分子单链塌缩的熔球中间态及其热力学解释

采用动态蒙特卡洛分子模拟研究了环形高分子单链在不良溶剂中发生塌缩转变时可逆地出现具有核-壳结构特征的熔球中间态,发现该结构特征与相同链长的线形单链基本相同,表明其只与链的长短有关,而与链端基的特殊效应无关.本工作将这一现象与单链单晶在其平衡熔点附近出现的类似现象相互关联,采用表面预溶模型来解释单链塌缩出现熔球中间态的热力学机理.分子量越低,熔球越小,表面预溶现象就越显著,塌缩转变随热力学条件变化就越缓慢.实际的高分子体系由于链内拓扑缠结,在表面未必能充分释放片段链,达不到理论预期的平衡态.表面预溶使得相分离临界点或晶体熔点附近在界面厚度方向上存在链单元能量状态不连续分布,这在微观分子水平上与临界界面连续浓度梯度的传统理论处理不一致,为我们深入理解高分子流体界面的微观结构带来帮助.     

良溶剂中接枝型聚两性电解质单链构象的布朗动力学模拟

采用布朗动力学研究了在良溶剂中荷电平衡的接枝聚两性电解质(GPA)的单链构象转变行为,讨论了主链链长、支链数及电荷密度对GPA分子链构象转变的影响.研究发现,随着静电相互作用的增强,GPA分子链构象转变过程由线团、主链与支链间的折叠、链段塌缩和电荷配对形成偶极子与四极子等4个阶段构成.与线型聚两性电解质不同,GPA存在的额外支链间空间排斥与静电排斥作用随着分子结构的变化而改变,并影响构象转变行为.在强静电相互作用下,良溶剂中的GPA链由于溶剂化作用会再伸展,以保证偶极子完全配对成四极子.减小主链长度或电荷密度或增加支链数目都会增大体系的排斥力和主链的刚性,阻滞分子链的塌缩,并使得分子链再伸展的幅度增大.     

高分子链坍塌转变动力学过程的动态蒙特卡罗模拟

基于键长涨落格子模型和动态蒙特卡罗模拟方法,引入疏水相互作用,对均聚高分子链坍塌转变动力学过程进行了模拟研究.模拟发现,其坍塌时间呈高斯分布,而平均坍塌时间随淬火深度的变化类似于蛋白质折叠,但难以发现局部最小;另外,平均坍塌时间随链长呈指数形式变化.在其坍塌动力学过程中,高分子链构象先由橄榄球状演变为项链状,进而演变为香肠状,最后形成近球状的熔融球;基于团簇数目、团簇大小和非球面参数等参量,对前人提出的动力学过程四阶段划分进行了更为清晰的界定.     

分子动力学方法研究单链聚乙烯的结晶过程

用分子动力学方法（ＭＤ）研究了单链聚乙烯在不同温度（１００Ｋ、２００Ｋ、３００Ｋ、４００Ｋ、５００Ｋ）下的结晶过程,并用能量和结构参数进行了描述．结果表明伸直分子链的结晶过程都经历了三个阶段,首先是伸直链的卷曲与聚集,然后通过链段的排列形成规整的片晶结构,最后是结晶形成的片晶在结构与能量上的涨落变化。研究表明,结晶温度越高,分子链的内聚速度越快．研究发现,分子链在内聚阶段经历一个局部凝聚的中间状态,在结晶温度很低（１００Ｋ）时,局部凝聚的结构是有序的．而在５００Ｋ时,该结构为无规线团．结晶温度的差异,一般来说,将导致得到的片晶厚度的不同．对于模拟的单链,随着结晶温度的降低而形成了较厚的片晶．该行为与聚乙烯本体结晶中片晶厚度对结晶温度的依赖性相反．在有序化阶段和之后的片晶调整运动阶段,分子链线团的回转半径基本保持不变．这与宏观多链体系的结果相同．另外,在模拟中发现,尺寸微小的单链聚乙烯晶片的扭转运动     

钴硫团簇ConS^＋n—1（n=2,3）的结构和稳定性

用ａｂ ｉｎｉｔｉｏ分子轨道方法（ＲＨＦ,ＵＨＦ）和密度泛涵（ＤＦＴ）方法研究了团簇Ｃｏ２Ｓ＾＋,Ｃｏ３Ｓ＾＋２的各种可能的几何构型和电子结构,并计算了相应的较稳定构型的振动光谱,发现Ｃｏ２Ｓ＾＋和Ｃｏ３Ｓ＾＋２团簇最稳定结构均具有Ｃｓ对称性。对团簇的成键作用机理进行了理论分析。     

乙腈＋氯乙烯体系的团簇产生与光电离

利用同步辐射和超声射流技术产生了团簇离子（ＣＨ＿３ＣＮ）＿ｍ（Ｃ＿２Ｈ＿３Ｃｌ）（ｍ≤４，ｎ≤４）及Ｃ２Ｈ３ＣｌＣＮ＋，Ｃ２Ｈ２ＣｌＣＮ＋由（ＣＨ３ＣＮ）（Ｃ２Ｈ３Ｃｌ）＋经团簇内离子。分子反应生成，反应过程中放出能量使Ｈ３Ｃ－ＣＮ键断裂。ａｂｉｎｉｔｉｏ计算表明Ｃ２Ｈ３ＣｌＣＮ＋离子是稳定的。同时测得了它们的电离势．     

同位索峰型计算在归属多元素团簇质谱中的应用

介绍了一种通过计算分子的同位素丰度模拟质谱峰型，根据比较质谱峰的位置和形状来帮助归属多元素团簇的飞行时间质谱的方法。这种方法不仅有助于归属完全分辨的低质量离子峰，还能从重叠的质谱峰中确定各个组份的相对含量。最后介绍了如何用这种方法来分析激光烧蚀ＭｎＣｌ２·４Ｈ２Ｏ和ＣｕＣｌ２·２Ｈ２Ｏ得到的正负团簇离子质谱     

聚乙烯串晶在单轴拉伸形变过程中的微结构变化和机理

本文采用电子显微镜和小角Ｘ－射线散射（ＳＡＸＳ）技术研究了含有串晶结构（Ｓｈｉｓｈ—ｋｅｂａｂ）的高密度聚乙烯（ＨＤＰＥ）／超高分子量聚乙烯（ＵＨＭＷＰＥ）共混物高取向膜在单轴拉伸过程中的微结构变化．深入探讨了拉伸温度对聚乙烯在形变过程中微结构变化的影响．室温拉伸时，聚乙烯串晶结构主要发生了解结晶过程；高温（１１５℃）形变时，主要表现为折叠链片晶直接转变为伸展链纤维晶的应变诱导结晶过程．     

参考答案

参考答案单元练习一参考答案及提示一、二、三、选择题四、２８．Ｏ２＋２ＫＩ＋Ｈ２Ｏ→２ＫＯＨ＋Ｉ２＋Ｏ２;Ｉ２,ＫＯＨ２９．１０００ｍ／１６ａ;１４．Ｚａ／ｂ;３０．ＣＨ４;Ｈ２;１：２;因为Ｃ：Ｈ＝３／１２：１＝１：４,ＣＨ４分子里Ｃ与Ｈ的质量比为３...     

均聚物/两嵌段共聚物/均聚物三元聚合物共混体系界面性质的Monte Carlo模拟

利用格子Monte Carlo(MC)模拟方法研究了两嵌段共聚物增容剂AB的链长及浓度对不相容性均聚物A/B共混体系界面性质的影响.研究结果表明,当两嵌段共聚物的体积分数φC=0.05时,随着两嵌段共聚物分子链长NC从10增至20,界面厚度剧烈减小,而当两嵌段共聚物的分子链长NC进一步增加到60时,界面厚度轻微增加;两嵌段共聚物的取向参数q随着分子链长的增长而增加,即共聚物分子在垂直界面方向的拉伸程度增大.当两嵌段共聚物AB的分子链长NC固定为10时,随着链浓度增大,界面厚度增加,共聚物分子链取向参数q减小,共聚物分子在垂直界面方向的拉伸程度减小.     

Molecular Dynamics Studies of Collapse Stages in the chain folding process of Polyethylene

Althoughtheequilibriumpropertiesofthepolymerhavebeenextensivelystudied,kineticphenomenasuchasthecondensingprocessandcollapsetransitionstillhavemanyunclearaspects,andmucheffortwastakentomakeathoroughinvestigationandstudy.Moleculardynamic(MD)simulationsofthefoldingandcollapseprocessforapolyethylenechainwasrecentlycarriedoutbymanyauthors1'2'3.Itwasreportedthatatwo-stagecollapseprocesswasseenwithouttorsionpotential',andthreestageswerefoundbysimplificationofthecomputationalmodel5.ButthecollaPsesta…     

Polymer association in poor solvents: from monomolecular micelles to clusters of chains and phase separation

We report some recent results obtained in our laboratory on the poor‐solvent behavior of macromolecules. We first discuss the globular collapse of short chains that, unlike long ones, may form compact ordered states. We then address the collapse of random AB copolymers, which may provide significant clues to understanding biophysical issues such as the protein folding problem or the DNA arrangement in a living cell. Afterwards, we turn to the many‐chain problem of homopolymer aggregation into polymolecular micelles or clusters of chains and eventually phase separation. The unifying feature of our approach consists in the self‐consistent free‐energy minimization with inclusion of intra‐ and inter‐molecular interactions, whenever they are required, that enables us to describe the chain conformation in detail.     

Collapse kinetics of vibrated granular chains

The kinetics of the collapse of the coil state into condensed states is studied with vibrated granular chain composed of N metal beads partially immersed in water. The radius of gyration of the chain, R(g) is measured. For short chains (N < 140), disk-like condensed state is formed and R(g) decreases with time such that the function ΔR(g)(2) (≡ R(g)(2) - R(g)(2)(∞)) = A e(-t/τ), where the relaxation time τ follows a power-law dependence on the chain length N with an exponent γ = 1.9 ± 0.2. For the chains with length N ≥ 300, rod-like clusters are observed during the initial stage of collapse and R(g)(2) = R(g)(2)(0) - Bt(β), with β = 0.6 ± 0.1. In the coarsening stage, the exponential dependence of ΔR(g)(2) on time still holds, however, the relaxation time τ fluctuates and has no simple dependence on N. Furthermore, the time dependence of the averaged radius of gyration of the individual clusters, R(g,cl) can be described by the theory of Lifshitz and Slyozov. A peak in the structure function of long chains is observed in the initial stage of the collapse transition. The collapse transition in the bead chains is a first order phase transition. However, features of the spinodal decomposition are also observed.     

Guest‐Directed Supramolecular Architectures of {W36} Polyoxometalate Crowns

The {W₃₆} isopolyoxotungstate cluster provides a stable inorganic molecular platform for the binding of inorganic and organic guest molecules. This is achieved by a binding pocket formed by six terminal oxo ligands located in the central cavity of the all‐inorganic cation binding host. Previously it was shown that the cluster can specifically bind primary amines and importantly, functionalized diamines through a combination of electrostatic and hydrogen bonding interactions. Here we transform this assembly strategy to utilize the binding of long‐chain alkyldiammonium guest cations to physically define the supramolecular structure of the clusters with respect to each other and demonstrate the structure direction as a function of alkyl chain length. The systematic variation of the chain length gives access to five supramolecular assemblies which were all fully characterized using single crystal XRD, TGA, ¹H NMR, and elemental analysis. In compound 1 , diprotonated 1,8‐diaminooctane molecules link the {W₃₆} clusters into infinite 1D zigzag chains, whereas compounds 2 and 3 feature trimeric {W₃₆} assemblies directly connected through protonated 1,9‐diaminononane ( 2 ) or 1,10‐diaminodecane ( 3 ) linkers . Compound 4 contains dumb‐bell shaped dimeric units as a result of direct center‐to‐center linkages between the {W₃₆} clusters formed by protonated 1,12‐diaminododecane. In compound 5 , triply protonated bis(hexamethylene)triamine was employed to obtain linear 1D chains of directly connected {W₃₆} cluster units.     

The phase behavior of polyethylene ring chains

The equilibrium properties of an isolated polyethylene ring chain are studied by using molecular dynamics (MD) simulations. The results of an 80-bond linear chain are also presented, which are in agreement with previous studies of square-well chains and Lennard-Jones (LJ) homopolymers. Mainly, we focus on the collapse of polyethylene ring chains. At high temperatures, a fully oblate structure is observed for the ring chains with different chain lengths. For such an oblate structure, a shape factor of delta(*)=0.25 and a rodlike scaling relation between the radius of gyration and chain lengths could be deduced easily in theory, and the same results are obtained by our MD simulations. Such an oblate structure can be obtained by Monte Carlo simulation only for sufficient stiff ring chains. When the temperature decreases, an internal energy barrier is observed. This induces a strong peak in the heat capacity, denoting a gas-liquid-like transition. This energy barrier comes mainly from the local monomer-monomer interactions, i.e., the bond-stretching, the bond-bending, and the torsion potentials. A low temperature peak is also observed in the same heat capacity curve, representing a liquid-solid-like transition. These numerical simulation results support a two-stage collapse of polyethylene ring chains; however, the nature should be different from the square-well and LJ ring chains.     

Folding of human telomerase RNA pseudoknot using ion-jump and temperature-quench simulations

Globally RNA folding occurs in multiple stages involving chain compaction and subsequent rearrangement by a number of parallel routes to the folded state. However, the sequence-dependent details of the folding pathways and the link between collapse and folding are poorly understood. To obtain a comprehensive picture of the thermodynamics and folding kinetics we used molecular simulations of coarse-grained model of a pseudoknot found in the conserved core domain of the human telomerase (hTR) by varying both temperature (T) and ion concentration (C). The phase diagram in the [T,C] plane shows that the boundary separating the folded and unfolded state for the finite 47-nucleotide system is relatively sharp, implying that from a thermodynamic perspective hTR behaves as an apparent two-state system. However, the folding kinetics following single C-jump or T-quench is complicated, involving multiple channels to the native state. Although globally folding kinetics triggered by T-quench and C-jump are similar, the kinetics of chain compaction are vastly different, which reflects the role of initial conditions in directing folding and collapse. Remarkably, even after substantial reduction in the overall size of hTR, the ensemble of compact conformations are far from being nativelike, suggesting that the search for the folded state occurs among the ensemble of low-energy fluidlike globules. The rate of unfolding, which occurs in a single step, is faster upon C-decrease compared to a jump in temperature. To identify "hidden" states that are visited during the folding process we performed simulations by periodically interrupting the approach to the folded state by lowering C. These simulations show that hTR reaches the folded state through a small number of connected clusters that are repeatedly visited during the pulse sequence in which the folding or unfolding is interrupted. The results from interrupted folding simulations, which are in accord with non-equilibrium single-molecule folding of a large ribozyme, show that multiple probes are needed to reveal the invisible states that are sampled by RNA as it folds. Although we have illustrated the complexity of RNA folding using hTR as a case study, general arguments and qualitative comparisons to time-resolved scattering experiments on Azoarcus group I ribozyme and single-molecule non-equilibrium periodic ion-jump experiments establish the generality of our findings.     

Polysoaps in Backbone‐Selective Solvents: Effects of Side‐Chain Length on Collapse Dynamics

Abstract

Molecular dynamics (MD) simulations of model comb‐graft heteropolymers were performed to understand general mechanistic features of coil‐to‐micelle relaxation after instantaneous quench from a nonselective solvent to solvent conditions selective for the backbone monomers and poor for the side‐chain monomers. The systems considered were single bead‐spring molecules with backbones of 30 monomers and 10 equally spaced side chains of 1, 5, 10, or 20 monomers each, immersed in dense liquids of 20,000 simple solvent particles. We find that the coil‐to‐micelle relaxation time, τ _r , averaged over 50 independent trajectories for each set of topological parameters considered, decreases with increasing side‐chain length. A two‐stage relaxation mechanism is observed: (1) a fast collapse and aggregation of neighboring side chains to form a chain of “protomicelles,” followed by (2) a slow intramolecular aggregation of protomicelles. Fast collapse dominates for molecules with relatively longer side chains due to relatively higher probabilities of initial contacts between side‐chain monomers in different side chains, while slow intramolecular aggregation dominates for molecules with relatively shorter side chains.     

Chain collapse by lattice simulation

Monte Carlo simulations have been performed on a self-avoiding simple cubic lattice chain with the nearest-neighbor interactions for a range of chain lengths N from 40 to 1000 segments to investigate equilibrium properties of polymer chains from an athermal to a collapsed state. Both the fraction of segments in the clusters and the number of contacts exhibit the three stage process for the chain collapse, consistent with our previous molecular dynamics simulations of a fully atomistic chain. In the collapse region corresponding to the nearest-neighbor interaction parameter larger than 0.5 for a segment-solvent pair, polymer chains are quite spherical and both ends lie nearly randomized within the sphere. The peak height of the specific heat is proportional to N(In N)^3/11, as predicted by the renormalization group theory.     

Self-organization in protein folding and the hydrophobic interaction

Self-organization is a critical aspect of living systems. During the folding of protein molecules, the hydrophobic interaction plays an important role in the collapse of the peptide chain to a compact shape. As the hydrophobic core tightens and excludes water, not only does the number of hydrophobic side chain contacts increase, but stabilization is further enhanced by an increase in strength of each hydrophobic interaction between side chains in the core. Thus, the self-organization of the protein folding process augments itself by enhancing the stability of the core against large-scale motions that would unfold the protein. Through calculations and computer simulations on a model four-helix bundle protein, we show how the strengthening of the hydrophobic interaction is crucial for stabilizing the core long enough for completion of the folding process and quantitatively manifests self-organizing dynamical behavior.     

Spacer‐Modulated Differentiation Between Self‐Assembly and Folding Pathways for Bichromophoric Merocyanine Dyes

We have synthesized a large series of bis(merocyanine) dyes with varying spacer unit and investigated in detail their self‐organization behavior by concentration‐ as well as solvent‐dependent UV/Vis spectroscopy. Our in‐depth studies have shown that the self‐organization of the present bis(merocyanine) dyes is subtly influenced by the nature of the spacer unit. The utilization of rigid spacers results in the formation of self‐associated bimolecular complexes with high binding strength, while flexible spacers drive the respective bichromophoric dyes to intramolecular folding. Our thorough investigations on the impact of alkyl spacer chain length on the folding tendency of the present series of bis(merocyanine) dyes revealed a biphasic behavior, that is, a steep increase of the folding tendency for the dyes containing C4 to C7 chains and then a gentle decrease for dyes with longer alkyl spacer chains as evidenced by free energy (ΔG) values for the folding of these dyes. Furthermore, analyses of aggregates’ optical properties based on exciton theory as well as quantum chemical calculations suggest a bimolecular aggregate structure for the dye possessing a rigid spacer and a rotationally twisted pleated structure for the bis(merocyanine) dyes having spacer units with less than seven carbon atoms, while the application of longer alkyl chain linkers (≥C7) provides enough flexibility to orient the chromophores in electrostatically most favored antiparallel fashion.