Anisotropic Poisson Effect and Deformation-Induced Fluorescence Change of Elastic 9,10-Dibromoanthracene Single Crystals

Elastic organic crystals have attracted considerable attention as next-generation flexible smart materials. However, the detailed information on both molecular packing change and macroscopic mechanical crystal deformations upon applied stress is still insufficient. Herein, we report that fluorescent single crystals of 9,10-dibromoanthracene are elastically bendable and stretchable, which allows a detailed investigation of the deformation behavior. We clearly observed a Poisson effect for the crystal, where the short axes (b and c-axes) of the crystal are contracted upon elongation along the long axis (a-axis). Moreover, we found that the Poisson's ratios along the b-axis and c-axis are largely different. Theoretical molecular simulation suggests that the tilting motion of the anthracene may be responsible for the large deformation along the c-axis. Spatially resolved photoluminescence (PL) measurement of the bent elastic crystals reveals that the PL spectra at the outer (elongated), central (neutral), and inner (contracted) sides are different from each other.     

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.     

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins

Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.     

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Fast multipole method for three-dimensional systems with periodic boundary condition in two directions

We derived a new expression for the electrostatic interaction of three-dimensional charge-neutral systems with two-dimensional periodic boundary conditions (slab geometry) using a fast multipole method (FMM). Contributions from all the image cells are expressed as a sum of real and reciprocal space terms, and a self-interaction term. The reciprocal space contribution consists of two parts: zero and nonzero terms of the absolute value of the reciprocal lattice vector. To test the new expressions, electrostatic interactions were calculated for a randomly placed charge distribution in a cubic box and liquid water produced by molecular dynamics calculation. The accuracy could be controlled by the degree of expansion of the FMM. In the present expression, the computational complexity of the electrostatic interaction of N-particle systems is order N, which is superior to that of the conventional two-dimensional periodic Ewald method for a slab geometry and the particle mesh Ewald method with a large empty space at an interface of the unit cell. © 2020 Wiley Periodicals, Inc.     

Reactions of fullerene C60 with methyl methacrylate radicals: A density functional theory study

We have investigated the stepwise addition of four growing methyl methacrylate (MMA) radicals to C₆₀ fullerene, taking into account all possible types of the formed adducts. This reaction set is a reliable approximation for understanding the MMA polymerization process in the presence of C₆₀ fullerene. We have analyzed the structures of the fullerene-MMA adducts and energy parameters of their formation (heat effects and activation enthalpies). We found that up to three MMA growing radicals are favorably attached to C₆₀ as the fullerene-MMA trisadduct is a stable radical of the allyl type. It is inactive for further radical addition, and the elimination of the hydrogen atom from the growing MMA radical becomes preferable. The effects of steric factors and structures of the products of multiple growing MMA radical additions to C₆₀ on the radical polymerization of MMA in the presence of C₆₀ fullerene are considered.     

The physicochemical properties role of a functionalized alkyl-peptide in nanofibre formation and neural progenitor cells viability and survival

Amphiphilic alkyl-peptides as novel biomaterials form 3D scaffolds that are applicable in tissue engineering. Here, the nanofibre formation capability of a distinct alkyl-peptide was investigated using coarse-grained molecular dynamics simulation (CGMD) and experimental methods. The alkyl-peptide (Ace-FAQRVPPEEEGGGAAAAK-Nhe(C16)) was functionalized with a peptide epitope (FAQRVPPP) which can help to maintenance and differentiation of neural stem cells. Two alkyl-peptide systems were investigated: the all-functionalized system (with only bioactive alkyl-peptides) and the distributed system (a combination of bioactive and non-bioactive alkyl-peptides with ratio 1:2). The CGMD and TEM results confirm elongated nanofibres for all-functionalized system and cylindrical nanofibres for the distributed one. Furthermore, PC12 cells show a reliable growth on both 2D alkyl-peptides coated surfaces. Because of the nanofibres negative surface charges, the cell morphologies show clustered form in the distributed system and rounded shape in the all-functionalized one. Since the stem cell state preserves in cluster form, the physicochemical property of these nanofibres allows a potential advantage in stem cell long-time maintains.     

两嵌段共聚物反相溶剂中组装结构转变动力学的模拟研究

利用耗散粒子动力学方法,分别研究了不同结构的组装体在改变溶剂的选择性后,在溶液及界面上的结构演变动力学.模拟结果表明,在改变溶剂的选择性后,大球形胶束在溶液中转变形成反向球形胶束,而在界面上则转变形成反向环状胶束,当前模拟结果与已有的实验结果一致.此外,模拟结果还预测出,在改变溶剂的选择性后,环状胶束在溶液中转变形成反向环状胶束,而在界面处受限形成反向的支化蠕虫状胶束;蠕虫状胶束则在溶液中转变形成反向环状胶束,而在界面处受限形成多层纳米球结构;囊泡在溶液中转变形成分散的小胶束聚集体,而在界面处受限形成球形的补丁纳米粒子.     

计算机分子模拟在分子印迹技术中的应用

传统的分子印迹技术对模板分子、功能单体、交联剂、致孔剂等的筛选往往依靠经验,常通过反复实验对合成条件进行优化,存在实验周期长、耗材量大等问题。计算机分子模拟技术的应用在实验过程中起到可预见性指导作用,可以实现精准识别位点的裁制、识别驱动力的设计,通过结合能等物化特征参数计算优化识别体系的稳定性,从而合理选择模板分子、功能单体、交联剂、致孔剂,优化聚合条件,以提高聚合物识别特异性和亲和力,缩短实验周期,更符合绿色化学的理念。本文简单介绍了计算机分子模拟技术,重点对其在分子印迹技术中的指导作用进行了综述,并对其在分子印迹技术中的应用进行了展望。     

Coherence transfer delay optimisation in PSYCOSY experiments

PSYCOSY is an f1 broadband homonuclear decoupled version of the COSY nuclear magnetic resonance pulse sequence. Here, we investigate by a combination of experimental measurements, spatially distributed spin dynamics simulations, and analytical predictions the coherence evolution delay necessary in PSYCOSY experiments to ensure intensity discrimination in favour of the correlations typically arising from short range (ⁿJ, n ≤ 3) ¹H–¹H couplings and show that, in general, a coherence evolution delay of around 35 ms is optimum.