Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study

Calreticulin (CRT) is localized to and has functions in multiple cellular compartments, including the cell surface, the endoplasmic reticulum, and the extracellular matrix. Mutagenesis studies have identified several residues on a concave β-sheet surface of CRT critical for CRT binding to carbohydrate and other proteins/peptides. How the mutations of these key residues in CRT affect the conformation and dynamics of CRT, further influencing CRT binding to carbohydrates and other proteins to signal the important biological activities remain unknown. In this study, we investigated the effect of three key point mutations (C105A, C137A and W319A) on CRT conformation and dynamics via atomistic molecular dynamics simulations. Results show that these three key residues mutations induced the changes of CRT local backbone flexibility and secondary structure of CRT N-domain, which could further affect CRT’s binding activity. C137A mutation led to dramatic decrease of the overall size of CRT due to the P-domain fold back to the globular domain and formed new inter-domain contacts, which can cause blockage of CRT’s binding with other large substrates. Furthermore, for CRT concave β-strand surface patch containing lectin binding site, CRT C105A, C137A and W319A point mutation resulted in the changes in solvent accessible surface area, key residues’ side chain atom positions and dynamical correlated motions between residues. All these changes could directly affect CRT binding behavior. Results of this study provide molecular and structural insights into understanding the role of key residues of CRT in its binding behavior.     

Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking

Multicanonical molecular dynamics based dynamic docking was used to exhaustively search the configurational space of an inhibitor binding to the N-terminal domain of heat-shock protein 90 (Hsp90). The obtained structures at 300 K cover a wide structural ensemble, with the top two clusters ranked by their free energy coinciding with the native binding site. The representative structure of the most stable cluster reproduced the experimental binding configuration, but an interesting conformational change in Hsp90 could be observed. The combined effects of solvation and ligand binding shift the equilibrium from a preferred loop-in conformation in the unbound state to an α-helical one in the bound state for the flexible lid region of Hsp90. Thus, our dynamic docking method is effective at predicting the native binding site while exhaustively sampling a wide configurational space, modulating the protein structure upon binding.     

Vibrations of a continuous web on elastic supports

We consider an infinite, homogenous linearly elastic beam resting on a system of linearly elastic supports, as an idealized model for a paper web in the middle of a cylinder-based dryer section. We obtain closed-form analytical expressions for the eigenfrequencies and the eigenmodes. The frequencies increase as the support rigidity is increased. Each frequency is bounded from above by the solution with absolutely rigid supports, and from below by the solution in the limit of vanishing support rigidity. Thus in a real system, the natural frequencies will be lower than predicted by commonly used models with rigid supports.     

Dynamic Variation of Excitonic Coupling in Excited Bilayer Graphene Quantum Dots?

The intermolecular interaction determines the photophysical properties of the organic aggregates, which are critical to the performance of organic photovoltaics. Here, excitonic coupling, an important intermolecular interaction in organic aggregates, between the π-stacking graphene quantum dots is studied by using transient absorption spectroscopy. We find that the spectral evolution of the ground state bleach arises from the dynamic variation of the excitonic coupling in the excited π-stacks. According to the spectral simulations, we demonstrate that the kinetics of the vibronic peak can be exploited as a probe to measure the dynamics of excitonic coupling in the excited π-stacks.     

Enabling the Operation of Highly Compatible LiI-3-Hydroxypropionitrile Small-Molecule Solid-State Electrolytes in Lithium Metal Batteries via Stepped-Amorphization Strategy

Integrating the advantages of both inorganic ceramic and organic polymer solid-state electrolytes, small-molecule solid-state electrolytes represented by LiI-3-hydroxypropionitrile (LiI-HPN) inorganic–organic hybrid systems possess good interfacial compatibility and high modulus. However, their lack of intrinsic Li⁺ conduction ability hinders potential application in lithium metal batteries until now, despite containing LiI phase composition. Herein, inspired by evolution tendency of ionic conduction behaviors together with first-principles molecular dynamics simulations, we propose a stepped-amorphization strategy to break the Li⁺ conduction bottleneck of LiI-HPN. It involves three progressive steps of composition (LiI-content increasing), time (long-time standing), and temperature (high-temperature melting) regulations, to essentially construct a small-molecule-based composite solid-state electrolyte with intensified amorphous degree, which realizes efficient conversion from an I⁻ to Li⁺ conductor and improved conductivity. As a proof, the stepped-optimized LiI-HPN is successfully operated in lithium metal batteries cooperated with Li₄Ti₅O₁₂ cathode to deliver considerable compatibility and stability over 250 cycles. This work not only clarifies the ionic conduction mechanisms of LiI-HPN inorganic–organic hybrid systems, but also provides a reasonable strategy to broaden the application scenarios of highly compatible small-molecule solid-state electrolytes.     

Efficient Reverse Intersystem Crossing in Carbene-Copper-Amide TADF Emitters via an Intermediate Triplet State

The mechanism behind reverse intersystem crossing (rISC) in metal-based TADF emitters is still under debate. Thermal rISC necessitates small singlet/triplet energy gaps as realized in donor-acceptor systems with charge-transfer excited states. However, their associated spin-orbit couplings are too small to account for effective rISC. Here, we report the first nonadiabatic dynamics simulation of the rISC process in a carbene-copper(I)-carbazolyl TADF emitter. Efficient rISC on a picosecond time scale is demonstrated for an initial triplet minimum geometry that exhibits a perpendicular orientation of the ligands. The dynamics involves an intermediate higher-lying triplet state of metal-to-ligand charge transfer character (³MLCT), which enables large spin-orbit couplings with the lowest singlet charge transfer state. The mechanism is completed in the S₁ state, where the complex can return to a co-planar coordination geometry that presents high fluorescence efficiency.     

Sustained Hydrogen Spillover on Pt/Cu(111) Single-Atom Alloy: Dynamic Insights into Gas-Induced Chemical Processes

Hydrogen spillover, involving the surface migration of dissociated hydrogen atoms from active metal sites to the relatively inert catalyst support, plays a crucial role in hydrogen-involved catalytic processes. However, a comprehensive understanding of how H atoms are driven to spill over from active sites onto the catalyst support is still lacking. Here, we examine the atomic-scale perspective of the H spillover process on a Pt/Cu(111) single atom alloy surface using machine-learning accelerated molecular dynamics calculations based on density functional theory. Our results show that when an impinging H₂ dissociates at an active Pt site, the Pt atom undergoes deactivation due to the dissociated hydrogen atoms that attach to it. Interestingly, collisions between H₂ and sticking H atoms facilitate H spillover onto the host Cu, leading to the reactivation of the Pt atom and the realization of a continuous H spillover process. This work underscores the importance of the interaction between gas molecules and adsorbates as a driving force in elucidating chemical processes under a gaseous atmosphere, which has so far been underappreciated in thermodynamic studies.     

Solvent Dependency of Catalyst-Substrate Aggregation Through π-π Stacking in Photoredox Catalysis

Assemblies of photoredox catalysts and their target substrates prior to photoexcitation is a phenomenon naïvely overlooked by the majority of synthetic chemists, but can have profound influences on reactivity and selectivity in photocatalytic reactions. In this study, we determine the aggregation states of triarylamine radical cationic photocatalysts with various target arene substrates in different solvents by specifically parameterized polarizable molecular dynamics simulations. A π-stacking interaction previously implicated by more expensive, less-representative quantum calculations is confirmed. Critically, this study presents new insights on: i) the ability of solvents (MeCN vs DMF) to make or break a photocatalytic reaction by promoting (MeCN) or demoting (DMF) its catalyst-substrate assemblies, which is a determining factor for reactivity, ii) the average “lifetimes” of assemblies in solution from a dynamic simulation. We find that both in the ground state and the photoexcited state, the cationic radical assemblies remain intact for periods often higher than 60 ps, rendering them ideally suitable to undergo intra-assembly electron transfer reactions upon photoexcitation. Such aspects have not addressed by previous studies on synthetic photocatalytic reactions involving non-covalent assemblies.     

A Universal equipment for biaxial stretching of polymer films

A biaxial stretching equipment was designed and constructed to enable fundamental studies of the relationship between film processing conditions and structures of oriented film products. With programmable drive motors and scissorlike mechanism, all stretching modes, including uniaxial stretching with constant and free width, simultaneous and sequential biaxial stretching, can be applied to a square-shaped sheet. Parameters related to film stretching manufacturing, such as temperature, draw ratio and stretching speed can be set independently to meet the requirement of different polymers. The force information during stretching is recorded by two miniature tension sensors in two directions independently, which can monitor the mechanical stimulus and stress response. Using this equipment, experiments are conducted to investigate the influence of stretching parameters on the structure of polypropylene films, which provides an effective method to tailor the processing conditions to obtain the films with desired properties.     

醚化PBS与CMC液体复合材料的相互作用

采用聚乙二醇(PEG)对聚丁二酸丁二醇酯(PBS)进行醚化改性,得到醚化PBS(PEG/PBS),PEG/PBS与羧甲基纤维素(CMC)共混制备了在水相均匀分散的新型(PEG/PBS)-CMC液体复合材料.结合分子模拟技术对PEG/PBS与CMC复合材料的相互作用机理进行了研究.结果表明,PEG/PBS具有预期的化学结构和优异的水润湿性;含醚链段PEG的引入有效提高了PBS分子链的极性和柔顺性,PEG/PBS与CMC之间存在氢键作用、范德华力作用、疏水作用和吸附作用.红外光谱(FTIR)中官能团(如—OH,—OCO—,—COOH,—C—O—C—等)的吸收峰频率发生偏移;光电子能谱(XPS)中C和O元素的结合能分布转移,表明PBS及PEG/PBS与CMC的官能团之间发生了相互作用;偏光显微镜(POM)和X射线衍射(XRD)结果表明,复合材料之间的相互作用为非共价键的结合;扫描电子显微镜(SEM)结果表明醚化改性后(PEG/PBS)-CMC复合材料间的相互作用增强,表面结合更紧密,相容性得到提高.