Reaction Coordinates by Nonlinear Dimensionality Reduction

Deriving reaction coordinates for the characterization of chemical reactions has long been a demanding task.In our previous work[ACS Cent.Sci.3,407(2017)],the reaction coordinate of a(retro-)Claisen rearrangement in aqueous solution optimized through a Bayesian measure,a linear combination of bond lengths formation and breakage,was judged to be optimal among all trails.Here,considering the nonlinearity of the transition state,we use isometric mapping and locally linear embedding to obtain one reaction coordinate which is composed of a few collective variables.With these methods,we find a more reasonable and powerful one-dimensional reaction coordinate,which can well describe the reaction progression.To explore the reaction mechanism,we analyze the contribution of intrinsic molecular properties and the solventsolute interactions to the nonlinear reaction coordinate.Furthermore,another coordinate is identified to characterize the heterogeneity of reaction mechanisms.

Enhanced Sampling Simulations on Transition-Metal-Catalyzed Organic Reactions:Zirconocene-Catalyzed Propylene Polymerization and Sharpless Epoxidation

The bond breaking and forming in chemical reactions is a typical rare event,which is one of the difficult problems in molecular dynamics simulations.Numerous enhanced sampling methods have been developed to extend the time scale covered by molecular simulations.However,the difficulties of obtaining appropriate collective variables from complicated reaction pathways and a controlled sampling over the desired phase space remain as challenges.Herein,we use MetaITS,which combines metadynamics and integrated tempered sampling,to increase the sampling efficiency for chemical reactions.Metadynamics with collective variables obtained by harmonic linear discriminant analysis can efficiently decrease the main energy barrier of chemical reaction.Meanwhile,integrated tempered sampling can enhance the exploration of other degrees of freedom.In this study,we applied the MetaITS method to two transition-metal-catalyzed organic reactions with complicated reaction coordinates.We simulated here a zirconocene-catalyzed propylene polymerization to investigate the regioselectivity and temperature effects.We also studied a Sharpless epoxidation reaction,for which both chiral products are observed through simulation.

High Li^(+)coordinated solvation sheaths enable high-quality Li metal anode

An advance Li-sphere possessing a definitely regular morphology in Li deposition enables a well-defined more robust structure and superior solid-electrolyte interphase(SEI)to achieve high-efficiency long-term cycles in Li metal anode.Here,a new sight of high Li^(+)cluster-like solvation sheaths coordinated in a localized high-concentration NO_(3)^(-)(LH-LiNO_(3))electrolyte fully clarifies for depositing advanced Li spheres.Moreover,we elucidate a critical amorphouscrystalline phase transition in the nanostructure evolution of Li-sphere deposits during the nucleation and growth.Li-sphere anode exhibits ultrastable structural engineering for suppressing Li dendrite growths and rendering ultralong life of 4000 cycles in symmetrical cells at 2 mAcm^(-2).The as-constructed Li spheres/3DCMjLiFePO_(4)(LFP)full cell delivers a high capacity retention of 90.5%at 1 C after 1000 cycles,and a robust dendrite-free structure also stably exists in Li-sphere anode.Combined with high-loading LFP cathodes(6.6 and 10.9 mg cm^(-2)),superb capacity retentions are up to 96.5%and 92.5%after 800 cycles at 1 C,respectively.Cluster-like solvation sheaths with high Li^(+)coordination exert significant influence on depositing a highquality Li-sphere anode.

Effect of stereoregularity on excitation-dependent fluorescence and room-temperature phosphorescence of poly(2-vinylpyridine)

Preparation of non-conjugated luminescent polymers(NCLPs)with excellent cluster luminescence(CL)performance is of great significance for scientific and industrious applications,and yet improving the performance of NCLPs through proper structural design is still a huge challenge.Herein,we report a non-conjugated ionized polymeric system consisting of(−)-camphorsulfonic acid((−)-CSA)and poly(2-vinylpyridine)(P2VP).These acid-base complexes exhibit typical excitationdependent fluorescence and room-temperature phosphorescence(RTP)with a lifetime up to 364 ms.We discover that changing the stereoregularity from atactic to isotactic significantly improves the CL performance of the complex.It(1)broadens the fluorescence emission spectra to cover the entire visible region,(2)enhances the fluorescence emission intensity at long wavelength beyond 500 nm,(3)enhances the phosphorescence intensity,and(4)extends the phosphorescence lifetime.Systematical experimental characterization and molecular dynamics simulation unravel the key role of stereoregularity in determining the formation of different pyridine aggregates that strongly influence the CL performance.Moreover,the different luminescence shows great potential in excitation divided information display and time-resolved encrypted display.This work not only points to a new direction for developing NCLPs with excellent performance,but also broadens the applications of NCLPs materials.

SPONGE:A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms

SPONGE(Simulation Package tOward Next GEneration molecular modeling)is a software package for molecular dynamics(MD)simulation of solution and surface molecular systems.In this version of SPONGE,the all-atom potential energy functions used in AMBER MD packages are used by default and other all-atom/coarse-grained potential energy functions are also supported.SPONGE is designed to extend the timescale being approached in MD simulations by utilizing the latest CUDA-enabled graphical processing units(GPU)and adopting highly efficient enhanced sampling algorithms,such as integrated tempering,selective integrated tempering and enhanced sampling of reactive trajectories.It is highly modular and new algorithms and functions can be incorporated con veniently.Particularly,a specialized Python plugin can be easily used to perform the machine learning MD simulation with MindSpore,TensorFlow,PyTorch or other popular machine learning frameworks.Furthermore,a plugin of Finite-Element Method(FEM)is also available to handle metallic surface systems.All these advanced features increase the power of SPONGE for modeling and simulation of complex chemical and biological systems.

Toward an understanding of the relation between gene regulation and 3D genome organization

Background:High-order chromatin structure has been shown to play a vital role in gene regulation.Previously we identified two types of sequence domains,CGI(CpG island)forest and CGI prairie,which tend to spatially segregate,but to different extent in different tissues.Here we aim to further quantify the association of domain segregation with gene regulation and therefore differentiation.Methods:By means of the published RNA-seq and Hi-C data,we identified tissue-specific genes and quantitatively investigated how their regulation is relevant to chromatin structure.Besides,two types of gene networks were constructed and the association between gene pair co-regulation and genome organization is discussed.Results:We show that compared to forests,tissue-specific genes tend to be enriched in prairies.Highly specific genes also tend to cluster according to their functions in a relatively small number of prairies.Furthermore,tissue-specific forest-prairie contact formation was associated with the regulation of tissue-specific genes,in particular those in the prairie domains,pointing to the important role of gene positioning,in the linear DNA sequence as well as in 3D chromatin structure,in gene regulatory network formation.Conclusion:We investigated how gene regulation is related to genome organization from the perspective of forest-prairie spatial interactions.Since unlike compartments A and B,forest and prairie are identified solely based on sequence properties.Therefore,the simple and uniform framework(forest-prairie domain segregation)provided here can be utilized to further understand the chromatin structure changes as well as the underlying biological significances in different stages,such as tumorgenesis.