Ab initio path‐integral calculations of kinetic and equilibrium isotope effects on base‐catalyzed RNA transphosphorylation models

Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self‐cleavage of RNA strands by 2′‐O‐transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2′‐O‐transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic‐structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold‐standard” coupled‐cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path‐integral method, that is, automated integration‐free path‐integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. © 2014 Wiley Periodicals, Inc.     

Surface diffusive motion in a periodic and asymmetric potential

9,10-Dithioanthracene adsorbed on Cu(111) diffuses exclusively along the high-symmetry axis of the molecule-substrate system. Further reduction of the symmetry of the system by asymmetric methylation does not reduce the symmetry of the motion although it has a substantial effect on the diffusion rate (100-fold reduction) and renders the diffusion barrier asymmetric. This is in contrast to the behavior expected of a classical particle, and it provides a direct single-molecule-scale vista on the validity of The Principle of Microscopic Reversibility first formulated by Tolman in 1924, which despite its fundamental role has attracted little visualization.     

Atomically thin MoS₂: a new direct-gap semiconductor

The electronic properties of ultrathin crystals of molybdenum disulfide consisting of N=1,2,…,6 S-Mo-S monolayers have been investigated by optical spectroscopy. Through characterization by absorption, photoluminescence, and photoconductivity spectroscopy, we trace the effect of quantum confinement on the material's electronic structure. With decreasing thickness, the indirect band gap, which lies below the direct gap in the bulk material, shifts upwards in energy by more than 0.6 eV. This leads to a crossover to a direct-gap material in the limit of the single monolayer. Unlike the bulk material, the MoS? monolayer emits light strongly. The freestanding monolayer exhibits an increase in luminescence quantum efficiency by more than a factor of 10? compared with the bulk material.     

Tuning the electronic properties of conjugated polymer by tethering low‐bandgap rhenium(I) complex on the main chain

Low‐bandgap rhenium(I) complex with absorption onset at 795 nm in solution was tethered onto π‐conjugated polymer. The conjugated copolymer provides solution processability of the metallopolymer, and the pendant allows the low energy‐absorbing Re(I) complex units to be evenly distributed on the thin film. The copolymer tethered with low‐bandgap rhenium complex was synthesized by Suzuki cross‐coupling reaction. The metal‐free polymer ( poly‐1 ) tethered with functionalized intramolecular charge transfer dye, 2‐phenyl‐3‐pyridin‐2‐yl‐5,7‐di‐2‐thienylthieno[3,4‐b]pyrazine, exhibited high molecular weight, good film‐forming properties, and excellent solution processability. The pendants of the conjugated polymer possess donor–acceptor characters and broaden the absorption band. These pendants can function as bidentate ligands for metal chelation. The solubilizing groups on the monomers provide good solubility to the polymer even with high content of metal chelation. Upon the complexation with rhenium(I) pentacarbonyl chloride, the absorption spectrum of the resulting metallopolymer was further extended toward the near‐infrared region. Photovoltaic performances based on this metallopolymer have been studied. The design approach of these metallopolymers provides synthetic feasibility for coordinating wide range of metal ions on the pendant, and the resulting low‐bandgap polymer can be a potential candidate for light harvesting material in solar cell applications. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 2311–2319, 2010     

A quantitative contour analysis of axisymmetric vesicles spontaneously adhering onto a substrate

The determination of membrane-substrate profile for adherent vesicle using confocal reflectance interference contrast microscopy (C-RICM) has pushed for the need of advanced mechanics model for interpreting adhesion mechanisms. In this work, a model for vesicles or cells adhesion is established, the governing equation is derived from the variation of the potential energy at the cohesive zone. A closed-form solution is found for vesicle spontaneously adheres to a substrate when its shear modulus, micro vanishes. Based on the model and C-RICM experiments the magnitude of the adhesion force is calculated for a lipid vesicle adheres to a glass substrate.     

Catalytic Phosphination and Arsination

The catalytic, user-friendly phosphination and arsination of aryl halides and triflates by triphenylphosphine and triphenylarsine using palladium catalysts have provided a facile synthesis of functionalized aryl phosphines and arsines in neutral media. Modification of the cynaoarisne yielded optically active N, As ligands which will be screened in various asymmetric catalysis.     

Crash Diagnosis and Price Rebound Prediction in NYSE Composite Index Based on Visibility Graph and Time-Evolving Stock Correlation Network

This study proposes a framework to diagnose stock market crashes and predict the subsequent price rebounds. Based on the observation of anomalous changes in stock correlation networks during market crashes, we extend the log-periodic power-law model with a metric that is proposed to measure network anomalies. To calculate this metric, we design a prediction-guided anomaly detection algorithm based on the extreme value theory. Finally, we proposed a hybrid indicator to predict price rebounds of the stock index by combining the network anomaly metric and the visibility graph-based log-periodic power-law model. Experiments are conducted based on the New York Stock Exchange Composite Index from 4 January 1991 to 7 May 2021. It is shown that our proposed method outperforms the benchmark log-periodic power-law model on detecting the 12 major crashes and predicting the subsequent price rebounds by reducing the false alarm rate. This study sheds light on combining stock network analysis and financial time series modeling and highlights that anomalous changes of a stock network can be important criteria for detecting crashes and predicting recoveries of the stock market.