With the extensive use of fossil fuels and CO 2 emission, the development of effective electrocatalysts to convert CO 2 into high-value-added chemical products has become an important issue in academia community. Single-atom alloys (SAA) integrate the advantages of single-atoms catalysts and alloys, which can improve the activity and selectivity of CO 2 electroreduction (CO 2 RR) by adjusting the electronic and geometric structure of the host and guest metals simultaneously. This article provides a comprehensive review on the research advances of SAA catalysts used for CO 2 RR, including the synthesis and characterizations, computational design, experimental performances, and electronic structure effects of different SAA. Specifically, the correlations between experimental results and theoretical studies have been highlighted and discussed clearly in this review, which provide unique fundamental insights on the CO 2 RR performances of SAA catalysts. Based on these understanding, we finally propose a workflow combining both computational and experimental methods to rationally design the SAA, which can help the further development of CO 2 RR catalysts in the future.

CONTEXT:The mesophase pitch prepared by acid catalytic method typically had the advantages of low softening point and high solubility. To fully understand the mechanism of acid-catalyzed reactions and gain a deeper understanding of the microstructure of mesophase pitch, this article studied the mechanism of hydrofluoride/boron trifluoride (HF/BF3)-catalyzed anthracene using molecular simulation methods. The results showed that there might be two types of carbocations present in the system: classical and non-classical carbocations, and five reactions might occur, protonation reaction, chain elongation reaction, intramolecular cyclization reaction, deprotonation reaction, and dehydrogenation reaction. Classical carbocations acted as reactive intermediates in the chain elongation reaction and intramolecular cyclization reaction. When anthracene occurred chain elongation reactions with carbocations to form polymers, the generation of the tetramer required lager energy barriers than that of the dimer and trimer. The stiffness and flatness of molecules could be increased via intramolecular cyclization reactions. The polymers of anthracene might also occurred dehydrogenation reactions when the non-classical carbocations played the role of reactive intermediates. The dehydrogenation reactions required large energy barriers, which might be the reason for the product having a high aliphatic hydrogen content.METHOD:The Materials Studio (MS) 2020 software was used to complete the simulation. The atomic charge distribution calculation and the structure optimization of molecules were carried out using the B3LYP functional and DNP basis. The DFT-D (TS) dispersion corrections were added to calculate the dispersion interaction between aromatic molecules. The complete LST/QST method was used to search the transition states and calculate the reaction energy barrier.

Electrocatalysis has been recognized as one of the key technologies toward a carbon-neutral cycle of energy and substances. The rational design of electrocatalysts is undoubtedly the most important approach for accelerating the application of electrocatalysis. Computational screening of electrocatalysts based on thermodynamic evaluation is an efficient method for initially estimating their catalytic performances. However, the reaction rate at the electrochemical interface can be affected by many kinetic factors. Recently, we have developed a method for modeling potential/pH dependence in electrocatalysis, namely, electric field controlling constant potential (EFC-CP), which is much cheaper compared to the widely used grand canonical density functional theory calculations. This method can explicitly determine the evolution of real transition structures at varying potentials. As a result, both the chemical and electrostatic contributions to potential-dependent properties can be explicitly analyzed. Meanwhile, the change of the intermediate dipole along reaction coordinates can also be studied, which can reflect the pH dependence of the kinetic barrier. In this Perspective, we review the significant progress in understanding reaction kinetics in the application of electrochemical nitrogen fixation, ammonia synthesis, and denitrification. These insights can effectively help us understand the underlying physics of electrocatalytic reactions and improve the capability of catalyst design and modification. It is anticipated that the synergy between thermodynamic estimation and kinetic validation will enable the rational design of electrocatalysts in working condition.

In the context of dealing with limited annotated data, this paper introduces a weakly supervised whole slide image (WSI) classification approach based on contrastive learning. The proposed method aims to detect whether cancer cells have metastasized in anterior lymph nodes of breast cancer in whole slide images. Initially, small patches are extracted from whole-slide pathology images, and an unsupervised pretraining is performed on the feature extraction model using the MoCo v2 framework. Subsequently, the feature extraction model is used to extract features from the small patches. Finally, CLAM is employed to aggregate the extracted features to obtain the overall whole slide image (WSI) classification results. Experimental results demonstrate that using MoCo v2 for unsupervised pretraining of the feature extraction model achieves an accuracy of 0.8808 in the small patch classification task. Moreover, under coarse-grained WSI-level labels, the proposed approach achieves area under the receiver operating characteristic curve (AUC) values of 0.957 ± 0.0276 and 0.9442 on different datasets, outperforming typical weakly supervised and partially supervised methods in terms of classification performance.

Nitrogen compounds in heavy oils have significant deleterious impacts on the petroleum products and processes. It is of great significance to characterize the structures of nitrogen compounds during hydrodenitrogenation (HDN) in heavy oils, but the low content of nitrogen compounds after HDN is not conducive to structural analysis. Zirconium tetrachloride (ZrCl4) was found as an efficient complexing agent to enrich both basic and non-basic nitrogen compounds in heavy oils. The molecular weight ranges of the basic and non-basic nitrogen compounds were similar before and after ZrCl4 enrichment. The distribution of carbon number and double bond equivalent (DBE) of basic N1 species in the enriched feedstock was very close to that of the original feedstock, while the basic N1 species in the enriched product behaved a higher DBE distribution. The non-basic nitrogen compounds with higher DBE in the feedstock and product were also more likely to be enriched. Moreover, multi-heteroatomic non-basic nitrogen compounds were more inclined to be enriched than the non-basic N1 species due to the possible synergism of multi-heteroatoms. The numbers of detected multi-heteroatomic non-basic N2, N1O1, and N1O2 compounds obtained by high resolution mass spectrometry increased by 40 to nearly 70 times. The double bond equivalent (DBE) of these refractory multi-heteroatomic non-basic nitrogen compounds in the deep HDN product was much lower than those in the feedstock, due to the hydrogenation saturation reaction during HDN. The representative core structures of refractory basic nitrogen compounds were deduced by ESI+ FT-ICR MS coupled with collision-induced dissociation (CID), and the side chains were proposed by ion mobility spectrometry (IMS). Two typical kinds of refractory basic N1 compounds were suggested in the HDN product. One was a compact structure with multiple naphthenic rings and short side chains. The other had a large molecular size with aromatic rings and long side chains. ZrCl4 as a complexing agent can effectively enrich nitrogen compounds in heavy oil, especially for the hydrotreated heavy oils. This enrichment method facilitates the structural characterization of refractory nitrogen compounds in heavy oil HDN process by FT-ICR MS and IMS. These results provide valuable information for the improvement of HDN processes and catalysts.

Viscosity and viscosity index are the crucial properties of lubricant base stocks. Molecular dynamics simulation and quantum calculation were used to simulate the five isomers of C26H54 to study the intrinsic relationship between viscosity, viscosity index, and the molecular structure of isoalkanes. The results showed that the intermolecular interaction energy and the volume of rigid-like groups were the intrinsic factors that affected the viscosity and which could describe the viscosity quantitatively. The molecule conformation was studied by calculating the rotational energy barrier of the dihedral angle in the isoalkane molecule, and combined with molecular dynamics, the effect of temperature on the molecular conformation at 313 K and 373 K was further investigated. The α, β, and γ carbon atoms adjacent to the tertiary carbon in the isoalkane molecule were difficult to rotate due to steric hindrance and could be regarded as rigid-like groups at 313 K. The tertiary carbon and the three adjacent carbon atoms formed a regular tetrahedral rigid-like group at 373 K. The changes in the intermolecular interaction energy and the volume of the rigid-like group with temperatures could better describe the viscosity index and reveal the fundamental reasons that affect the viscosity and the viscosity index. The molecular-level understanding of the relationship between the molecular structure and properties of isoalkanes provided theoretical support and scientific guidance for designing isoalkane molecules with specific properties. Molecular dynamics simulation and quantum calculation were performed using Material Studio 8.0 software. The Amorphous Cell module was used to create an amorphous cell. The Foricite module was used for molecular dynamics simulation; the forcefield was assigned as COMPASS II. Nose–Hoover thermostat and Berendsen barostat were applied to maintain the temperature and pressure, respectively. To describe the non-bond interactions, the Ewald method was applied to calculate the van der Waals and electrostatic interactions. The Conformers module was used to study the conformation and the Dmol3 module was used to calculate the conformational energy with fine quality; the functional of GGA-PW91 and the basis set of DNP were used to calculate the energy.

The active catalysts of the BF3/n-C4H9OH-catalyzed 1-decene oligomerization reaction,as well as the distribution of the reaction products,was investigated by molecular simulation.The calculation results show that(BF3)2·n-C4H9OH catalyzes the 1-decene oligomerization reaction with higher activity compared to BF3·n-C4H9OH,which is the most catalytically active substance in the BF3/n-C4H9OH catalyst system.The reaction energy barriers and heats of reaction of chain initiation,chain growth,and chain termination in BF3/n-C4H9OH-catalyzed 1-decene oligomerization are calculated to reveal the product distribution.The calculation results show that the contents of the oligomerization reaction products in descending order are trimer,tetramer,pentamer,and dimer.The calculated results were consistent with the experimentally obtained product distribution.

Supplementary Figure 6 from Hedgehog-Producing Cancer Cells Respond to and Require Autocrine Hedgehog Activity

Supplementary Figure 1 from Hedgehog-Producing Cancer Cells Respond to and Require Autocrine Hedgehog Activity

Density functional theory (DFT) was rapidly developed and achieved a great success in the last decades. As the advancement of general concepts in heterogeneous catalysis, theoretical study of chemical reactions based on DFT calculations has become more and more feasible, which provides a guideline for the rational design of novel catalysts toward higher reaction activity and specific selectivity. Here, we review an innovate scheme, namely reaction phase diagram (RPD), which can offer not only an in-depth understanding of reaction mechanisms, but also the prediction of catalytic activity and selectivity trend over a collection of catalysts. The RPD analysis was successfully applied to understand the activity variation of CO2 electroreduction to CO and formic acid, as well as thermochemical hydrogenation and dehydrogenation. Meanwhile, the RPD analysis also exhibits a success of studying the product selectivity in syngas conversion to methane, ethanol, and methanol with complicated reaction pathways. At the end, we review a successful case of catalyst rational design with a target of NO selective electroreduction to ammonia. The foundation of RPD analysis is based on the scaling relation of adsorption energies and the correlation between kinetic barriers and reaction energies at elementary steps. Therefore, microkinetic modeling is complementary to the RPD analysis. A few of limitations and the prospect of the development regarding the RPD analysis are addressed in this review. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis

Electrocatalytic reduction of dinitrogen has emerged as a new strategy for ammonia synthesis. Despite being environmentally benign and energy-saving, it suffers from low conversion efficiency and short yield of ammonia because of the challenges of activating the inert N≡N bond at room temperature and atmospheric pressure. As a result of this, researchers proposed to reduce the nitrogenous species, one category of air and water pollutants, into valuable ammonia. Although remaining largely underexplored, this alternative approach shows promising efficiency for ammonia synthesis, while achieving high catalytic activity and selectivity remains challenging. In this Minireview, we summarize recent electrocatalytic performances of denitrification with selective formation to ammonia in terms of proposed active sites and reaction mechanisms. Additionally, we discuss the common issues in the state-of-the-art experimental tests and highlight the breakthroughs via computational screening of electrode materials. The aim of this is to steer the future research directions in the field, which is aiming for an optimal catalytic system with higher activity and selectivity for electrocatalytic denitrification.

Asphaltenes generally exist in the form of molecular aggregates in crude oil or in petroleum residues, and asphaltene aggregates can usually cause serious problems to oil exploitation, transportation, and processing. Achieving deaggregation and separation of asphaltene aggregates is a premise and basis for molecular characterization and processing of heavy oils. Aiming at the intermolecular interactions in asphaltene molecular aggregates, it has proposed and summarized that aspahltene aggregates can be subject to deaggregation by means of five approaches, including solvent diluting, removing active sites, moderate heating, ultrasonication and on-line molecular collision. Moreover, asphaltenes can be further separated to narrow fractions for molecular-level research based on polarity difference, molecular size difference, acid-base properties, and reactivity difference.

In order to elucidate deeply the mechanism of gasoline oxidation during its storage and usage,the typical hydrocarbon molecules with the same carbon number were selected as the model compounds.Using the ab initio quantum method based on density functional theory,we calculated the chain free radical oxidation reaction network which produced deposit with high relative molecular mass and high polarity.By comparing the reaction energy barrier of different reaction paths,the key step of the deposit formation was obtained.Thus,structure characteristics of gasoline molecules contributing to the formation of deposit have been draw n up.T he results show ed that it is easy to initiate free radical chain reaction for the gasoline molecules w hich have C—H in α position of C=C,tert C— H or C—H in αposition of phenyl.However,it depends on the structure of the intermediate products w hether they could continue to react.Whether there w as still a C—H in αposition of C=C,tert C—H,C—H in αposition of phenyl or whether bonds like C= O were generated,the electron-withdrawing group in the reaction process was the critical factor. Furthermore,ROOH and ROO · were the most critical intermediates.The crucial step is to remove the two free radicals.

A DFT study of oxidation initiation reaction for same carbon number but different type hydrocarbon compound in gasoline was performed. Firstly, the homolytic dissociation energies of the C-H bond in various hydrocarbon molecules were calculated and the C-H active site which was most likely to be attacked by oxygen molecules was obtained. Then, the reaction barrier of oxidation initiation reaction for different gasoline hydrocarbon molecules was compared. Furthermore, frontier orbital theory was used to analyze the chain initiation mechanism. It was found that the symmetry and energy gap of the HOMO orbitals of gasoline hydrocarbon molecules and the LUMO orbitals of oxygen molecule are the decisive factors in the oxidation initiation reaction. The results indicate that the reaction barrier of the olefin is much lower than other hydrocarbons. On the other hand, the energy gap between the HOMO orbital of 2, 4-hexadiene and the LUMO orbital of the oxygen is much lower than other molecules just followed by 1-hexene.

To understand the alkylation mechanism of isobutane with butene, it is of great importance to elucidate the difference of protonation behaviours among butene isomers at molecular scale, because it is the starting point of this reaction. Herein, we have calculated the protonation processing of isobutene and 2-butene on a 120T HY cluster model, using an embedded QM/MM (quantum mechanical/molecular mechanical) method. The formation energy of p-complex from isobutene is higher than that of 2-butene owing to the effect of electronic interaction and steric hindrance between the C=C bond of butene and the H atom of the HY zeolite. Moreover, the energy of t-butyl alkoxide (TBA) produced via isobutene protonation is higher than that of s-butyl alkoxide (SBA) from 2-butene, as the C-O bond of TBA is longer. In addition, the transition state of isobutene protonation is a t-butyl carbonium ion, while the corresponding structure during 2-butene protonation is a s-butyl carbonium ion, which is less stable. In conclusion, isobutene is much easier to be activated by Bronsted acid site of HY zeolite than 2-butene.

Catalytic combustion is an important technique for utilization of fossil fuels, and the research on catalytic combustion mechanism could provide theoretical basis for the selection of catalyzer. In this paper, we adopt the Ni catalyst to promote the oxidation combustion reaction, and carry out study on carbon oxygen catalytic combustion mechanism based on density functional theory. The result suggests that Ni catalyst could significantly improve the carbon - oxygen catalytic combustion performance.

Coke formation during the refining of heavy oils has attracted extensive attention as a result of the effects on the liquid yield, catalyst deactivation, and operating period. Polycydic aromatic hydrocarbons (PAHs) generally have the strongest tendencies to form coke during the refining processes, which are considered as coke precursors. In this work, a vacuum residue was treated by thermal conversion and deep hydroprocessing. The feedstock and products were characterized by Fourier transform ion cyclotron resonance mass spectrometry. The detailed distributions of aromatic hydrocarbons of the products behaved with clear boundaries, which were described in limit lines. The slopes of the limit lines differed greatly between the two kinds of products, indicating different mechanisms for the growth of PAHs. Thermal conversion and deep hydroprocessing of model compounds were also conducted. Thermal conversion products of phenanthrene and pyrene proved that only condensation reactions occurred at a temperature of 450 degrees C and the aromatic rings were not ruptured. Deep hydroprocessing of pyrene revealed that the aromatic ring structures were cracked and then the smaller aromatic substrates combined together to form highly condensed aromatic rings. As a conclusion, the different mechanisms of coke precursor formation resulted in the different slopes of limit lines for thermal conversion and deep hydroprocessing products.