First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne.

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

Screening novel candidates of ZL003-based organic dyes for dye-sensitized solar cells by modifying auxiliary electron acceptors: A theoretical study.

In this work, a series of ZL003-based free-metal sensitizers with the donor-acceptor-π- conjugated spacer-acceptor (D-A-π-A) structure were designed by modifying auxiliary electron acceptors for the potential application in dye-sensitized solar cells. The energy levels of frontier molecular orbitals, absorption spectra, electronic transition, and photovoltaic parameters for all studied dyes were systematically evaluated using density functional theory (DFT)/time-dependent DFT calculations. Results illustrated that thienopyrazine (TPZ), selenadiazolopyridine (SDP), and thiadiazolopyridine (TDP) are excellent electron acceptors, and dye sensitizers functionalized by these acceptors have smaller HOMO-LUMO gaps, obviously red-shifted absorption bands and stronger light harvesting. The present study revealed that the photoelectric conversion efficiency (PCE) of ZL003 is around 13.42 % with a JSC of 20.21 mA·cm-2, VOC of 966 mV and FF of 0.688 under the AM 1.5G sun exposure, in good agreement with its experimental value (PCE = 13.6 ± 0.2 %, JSC = 20.73 ± 0.20 mA·cm-2, VOC = 956 ± 5 mV, and FF = 0.685 ± 0.005.). With the same procedure, the PCE values for M4, M6, and M7 were estimated to be as high as 19.93 %, 15.38 %, and 15.80 % respectively. Hence, these three dyes are expected to be highly efficient organic sensitizers applied in practical DSSCs.

Review of Theoretical and Computational Studies of Bulk and Single Atom Catalysts for H2 S Catalytic Conversion.

Catalytic conversion of hydrogen sulfide (H2 S) plays a vital role in environmental protection and safety production. In this review, recent theoretical advances for catalytic conversion of H2 S are systemically summarized. Firstly, different mechanisms of catalytic conversion of H2 S are elucidated. Secondly, theoretical studies of catalytic conversion of H2 S on surfaces of metals, metal compounds, and single-atom catalysts (SACs) are systematically reviewed. In the meantime, various strategies which have been adopted to improve the catalytic performance of catalysts in the catalytic conversion of H2 S are also reviewed, mainly including facet morphology control, doped heteroatoms, metal deposition, and defective engineering. Finally, new directions of catalytic conversion of H2 S are proposed and potential strategies to further promote conversion of H2 S are also suggested: including SACs, double atom catalysts (DACs), single cluster catalysts (SCCs), frustrated Lewis pairs (FLPs), etc. The present comprehensive review can provide an insight for the future development of new catalysts for the catalytic conversion of H2 S.

Tailoring the coordination environment of double-atom catalysts to boost electrocatalytic nitrogen reduction: a first-principles study.

Tailoring the coordination environment is an effective strategy to modulate the electronic structure and catalytic activity of atomically dispersed transition-metal (TM) catalysts, which has been widely investigated for single-atom catalysts but received less attention for emerging double-atom catalysts (DACs). Herein, based on first-principles calculations, taking the commonly studied N-coordinated graphene-based DACs as references, we explored the effect of coordination engineering on the catalytic behaviors of DACs towards the electrocatalytic nitrogen reduction reaction (NRR), which is realized through replacing one N atom by the B or O atom to form B, N or O, N co-coordinated DACs. We found that B, N or O, N co-coordination could significantly strengthen N2 adsorption and alter the N2 adsorption pattern of the TM dimer active center, which greatly facilitates N2 activation. Moreover, on the studied DACs, the linear scaling relationship between the binding strengths of key intermediates can be attenuated. Consequently, the O, N co-coordinated Mn2 DACs, exhibiting an ultralow limiting potential of -0.27 V, climb to the peak of the activity volcano. In addition, the experimental feasibility of this DAC system was also identified. Overall, benefiting from the coordination engineering effect, the chemical activity and catalytic performance of the DACs for NRR can be significantly boosted. This phenomena can be understood from the adjusted electronic structure of the TM dimer active center due to the changes of its coordination microenvironment, which significantly affects the binding strength (pattern) of key intermediates and changes the reaction pathways, leading to enhanced NRR activity and selectivity. This work highlights the importance of coordination engineering in developing DACs for the electrocatalytic NRR and other important reactions.

Laccase Lac-W detoxifies aflatoxin B1 and degrades five other major mycotoxins in the absence of redox mediators.

A multicopper oxidase Lac-W from Weizmannia coagulans 36D1 was identified and characterized as a laccase (Lac-W) with a robust enzymatic activity, which was used in various mycotoxins degradation. We demonstrated that Lac-W could directly degrade six major mycotoxins in the absence of redox mediators in pH 9.0, 24h static incubation at room temperature, including aflatoxin B1 (AFB1, 88%), zearalenone (60%), deoxynivalenol (34%), T-2 toxin (19%), fumonisin B1 (18%), and ochratoxin A (12%). The optimal condition for Lac-W to degrade AFB1 was 30 °C, pH 9.0, enzyme-substrate ratio 3U/µg in 24h static condition. Furthermore, we characterized aflatoxin Q1 as a Lac-W-mediated degradation product of AFB1 using UHPLC-MS/MS. Interestingly, degradation products of AFB1 failed to generate cell death and apoptosis of intestinal porcine epithelial cells. Finally, our molecular docking simulation results revealed that the substrate-binding pocket of Lac-W was large enough to allow the entry of six mycotoxins with different structures, and their degradation rates were positively correlated to their interacting affinity with Lac-W. In summary, the unique properties of the Lac-W make it a great candidate for detoxifying multiple mycotoxins contaminated food and feed cost-effectively and eco-friendly. Our study provides new insights into development of versatile enzymes which could simultaneously degrade multiple mycotoxins.

A stable and strongly ferromagnetic Fe17O10- cluster with an accordion-like structure.

Isolated clusters are ideal systems for tailoring molecule-based magnets and investigating the evolution of magnetic order from microscopic to macroscopic regime. We have prepared pure Fen- (n = 7-31) clusters and observed their gas-collisional reactions with oxygen in a flow tube reactor. Interestingly, only the larger Fen- (n ≥ 15) clusters support the observation of O2-intake, while the smaller clusters Fen- (n = 7-14) are nearly nonreactive. What is more interesting is that Fe17O10- shows up with prominent abundance in the mass spectra indicative of its distinct inertness. In combination with DFT calculations, we unveil the stability of Fe17O10- within an interesting acordion-like structure and elucidate the spin accommodation in such a strongly ferromagnetic iron cluster oxide.

Sabatier Phenomenon in Hydrogenation Reactions Induced by Single-Atom Density.

The Sabatier principle is a fundamental concept in heterogeneous catalysis that provides guidance for designing optimal catalysts with the highest activities. For the first time, we here report a new Sabatier phenomenon in hydrogenation reactions induced by single-atom density at the atomic scale. We produce a series of Ir single-atom catalysts (SACs) with a predominantly Ir1-P4 coordination structure with densities ranging from 0.1 to 1.7 atoms/nm2 through a P-coordination strategy. When used as the catalysts for hydrogenation, a volcano-type relationship between Ir single-atom density and hydrogenation activity emerges, with a summit at a moderate density of 0.7 atoms/nm2. Mechanistic studies show that the balance between adsorption and desorption strength of the activated H* on Ir single atoms is found to be a key factor for the Sabatier phenomenon. The transferred Bader charge on these Ir SACs is proposed as a descriptor to interpret the structure-activity relationship. In addition, the maximum activity and selectivity can be simultaneously achieved in chemoselective hydrogenation reactions with the optimized catalyst due to the uniform geometric and electronic structures of single sites in SACs. The present study reveals the Sabatier principle as an insightful guidance for the rational design of more efficient and practicable SACs for hydrogenation reactions.

Recent progress of theoretical studies on electro- and photo-chemical conversion of CO2 with single-atom catalysts.

The CO2 reduction reaction (CO2RR) into chemical products is a promising and efficient way to combat the global warming issue and greenhouse effect. The viability of the CO2RR critically rests with finding highly active and selective catalysts that can accomplish the desired chemical transformation. Single-atom catalysts (SACs) are ideal in fulfilling this goal due to the well-defined active sites and support-tunable electronic structure, and exhibit enhanced activity and high selectivity for the CO2RR. In this review, we present the recent progress of quantum-theoretical studies on electro- and photo-chemical conversion of CO2 with SACs and frameworks. Various calculated products of CO2RR with SACs have been discussed, including CO, acids, alcohols, hydrocarbons and other organics. Meanwhile, the critical challenges and the pathway towards improving the efficiency of the CO2RR have also been discussed.

Adsorption of Transition-Metal Clusters on Graphene and N-Doped Graphene: A DFT Study.

Using the dispersion-corrected density functional theory (DFT-D3) method, we systematically studied the adsorption of 15 kinds of transition-metal (TM) clusters on pristine graphene (Gr) and N-doped graphene (N-Gr). It has been found that TMn (n = 1-4) clusters adsorbed on the N-Gr surface are much stronger than those on the pristine Gr surface, while 3d series clusters present similar geometries on Gr and N-Gr surfaces. The most preferred sites of TMs migrate from hollow to bridge to the top site on the Gr surface along the d series in the periodic table, while the preferred sites of TMs migrate in a much more complex manner on the N-Gr surface. It has also been found that charge transfer decreases along the d series for adsorbed clusters on both surfaces, but adsorbed clusters present less charge transfer on the N-Gr surface than on the Gr surface. What is more interesting is that some TM (Tc, Ru, and Re) clusters change the growth mechanism from the three-dimensional (3D) growth mode on the Gr surface to the two-dimensional (2D) growth mode on the N-Gr surface. At last, it has been found that adsorbed clusters are more dispersed on the N-Gr surface than on the pristine Gr surface due to growth and average aggregation energies.

Unprecedentedly high activity and selectivity for hydrogenation of nitroarenes with single atomic Co1-N3P1 sites.

Transition metal single atom catalysts (SACs) with M1-Nx coordination configuration have shown outstanding activity and selectivity for hydrogenation of nitroarenes. Modulating the atomic coordination structure has emerged as a promising strategy to further improve the catalytic performance. Herein, we report an atomic Co1/NPC catalyst with unsymmetrical single Co1-N3P1 sites that displays unprecedentedly high activity and chemoselectivity for hydrogenation of functionalized nitroarenes. Compared to the most popular Co1-N4 coordination, the electron density of Co atom in Co1-N3P1 is increased, which is more favorable for H2 dissociation as verified by kinetic isotope effect and density functional theory calculation results. In nitrobenzene hydrogenation reaction, the as-synthesized Co1-N3P1 SAC exhibits a turnover frequency of 6560 h-1, which is 60-fold higher than that of Co1-N4 SAC and one order of magnitude higher than the state-of-the-art M1-Nx-C SACs in literatures. Furthermore, Co1-N3P1 SAC shows superior selectivity (>99%) toward many substituted nitroarenes with co-existence of other sensitive reducible groups. This work is an excellent example of relationship between catalytic performance and the coordination environment of SACs, and offers a potential practical catalyst for aromatic amine synthesis by hydrogenation of nitroarenes.

N-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide: design, synthesis, crystal structure, antiproliferative activity, DFT, Hirshfeld surface analysis and molecular docking study.

The compound N-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide (8) was synthesized by the condensation of 3-methoxybenzoic acid (7) with N1-(2-chlorothieno[3,2-d]pyrimidin-4-yl)ethane-1,2-diamine (6). This intermediate was prepared from methyl 3-aminothiophene-2-carboxylate (1) by the condensation with urea, chlorination with phosphorus oxychloride and then condensation with ethane-1,2-diamine. The crystal structure of the title compound was determined and the crystal of the title compound belongs to the tetragonal system, space group P4(3) with a = 9.4694(10) Å, b = 9.4694(10) Å, c = 18.886(3) Å, α = 90°, ß = 90°, γ = 90°. The optimized geometric bond lengths and bond angles obtained by using density functional theory (DFT) have been compared with X-ray diffraction values. The calculated HOMO and LUMO energies showed the character of the title compound. The molecular electrostatic potential (MEP) surface map of the related molecule was investigated with theoretical calculations at the B3LYP/6-311 + G(d,p) levels. A quantitative analysis of the intermolecular interactions in the crystal structures has been performed using Hirshfeld surface analysis. In addition, the title compound possesses marked inhibition against the proliferation of human colon cancer cell line HT-29 (IC50 = 1.76 µM), human lung adenocarcinoma cell line A549 (IC50 = 1.98 µM) and human gastric cancer cell line MKN45 (IC50 = 2.32 µM), displaying promising anticancer activitiy. The molecular docking studies revealed that the title compound may exhibit activity inhibiting PDB:3D15.Communicated by Ramaswamy H. Sarma.

Direct Observation of Metal Oxide Nanoparticles Being Transformed into Metal Single Atoms with Oxygen-Coordinated Structure and High-Loadings.

Direct conversion of bulk metal or nanoparticles into metal single atoms under thermal pyrolysis conditions is a highly efficient and promising strategy to fabricate single-atom catalysts (SACs). Usually, nitrogen-doped carbon is used as the anchoring substrate to capture the migrating metal ion species at high temperatures, and stable isolated SACs with nitrogen coordination are formed during the process. Herein, we report unexpected oxygen-coordinated metal single-atom catalysts (Fe-, Co-, Ni-, Mn-SACs) with high loadings (above 10 wt %) through direct transformation of metal oxide nanoparticles (Fe-, Co-, Ni-, Mn-NPs) in an inert atmosphere at 750 °C for 2 h. The atomic dispersion of metal single atoms and their coordinated structures were confirmed by aberration-corrected scanning transmission electron microscopy and X-ray absorption fine structures. In addition, the dynamic process of nanoparticles to atoms was directly observed by in situ transmission electron microscopy. The as-prepared Fe SAC exhibited high activity and superior selectivity for catalytic oxidation of benzene to phenol with hydrogen peroxide.

Spherical trihedral metallo-borospherenes.

The discovery of borospherenes unveiled the capacity of boron to form fullerene-like cage structures. While fullerenes are known to entrap metal atoms to form endohedral metallofullerenes, few metal atoms have been observed to be part of the fullerene cages. Here we report the observation of a class of remarkable metallo-borospherenes, where metal atoms are integral parts of the cage surface. We have produced La3B18- and Tb3B18- and probed their structures and bonding using photoelectron spectroscopy and theoretical calculations. Global minimum searches revealed that the most stable structures of Ln3B18- are hollow cages with D3h symmetry. The B18-framework in the Ln3B18- cages can be viewed as consisting of two triangular B6 motifs connected by three B2 units, forming three shared B10 rings which are coordinated to the three Ln atoms on the cage surface. These metallo-borospherenes represent a new class of unusual geometry that has not been observed in chemistry heretofore.

Efficient synthesis of highly dispersed ultrafine Pd nanoparticles on a porous organic polymer for hydrogenation of CO2 to formate.

Precise design of catalytic supports is an encouraging technique for simultaneously improving the activity and stability of the catalyst. However, development of efficient heterogeneous catalysts for transforming CO2 into formic acid (FA) is still a big challenge. Herein, we report that Pd nanoparticles (NPs) based on a porous organic polymeric support containing amide and pyridine functional groups (AP-POP) can be an efficient catalyst for selective hydrogenation of CO2 to form formate with high efficiency even under mild reaction conditions (6.0 MPa, 80 °C). Electron density of the active Pd species modulated via the interaction between pyridine nitrogen and Pd play important roles in dramatic enhancement of catalytic activity and was indicated by X-ray photoelectron spectroscopy (XPS) along with CO chemisorption. This work provides an interesting and effective strategy for precise support design to improve the catalytic performance of nanoparticles.

Atmospheric chemistry of the self-reaction of HO2 radicals: stepwise mechanism versus one-step process in the presence of (H2O)n (n = 1-3) clusters.

The effects of water on radical-radical reactions are of great importance for the elucidation of the atmospheric oxidation process of free radicals. In the present work, the HO2 + HO2 reactions with (H2O)n (n = 1-3) have been investigated using quantum chemical methods and canonical variational transition state theory with small curvature tunneling. We have explored both one-step and stepwise mechanisms, in particular the stepwise mechanism initiated by ring enlargement. The calculated results have revealed that the stepwise mechanism is the dominant one in the HO2 + HO2 reaction that is catalyzed by one water molecule. This is because its pseudo-first-order rate constant (kRWM1') is 3 orders of magnitude larger than that of the corresponding one-step mechanism. Additionally, the value of kRWM1' at 298 K has been found to be 4.3 times larger than that of the rate constant of the HO2 + HO2 reaction (kR1) without catalysts, which is in good agreement with the experimental findings. The calculated results also showed that the stepwise mechanism is still dominant in the (H2O)2 catalyzed reaction due to its higher pseudo-first-order rate constant, which is 3 orders of magnitude larger than that of the corresponding one-step mechanism. On the other hand, the one-step process is much faster than the stepwise mechanism by a factor of 105-106 in the (H2O)3 catalyzed reaction. However, the pseudo-first-order rate constants for the (H2O)2 and (H2O)3-catalyzed reactions are lower than that of the H2O-catalyzed reaction by 3-4 orders of magnitude, which indicates that the water monomer is the most efficient one among all the catalysts of (H2O)n (n = 1-3). The present results have provided a definitive example that water and water clusters have important influences on atmospheric reactions.

Correction: The stability and unexpected chemistry of oxide clusters.

Correction for 'The stability and unexpected chemistry of oxide clusters' by Xiaohu Yu et al., Phys. Chem. Chem. Phys., 2018, 20, 30437-30444.

Effects of water, ammonia and formic acid on HO2 + Cl reactions under atmospheric conditions: competition between a stepwise route and one elementary step.

Quantum chemical calculations at M06-2X and CCSD(T) levels of theory have been performed to investigate the effects of H2O, NH3, and HCOOH on the HO2 + Cl → HCl + O2 reaction. The results show that catalyzed reactions with three catalysts could proceed through two different mechanisms, namely a stepwise route and one elementary step, where the former reaction is more favorable than the latter. Meanwhile, for the stepwise route, a single hydrogen atom transfer pathway in the presence of all catalysts has more advantages than the respective double hydrogen atom transfer pathway. Then, the relative impacts of catalysts under tropospheric conditions were investigated by considering the temperature dependence of the rate constants and the altitude dependence of catalyst concentrations. The calculated results show that at 0 km altitude, the HO2 + Cl → HCl + O2 reaction with catalysts, such as H2O, NH3, or HCOOH, cannot compete with the reaction without a catalyst, as the effective rate constant with a catalyst is smaller by 2-6 orders of magnitude than the naked reaction within the temperature range 280-320 K. The calculated results also show that at altitudes of 5, 10 and 15 km, the effective rate constant of the HCOOH-catalyzed reaction increases obviously with an increase in altitude. At 15 km altitude, its value is up to 9.63 × 10-11 cm3 per molecule per s, which is close to the corresponding value of the reaction without a catalyst, showing that the contribution of HCOOH to the HO2 + Cl → HCl + O2 reaction cannot be neglected at high altitudes. The new findings in this investigation are not only of great necessity and importance for elucidating the gas-phase reaction of HO2 with Cl in the presence of acidic, neutral and basic catalysts, but are also of great interest for understanding the importance of other types of hydrogen abstraction in the atmosphere.

Catalytic effect of (H2O) n (n = 1-3) clusters on the HO2 + SO2 → HOSO + 3O2 reaction under tropospheric conditions.

The HO2 + SO2 → HOSO + 3O2 reaction, both without a catalyst and with (H2O) n (n = 1-3) as a catalyst, has been investigated using CCSD(T)/CBS//M06-2X/aug-cc-pVTZ methods, and canonical variational transition state theory with small curvature tunneling (CVT/SCT). The calculated results show that H2O exerts the strongest catalytic role in the hydrogen atom transfer processes of HO2 + SO2 → HOSO + 3O2 as compared with (H2O)2 and (H2O)3. In the atmosphere at 0 km altitude within the temperature range of 280.0-320.0 K, the reaction with H2O is dominant, compared with the reaction without a catalyst, with an effective rate constant 2-3 orders of magnitude larger. In addition, at 0 km, it is worth mentioning that the relevance of the HO2 + SO2 → HOSO + 3O2 reaction with H2O depends heavily on its ability to compete with the primary loss mechanism of HO2 radicals (such as the HO2 + HO2 and HO2 + NO3 reactions) and SO2 (such as the SO2 + HO reaction). The calculated results show that the HO2 + SO2 → HOSO + 3O2 reaction with H2O cannot be neglected in the primary loss mechanism of the HO2 radical and SO2. The calculated results also show that for the formation of HOSO and 3O2, the contribution of H2O decreases from 99.98% to 27.27% with an increase in altitude from 0 km to 15 km, due to the lower relative concentration of water. With the altitude increase, the HO2 + SO2 → HOSO + 3O2 reaction with H2O cannot compete with the primary loss mechanism of HO2 radicals. The present results provide new insight into (H2O) n (n = 1-3) catalysts, showing that they not only affect energy barriers, but also have an influence on loss mechanisms. The present findings should have broad implications in computational chemistry and atmospheric chemistry.

Correction: Effects of water, ammonia and formic acid on HO2 + Cl reactions under atmospheric conditions: competition between a stepwise route and one elementary step.

[This corrects the article DOI: 10.1039/C9RA03541A.].

The stability and unexpected chemistry of oxide clusters.

Using evolutionary structure prediction and ab initio thermodynamics, we determine stable compositions and structures of small CemOn and FemOn clusters at realistic temperatures and oxygen pressures. We use second energy differences as the criterion determining clusters of particular stability ("magic" clusters), whereas HOMO-LUMO gaps are used to gauge chemical inertness - i.e. the ability of a cluster to survive in a complex chemical environment. We find that, similar to atomic nuclei (which are clusters made of neutrons and protons), compositional space of two-component clusters also has ridges and islands of stability, surrounded by sea of instability. Long ridges of stability correspond to stoichiometric compositions - e.g., (CeO2)k, (Ce2O3)k, (FeO)k, (Fe2O3)k and (Fe3O4)k series of clusters, while "islands of stability" can have very unexpected compositions. For example, at room temperature and ambient atmosphere, superoxidized Fe4O8 clusters will be dominant among the Fe4On clusters. We emphasize that stability is dictated not only by closed geometric and electronic shells, but also by magnetism.