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.

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.

Energetic and Kinetic Competition on the Stability of Pd13 Clusters: Ab Initio Molecular Dynamics Simulations.

Material stability is the focus on both experiments and calculations, which includes the energetic stability at the static state and the thermodynamic stability at the kinetic state. To show whether energetics or kinetics dominates on material stability, this study focuses on the Pd13 clusters, because of their observable magnetic moment in experiment. Energetically, the CALYPSO searching method and first-principles calculations find that Pd13(C2) is the ground state at 0 K while the static frequency calculations demonstrate that the icosahedron Pd13(Ih) becomes more favorable on free energy as temperature increases. However, their magnetic moments (8 µB) are not in agreement with the experimental value (<5.2 µB). Kinetically, ab initio molecular dynamics simulations reveal that Pd13(C3v) (6 µB) has supreme isomerization temperature and the other 11 low-lying isomers transform to Pd13(C3v) directly or indirectly, demonstrating that Pd13(C3v) has the maximum probability to be observed in experiment. The magnetic moment difference between experiment (<5.2 µB) and this calculation (6 µB) may be due to the spin multiplicities. Our result suggests that the magnetic moment disparity between theory and experiment (in Pd13 clusters) originates from the kinetic stability.

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.

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.

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.

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.

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.

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.

Molecular and dissociative O2 adsorption on the Cu2O(111) surface.

The adsorption of O2 on the Cu2O(111) surface at different coverages has been studied by spin-polarized density functional theory (DFT+U) calculations and atomic thermodynamics. It has been found that the dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface at low coverages (1/4 to 1 monolayer), while totally dissociative and mixed molecular and dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface thermodynamically at higher coverages (5/4 to 7/4 monolayers). More interesting is that the CuO film can be automatically formed on the Cu2O(111) surface that was induced by the surface reconstruction of the Cu2O(111) surface and adsorption of four dissociative O2 molecules (1 monolayer), which agrees well with the recent experimental results. Along higher coverages of O2 adsorption (5/4 to 7/4 monolayers), much stronger surface reconstruction and relaxation was found. The probability distribution of different single-O2 adsorbed states on the Cu2O(111) surface as a function of temperature was analyzed using a Boltzmann model. The adsorption mechanism of O2 on the Cu2O(111) surface was analyzed using the phase diagram and compared with other metal oxides.

Role of the (H2O)n (n = 1-3) cluster in the HO2 + HO →3O2 + H2O reaction: mechanistic and kinetic studies.

To study the catalytic effects of (H2O)n (n = 1-3), the mechanisms of the reaction HO2 + HO →3O2 + H2O without and with (H2O)n (n = 1-3) have been investigated theoretically at the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ level of theory, coupled with rate constant calculations using the conventional transition state theory. Our results show that upon incorporation of (H2O)n (n = 1-3) into the channel of H2O + 3O2 formation, two different reactions, i.e. HO + HO2(H2O)n (n = 1-3) and HO2 + HO(H2O)n (n = 1-3), have been observed, and these two reactions are competitive with each other. The catalytic effects of (H2O)n (n = 1-3) mainly arise from the contribution of a single water vapor molecule; this is because the effective rate constants with water are respectively larger by 2-3 and 3-4 orders of magnitude than those of the reactions with (H2O)2 and (H2O)3. Furthermore, the catalytic effects of the water monomer mainly arise from the H2OHO2 + HO reaction, and the enhancement factor of this reaction is obvious within the temperature range of 240.0-425.0 K, with the branching ratio (k'(RW)/ktot) of 17.27-80.77%. Overall, the present results provide a new example of how water and water clusters catalyze gas phase reactions under atmospheric conditions.

High coverage water adsorption on CuO(011) surface.

Spin-polarized density functional theory calculations (GGA+U) and atomic thermodynamics have been used to study the adsorption of water on the CuO(011) surface at different coverages. It was found that H2O molecular adsorption on CuO(011) surface is energetically favorable for one H2O molecule, but dissociative adsorption is preferred for two and three molecules, while a mixed molecular and dissociative coadsorption is favorable for four water molecules. The phase diagram of water adsorption on the CuO(011) surface shows that the adsorption of three and four water molecules is favorable thermodynamically. Different single-water adsorption states were analyzed by the Boltzmann model at different temperatures. The adsorption energy is contributed to by the surface uncoordinated copper and oxygen atoms, and by hydrogen chemical bonding. The energetic trends are related to the underlying electronic mechanisms.

CO adsorption, oxidation and carbonate formation mechanisms on Fe3O4 surfaces.

By means of density functional theory calculations that account for the on-site Coulomb interaction via a Hubbard term (DFT+U), we systematically investigated CO adsorption on Fe3O4 surfaces at different coverages. It has been found that more than one CO can coadsorb on one surface iron atom on both Fetet1 and Feoct2 terminations of Fe3O4(111). The uncapped oxygen atom is the active site for CO oxidation on both Fetet1 and Feoct2 terminations of Fe3O4(111). For Fe3O4(110), two CO molecules prefer to coadsorb on one surface iron atom on the A layer; CO prefers to adsorb at the bridge site of the surface octahedral iron atoms at low coverage, while CO prefers to adsorb at the surface tetrahedral iron atom at high coverage on the B layer. It has been found that the surface oxygen atom which is not coordinated to the tetrahedral iron atom is the active site for CO oxidation on the B termination of Fe3O4(001). On the Fe3O4 surfaces, the formation of carbonate has been found to be very stable thermodynamically, which agrees well with experiments. The adsorption mechanism has been analyzed on the basis of projected density of states (PDOS).

d-AO spherical aromaticity in Ce6O8.

After the first introduction of π aromaticity in chemistry to explain the bonding, structure, and reactivity of benzene and its derivatives, this concept was further applied to many other compounds featuring other types of aromaticity (i.e., σ, δ). Thus far, there have been no reports on d-AO-based spherical σ aromaticity. Here, we predict a highly stable bare Ce6O8 cluster of a spherical shape using evolutionary algorithm USPEX and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that bare Ce6O8 cluster exhibits d-AO spherical σ aromaticity, thus explaining its exotic geometry and stability. Ce6O8 complex plays an important role in many reactions and is known to exist in many forms, such as in NH4[Ce6(µ(3)O)5(µ(3)OH)3(µ(2)-C6H5COO)9(NO3)3(DMF)3]*DMF*H2O compound, which is prepared under room temperature, and acts as an oxidizing agent.

Antiferromagnetic Stabilization in the Ti8O12 Cluster.

Using the evolutionary algorithm USPEX and DFT+U calculations, we predicted a high-symmetry geometric structure of the bare Ti8 O12 cluster composed of 8 Ti atoms forming a cube, in which O atoms are at midpoints of all of its edges, in excellent agreement with experimental results. Using natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots, we find the origin of the particular stability of bare Ti8 O12 cluster: unique chemical bonding where eight electrons of Ti atoms interacting with each other in antiferromagnetic fashion to lower the total energy of the system. The bare Ti8 O12 is thus an unusual molecule stabilized by d-orbital antiferromagnetic coupling.

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.

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.

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.

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.