How spin state and oxidation number of transition metal atoms determine molecular adsorption: a first-principles case study for NH3.

Understanding how the electronic state of transition metal atoms can influence molecular adsorption on a substrate is of great importance for many applications. Choosing NH3 as a model molecule, its adsorption behavior on defected SnS2 monolayers is investigated. The number of valence electrons n is controlled by decorating the monolayer with different transition metal atoms, ranging from Sc to Zn. Density-Functional Theory based calculations show that the adsorption energy of NH3 molecules oscillates with n and shows a clear odd-even pattern. There is also a mirror symmetry of the adsorption energies for large and low electron numbers. This unique behavior is mainly governed by the oxidation state of the TM ions. We trace back the observed trends of the adsorption energy to the orbital symmetries and ligand effects which affect the interaction between the 3σ orbitals (NH3) and the 3d orbitals of the transition metals. This result unravels the role which the spin state of TM ions plays in different crystal fields for the adsorption behavior of molecules. This new understanding of the role of the electronic structure on molecular adsorption can be useful for the design of high efficiency nanodevices in areas such as sensing and photocatalysis.

Polycrystalline Few-Layer Graphene as a Durable Anticorrosion Film for Copper.

Corrosion of metals in atmospheric environments is a worldwide problem in industry and daily life. Traditional anticorrosion methods including sacrificial anodes or protective coatings have performance limitations. Here, we report atomically thin, polycrystalline few-layer graphene (FLG) grown by chemical vapor deposition as a long-term protective coating film for copper (Cu). A six-year old, FLG-protected Cu is visually shiny and detailed material characterizations capture no sign of oxidation. The success of the durable anticorrosion film depends on the misalignment of grain boundaries between adjacent graphene layers. Theoretical calculations further found that corrosive molecules always encounter extremely high energy barrier when diffusing through the FLG layers. Therefore, the FLG is able to prevent the corrosive molecules from reaching the underlying Cu surface. This work highlights the interesting structures of polycrystalline FLG and sheds insight into the atomically thin coatings for various applications.

Efficient UV-induced charge separation and recombination in an 8-oxoguanine-containing dinucleotide.

During the early evolution of life, 8-oxo-7,8-dihydro-2'-deoxyguanosine (O) may have functioned as a proto-flavin capable of repairing cyclobutane pyrimidine dimers in DNA or RNA by photoinduced electron transfer using longer wavelength UVB radiation. To investigate the ability of O to act as an excited-state electron donor, a dinucleotide mimic of the FADH2 cofactor containing O at the 5'-end and 2'-deoxyadenosine at the 3'-end was studied by femtosecond transient absorption spectroscopy in aqueous solution. Following excitation with a UV pulse, a broadband mid-IR pulse probed vibrational modes of ground-state and electronically excited molecules in the double-bond stretching region. Global analysis of time- and frequency-resolved transient absorption data coupled with ab initio quantum mechanical calculations reveal vibrational marker bands of nucleobase radical ions formed by electron transfer from O to 2'-deoxyadenosine. The quantum yield of charge separation is 0.4 at 265 nm, but decreases to 0.1 at 295 nm. Charge recombination occurs in 60 ps before the O radical cation can lose a deuteron to water. Kinetic and thermodynamic considerations strongly suggest that all nucleobases can undergo ultrafast charge separation when π-stacked in DNA or RNA. Interbase charge transfer is proposed to be a major decay pathway for UV excited states of nucleic acids of great importance for photostability as well as photoredox activity.

UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes.

The excited-state dynamics of two cyclic DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrared spectroscopy. As in longer DNA duplexes, intrastrand electron transfer induced by UV excitation triggers interstrand proton transfer in the alternating miniduplex containing two out-of-phase G·C base pairs. The resulting excited state decays on a time scale of several tens of picoseconds. This state is absent when one of the two G residues is substituted by 8-oxo-7,8-dihydroguanine, a modification that is suggested to disrupt base stacking, while maintaining base pairing. These findings demonstrate that a nucleobase tetramer arranged as two stacked base pairs accurately captures the interplay between intrastrand and interstrand decay channels. The similar signals seen in the miniduplexes and longer sequences suggest that excited states in the latter rapidly localize on two adjacent base pairs.

The influence of edge and corner evolution on plasmon properties and resonant edge effect in gold nanoplatelets.

In this paper a simulation of the properties of surface plasmons on gold nanoplatelets with various cross-sections inscribed in a circle and an investigation of their field distributions to assign multiple SPRs are described. The manipulated propagation can be obtained through the evolution of edges and corners. Furthermore, the particle morphology and the associated spectral positions alone do not uniquely reflect the important details of the local field distribution or the resonance modes. The plasmon modes were investigated and found to be mainly excited along the edges and in the side and sloped side surfaces. The strong field distributions can generally be found around the corners and how the plasmons transmit through the corners to adjacent edges was also investigated. Besides the plasmons excited along the edges as were found for the triangular nanoplatelets, plasmons were excited in the interior region of the triangular surfaces and were also investigated. Despite this in the infrared region, plasmon modes were found to be along the edges for the hexagonal nanoplatelets. Also, it can be seen that the change of nanoplatelet thickness can support different plasmon modes ranging from dipolar resonance mode to quadrupole resonance mode. The thickness far below the skin depth can display complex plasmon modes along the edges and on the side and sloping side surfaces as well as the strong coupling between the top and bottom surfaces. The observed plasmon resonance modes in this simulation reflect the interference of all these contributions including the plasmons along the edges and on the side surfaces. This is an essential step towards a thorough understanding of plasmon modes and the effect of edge and corner evolution in polygonous nanoplatelets.

Adaptive cluster expansion approach for predicting the structure evolution of graphene oxide.

An adaptive cluster expansion (CE) method is used to explore surface adsorption and growth processes. Unlike the traditional CE method, suitable effective cluster interaction (ECI) parameters are determined, and then the selected fixed number of ECIs is continually optimized to predict the stable configurations with gradual increase of adatom coverage. Comparing with traditional CE method, the efficiency of the adaptive CE method could be greatly enhanced. As an application, the adsorption and growth of oxygen atoms on one side of pristine graphene was carefully investigated using this method in combination with first-principles calculations. The calculated results successfully uncover the structural evolution of graphene oxide for the different numbers of oxygen adatoms on graphene. The aggregation behavior of the stable configurations for different oxygen adatom coverages is revealed for increasing coverages of oxygen atoms. As a targeted method, adaptive CE can also be applied to understand the evolution of other surface adsorption and growth processes.

Diverse and tunable electronic structures of single-layer metal phosphorus trichalcogenides for photocatalytic water splitting.

The family of bulk metal phosphorus trichalcogenides (APX3, A = M(II), M(I)(0.5)M(III)(0.5); X = S, Se; M(I), M(II), and M(III) represent Group-I, Group-II, and Group-III metals, respectively) has attracted great attentions because such materials not only own magnetic and ferroelectric properties, but also exhibit excellent properties in hydrogen storage and lithium battery because of the layered structures. Many layered materials have been exfoliated into two-dimensional (2D) materials, and they show distinct electronic properties compared with their bulks. Here we present a systematical study of single-layer metal phosphorus trichalcogenides by density functional theory calculations. The results show that the single layer metal phosphorus trichalcogenides have very low formation energies, which indicates that the exfoliation of single layer APX3 should not be difficult. The family of single layer metal phosphorus trichalcogenides exhibits a large range of band gaps from 1.77 to 3.94 eV, and the electronic structures are greatly affected by the metal or the chalcogenide atoms. The calculated band edges of metal phosphorus trichalcogenides further reveal that single-layer ZnPSe3, CdPSe3, Ag0.5Sc0.5PSe3, and Ag0.5In0.5PX3 (X = S and Se) have both suitable band gaps for visible-light driving and sufficient over-potentials for water splitting. More fascinatingly, single-layer Ag0.5Sc0.5PSe3 is a direct band gap semiconductor, and the calculated optical absorption further convinces that such materials own outstanding properties for light absorption. Such results demonstrate that the single layer metal phosphorus trichalcogenides own high stability, versatile electronic properties, and high optical absorption, thus such materials have great chances to be high efficient photocatalysts for water-splitting.

Theoretical calculations and experimental verification of carbon dioxide reduction electrocatalyzed by metalloporphyrin.

Metal-functionalized porphyrin-like graphene structures are promising electrocatalysts for carbon dioxide reduction reaction (CO2RR) as their metal centers can modulate activity. Yet, the role of metal center of metalloporphyrins (MTPPs) in CO2 reaction activity is still lacking deep understanding. Here, CO2RR mechanism on MTPPs with five different metal centers (M = Fe, Co, Cu, Zn and Ni) are examined by first-principles calculations. The *COOH formation is the rate determined step on the five MTPP structures, and the CoTPP exhibits the best CO2RR activity while ZnTPP and NiTPP are the worst, which is also verified by our experiment. The CO2RR activity is controlled by adsorption states of intermediates (*CO, *COOH), i.e., chemisorption (e.g., on CoTPP) and physisorption (on ZnTPP and NiTPP) of intermediates will lead to good and poor activity, respectively. The deeper the d-band center of the porphyrin ring complexed metal atom, the weaker bonding of MTPP with CO and COOH. Theoretical calculations and experimental results indicate that MTPPs with Co and Fe centers lead to a reduction in the energy barriers for the two uphill reaction steps in the electrocatalytic CO2 reduction process, thereby enhancing CO2 reduction electrocatalytic activity. Faradaic efficiency of CO is correlated with the reaction energy barrier of the first proton-coupled electron reduction process, displaying a strong linear correlation. This work provides a fundamental understanding of MTPPs used as electrocatalysts for CO2RR.

Ultrafast excited-state dynamics and vibrational cooling of 8-oxo-7,8-dihydro-2'-deoxyguanosine in D2O.

Nguyen and Burrows recently demonstrated that UV-B irradiation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a signature product of oxidatively damaged DNA, can repair cyclobutane pyrimidine dimers in double-stranded DNA (J. Am. Chem. Soc. 2011, 133, 14586 - 14589). In order to test the hypothesis that repair occurs by photoinduced electron transfer, it is critical to determine basic photophysical parameters of 8-oxodG including the excited-state lifetime. Here, femtosecond transient absorption spectroscopy was used to study the ultrafast excited-state dynamics of 8-oxodG with excitation in the UV and probing at visible and mid-IR wavelengths. The excited-state lifetimes of both neutral and basic forms of 8-oxodG in D2O are reported for the first time by monitoring the disappearance of excited-state absorption at 570 nm. The lifetime of the first excited state of the neutral form is 0.9 ± 0.1 ps, or nearly twice as long as that of 2'-deoxyguanosine. The basic form of 8-oxodG exhibits a much longer excited-state lifetime of 43 ± 3 ps. Following ultrafast internal conversion by neutral 8-oxodG, a vibrationally hot ground state is created that dissipates its excess vibrational energy to the solvent on a time scale of 2.4 ± 0.4 ps. Femtosecond time-resolved IR experiments provide additional insights into excited-state dynamics and the vibrational relaxation of several modes in the fingerprint region.

[Surface-enhanced raman spectra of thymine calculated by DFT and ab inition HF].

In the present paper, B3LYP (Becke's three-parameter hybrid method with the Lee, Yang, and Parr gradient corrected correlation functional) and HF (Hartree-Fock) methods at 6-31+G* * (C, H, N, O)/LANL2DZ(Ag) level were used to optimize molecular configurations of thymine. Base on the optimized structure, the normal Raman spectrum (NRS) of thymine and the surface-enhanced Raman spectrum (SERS) of thymine adsorbed on Ag and Ag2 were calculated, which were compared with the experimental values. The calculation results indicated that the result of the DFT for NRS was more approximate to the ever reported experimental date than those of HF results. A better conformity of SERS was found between the HF computed and the experimental results. At the end, detailed analysis of the Raman spectrum and more comprehensive assignments of the vibration mode for thymine were studied by the software of GaussView.

Which Is Better for Hydrogen Evolution on Metal@MoS2 Heterostructures from a Theoretical Perspective: Single Atom or Monolayer?

Single atom (SA)- and monolayer (ML)-supported catalysts are two main technical routines to increase electrochemical catalytic performance and reduce cost. To date, it is still a debate which one is better for catalysis in experiments as both routines face a puzzling problem of searching for balance between stability and catalytic activity. Here, hydrogen evolution on two-dimensional 2H-MoS2 with SA- and ML-adsorbed metal atoms (23 kinds in total) is taken as an example to solve this question by first-principles calculations. The thermodynamic stability during synthesis, in vacuum, and in electrochemical reaction conditions is determined to access the stability of MoS2 loaded with single (MS@MoS2) and monolayer metal atoms (MM@MoS2). The realistic catalytic surfaces determined by surface Pourbaix diagrams, the free energy changes of hydrogen atoms at different coverages, and the exchange current densities are applied to determine hydrogen evolution reaction (HER) activity. The results show that all MM@MoS2 are much more stable than the corresponding MS@MoS2 as the metal-metal interaction in MLs could make the former structures more stable. In general, MM@MoS2 show higher hydrogen evolution activities than those of MS@MoS2. In detail, the exchange current densities of MoS2 loaded by Pd ML and Au ML are 6.208, and 1.109 mA/cm-2, respectively, which are comparable to Pt(111). Combining with small binding energies, the Pd and Au MLs are the most promising catalysts for hydrogen evolution. The purpose of this work is to highlight the advantages and disadvantages of SA- and ML-supported surfaces as HER catalysts and provide a fundamental standard for studying them.

The unique photoelectronic properties of the two-dimensional Janus MoSSe/WSSe superlattice: a first-principles study.

Designing photocatalysts with suitable band alignment and considerable carrier mobility is extremely important. Here, by means of first-principles calculation, we systematically investigated the structural, photoelectronic, and carrier mobility behavior of the two-dimensional Janus MoSSe/WSSe superlattice. The results show that both armchair-type (AN-SL) and zigzag-type (ZN-SL) superlattices are relatively stable with negative Ef values in the range of -2.35 to -1.16 eV. Band gap and band edge position calculations demonstrate that these superlattices are completely suitable for water splitting by visible light. Particularly, the interface contact of the superlattice can be spontaneously changed from type-I to type-II when N > 4, facilitating separation of photogenerated carriers. Furthermore, the hole carrier mobility (µh) in AN-SL can be effectively regulated from 1200 to 2200 cm2 V-1 s-1, much larger than that of the isolated components. Interestingly, the disparity of hole/electron carrier mobility is remarkably large with an approximately 20-fold difference, showing the potential in prohibiting the recombination of photogenerated carriers. This unique behavior is further illustrated by the relaxation times of carriers, where the lifetime of hole carriers is about 7 times larger than that of electron carriers. These findings suggest that forming a Janus superlattice is a promising approach for regulating the photoelectronic properties of semiconductors, providing a promising way to design high efficiency photocatalysts.

Crucial Role of Crystal Field on Determining the Evolution Process of Janus MoSSe Monolayer: A First-Principles Study.

Two-dimensional Janus MXY materials have been successfully synthesized from their parent species by CVD, SEAR, or PLD techniques. However, their detailed evolution process and underlying atomistic mechanism are far from understood conclusively, which are prompts for further research. Here, taking Janus MoSSe as a representation, the evolution process from MoS2 is systematically investigated by first-principles calculation. The simulation shows that the lowest formation energy of MoS(2-δ)Seδ increases with selenylation ratio δ. Unexpectedly, Se atoms prefer to form a pair in next-nearest neighboring state (Se-NN-Se), eventually transferred into a growth rule of (6n + 1) during the evolution process. Particularly, it is demonstrated that the stability of the intermediate is mainly governed by the Mo 4d orbitals in different distorted triangular crystal fields, rendering a different degree of orbital splitting. Both the occupied and unoccupied Mo 4d orbitals of Se-NN-Se are farther from the Fermi level than other cases, which is clearly illustrated by d-band center theory. These findings will be helpful to understand the evolution process and the underlying atomistic mechanism of Janus MXY.

The role of permanent and induced electrostatic dipole moments for Schottky barriers in Janus MXY/graphene heterostructures: a first-principles study.

The Schottky barrier height (ESBH) is a crucial factor in determining the transport properties of semiconductor materials and it directly regulates the carrier mobility in opto-electronics devices. In principle, van der Waals (vdW) Janus heterostructures offer an appealing avenue for controlling the ESBH. However, the underlying atomistic mechanisms are far from understood conclusively, which prompts further research in the topic. To this end, here we carry out an extensive first-principles study of the electronic properties and ESHB of several vdW Janus MXY/graphene (M = Mo, W; X, Y = S, Se, Te) heterostructures. The results of the simulations show that by changing the composition and geometry of the heterostructure's interface, it is possible to control its electrical contact, and thence electron transport properties, from ohmic to Schottky with up to a factor seven variation in the ESBH. Detailed analysis of the simulations enables rationalization of this highly attractive property on the basis of the interplay between the permanent dipole moment of the Janus MXY sheet and the induced one due to interfacial charge redistribution at the MXY/Gr interface. Such an interplay is shown to be highly effective in altering the electrostatic potential difference across the vdW Janus heterostructure, determining its ESBH, and thence Schottky (ohmic) contact type. These computational findings contribute guidelines to control the electrical contacts in Janus heterostructures towards the rational design of electrical contacts in nanoscale devices.

The unique carrier mobility of monolayer Janus MoSSe nanoribbons: a first-principles study.

Charge-carrier mobility is a determining factor of the transport properties of semiconductor materials and is strongly related to the optoelectronic performance of nanoscale devices. Here, we investigate the electronic properties and charge carrier mobility of monolayer Janus MoSSe nanoribbons by means of first-principles simulations coupled with deformation potential theory. These simulations indicate that zigzag nanoribbons are metallic. Conversely, armchair nanoribbons are semiconducting and show oscillations in the calculated band gap as a function of edge-width according to the 3p < 3p + 1 < 3p + 2 rule, with p being the integer number of repeat units along the non-periodic direction of the nanoribbon. Although the charge-carrier mobility of armchair nanoribbons oscillates with the edge-width, its magnitude is comparable to its two-dimensional sheet counterpart. A robust room-temperature carrier mobility is calculated for 3.5 nm armchair nanoribbons with values ranging from 50 cm2 V-1 s-1 to 250 cm2 V-1 s-1 for electrons (e) and holes (h), respectively. A comparison of these values with the results for periodic flat sheet (e: 73.8 cm2 V-1 s-1; h: 157.2 cm2 V-1 s-1) reveals enhanced (suppressed) hole (electron) mobility in the Janus MoSSe nanoribbons. This is in contrast to what was previously found for MoS2 nanoribbons, namely larger mobility for electrons in comparison with holes. These differences are rationalized on the basis of the different structures, edge electronic states and deformation potentials present in the MoSSe nanoribbons. The present results provide the guidelines for the structural and electronic engineering of MoSSe nanoribbon edges towards tailored electron transport properties.

Cyclopropylazetoindolines as precursors to C(3)-quaternary-substituted indolines.

This manuscript describes the generation and use of a cyclopropylazetoindoline, a novel fused heterocycle, in coupling reactions with hetero- and carbon nucleophiles to give C(3)-quaternary-substituted pyrroloindolines.

Activity and selectivity of CO2 photoreduction on catalytic materials.

Photoreduction of molecular CO2 by solar light into added-value fuels or chemical feedstocks is an appealing strategy to simultaneously overcome environmental problems and energy challenges. However, multiple reaction steps and a large number of possible products have significantly hindered the development of highly selective catalysts capable of delivering CO2 conversion with high efficiency. Recently, several strategies associated with different conversion mechanisms have been proposed to improve the activity and product selectivity of CO2 photocatalysts. These are based on development of low dimensional nanomaterials, defect or facet engineering, design of tailored heterostructures, and carrier conductivity enhancement. In spite of impressive progress in the field, real-world applications are yet to be delivered. To sustain further research in this promising field, here we provide a short frontier of recent advances in activity and selectivity of CO2 reduction photocatalysts, together with a critical discussion of further avenues of research in this field.

Correlations of the stability, static dipole polarizabilities, and electronic properties of yttrium clusters.

Static dipole polarizabilities for the ground-state geometries of yttrium clusters (Yn, n < or = 15) are investigated by using the numerically finite field method in the framework of density functional theory. The structural size dependence of electronic properties, such as the highest occupied molecular orbital-lowest occupied molecular orbital (HOMO-LUMO) gap, ionization energy, electron affinity, chemical hardness and softness, etc., has been determined for yttrium clusters. The energetic analysis, minimum polarizability principle, and principle of maximum hardness are used to characterize the stability of yttrium clusters. The correlations of stability, static dipole polarizabilities, and electronic properties are analyzed especially. The results show that static polarizability and electronic structure can reflect obviously the stability of yttrium clusters. The static polarizability per atom decreases slowly with an increase in the cluster size and exhibits a local minimum at the magic number cluster. The ratio of the mean static polarizability to the HOMO-LUMO gap has a much lower value for the most stable clusters. The static dipole polarizabilities of yttrium clusters are highly dependent on their electronic properties and are also partly related to their geometrical characteristics. A large HOMO-LUMO gap of an yttrium cluster usually corresponds to a large dipole moment. Strong correlative relationships of the ionization potential, softness, and static dipole polarizability are observed for yttrium clusters.

Electrochemical Hydrogen Evolution at the Interface of Monolayer VS2 and Water from First-Principles Calculations.

Density functional theory calculations are carried out to study the hydrogen evolution reaction (HER) at the electrochemical double-layer interface of monolayer 2H phase VS2 and water. Under typical conditions of HER, the catalyst surface is predicted to have a low hydrogen coverage of about 12%, whereas the aqueous solution side features a high hydronium concentration of about 8.3%. As a result, the HER takes place through the Volmer-Heyrovsky route, with an overall reaction barrier of about 1.0 eV, much larger than that of 1T phase VS2. This result demonstrates that 2H phase VS2 is much less reactive than its 1T phase counterpart, and the 1T-to-2H phase transformation induced by thickness reduction may deteriorate the HER activity of VS2.

Development of novel prediction model for drug-induced mitochondrial toxicity by using naïve Bayes classifier method.

Mitochondrial dysfunction has been considered as an important contributing factor in the etiology of drug-induced organ toxicity, and even plays an important role in the pathogenesis of some diseases. The objective of this investigation was to develop a novel prediction model of drug-induced mitochondrial toxicity by using a naïve Bayes classifier. For comparison, the recursive partitioning classifier prediction model was also constructed. Among these methods, the prediction performance of naïve Bayes classifier established here showed best, which yielded average overall prediction accuracies for the internal 5-fold cross validation of the training set and external test set were 95 ± 0.6% and 81 ± 1.1%, respectively. In addition, four important molecular descriptors and some representative substructures of toxicants produced by ECFP_6 fingerprints were identified. We hope the established naïve Bayes prediction model can be employed for the mitochondrial toxicity assessment, and these obtained important information of mitochondrial toxicants can provide guidance for medicinal chemists working in drug discovery and lead optimization.