State Key Laboratory for Structural Chemistry of Unstable and Stable Species

The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/.

Defects usually play an important role in tailoring various properties of two-dimensional materials. Defects in two-dimensional monolayer molybdenum disulphide may be responsible for large variation of electric and optical properties. Here we present a comprehensive joint experiment-theory investigation of point defects in monolayer molybdenum disulphide prepared by mechanical exfoliation, physical and chemical vapour deposition. Defect species are systematically identified and their concentrations determined by aberration-corrected scanning transmission electron microscopy, and also studied by ab-initio calculation. Defect density up to 3.5 × 10(13) cm(-2) is found and the dominant category of defects changes from sulphur vacancy in mechanical exfoliation and chemical vapour deposition samples to molybdenum antisite in physical vapour deposition samples. Influence of defects on electronic structure and charge-carrier mobility are predicted by calculation and observed by electric transport measurement. In light of these results, the growth of ultra-high-quality monolayer molybdenum disulphide appears a primary task for the community pursuing high-performance electronic devices.

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Graphene is a monolayer of carbon atoms packed into a two-dimensional (2D) honeycomb crystal structure, which is a special material with many excellent properties. In the present study, we will discuss the possibility that graphene can be used as a substrate for enhancing Raman signals of adsorbed molecules. Here, phthalocyanine (Pc), rhodamine 6G (R6G), protoporphyin IX (PPP), and crystal violet (CV), which are popular molecules widely used as a Raman probe, are deposited equally on graphene and a SiO(2)/Si substrate using vacuum evaporation or solution soaking. By comparing the Raman signals of molecules on monolayer graphene and on a SiO(2)/Si substrate, we observed that the intensities of the Raman signals on monolayer graphene are much stronger than on a SiO(2)/Si substrate, indicating a clear Raman enhancement effect on the surface of monolayer graphene. For solution soaking, the Raman signals of the molecules are visible even though the concentration is low to 10(-8) mol/L or less. What's more interesting, the enhanced efficiencies are quite different on monolayer, few-layer, multilayer graphene, graphite, and highly ordered pyrolytic graphite (HOPG). The Raman signals of molecules on multilayer graphene are even weaker than on a SiO(2)/Si substrate, and the signals are even invisible on graphite and HOPG. Taking the Raman signals on the SiO(2)/Si substrate as a reference, Raman enhancement factors on the surface of monolayer graphene can be obtained using Raman intensity ratios. The Raman enhancement factors are quite different for different peaks, changing from 2 to 17. Furthermore, we found that the Raman enhancement factors can be distinguished through three classes that correspond to the symmetry of vibrations of the molecule. We attribute this enhancement to the charge transfer between graphene and the molecules, which result in a chemical enhancement. This is a new phenomenon for graphene that will expand the application of graphene to microanalysis and is good for studying the basic properties of both graphene and SERS.

CO2 hydrogenation for the acquisition of value-added chemicals is an economical means to deal with the CO2-relevant environmental problems, among which CO2 reduction to CH4 is an excellent model reaction for investigating the initial steps of CO2 hydrogenation. For the supported catalysts commonly used in such reactions, the tailoring of the interfacial effect between metal centers and supporting materials so as to obtain superior low-temperature CO2 methanation performance is a significant but challenging subject. In this work, we altered the size regimes of the Ru deposits in Ru/CeO2 assemblies and uncovered the competitive relationship between the strong metal–support interactions (SMSI) and the H-spillover effect in determining the methanation activities by some ex situ and in situ spectroscopic techniques coupled with density functional theory (DFT) calculations. For CeO2 nanowire supported single Ru atoms, Ru nanoclusters (ca. 1.2 nm in size), and large Ru nanoparticles (ca. 4.0 nm in size), the nanoclusters show the most outstanding low-temperature CO2 methanation activity and 98–100% selectivity, with a turnover frequency (TOF) of 7.41 × 10–3 s–1 at 190 °C. The negative CO2 reaction order decreases their absolute values from single atoms to nanoclusters and turns positive in nanoparticles, while the positive H2 reaction order follows the reverse tendency. In situ DRIFTS measurements demonstrate that the dominant reaction pathway is the CO route, in which metal carbonyls are the critical intermediates and the active sites are those Ce3+–OH sites and Ru sites near the metal–support interfaces in charge of CO2 dissociation and carbonyl hydrogenation, respectively. Meanwhile, the strongest SMSI and H-spillover effect are respectively encountered in supported single Ru atoms and large Ru nanoparticles, with the activation of metal carbonyls and the dehydration of the support surfaces suppressed correspondingly. The two factors reach a balance in CeO2-supported Ru nanoclusters, and the methanation activity is therefore maximized. A mechanistic understanding of the interfacial effect in tuning the CO2 methanation activities would shed light on the ingenious design of the CO2 hydrogenation catalysts to utilize the SMSI and H-spillover effect to an appropriate degree and avoid their possible suppressions that would take place in extreme cases.

Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~10(5) to 10(6) cycles for stochastic switching).

A facile strategy to grow nitrogen-doped graphene using embedded nitrogen and carbon in metal substrate via a segregation method is reported. As doping is concurrently carried out in the segregation process of the carbon species, N atoms can be substitutionally doped into the graphene lattice. This approach allows precise control of the doping degree and location, which enables growing various heterojunctions at the desired location.

Stable cycling of lithium metal anode is challenging due to the dendritic lithium formation and high chemical reactivity of lithium with electrolyte and nearly all the materials. Here, we demonstrate a promising novel electrode design by growing two-dimensional (2D) atomic crystal layers including hexagonal boron nitride (h-BN) and graphene directly on Cu metal current collectors. Lithium ions were able to penetrate through the point and line defects of the 2D layers during the electrochemical deposition, leading to sandwiched lithium metal between ultrathin 2D layers and Cu. The 2D layers afford an excellent interfacial protection of Li metal due to their remarkable chemical stability as well as mechanical strength and flexibility, resulting from the strong intralayer bonds and ultrathin thickness. Smooth Li metal deposition without dendritic and mossy Li formation was realized. We showed stable cycling over 50 cycles with Coulombic efficiency ∼97% in organic carbonate electrolyte with current density and areal capacity up to the practical value of 2.0 mA/cm(2)and 5.0 mAh/cm(2), respectively, which is a significant improvement over the unprotected electrodes in the same electrolyte.

The facile synthesis of highly ordered mesoporous aluminas with high thermal stability and tunable pore sizes is systematically investigated. The general synthesis strategy is based on a sol-gel process associated with nonionic block copolymer as templates in ethanol solvent. Small-angle XRD, TEM, and nitrogen adsorption and desorption results show that these mesoporous aluminas possess a highly ordered 2D hexagonal mesostructure, which is resistant to high temperature up to 1000 degrees C. Ordered mesoporous structures with tunable pore sizes are obtained with various precursors, different acids as pH adjustors, and different block copolymers as templates. These mesoporous aluminas have large surface areas (ca. 400 m2/g), pore volumes (ca. 0.70 cm3/g), and narrow pore-size distributions. The influence of the complexation ability of anions and hydro-carboxylic acid, acid volatility, and other important synthesis conditions are discussed in detail. Utilizing this simple strategy, we also obtained partly ordered mesoporous alumina with hydrous aluminum nitrate as the precursor. FTIR pyridine adsorption measurements indicate that a large amount of Lewis acid sites exist in these mesoporous aluminas. These materials are expected to be good candidates in catalysis due to the uniform pore structures, large surface areas, tunable pore sizes, and large amounts of surface Lewis acid sites. Loaded with ruthenium, the representative mesoporous alumina exhibits reactant size selectivity in hydrogenation of acetone, D-glucose, and D-(+)-cellobiose as a test reaction, indicating the potential applications in shape-selective catalysis.

Unique spindle-shaped nanoporous anatase TiO(2) mesocrystals with a single-crystal-like structure and tunable sizes were successfully fabricated on a large scale through mesoscale assembly in the tetrabutyl titanate-acetic acid system without any additives under solvothermal conditions. A complex mesoscale assembly process involving slow release of soluble species from metastable solid precursors for the continuous formation of nascent anatase nanocrystals, oriented aggregation of tiny anatase nanocrystals, and entrapment of in situ produced butyl acetate as a porogen was put forward for the formation of the anatase mesocrystals. It was revealed that the acetic acid molecules played multiple key roles during the nonhydrolytic processing of the [001]-oriented, single-crystal-like anatase mesocrystals. The obtained nanoporous anatase mesocrystals exhibited remarkable crystalline-phase stability (i.e., the pure phase of anatase can be retained after being annealed at 900 °C) and improved performance as anode materials for lithium ion batteries, which could be largely attributed to the intrinsic single-crystal-like nature as well as high porosity of the nanoporous mesocrystals.

The transferring and identification of single- and few- layer graphene sheets from SiO2/Si substrates to other types of substrates is presented. Features across large areas (∼cm2) having single and few-layer graphene flakes, obtained by the microcleaving of highly oriented pyrolytic graphite (HOPG), can be transferred reliably. This method enables the fast localization of graphene sheets on substrates on which optical microscopy does not allow direct and fast visualization of the thin graphene sheets. No major morphological deformations, corrugations, or defects are induced on the graphene films when transferred to the target surface. Moreover, the differentiation between single and bilayer graphene via the G′ (∼2700 cm−1) Raman peak is demonstrated on various substrates. This approach opens up possibilities for the fabrication of graphene devices on a substrate material other than SiO2/Si.

In the absence of any usual protective agent, stable platinum, rhodium, and ruthenium metal nanoclusters with small particle size in organic media are effectively prepared by heating corresponding metal hydroxide colloids in ethylene glycol containing NaOH for the first time. The average diameters of the Pt, Rh, and Ru nanoclusters determined by means of transmission electron microscopy are in a range from 1 to 2 nm. The particle size distribution in each colloidal solution is sharp, within 2 nm wide. Studies on the preparation conditions and some properties of the “unprotected” Pt metal nanoclusters have been carried out. By adjusting pH, it is convenient to separate the Pt nanocluster as a precipitate from glycol solvent, and the precipitated Pt nanoclusters can easily be “dissolved” in many organic solvents to form transparent Pt nanocluster solutions with high concentration in the absence of usual protective agents. The “unprotected” Pt nanoclusters can also be easily transformed to various protected Pt nanoclusters with the same Pt cores and can be extracted into toluene by forming PPh3-modified Pt clusters.

Realizing Raman enhancement on a flat surface has become increasingly attractive after the discovery of graphene-enhanced Raman scattering (GERS). Two-dimensional (2D) layered materials, exhibiting a flat surface without dangling bonds, were thought to be strong candidates for both fundamental studies of this Raman enhancement effect and its extension to meet practical applications requirements. Here, we study the Raman enhancement effect on graphene, hexagonal boron nitride (h-BN), and molybdenum disulfide (MoS2), by using the copper phthalocyanine (CuPc) molecule as a probe. This molecule can sit on these layered materials in a face-on configuration. However, it is found that the Raman enhancement effect, which is observable on graphene, hBN, and MoS2, has different enhancement factors for the different vibrational modes of CuPc, depending strongly on the surfaces. Higher-frequency phonon modes of CuPc (such as those at 1342, 1452, 1531 cm(-1)) are enhanced more strongly on graphene than that on h-BN, while the lower frequency phonon modes of CuPc (such as those at 682, 749, 1142, 1185 cm(-1)) are enhanced more strongly on h-BN than that on graphene. MoS2 demonstrated the weakest Raman enhancement effect as a substrate among these three 2D materials. These differences are attributed to the different enhancement mechanisms related to the different electronic properties and chemical bonds exhibited by the three substrates: (1) graphene is zero-gap semiconductor and has a nonpolar C-C bond, which induces charge transfer (2) h-BN is insulating and has a strong B-N bond, while (3) MoS2 is semiconducting with the sulfur atoms on the surface and has a polar covalent bond (Mo-S) with the polarity in the vertical direction to the surface. Therefore, the different Raman enhancement mechanisms differ for each material: (1) charge transfer may occur for graphene; (2) strong dipole-dipole coupling may occur for h-BN, and (3) both charge transfer and dipole-dipole coupling may occur, although weaker in magnitude, for MoS2. Consequently, this work studied the origin of the Raman enhancement (specifically, chemical enhancement) and identifies h-BN and MoS2 as two different types of 2D materials with potential for use as Raman enhancement substrates.

Surface enhanced Raman spectroscopy (SERS) is an attractive analytical technique, which enables single-molecule sensitive detection and provides its special chemical fingerprints. During the past decades, researchers have made great efforts towards an ideal SERS substrate, mainly including pioneering works on the preparation of uniform metal nanostructure arrays by various nanoassembly and nanotailoring methods, which give better uniformity and reproducibility. Recently, nanoparticles coated with an inert shell were used to make the enhanced Raman signals cleaner. By depositing SERS-active metal nanoislands on an atomically flat graphene layer, here we designed a new kind of SERS substrate referred to as a graphene-mediated SERS (G-SERS) substrate. In the graphene/metal combined structure, the electromagnetic "hot" spots (which is the origin of a huge SERS enhancement) created by the gapped metal nanoislands through the localized surface plasmon resonance effect are supposed to pass through the monolayer graphene, resulting in an atomically flat hot surface for Raman enhancement. Signals from a G-SERS substrate were also demonstrated to have interesting advantages over normal SERS, in terms of cleaner vibrational information free from various metal-molecule interactions and being more stable against photo-induced damage, but with a comparable enhancement factor. Furthermore, we demonstrate the use of a freestanding, transparent and flexible "G-SERS tape" (consisting of a polymer-layer-supported monolayer graphene with sandwiched metal nanoislands) to enable direct, real time and reliable detection of trace amounts of analytes in various systems, which imparts high efficiency and universality of analyses with G-SERS substrates.

We have measured resonance Raman spectra with greatly suppressed fluorescence (FL) background from rhodamine 6G (R6G) and protoporphyrin IX (PPP) adsorbed on graphene. The FL suppression is estimated to be approximately 10(3) times for R6G. The successful observation of resonance Raman peaks demonstrates that graphene can be used as a substrate to suppress FL in resonance Raman spectroscopy (RRS), which has potential applications in low-concentration detection and RRS study of fluorescent molecules.

Graphene has a unique atom-thick two-dimensional structure and excellent properties, making it attractive for a variety of electrochemical applications, including electrosynthesis, electrochemical sensors or electrocatalysis, and energy conversion and storage. However, the electrochemistry of single-layer graphene has not yet been well understood, possibly due to the technical difficulties in handling individual graphene sheet. Here, we report the electrochemical behavior at single-layer graphene-based electrodes, comparing the basal plane of graphene to its edge. The graphene edge showed 4 orders of magnitude higher specific capacitance, much faster electron transfer rate and stronger electrocatalytic activity than those of graphene basal plane. A convergent diffusion effect was observed at the sub-nanometer thick graphene edge-electrode to accelerate the electrochemical reactions. Coupling with the high conductivity of a high-quality graphene basal plane, graphene edge is an ideal electrode for electrocatalysis and for the storage of capacitive charges.

Surface-enhanced Raman spectroscopy (SERS) imparts Raman spectroscopy with the capability of detecting analytes at the single-molecule level, but the costs are also manifold, such as a loss of signal reproducibility. Despite remarkable steps having been taken, presently SERS still seems too young to shoulder analytical missions in various practical situations. By the virtue of its unique molecular structure and physical/chemical properties, the rise of graphene opens up a unique platform for SERS studies. In this review, the multi-role of graphene played in SERS is overviewed, including as a Raman probe, as a substrate, as an additive, and as a building block for a flat surface for SERS. Apart from versatile improvements of SERS performance towards applications, graphene-involved SERS studies are also expected to shed light on the fundamental mechanism of the SERS effect.

We demonstrated a highly electron-deficient system 1 as a turn-on fluorescence sensor for intracellular imaging of Cys/Hcy in biological samples. On the basis of the specific nucleophilic ability of thiols of Cys and Hcy, 1 exhibited high selectivity and sensitivity for Cys/Hcy over other amino acids and thiol biomolecules. This probe is the first Cys/Hcy sensor with excitation in the visible region and turn-on (75-fold) fluorescence emission and also gives a significant increase in two-photon excited fluorescence for sensing Cys/Hcy. Moreover, confocal laser scanning microscopy and two-photon laser scanning microscopy experiments further established that 1 can be used for sensing Cys/Hcy within biological samples.

Highly ordered TiO2 single-crystalline nanowire arrays have been fabricated within the pores of anodic aluminum oxide (AAO) template by a cathodically induced sol−gel method. Raman spectra confirmed that the nanowires are composed of pure anatase TiO2. TEM investigations indicated that these nanowires have a uniform tetragonal single-crystal structure. Finally, a possible growth mechanism of the TiO2 nanowires is discussed.

The effect of the additive Ce on V2O5-WO3/TiO2 with low vanadium loadings for the selective catalytic reduction (SCR) of NOx with NH3 was investigated. The catalytic activity of 0.1% V2O5-6% WO3/TiO2 (V0.1W6Ti) was greatly enhanced by the addition of 10 wt % of Ce in the broad temperature range of 200−500 °C. The catalysts were characterized by BET, XRD, XPS, TPD, H2-TPR, and DRIFTS. The results indicated that the active components of V and W were well-dispersed, while a small cluster of cubic CeO2 appeared over the V0.1W6Ce10Ti catalyst. The Ce additive could enhance the NOx adsorption and then accelerate the SCR reaction due to the synergetic interaction among the Ce and V,W species. Ce mainly existed in the form of Ce3+ oxide in V0.1W6Ce10Ti catalysts, which was beneficial for the oxidation of NO to NO2. Moreover, the DRIFTS results showed that the Ce additive on V0.1W6Ti could provide stronger and more active Brønsted acid sites, which were beneficial for the SCR reaction. The Ce additive also enhanced the reaction rate because the ad-NH4+ disappeared quickly in the presence of NO and O2. NO2, nitrate, and nitrite species formed on the Ce-doped VWTi catalyst because NO was easily oxidized due to the addition of Ce on V0.1W6Ti.