Jishi Chen

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza.

Ferroelectric transition of Aurivillius compounds Bi5Ti3FeO15 and Bi6Ti3Fe2O18

Single-phase Bi5Ti3FeO15 and Bi6Ti3Fe2O18 ceramics have been synthesized by solid state reaction. The ferroelectric transition of the compounds was studied by differential scanning calorimetry, high-temperature x-ray diffraction, and temperature-dependent dielectric measurements. Two solid-state structural transitions were observed in both compounds, one is the orthorhombic↔tetragonal transition (ferroelectric transition) at 1021 K for Bi5Ti3FeO15 and 973 K for Bi6Ti3Fe2O18, and the other is accompanied by an abrupt lattice expansion of the tetragonal phase at about 1110 K for Bi5Ti3FeO15 and about 1090 K for Bi6Ti3Fe2O18.

Adding Two Active Silver Atoms on Au25 Nanoparticle

Alloy nanoparticles with atomic monodispersity is of importance for some fundamental research (e.g., the investigation of active sites). However, the controlled preparation of alloy nanoparticles with atomic monodispersity has long been a major challenge. Herein, for the first time a unique method, antigalvanic reduction (AGR), is introduced to synthesize atomically monodisperse Au25Ag2(SC2H4Ph)18 in high yield (89%) within 2 min. Interestingly, the two silver atoms in Au25Ag2(SC2H4Ph)18 do not replace the gold atoms in the precursor particle Au25(SC2H4Ph)18 but collocate on Au25, which was supported by experimental and calculated results. Also, the two silver atoms are active to play roles in stabilizing the alloy nanoparticle, triggering the nanoparticle fluorescence and catalyzing the hydrolysis of 1,3-diphenylprop-2-ynyl acetate.

Magnetic properties of Bi(Fe1−xCrx)O3 synthesized by a combustion method

Single-phase samples of Bi(Fe1−xCrx)O3 with x=0, 0.1, and 0.2 were synthesized by a combustion method. X-ray diffraction reveals that the lattice parameters of Bi(Fe1−xCrx)O3 perovskites decrease linearly with the Cr content, indicating that Cr ions substitute for Fe ions to form a solid solution. X-ray photoelectron spectroscopy investigation shows that Cr ions have the Cr3+ valence state in Bi(Fe1−xCrx)O3. The frequency dependence of dielectric constants was investigated at room temperature. Magnetic measurements show hysteresis loops at both 5 and 300K and the substitution of Cr for Fe enhances the magnetization.

Structure of Chiral Au44(2,4-DMBT)26 Nanocluster with an 18-Electron Shell Closure

The 18-electron shell closure structure of Au nanoclusters protected by thiol ligands has not been reported until now. Herein, we synthesize a novel nanocluster bearing the same gold atom number but a different thiolate number as another structurally resolved nanocluster Au44(TBBT)28 (TBBTH = 4-tert-butylbenzenelthiol). The new cluster was determined to be Au44(2,4-DMBT)26 (2,4-DMBTH = 2,4-dimethylbenzenethiol) using multiple techniques, including mass spectrometry and single crystal X-ray crystallography (SCXC). Au44(2,4-DMBT)26 represents the first 18-electron closed-shell gold nanocluster. SCXC reveals that the atomic structure of Au44(2,4-DMBT)26 is completely different from that of Au44(TBBT)28 but is similar to the structure of Au38Q. The arrangement of staples (bridging thiolates) and part of the Au29 kernel atom induces the chirality of Au44(2,4-DMBT)26. The finding that a small portion of the gold kernel exhibits chirality is interesting because it has not been previously reported to the best of our knowledge. Although Au44(2,4-DMBT)26 bears an 18-electron shell closure structure, it is less thermostable than Au44(TBBT)28, indicating that multiple factors contribute to the thermostability of gold nanoclusters. Surprisingly, the small difference in Au/thiolate molar ratio between Au44(2,4-DMBT)26 and Au44(TBBT)28 leads to a dramatic distinction in Au 4f X-ray photoelectron spectroscopy, where it is found that the charge state of Au in Au44(2,4-DMBT)26 is remarkably more positive than that in Au44(TBBT)28 and even slightly more positive than the charge states of gold in Au-(2,4-DMBT) or Au-TBBT complexes.

The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au–S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au–S bonding and solid photoluminescence of gold nanoclusters.

Fluorescent Gold Nanoclusters with Interlocked Staples and a Fully Thiolate‐Bound Kernel

The structural features that render gold nanoclusters intrinsically fluorescent are currently not well understood. To address this issue, highly fluorescent gold nanoclusters have to be synthesized, and their structures must be determined. We herein report the synthesis of three fluorescent Au24 (SR)20 nanoclusters (R=C2 H4 Ph, CH2 Ph, or CH2 C6 H4 (t) Bu). According to UV/Vis/NIR, differential pulse voltammetry (DPV), and X-ray absorption fine structure (XAFS) analysis, these three nanoclusters adopt similar structures that feature a bi-tetrahedral Au8 kernel protected by four tetrameric Au4 (SR)5 motifs. At least two structural features are responsible for the unusual fluorescence of the Au24 (SR)20 nanoclusters: Two pairs of interlocked Au4 (SR)5 staples reduce the vibration loss, and the interactions between the kernel and the thiolate motifs enhance electron transfer from the ligand to the kernel moiety through the Au-S bonds, thereby enhancing the fluorescence. This work provides some clarification of the structure-fluorescence relationship of such clusters.

Transition-sized Au92 nanoparticle bridging non-fcc-structured gold nanoclusters and fcc-structured gold nanocrystals

Herein, we report the intriguing structure, optical absorption and electrochemical properties of the transition-sized Au92(TBBT)44 (Au92 for short, TBBT = 4-tert-butylbenzenethiolate) nanoparticle. An interesting observation is the 4H phase array of Au92 nanoparticles in the unit cells of single crystals.

Synthesis and Properties Evolution of a Family of Tiara-like Phenylethanethiolated Palladium Nanoclusters

Tiara-like thiolated group 10 transition metal (Ni, Pd, Pt) nanoclusters have attracted extensive interest due to their fundamental scientific significance and potential application in a number of fields. However, the properties (e.g. the absorption) evolution with the ring size’s increase was not investigated so far to our best knowledge, due to the challenge of obtaining a series of nanocluster analogues. Herein, we successfully synthesized, isolated and identified a family of [Pd(SC2H4Ph)2]n nanoclusters (totally 17 novel clusters, n = 4–20). Their structures were determined to be tiara-like by single crystal X-ray crystallography together with theoretical calculation; their formation mechanism was proposed to be a substitution—polycondensation—ring-closure process based on experimental observations. All of these clusters are rather robust (anti-reductive and anti-oxidative) owing to their tiara-like structures with large HOMO-LUMO gaps. Finally, the optical and electrochemical evolution with the increase of ring size was investigated, and it is found that both optical and electrochemical gaps have a “turning point” at a size corresponding to n = 8 for [Pd(SR)2]n nanoclusters.

Investigation of interface in silicon-on-insulator by fractal analysis

Abstract In this study, RMS roughness values of the interface between top silicon and buried layer in SIMOX–SOI (SIMOX, separation by implantation of oxygen; SOI, silicon-on-insulator) were directly measured by AFM. The results revealed that they were self-affine fractal. Based on the variation of the RMS values with scan sizes, the fractal dimensions and horizontal cutoffs of the fractal interfaces were calculated. It was found that the cutoff values varied with the different processes suggesting that the cutoff is sensitive to process and can be used to characterize the quality of SIMOX–SOI wafer.