DNA methylation of promoter region inhibits galectin-1 expression in BMSCs of aged mice.

Senile osteoporosis increases fracture risks. Bone marrow stromal cells (BMSCs) are sensitive to aging. Deep insights into BMSCs aging are vital to elucidate the mechanisms underlying age-related bone loss. Recent advances showed that osteoporosis is associated with aberrant DNA methylation of many susceptible genes. Galectin-1 (Gal-1) has been proposed as a mediator of BMSCs functions. In our previous study, we showed that Gal-1 was downregulated in aged BMSCs and global deletion of Gal-1 in mice caused bone loss via impaired osteogenesis potential of BMSCs. Gal-1 promoter is featured by CpG islands. However, there are no reports concerning the DNA methylation status in Gal-1 promoter during osteoporosis. In the current study, we sought to investigate the role of DNA methylation in Gal-1 downregulation in aged BMSCs. The potential for anti-bone loss therapy based on modulating DNA methylation is explored. Our results showed that Dnmt3b-mediated Gal-1 promoter DNA hypermethylation plays an important role in Gal-1 downregulation in aged BMSCs, which inhibited ß-catenin binding on Gal-1 promoter. Bone loss of aged mice was alleviated in response to in vivo deletion of Dnmt3b from BMSCs. Finally, when bone marrow of young wild-type (WT) mice or young Dnmt3bPrx1-Cre mice was transplanted into aged WT mice, Gal-1 level in serum and trabecular bone mass were elevated in recipient aged WT mice. Our study will benefit for deeper insights into the regulation mechanisms of Gal-1 expression in BMSCs during osteoporosis development, and for the discovery of new therapeutic targets for osteoporosis via modulating DNA methylation status.NEW & NOTEWORTHY There is Dnmt3b-mediated DNA methylation in Gal-1 promoter in aged bone marrow stromal cell (BMSC). DNA methylation causes Gal-1 downregulation and osteogenesis attenuation of aged BMSC. DNA methylation blocks ß-catenin binding on Gal-1 promoter. Bone loss of aged mice is alleviated by in vivo deletion of Dnmt3b from BMSC.

Understanding the Electronic Structure and Chemical Bonding in the 2D Fullerene Monolayer.

Recently synthesized two-dimensional (2D) monolayer quasi-hexagonal-phase fullerene (qHPC60) demonstrates excellent thermodynamic stability. Within this monolayer, each fullerene cluster is surrounded by six adjacent C60 cages along an equatorial plane and is connected by both C-C single bonds and [2 + 2] cycloaddition bonds that serve as bridges. In this study, we investigate the stability mechanism of the 2D qHPC60 monolayer by examining the electronic structure and chemical bonding through state-of-the-art theoretical methodologies. Density functional theory (DFT) studies reveal that 2D qHPC60 possesses a moderate direct electronic band gap of 1.46 eV, close to the experimental value (1.6 eV). It is found that the intermolecular bridge bonds play a crucial role in enhancing the charge flow and redistribution among C60 cages, leading to the formation of dual π-aromaticity within the C60 sphere and stabilizing the 2D framework structure. Furthermore, we identify a series of delocalized superatom molecular orbitals (SAMOs) within the 2D qHPC60 monolayer, exhibiting atomic orbital-like behavior and hybridization to form nearly free-electron (NFE) bands with σ/π bonding and σ*/π* antibonding properties. Our findings provide insights into the design and potential applications of NFE bands derived from SAMOs in 2D qHPC60 monolayers.

Chelating Effect of Siderophore Desferrioxamine-B on Uranyl Biomineralization Mediated by Shewanella putrefaciens.

In contaminated water and soil, little is known about the role and mechanism of the biometabolic molecule siderophore desferrioxamine-B (DFO) in the biogeochemical cycle of uranium due to complicated coordination and reaction networks. Here, a joint experimental and quantum chemical investigation is carried out to probe the biomineralization of uranyl (UO22+, referred to as U(VI) hereafter) induced by Shewanella putrefaciens (abbreviated as S. putrefaciens) in the presence of DFO and Fe3+ ion. The results show that the production of mineralized solids {hydrogen-uranium mica [H2(UO2)2(PO4)2·8H2O]} via S. putrefaciens binding with UO22+ is inhibited by DFO, which can both chelate preferentially UO22+ to form a U(VI)-DFO complex in solution and seize it from U(VI)-biominerals upon solvation. However, with Fe3+ ion introduced, the strong specificity of DFO binding with Fe3+ causes re-emergence of biomineralization of UO22+ {bassetite [Fe(UO2)2(PO4)2·8(H2O)]} by S. putrefaciens, owing to competitive complexation between Fe3+ and UO22+ for DFO. As DFO possesses three hydroxamic functional groups, it forms hexadentate coordination with Fe3+ and UO22+ ions via these functional groups. The stability of the Fe3+-DFO complex is much higher than that of U(VI)-DFO, resulting in some DFO-released UO22+ to be remobilized by S. putrefaciens. Our finding not only adds to the understanding of the fate of toxic U(VI)-containing substances in the environment and biogeochemical cycles in the future but also suggests the promising potential of utilizing functionalized DFO ligands for uranium processing.

Chitosan alleviates ovarian aging by enhancing macrophage phagocyte-mediated tissue homeostasis.

BACKGROUND: Age-related changes in the ovarian microenvironment are linked to impaired fertility in women. Macrophages play important roles in ovarian tissue homeostasis and immune surveillance. However, the impact of aging on ovarian macrophage function and ovarian homeostasis remains poorly understood. METHODS: Senescence-associated beta-galactosidase staining, immunohistochemistry, and TUNEL staining were used to assess senescence and apoptosis, respectively. Flow cytometry was employed to evaluate mitochondrial membrane potential (MMP) and apoptosis in granulosa cells lines (KGN), and macrophages phagocytosis. After a 2-month treatment with low molecular weight Chitosan (LMWC), ovarian tissues from mice were collected for comprehensive analysis. RESULTS: Compared with the liver and uterus, the ovary displayed accelerated aging in an age-dependent manner, which was accompanied by elevated levels of inflammatory factors and apoptotic cells, and impaired macrophage phagocytic activity. The aged KGN cells exhibited elevated reactive oxygen species (ROS) and apoptotic levels alongside decreased MMP. H2O2-induced aging macrophages showed reduced phagocytosis function. Moreover, there were excessive aging macrophages with impaired phagocytosis in the follicular fluid of patients with diminished ovarian reserve (DOR). Notably, LMWC administration alleviated ovarian aging by enhancing macrophage phagocytosis and promoting tissue homeostasis. CONCLUSIONS: Aging ovarian is characterized by an accumulation of aging and apoptotic granulosa cells, an inflammatory response and macrophage phagocytosis dysfunction. In turn, impaired phagocytosis of macrophage contributes to insufficient clearance of aging and apoptotic granulosa cells and the increased risk of DOR. Additionally, LMWC emerges as a potential therapeutic strategy for age-related ovarian dysfunction.

Spectroscopic snapshot for neutral water nonamer (H2O)9: Adding a H2O onto a hydrogen bond-unbroken edge of (H2O)8.

Structural characterization of neutral water clusters is crucial to understanding the structures and properties of water, but it has been proven to be a challenging experimental target due to the difficulty in size selection. Here, we report the size-specific infrared spectra of confinement-free neutral water nonamer (H2O)9 based on threshold photoionization, using a tunable vacuum ultraviolet free-electron laser. Distinct OH stretch vibrational fundamentals in the 3200-3350 cm-1 region are observed, providing unique spectral signatures for the formation of an unprecedented (H2O)9 structure evolved by adding a ninth water molecule onto a hydrogen bond-unbroken edge of the (H2O)8 octamer with D2d symmetry. This nonamer structure coexists with the five previously identified structures that can be viewed as derived by inserting a ninth water molecule into a hydrogen bond-broken edge of the D2d/S4 octamer. These findings provide key microscopic information for systematic understanding of the formation and growth mechanism of dynamical hydrogen-bonding networks that are responsible for the structure and properties of condensed-phase water.

Infrared spectroscopy of neutral water clusters at finite temperature: Evidence for a noncyclic pentamer.

Infrared spectroscopic study of neutral water clusters is crucial to understanding of the hydrogen-bonding networks in liquid water and ice. Here we report infrared spectra of size-selected neutral water clusters, (H2O) n (n = 3-6), in the OH stretching vibration region, based on threshold photoionization using a tunable vacuum ultraviolet free-electron laser. Distinct OH stretch vibrational fundamentals observed in the 3,500-3,600-cm-1 region of (H2O)5 provide unique spectral signatures for the formation of a noncyclic pentamer, which coexists with the global-minimum cyclic structure previously identified in the gas phase. The main features of infrared spectra of the pentamer and hexamer, (H2O) n (n = 5 and 6), span the entire OH stretching band of liquid water, suggesting that they start to exhibit the richness and diversity of hydrogen-bonding networks in bulk water.

Correlation between changes in flavor compounds and microbial community ecological succession in the liquid fermentation of rice wine.

Microorganisms play an important role in regulating flavor compounds in rice wine, whereas we often don't understand how did they affect flavor compounds. Here, the relations between flavor compounds and microbial community ecological succession were investigated by monitoring flavor compounds and microbial community throughout the fermentation stage of rice wine. The composition of microbial community showed a dynamic change, but 13 dominant bacterial genera and 4 dominant fungal genera were detected throughout the fermentation stages. Saccharomyces presented a strong negative correlation with fungi genera but had positive associations with bacteria genera. Similarly, flavor compounds in rice wine were also showed the dynamic change, and 112 volatile compounds and 17 free amino acids were identified in the whole stages. The alcohol-ester ratio was decreased in the LTF stage, indicating that low temperature boosts ester formation. The potential correlation between flavor compounds and microbial community indicated that Delftia, Chryseobacterium, Rhizopus and Wickerhamomyces were the core functional microorganisms in rice wine. These findings clarified the correlation between changes in flavor compounds and in microbial community in the liquid fermentation of rice wine, and these results have some reference value for the quality improvement and technological optimization in liquid fermentation of rice wine.

A Supramolecular Naphthalene Diimide Radical Anion with Efficient NIR-II Photothermal Conversion for E. coli-Responsive Photothermal Therapy.

We report a supramolecular naphthalene diimide (NDI) radical anion with efficient NIR-II photothermal conversion for E. coli-responsive photothermal therapy. The supramolecular radical anion (NDI-2CB[7])⋅- , which is obtained from the E. coli-induced in situ reduction of NDI-2CB[7] neutral complex, formed by the host-guest interaction between an NDI derivative and cucurbit[7]uril (CB[7]), exhibits unexpectedly strong NIR-II absorption and remarkable photothermal conversion capacity in aqueous solution. The NIR-II absorption is caused by the self-assembly of NDI radical anions to form supramolecular dimer radicals in aqueous solution, which is supported by theoretically predicted spectra. The (NDI-2CB[7])⋅- demonstrates excellent NIR-II photothermal antimicrobial activity (>99 %). This work provides a new approach for constructing NIR-II photothermal agents and non-contact treatments for bacterial infections.

Single-cell transcriptomic analysis reveals differential cell subpopulations and distinct phenotype transition in normal and dissected ascending aorta.

BACKGROUND: Acute thoracic aortic dissection (ATAD) is a fatal condition characterized by tear of intima, formation of false lumen and rupture of aorta. However, the subpopulations of normal and dissected aorta remain less studied. METHODS: Single-cell RNA sequencing was performed including 5 patients with ATAD and 4 healthy controls. Immunohistochemistry and immunofluorescence were used to verify the findings. RESULTS: We got 8 cell types from human ascending aorta and identified 50 subpopulations including vascular smooth muscle cells (VSMCs), endothelial cells, fibroblasts, neutrophils, monocytes and macrophages. Six transmembrane epithelial antigen of prostate 4 metalloreductase (STEAP4) was identified as a new marker of synthetic VSMCs. CytoTRACE identified subpopulations with higher differentiation potential in specified cell types including synthetic VSMCs, enolase 1+ fibroblasts and myeloid-derived neutrophils. Synthetic VSMCs-derived C-X-C motif chemokine ligand 12 (CXCL12) might interact with neutrophils and fibroblasts via C-X-C motif chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3), respectively, which might recruit neutrophils and induce transdifferentitation of fibroblasts into synthetic VSMCs. CONCLUSION: We characterized signatures of different cell types in normal and dissected human ascending aorta and identified a new marker for isolation of synthetic VSMCs. Moreover, we proposed a potential mechanism that synthetic VSMCs might interact with neutrophils and fibroblasts via CXCL12-CXCR4/ACKR3 axis whereby deteriorating the progression of ATAD, which might provide new insights to better understand the development and progression of ATAD.

Epitaxial Growth of High-Energy Copper Facets for Promoting Hydrogen Evolution Reaction.

Copper is known as a conductive metal but an inert catalyst for the hydrogen evolution reaction due to its inappropriate electronic structure. In this work, an active copper catalyst is prepared with high-energy surfaces by adopting the friction stir welding (FSW) technique. FSW can mix the immiscible Fe and Cu materials homogenously and heat them to a high temperature. Resultantly, α-Fe transforms into γ-Fe, and low-energy γ-Fe (100) and (110) surfaces induce the epitaxial growth of high-energy Cu (110) and (100) planes, respectively. After the removal of γ-Fe by acid etching, the copper electrode exposes high-energy surface and exhibits excellent acidic HER activity, even being superior to Pt foil at high current densities (>66 mA cm-2 ). Density functional theory calculation reveals that the high-energy surface favors the adsorption of hydrogen intermediate, thus accelerating the hydrogen evolution reaction. The epitaxial growth induced by FSW opens a new avenue toward engineering high-performance catalysts. In addition, FSW makes it possible to massively fabricate low-cost catalyst, which is advantageous to industrial application.

12-Membered Ring Carbides with Stabilization of Actinide Atoms.

Actinide (Th and U) carbides as the potential nuclear fuels in nuclear reactors require basic research in order to understand the thermodynamic stability and performance of these substances. Here we report the structural characterization and bonding analyses of [C12], ThC12, and UC12 clusters via a global-minimum search combined with relativistic quantum chemistry calculations to elucidate the stability and bonding nature of An-C bonds. We predict that these [C12], ThC12, and UC12 compounds have a planar structure with C6h, D12h, and D12h symmetry, respectively. [C12] has a hyperconjugation structure containing alternating single and double bonds. The significant stabilization when forming AnC12 predominantly comes from the electrostatic interaction between An4+ and [C12]4- and also from a certain degree of orbital interaction between the An 5f6d7s valence shell and [C12] π orbitals. The covalent character of the An-C bonds exhibits a direct in-plane σ-type overlap of the C 2p-derived MOs of [C12] and the An 5fϕ AO, thus leading to an unprecedented electronic configuration of d1f1 for U in UC12. Our results present an example of the novel properties that can be expected for actinide compounds and would provide the knowledge required to obtain novel structures of AnC12 in future experiments.

Semisynthesis and Non-Small-Cell Lung Cancer Cytotoxicity Evaluation of Germacrane-Type Sesquiterpene Lactones from Elephantopus scaber.

Two series of germacrane-type sesquiterpene lactones were produced by semisynthetic modulation of scaberol C, which was prepared by a standard chemical transformation from an Elephantopus scaber extract. Their inhibition activities against non-small-cell lung cancer cells were screened, and preliminary structure-activity relationships were also established. Among them, monomeric analog 1u and dimeric analog 3d exhibited superior anti-non-small-cell lung cancer cytotoxic potencies with IC50 values of 4.3 and 0.7 µM against A549 cells, respectively, and were more active than cisplatin and the standard sesquiterpene lactones, parthenolide and scabertopin. Further studies revealed that compounds 1u and 3d cause G2/M phase arrest and induce apoptosis through the activation of mitochondrial pathways in A549 cells. Collectively, the results obtained suggest that compounds 1u and 3d are promising anti-non-small-cell lung cancer lead compounds.

Genistein Modified with 8-Prenyl Group Suppresses Osteoclast Activity Directly via Its Prototype but Not Metabolite by Gut Microbiota.

Postmenopausal osteoporosis is a significant threat to human health globally. Genistein, a soy-derived isoflavone, is regarded as a promising anti-osteoporosis drug with the effects of promoting osteoblastogenesis and suppressing osteoclastogenesis. However, its oral bioavailability (6.8%) is limited by water solubility, intestinal permeability, and biotransformation. Fortunately, 8-prenelylated genistein (8PG), a derivative of genistein found in Erythrina Variegate, presented excellent predicted oral bioavailability (51.64%) with an improved osteoblastogenesis effect, although its effects on osteoclastogenesis and intestinal biotransformation were still unclear. In this study, an in vitro microbial transformation platform and UPLC-QTOF/MS analysis method were developed to explore the functional metabolites of 8PG. RANKL-induced RAW264.7 cells were utilized to evaluate the effects of 8PG on osteoclastogenesis. Our results showed that genistein was transformed into dihydrogenistein and 5-hydroxy equol, while 8PG metabolites were undetectable under the same conditions. The 8PG (10-6 M) was more potent in inhibiting osteoclastogenesis than genistein (10-5 M) and it down-regulated NFATC1, cSRC, MMP-9 and Cathepsin K. It was concluded that 8-prenyl plays an important role in influencing the osteoclast activity and intestinal biotransformation of 8PG, which provides evidence supporting the further development of 8PG as a good anti-osteoporosis agent.

CDKN2B-AS1 gene rs4977574 A/G polymorphism and coronary heart disease: A meta-analysis of 40,979 subjects.

It has been implied that there is a possible relationship between cyclin-dependent protein kinase inhibitors antisense RNA 1 (CDKN2B-AS1) gene rs4977574 A/G polymorphism and coronary heart disease (CHD) susceptibility. However, as the research results are discrepant, no distinct consensus on this issue has been reached so far. In order to further elaborate the latent association of the CDKN2B-AS1 gene rs4977574 A/G polymorphism and CHD, this present meta-analysis was conducted. There were 40,979 subjects of 17 individual studies in the present meta-analysis. The pooled odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were estimated to determine the association strength. Considering the significant heterogeneity among the individual studies, the random-effect models were used. In the current meta-analysis, a significant association between CDKN2B-AS1 gene rs4977574 A/G polymorphism and CHD was found under allelic (OR: 1.18, 95% CI: 1.08-1.29, p = 4.83×10-4 ), recessive (OR: 1.36, 95% CI: 1.11-1.67, p = 0.003), dominant (OR: 0.71, 95% CI: 0.58-0.86, p = 6.26×10-4 ), heterozygous (OR:1.210, 95% CI: 1.076-1.360, p = 0.001), homozygous (OR: 1.394, 95% CI: 1.163-1.671, p = 3.31×10-4 ) and additive (OR: 1.180, 95% CI: 1.075-1.295, p = 4.83×10-4 ) genetic models. A more significant association between them was found in the Asian population than that in the whole population under these genetic models (p < 0.05). However, no significant association between them was found in the Caucasian population (p > 0.05). CDKN2B-AS1 gene rs4977574 A/G polymorphism was associated with CHD susceptibility, especially in the Asian population. G allele of CDKN2B-AS1 gene rs4977574 A/G polymorphism is the risk allele for CHD.

Double σ-Aromaticity in a Planar Zinc-Doped Gold Cluster: Au9Zn.

The strong relativistic effects result in many interesting chemical and physical properties for gold and gold compounds. One of the most surprising findings has been that small gold clusters prefer planar structures. Dopants can be used to tune the electronic and structural properties of gold nanoclusters. Here we report an experimental and theoretical investigation of a Zn-doped gold cluster, Au9Zn-. Photoelectron spectroscopy reveals that Au9Zn- is a highly stable electronic system with an electron binding energy of 4.27 eV. Quantum chemical studies show that the global minimum of Au9Zn- has a D3h structure with a closed-shell electron configuration (1A1'), which can be viewed as replacing the central Au atom by Zn in the open-shell parent Au10- cluster. The high electronic stability of Au9Zn- is corroborated by its extremely large HOMO-LUMO gap of 3.3 eV. Chemical bonding analyses revealed that the D3h Au9Zn- are bonded by two sets of delocalized σ bonds, giving rise to double σ aromaticity and its remarkable stability. Two planar low-lying isomers are also observed, corresponding to a similar triangular structure with the Zn atom on the edge and another one with one of the corner Au atoms moved to the edge of the triangle.

Neuronal Differentiation 1 gene Ala45Thr polymorphism and type 2 diabetes mellitus: A meta-analysis of 7,940 subjects.

BACKGROUND AND AIMS: Previous studies have shown that there was a possible relationship between human Neuronal Differentiation 1 (NEUROD1) gene Ala45Thr polymorphism and type 2 diabetes mellitus (T2DM) susceptibility. Nevertheless, no public opinion has been formed because of the conflicting results in the past studies. In order to illuminate the potential association of human NEUROD1 gene Ala45Thr polymorphism and T2DM, the present meta-analysis was conducted. METHODS AND RESULTS: In the current meta-analysis, 7940 subjects from 14 individual studies were included. The fixed or random effects models were used to evaluate the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). The current meta-analysis found a significant association between NEUROD1 gene Ala45Thr polymorphism and T2DM under allelic (OR: 1.21, 95% CI: 1.04-1.41, P = 0.01), dominant (OR: 0.819, 95% CI: 0.734-0.913, P = 3.31 × 10-4), heterozygous (OR:1.199, 95% CI: 1.068-1.346, P = 0.002), and additive (OR: 1.33, 95% CI: 1.09-1.62, P = 0.004) genetic models. CONCLUSIONS: NEUROD1 gene Ala45Thr polymorphism was significantly related to T2DM, especially in the Asian population. More particularly, the Thr45 allele carriers of the NEUROD1 gene may be more susceptible to T2DM.

FVII gene R353Q polymorphism and coronary heart disease: a meta-analysis including 3258 subjects.

The coagulation factor VII (FVII) gene R353Q polymorphism is suggested to be relevant to the coronary heart disease (CHD) susceptibility. However, the results of separate studies are not consistent with one another. A meta-analysis including 3258 participants from nine studies was conducted to investigate the relationship between the FVII gene R353Q polymorphism and the CHD in the Chinese population. The fixed-effect models were used to assess the pooled odds ratios (ORs) and their corresponding 95% confidence intervals. A significant association was observed between the FVII gene R353Q polymorphism and the CHD in the Chinese population under allelic (OR 1.34, 95% CI 1.10-1.65, P = 0.004), dominant (OR 0.68, 95% CI 0.55-0.85, P = 0.0006), and heterozygous (OR 0.68, 95% CI 0.55-0.85, P = 0.0007) genetic models. The FVII gene R353Q polymorphism was significantly correlated with the CHD susceptibility in the Chinese population. Persons with the R allele of the FVII gene R353Q polymorphism might have greater CHD risk than others.

The identification of alkaloids from the stems of Picrasma quassioides via computer-assisted structure elucidation and quantum chemical calculations.

Four new alkaloids (1-4) and one known alkaloid were isolated from the stems of Picrasma quassioides. The structures of these isolated compounds were elucidated by spectroscopic analyses, a combination of computer-assisted structure elucidation software (ACD/Structure Elucidator) and gauge-including atomic orbital (GIAO) calculation of 1 D NMR data. All compounds were evaluated for their cytotoxic activities against hepatocellular carcinoma HepG2 and Hep3B cells. However, they did not show obvious inhibitory activities.[Figure: see text].

Targeted isolation of cytotoxic germacranolide sesquiterpenes from Elephantopus scaber L. using small molecule accurate recognition technology.

Small molecule accurate recognition technology (SMART) is an emerging method for the rapid structural prediction of major constituents from crude extracts and fractions. In the present study, a targeted isolation of an Elephantopus scaber extract by SMART resulted in the obtention of 15 new (1-15) and five known germacranolide sesquiterpenes (16-20). Their structures were assigned by extensively analyzing HRESIMS, NMR, X-ray crystallographic analyses, modified Mosher's method results, and quantum chemical calculate electronic circular dichroism (ECD) spectra. All germacranolide sesquiterpenes were screened to determine their inhibitory effects with two hepatoma cell lines (HepG2 and Hep3B), and compounds 14, 16, 18, 19 and 20 showed significant cytotoxic activities against the HepG2 (IC50, 3.3-9.9 µM) and Hep3B (IC50, 4.5-8.6 µM) cell lines. Further study suggested that 18 can induce the apoptosis of hepatoma cells via mitochondrial dysfunction.

TGMin: An efficient global minimum searching program for free and surface-supported clusters.

In this article, we introduce an efficient global-minimum structural search program named Tsinghua Global Minimum 2 (TGMin-2), which is the successor of the original TGMin algorithm that was developed in our group in 2011. We have introduced a number of new features and improvements into TGMin-2, including a symmetric structure generation algorithm that can produce good initial seeds for small- and medium-size clusters, the duplicated structure identification algorithm, and the improved structure adaption algorithm that was implemented in the original TGMin code. To predict the simulated photoelectron spectrum (PE spectrum) automatically, we also implemented a standalone program named AutoPES (Auto Photoelectron Spectroscopy), which can be used to simulate PE spectra and compare them with experimental results automatically. We have demonstrated that TGMin-2 and AutoPES are powerful tools for studying free and surface-supported molecules, clusters, and nanoclusters. © 2018 Wiley Periodicals, Inc.