Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn2+ coordination and substrate binding.

Members of glycosyltransferase family 75 (GT75) not only reversibly catalyze the autoglycosylation of a conserved arginine residue with specific NDP-sugars but also exhibit NDP-pyranose mutase activity that reversibly converts specific NDP-pyranose to NDP-furanose. The latter activity provides valuable NDP-furanosyl donors for glycosyltransferases and requires a divalent cation as a cofactor instead of FAD used by UDP-D-galactopyranose mutase. However, details of the mechanism for NDP-pyranose mutase activity are not clear. Here we report the first crystal structures of GT75 family NDP-pyranose mutases. The novel structures of GT75 member MtdL in complex with Mn2+ and GDP, GDP-D-glucopyranose, GDP-L-fucopyranose, GDP-L-fucofuranose, respectively, combined with site-directed mutagenesis studies, reveal key residues involved in Mn2+ coordination, substrate binding, and catalytic reactions. We also provide a possible catalytic mechanism for this unique type of NDP-pyranose mutase. Taken together, our results highlight key elements of an enzyme family important for furanose biosynthesis.

Bimetallic Ag125Cu8 Nanocluster, Structure Determination, and Nonlinear Optical Properties.

The atomic precision of the subnanometer nanoclusters has provided sound proof on the structural correlation of metal complexes and larger-sized metal nanoparticles. Herein, we report the synthesis, crystallography, structural characterization, electrochemistry, and optical properties of a 133-atom intermetallic nanocluster protected by 57 thiolates (3-methylbenzenethiol, abbreviated as m-MBTH) and 3 chlorides, with the formula of Ag125Cu8(m-MBT)57Cl3. This is the largest Ag-Cu bimetallic cluster ever reported. Crystallographic analysis revealed that the nanocluster has a three-layer concentric core-shell structure, Ag7@Ag47@Ag71Cu8S57Cl3, and the Ag54 metal kernel adopts a D5h symmetry. The nuclei number is between that of the previously reported large silver cluster [Ag136(SR)64Cl3Ag0.45]- and the large silver-rich cluster Au130-xAgx(SR)55 (x = 98). All these three clusters bear a similar metallic core structure, while the main structural difference lies in the shell motif structures. Electron counting revealed an open electron shell with 73 delocalized electrons, which was verified by the electron paramagnetic resonance analysis. The DPV electrochemical measurement indicates a multielectron state quantization double-layer charging shape and single-electron sequential charging and discharging characteristic of the AgCu alloy cluster. In addition, the open-hole Z-scan test reveals the nonlinear optical absorption (2-3 optical absorption in the NIR-II/III region) of Ag125Cu8 nanoclusters.

Symmetry Breaking Enhancing the Activity of Electrocatalytic CO2 Reduction on an Icosahedron-Kernel Cluster by Cu Atoms Regulation.

Recently, CO2 hydrogenation had a new breakthrough resulting from the design of catalysts to effectively activate linear CO2 with symmetry-breaking sites. However, understanding the relationship between symmetry-breaking sites and catalytic activity at the atomic level is still a great challenge. In this study, a set of gold-copper alloy Au13 Cux (x=0-4) nanoclusters were used as research objects to show the symmetry-controlled breaking structure on the surface of nanoclusters with the help of manipulability of the Cu atoms. Among them, Au13 Cu3 nanocluster displays the highest degree of symmetry-breaking on its crystal structure compared with the other nanoclusters in the family. Where the three copper atoms occupying the surface of the icosahedral kernel unevenly with one copper atom is coordinately unsaturated (CuS2 motif relative to CuS3 motif). As expected, Au13 Cu3 has an excellent hydrogenation activity of CO2 , in which the current density is as high as 70 mA cm-2 (-0.97 V) and the maximum FECO reaches 99 % at -0.58 V. Through the combination of crystal structures and theoretical calculations, the excellent catalytic activity of Au13 Cu3 is revealed to be indeed closely related to its asymmetric structure.

Cu(I)-Glutathione Assembly Supported on ZIF-8 as Robust and Efficient Catalyst for Mild CO2 Conversions.

The Cu-glutathione (GSH) redox system, essential in biology, is designed here as a supramacromolecular assembly in which the tetrahedral 18e Cu(I) center loses a thiol ligand upon adsorption onto ZIF-8, as shown by EXAFS and DFT calculation, to generate a very robust 16e planar trigonal single-atom Cu(I) catalyst. Synergy between Cu(I) and ZIF-8, revealed by catalytic experiments and DFT, affords CO2 conversion into high-value-added chemicals with a wide scope of substrates by reaction with terminal alkynes or propargyl amines in excellent yields under mild conditions and reuse at least 10 times without significant decrease in catalytic efficiency.

Cd Atom Goes into the Interior of Cluster Induced by Directional Consecutive Assembly of Tetrahedral Units on an Icosahedron Kernel.

"Core sliding" in metal nanoclusters drives the reconstruction of external structural units and provides an ideal platform for mapping their precise transformation mechanism and evolution pathway. However, observing the movement behavior of metal atoms in experiments is still challenging because of the uncertain stability of intermediates. In this work, a series of Au-Cd alloy nanoclusters with continuously assembled kernels (one icosahedral building block assembled with 0 to 3 tetrahedral units) were constructed. As the assembly continued, it eventually led to the Cd atom doping into the inner positions of the clusters. Importantly, the Cd doped into the interior of the cluster exhibits a different behavior than the surface or external Cd atoms (dispersion doping vs localized occupy), which provides experimental evidence of the sliding behavior in the nanocluster kernel. Furthermore, density functional theory (DFT) calculations reveal that this sliding behavior in the inner sites of nanoclusters is an energetically favorable process. In addition, these Au-Cd nanoclusters exhibit tunable optical properties with different assembly patterns in their kernels.

DFT Insights into the Variety in the Coordination Modes of the Equatorial Halides in [Au13 Ag12 (PR3 )10 X8 ]+ (X=Cl/Br) Clusters.

The bonding character within metal nanoclusters represents an intriguing topic, shedding light on the inherent driving force for the packing preference in nanomaterials. Herein, density functional theory (DFT) calculations were conducted to investigate the correlation of the series of isomeric [Au13 Ag12 (PR3 )10 X8 ]+ (X=Cl/Br) clusters, which are mainly differentiated by the coordination mode of the equatorial halides (µ2 -, µ3 - and µ4 -) in the rod-like, bi-icosahedral framework. The theoretical simulation corroborates the variety in the configuration of the Au13 Ag12 clusters and elucidates the fast isomerization kinetics among the different configurations. The easy tautomerization and the variety in chloride binding modes correspond to a fluxionality character of the equatorial halides and are verified by the potential energy curve analysis. The structural flexibility of the central Au3 Ag10 block is the main driving force, while the relatively stronger Ag-X bonding interaction (compared to that of Au-X), and a sufficient number of halides are also requisite for the associating Ag-X tautomerizations.

Motif-to-Core Nucleation in a Decahedral Evolution Pattern.

The atomic precision of ultrasmall metal nanoclusters has opened the door to elucidating the structural evolution principles of metal nanomaterials at the molecular level. Here, we report a novel set of super-atomic Ag clusters, including [Ag19(TBBT)16(DPPP)4]+ (Ag19), [Ag22(DMAT)8(DPPM)4Cl8]2+ (Ag22), Ag26(SPh3,5-CF3)15(DPPF)4Cl5 (Ag26), and [Ag30(DMAT)12(DPPP)4Cl8]2+ (Ag30). The core structures of these clusters correspond to one decahedral Ag7, perpendicular bi-decahedrons, three-dimensional penta-decahedrons, and hexa-decahedrons, respectively. The Ag atoms in AgS2 blocks show a strong correlation with the decahedral cores: the five equatorial Ag atoms in the decahedral Ag7 core of Ag19 all adopt the AgS2 coordination, while the Ag atoms in AgS2 blocks of Ag22, Ag26, and Ag30 unexceptionally constitute additional decahedral structures with the core Ag atoms. Specifically, two and four core Ag atoms of Ag26 and Ag30 clusters occupy positions that highly resemble that of Ag (in AgS2 motifs) of Ag22. The strong structural correlation demonstrates the motif-to-core evolution of the surface Ag (on AgS2) to build extra-decahedral blocks. Density functional theory calculations indicate that the 2e, 4e, 6e, and 8e clusters (from Ag19 to Ag30) adopt 1S2, 1S21P2, 1S21P4, and 1S21P6 electron configurations, all of which feature excellent super-atomic characters.

Activity of Different AunSn+1 Staples in the Ligand Exchange of Au23(SR)16- with a Single Foreign Thiolate Ligand.

Ligand exchange has been widely used to synthesize novel thiolated gold nanoclusters and to regulate their specific properties. Herein, density functional theory (DFT) calculations were conducted to investigate the kinetic profiles of the ligand exchange of the [Au23(SCy)16]- nanocluster with an aromatic thiolate (2-napthalenethiol). The three types of staple motifs (i.e., trimetallic Au3S4, monometallic AuS2, and the bridging thiolates) of the Au23 cluster precursor could be categorized into eight groups of S sites with different chemical environments. The ligand exchange of all of them occurs favorably via the SN1-like pathway, with one site starting with the Au-S dissociation and seven other sites starting with the H-transfer steps. By contrast, the SN2-like pathway (i.e., the synergistic SCy-to-SAr exchange prior to the H-transfer step) is unlikely in the target systems. Meanwhile, the Au-S bond on the capping Au atom of the bicapped icosahedral Au15 core is the most active one, while the S sites on Au3S4 (except for the one remote from the metallic core) are all competitive exchanging sites. The ligand exchange activity of the bridging thiolate and the remote S site on Au3S4 is significantly less reactive. The calculation results correlate with the multiple ligand exchange within only a few minutes and the preferential etching of the AuS2 staple with the foreign ligands reported in earlier experiments. The relative activity of different staples might be helpful in elucidating the inherent principles in the ligand exchange-induced size-evolution of metal nanoclusters.

Mechanistic Insights into Oxidation-Induced Size Conversion of [Au6(dppp)4]2+ to [Au8(dppp)4Cl2]2.

Oxidation-induced conversion of gold nanoclusters is an important strategy for preparing novel atomically precise clusters and elucidating the kinetic correlations of different clusters. Herein, the oxidation-induced growth from [Au6(dppp)4]2+ to [Au8(dppp)4Cl2]2+ (reported by Konishi and co-workers) has been studied by density functional theory calculations. A successive oxidation → Cl- coordination → oxidation → Cl- coordination sequence occurs first to activate the Au6 structure, resulting in the high Au(core)-Au(corner) bond cleavage activity and the subsequent formation of [Au2(dppp)2Cl]+ and [Au4(dppp)2Cl]+ fragments. Then, the dimerization of two Au4 fragments and the rearrangement of the diphosphine coordination occur to generate the thermodynamically stable [Au8(dppp)4Cl2]2+ products. The proposed mechanism agrees with the experimental outcome for the fast reaction rate and the residual of the Au2 components. Specifically, a multivariate linear regression analysis indicates the strong correlation of the oxidation potential of Au6, Au8, Au23, and Au25 clusters with the HOMO energy, the number of Au atoms, and cluster charge state. The main conclusions [e.g., oxidation-induced Au(corner)-Au(core) bond activation, easy 1,2-P transfer steps, etc.] of this study might be widely applicable in improving our understanding of the mechanism of other cluster-conversion reactions.

Insight into the Role of Copper in the Transformation of a [Ag25(2,5-DMBT)16(DPPF)3]+ Nanocluster: Doping or Oxidation.

Structural transformation in nanoclusters is important not only in obtaining functional nanoclusters controllably but also in understanding their structural evolution. This study investigated the role of Cu2+ ions in structural transformation. It was revealed that Cu2+ exhibits two different functions, doping and oxidation, in determining the final products. Starting with a new silver nanocluster, [Ag25(2,5-DMBT)16(DPPF)3]+ (Ag25), a doping process would occur when no more than 0.5 equiv of Cu2+ was added, resulting in the formation of [Ag25-xCux(2,5-DMBT)16(DPPF)3]+ (Ag25-xCux). When 1 equiv of Cu2+ was introduced to Ag25, a structural transformation process would occur instead, forming [Ag22-xCux(2,5-DMBT)12(DPPF)4Cl4]2+ (Ag22-xCux). Considering the similar Cu doping amounts in Ag25-xCux and Ag22-xCux, an oxidation process induced by Cu2+ in the solution can account for this transformation process, which was further demonstrated by the addition of other oxidant substitutions. On the other hand, the role of other valence states of copper in the transformation of the Ag25 cluster was explored. It was found that copper powder can hardly change Ag25 and Cu+ can only proceed the doping process, both of which are different from the role of Cu2+. Overall, this work explores the role of copper in the transformation of the Ag25 cluster in detail, including its concentrations and valence states.

Nucleophilicity Prediction Using Graph Neural Networks.

The quantitative description between chemical reaction rates and nucleophilicity parameters plays a crucial role in organic chemistry. In this regard, the formula proposed by Mayr et al. and the constructed reactivity database are important representatives. However, the determination of Mayr's nucleophilicity parameter N often requires time-consuming experiments with reference electrophiles in the solvent. Several machine learning (ML)-based models have been proposed to realize the data-driven prediction of N in recent years. However, in addition to DFT-calculated electronic descriptors, most of them also use a set of artificially predefined structural descriptors as input, which may result in a biased representation of the nucleophile's structural information depending on descriptors' definition preference. Compared with traditional ML algorithms, graph neural networks (GNNs) can naturally take the molecule's structural information into account by applying the message passing technique. We herein proposed a SchNet-based GNN model that only takes the molecular conformation and solvent type as input. The model achieves a comparable performance to the previous benchmark study on 10-fold cross-validation of 894 data points (R2 = 0.91, RMSE = 2.25). To enhance the model's ability to capture the molecule's electronic information, some DFT-calculated parameters are then incorporated into the model via graph global features, and substantial improvement is achieved in the prediction precision (R2 = 0.95, RMSE = 1.63). These results demonstrate that both structural and electronic information are important for the prediction of N, and GNN can integrate these two kinds of information more effectively.

An Oligopeptide-Protected Ultrasmall Gold Nanocluster with Peroxidase-Mimicking and Cellular-Imaging Capacities.

Recent decades have witnessed the rapid progress of nanozymes and their high promising applications in catalysis and bioclinics. However, the comprehensive synthetic procedures and harsh synthetic conditions represent significant challenges for nanozymes. In this study, monodisperse, ultrasmall gold clusters with peroxidase-like activity were prepared via a simple and robust one-pot method. The reaction of clusters with H2O2 and 3,3',5,5'-tetramethylbenzidine (TMB) followed the Michaelis-Menton kinetics. In addition, in vitro experiments showed that the prepared clusters had good biocompatibility and cell imaging ability, indicating their future potential as multi-functional materials.

Reference equations for the six-minute walking distance in obese Chinese subjects more than 40 years old.

BACKGROUND: Studies have shown that the reference equations for the six-minute walking distance (6MWD), which were mainly derived from healthy, normal-weight people, are not suitable for individuals with obesity. The main purpose of this study was to establish reference equations for the 6MWD in obese Chinese subjects. METHODS: In our study, a total of 214 individuals with obesity performed the six-minute walking tests (6MWTs) according to the American thoracic society (ATS) guidelines, and the longer 6MWD was used for further analysis. The reference equations for the 6MWD were developed using stepwise multiple regression analysis. The newly established equations for the 6MWD were compared to the existing prediction equations. RESULTS: The mean 6MWD for the cohort was 523 ± 56 m. We found that the reliability of two 6MWTs was good. Age and BMI were identified as independent factors, and explained 31% and 27% of the variance in the 6MWD for the male and female participants, respectively. Thus, the reference equations reported in the previous studies did not accurately predict the 6MWD in our subjects. CONCLUSION: Our study was the first to describe the 6MWD in obese Chinese subjects and to propose new predictive equations. These established equations can improve the assessment of the health of obese Chinese patients whose exercise capacity is affected by the disease. LEVEL OF EVIDENCE: III, Cohort study.

Multiple Ways Realizing Charge-State Transform in AuCu Bimetallic Nanoclusters with Atomic Precision.

Thiolate-protected nanoclusters with different charge states usually show similar structure frameworks but different electronic configurations, which are proved to dramatically affect their properties such as magnetism, photoluminescence, and catalytic activity. Until now, few nanoclusters with alterable charge states have been reported and only some of them are structurally solved, limiting the in-depth studies on their interesting properties. Here, a new AuCu alloy nanocluster [Au18 Cu32 (SPhCl)36 ]2- (HSPhCl = 4-chlorophenylthiophenol) is synthesized and structurally solved by X-ray crystallography. Interestingly, it is found that this nanocluster can be reduced to another nanocluster with a different charge state, that is, [Au18 Cu32 (SPhCl)36 ]3- . This change in charge states is clearly proved by X-ray crystallography, electrospray ionization mass spectrometry, thermogravimetric analysis, and electron paramagnetic resonance. Furthermore, several redox methods are carried out to realize the reversible interconversion between these two nanoclusters, including electrochemical redox, introduction of H2 O2 /NaBH4 , and oxidation with silica under air atmosphere. This work offers new insight into the transform progress of charge states with AuCu alloy nanoclusters which contributes to the understanding of the relationship between electronic structure and properties of nanoclusters and further development of AuCu nanoclusters with excellent performance.

Pivotal Electron Delivery Effect of the Cobalt Catalyst in Photocarboxylation of Alkynes: A DFT Calculation.

Photocarboxylation of alkyne with carbon dioxide represents a highly attractive strategy to prepare functionalized alkenes with high efficiency and atomic economy. However, the reaction mechanism, especially the sequence of elementary steps (leading to different reaction pathways), reaction modes of the H-transfer step and carboxylation step, spin and charge states of the cobalt catalyst, etc., is still an open question. Herein, density functional theory calculations are carried out to probe the mechanism of the Ir/Co-catalyzed photocarboxylation of alkynes. The overall catalytic cycle mainly consists of four steps: reductive-quenching of the Ir catalyst, hydrogen transfer (rate-determining step), outer sphere carboxylation, and the final catalyst regeneration step. Importantly, the cobalt catalyst can facilitate the H-transfer by an uncommon hydride coupled electron transfer (HCET) process. The pivotal electron delivery effect of the Co center enables a facile H-transfer to the α-C(alkyne) of the aryl group, resulting in the high regioselectivity for ß-carboxylation.

Redox-Induced Interconversion of Two Au8 Nanoclusters: the Mechanism and the Structure-Bond Dissociation Activity Correlations.

The interconversion of atomically precise nanoclusters represents an excellent platform to understand the structural correlations of nanomaterials at the atomic level. Herein, density functional theory calculations were performed to elucidate the mechanism of the redox-induced interconversion of [Au8(dppp)4]2+ and [Au8(dppp)4Cl2]2+ (dppp is short for 1,3-bis(diphenylphosphino)propane) nanoclusters. Reduction is the driving force for the conversion of [Au8(dppp)4Cl2]2+ to [Au8(dppp)4]2+, while the Au-Au and first Au-Cl bond dissociations occur asynchronously on the two different corner Au atoms to avoid the formation of an electron-deficient Au atom. By contrast, the reduced electron density of [Au8(dppp)4]2+ by oxidation with O2 weakens the outmost Au-Au bond therein and facilitates the coordination of the electron-rich chloride(s). The reduction- and oxidation-induced activations, respectively, of Au-Cl and Au-Au bonds and the elucidated principles on the structure-activity correlations might also be generalized to other size conversions upon redox treatment.

Structure Determination of the Cl-Enriched [Ag52(SAdm)31Cl13]2+ Nanocluster.

Cl atoms can serve as the innermost core, the peripheral ligand, or the counterions of metal nanoclusters. Herein, we report the structural determination a Cl-enriched [Ag52(SAdm)31Cl13]2+. The ratio of Cl to AdmSH is quite high compared to those of other nanoclusters. Structurally, nine Cl atoms, existing at the interlayer of the inner kernel and the surface motif, serve as the bridging ligands to sustain the robustness of the whole structure. Interestingly, four Cl atoms on the motif structure can be substituted by Br. This work allows us to clear the regulation of Cl ligands in the structural construction of metal nanoclusters.

Core Charge Density Dominated Size-Conversion from Au6 P8 to Au8 P8 Cl2.

The stimulus-response of metal nanoclusters is crucial to their applications in catalysis and bio-clinics, etc. However, its mechanistic origin has not been well studied. Herein, the mechanism of the AuI PPh3 Cl-induced size-conversion from [Au6 (DPPP)4 ]2+ to [Au8 (DPPP)4 Cl2 ]2+ (DPPP is short for 1,3-bis(diphenylphosphino)propane) is theoretically investigated with density functional theory (DFT) calculations. The optimal size-growth pathway, and the key structural parameters were elucidated. The Au-P bond dissociation steps are key to the size-growth, the easiness of which was determined by the charge density of the metallic core of the cluster precursors (i.e., "core charge density"). This study sheds light on the inherent structure-reactivity relationships during the size-conversion, and will benefit the deep understanding on the kinetics of more complex systems.

Steric and Electrostatic Control of the pH-Regulated Interconversion of Au16(SR)12 and Au18(SR)14 (SR: Deprotonated Captopril).

An understanding of the response of nanomaterials to specific environmental parameters is an essential prerequisite for their practical use, especially in living systems. Herein, we disclose the preparation of a water-soluble nanocluster Au16(SR)12 (SR denotes deprotonated captopril) and its characterization by a combination of theoretical (e.g., density functional theory calculations) and experimental (UV-vis, electrospray ionization mass spectrometry, etc.) methods. Interestingly, Au16(SR)12 was found to convert to Au18(SR)14 under acidic conditions, while the reverse conversion from Au18(SR)14 to Au16(SR)12 occurred upon the addition of base. A mechanistic investigation determined this pH regulation to originate from the distinct steric and electrostatic properties of these two clusters. This study is the first to report the susceptibility of Au18(SR)14 and Au16(SR)12 to pH, and the distinct pH stability unambiguously reveals the importance of size-tracking of nanomaterials in living systems for future clinical applications.

A mechanistic study on Cu(i) catalyzed carboxylation of the C-F bond with CO2: a DFT study.

The Cu(i) catalyzed carboxylation of the C-F bond recently reported by Yu and co-workers is an excellent method for the construction of complex fluoroacrylate compounds with high regioselectivity. In the present study, theoretical calculations were carried out to investigate the detailed mechanism of the catalytic cycle and the origin of regioselectivity. The calculation results reveal that the overall catalytic cycle proceeds via the migratory insertion of difluoroalkene on the boryl-Cu(i) species, synß-F elimination, transmetalation, and carboxylation steps. The rate determining step is the carboxylation step, and the migration insertion is the regioselectivity determining step. The regioselectivity for 2,1-insertion is consistent with Yu's experiment, and is determined by both steric and electronic effects.