Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

Hydrogen–deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Dynamics simulation and reaction pathway analysis of characteristics of soot particles in ethylene oxidation at high temperature

Soot particles characteristics were investigated numerically for high temperature oxidation of C₂H₄/O₂/N₂ (C/O ratio of 2.2) in a closed jet-stirred/plug-flow reactor (JSR/PFR) system. Based on the growth mechanism of polycyclic aromatic hydrocarbons (PAHs), two mechanisms were used to explore the formation pathways of soot precursors and soot. Numerical results were compared with the experimental and reference data. The simulation results show that the value predicted for small molecule intermediates within A1 gives a strong regularity, consistent trend with reference data. However, with the hydrogen-abstraction-carbon-addition (HACA) growth mechanism, the predicted value for beyond-A1 PAH macromolecules and soot volume fraction are smaller than the experimental data. The results also show that the predicted soot volume fraction is in good agreement with experimental data when a combination of the HACA and PAHs condensation (HACA + PAH-PAH) growth mechanisms is used. Analyses of the A1 sensitivity and reaction pathway elucidated that A1 are mainly formed from C₂H₃, C₂H₂, C₃H₃, C₆H₅OH, A1C₂H and A1-. The reaction 2C₃H₃ → A1 is the dominant route of benzene formation. The prediction results and an analysis of the A3 reaction pathway indicate that the growth process from benzene to larger aromatic hydrocarbons (beyond two-ring polycyclic aromatic hydrocarbons [PAHs]) goes by two pathways, i.e., HACA combined with the PAH-PAH radical recombination and addition reaction growth mechanisms.     

Catalytic epoxidation of alkenes over supported manganese oxide with hydrogen peroxide: effect of supports and manganese loading

Manganese oxides supported on γ-Al₂O₃, amorphous SiO₂, MCM-41, and TiO₂ prepared by an impregnation method were used as heterogeneous catalysts for epoxidation of alkenes with 30 % H₂O₂ in the presence of NaHCO₃ aqueous solution. The effect of support and manganese loading on their activity was studied. The 1.3-MnO _x /γ-Al₂O₃ exhibited superior epoxidazing activity of styrene, compared with other supported MnO _x . Hydrogen temperature-programmed reduction, UV–vis and ESR analyses suggested that Mn²⁺ (catalytic activity species) dominated in 1.3 % MnO _x /γ-Al₂O₃ due to a strong interaction between MnO _x and γ-Al₂O₃. Recycling studies showed the catalyst was a heterogeneous one and retained its activity after recycling four times.     

Enzymatic Building-Block Synthesis for Solid-Phase Automated Glycan Assembly

Automated chemical oligosaccharide synthesis is an attractive concept that has been successfully applied to a large number of target structures, but requires excess quantities of suitably protected and activated building blocks. Herein we demonstrate the use of biocatalysis to supply such reagents for automated synthesis. By using the promiscuous NmLgtB-B β1-4 galactosyltransferase from Neisseria meningitidis we demonstrate fast and robust access to the LacNAc motif, common to many cell-surface glycans, starting from either lactose or sucrose as glycosyl donors. The enzymatic product was shown to be successfully incorporated as a complete unit into a tetrasaccharide target by automated assembly.     

Divergent Total Synthesis of Euphoranginol C,Euphoranginone D,ent-Trachyloban-3β-ol,ent-Trachyloban-3-one,Excoecarin E,and ent-16α-Hydroxy-atisane-3-one

A divergent synthetic approach to biogenetically related diterpenoids such as ent-kauranes, ent-trachylobanes, ent-beyerane, and ent-atisane has been developed. The unified synthetic route involves the De Mayo reaction to rapidly generate the bicyclo[3.2.1]-octane moiety of ent-kaurane. The key reactions also include bioinspired nucleophilic cyclopropanation generating the [3.2.1.0^2,7]-tricyclic core of ent-trachylobane and regioselective cyclopropane fragmentation furnishing ent-beyerane and ent-atisane through the nucleophilic attack and protonation of the cyclopropane ring. This strategy enables the asymmetric total syntheses of six diterpenoids from the commercially available geraniol.     

Bioorthogonal Ligation and Cleavage by Reactions of Chloroquinoxalines with ortho-Dithiophenols

A bioorthogonal ligation and cleavage method via reactions of chloroquinoxalines (CQ) and ortho-dithiophenols (DT) is presented. Double nucleophilic substitutions of ortho-dithiophenols to chloroquinoxalines provide conjugates containing tetracyclic benzo[5,6][1,4]dithiino[2,3-b]quinoxaline with strong built-in fluorescence together with release of the other functional molecules. Three cleavable linkers were designed and successfully used in release of the molecules containing biotin from the protein conjugates. The CQ-DT bioorthogonal reactions can be applied for the bioorthogonal ligations, bioorthogonal cleavages, and trans-tagging of proteins, and show advantages of readily accessible unnatural orthogonal groups, appealing reaction kinetics (k₂≈1.3 m ⁻¹ s⁻¹), excellent biocompatibility of orthogonal groups, and high stability of conjugates. This complements previous bioorthogonal reactions and is a new route for protein-fishing applications and in-gel fluorescence analysis.     

Rationally Designed Three-Layered Cu2S@Carbon@MoS2 Hierarchical Nanoboxes for Efficient Sodium Storage

Hybrid materials, integrating the merits of individual components, are ideal structures for efficient sodium storage. However, the construction of hybrid structures with decent physical/electrochemical properties is still challenging. Now, the elaborate design and synthesis of hierarchical nanoboxes composed of three-layered Cu₂S@carbon@MoS₂ as anode materials for sodium-ion batteries is reported. Through a facile multistep template-engaged strategy, ultrathin MoS₂ nanosheets are grown on nitrogen-doped carbon-coated Cu₂S nanoboxes to realize the Cu₂S@carbon@MoS₂ configuration. The design shortens the diffusion path of electrons/Na⁺ ions, accommodates the volume change of electrodes during cycling, enhances the electric conductivity of the hybrids, and offers abundant active sites for sodium uptake. By virtue of these advantages, these three-layered Cu₂S@carbon@MoS₂ hierarchical nanoboxes show excellent electrochemical properties in terms of decent rate capability and stable cycle life.     

Fabrication of Heterostructured Fe2TiO5–TiO2 Nanocages with Enhanced Photoelectrochemical Performance for Solar Energy Conversion

Photocatalysts with well‐designed compositions and structures are desirable for achieving highly efficient solar‐to‐chemical energy conversion. Heterostructured semiconductor photocatalysts with advanced hollow structures possess beneficial features for promoting the activity towards photocatalytic reactions. Here we develop a facile synthetic strategy for the fabrication of Fe₂TiO₅–TiO₂ nanocages (NCs) as anode materials in photoelectrochemical (PEC) water splitting cells. A hydrothermal reaction is performed to transform MIL‐125(Ti) nanodisks (NDs) to Ti–Fe–O NCs, which are further converted to Fe₂TiO₅–TiO₂ NCs through a post annealing process. Owing to the compositional and structural advantages, the heterostructured Fe₂TiO₅–TiO₂ NCs show enhanced performance for PEC water oxidation compared with TiO₂ NDs, Fe₂TiO₅ nanoparticles (NPs) and Fe₂TiO₅–TiO₂ NPs.     

On Symmetric Cayley Graphs of Valency Eleven

A Cayley graph Γ=Cay(G,S)is said to be normal if G is normal in Aut Γ.In this paper,we investigate the normality problem of the connected 11-valent symmetric Cayley graphs Γ of finite nonabelian simple groups G,where the vertex stabilizer Av is soluble for A=Aut Γ and v ∈ VΓ.We prove that either Γ is normal or G=A5,A10,A54,A274,A549 or A1099.Further,11-valent symmetric nonnormal Cayley graphs of A5,A54 and A274 are constructed.This provides some more examples of nonnormal 11-valent symmetric Cayley graphs of finite nonabelian simple groups after the first graph of this kind(of valency 11)was constructed by Fang,Ma and Wang in 2011.     

Quantification of Venetoclax for Therapeutic Drug Monitoring in Chinese Acute Myeloid Leukemia Patients by a Validated UPLC-MS/MS Method

Venetoclax has emerged as a breakthrough for treatment of leukemia with a wide interindividual variability in pharmacokinetics. Herein, a rapid, sensitive, and reliable UPLC-MS/MS method for quantification of venetoclax in plasma was developed and validated. The method was operated in the multiple-reaction monitoring (MRM) mode to detect venetoclax at m/z transition 868.5 > 321.0 and IS at 875.5 > 321.0, respectively. Protein precipitation prior to injection into the LC-MS/MS and the analyte was separated on an ACQUITY UPLC BEH C18 column by gradient elution with acetonitrile and 0.1% formic acid in water. Linear calibration curves were obtained in the range of 25–8000 ng/mL. The specificity, recovery, matrix effect, and stability also met the acceptance criteria of FDA guidance. The method was successfully applied to analyze plasma in acute myeloid leukemia (AML) patients. The peak plasma concentration (C_max) of venetoclax in Chinese AML patient was 2966.0 ± 1595.0 ng/mL while the trough concentration (C_min) was 1018.0 ± 729.4 ng/mL. Additionally, C_max and C_min showed a positive correlation with AST levels. Furthermore, C_max was significantly higher in the older patients. The present method can be applied for TDM of venetoclax in treatment of hematological cancers.