Article
Energy & Fuels
Wanru Li, Jeremy M. Manheim, Yue Fu, Tiina Laaksonen, Gozdem Kilaz, Hilkka I. Kenttamaa
Summary: The performance of APCI LQIT Orbitrap MS and GCxGC/EI TOF MS were compared for the analysis of heavy base oils. APCI predominantly ionized compounds via protonation, while GCxGC/EI enabled chromatographic separation. APCI provided more information for large compounds, while GCxGC/EI gave more accurate results for aromatic hydrocarbons and small alkanes.
Article
Computer Science, Theory & Methods
Fahad Saeed, Muhammad Haseeb, S. S. Iyengar
Summary: This paper demonstrates the communication bounds reached by existing parallel proteomics algorithms and argues for the need for next-generation parallel algorithms for MS based large systems biology studies.
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING
(2022)
Article
Food Science & Technology
Chengyu Wang, Hongyan Bi
Summary: The study compared several one-step methods for pretreating seafood muscle tissues, and found that the acid processing method showed the best performance in achieving good spectral resolution when using MALDI-MS for analysis, allowing for rapid and efficient differentiation of fish samples.
Article
Mathematics, Applied
Liwen Ma
Summary: Finite topological spaces have been attracting more attention due to their wide applications, especially in fields like data mining and computing where interior and closure operators are important. The concept of base matrix of the topology is introduced, along with matrix computation formulas for interior, closure, boundary, and Kuratowski 14 sets. A Generalized 14 Sets Theorem is also proposed, with matrix representations provided for the generalized 14 sets. The use of matrix methods simplifies computations, improves efficiency, accuracy, and can be easily implemented by computer programs, expanding the application scope of finite topological spaces in various fields.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Article
Polymer Science
Fanfan Li, Yi Yu, Hanyu Lv, Guiting Cai, Yanwu Zhang
Summary: Twisted ZnTHP-Me2Si and layered ZnTHP-Ph2Si, synthesized by cross-linking ZnTHP, show high active site loadings and are effective photocatalysts for the polymerization of NIPAm. Twisted ZnTHP-Me2Si, with a larger surface area and more uniform pore distribution, accelerates the polymerization reaction more effectively.
Article
Instruments & Instrumentation
Georg Rugel, Rene Ziegenrucker, Axel D. Renno, Dominik Koll, Johannes Lachner, Pavol Noga, Carlos Vivo-Vilches, Anton Wallner, Michael Wiedenbeck
Summary: The DREAMS Super-SIMS project aims to provide quantitative concentration data of ultra-trace elements in geological samples through the use of Super-SIMS technology. The lack of well characterized calibration materials poses a challenge for accurate measurement of trace and ultra-trace element contents.
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS
(2022)
Article
Chemistry, Multidisciplinary
Oliver J. Hale, Helen J. Cooper
Summary: This study demonstrates a mass spectrometry analysis method for the direct analysis of intact oligomeric membrane proteins from tissue. By characterizing protein assembly directly from sheep eye lens sections without sample pre-treatment, our approach allows for simultaneous analysis of soluble protein assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Neng-Bin Xie, Min Wang, Tong-Tong Ji, Xia Guo, Jiang-Hui Ding, Bi-Feng Yuan, Yu-Qi Feng
Summary: The study presents an engineered deaminase-mediated sequencing (EDM-seq) method for the quantitative detection of 5hmC in DNA at single-nucleotide resolution. The method uses an engineered A3A protein to deaminate C and 5mC, while leaving 5hmC unaffected, allowing for the direct and quantitative detection of 5hmC in DNA.
Editorial Material
Chemistry, Multidisciplinary
Muhammad A. Zenaidee, Joseph A. Loo
Summary: Extending mass spectrometry measurements of biomolecules into the megadalton regime is challenging. However, using single ion-charge detection Orbitrap mass spectrometry, a mass accuracy of 0.001% has been demonstrated for protein particles larger than 9 MDa.
Article
Biochemical Research Methods
Yin Ji, Heming Li, Jinghan Dong, Jiashi Lin, Zian Lin
Summary: For the first time, two-dimensional covalent organic framework nanosheets (NUS-9) were used for highly efficient enrichment of glycopeptides. NUS-9 displayed ultra-high graft density of sulfonic groups and super-hydrophilicity, which enabled remarkable efficiency for glycopeptide enrichment with excellent detection sensitivity, outstanding enrichment capability, and good enrichment selectivity.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemistry & Molecular Biology
Ozgur Yurekten, Thomas Payne, Noemi Tejera, Felix Xavier Amaladoss, Callum Martin, Mark Williams, Claire O'Donovan
Summary: MetaboLights is a global database for metabolomics studies that contains raw experimental data and associated metadata. It includes metabolite structures, reference spectra, and biological roles. This article discusses the growth and diversity of submissions to the database and highlights the development of MetaboLights Labs, a standardized workflow platform. The reuse of data by the community is also emphasized.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xiaotong Luo, Yuantai Huang, Huiqin Li, Yihai Luo, Zhixiang Zuo, Jian Ren, Yubin Xie
Summary: The SPENCER database compiles research on ncRNA-encoded small peptides in cancer, identifying 29,526 ncPEPs across 15 different cancer types. Of these, 22,060 have been experimentally validated. Additionally, SPENCER predicted the immunogenicity of 4497 ncPEPs, making it a valuable resource for cancer research.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Medical Laboratory Technology
Kenichi Tamama
Summary: Drugs of abuse testing is commonly used in clinical and forensic settings, with urine being the preferred specimen type but other emerging types include saliva, sweat, hair, and meconium. Liquid chromatography-tandem mass spectrometry (LC-tandem-MS) has become the new gold standard for confirmatory drug testing due to its ability to analyze a wider range of analytes compared to gas chromatography-mass spectrometry (GC-MS). Technical advancements such as high-resolution mass spectrometry and miniature ambient ionization mass spectrometry have improved the speed and efficiency of drugs of abuse testing.
CLINICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Michael S. Westphall, Kenneth W. Lee, Colin Hemme, Austin Z. Salome, Keaton Mertz, Timothy Grant, Joshua J. Coon
Summary: This article describes an apparatus that can cryogenically land particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. The study demonstrates that using this cryogenic landing device significantly improves the structural preservation of deposited protein-protein complexes compared to room temperature landings, and landing under cryogenic conditions can increase the diversity of particle orientations, enabling improved 3D structural interpretation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Linlin Sun, Xueliang Liu, Sihui Liu, Xiaofeng Chen, Zheng Li
Summary: The on-chip strategy combining conductive nanosensors with a chaotic gas micromixer enables real-time monitoring of volatile metabolites from urine for accurate diagnosis and classification of urinary tract cancers.
ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Analytical
Lehua Lu, Menghui Xiang, Haoran Lu, Zhixin Tian, Yihan Gao
Summary: Each e-cigarette is a battery-powered system that heats e-liquids to make them inhalable, containing components like vegetable glycerin, propylene glycol, nicotine, organic acid, and flavor ingredients. Research focuses on quantifying nicotine content and form distribution, utilizing technologies like GC-MS and quantitation strategies using LC-MS. Various methods, such as pH value derivation, solvent extraction, SPME, and NMR, are used to determine nicotine forms distribution, crucial for e-cigarette product upgrade and development.
ANALYTICAL METHODS
(2022)
Article
Chemistry, Physical
Kimihiko Hirao, Takahito Nakajima, Bun Chan, Ho-Jin Lee
Summary: The core ionization energies of second-period and third-period elements are investigated using Lambda SCF and Slater's transition state (STS) theory with Hartree-Fock (HF) and Kohn-Sham (KS) approximations. Electron correlation increases the estimated core ionization energies, while the self-interaction error (SIE) decreases them, especially for the third-period elements. HF predictions of core ionization energies are reasonably accurate due to the lack of SIE, while KS calculations are sensitive to the functional used. Overall, the study highlights the importance of considering electron correlation and SIE when predicting core ionization energies. Rating: 7 out of 10.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Carina Yi Jing Lim, Meltem Yilmaz, Juan Manuel Arce-Ramos, Albertus D. Handoko, Wei Jie Teh, Yuangang Zheng, Zi Hui Jonathan Khoo, Ming Lin, Mark Isaacs, Teck Lip Dexter Tam, Yang Bai, Chee Koon Ng, Boon Siang Yeo, Gopinathan Sankar, Ivan P. Parkin, Kedar Hippalgaonkar, Michael B. Sullivan, Jia Zhang, Yee-Fun Lim
Summary: The authors report a histidine-functionalized Cu catalyst for CO2 reduction to multi-carbon products and reveal the correlation between catalyst surface charge and catalytic performance. The histidine-functionalized Cu exhibits high and stable selectivity for multi-carbon products across a wide potential range. The results provide important insights for explaining CO2 reduction activity and discovering new catalysts.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Bun Chan, Seiji Shirakawa
Summary: In this study, computational quantum chemistry was used to investigate the cation affinity of various nucleophiles. The results suggest that organochalcogens may serve as catalysts for cation transfer. The study also found that certain DFT methods, such as DSD-PBEP86, can be used to study these cation transfer processes.
CANADIAN JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Physical
Wen-Qing Li, Juan Manuel Arce-Ramos, Michael B. Sullivan, Chee Kok Poh, Luwei Chen, Armando Borgna, Jia Zhang
Summary: In this study, a novel mechanism involving previously unexplored surface diffusion of partially hydrogenated intermediates (CH, CHCH) was proposed through density functional theory simulations. This mechanism significantly reduces the energy barrier of CH2CH2, resulting in the production of C2H4 in CO-derived surface C hydrogenation. Studies on the correlation between the average Bader charge of surface Fe and the energy barrier of CH4 and CH2CH2 formation suggest that an increase in the positive charge of iron can enhance the activity and selectivity of ethylene formation.
JOURNAL OF CATALYSIS
(2023)
Article
Chemistry, Physical
Bun Chan
Summary: In this study, the performance of various small basis sets and their geometric counterpoise (gCP) corrections for DFT computations were examined. It was found that a simplified scheme, unity-gCP, using a single scaling parameter, can yield fair results for an arbitrary basis set. The optimal balance between accuracy and computational efficiency was found to be 6-31+G(2d) for medium-sized basis sets. On the other hand, less balanced basis sets, even larger ones, can show significantly worse accuracy, and the inclusion of gCP may lead to overcorrections.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Guanyu Liu, Quang Thang Trinh, Haojing Wang, Shuyang Wu, Juan Manuel Arce-Ramos, Michael B. Sullivan, Markus Kraft, Joel W. W. Ager, Jia Zhang, Rong Xu
Summary: The electroreduction of CO2 to fuels is a viable method for renewable energy sources. This study investigates various catalyst design strategies, such as electronic metal-support interaction, to improve catalytic selectivity. A solvent-free synthesis method is used to prepare a copper-based metal-organic framework (MOF) that undergoes in situ decomposition/redeposition processes upon CO2 reduction, forming interfaces between Cu nanoparticles and amorphous carbon supports. This Cu/C catalyst shows high selectivity and stability in producing CH4, with a Faradaic efficiency of approximately 55% at -1.4 V versus reversible hydrogen electrode (RHE) for 12.5 h. Density functional theory calculation demonstrates the importance of interfacial sites between Cu and amorphous carbon support in stabilizing key intermediates for CO2 reduction to CH4. Adsorption of COOH* and CHO* at the Cu/C interface is significantly stronger than on Cu(111), promoting CH4 formation. Therefore, regulating electronic metal-support interaction can improve the selectivity and stability of catalysts for electrochemical CO2 reduction.
Article
Nanoscience & Nanotechnology
Yakui Mu, Tan Wang, Zeyu Deng, Bun Chan, Tiesheng Wang
Summary: Organic crystals assembled by TTF-based molecules hold potential for electronics, smart materials, and superconductors. A fragment charge difference method was used to investigate the charge transfer properties of these crystals, and the results were consistent with another established method. The study also demonstrated the influence of structure and chemistry on charge transfer properties.
Article
Chemistry, Multidisciplinary
Kimihiko Hirao, Takahito Nakajima, Bun Chan, Ho-Jin Lee
Summary: This study calculates the core ionization energies of various molecules using different methods and compares the results. The use of the shifted STS methods is shown to be effective in predicting the core ionization energies.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Bun Chan
Summary: In this study, computational quantum chemistry is used to obtain lattice energies (LEs) for various ionic clusters with the NaCl structure. Different methods are applied to small and large clusters, and species-specific adjustments are made to account for systematic deviations. The results provide a straightforward means to estimate LEs for similarly structured ionic compounds.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Zhiqiang Hao, Qiang Guo, Yuanyuan Feng, Zihan Zhang, Tiantian Li, Zhixin Tian, Jianting Zheng, Lin-Tai Da, Wenjie Peng
Summary: The study reveals the molecular mechanism of substrate recognition and catalysis by Actinobacillus pleuropneumoniae soluble N-glycosyltransferase (ApNGT). Key structural motifs and residues involved in peptide substrate recognition were identified. The study also achieved site-selective N-glycosylation of specific sequences within the SARS-CoV-2 spike protein, enabling investigation of the biological roles of N-glycosylation in virus entry. This research provides insights into ApNGT and the synthesis of chemically defined N-glycoproteins for exploring the importance of N-glycosylation.
Article
Chemistry, Physical
Bun Chan, Amir Karton
Summary: In this study, the energy differences between singlet and triplet states of small fullerenes were investigated using density functional theory (DFT), along with the ionization energy (IE) and electron affinity (EA). The DFT methods consistently showed qualitative observations. Among the 812 fullerene isomers, approximately 80-90% had a singlet ground state, while the rest had ground-state triplets. Some of these may enhance the efficiency of singlet-fission materials for light harvesting. The triplet-singlet energy difference correlated well with the IE-EA differences, which serve as indicators for charge-transfer capabilities. Larger fullerenes were surveyed to identify candidates with superior charge-transfer properties, suggesting that optimally shaped medium-sized fullerenes are the most promising.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Qinyi Gu, Zi-Han Zhao, Bun Chan, Tong Yan, Jing-Lin Zuo, Deanna M. D'Alessandro, Cheng-Hui Li
Summary: A new Ni-dithiolene ligand was used to prepare a photothermal metal-organic framework (MOF) that showed efficient conversion of light into heat. The MOF had strong absorption in the near-infrared region due to the radical monoanion of the ligands, and the structure played an important role in the photothermal properties. The photothermal MOF was then doped into a self-healing polymer, enabling the composites to recover from dynamic damage using the heat generated by photostimulus.
ACS MATERIALS LETTERS
(2023)
Article
Multidisciplinary Sciences
Chisato Terada, Kaho Oh, Ryutaro Tsubaki, Bun Chan, Nozomi Aibara, Kaname Ohyama, Masa-Aki Shibata, Takehiko Wada, Mariko Harada-Shiba, Asako Yamayoshi, Tsuyoshi Yamamoto
Summary: In this study, a toehold-bearing ASO architecture is developed to mitigate a broad spectrum of off-target interactions, significantly enhancing the safety profile of ASO drugs.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Haitao Liu, Feng Chen, Nannan Zhao, Sai V. C. Vummaleti, Michael B. Sullivan, Jackie Y. Ying, Lei Wang
Summary: Ring expansion reactions are efficient tools in synthetic and medicinal chemistry, but the strategy involving sulfur ylide-initiated [1,4]-sigmatropic rearrangement is still underexploited. In this study, a rhodium-catalyzed ring expansion of thiochromenes and aromatic thiophenes was disclosed, enabling the straightforward assembly of polyaromatic oxathionines and oxathiocines with diverse functionalities.
