Article
Chemistry, Organic
Aaron M. Fleming, Songjun Xiao, Cynthia J. Burrows
Summary: The differential reactions of pseudouridine (Psi) and 5-methylcytidine (m(5)C) with NaHSO3 at pH 5 were used to locate their positions in RNA. The study found that NaHSO3 was unique in achieving quantitative yields compared to other reagents. The reaction selectivity of pseudouridine with NaHSO3 was supported by the reaction rate constants at pH 7. Additionally, the Psi derivative N1-methylpseudouridine in mRNA vaccines formed ribose adducts through a similar reaction with bisulfite.
Review
Chemistry, Multidisciplinary
Cynthia J. Burrows, Aaron M. Fleming
Summary: This article discusses the reaction mechanism of bisulfite with pseudouridine and introduces a chemical method for sequencing modified bases in the epitranscriptome. Through the study of structure and mechanism, a sequencing reaction specific to pseudouridine was designed, and psi sites were mapped using nanopore direct RNA sequencing.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Shashanka Aroli, Eui-Jeon Woo, Balasubramanian Gopal, Umesh Varshney
Summary: UdgX removes uracil from uracil-containing DNA and forms a covalent bond with the resulting AP-DNA. It is structurally similar to family-4 UDGs (F4-UDGs) but unique in possessing a flexible R-loop (105KRRIH109). Mutations in UdgX reveal the role of specific amino acids in its enzymatic activity and substrate binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Yuta Miura, Yo-ichi Yamamoto, Shutaro Karashima, Natsumi Orimo, Ayano Hara, Kanae Fukuoka, Tatsuya Ishiyama, Toshinori Suzuki
Summary: Ultrafast electronic relaxation plays a crucial role in the photostability of DNA. However, some nucleobases in aqueous solutions can form long-lived dark states from the excited states with a high quantum yield. By using extreme ultraviolet time-resolved photoelectron spectroscopy, we investigated the electronic relaxation in pyrimidine nucleobases in both aqueous solutions and the gas phase. We found that the quantum yields of the long-lived dark states were considerably lower for cytidine and uracil derivatives in aqueous solutions, while thymine and thymidine showed a longer excited state lifetime and a higher quantum yield. The reduction of the quantum yield in aqueous solutions is attributed to the destabilization of the dark states induced by hydrogen bonding.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Genetics & Heredity
Sae Rom Hong, Kyoung-Jin Shin
Summary: This study introduces a multiplex quantitative real-time PCR system named BisQuE, which can simultaneously analyze three key features of BS conversion, including efficiency, recovery, and degradation levels. Six BS conversion kits were tested, with NEBNext kit showing the lowest conversion efficiency but also the lowest degradation level among them.
FRONTIERS IN GENETICS
(2021)
Article
Chemistry, Physical
Leila Shahrokh, Reza Omidyan, Gholamhassan Azimi
Summary: The study utilizes ab initio and surface-hopping nonadiabatic dynamics simulation methods to investigate relaxation mechanisms in protonated thymine (TH+) and cytosine (CH+). Multiple conical intersections were located between (1)pi pi* and S-0 states for each system, with particular focus on the barrier-free out-of-plane deformation governing relaxation from the (1)pi pi* state to the ground state. The ring puckering coordinate from the C-6 position of the heterocycle ring was found to play a prominent role in the deactivation mechanism of the considered systems, supported by excited-state nonadiabatic dynamics simulations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yanhui Yi, Shangkun Li, Zhaolun Cui, Yingzi Hao, Yang Zhang, Li Wang, Pei Liu, Xin Tu, Xianming Xu, Hongchen Guo, Annemie Bogaerts
Summary: Using Ni-based catalysts in a plasma environment for the selective oxidation of methane to methanol is an efficient method with high selectivity and good catalytic stability. Chemical kinetics modeling shows that methanol is mainly produced through radical reactions. Improvements in catalyst characterization help promote methanol production and increase yield.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2021)
Article
Engineering, Environmental
Qian Yang, Yufei Zhong, Zhuqin Zhang, Zhi Dang, Fangbai Li, Lijuan Zhang
Summary: A novel flexible self-supporting Fe-CuAl2O3 nanofibrous membrane was synthesized and used for simultaneous degradation of SMT and removal of Cr(VI). The membrane exhibited excellent catalytic selectivity and recycling performance over a wide range of environmental pH. This work provides new insights and a feasible strategy for the remediation of organic-inorganic composite pollutions.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Shidong Zhao, Lishuang Ma, Yanyan Xi, Hongyan Shang, Xufeng Lin
Summary: The research found that HAT reaction mediated by CrOOH clusters is more likely to lead to methane C-H activation. PCET pathways are regulated by the nucleophilicity of the O-t site and the electrophilicity of the metal center, with no significant difference in energy consumption among the four reactions. The introduction of a silica support can subtly influence intermolecular interactions and the thermodynamics of methane C-H activation.
Article
Chemistry, Inorganic & Nuclear
Jia-Yi Chen, Man Li, Rong-Zhen Liao
Summary: In this study, density functional theory (DFT) calculations were performed to investigate the reaction mechanism and product selectivity of the iron tetraphenylporphyrin complex-catalyzed photochemical reduction of CO2 to CH4. The results showed that the initial catalyst Fe-p-TMA undergoes three reduction steps, accompanied by the dissociation of the chloride ion. The redox non-innocent tetraphenylporphyrin ligand plays an important role in the CO2 reduction, keeping the ferrous ion at a relatively high oxidation state.
INORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)