Article
Chemistry, Organic
Nan-Fang Mo, Ying Zhang, Zheng-Hui Guan
Summary: An asymmetric organocatalyzed three-component Povarov reaction has been developed to construct azaspirocycles. A chiral phosphoric acid catalyst with a unique structure was highly efficient in the reaction, leading to a wide range of azaspirocycles in high yields and excellent enantioselectivities. This reaction has expanded the scope of the traditional Povarov reaction.
Article
Chemistry, Multidisciplinary
Hong Zhang, Alexander J. E. Novak, Cooper S. Jamieson, Xiao-Song Xue, Shuming Chen, Dirk Trauner, K. N. Houk
Summary: Computational studies using omega B97X-D density functional theory have revealed and refined the mechanisms of unique processes in Trauner's biomimetic synthesis of preuisolactone A. The research identified an ambimodal transition state for the cycloaddition between o-quinone and hydroxy-o-quinone, leading to both (5 + 2) and (4 + 2) cycloaddition products. A new mechanism for benzilic acid rearrangement resulting in ring contraction was proposed based on the study.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Masao Ohashi, Dan Tan, Jiayan Lu, Cooper S. Jamieson, Daiki Kanayama, Jiahai Zhou, K. N. Houk, Yi Tang
Summary: The synthesis of cis-decalin structures using [4 + 2] cycloaddition with high stereoselectivity is challenging. In this study, we investigated the biosynthetic pathway of the fungal natural product fischerin (1) and identified a novel pericyclase, FinI, which catalyzes this reaction. The cocrystal structure of FinI, a predicted O-methyltransferase, with the product and SAM provides valuable insights into the natural formation of cis-decalin.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
Marek Poschl, Shibulal Gopi Sathi, Radek Stocek, Ondrej Kratina
Summary: The addition of maleide F results in significantly improved curing torque and tensile properties of NR and CR blends, even retaining these properties under high-temperature aging conditions.
Article
Chemistry, Organic
Yan Jiang, Hao-Jie Ma, Xue-Long Wang, Yi Yang
Summary: A Yb(OTf)(3)-catalyzed formal (4 + 3) cycloaddition reaction was successfully achieved using donor-acceptor cyclopropanes and 3-benzylideneindoline-2-thiones as reactants. Functionalized 5,10-dihydro-2H-thiepino[2,3-b]indole derivatives were synthesized with good yields and moderate to good diastereoselectivity. This reaction represents the first (4 + 3) cycloaddition of 3-benzylideneindoline-2-thiones.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Ming Lai, Ying Zhang, Liang Zhao, Yu-Hua Huang, Lei Zhang, Wenlong Fu, Pu Chen, Xu-Dong Wang, Tingshun Zhu, Zhenyu Yang
Summary: Colloidal silicon nanocrystals (SiNCs) have attracted significant attention in optoelectronics and biomedical applications. A metal-free method is demonstrated for directly functionalizing SiNCs with aryl-based ligands. This method allows efficient arylation on silicon surfaces under mild conditions and the resulting aryl-functionalized SiNCs exhibit strong blue emissions with nanosecond-scaled decay.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Julia O. Strelnikova, Alexander N. Koronatov, Nikolai Rostovskii, Alexander F. Khlebnikov, Olesya Khoroshilova, Mariya A. Kryukova, Mikhail S. Novikov
Summary: The domino reaction catalyzed by Rh-2(Piv)(4) leads to the formation of N-sulfonylated (Z)-2-(2-aminovinyl)imidazoles, providing a direct and flexible access to the desired compounds.
Article
Chemistry, Physical
Natalia Rodriguez Quiroz, Tso-Hsuan Chen, Stavros Caratzoulas, Dionisios G. Vlachos
Summary: We report the direct Brønsted acid-catalyzed glucose dehydration in methyl isobutyl ketone solvent doped with small fractions of water to a high yield of 5-hydroxymethylfurfural (HMF) without using a Lewis acid catalyst. Our findings highlight the importance of solvent selection in facilitating the desired reaction and minimizing undesired byproducts.
Article
Chemistry, Organic
Gary L. Points, Christopher M. Beaudry
Summary: Substituted carbazoles are efficiently synthesized from 3-triflato-2-pyrones and alkynyl anilines, allowing for multiple substituents with complete control of regiochemistry, resulting in complex substitution patterns. This strategy can also be applied to prepare substituted bicarbazoles and related biaryls, and has been demonstrated in the synthesis of the carbazole natural product clausine C.
Article
Chemistry, Organic
Tao Wang, Wen-Bin Wang, Yan-Ming Fu, Cheng-Feng Zhu, Lan-Jun Cheng, Yang-En You, Xiang Wu, You-Gui Li
Summary: An asymmetric double oxidative [3 + 2] cycloaddition is reported, which generates highly functionalized chiral CF3-containing spiro[pyrrolidin-3,2'-oxindole] with four contiguous stereocenters stereoselectively. This method directly constructs two C-C bonds from four C(sp3)-H bonds, and it features mild conditions, broad substrate scope, and excellent functional group compatibility.
Article
Chemistry, Organic
Yan Jiang, Hao-Jie Ma, Xue-Long Wang, Yi Yang
Summary: A new compound was synthesized successfully in this study by using Yb-(OTf)(3) catalyst to react donor-acceptor cyclopropanes with sulfur-containing 4π components. The reaction showed high yields and moderate to good diastereoselectivity.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Marlene Fadel, Erick M. Carreira
Summary: The first total synthesis of (+)-pedrolide, a tigliane-derived diterpenoid featuring an unprecedented 5-5-6-6-3 carbon skeleton, was achieved. A key step in the synthesis involved the construction of the bicyclo[2.2.1]heptane core via an intramolecular cyclopentadiene-Diels-Alder cycloaddition. A norbornadiene was used as a surrogate for cyclopentadiene, and the unmasking of the cyclopentadiene was achieved through a complex Diels-Alder reaction cascade. This synthesis also provided a novel approach to a densely functionalized carane in an efficient and enantioselective manner.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
S. Gopi Sathi, E. Harea, A. Machu, R. Stocek
Summary: This study investigates the curing behavior of natural rubber with different bismaleimides in an accelerated-sulfur system, showing that Maleide F interacts directly with NR to form stable bismaleimide crosslinks, while Perkalink 900 does not. A synergistic combination of Maleide F and Perkalink has been identified as necessary for high-temperature curing without reversion.
EXPRESS POLYMER LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Gleb M. Averochkin, Evgeniy G. Gordeev, Matvei K. Skorobogatko, Fedor A. Kucherov, Valentine P. Ananikov
Summary: This study explores the reaction space of furanics-to-aromatics conversion process for HMF-based platform chemicals through experimental and quantum chemistry methods. A structure-activity relationship for furan-yne cycloaddition in different HMF derivatives was established, along with correlations between activation energy and substrate structure. Analysis of cycloaddition mechanisms in singlet and triplet electronic states was conducted, leading to the synthesis of biobased 7-oxanorbornadienes and examination of various aromatization methods for the obtained adducts.
Article
Chemistry, Physical
Jia-Ning Wang, Yuanfei Xue, Pengfei Li, Xiaoliang Pan, Meiting Wang, Yihan Shao, Yan Mo, Ye Mei
Summary: In silico investigations of enzymatic reactions and chemical reactions in condensed phases often require expensive computational resources due to the high number of degrees of freedom and large phase space. Reference-potential methods provide an alternative approach to achieve accurate simulations without significant loss of efficiency. This Perspective summarizes the concept of reference-potential methods, showcases recent applications, discusses pitfalls, and presents remedies.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Review
Biochemistry & Molecular Biology
Yaoyukun Jiang, Xinchun Ran, Zhongyue J. Yang
Summary: Identifying function-enhancing enzyme variants is a challenging task in protein science, and data-driven strategies, such as statistical modeling and machine learning, have advanced our understanding of enzyme relationships. These approaches have facilitated the prediction and design of new enzymes for catalyzing new reactions.
PROTEIN ENGINEERING DESIGN & SELECTION
(2023)
Review
Chemistry, Multidisciplinary
Carole A. Bewley, Gary A. Sulikowski, Zhongyue J. Yang, Giuseppe Bifulco, Hyo-Moon Cho, Christopher R. Fullenkamp
Summary: Natural products, produced by enzymatic assembly lines, have played a crucial role in the discovery of antibiotics, antineoplastics, and therapeutics. They have unique three-dimensional shapes and stereochemistry, which determine their diverse functions and biological activities. With advancements in methods and tools, research on atropisomerism in natural products and related scaffolds is progressing.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Engineering, Environmental
Lei Jiang, Ning Han, Tingting Luo, Zhe Zhang, Fenghao Liang, Daoning Wu, Xiaochun Li, Fengjiao Liu, Yichuan Rui, Wei Zhang, Yi Qu, Bohejin Tang
Summary: The solid molten salt-Fe2O3@Polypyrrole (SMS-Fe2O3@PPy) materials have been successfully synthesized and applied as anode electrode for lithium-ion batteries (LIBs) through a two-step method. The SMS-Fe2O3@PPy electrode consists of Fe-based solid molten salt (SMS), PPy, and octahedral Fe2O3 nanoparticles. The introduction of PPy not only provides a coating to suppress volume expansion but also improves the electrical conductivity, effectively reducing the volume expansion during Li+ insertion/extraction. The SMS-Fe2O3@PPy electrode exhibits excellent electrochemical performance, including high reversible capacities, good cycle stability, and excellent rate performance.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Medicinal
Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang
Summary: LassoHTP is a software developed for automatic construction and modeling of lasso peptide structures, enabling efficient prediction and design of lasso peptides. The software was used to construct eight known lasso peptide structures and simulate their conformational ensembles. The results show that the LassoHTP-initiated ensembles are similar to those initiated from the PDB structures. LassoHTP provides a computational platform for lasso peptide prediction and design.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Songyuan Yao, Richard Van, Xiaoliang Pan, Ji Hwan Park, Yuezhi Mao, Jingzhi Pu, Ye Mei, Yihan Shao
Summary: Inspired by recent work, this study investigates the possibility of deriving an implicit solvent model from explicit solvent molecular dynamics simulations using machine learning techniques. The authors successfully trained a machine learning potential for alanine dipeptide to capture its interactions with the average solvent environment configuration. The predicted forces and free energy surface were in good agreement with reference values, demonstrating the potential of machine learning-based implicit solvent models for ab initio-QM MD simulations.
Review
Chemistry, Multidisciplinary
Wook Shin, Zhongyue J. Yang
Summary: Computational simulations of entropy play a crucial role in understanding the thermodynamics of chemical reactions at the molecular scale. This review highlights four specific methods used for calculating entropy: normal mode analysis, free volume theory, two-phase thermodynamics, and configurational entropy modeling. The technical aspects, applications, and limitations of each method are discussed in detail.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Chemistry, Physical
Wook Shin, Xinchun Ran, Zhongyue J. Yang
Summary: The study focuses on understanding the role of entropy in chemical reactions and developing a more efficient method for computing entropic profiles. The authors utilized a deep generative model to accelerate the computation of entropy along reaction trajectories. The new approach, called bidirectional generative adversarial network-entropic path sampling, successfully reproduced reference entropic profiles using significantly fewer trajectories. The method was further validated with three reactions, revealing the presence of a hidden entropic intermediate.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Jia-Ning Wang, Yuanfei Xue, Pengfei Li, Xiaoliang Pan, Meiting Wang, Yihan Shao, Yan Mo, Ye Mei
Summary: In silico investigations of enzymatic reactions and chemical reactions in condensed phases often require expensive computational resources due to the high number of degrees of freedom and large phase space. Reference-potential methods provide an alternative approach to achieve accurate simulations without significant loss of efficiency. This Perspective summarizes the concept of reference-potential methods, showcases recent applications, discusses pitfalls, and presents remedies.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Alina Thokkadam, Truc Do, Xinchun Ran, Mark P. Brynildsen, Zhongyue J. Yang, A. James Link
Summary: The Burkholderia cepacia complex (Bcc) is a group of bacteria that can cause serious infections in immunocompromised individuals and cystic fibrosis patients. Ubonodin, a lasso peptide, has shown potential in inhibiting Bcc species by targeting RNA polymerase. Through a high-throughput screening and next-generation sequencing, a library of over 90,000 ubonodin variants was created, providing valuable insights into the structure-activity relationship of ubonodin. One variant with improved activity and a submicromolar minimum inhibitory concentration (MIC) against Burkholderia cenocepacia, a Bcc member, was identified. Additionally, some variants had lower MICs against certain Bcc strains compared to clinically approved antibiotics. The large library size also allowed the development of DeepLasso, a deep learning model for predicting the RNAP inhibitory activity of ubonodin variants.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Medicinal
Qianzhen Shao, Yaoyukun Jiang, Zhongyue J. Yang
Summary: This study developed a computational directed evolution protocol based on EnzyHTP and implemented an adaptive resource allocation strategy to improve throughput efficiency. The application of adaptive resource allocation saved significant amounts of CPU and GPU hours. Furthermore, the protocol successfully identified target variants in experimental screenings.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Review
Chemistry, Physical
Zhongyue J. Yang, Qianzhen Shao, Yaoyukun Jiang, Christopher Jurich, Xinchun Ran, Reecan J. Juarez, Bailu Yan, Sebastian L. Stull, Anvita Gollu, Ning Ding
Summary: Protein engineering is a promising field in biomedicine and biotechnology, and Mutexa is a computational ecosystem designed to enable intelligent protein engineering. Researchers can use Mutexa to obtain protein variants with desired functions and apply them in various areas.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Organic
Yi Sun, Fengjiao Liu, Jacob N. Sanders, K. N. Houk
Summary: The influence of steric effects on the rates of hydrogen atom transfer reactions between oxyradicals and alkanes is explored computationally. The study shows that bulky substituents on the radical significantly affect activation barriers and reaction enthalpies, while substituents on the alkane have little effect. The results suggest that the Evans-Polanyi relationship can still describe the HAT reactions between bulky molecules even when steric repulsion effects become important.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Chemistry, Physical
Peipei Jin, Jia-Ning Wang, Xueli Wang, Menghui Jia, Haifeng Pan, Ye Mei, Jinquan Chen
Summary: Methylation of cytosine at the C5 position is highly correlated with mutational hotspots in diseases such as skin cancer. However, the photophysical and photochemical properties of dinucleotides and polynucleotides containing 5-methylcytosine (C-5m) are still unclear. In this study, a charge transfer triplet state generated by intersystem crossing from a charge transfer singlet state is observed for the first time in the (TC)-C-5m dimer using femtosecond transient absorption and time-resolved mid-infrared spectroscopy.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Medicinal
Reecan J. Juarez, Yaoyukun Jiang, Matthew Tremblay, Qianzhen Shao, A. James Link, Zhongyue J. Yang
Summary: Lasso peptides are ribosomally synthesized and posttranslationally modified peptides with a slipknot conformation, showing great potential in bioengineering and pharmaceutical applications. To facilitate computational prediction and design of lasso peptides, we developed a software called LassoHTP, which enables automatic structure construction and modeling. LassoHTP has been successfully used to generate de novo structures and simulate conformational ensembles for known lasso peptides.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Xinchun Ran, Yaoyukun Jiang, Qianzhen Shao, Zhongyue J. Yang
Summary: EnzyKR is a new approach based on a deep learning framework for predicting enantiomeric outcomes in hydrolase-catalyzed kinetic resolution reactions. It automates the selection of enzyme scaffolds for separating a racemic substrate mixture and achieves good prediction performance using a structure-based encoding strategy.
