Article
Chemistry, Physical
Arkajyoti Sengupta, K. N. Houk
Summary: This study investigates the reaction mechanism for intramolecular cycloadditions of a heptafulvenyl-fulvene tethered by a trimethylene chain using quantum mechanical calculations and molecular dynamics simulations. The experimental reports of temperature dependence on the periselectivity of intramolecular cycloadditions are explained by the mechanistic details. Furthermore, additional calculations with multireference-based methods highlight the limitations of DFT methods and single-reference wavefunction-based CCSD(T) in describing the complete potential energy surface involving various cycloadditions of the heptafulvenyl-fulvene.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Multidisciplinary
Qingyang Zhou, Mathias K. Thogersen, Nomaan M. Rezayee, Karl Anker Jorgensen, K. N. Houk
Summary: The thermal dimerization of cycloheptatriene can occur through a concerted [6 + 4] cycloaddition via an ambimodal [6 + 4]/[4 + 6] transition state or a stepwise diradical (6 + 2) cycloaddition. The resulting dimers undergo intramolecular [4 + 2] cycloadditions to form thermally stable tetracyclic products. The energy barrier in cycloheptatriene dimerization is attributed to its high distortion energy. Experimental studies confirmed the predicted reaction pathways.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Hong Zhang, Mathias Kirk Thogersen, Cooper S. Jamieson, Xiao-Song Xue, Karl Anker Jorgensen, Kendall N. Houk
Summary: This study investigates the Diels-Alder reactions of tropolone and its conjugate base with N-methylmaleimide through computational and experimental approaches. The results reveal that the reaction forms both endo- and exo-products in similar, but variable amounts under basic conditions, with the endo-product being thermodynamically more stable. Computational explorations suggest the reaction involves an ambimodal transition state, and longer reaction times lead to a slight excess of the exo-product.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
Yike Zou, K. N. Houk
Summary: The study investigates the mechanism and dynamics of the formation of the delitschiapyrone family of natural products. It is found that under different conditions, different reaction pathways occur, and the presence of enzymes may lead to changes in product selectivity.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Cooper S. Jamieson, Arkajyoti Sengupta, K. N. Houk
Summary: Through quantum mechanical studies and molecular dynamics simulations, it was found that the cycloadditions of cyclopentadiene and cycloheptatriene with tropone involve ambimodal transition states, leading to a complex network of products. This general concept was supported by calculations of simple parent systems and a thorough meta-analysis of literature examples.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Mikk Kaasik, Pan-Pan Chen, Sebastijan Ricko, Karl Anker Jorgensen, K. N. Houk
Summary: This study describes the novel asymmetric aminocatalytic cycloadditions between formyl cycloheptatrienes and 6,6-dimethylfulvene. The reactions result in [4 + 2], [6 + 2], and [4 + 6] cycloadducts. The position of the formyl functionality in the cycloheptatriene core determines the reaction course and each formyl cycloheptatriene isomer exhibits distinct reactivity patterns.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Kenta Tanaka, Yosuke Asada, Yujiro Hoshino
Summary: Visible-light-induced [6+4] cycloaddition reactions of ortho-quinone methides have been developed as a promising tool for the synthesis of natural products and bioactive compounds that contain a benzoxepine structure.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Organic
Xiumei Liu, Wenhua Xu, Fang Fang, Nengni Xu, Zhishuang Lin, Xinjun Luan, Jinfeng Zhang, Hui Wang
Summary: This study reports the synthesis of polysubstituted azulen-6-ones through ring opening and scaffold rearrangement of spirocycles under the catalysis of ferric chloride at ambient conditions. Control experiments suggest a radical cation mechanism for the reaction, with theoretical calculations indicating the crucial role of electronic distribution in the oxidative rearrangement. Azulen-6-one 2a exhibits interesting photophysical properties, such as aggregation-induced emission, halochromism, and two-photon fluorescence, making them promising functional materials in optical-related fields.
Article
Chemistry, Organic
Maya L. Milrod, Brian H. Northrop
Summary: Thermally promoted cycloaddition reactions of tropone-3,4-dimethylester and cyclopentadiene have been investigated computationally, revealing that substitution of the tropone component with methyl esters leads to lower energy barriers, higher thermodynamic driving forces, and a greater number of possible reaction pathways.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
K. N. Houk, Xiao-Song Xue, Fang Liu, Yu Chen, Xiangyang Chen, Cooper Jamieson
Summary: The concept of pericyclic reactions was developed by Woodward and Hoffmann 56 years ago, and has been further studied through high-accuracy quantum mechanical calculations and computational methods in recent years. This has enriched our understanding of pericyclic reactions, outlining the subtleties of bond formation and the involvement of enzymes in catalyzing such reactions.
ISRAEL JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Ben-Hong Chen, Shuai-Jiang Liu, Qian Zhao, Qiumeng Hou, Jia-Li Yuan, Gu Zhan, Qian-Qian Yang, Wei Huang
Summary: Here, a palladium-catalyzed strategy is developed for the synthesis of a diverse set of chiral spiro derivatives of benzoxazine compounds by reacting vinyl benzoxazinanones with pyrazolone 4,5-diones. This method extends the application of vinyl benzoxazinanones with ketones and demonstrates broad substrate scope and functional group tolerance, with yields up to 76% and enantioselectivity up to 96% ee. The facile scale-up and conversion to diversified products confirm the synthetic utility of this approach.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yu-Jiao Wang, Li-Ming Zhao
Summary: A catalytic formal [6+4] cycloaddition reaction was developed for the synthesis of 10-membered azecines, which produced benzofuran-fused azecines with high diastereoselectivity in moderate to good yields through the reaction of delta-vinylvalerolactones and benzofuran-derived azadienes under palladium catalysis. The unique transformations involving the transannular reaction of these compounds for the construction of polycyclic compounds were also demonstrated.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Melissa Ramirez, Dennis Svatunek, Fang Liu, Neil K. Garg, Kendall N. Houk
Summary: The Diels-Alder reactions of furans and pyrroles with 1,2-cyclohexadiene and oxa- and azaheterocyclic analogs exhibit endo selectivity, which is determined by the interaction of molecular orbitals and electrostatic effects. This selectivity, based on stabilizing interactions, is expected to lead to the increased use of strained cyclic allenes in chemical synthesis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Georgia Gomatou, Ioannis Trontzas, Stephanie Ioannou, Maria Drizou, Nikolaos Syrigos, Elias Kotteas
Summary: CDK 4/6 inhibitors have shown promise in treating breast cancer, but patients often develop resistance. Studies indicate that resistance mechanisms involve aberrations of cell cycle molecules and rewiring of the cell to reduce dependence on CDK 4/6.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Jia Qiu, Yougen Xu, Shimin Su, Yadong Gao, Peiyuan Yu, Zhixiong Ruan, Kuangbiao Liao
Summary: This study developed an auto machine learning model to predict the yield of TEMPO-catalyzed oxidation reactions of primary alcohols. By utilizing a large dataset of high-throughput experimentation data and descriptors, the model demonstrated excellent predictive performance in independent and external tests, and revealed a new relevant descriptor for yield prediction.
CHINESE JOURNAL OF CHEMISTRY
(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
Chemistry, Applied
Velabo Mdluli, Dan Lehnherr, Yu-hong Lam, Yining Ji, Justin A. Newman, Jungchul Kim
Summary: A photochemical synthetic method for the synthesis of sulfones from aryl halides and sodium alkylsulfinates in the presence of CuCl is described. The sulfonylation of polyhalogenated arenes exhibits regio- and chemoselectivity. Mechanistic studies suggest the formation of a copper sulfinate reagent in situ from CuCl and sodium sulfinate, as evidenced by NMR experiments. Density functional theory calculations reveal energetically accessible non-planar triplet geometries for potential reaction intermediates, including excited state aryl halides.
ADVANCED SYNTHESIS & CATALYSIS
(2023)
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, Multidisciplinary
Le Wang, Wenfu Zheng, Leni Zhong, Yingkun Yang, Yao Chen, Qinghong Hou, Peiyuan Yu, Xingyu Jiang
Summary: This study focuses on the issues of drug resistance and high toxicity in vancomycin, and presents mercaptophenylboronic acid (MBA)-modified gold nanoclusters (Au-44(MBA)(18)) as a solution. The results show that Au-44(MBA)(18) exhibits excellent antibacterial activities against drug-resistant bacteria and can interact with bacteria by attaching to teichoic-acid and destroying the cell wall, as well as binding to bacterial DNA. It has multiple administration routes and high biosafety, making it a potential nanoantibiotic for treating multidrug-resistant bacterial infections.
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)
Proceedings Paper
Automation & Control Systems
Yunlong Hu, Peiyuan Yu, Bochen Teng, Jia Song
Summary: Compound-wing unmanned aerial vehicle (UAV) has broad application prospects in the industry due to its vertical take-off and landing and high-speed cruise functions. However, the level flight process of compound-wing UAV is interfered by the rotor, resulting in reduced control performance and flight stability. This paper presents a controller that effectively reduces rotor disturbances on the attitude of a compound-wing UAV.
PROCEEDINGS OF 2022 INTERNATIONAL CONFERENCE ON AUTONOMOUS UNMANNED SYSTEMS, ICAUS 2022
(2023)
Article
Chemistry, Organic
Jinxia Li, Dingyi Tang, Yu Zhang, Weichi Chen, Xiaoxi Su, Peiyuan Yu, Shuanglin Qu
Summary: Here, we investigate the mechanism and selectivity of the intramolecular cyclization of alkynones catalyzed by Ni catalysts using DFT computations. The Ni(0) catalyst system forms 5-exocyclic products, while the Ni(II) catalyst system generates 6-endocyclic or 5-exocyclic products due to different reaction pathways. The regioselectivity is determined by the alkyne insertion and the enantioselectivity is determined by the carbonyl insertion.
ORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Organic
Zhibin Yue, Boming Shen, Jie Cao, Xuling Chen, Fang Fang, Pengfei Li, Peiyuan Yu, Wenjun Li
Summary: With the use of chiral phosphoric acid as a catalyst, an enantioselective 1,6-addition of tryptamines to alkynyl 7-methylene-7H-indoles derived from tertiary alpha-(7-indolyl)methanols has been developed. This reaction provides a wide range of axially chiral tetrasubstituted allenes featuring indole and hexahydropyrrolo[2,3-b]indole units in good to high yields and with asymmetric induction. DFT calculations have been performed to elucidate the reaction mechanism and understand the origin of stereoselectivity.
ORGANIC CHEMISTRY FRONTIERS
(2023)
Article
Chemistry, Multidisciplinary
Ye-Hui Chen, Meng Duan, Si-Li Lin, Yu-Wei Liu, Jun Kee Cheng, Shao-Hua Xiang, Peiyuan Yu, Kendall N. Houk, Bin Tan
Summary: This article introduces an effective strategy for umpolung functionalization of imines through aromatization. The attachment of strongly electron-withdrawing groups to imines enhances their reactivity, enabling direct amination of (hetero)arenes. Additionally, the use of chiral catalysts allows for the synthesis of (hetero)aryl C-N atropisomers or enantioenriched aliphatic amines.
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.
Article
Chemistry, Multidisciplinary
Ming Wu, Yi-Wei Chen, Qian Lu, Yong-Bin Wang, Jun Kee Cheng, Peiyuan Yu, Bin Tan
Summary: Chiral organosilanes are important chemical entities in the development of functional organic materials, asymmetric catalysis, and medicinal chemistry. An efficient method for atroposelective synthesis of biaryl siloxane atropisomers via organocatalytic Si-C bond functionalization of dinaphthosiloles with silanol nucleophiles is presented. The reaction proceeds through an asymmetric protonation and simultaneous Si-C bond cleavage/silanolysis sequence in the presence of a newly developed chiral Bronsted acid catalyst. The versatile nature of the Si-C bond expands the applicability of this method.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)