Article
Chemistry, Medicinal
Masato Sumita, Kei Terayama, Ryo Tamura, Koji Tsuda
Summary: This article introduces a Python library called QCforever, which automates the computation of molecular properties and chemical phenomena. By incorporating this tool, it is possible to explore molecules with desired properties within the framework of black-box optimization.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Medicinal
Raghuram Srinivas, Niraj Verma, Elfi Kraka, Eric C. Larson
Summary: In this study, the implicit fingerprint method is extended using deep learning techniques to translate latent descriptors into discrete representations of molecules. The generated compounds exhibit properties of chemically feasible compounds and are predicted to be excellent binders to known proteins, indicating the effectiveness of the approach in designing new drug-like compounds.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Nuclear Science & Technology
Marco Colombo, Roland Rzehak, Michael Fairweather, Yixiang Liao, Dirk Lucas
Summary: This paper benchmarks CFD models developed at the University of Leeds and Helmholtz-Zentrum Dresden-Rossendorf against a large database of bubbly flows in vertical pipes, aiming to identify a universal set of widely applicable closures. The focus is on interfacial momentum transfer and turbulence modeling closures, with the models proving to be reliable and robust over the tested parameters. Areas for further development are identified, and a benchmark is established for testing other models in the future.
NUCLEAR ENGINEERING AND DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Ryan D. D. Cohen, Jared S. S. Wood, Yu-Hong Lam, Alexei V. V. Buevich, Edward C. C. Sherer, Mikhail Reibarkh, R. Thomas Williamson, Gary E. E. Martin
Summary: Density functional theory (DFT) benchmark studies were conducted to evaluate the accuracy of predicting H-1 and C-13 NMR chemical shifts. A carefully selected dataset of 50 small organic molecules was used to assess the performance of different DFT methodologies, basis sets, solvent models, and gauge-referencing schemes. The best results were obtained using WP04/6-311++G(2d,p) and omega B97X-D/def2-SVP for H-1 and C-13 NMR chemical shift predictions, respectively, when combined with the PCM solvent model and GIAO method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions for 20 organic compounds and natural products showed good agreement with experimental values, with maximum deviations of less than 0.5 ppm for H-1 and 6.5 ppm for C-13.
Article
Environmental Sciences
Pietro Cozzini, Francesca Cavaliere, Giulia Spaggiari, Gianluca Morelli, Marco Riani
Summary: According to Eurostat, the production of hazardous chemicals in the EU reached 211 million tonnes in 2019, which has attracted considerable attention from the scientific community. Due to the large number of chemical compounds, it is impossible to identify all possible toxic interactions using traditional in vitro/in vivo tests. Therefore, this study uses computational approaches to screen the interactions of food contact chemicals with the nuclear receptor family, providing a cost and time-effective solution.
Article
Biochemistry & Molecular Biology
Mahfuzur Rahman, Maximilian Billmann, Michael Costanzo, Michael Aregger, Amy H. Y. Tong, Katherine Chan, Henry N. Ward, Kevin R. Brown, Brenda J. Andrews, Charles Boone, Jason Moffat, Chad L. Myers
Summary: FLEX is a pipeline that establishes reference standards for benchmarking human genome-wide CRISPR screen data, identifying a predominant mitochondria-associated signal within co-essentiality networks. By characterizing functional bias associated with mitochondria genes, it provides insights into interpreting differential hits in CRISPR screening. The utility of the FLEX pipeline for performing robust comparative evaluations of CRISPR screens or methods for processing them is demonstrated.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Elif Sorkun, Qi Zhang, Abhishek Khetan, Murat Cihan Sorkun, Suleyman Er
Summary: An increasing number of electroactive compounds have been explored for high-performance redox flow batteries for grid-scale energy storage. High-throughput virtual screening approaches are indispensable tools for accessing the physicochemical properties of these compounds in a speedy way. This study presents RedDB, a computational database containing 31,618 molecules from two classes of organic electroactive compounds, and provides useful information for battery performance.
Article
Multidisciplinary Sciences
Kevin Spiekermann, Lagnajit Pattanaik, William H. Green
Summary: Quantitative chemical reaction data is crucial for understanding reaction kinetics and predicting reaction outcomes, but high-quality data is often difficult to obtain. In this study, we used quantum chemistry calculations to generate a kinetics dataset for nearly 12,000 gas-phase reactions, involving various elements and heavy atoms.
Article
Chemistry, Medicinal
Xujun Zhang, Chao Shen, Ben Liao, Dejun Jiang, Jike Wang, Zhenxing Wu, Hongyan Du, Tianyue Wang, Wenbo Huo, Lei Xu, Dongsheng Cao, Chang-Yu Hsieh, Tingjun Hou
Summary: The development of accurate machine-learning-based scoring functions for virtual screening requires unbiased and diverse datasets. However, most existing datasets may suffer from hidden biases and data insufficiency. In this study, we developed a new approach named TocoDecoy to generate unbiased and expandable datasets, and evaluated its performance compared to other datasets.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Tobias Hilche, Tim Krebs, Hendrik Weissbarth, Fabian Lang, Gregor Schnakenburg, Andreas Gansaeuer
Summary: The synthesis of enantiomerically pure titanocenes is currently limited to cases with enantiomerically pure substituents at the cyclopentadienyl ligands and to ansa-titanocenes. Here, a new synthetic method is introduced using enantiomerically pure camphorsulfonate (CSA) ligands to control the absolute and relative configuration of titanocene complexes. The desired enantiomerically and diastereomerically pure complexes can be obtained in just two steps.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Chemistry, Physical
Sebastian Spicher, Eike Caldeweyher, Andreas Hansen, Stefan Grimme
Summary: Charged atoms or molecules interacting with pi-systems through ion-pi interactions play a major role in various chemical and biological systems. This study compiled a molecular test set IONPI19 to evaluate different density functional approximations for interaction energies, finding that the double-hybrids PWPB95-D4/QZ and revDSD-PBEP86-D4/QZ are the most reliable methods for describing ion-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Medicinal
Yuqi Zhang, Marton Vass, Da Shi, Esam Abualrous, Jennifer M. Chambers, Nikita Chopra, Christopher Higgs, Koushik Kasavajhala, Hubert Li, Prajwal Nandekar, Hideyuki Sato, Edward B. Miller, Matthew P. Repasky, Steven Jerome
Summary: The AlphaFold2 (AF2) algorithm predicts proteins' 3D structures from amino acid sequences. The open AlphaFold protein structure database covers the complete human proteome. Through virtual screening, AF2 structures show comparable early enrichment of known active compounds to apo structures, and with refinement using an induced-fit protocol, the performance in structure-based virtual screening can be improved. Thus, AF2 structures hold promise for in silico hit identification.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Pantaleo Musci, Marco Colella, Angela Altomare, Giuseppe Romanazzi, Nadeem S. Sheikh, Leonardo Degennaro, Renzo Luisi
Summary: This study demonstrates the stereoconvergence of the lithiation reaction of enantiomerically enriched N-alkyl 2-oxazolinylazetidines, leading to highly stereoselective products. The dynamics at the azetidine nitrogen atom and the inversion at the C-Li center contribute to the configurational instability of the diastereomeric lithiated azetidines.
Article
Construction & Building Technology
Miles J. S. Gulliford, Richard H. Orlebar, Max H. Bird, Salvador Acha, Nilay Shah
Summary: This study introduces a novel benchmarking method to evaluate the emission and cost performances of food retail stores, and proposes a benchmark for investment decision-making. The decision tree technique is found to be the most effective, accurately classifying buildings and highlighting the need for further research on natural gas consumption benchmarking and humidity data.
ENERGY AND BUILDINGS
(2022)
Article
Construction & Building Technology
Xuan Zhou, Yukun Mei, Liequan Liang, Zhubing Fan, Junwei Yan, Dongmei Pan
Summary: This study aims to develop a dynamic room-level energy benchmarking method to evaluate energy performance of all rooms in an office building. By analyzing room types and energy consumption patterns, it provides detailed information to help building managers and engineers develop targeted energy-saving measures. The potential energy saving for each room accounts for 24.69% of the total energy consumption, and the energy benchmarking could be periodically updated with increasing awareness of occupants for energy conservation.
JOURNAL OF BUILDING ENGINEERING
(2021)
Article
Energy & Fuels
Qi Lei, Qianli Si, Ji Zhang, Yifeng Jiang, Long Hu, Liang Qiao, Xiaotao Zu, Gang Xiao, Jack Yang, Sean Li
Summary: This study investigated the thermal properties of CaMnO3, a perovskite manganite, for its potential application in high-temperature redox cycling. The material demonstrated high energy storage capacity and stability, making it a promising energy storage material for future solar thermal power plants.
Article
Chemistry, Multidisciplinary
Chao Cai, Shaobo Han, Xiaotao Zhang, Jingxia Yu, Xia Xiang, Jack Yang, Liang Qiao, Xiaotao Zu, Yuanzheng Chen, Sean Li
Summary: The oxygen evolution reaction (OER) has been a focus of research in water electrolysis. In this study, the authors used single-atom Au doped Co-based nanosheets to evaluate the OER activity and the interaction between Co and Au. The results showed that Au-Co(OH)(2) nanosheets exhibited superior performance compared to state-of-the-art Co-based catalysts. The authors also provided new insights into the mechanisms of OER activity and the synthesis of efficient OER electrocatalysts.
Article
Nanoscience & Nanotechnology
Xun Geng, Tianci Chang, Jiaxin Fan, Yu Wang, Xiaotian Wang, Yunlong Sun, Premkumar Selvarajan, Chuang Liu, Chun-Ho Lin, Xiaolin Wang, Jack Yang, Zhenxiang Cheng, Kourosh Kalantar-Zadeh, Xun Cao, Danyang Wang, Ajayan Vinu, Jiabao Yi, Tom Wu
Summary: Cobalt-doped VO2 thin films were successfully fabricated in this study, with the highest doping concentration reducing the transition temperature of VO2 and increasing the luminous transmittance. Experimental and modeling analysis provided a comprehensive explanation of the effects of cobalt doping on VO2 properties, highlighting the promising future of cobalt-doped VO2 in smart window applications.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Chemistry, Inorganic & Nuclear
Yuqi Zhang, Jack Yang, Riyue Ge, Jiujun Zhang, Julie M. Cairney, Ying Li, Mingyuan Zhu, Sean Li, Wenxian Li
Summary: Single-atom catalysts (SACs) have emerged as a promising solution to enhance catalytic efficiency and reduce costs. However, the agglomeration of metal atoms in SACs remains a challenge. Strong coordination bonds between single-atoms and their supports can address this issue. Characterization of SACs at the atomic level is crucial to identify and regulate the coordination environments of single-atoms.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Chemistry, Physical
Shuangyue Wang, Ni Yang, Mengyao Li, Ji Zhang, Ashraful Azam, Yin Yao, Xiaotao Zu, Liang Qiao, Peter Reece, John Stride, Jack Yang, Sean Li
Summary: The step edges and intrinsic atomic structure of single-crystal substrate play a crucial role in determining the growth pathways of transition metal dichalcogenide grains. The substrate can modulate the orientation and morphology of the grains. Oxygen treatment on the substrate and its structural anisotropy also affect the growth behavior.
Article
Multidisciplinary Sciences
Jing-Kai Huang, Yi Wan, Junjie Shi, Ji Zhang, Zeheng Wang, Wenxuan Wang, Ni Yang, Yang Liu, Chun-Ho Lin, Xinwei Guan, Long Hu, Zi-Liang Yang, Bo-Chao Huang, Ya-Ping Chiu, Jack Yang, Vincent Tung, Danyang Wang, Kourosh Kalantar-Zadeh, Tom Wu, Xiaotao Zu, Liang Qiao, Lain-Jong Li, Sean Li
Summary: The scaling of silicon metal-oxide-semiconductor field-effect transistors has been successful, but with the thinning of silicon at smaller technology nodes, new challenges arise. In this study, researchers explore the use of ultrahigh-kappa single-crystalline perovskite strontium-titanium-oxide membranes as gate dielectrics for 2D field-effect transistors. These membranes have desirable properties and can mitigate the issues related to using ultrahigh-kappa dielectrics.
Review
Chemistry, Applied
Huidong Xu, Jack Yang, Riyue Ge, Jiujun Zhang, Ying Li, Mingyuan Zhu, Liming Dai, Sean Li, Wenxian Li
Summary: This article reviews different types of bifunctional ORR/OER electrocatalysts with activated surface sites and discusses methods to improve catalytic performance by controlling the microstructure of the catalysts and optimizing their electronic structures. It also analyzes the challenges in structural design and surface engineering of bifunctional ORR/OER catalysts and proposes potential solutions.
JOURNAL OF ENERGY CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jiaxin Fan, Wenxian Li, Sean Li, Jack Yang
Summary: Ammonia has gained attention as a carrier for hydrogen usage in the hydrogen economy, but new synthesis techniques are needed to overcome high energy consumption. Chemical looping ammonia synthesis (CLAS) is a promising approach, but ideal redox materials are yet to be discovered. This study screens 1699 bicationic redox pairs using the MP database and employs machine learning to broaden the search for potential redox materials. Bicationic compounds containing alkali/alkaline-earth metals and transition metal/metalloid elements show promise in CLAS.
Article
Green & Sustainable Science & Technology
Jiancheng Li, Yao Xu, Liping Liang, Riyue Ge, Jack Yang, Bin Liu, Jing Feng, Ying Li, Jiujun Zhang, Mingyuan Zhu, Sean Li, Wenxian Li
Summary: The development of efficient catalysts is essential for utilizing green energy in clean electrochemical energy conversion systems. In this study, cobalt phosphides nanorods anchored in N-doped carbon nanosheets were synthesized through a cation-induced strategy. The optimized Co2P/CoP-NC nanomaterial exhibited high catalytic activity for both the HER and OER in alkaline media, as well as considerable durability.
SUSTAINABLE MATERIALS AND TECHNOLOGIES
(2022)
Article
Nanoscience & Nanotechnology
Riyue Ge, Juanli Zhao, Juanjuan Huo, Jiangtao Qu, Jack Yang, Ying Li, Mingyuan Zhu, Julie M. Cairney, Rongkun Zheng, Sean Li, Jiujun Zhang, Bin Liu, Wenxian Li
Summary: In this study, a Ni/Mo2C@NC electrocatalyst was fabricated through interfacial engineering, which exhibited excellent hydrogen evolution reaction (HER) activity and stability in alkaline solution, providing a high-performance catalyst for water splitting.
MATERIALS TODAY NANO
(2022)
Review
Chemistry, Applied
Yao Xu, Riyue Ge, Jack Yang, Jiancheng Li, Sean Li, Ying Li, Jiujun Zhang, Jing Feng, Bin Liu, Wenxian Li
Summary: This paper comprehensively reviews MoS2-based electrocatalysts for hydrogen evolution reaction (HER), focusing on the manipulation of crystal structure, microstructure, surface, and interface to enhance their catalytic performance. Recent advances in surface/interface engineering are analyzed, and the perspectives, challenges, and future research directions of HER electrocatalysis are discussed.
JOURNAL OF ENERGY CHEMISTRY
(2022)
Article
Green & Sustainable Science & Technology
Yuqi Zhang, Haobo Liu, Riyue Ge, Jack Yang, Sean Li, Yang Liu, Lingyan Feng, Ying Li, Mingyuan Zhu, Wenxian Li
Summary: Transition metal phosphides (TMPs) are promising materials for water splitting due to their high electrical conductivity and stability. Doping and constructing heterostructure electrocatalysts can optimize the catalytic activity and efficiency of TMPs.
SUSTAINABLE MATERIALS AND TECHNOLOGIES
(2022)
Article
Engineering, Electrical & Electronic
Ni Yang, Ji Zhang, Jing-Kai Huang, Yang Liu, Junjie Shi, Qianli Si, Jack Yang, Sean Li
Summary: The emergence of in-memory computing solves the high-power consumption and low efficiency problems of traditional computers. Memristors, which exhibit history-dependent conductivity modulation, can simulate synaptic behaviors in the brain. Researchers have successfully developed a memristor with various synaptic plasticity and stable switching responses over repetitive operating cycles.
ACS APPLIED ELECTRONIC MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Jack Yang, Sean Li
Summary: This study uses high-throughput computational screening to map out room-temperature stabilities and vibrational anharmonicity landscapes for 3819 cubic ABX(3) perovskites, finding that halides are systematically more stable and less anharmonic than oxides/chalcogenides. New metrics have been developed to quantify the significance of higher order force constants to the strong anharmonicities in room-temperature stable perovskites.
MATERIALS HORIZONS
(2022)
Article
Chemistry, Physical
Jiancheng Li, Riyue Ge, Panpan Lan, Jack Yang, Jing Feng, Ying Li, Sean Li, Bin Liu, Wenxian Li
Summary: In this study, a series of transition metal and MoC/Mo2C heterostructures catalysts were prepared through an in situ phase transition strategy, which effectively improved the kinetics of the hydrogen evolution reaction. The catalyst with 0.5% molar ratio of Co and Mo showed low overpotential and good stability.
JOURNAL OF MATERIALS CHEMISTRY A
(2022)