Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第2页

Spillover Dynamics in Heterogeneous Catalysis on Singe-Atom Alloys: A Theoretical Perspective 单原子合金非均相催化的溢出动力学：一个理论视角

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-03-24 DOI: 10.1002/wcms.70011

Sutao Lin, Rui Xiong, Jun Chen, Sen Lin

{"title":"Spillover Dynamics in Heterogeneous Catalysis on Singe-Atom Alloys: A Theoretical Perspective","authors":"Sutao Lin, Rui Xiong, Jun Chen, Sen Lin","doi":"10.1002/wcms.70011","DOIUrl":"https://doi.org/10.1002/wcms.70011","url":null,"abstract":"<div>\u0000 \u0000 <p>Recent advances in single-atom alloy (SAA) catalysts provide a unique platform for understanding spillover, due to the well-defined nature of the active site for dissociative chemisorption. In particular, the use of spilled adsorbates following molecular dissociation on the host metal surface facilitates the generation of high-value chemicals in subsequent catalytic reactions. Nevertheless, the factors that control the spillover process remain to be fully elucidated. This perspective discusses recent theoretical advances in the spillover dynamics on SAAs, with a particular focus on the dissociation and spillover processes of H<sub>2</sub> and CH<sub>4</sub>. It provides valuable insights into how various factors, such as energy transfer, nuclear quantum effects, gas-adsorbate interactions, and adsorbate size, impact the diffusion behavior of hydrogen and methyl species on SAA surfaces. The article concludes with a discussion of future prospects. This perspective underscores the significance of spillover dynamics in heterogeneous catalysis, with important implications for improving catalytic performance.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing GPU-Acceleration in the Python-Based Simulations of Chemistry Frameworks 在基于 Python 的化学框架模拟中增强 GPU 加速能力

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-03-23 DOI: 10.1002/wcms.70008

Xiaojie Wu, Qiming Sun, Zhichen Pu, Tianze Zheng, Wenzhi Ma, Wen Yan, Yu Xia, Zhengxiao Wu, Mian Huo, Xiang Li, Weiluo Ren, Sheng Gong, Yumin Zhang, Weihao Gao

{"title":"Enhancing GPU-Acceleration in the Python-Based Simulations of Chemistry Frameworks","authors":"Xiaojie Wu, Qiming Sun, Zhichen Pu, Tianze Zheng, Wenzhi Ma, Wen Yan, Yu Xia, Zhengxiao Wu, Mian Huo, Xiang Li, Weiluo Ren, Sheng Gong, Yumin Zhang, Weihao Gao","doi":"10.1002/wcms.70008","DOIUrl":"https://doi.org/10.1002/wcms.70008","url":null,"abstract":"<div>\u0000 \u0000 <p>We describe our contribution as industrial stakeholders to the existing open-source GPU4PySCF project (https://github.com/pyscf/gpu4pyscf), a GPU-accelerated Python quantum chemistry package. We have integrated GPU acceleration into other PySCF functionalities including Density Functional Theory (DFT), geometry optimization, frequency analysis, solvent models, and the density fitting technique. Through these contributions, GPU4PySCF v1.0 can now be regarded as a fully functional and industrially relevant platform, which we demonstrate in this work through a range of tests. When performing DFT calculations with the density fitting scheme on modern GPU platforms, GPU4PySCF delivers a 30 times speedup over a 32-core CPU node, resulting in approximately 90% cost savings for most DFT tasks. The performance advantages and productivity improvements have been found in multiple industrial applications, such as generating potential energy surfaces, analyzing molecular properties, calculating solvation free energy, identifying chemical reactions in lithium-ion batteries, and accelerating neural-network methods. With the improved design that makes it easy to integrate with the Python and PySCF ecosystem, GPU4PySCF is a natural choice that we can now recommend for many industrial quantum chemistry applications.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances and Challenges of SCAN and r2SCAN Density Functionals in Transition-Metal Compounds 过渡金属化合物中SCAN和r2SCAN密度泛函的研究进展与挑战

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-03-23 DOI: 10.1002/wcms.70007

Yubo Zhang, Akilan Ramasamy, Kanun Pokharel, Manish Kothakonda, Bing Xiao, James W. Furness, Jinliang Ning, Ruiqi Zhang, Jianwei Sun

{"title":"Advances and Challenges of SCAN and r2SCAN Density Functionals in Transition-Metal Compounds","authors":"Yubo Zhang, Akilan Ramasamy, Kanun Pokharel, Manish Kothakonda, Bing Xiao, James W. Furness, Jinliang Ning, Ruiqi Zhang, Jianwei Sun","doi":"10.1002/wcms.70007","DOIUrl":"https://doi.org/10.1002/wcms.70007","url":null,"abstract":"<div>\u0000 \u0000 <p>Transition-metal compounds (TMCs) with open-shell <i>d</i>-electrons are characterized by a complex interplay of lattice, charge, orbital, and spin degrees of freedom, giving rise to various fascinating applications. Often exhibiting exotic properties, these compounds are commonly classified as correlated systems due to strong inter-electronic interactions called Hubbard <i>U</i>. This inherent complexity presents significant challenges to Kohn-Sham density functional theory (KS-DFT), the most widely used electronic structure method in condensed matter physics and materials science. While KS-DFT is, in principle, exact for the ground-state total energy, its exchange-correlation energy must be approximated in practice. The mean-field nature of KS implementations, combined with the limitations of current exchange-correlation density functional approximations, has led to the perception that DFT is inadequate for correlated systems, particularly TMCs. Consequently, a common workaround involves augmenting DFT with an on-site Hubbard-like <i>U</i> correction. In recent years, the <i>strongly constrained and appropriately normed</i> (SCAN) density functional, along with its refined variant r<sup>2</sup>SCAN, has achieved remarkable progress in accurately describing the structural, energetic, electronic, magnetic, and vibrational properties of TMCs, challenging the traditional perception of DFT's limitations. This review explores the design principles of SCAN and r<sup>2</sup>SCAN, highlights their key advancements in studying TMCs, explains the mechanisms driving these improvements, and addresses the remaining challenges in this evolving field.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing Molecular Dynamics Simulations of Electrical Double Layers: From Simplified to Realistic Models 加强电双层分子动力学模拟：从简化到现实模型

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-03-23 DOI: 10.1002/wcms.70009

Liang Zeng, Xiangyu Ji, Jinkai Zhang, Nan Huang, Zhenxiang Wang, Ding Yu, Jiaxing Peng, Guang Feng

{"title":"Enhancing Molecular Dynamics Simulations of Electrical Double Layers: From Simplified to Realistic Models","authors":"Liang Zeng, Xiangyu Ji, Jinkai Zhang, Nan Huang, Zhenxiang Wang, Ding Yu, Jiaxing Peng, Guang Feng","doi":"10.1002/wcms.70009","DOIUrl":"https://doi.org/10.1002/wcms.70009","url":null,"abstract":"<div>\u0000 \u0000 <p>Molecular dynamics (MD) simulations have become a powerful tool for studying double-layer systems, offering atomistic insights into their equilibrium properties and dynamic behaviors. These simulations have significantly advanced the understanding of key electrochemical mechanisms and the design of electrochemical devices. However, challenges remain in aligning simulations with the complexities of realistic applications. In this perspectiv, we highlight critical areas for enhancing the realism of MD simulations, including refining methods for representing electrode polarization, improving electrode and electrolyte models to incorporate structural and compositional complexities, and simulating charging and discharging processes under realistic conditions while considering associated thermal behaviors. We also stress the importance of scaling simulation results to experimental dimensions through multiscale modeling and dimensionless analysis. Overcoming these challenges will allow MD simulations to advance our understanding of electrical double-layer behaviors and drive innovations in the development of future electrochemical technologies.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insight Into the Dynamic Active Sites and Catalytic Mechanism for CO2 Hydrogenation Reaction CO2加氢反应动力学活性位点及催化机理研究

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-02-06 DOI: 10.1002/wcms.70006

You Han, Qin Hong, Chang-Jun Liu, Yao Nian

{"title":"Insight Into the Dynamic Active Sites and Catalytic Mechanism for CO2 Hydrogenation Reaction","authors":"You Han, Qin Hong, Chang-Jun Liu, Yao Nian","doi":"10.1002/wcms.70006","DOIUrl":"https://doi.org/10.1002/wcms.70006","url":null,"abstract":"<div>\u0000 \u0000 <p>The catalytic CO<sub>2</sub> hydrogenation to produce valuable fuels and chemicals holds immense importance in addressing energy scarcity and environmental degradation. Given that the real catalytic reaction system is complex and dynamic, the structure of catalysts might experience dynamic evolution under real reaction conditions. It implies that the real active sites might only generated during the reaction process. The induction factor of dynamic evolution of active sites could be reactants, intermediates, products, and other local chemical environments. Utilizing in-situ/operando characterization techniques allows for the real-time observation of the dynamic evolution process, further combining multiscale theoretical simulations can effectively reveal the refined structure of real active sites and catalytic mechanisms. Herein, we summarized the latest advancements in understanding the dynamic active sites and catalytic mechanisms during the real reaction process for the CO<sub>2</sub> hydrogenation to C<sub>1</sub> products (CH<sub>3</sub>OH, CO, and CH<sub>4</sub>). The dynamic evolutions of the catalyst in morphology, size, valence state, and interface between active component and support were discussed, respectively. Future research could benefit from more in-situ characterization and theoretical simulation to explore the microstructure and reaction mechanism, aiming to produce high conversion and selectivity catalysts for CO<sub>2</sub> hydrogenation reactions.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143248888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Condensed-Phase Quantum Chemistry 凝聚态量子化学

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-20 DOI: 10.1002/wcms.70005

Paul J. Robinson, Adam Rettig, Hieu Q. Dinh, Meng-Fu Chen, Joonho Lee

引用次数: 0

Time-Dependent Vibrational Coupled Cluster Theory With Static and Dynamic Basis Functions 具有静态和动态基函数的时变振动耦合聚类理论

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-19 DOI: 10.1002/wcms.70001

Mads Greisen Højlund, Alberto Zoccante, Andreas Buchgraitz Jensen, Ove Christiansen

{"title":"Time-Dependent Vibrational Coupled Cluster Theory With Static and Dynamic Basis Functions","authors":"Mads Greisen Højlund, Alberto Zoccante, Andreas Buchgraitz Jensen, Ove Christiansen","doi":"10.1002/wcms.70001","DOIUrl":"https://doi.org/10.1002/wcms.70001","url":null,"abstract":"<div>\u0000 \u0000 <p>In recent decades, coupled cluster theory has proven valuable in accurately describing correlation in many-body systems, particularly in time-independent computations of molecular electronic structure and vibrations. This review describes recent advancements in using coupled cluster parameterizations for time-dependent wave functions for the efficient computation of the quantum dynamics associated with the motion of nuclei. It covers time-dependent vibrational coupled cluster (TDVCC) and time-dependent modal vibrational coupled cluster (TDMVCC), which employ static and adaptive basis sets, respectively. We discuss the theoretical foundation, including many-mode second quantization, bivariational principles, and various parameterizations of time-dependent bases. Additionally, we highlight key features that make TDMVCC promising for future quantum dynamical simulations. These features include fast configuration-space convergence, the use of a compact adaptive basis set, and the possibility of efficient implementations with a computational cost that scales only polynomially with system size.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Strategies for Redesigning Withdrawn Drugs to Enhance Therapeutic Efficacy and Safety: A Review 重新设计已撤销药物以提高疗效和安全性的策略综述

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-19 DOI: 10.1002/wcms.70004

Chirag N. Patel, Adeeba Shakeel, Raghvendra Mall, Khadija M. Alawi, Ivan V. Ozerov, Alex Zhavoronkov, Filippo Castiglione

{"title":"Strategies for Redesigning Withdrawn Drugs to Enhance Therapeutic Efficacy and Safety: A Review","authors":"Chirag N. Patel, Adeeba Shakeel, Raghvendra Mall, Khadija M. Alawi, Ivan V. Ozerov, Alex Zhavoronkov, Filippo Castiglione","doi":"10.1002/wcms.70004","DOIUrl":"https://doi.org/10.1002/wcms.70004","url":null,"abstract":"<div>\u0000 \u0000 <p>Drug toxicity and market withdrawals are two issues that often obstruct the lengthy and intricate drug discovery process. In order to enhance drug effectiveness and safety, this review examines withdrawn drugs and presents a novel paradigm for their redesign. In addition to addressing methodological issues with toxicity datasets, this study highlights important shortcomings in in silico drug toxicity prediction models and suggests solutions. High-throughput screening (HTS) has greatly progressed with the advent of 3D organoid and organ-on-chip (OoC) technologies, which provide physiologically appropriate systems that replicate the structure and function of human tissue. These systems provide accurate, human-relevant data for drug development, toxicity evaluation, and disease modeling, overcoming the limitations of traditional 2D cell cultures and animal models. Their integration into HTS pipelines has shown to have a major influence, promoting drug redesign efforts and enabling improved accuracy in preclinical research. The potential of fragment-based drug discovery to enhance pharmacokinetics (PK) and pharmacodynamics (PD) when combined with conventional techniques is highlighted in this study. The limits of animal models are discussed, with a focus on the need of bioengineered humanized systems such OoC technologies and 3D organoids. To improve drug candidate screening and simulate real illnesses, advanced models are crucial. This leads to improved target affinity and fewer adverse effects.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age 人工智能时代来临之际酶反应性模拟的研究进展

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-19 DOI: 10.1002/wcms.70003

Katarzyna Świderek, Joan Bertran, Kirill Zinovjev, Iñaki Tuñón, Vicent Moliner

{"title":"Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age","authors":"Katarzyna Świderek, Joan Bertran, Kirill Zinovjev, Iñaki Tuñón, Vicent Moliner","doi":"10.1002/wcms.70003","DOIUrl":"https://doi.org/10.1002/wcms.70003","url":null,"abstract":"<p>The study of natural enzyme catalytic processes at a molecular level can provide essential information for a rational design of new enzymes, to be applied in more efficient and environmentally friendly industrial processes. The use of computational tools, combined with experimental techniques, is providing outstanding milestones in the last decades. However, apart from the complexity associated with the nature of these large and flexible biomolecular machines, the full enzyme catalyzed process involves different physical and chemical steps. Consequently, from the computational point of view, a deep understanding of every single step requires the selection of a proper computational technique to get reliable, robust and useful results. In this article, we summarize the different computational techniques and their use in the study of every single step of the catalytic process, including conformational diversity, allostery and those to study the chemical steps, as well as in the design of new enzymes. Because of the impact of artificial intelligence in all aspects of science during the last years, special attention has been applied to methods based on these techniques, their foundations and some selected recent applications.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Theoretical Investigation of Singlet Fission Processes in Organic Photovoltaics 有机光伏单线态裂变过程的理论研究

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-19 DOI: 10.1002/wcms.70002

Zhangxia Wang, Xiaoyu Xie, Haibo Ma

引用次数: 0