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

Building Nucleosome Positioning Maps: Discovering Hidden Gems 构建核小体定位图：发现隐藏的宝石

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-05-10 DOI: 10.1002/wcms.70029

Yosef Masoudi-Sobhanzadeh, Anisur Rahman, Shuxiang Li, Saman Bazmi, Sushant Kumar, Anna R. Panchenko

{"title":"Building Nucleosome Positioning Maps: Discovering Hidden Gems","authors":"Yosef Masoudi-Sobhanzadeh, Anisur Rahman, Shuxiang Li, Saman Bazmi, Sushant Kumar, Anna R. Panchenko","doi":"10.1002/wcms.70029","DOIUrl":"https://doi.org/10.1002/wcms.70029","url":null,"abstract":"<p>Nucleosomes serve as fundamental units of chromatin packaging and play a crucial role as central hubs in epigenetic regulation. Their positions throughout the genome are not random and follow certain patterns, influenced by DNA sequence, histone-DNA interactions, chromatin physical barriers, nucleosome sliding and unwrapping, and chromatin modifications. There are many experimental techniques for identifying nucleosome positions, but these methods often involve a trade-off between achieving high resolution and covering the entire genome. In this regard, computational approaches may offer a fast alternative, with the benefit of aiding experimental analysis by denoising data, refining nucleosome boundaries, and identifying features critical for nucleosome positioning. Moreover, computational predictions enable the integration of nucleosome positioning data with other genomic and epigenomic datasets, providing a more comprehensive view of chromatin organization and gene regulation. In this review, we focus on various nucleosome positioning methods, including experimental techniques of nucleosome boundaries identification and in silico methods of nucleosome positioning data denoising and prediction of nucleosome positioning from the DNA sequence.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143930298","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

Understanding Surface/Interface-Induced Chemical and Physical Properties at Atomic Level by First Principles Investigations 通过第一性原理研究了解表面/界面在原子水平上引起的化学和物理性质

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-05-06 DOI: 10.1002/wcms.70030

Jingyu Yang, Jinbo Pan, Shixuan Du

{"title":"Understanding Surface/Interface-Induced Chemical and Physical Properties at Atomic Level by First Principles Investigations","authors":"Jingyu Yang, Jinbo Pan, Shixuan Du","doi":"10.1002/wcms.70030","DOIUrl":"https://doi.org/10.1002/wcms.70030","url":null,"abstract":"<div>\u0000 \u0000 <p>The scientific trajectory in contemporary materials research has transitioned toward surface and interface engineering as critical determinants of functional performance, facilitating atomic-level precision in modulating physical and chemical properties for advanced applications spanning functional device architectures, catalytic systems, and electrochemical technologies. However, persistent challenges in atomic-scale characterization and the resource-intensive nature of empirical optimization necessitate systematic implementation of first-principles calculations to elucidate fundamental mechanisms underlying experimental observations and enable rational design of surface/interface modifications. This review examines three advancements in ab initio calculations for interfacial engineering: (1) revealing the mechanism of selective assembly and activation phenomena on surfaces, (2) theoretical predictions of interface engineering strategies, and (3) developing material databases with ionic/van der Waals components. We further address computational challenges while proposing quantum-mechanical methods to design next-gen materials with customized interfacial properties.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143914251","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

Ab Initio Vibrational Spectroscopy of Water and Aqueous Solutions in a Wide Pressure–Temperature Range 宽压力-温度范围内水和水溶液的从头算振动光谱

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-05-06 DOI: 10.1002/wcms.70017

Tao Li, Jiajia Huang, Chu Li, Cui Zhang, Ding Pan

{"title":"Ab Initio Vibrational Spectroscopy of Water and Aqueous Solutions in a Wide Pressure–Temperature Range","authors":"Tao Li, Jiajia Huang, Chu Li, Cui Zhang, Ding Pan","doi":"10.1002/wcms.70017","DOIUrl":"https://doi.org/10.1002/wcms.70017","url":null,"abstract":"<p>Vibrational spectroscopy is commonly applied for investigating the chemical and physical properties of water and aqueous solutions. Ab initio spectroscopy methods are used to analyze experimental spectra, offering valuable insights into structural and dynamic properties. In cases where experimental data is limited or contentious for aqueous systems subjected to high pressure–temperature conditions or extreme spatial confinement, ab initio methods can provide guidance for experiments. Recent progress in algorithms and computational power has driven substantial development in ab initio spectroscopy. In this review, we summarize first principles methods for calculating dipole moments and electronic polarizabilities, as well as demonstrate the use of time correlation functions for calculating infrared (IR) and Raman spectra. Additionally, we summarize recent advances in machine learning methods developed to expedite spectrum calculations and discuss the existing challenges that require further advancements in the field.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143909189","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

Multiscale Simulations and Property Predictions for Organic Luminescent Aggregates 有机发光聚集体的多尺度模拟与性质预测

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-28 DOI: 10.1002/wcms.70021

Xiaoyan Zheng, Qian Peng

{"title":"Multiscale Simulations and Property Predictions for Organic Luminescent Aggregates","authors":"Xiaoyan Zheng, Qian Peng","doi":"10.1002/wcms.70021","DOIUrl":"https://doi.org/10.1002/wcms.70021","url":null,"abstract":"<div>\u0000 \u0000 <p>Precise regulation of aggregation-state luminescence is a crucial and challenging task in the field of organic luminescence. The luminescence properties of organic molecular aggregates are intricately governed by both molecular conformations and intermolecular packing structures. The inherent conformational flexibility and the cooperative interplay of diverse intermolecular interactions in organic molecular aggregates give rise to numerous kinetically stable states besides the thermodynamically stable state, as well as multi-level couplings associated with excited states, which make the prediction of luminescent properties extraordinarily complicated and challenging. In this review, we first introduce a general theoretical protocol that combines multiscale modeling, kinetic network model, and excited-state decay rate theory. Then, the mechanism of luminescence and its regulation are presented for various organic molecular aggregates ranging from homogenous crystals, cocrystals, heterogenous amorphous aggregates, to kinetically controlled assemblies. Importantly, the mapping relationship is established between the formation processes of organic molecular aggregates and the corresponding dynamic luminescent properties, which provide valuable insights for a deeper understanding of aggregation-state luminescent properties and facilitate the precise regulation of organic luminescent materials.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143879869","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

Software Update: The ORCA Program System—Version 6.0 软件更新：ORCA程序系统6.0版本

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-28 DOI: 10.1002/wcms.70019

Frank Neese

引用次数: 0

Everything You Want to Know About Coarse-Graining and Never Dared to Ask: Macromolecules as a Key Example 您想知道却从未敢问的粗粒度问题：以大分子为例

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-23 DOI: 10.1002/wcms.70022

Marina G. Guenza

{"title":"Everything You Want to Know About Coarse-Graining and Never Dared to Ask: Macromolecules as a Key Example","authors":"Marina G. Guenza","doi":"10.1002/wcms.70022","DOIUrl":"https://doi.org/10.1002/wcms.70022","url":null,"abstract":"<p>Coarse-graining (CG) is transforming the study of molecular systems, allowing researchers to explore by computer simulations larger and more complex structures than ever before. Continued advancements in CG techniques are making simulations more efficient, establishing this approach as a cornerstone for designing innovative materials and eco-friendly alternatives to traditional plastics. Additionally, CG methods are becoming indispensable for unraveling the complexities and functional mechanisms of large-scale macromolecular machines within cells. Yet, crafting an effective coarse-grained model demands a nuanced understanding of its advantages and limitations. Faster simulations come at the cost of molecular detail and accuracy in some properties, so that it is essential to balance computational efficiency with the specific needs of the system one wants to simulate. By asking the right questions, researchers can select models that offer the desired benefits while managing trade-offs. This article delves into the potential of different CG models and the compromises inherent in their adoption, highlighting their role in shaping the future of material science and biophysics.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865553","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

Recent Progresses in Two-Dimensional Carbon-Metal Composites for Catalysis Applications 用于催化应用的二维碳-金属复合材料的最新进展

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-16 DOI: 10.1002/wcms.70014

Yongjie Zhang, Kah-Meng Yam, Hao Wang, Na Guo, Chun Zhang

{"title":"Recent Progresses in Two-Dimensional Carbon-Metal Composites for Catalysis Applications","authors":"Yongjie Zhang, Kah-Meng Yam, Hao Wang, Na Guo, Chun Zhang","doi":"10.1002/wcms.70014","DOIUrl":"https://doi.org/10.1002/wcms.70014","url":null,"abstract":"<div>\u0000 \u0000 <p>Catalysis stands as a cornerstone for the global economy and human society, with metals and metal oxides assuming significant roles in catalytic research. The emergence of two-dimensional (2D) carbon materials, such as graphene (GR), graphyne (GY), and graphdiyne (GDY), boasting unique structural and tunable electronic properties, opens up new avenues for the exploration of heterogeneous catalysts. In this review, we initially analyze the limitations inherent in metal- and metal oxide-based catalysts. Subsequently, we present an overview of the latest advancements in heterogeneous catalysts pertaining to 2D carbon-metal composites. We categorize these composites into two groups: support-induced catalysts with disordered lattices and metal-carbon crystals. The realm of 2D support-induced catalysts predominantly encompasses GR-, GY-, and GDY-supported single-atom catalysts (SACs), dual-atom catalysts (DACs), and single-cluster catalysts (SCCs). Meanwhile, the domain of 2D metal-carbon crystals primarily includes metal organic frameworks (MOFs), transition metal carbides (MXenes), and graphite metal carbides (g-MCs). This review encapsulates a comprehensive understanding of the structure, stability, and catalytic application of all these 2D carbon-metal composites from a theoretical standpoint, placing particular emphasis on the coordination structure –performance relationship. To conclude, a brief summary and outlook are provided, offering insights for the future study of 2D carbon-metal composites.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143836456","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

Dissipative Particle Dynamics Modeling in Polymer Science and Engineering 聚合物科学与工程中的耗散粒子动力学建模

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-15 DOI: 10.1002/wcms.70018

Sousa Javan Nikkhah, Matthias Vandichel

{"title":"Dissipative Particle Dynamics Modeling in Polymer Science and Engineering","authors":"Sousa Javan Nikkhah, Matthias Vandichel","doi":"10.1002/wcms.70018","DOIUrl":"https://doi.org/10.1002/wcms.70018","url":null,"abstract":"<p>Polymeric materials are intricate systems with unique properties across different length and time scales, presenting challenges in understanding the hierarchical features that govern their behavior. Advancing innovative polymeric systems requires a deep comprehension of these complexities. Dissipative particle dynamics (DPD), a mesoscale simulation technique, has proven instrumental in elucidating polymer behavior. Unlike molecular dynamics, which tracks individual molecules, DPD employs a coarse-graining approach, to describe molecular systems as particles interacting via soft potentials. Thanks to its computational efficiency, DPD has enabled researchers to numerically study several complex fluid applications in detail. Moreover, with the ever-increasing high-performance computing resources, it has become possible to tackle larger molecular systems beyond the nanoscale, typically micrometer-sized systems. An in-depth analysis of the theoretical foundations of DPD is presented, focusing on its methodology, mathematical formulations, and computational implementation. This review then explores various applications of DPD simulations for polymeric systems, demonstrating DPD's ability to accurately capture phenomena such as polymer self-assembly, polymer behavior in solutions and blends, charged polymers, polymer interfaces, polymer rheology, polymeric membranes, polymerization reactions, and polymeric composites. Overall, this review examines the adoption of DPD as a predictive modeling tool for polymeric materials, focusing on its key features and its integration with methods such as atomistic molecular dynamics to determine the interaction parameters. Building on these advancements, future directions for DPD include its potential applications in other systems like biological membranes, macromolecules, and shape-memory materials.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70018","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831030","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

Multireference Coupled-Cluster Theory: The Internally Contracted Route 多参考耦合集群理论：内部收缩路线

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-04-15 DOI: 10.1002/wcms.70023

Robert G. Adam, Alexander Waigum, Andreas Köhn

{"title":"Multireference Coupled-Cluster Theory: The Internally Contracted Route","authors":"Robert G. Adam, Alexander Waigum, Andreas Köhn","doi":"10.1002/wcms.70023","DOIUrl":"https://doi.org/10.1002/wcms.70023","url":null,"abstract":"<p>Transferring the success of the coupled-cluster expansion for single-determinant references to multireference cases remains a challenge. The main dilemma is a proper merge of the exponential ansatz, required for extensivity of the correlation energy, with a linear ansatz, required for an unbiased treatment of near-degenerate state interactions. We argue that the state interaction aspect is important and that therefore the Bloch equations are the necessary starting point for all true multireference coupled-cluster theories. Considering the aspect of spin-adaptation and orbital invariance, we arrive at internally contracted expansions, which indeed have a number of appealing formal properties, but also incur a tremendous increase in the complexity of the resulting working equations. The most striking property of internally contracted expansions is probably that a simple transformation of the reference space turns the multistate equations into state-specific equations without introducing further approximations. We discuss the present shortcomings and perspectives of the internally contracted multireference coupled-cluster theory and discuss issues like the completeness of the equations, alternative expansions using normal ordering, and perspectives for large active spaces and large molecules.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 2","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143831029","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

Rational Proteolysis Targeting Chimera Design Driven by Molecular Modeling and Machine Learning 分子建模和机器学习驱动的合理蛋白质分解靶向嵌合体设计

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-03-24 DOI: 10.1002/wcms.70013

Shuoyan Tan, Zhenglu Chen, Ruiqiang Lu, Huanxiang Liu, Xiaojun Yao

{"title":"Rational Proteolysis Targeting Chimera Design Driven by Molecular Modeling and Machine Learning","authors":"Shuoyan Tan, Zhenglu Chen, Ruiqiang Lu, Huanxiang Liu, Xiaojun Yao","doi":"10.1002/wcms.70013","DOIUrl":"https://doi.org/10.1002/wcms.70013","url":null,"abstract":"<div>\u0000 \u0000 <p>Proteolysis targeting chimera (PROTAC) induces specific protein degradation through the ubiquitin–proteasome system and offers significant advantages over small molecule drugs. They are emerging as a promising avenue, particularly in targeting previously “undruggable” targets. Traditional PROTACs have been discovered through large-scale experimental screening. Extensive research efforts have been focused on unraveling the biological and pharmacological functions of PROTACs, with significant strides made toward transitioning from empirical discovery to rational, structure-based design strategies. This review provides an overview of recent representative computer-aided drug design studies focused on PROTACs. We highlight how the utilization of the targeted protein degradation database, molecular modeling techniques, machine learning algorithms, and computational methods contributes to facilitating PROTAC discovery. Furthermore, we conclude the achievements in the PROTAC field and explore challenges and future directions. We aim to offer insights and references for future computational studies and the rational design of PROTACs.</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":"143689723","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