Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献

{"title":"Computation of Time-Resolved Nonlinear Electronic Spectra From Classical Trajectories","authors":"Maxim F. Gelin,&nbsp;Zhenggang Lan,&nbsp;Nađa Došlić,&nbsp;Wolfgang Domcke","doi":"10.1002/wcms.70012","DOIUrl":"https://doi.org/10.1002/wcms.70012","url":null,"abstract":"<p>A variety of time-resolved spectroscopic techniques employing femtosecond pump and probe pulses are nowadays widely used to unravel the fundamental mechanisms of photophysical and photochemical processes in molecules and materials. Theoretical support based on first-principles electronic-structure calculations is essential for the interpretation of the observed time and frequency resolved signals. Accurate calculations of nonlinear spectroscopic signals based on a quantum wave-packet description of the nonadiabatic excited-state dynamics have been demonstrated for diatomic and triatomic molecules. For polyatomic molecules with many nuclear degrees of freedom, quasi-classical trajectory descriptions of the excited-state dynamics are more practical. While the computation of time-dependent electronic population probabilities with quasi-classical trajectory methods has become routine, the simulation of time and frequency resolved pump-probe signals is more challenging. This article presents a theoretical framework for first-principles simulations of various femtosecond signals that is based on the third-order polarization and the quasi-classical implementation of the doorway-window approximation. The latter approximation is applicable for non-overlapping pump and probe pulses that are reasonably short on the characteristic time scale of the system dynamics. Apart from a systematic derivation of the theory, explicit computational protocols for the calculation of pump-probe signals are provided. Transient absorption pump-probe spectroscopy with UV pump and UV or X-ray probe pulses, two-dimensional electronic spectroscopy, and femtosecond time-resolved photoelectron spectroscopy are considered as specific examples. Recent applications of these computational methods to prototypical chromophores are briefly reviewed.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100861","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}

{"title":"Theoretical Studies of Molecular Reactions at the Air–Water Interface: Recent Progress and Perspective","authors":"Jing Kang,&nbsp;Shixuan Wang,&nbsp;Chenruyuan Li,&nbsp;Guichuan Cao,&nbsp;Xinyue Gong,&nbsp;Chongqin Zhu","doi":"10.1002/wcms.70031","DOIUrl":"https://doi.org/10.1002/wcms.70031","url":null,"abstract":"<div>\u0000 \u0000 <p>Water microdroplets have been shown to possess unique properties. For instance, compared to bulk water, microdroplets can accelerate chemical reactions by several orders of magnitude and trigger reactions that cannot occur in bulk water. These phenomena have generated significant interest in various fields like atmospheric science, green synthesis, and materials preparation. These unique properties and phenomena are associated with reactions at the air–water interface; however, the underlying mechanisms remain unclear. Studying the microscopic details of phenomena at the air–water interface remains a substantial experimental challenge. Meanwhile, molecular dynamics (MD) simulations and related computational methods provide powerful tools for studying chemical reactions at the air–water interface. This review aims to summarize processes and reactions at the air–water interface from the perspective of theoretical simulations. First, we discuss the physical and chemical properties of the air–water interface. Subsequently, we systematically introduce simulation methods and strategies for four categories of interfacial reactions: (a) simulations of near-barrierless chemical reactions, (b) simulations of chemical reactions with some energy barriers, (c) simulations of chemical reactions employing high-level quantum chemical methods, and (d) simulations of photochemical reactions. Finally, we focus on simulating thermal chemical and photochemical reactions at the air–water interface, with particular emphasis on atmospheric chemistry. The thermal chemical reactions discussed involve Criegee intermediates, nitrogen-containing compounds, and chlorine-containing compounds, while the photochemical reactions discussed include H₂O₂ and phenol. The results discussed here enable an improved understanding of the simulation methods and strategies for chemical reactions at the air–water interface, as well as atmospheric processes.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100549","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}

{"title":"Current Advances in Genome Modeling Across Length Scales","authors":"Eric R. Schultz,&nbsp;Jay L. Kaplan,&nbsp;Yiheng Wu,&nbsp;Soren Kyhl,&nbsp;Rebecca Willett,&nbsp;Juan J. de Pablo","doi":"10.1002/wcms.70024","DOIUrl":"https://doi.org/10.1002/wcms.70024","url":null,"abstract":"<p>The physical organization of DNA within the nucleus is fundamental to a wide range of biological processes. The experimental investigation of the structure of genomic DNA remains challenging due to its large size and hierarchical arrangement. These challenges present considerable opportunities for combined experimental and modeling approaches. Physics-based computational models, in particular, have emerged as essential tools for probing chromatin structure and dynamics across a wide range of length scales. Such models must necessarily be capable of bridging scales, and each scale presents its own subtleties and intricacies. This review discusses recent methodological advances in genomic structural modeling, emphasizing the need for multiscale integration to capture the hierarchical organization and molecular mechanisms that underlie chromatin structure and function. We present an analysis of state-of-the-art methods, as well as a perspective on challenges and future opportunities across length scales ranging from bare DNA to nucleosomes and chromatin fibers, up to TAD and chromosome-scale models. We emphasize models that connect genome organization to gene expression, models that leverage emerging machine learning capabilities, and models that develop multiscale approaches. We examine gaps in experimental data that computational models are poised to address and propose directions for future research that bridge theory and experiment in DNA structural biology.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144100860","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}

{"title":"Cover Image, Volume 14, Issue 4","authors":"Anastasiia S. Fedulova,&nbsp;Grigoriy A. Armeev,&nbsp;Tatiana A. Romanova,&nbsp;Lovepreet Singh-Palchevskaia,&nbsp;Nikita A. Kosarim,&nbsp;Nikita A. Motorin,&nbsp;Galina A. Komarova,&nbsp;Alexey K. Shaytan","doi":"10.1002/wcms.70026","DOIUrl":"https://doi.org/10.1002/wcms.70026","url":null,"abstract":"<p>The cover image is based on the article <i>Molecular dynamics simulations of nucleosomes are coming of age</i> by Alexey Shaytan et al., https://doi.org/10.1002/wcms.1728.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 4","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144091413","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}

{"title":"Quantum Algorithms for Quantum Molecular Systems: A Survey","authors":"Yukun Zhang,&nbsp;Xiaoming Zhang,&nbsp;Jinzhao Sun,&nbsp;Heng Lin,&nbsp;Yifei Huang,&nbsp;Dingshun Lv,&nbsp;Xiao Yuan","doi":"10.1002/wcms.70020","DOIUrl":"https://doi.org/10.1002/wcms.70020","url":null,"abstract":"<p>Solving quantum molecular systems presents a significant challenge for classical computation. The advent of early fault-tolerant quantum computing devices offers a promising avenue to address these challenges, leveraging advanced quantum algorithms with reduced hardware requirements. This review surveys the latest developments in quantum computing algorithms for quantum molecular systems in the fault-tolerant quantum computing era, covering encoding schemes, advanced Hamiltonian simulation techniques, and ground-state energy estimation methods. We highlight recent progress in overcoming practical barriers, such as reducing circuit depth and minimizing the use of ancillary qubits. Special attention is given to the potential quantum advantages achievable through these algorithms, as well as the limitations imposed by dequantization and classical simulation techniques. The review concludes with a discussion of future directions, emphasizing the need for optimized algorithms and experimental validation to bridge the gap between theoretical developments and practical implementation for quantum molecular systems.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144085327","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}

{"title":"Coarse-Grained DNA Models: Bridging Scales Through Extended Dynamics","authors":"Martín Soñora,&nbsp;Lucianna Helene Silva Santos,&nbsp;Antonella Alba,&nbsp;Andrés Ballesteros-Casallas,&nbsp;Sergio Pantano","doi":"10.1002/wcms.70028","DOIUrl":"https://doi.org/10.1002/wcms.70028","url":null,"abstract":"<div>\u0000 \u0000 <p>The cost-effective simulation of biomolecular assemblies using simplified molecular representations has seen significant developments since the beginning of the century. Residue-based coarse-grained (CG) models have become increasingly popular in modeling membranes and protein systems thanks to the speed-up they provide while still offering pseudo-atomistic resolution. However, CG models of DNA have lagged, primarily due to intrinsic complexities such as the dominant role of electrostatics and stacking interactions. This unique challenge has intrigued researchers, leading to significant contributions in the field by the end of the first decade of the century. Here, we provide a comprehensive historical overview of the developments of all-atoms and CG DNA models since the early 1980s. This journey through four decades of DNA modeling aims to highlight the significance of landmark works that shape the development of more complete and accurate simulation tools today.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074587","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}

{"title":"Building Nucleosome Positioning Maps: Discovering Hidden Gems","authors":"Yosef Masoudi-Sobhanzadeh,&nbsp;Anisur Rahman,&nbsp;Shuxiang Li,&nbsp;Saman Bazmi,&nbsp;Sushant Kumar,&nbsp;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}

{"title":"Understanding Surface/Interface-Induced Chemical and Physical Properties at Atomic Level by First Principles Investigations","authors":"Jingyu Yang,&nbsp;Jinbo Pan,&nbsp;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}

{"title":"Ab Initio Vibrational Spectroscopy of Water and Aqueous Solutions in a Wide Pressure–Temperature Range","authors":"Tao Li,&nbsp;Jiajia Huang,&nbsp;Chu Li,&nbsp;Cui Zhang,&nbsp;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}

{"title":"Multiscale Simulations and Property Predictions for Organic Luminescent Aggregates","authors":"Xiaoyan Zheng,&nbsp;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}