Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献

{"title":"A Journey With THeSeuSS: Automated Python Tool for Modeling IR and Raman Vibrational Spectra of Molecules and Solids","authors":"Ariadni Boziki,&nbsp;Frédéric Ngono Mebenga,&nbsp;Philippe Fernandes,&nbsp;Alexandre Tkatchenko","doi":"10.1002/wcms.70033","DOIUrl":"https://doi.org/10.1002/wcms.70033","url":null,"abstract":"<p>Vibrational spectroscopy is an indispensable analytical tool that provides structural fingerprints for molecules, solids, and interfaces thereof. This study introduces THeSeuSS (THz Spectra Simulations Software)—an automated computational platform that efficiently simulates IR and Raman spectra for both periodic and non-periodic systems. Using DFT, DFTB and machine-learning force field, THeSeuSS offers robust capabilities for detailed vibrational spectra simulations. Our extensive evaluations and benchmarks demonstrate that THeSeuSS accurately reproduces both previously calculated and experimental spectra, enabling precise comparisons and interpretations of vibrational characteristics in various test cases, including H₂O and glycine molecules in the gas phase, as well as solid ammonia and solid ibuprofen. Designed with a user-friendly interface and seamless integration with existing computational chemistry tools, THeSeuSS enhances the accessibility and applicability of advanced spectroscopic simulations, supporting research and development in chemical, pharmaceutical, and material sciences.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.70033","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144171861","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":"Floquet Nonadiabatic Dynamics in Open Quantum Systems: Overview","authors":"Vahid Mosallanejad,&nbsp;Yu Wang,&nbsp;Jingqi Chen,&nbsp;Wenjie Dou","doi":"10.1002/wcms.70032","DOIUrl":"https://doi.org/10.1002/wcms.70032","url":null,"abstract":"<div>\u0000 \u0000 <p>The Born–Oppenheimer (BO) approximation has shaped our understanding on molecular dynamics microscopically in many physical and chemical systems. However, there are many cases that we must go beyond the BO approximation, particularly when strong light-matter interactions are considered. Floquet theory offers a powerful tool to treat time-periodic quantum systems. In this overview, we briefly review recent developments on Floquet nonadiabatic dynamics, with a special focus on open quantum systems. We first present the general Floquet Liouville von-Neumann (LvN) equation. We then show how to connect Floquet operators to real time observables. We proceed to outline the derivation of the Floquet quantum master equation in treating the dynamics under periodic driving in open quantum systems. We further present the Floquet mixed quantum classical Liouville equation (QCLE) to deal with coupled electron-nuclear dynamics. Finally, we embed FQCLE into a classical master equation (CME) to deal with Floquet nonadiabatic dynamics in open quantum systems. The formulations are general platforms for developing trajectory based dynamical approaches. As an example, we show how Floquet QCLE and Floquet CME can be implemented into a Langevin dynamics with Lorentz force and surface hopping algorithms.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148451","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":"ByteQC: GPU-Accelerated Quantum Chemistry Package for Large-Scale Systems","authors":"Zhen Guo,&nbsp;Zigeng Huang,&nbsp;Qiaorui Chen,&nbsp;Jiang Shao,&nbsp;Guangcheng Liu,&nbsp;Hung Q. Pham,&nbsp;Yifei Huang,&nbsp;Changsu Cao,&nbsp;Ji Chen,&nbsp;Dingshun Lv","doi":"10.1002/wcms.70034","DOIUrl":"https://doi.org/10.1002/wcms.70034","url":null,"abstract":"<div>\u0000 \u0000 <p>Applying quantum chemistry algorithms to large-scale systems requires substantial computational resources scaling with the system size and the desired accuracy. To address this, ByteQC, a fully functional and efficient package for large-scale quantum chemistry simulations, has been open sourced at https://github.com/bytedance/byteqc, leveraging recent advances in computational power and many-body algorithms. Regarding computational power, several standard algorithms are efficiently implemented on modern GPUs, ranging from mean-field calculations (Hartree-Fock and density functional theory) to post-Hartree-Fock methods such as Møller-Plesset perturbation theory and coupled cluster methods. For the algorithmic approach, we also employ a quantum embedding method, which significantly expands the tractable system size while preserving high accuracy at the gold-standard level. All these features have been systematically benchmarked. For standalone algorithms, the benchmark results demonstrate up to a 60× speedup when compared to 100-core CPUs. Additionally, the tractable system sizes have been significantly expanded: 1610 orbitals for coupled cluster with single and double excitations (1380 orbitals with perturbative triple excitations), 11,040 orbitals for Møller-Plesset perturbation theory of second order, 37,120 orbitals for mean-field calculations under open boundary conditions, and over 100,000 orbitals for periodic boundary conditions. For the advanced quantum embedding feature, two representative examples are demonstrated: the water cluster problem (2752 orbitals) and a water monomer adsorbed on a boron nitride surface (3929 orbitals), achieving the gold-standard accuracy. With these efforts, ByteQC is expected to significantly advance research in quantum chemistry, particularly in large-scale, high-accuracy calculations.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 3","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144171203","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":"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}