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

Time-Dependent Vibrational Coupled Cluster Theory With Static and Dynamic Basis Functions

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Strategies for Redesigning Withdrawn Drugs to Enhance Therapeutic Efficacy and Safety: A Review

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

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

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

From Perception to Prediction and Interpretation: Enlightening the Gray Zone of Molecular Bricks of Life With the Help of Machine Learning and Quantum Chemistry

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-06 DOI: 10.1002/wcms.70000

Vincenzo Barone

{"title":"From Perception to Prediction and Interpretation: Enlightening the Gray Zone of Molecular Bricks of Life With the Help of Machine Learning and Quantum Chemistry","authors":"Vincenzo Barone","doi":"10.1002/wcms.70000","DOIUrl":"https://doi.org/10.1002/wcms.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>The latest developments of a general exploration/exploitation strategy for the computational study of molecular bricks of life in the gas-phase are presented and illustrated by means of prototypical semi-rigid and flexible systems. In the first step, generalized natural internal coordinates are employed to obtain a clear-cut separation between different degrees of freedom, and machine-learning algorithms based on chemical descriptors (synthons) drive fast quantum chemical methods in the exploration of rugged potential energy surfaces ruled by soft degrees of freedom. Then, different quantum chemical models are carefully selected for exploiting energies, geometries, and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional is employed for geometries and harmonic frequencies and a cheaper global hybrid functional for anharmonic contributions. A panel of molecular bricks of life containing up to 50 atoms is employed to show that the proposed strategy draws closer to the accuracy of state-of-the-art composite wave-function methods for small semi-rigid molecules, but is applicable to much larger systems. The implementation of the whole computational workflow in terms of preprocessing and postprocessing of data provided by standard electronic structure codes paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by a user-friendly black-box tool exploitable also by experiment-oriented researchers.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112602","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

Good Practices in Database Generation for Benchmarking Density Functional Theory

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2025-01-05 DOI: 10.1002/wcms.1737

Amir Karton, Marcelo T. de Oliveira

{"title":"Good Practices in Database Generation for Benchmarking Density Functional Theory","authors":"Amir Karton, Marcelo T. de Oliveira","doi":"10.1002/wcms.1737","DOIUrl":"https://doi.org/10.1002/wcms.1737","url":null,"abstract":"<div>\u0000 \u0000 <p>The hundreds of density functional theory (DFT) methods developed over the past three decades are often referred to as the “zoo” of DFT approximations. In line with this terminology, the numerous DFT benchmark studies might be considered the “safari” of DFT evaluation efforts, reflecting their abundance, diversity, and wide range of application and methodological aspects. These benchmarks have played a critical role in establishing DFT as the dominant approach in quantum chemical applications and remain essential for selecting an appropriate DFT method for specific chemical properties (e.g., reaction energy, barrier height, or noncovalent interaction energy) and systems (e.g., organic, inorganic, or organometallic). DFT benchmark studies are a vital tool for both DFT users in method selection and DFT developers in method design and parameterization. This review provides best-practice guidance on key methodological aspects of DFT benchmarking, such as the quality of benchmark reference values, dataset size, reference geometries, basis sets, statistical analysis, and electronic availability of the benchmark data. Additionally, we present a flowchart to assist users in systematically choosing these methodological aspects, thereby enhancing the reliability and reproducibility of DFT benchmarking studies.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"15 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112260","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

Nonequilibrium Dynamics at Cellular Interfaces: Insights From Simulation and Theory 非平衡动力学在细胞界面：从模拟和理论的见解

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-12-09 DOI: 10.1002/wcms.1736

Zheng Jiao, Lijuan Gao, Xueqing Jin, Jiaqi Li, Yuming Wang, Wenlong Chen, Li-Tang Yan

{"title":"Nonequilibrium Dynamics at Cellular Interfaces: Insights From Simulation and Theory","authors":"Zheng Jiao, Lijuan Gao, Xueqing Jin, Jiaqi Li, Yuming Wang, Wenlong Chen, Li-Tang Yan","doi":"10.1002/wcms.1736","DOIUrl":"https://doi.org/10.1002/wcms.1736","url":null,"abstract":"<div>\u0000 \u0000 <p>Active matters, which consume energy to exert mechanical forces, include molecular motors, synthetic nanomachines, actively propelled bacteria, and viruses. A series of unique phenomena emerge when active matters interact with cellular interfaces. Activity changes the mechanism of nanoparticle intracellular delivery, while active mechanical processes generated in the cytoskeleton play a major role in membrane protein distribution and transport. This review provides a comprehensive overview of the theoretical and simulation models used to study these nonequilibrium phenomena, offering insights into how activity enhances cellular uptake, influences membrane deformation, and governs surface transport dynamics. Furthermore, we explore the impact of membrane properties, such as fluidity and viscosity, on transport efficiency and discuss the slippage dynamics and active rotation behaviors on the membrane surface. The interplay of active particles and membranes highlights the essential role of nonequilibrium dynamics in cellular transport processes, with potential applications in drug delivery and nanotechnology. Finally, we provide an outlook highlighting the significance of deeper theoretical and simulation-based investigations to optimize active particles and understand their behavior in complex biological environments.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 6","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142860656","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

Unveiling Drug Discovery Insights Through Molecular Electrostatic Potential Analysis 通过分子静电势分析揭示药物发现的见解

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-12-03 DOI: 10.1002/wcms.1735

Mambatta Haritha, Cherumuttathu H. Suresh

{"title":"Unveiling Drug Discovery Insights Through Molecular Electrostatic Potential Analysis","authors":"Mambatta Haritha, Cherumuttathu H. Suresh","doi":"10.1002/wcms.1735","DOIUrl":"https://doi.org/10.1002/wcms.1735","url":null,"abstract":"<div>\u0000 \u0000 <p>Molecular electrostatic potential (MESP) analysis has emerged as a pivotal tool in drug discovery, providing insights into molecular reactivity and noncovalent interactions essential for drug function. While widely used MESP-on-isodensity surface analysis offers interpretations of electron-rich or deficient regions of a drug molecule, the MESP topology parameters such as spatial minimum (<i>V</i><sub>min</sub>) and MESP at nuclei (<i>V</i><sub>n</sub>) provide a quantitative understanding. The investigation into the correlation between MESP parameters and various molecular properties such as lipophilicity, pK<sub>a</sub> (acidity/basicity), conformations, and tautomeric forms is crucial for understanding the impact on biological activity of drugs and facilitating drug design. Moreover, MESP topology analysis serves as a fundamental tool in elucidating the pharmacological behavior of compounds and optimizing their therapeutic efficacy. A quantitative study utilizing <i>V</i><sub>n</sub> parameters to assess the hydrogen bond propensity of a drug presents a novel strategy for investigating drug-receptor interactions with increased precision. The qualitative and quantitative analysis of the MESP features of various drugs, including their applications in cancer, tuberculosis, tumors, inflammation, and infectious diseases such as malaria, bacterial infections, fungal infections, and viral infections, is conducted in this review.</p>\u0000 </div>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 6","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764056","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

Embedded Many-Body Green's Function Methods for Electronic Excitations in Complex Molecular Systems 复杂分子系统中电子激发的嵌入式多体格林函数方法

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-11-17 DOI: 10.1002/wcms.1734

Gianluca Tirimbó, Vivek Sundaram, Björn Baumeier

{"title":"Embedded Many-Body Green's Function Methods for Electronic Excitations in Complex Molecular Systems","authors":"Gianluca Tirimbó, Vivek Sundaram, Björn Baumeier","doi":"10.1002/wcms.1734","DOIUrl":"https://doi.org/10.1002/wcms.1734","url":null,"abstract":"<p>Many-body Green's function theory in the <i>GW</i> approximation with the Bethe–Salpeter equation (BSE) provides a powerful framework for the first-principles calculations of single-particle and electron–hole excitations in perfect crystals and molecules alike. Application to complex molecular systems, for example, solvated dyes, molecular aggregates, thin films, interfaces, or macromolecules, is particularly challenging as they contain a prohibitively large number of atoms. Exploiting the often localized nature of excitation in such disordered systems, several methods have recently been developed in which <i>GW</i>-BSE is applied to a smaller, tractable region of interest that is embedded into an environment described with a lower-level method. Here, we review the various strategies proposed for such embedded many-body Green's functions approaches, including quantum–quantum and quantum–classical embeddings, and focus in particular on how they include environment screening effects either intrinsically in the screened Coulomb interaction in the <i>GW</i> and BSE steps or via extrinsic electrostatic couplings.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 6","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1734","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142665090","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

ROBERT: Bridging the Gap Between Machine Learning and Chemistry 罗伯特：缩小机器学习与化学之间的差距

IF 16.8 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-10-22 DOI: 10.1002/wcms.1733

David Dalmau, Juan V. Alegre-Requena

{"title":"ROBERT: Bridging the Gap Between Machine Learning and Chemistry","authors":"David Dalmau, Juan V. Alegre-Requena","doi":"10.1002/wcms.1733","DOIUrl":"https://doi.org/10.1002/wcms.1733","url":null,"abstract":"<p>Beyond addressing technological demands, the integration of machine learning (ML) into human societies has also promoted sustainability through the adoption of digitalized protocols. Despite these advantages and the abundance of available toolkits, a substantial implementation gap is preventing the widespread incorporation of ML protocols into the computational and experimental chemistry communities. In this work, we introduce ROBERT, a software carefully crafted to make ML more accessible to chemists of all programming skill levels, while achieving results comparable to those of field experts. We conducted benchmarking using six recent ML studies in chemistry containing from 18 to 4149 entries. Furthermore, we demonstrated the program's ability to initiate workflows directly from SMILES strings, which simplifies the generation of ML predictors for common chemistry problems. To assess ROBERT's practicality in real-life scenarios, we employed it to discover new luminescent Pd complexes with a modest dataset of 23 points, a frequently encountered scenario in experimental studies.</p>","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 5","pages":""},"PeriodicalIF":16.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1733","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142525092","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