Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第3页

The role of stereochemistry in combustion processes 立体化学在燃烧过程中的作用

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-03-21 DOI: 10.1002/wcms.1710

Sarah N. Elliott, Kevin B. Moore III, Clayton R. Mulvihill, Andreas V. Copan, Luna Pratali Maffei, Stephen J. Klippenstein

{"title":"The role of stereochemistry in combustion processes","authors":"Sarah N. Elliott, Kevin B. Moore III, Clayton R. Mulvihill, Andreas V. Copan, Luna Pratali Maffei, Stephen J. Klippenstein","doi":"10.1002/wcms.1710","DOIUrl":"https://doi.org/10.1002/wcms.1710","url":null,"abstract":"Stereochemical effects significantly influence chemical processes, yet it is not well understood if they are a leading source of uncertainty in combustion modeling. Stereochemistry influences a combustion model (i) at the earliest stage of its construction when mapping the reaction network, (ii) in the computation of individual thermochemical and rate parameters, and (iii) in the prediction of combustion observables. The present work reviews the importance of enumerating stereochemical species and reactions at each of these steps. Further, it analyzes the separate influence of several types of stereochemistry, including geometric, optical, and fleeting transition state diastereomers. Three reaction networks serve to examine which stages of low-temperature oxidation are most affected by stereochemistry, including the first and second oxidation of n-butane, the third oxidation of n-pentane, and the early stages of pyrolysis of 1- and 2-pentene. The 149 reactions in the n-butane mechanism are expanded to 183 reactions when accounting for diastereomerism. Each of these 183 reactions is parameterized with ab initio kinetics computations to determine that, for the n-butane mechanism, the median factor of diastereomeric deviation is 3.5 at 360 K for rate constants and as high as 1.6 for mechanism reactivity, in terms of ignition delay times, as opposed to a mechanism without stereochemical expansion.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1710","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140188539","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

Making quantum chemistry compressive and expressive: Toward practical ab-initio simulation 使量子化学具有压缩性和表现力：实现实用的模拟仿真

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-03-12 DOI: 10.1002/wcms.1706

Jun Yang

{"title":"Making quantum chemistry compressive and expressive: Toward practical ab-initio simulation","authors":"Jun Yang","doi":"10.1002/wcms.1706","DOIUrl":"https://doi.org/10.1002/wcms.1706","url":null,"abstract":"Ab-initio quantum chemistry simulations are essential for understanding electronic structure of molecules and materials in almost all areas of chemistry. A broad variety of electronic structure theories and implementations has been developed in the past decades to hopefully solve the many-body Schrödinger equation in an approximate manner on modern computers. In this review, we present recent progress in advancing low-rank electronic structure methodologies that rely on the wavefunction sparsity and compressibility to select the important subset of electronic configurations for both weakly and strongly correlated molecules. Representative chemistry applications that require the many-body treatment beyond traditional density functional approximations are discussed. The low-rank electronic structure theories have further prompted us to highlight compressive and expressive principles that are useful to catalyze idea of quantum learning models. The intersection of the low-rank correlated feature design and the modern deep neural network learning provides new feasibilities to predict chemically accurate correlation energies of unknown molecules that are not represented in the training dataset. The results by others and us are discussed to reveal that the electronic feature sets from an extremely low-rank correlation representation, which is very poor for explicit energy computation, are however sufficiently expressive for capturing and transferring electron correlation patterns across distinct molecular compositions, bond types and geometries.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1706","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140114230","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

Computational high-pressure chemistry: Ab initio simulations of atoms, molecules, and extended materials in the gigapascal regime 计算高压化学：原子、分子和扩展材料在千兆帕制度下的 Ab initio 模拟

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-03-07 DOI: 10.1002/wcms.1708

Felix Zeller, Chieh-Min Hsieh, Wilke Dononelli, Tim Neudecker

{"title":"Computational high-pressure chemistry: Ab initio simulations of atoms, molecules, and extended materials in the gigapascal regime","authors":"Felix Zeller, Chieh-Min Hsieh, Wilke Dononelli, Tim Neudecker","doi":"10.1002/wcms.1708","DOIUrl":"https://doi.org/10.1002/wcms.1708","url":null,"abstract":"The field of liquid-phase and solid-state high-pressure chemistry has exploded since the advent of the diamond anvil cell, an experimental technique that allows the application of pressures up to several hundred gigapascals. To complement high-pressure experiments, a large number of computational tools have been developed. These techniques enable the simulation of chemical systems, their sizes ranging from single atoms to infinitely large crystals, under high pressure, and the calculation of the resulting structural, electronic, and spectroscopic changes. At the most fundamental level, computational methods using carefully tailored wall potentials allow the analytical calculation of energies and electronic properties of compressed atoms. Molecules and molecular clusters can be compressed either via mechanochemical approaches or via more sophisticated computational protocols using implicit or explicit solvation approaches, typically in combination with density functional theory, thus allowing the simulation of pressure-induced chemical reactions. Crystals and other periodic systems can be routinely simulated under pressure as well, both statically and dynamically, to predict the changes of crystallographic data under pressure and high-pressure crystal structure transitions. In this review, the theoretical foundations of the available computational tools for simulating high-pressure chemistry are introduced and example applications demonstrating the strengths and weaknesses of each approach are discussed.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 2","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1708","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140063840","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

Toward generalizable structure-based deep learning models for protein–ligand interaction prediction: Challenges and strategies 为蛋白质配体相互作用预测建立可通用的基于结构的深度学习模型：挑战与策略

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-25 DOI: 10.1002/wcms.1705

Seokhyun Moon, Wonho Zhung, Woo Youn Kim

引用次数: 0

Correction to “The versatility of the Cholesky decomposition in electronic structure theory” 对 "乔利斯基分解在电子结构理论中的多功能性 "的更正

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-17 DOI: 10.1002/wcms.1707

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A brief history of amyloid aggregation simulations 淀粉样蛋白聚集模拟简史

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-15 DOI: 10.1002/wcms.1703

Hebah Fatafta, Mohammed Khaled, Batuhan Kav, Olujide O. Olubiyi, Birgit Strodel

{"title":"A brief history of amyloid aggregation simulations","authors":"Hebah Fatafta, Mohammed Khaled, Batuhan Kav, Olujide O. Olubiyi, Birgit Strodel","doi":"10.1002/wcms.1703","DOIUrl":"https://doi.org/10.1002/wcms.1703","url":null,"abstract":"Amyloid proteins are characterized by their tendency to aggregate into amyloid fibrils, which are often associated with devastating diseases. Aggregation pathways typically involve unfolding or misfolding of monomeric proteins and formation of transient oligomers and protofibrils before the final aggregation product is formed. The conformational dynamics and polymorphic and volatile nature of these aggregation intermediates make their characterization by experimental techniques alone insufficient and also require computational approaches. Over the past 25 years, the size of simulated amyloid aggregation systems and the length of these simulations have increased significantly. These advances are discussed here. The review includes simulation approaches that model the aggregating peptides or proteins at both the all-atom and coarse-grained levels, use molecular dynamics simulations or Monte Carlo sampling to simulate the conformational changes, and present results for various amyloid peptides and proteins ranging from Lys-Phe-Phe-Glu (KFFE) as the smallest system to <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>Aβ</mi>\u0000 </mrow>\u0000 <annotation>$$ mathrm{A}upbeta $$</annotation>\u0000 </semantics></math> as an intermediate-sized peptide to α-synuclein. The presentation of the history of amyloid aggregation simulations concludes with a discussion of where the future of these simulations may lie.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1703","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139744921","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

Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design 揭开钾通道秘密的计算方法：结构、机理和药物设计

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-02-15 DOI: 10.1002/wcms.1704

Lingling Wang, Qianqian Zhang, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Guohui Li

{"title":"Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design","authors":"Lingling Wang, Qianqian Zhang, Henry H. Y. Tong, Xiaojun Yao, Huanxiang Liu, Guohui Li","doi":"10.1002/wcms.1704","DOIUrl":"https://doi.org/10.1002/wcms.1704","url":null,"abstract":"Potassium (K+) channels play vital roles in various physiological functions, including regulating K+ flow in cell membranes, impacting nervous system signal transduction, neuronal firing, muscle contraction, neurotransmitters, and enzyme secretion. Their activation and switch-off are directly linked to diseases like arrhythmias, atrial fibrillation, and pain etc. Although the experimental methods play important roles in the studying the structure and function of K+ channels, they are still some limitations to enclose the dynamic molecular processes and the corresponding mechanisms of conformational changes during ion transport, permeation, and gating control. Relatively, computational methods have obvious advantages in studying such problems compared with experimental methods. Recently, more and more three-dimensional structures of K+ channels have been disclosed based on experimental methods and in silico prediction methods, which provide a good chance to study the molecular mechanism of conformational changes related to the functional regulations of K+ channels. Based on these structural details, molecular dynamics simulations together with related methods such as enhanced sampling and free energy calculations, have been widely used to reveal the conformational dynamics, ion conductance, ion channel gating, and ligand binding mechanisms. Additionally, the accessibility of structures also provides a large space for structure-based drug design. This review mainly addresses the recent progress of computational methods in the structure, mechanism, and drug design of K+ channels. After summarizing the progress in these fields, we also give our opinion on the future direction in the area of K+ channel research combined with the cutting edge of computational methods.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139744922","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

Two-dimensional hypercoordinate chemistry: Challenges and prospects 二维超配位化学：挑战与前景

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-30 DOI: 10.1002/wcms.1699

Bingyi Song, Li-Ming Yang

{"title":"Two-dimensional hypercoordinate chemistry: Challenges and prospects","authors":"Bingyi Song, Li-Ming Yang","doi":"10.1002/wcms.1699","DOIUrl":"https://doi.org/10.1002/wcms.1699","url":null,"abstract":"Planar hypercoordinate compounds are fascinating but challenging to be realized. The difficulty in stabilizing and fabricating such compounds prevent us from in-deep understanding these compounds and exploring potential applications. Molecular-level insights on underlying mechanism for the formation of viable hypercoordinate compounds is the key towards the development of this field. This review aims to summarize recent advances in this direction. Regular polygons ALCN (A and L are central and ligand atoms, CN is coordination number) are generally applicable models used to derive the unified mathematical relations between the radii of constitute atoms and the angles of regular polygons as exemplified by two typical examples Gr14LCN and TMBCN (Gr14 is Group 14 element, TM is transition metal, B is boron). Effective schemes and some useful rule of thumb are proposed towards the architecture of 2D hypercoordinate crystals ALx (x is composition ratio). A set of design flow chart and several effective design strategies and principles are suggested for 2D-HyperMaters. Potential diverse applications of 2D-HyperMaters are discussed and summarized. Grand blueprint for planar hypercoordinate chemistry is drew. Finally, future prospects of 2D-HyperChem is outlooked.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139655510","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

Subsystem density-functional theory (update) 子系统密度函数理论（更新）

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-30 DOI: 10.1002/wcms.1700

Christoph R. Jacob, Johannes Neugebauer

引用次数: 0

Complexity of life sciences in quantum and AI era 量子和人工智能时代生命科学的复杂性

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-01-17 DOI: 10.1002/wcms.1701

Alexey Pyrkov, Alex Aliper, Dmitry Bezrukov, Dmitriy Podolskiy, Feng Ren, Alex Zhavoronkov

{"title":"Complexity of life sciences in quantum and AI era","authors":"Alexey Pyrkov, Alex Aliper, Dmitry Bezrukov, Dmitriy Podolskiy, Feng Ren, Alex Zhavoronkov","doi":"10.1002/wcms.1701","DOIUrl":"https://doi.org/10.1002/wcms.1701","url":null,"abstract":"Having made significant advancements in understanding living organisms at various levels such as genes, cells, molecules, tissues, and pathways, the field of life sciences is now shifting towards integrating these components into the bigger picture to understand their collective behavior. Such a shift of perspective requires a general conceptual framework for understanding complexity in life sciences which is currently elusive, a transition being facilitated by large-scale data collection, unprecedented computational power, and new analytical tools. In recent years, life sciences have been revolutionized with AI methods, and quantum computing is touted to be the next most significant leap in technology. Here, we provide a theoretical framework to orient researchers around key concepts of how quantum computing can be integrated into the study of the hierarchical complexity of living organisms and discuss recent advances in quantum computing for life sciences.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"14 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139488608","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