Wiley Interdisciplinary Reviews: Computational Molecular Science最新文献_第10页

Cover Image, Volume 13, Issue 1 封面图片，第13卷，第1期

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-01-20 DOI: 10.1002/wcms.1657

Siri C. van Keulen, Juliette Martin, Francesco Colizzi, Elisa Frezza, Daniel Trpevski, Nuria Cirauqui Diaz, Pietro Vidossich, Ursula Rothlisberger, Jeanette Hellgren Kotaleski, Rebecca C. Wade, Paolo Carloni

引用次数: 0

Atomistic simulations of pristine and nanoparticle reinforced hydrogels: A review 原始和纳米颗粒增强水凝胶的原子模拟:综述

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-01-18 DOI: 10.1002/wcms.1655

Raju Kumar, Avinash Parashar

{"title":"Atomistic simulations of pristine and nanoparticle reinforced hydrogels: A review","authors":"Raju Kumar, Avinash Parashar","doi":"10.1002/wcms.1655","DOIUrl":"https://doi.org/10.1002/wcms.1655","url":null,"abstract":"Hydrogel is a three-dimensional cross-linked hydrophilic network that can imbibe a large amount of water inside its structure (up to 99% of its dry weight). Due to their unique characteristics of biocompatibility and flexibility, it has found applications in diversified fields, including tissue engineering, drug delivery, biosensors, and agriculture. Even though hydrogels are widely used in the biomedical field, their lower mechanical strength still limits their application to its full potential. Hydrogels can be reinforced with organic, inorganic, and metal-based nanofillers to improve their mechanical strength. Due to improved computational power, computational-based techniques are emerging as a leading characterization technique for nanocomposites and hydrogels. In nanomaterials, atomistic description governs the mechanical strength and thermal behavior that realized atomistic level simulations as an appropriate approach to capture the deformation governing mechanism. Among atomistic simulations, the molecular dynamics (MD)-based approach is emerging as a prospective technique for simulating neat and nanocomposite-based hydrogels' mechanical and thermal behavior. The success and accuracy of MD simulation entirely depend on the force field. This review article will compile the force field employed by the research community to capture the atomistic interactions in different nanocomposite-based hydrogels. This article will comprehensively review the progress made in the atomistic approach to study neat and nanocomposite-based hydrogels' properties. The authors have enlightened the challenges and limitations associated with the atomistic modeling of hydrogels.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2023-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5917459","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: 3

Graph neural networks for conditional de novo drug design 有条件从头药物设计的图神经网络

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2023-01-12 DOI: 10.1002/wcms.1651

Carlo Abate, Sergio Decherchi, Andrea Cavalli

引用次数: 1

Rational design of catalysts with earth-abundant elements 富土元素催化剂的合理设计

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-30 DOI: 10.1002/wcms.1654

Gaomou Xu, Cheng Cai, Wanghui Zhao, Yonghua Liu, Tao Wang

{"title":"Rational design of catalysts with earth-abundant elements","authors":"Gaomou Xu, Cheng Cai, Wanghui Zhao, Yonghua Liu, Tao Wang","doi":"10.1002/wcms.1654","DOIUrl":"https://doi.org/10.1002/wcms.1654","url":null,"abstract":"Catalysis has played a crucial role in energy sustainability, environment control, and chemical production, while the design of high-performance catalysts is a key scientific question. In nature, biological organisms carry out catalysis with earth-abundant metals, whereas modern industrial processes rely heavily on precious metals. This points out the necessity of designing state-of-the-art catalysts with earth-abundant elements to maintain sustainable catalysis. In this review, we will start with the fact that nature uses earth-abundant metals to feed the planet, followed by a few successful examples of catalyst design for water oxidation. Then, we will systematically introduce the practical methods in computational catalyst design and their applications in the rational modification of EAM catalysts for various reactions. In addition, the roles of high-throughput computations and artificial intelligence in this framework are summarized and discussed. We will also discuss the potential limitations of the framework and the strategies to overcome these challenges. Finally, we emphasize the importance of the synergistic efforts between theory and experiments in rational catalyst design with earth-abundant elements.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 4","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6108357","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

Combining machine-learning and molecular-modeling methods for drug-target affinity predictions 结合机器学习和分子建模方法进行药物靶标亲和力预测

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-27 DOI: 10.1002/wcms.1653

Carles Perez-Lopez, Alexis Molina, Estrella Lozoya, Victor Segarra, Marti Municoy, Victor Guallar

引用次数: 1

Perspective: Simultaneous treatment of relativity, correlation, and QED 观点:同时处理相对性、相关性和QED

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-22 DOI: 10.1002/wcms.1652

Wenjian Liu

引用次数: 2

Brownian dynamics simulations of biomolecular diffusional association processes 生物分子扩散结合过程的布朗动力学模拟

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-14 DOI: 10.1002/wcms.1649

Abraham Mu?iz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade

{"title":"Brownian dynamics simulations of biomolecular diffusional association processes","authors":"Abraham Mu?iz-Chicharro, Lane W. Votapka, Rommie E. Amaro, Rebecca C. Wade","doi":"10.1002/wcms.1649","DOIUrl":"https://doi.org/10.1002/wcms.1649","url":null,"abstract":"Brownian dynamics (BD) is a computational method to simulate molecular diffusion processes. Although the BD method has been developed over several decades and is well established, new methodological developments are improving its accuracy, widening its scope, and increasing its application. In biological applications, BD is used to investigate the diffusive behavior of molecules subject to forces due to intermolecular interactions or interactions with material surfaces. BD can be used to compute rate constants for diffusional association, generate structures of encounter complexes for molecular binding partners, and examine the transport properties of geometrically complex molecules. Often, a series of simulations is performed, for example, for different protein mutants or environmental conditions, so that the effects of the changes on diffusional properties can be estimated. While biomolecules are commonly described at atomic resolution and internal molecular motions are typically neglected, coarse-graining and the treatment of conformational flexibility are increasingly employed. Software packages for BD simulations of biomolecules are growing in capabilities, with several new packages providing novel features that expand the range of questions that can be addressed. These advances, when used in concert with experiment or other simulation methods, such as molecular dynamics, open new opportunities for application to biochemical and biological systems. Here, we review some of the latest developments in the theory, methods, software, and applications of BD simulations to study biomolecular diffusional association processes and provide a perspective on their future use and application to outstanding challenges in biology, bioengineering, and biomedicine.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1649","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5849808","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: 1

Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems 复杂分子和凝聚相体系的量子碎片化研究进展

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-13 DOI: 10.1002/wcms.1650

Jinfeng Liu, Xiao He

{"title":"Recent advances in quantum fragmentation approaches to complex molecular and condensed-phase systems","authors":"Jinfeng Liu, Xiao He","doi":"10.1002/wcms.1650","DOIUrl":"https://doi.org/10.1002/wcms.1650","url":null,"abstract":"Quantum mechanical (QM) calculations are critical in quantitatively understanding the relationship between the structure and physicochemical properties of various chemical systems. However, the sharply increasing computational cost with the system size has severely hindered applying direct QM calculations on large-sized systems. Hence, linear-scaling and/or fragmentation QM methods have been proposed to overcome this difficulty. In this review, we focus on the recent development and applications of the electrostatically embedded generalized molecular fractionation with the conjugate caps (EE-GMFCC) method in probing various properties of complex large molecules and condensed-phase systems. The EE-GMFCC method is now capable of describing the localized excited states of biomolecules and molecular crystals with a chromophore. The EE-GMF method is also combined with anharmonic vibrational calculations for accurate simulation of the infrared spectrum of the magic number H+(H2O)21 cluster at the coupled cluster level. With an adaptive fragmentation scheme, the EE-GMF-based ab initio molecular dynamics is able to directly simulate chemical reactions occurred in atmospheric molecular clusters. Furthermore, by combining the EE-GMF(CC) method and deep machine learning techniques, neural network potentials can be efficiently constructed for accurate simulations of complex systems with the accuracy of high-level wave function methods. The EE-GMF(CC) method is expected to become a practical tool for quantitative description of complex large molecules and condensed-phase systems with high-level ab initio theories or ab initio quality potentials.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6219897","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: 5

The subsystem quantum chemistry program Serenity 子系统量子化学项目宁静号

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-12-07 DOI: 10.1002/wcms.1647

Niklas Niemeyer, Patrick Eschenbach, Moritz Bensberg, Johannes T?lle, Lars Hellmann, Lukas Lampe, Anja Massolle, Anton Rikus, David Schnieders, Jan P. Unsleber, Johannes Neugebauer

{"title":"The subsystem quantum chemistry program Serenity","authors":"Niklas Niemeyer, Patrick Eschenbach, Moritz Bensberg, Johannes T?lle, Lars Hellmann, Lukas Lampe, Anja Massolle, Anton Rikus, David Schnieders, Jan P. Unsleber, Johannes Neugebauer","doi":"10.1002/wcms.1647","DOIUrl":"https://doi.org/10.1002/wcms.1647","url":null,"abstract":"SERENITY [J Comput Chem. 2018;39:788–798] is an open-source quantum chemistry software that provides an extensive development platform focused on quantum-mechanical multilevel and embedding approaches. In this study, we give an overview over the developments done in Serenity since its original publication in 2018. This includes efficient electronic-structure methods for ground states such as multilevel domain-based local pair natural orbital coupled cluster and Møller–Plesset perturbation theory as well as the multistate frozen-density embedding quasi-diabatization method. For the description of excited states, SERENITY features various subsystem-based methods such as embedding variants of coupled time-dependent density-functional theory, approximate second-order coupled cluster theory and the second-order algebraic diagrammatic construction technique as well as GW/Bethe–Salpeter equation approaches. SERENITY's modular structure allows combining these methods with density-functional theory (DFT)-based embedding through various practical realizations and variants of subsystem DFT including frozen-density embedding, potential-reconstruction techniques and projection-based embedding.This article is categorized under:\u0000 ","PeriodicalId":236,"journal":{"name":"Wiley Interdisciplinary Reviews: Computational Molecular Science","volume":"13 3","pages":""},"PeriodicalIF":11.4,"publicationDate":"2022-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1647","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"6111307","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: 7

Growing Spicy ONIOMs: Extending and generalizing concepts of ONIOM and many body expansions 种植辣洋葱:扩展和概括洋葱和许多身体扩展的概念

IF 11.4 2区化学

Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2022-11-22 DOI: 10.1002/wcms.1644

Phillip Seeber, Sebastian Seidenath, Johannes Steinmetzer, Stefanie Gr?fe

引用次数: 2