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Navigating the landscape of enzyme design: from molecular simulations to machine learning 酶设计的导航:从分子模拟到机器学习。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-11 DOI: 10.1039/D4CS00196F
Jiahui Zhou and Meilan Huang

Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is challenging to navigate the vast sequence space to identify those proteins with admirable biocatalytic functions. The recent development of deep-learning based structure prediction methods such as AlphaFold2 reinforced by different computational simulations or multiscale calculations has largely expanded the 3D structure databases and enabled structure-based design. While structure-based approaches shed light on site-specific enzyme engineering, they are not suitable for large-scale screening of potential biocatalysts. Effective utilization of big data using machine learning techniques opens up a new era for accelerated predictions. Here, we review the approaches and applications of structure-based and machine-learning guided enzyme design. We also provide our view on the challenges and perspectives on effectively employing enzyme design approaches integrating traditional molecular simulations and machine learning, and the importance of database construction and algorithm development in attaining predictive ML models to explore the sequence fitness landscape for the design of admirable biocatalysts.

全球环境问题和可持续发展呼唤精细化学品合成和废物价值化的新技术。作为传统有机合成的替代技术,生物催化技术备受关注。然而,要在浩瀚的序列空间中识别出具有令人钦佩的生物催化功能的蛋白质是一项挑战。最近,基于深度学习的结构预测方法(如 AlphaFold2)得到了不同计算模拟或多尺度计算的加强,在很大程度上扩展了三维结构数据库,实现了基于结构的设计。虽然基于结构的方法为特定位点的酶工程提供了启示,但并不适合大规模筛选潜在的生物催化剂。利用机器学习技术有效利用大数据开辟了加速预测的新时代。在此,我们回顾了基于结构和机器学习指导的酶设计方法和应用。我们还就有效利用传统分子模拟和机器学习相结合的酶设计方法所面临的挑战和前景,以及数据库建设和算法开发在获得预测性 ML 模型以探索序列适配性景观以设计理想的生物催化剂方面的重要性提出了自己的看法。
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引用次数: 0
Nucleic acid-based wearable and implantable electrochemical sensors 基于核酸的可穿戴和植入式电化学传感器。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-10 DOI: 10.1039/D4CS00001C
Cui Ye, Heather Lukas, Minqiang Wang, Yerim Lee and Wei Gao

The rapid advancements in nucleic acid-based electrochemical sensors for implantable and wearable applications have marked a significant leap forward in the domain of personal healthcare over the last decade. This technology promises to revolutionize personalized healthcare by facilitating the early diagnosis of diseases, monitoring of disease progression, and tailoring of individual treatment plans. This review navigates through the latest developments in this field, focusing on the strategies for nucleic acid sensing that enable real-time and continuous biomarker analysis directly in various biofluids, such as blood, interstitial fluid, sweat, and saliva. The review delves into various nucleic acid sensing strategies, emphasizing the innovative designs of biorecognition elements and signal transduction mechanisms that enable implantable and wearable applications. Special perspective is given to enhance nucleic acid-based sensor selectivity and sensitivity, which are crucial for the accurate detection of low-level biomarkers. The integration of such sensors into implantable and wearable platforms, including microneedle arrays and flexible electronic systems, actualizes their use in on-body devices for health monitoring. We also tackle the technical challenges encountered in the development of these sensors, such as ensuring long-term stability, managing the complexity of biofluid dynamics, and fulfilling the need for real-time, continuous, and reagentless detection. In conclusion, the review highlights the importance of these sensors in the future of medical engineering, offering insights into design considerations and future research directions to overcome existing limitations and fully realize the potential of nucleic acid-based electrochemical sensors for healthcare applications.

过去十年间,用于植入式和可穿戴式应用的核酸电化学传感器取得了突飞猛进的发展,标志着个人医疗保健领域实现了重大飞跃。这项技术有助于早期诊断疾病、监测疾病进展和定制个性化治疗方案,有望彻底改变个性化医疗保健。本综述介绍了这一领域的最新发展,重点是核酸传感策略,这种策略可直接在血液、组织间液、汗液和唾液等各种生物流体中进行实时和连续的生物标记分析。综述深入探讨了各种核酸传感策略,强调了生物识别元件和信号转导机制的创新设计,从而实现植入式和可穿戴式应用。文章特别关注如何提高核酸传感器的选择性和灵敏度,这对于准确检测低水平生物标记物至关重要。将此类传感器集成到植入式和可穿戴式平台(包括微针阵列和柔性电子系统)中,可将其用于健康监测的体外设备。我们还探讨了这些传感器开发过程中遇到的技术挑战,如确保长期稳定性、管理生物流体动态的复杂性,以及满足实时、连续和无残留检测的需求。总之,这篇综述强调了这些传感器在未来医学工程中的重要性,对设计考虑因素和未来研究方向提出了见解,以克服现有限制,充分发挥基于核酸的电化学传感器在医疗保健应用中的潜力。
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引用次数: 0
Nature-inspired adhesive systems 受大自然启发的粘合剂系统。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-10 DOI: 10.1039/D3CS00764B
Ming Li, Anran Mao, Qingwen Guan and Eduardo Saiz

Many organisms in nature thrive in intricate habitats through their unique bio-adhesive surfaces, facilitating tasks such as capturing prey and reproduction. It's important to note that the remarkable adhesion properties found in these natural biological surfaces primarily arise from their distinct micro- and nanostructures and/or chemical compositions. To create artificial surfaces with superior adhesion capabilities, researchers delve deeper into the underlying mechanisms of these captivating adhesion phenomena to draw inspiration. This article provides a systematic overview of various biological surfaces with different adhesion mechanisms, focusing on surface micro- and nanostructures and/or chemistry, offering design principles for their artificial counterparts. Here, the basic interactions and adhesion models of natural biological surfaces are introduced first. This will be followed by an exploration of research advancements in natural and artificial adhesive surfaces including both dry adhesive surfaces and wet/underwater adhesive surfaces, along with relevant adhesion characterization techniques. Special attention is paid to stimulus-responsive smart artificial adhesive surfaces with tunable adhesive properties. The goal is to spotlight recent advancements, identify common themes, and explore fundamental distinctions to pinpoint the present challenges and prospects in this field.

自然界中的许多生物通过其独特的生物粘附表面在错综复杂的栖息地中茁壮成长,为捕捉猎物和繁殖等任务提供便利。值得注意的是,这些天然生物表面所具有的显著粘附特性主要源于它们独特的微纳米结构和/或化学成分。为了创造出具有卓越粘附能力的人造表面,研究人员深入研究了这些迷人的粘附现象的内在机理,从中汲取灵感。本文系统概述了具有不同粘附机制的各种生物表面,重点介绍了表面的微纳米结构和/或化学成分,为人工表面的设计提供了原则。本文首先介绍了天然生物表面的基本相互作用和粘附模型。随后将探讨天然和人工粘附表面的研究进展,包括干粘附表面和湿/水下粘附表面,以及相关的粘附表征技术。特别关注具有可调粘合特性的刺激响应型智能人工粘合表面。其目的是聚焦最新进展,确定共同主题,探讨基本区别,从而明确该领域当前的挑战和前景。
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引用次数: 0
Functionalized 2D membranes for separations at the 1-nm scale 用于 1 纳米尺度分离的功能化二维膜。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-10 DOI: 10.1039/D4CS00272E
Yuan Kang, Yuqi Wang, Hao Zhang, Zhouyou Wang, Xiwang Zhang and Huanting Wang

The ongoing evolution of two-dimensional (2D) material-based membranes has prompted the realization of mass separations at the 1-nm scale due to their well-defined selective nano- and subnanochannels. Strategic membrane functionalization is further found to be key to augmenting channel accuracy and efficiency in distinguishing ions, gases and molecules within this range and is thus trending as a research focus in energy-, resource-, environment- and pharmaceutical-related applications. In this review, we present the fundamentals underpinning functionalized 2D membranes in various separations, elucidating the critical “method–interaction–property” relationship. Starting with an introduction to various functionalization strategies, we focus our discussion on functionalization-induced channel-species interactions and reveal how they shape the transport- and operation-related features of the membrane in different scenarios. We also highlight the limitations and challenges of current functionalized 2D membranes and outline the necessary breakthroughs needed to apply them as reliable and high-performance separation units across industries in the future.

基于二维(2D)材料的膜不断发展,由于其具有明确的选择性纳米和亚纳米通道,促使实现了 1 纳米尺度的质量分离。战略性膜功能化被进一步发现是提高通道精度和效率的关键,可在此范围内区分离子、气体和分子,因此成为能源、资源、环境和制药相关应用的研究重点。在本综述中,我们介绍了各种分离中功能化二维膜的基本原理,阐明了关键的 "方法-相互作用-性能 "关系。从介绍各种官能化策略开始,我们重点讨论官能化引起的通道-物种相互作用,并揭示它们如何在不同情况下塑造膜的传输和操作相关特性。我们还强调了当前功能化二维膜的局限性和挑战,并概述了未来将其作为可靠、高性能分离装置应用于各行各业所需的必要突破。
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引用次数: 0
One-pot chemo- and photo-enzymatic linear cascade processes 一锅化学和光酶线性级联过程。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-05 DOI: 10.1039/D3CS00595J
J. M. Carceller, K. S. Arias, M. J. Climent, S. Iborra and A. Corma

The combination of chemo- and photocatalyses with biocatalysis, which couples the flexible reactivity of the photo- and chemocatalysts with the highly selective and environmentally friendly nature of enzymes in one-pot linear cascades, represents a powerful tool in organic synthesis. However, the combination of photo-, chemo- and biocatalysts in one-pot is challenging because the optimal operating conditions of the involved catalyst types may be rather different, and the different stabilities of catalysts and their mutual deactivation are additional problems often encountered in one-pot cascade processes. This review explores a large number of transformations and approaches adopted for combining enzymes and chemo- and photocatalytic processes in a successful way to achieve valuable chemicals and valorisation of biomass. Moreover, the strategies for solving incompatibility issues in chemo-enzymatic reactions are analysed, introducing recent examples of the application of non-conventional solvents, enzyme–metal hybrid catalysts, and spatial compartmentalization strategies to implement chemo-enzymatic cascade processes.

化学催化和光催化与生物催化的结合,将光催化剂和化学催化剂的灵活反应性与酶的高选择性和环境友好性结合在一起,形成了一种强大的有机合成工具。然而,将光催化剂、化学催化剂和生物催化剂结合在一起进行单级反应具有挑战性,因为所涉及的催化剂类型的最佳操作条件可能相当不同,而且催化剂的不同稳定性及其相互失活是单级反应过程中经常遇到的额外问题。本综述探讨了将酶与化学和光催化过程成功结合起来,以实现有价值化学品和生物质增值的大量转化和方法。此外,还分析了解决化学-酶反应中不相容问题的策略,介绍了应用非常规溶剂、酶-金属混合催化剂和空间分隔策略实施化学-酶级联过程的最新实例。
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引用次数: 0
Sodium layered oxide cathodes: properties, practicality and prospects 钠层状氧化物阴极:特性、实用性和前景。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-04 DOI: 10.1039/D4CS00415A
Yu-Jie Guo, Ruo-Xi Jin, Min Fan, Wen-Peng Wang, Sen Xin, Li-Jun Wan and Yu-Guo Guo

Rechargeable sodium-ion batteries (SIBs) have emerged as an advanced electrochemical energy storage technology with potential to alleviate the dependence on lithium resources. Similar to Li-ion batteries, the cathode materials play a decisive role in the cost and energy output of SIBs. Among various cathode materials, Na layered transition-metal (TM) oxides have become an appealing choice owing to their facile synthesis, high Na storage capacity/voltage that are suitable for use in high-energy SIBs, and high adaptivity to the large-scale manufacture of Li layered oxide analogues. However, going from the lab to the market, the practical use of Na layered oxide cathodes is limited by the ambiguous understanding of the fundamental structure-performance correlation of cathode materials and lack of customized material design strategies to meet the diverse demands in practical storage applications. In this review, we attempt to clarify the fundamental misunderstandings by elaborating the correlations between the electron configuration of the critical capacity-contributing elements (e.g., TM cations and oxygen anion) in oxides and their influence on the Na (de)intercalation (electro)chemistry and storage properties of the cathode. Subsequently, we discuss the issues that hinder the practical use of layered oxide cathodes, their origins and the corresponding strategies to address their issues and accelerate the target-oriented research and development of cathode materials. Finally, we discuss several new Na layered cathode materials that show prospects for next-generation SIBs, including layered oxides with anion redox and high entropy and highlight the use of layered oxides as cathodes for solid-state SIBs with higher energy and safety. In summary, we aim to offer insights into the rational design of high-performance Na layered oxide cathode materials towards the practical realization of sustainable electrochemical energy storage at a low cost.

可充电钠离子电池(SIB)是一种先进的电化学储能技术,具有减轻对锂资源依赖的潜力。与锂离子电池类似,正极材料对 SIB 的成本和能量输出起着决定性作用。在各种阴极材料中,Na 层状过渡金属(TM)氧化物因其易于合成、适合用于高能量 SIB 的高 Na 储存容量/电压以及对大规模制造 Li 层状氧化物类似物的高度适应性而成为一种有吸引力的选择。然而,从实验室到市场,Na 层状氧化物阴极的实际应用受到了限制,因为人们对阴极材料的基本结构-性能相关性认识不清,而且缺乏定制的材料设计策略来满足实际存储应用中的各种需求。在本综述中,我们试图通过阐述氧化物中关键容量贡献元素(如 TM 阳离子和氧阴离子)的电子构型与它们对纳(脱)闰(电)化学和阴极存储特性的影响之间的相关性来澄清基本误解。随后,我们讨论了阻碍层状氧化物阴极实际应用的问题、这些问题的根源以及解决这些问题的相应策略,从而加快以目标为导向的阴极材料研发。最后,我们讨论了几种新型 Na 层状阴极材料,包括具有阴离子氧化还原和高熵的层状氧化物,这些材料显示了下一代 SIB 的发展前景,并强调了将层状氧化物作为阴极用于具有更高能量和安全性的固态 SIB 的可能性。总之,我们的目标是为高性能 Na 层状氧化物阴极材料的合理设计提供见解,以切实实现低成本的可持续电化学储能。
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引用次数: 0
Outstanding Reviewers for Chemical Society Reviews in 2023 2023 年化学学会评论杰出审稿人。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-03 DOI: 10.1039/D4CS90046D

We would like to take this opportunity to thank all of Chemical Society Reviews’ reviewers for helping to preserve quality and integrity in chemical science literature. We would also like to highlight the Outstanding Reviewers for Chemical Society Reviews in 2023.

我们想借此机会感谢《化学学会评论》的所有审稿人,感谢他们帮助维护化学科学文献的质量和完整性。我们还想特别介绍一下 2023 年《化学学会评论》的杰出审稿人。
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引用次数: 0
Lymphoid organ-targeted nanomaterials for immunomodulation of cancer, inflammation, and beyond 淋巴器官靶向纳米材料用于癌症、炎症及其他免疫调节。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-03 DOI: 10.1039/D4CS00421C
Jessica C. Hsu, Peng Liu, Yangmeihui Song, Wenyu Song, Rachel J. Saladin, Ying Peng, Shuo Hu, Xiaoli Lan and Weibo Cai

Nanomaterials exhibit significant potential for stimulating immune responses, offering both local and systemic modulation across a variety of diseases. The lymphoid organs, such as the spleen and lymph nodes, are home to various immune cells, including monocytes and dendritic cells, which contribute to both the progression and prevention/treatment of diseases. Consequently, many nanomaterial formulations are being rationally designed to target these organs and engage with specific cell types, thereby inducing therapeutic and protective effects. In this review, we explore crucial cellular interactions and processes involved in immune regulation and highlight innovative nano-based immunomodulatory approaches. We outline essential considerations in nanomaterial design with an emphasis on their impact on biological interactions, targeting capabilities, and treatment efficacy. Through selected examples, we illustrate the strategic targeting of therapeutically active nanomaterials to lymphoid organs and the subsequent immunomodulation for infection resistance, inflammation suppression, self-antigen tolerance, and cancer immunotherapy. Additionally, we address current challenges, discuss emerging topics, and share our outlook on future developments in the field.

纳米材料在刺激免疫反应方面具有巨大潜力,可对多种疾病进行局部和全身调节。淋巴器官(如脾脏和淋巴结)是各种免疫细胞(包括单核细胞和树突状细胞)的家园,它们有助于疾病的发展和预防/治疗。因此,许多纳米材料配方正被合理设计为针对这些器官并与特定细胞类型接触,从而产生治疗和保护效果。在本综述中,我们将探讨参与免疫调节的关键细胞相互作用和过程,并重点介绍基于纳米的创新免疫调节方法。我们概述了纳米材料设计的基本考虑因素,重点是它们对生物相互作用、靶向能力和治疗效果的影响。通过精选的实例,我们说明了具有治疗活性的纳米材料对淋巴器官的战略靶向作用,以及随后对抗感染、炎症抑制、自我抗原耐受和癌症免疫疗法的免疫调节作用。此外,我们还探讨了当前面临的挑战,讨论了新出现的话题,并分享了我们对该领域未来发展的展望。
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引用次数: 0
Metal nanowire-based transparent electrode for flexible and stretchable optoelectronic devices 用于柔性和可拉伸光电器件的基于金属纳米线的透明电极
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-07-02 DOI: 10.1039/D4CS00080C
Yu Ding, Sixing Xiong, Lulu Sun, Yiying Wang, Yinhua Zhou, Yaowen Li, Jun Peng, Kenjiro Fukuda, Takao Someya, Ruiyuan Liu and Xiaohong Zhang

High-quality transparent electrodes are indispensable components of flexible optoelectronic devices as they guarantee sufficient light transparency and electrical conductivity. Compared to commercial indium tin oxide, metal nanowires are considered ideal candidates as flexible transparent electrodes (FTEs) owing to their superior optoelectronic properties, excellent mechanical flexibility, solution treatability, and higher compatibility with semiconductors. However, certain key challenges associated with material preparation and device fabrication remain for the practical application of metal nanowire-based electrodes. In this review, we discuss state-of-the-art solution-processed metal nanowire-based FTEs and their applications in flexible and stretchable optoelectronic devices. Specifically, the important properties of FTEs and a cost-benefit analysis of existing technologies are introduced, followed by a summary of the synthesis strategy, key properties, and fabrication technologies of the nanowires. Subsequently, we explore the applications of metal-nanowire-based FTEs in different optoelectronic devices including solar cells, photodetectors, and light-emitting diodes. Finally, the current status, future challenges, and emerging strategies in this field are presented.

高质量的透明电极是柔性光电器件不可或缺的组成部分,因为它们能保证足够的光透明度和导电性。与商用氧化铟锡相比,金属纳米线因其优越的光电特性、出色的机械灵活性、溶液处理能力以及与半导体更高的兼容性,被认为是柔性透明电极(FTE)的理想候选材料。然而,在基于金属纳米线的电极的实际应用中,与材料制备和器件制造相关的某些关键挑战依然存在。在本综述中,我们将讨论最先进的溶液处理金属纳米线基 FTE 及其在柔性和可拉伸光电器件中的应用。具体来说,首先介绍了 FTE 的重要特性和现有技术的成本效益分析,然后总结了纳米线的合成策略、关键特性和制造技术。随后,我们探讨了基于金属纳米线的 FTE 在太阳能电池、光电探测器和发光二极管等不同光电器件中的应用。最后,介绍了该领域的现状、未来挑战和新兴战略。
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引用次数: 0
SERS microscopy as a tool for comprehensive biochemical characterization in complex samples 将 SERS 显微镜作为复杂样品中全面生化特征描述的工具。
IF 40.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-06-27 DOI: 10.1039/D4CS00460D
Janina Kneipp, Stephan Seifert and Florian Gärber

Surface enhanced Raman scattering (SERS) spectra of biomaterials such as cells or tissues can be used to obtain biochemical information from nanoscopic volumes in these heterogeneous samples. This tutorial review discusses the factors that determine the outcome of a SERS experiment in complex bioorganic samples. They are related to the SERS process itself, the possibility to selectively probe certain regions or constituents of a sample, and the retrieval of the vibrational information in order to identify molecules and their interaction. After introducing basic aspects of SERS experiments in the context of biocompatible environments, spectroscopy in typical microscopic settings is exemplified, including the possibilities to combine SERS with other linear and non-linear microscopic tools, and to exploit approaches that improve lateral and temporal resolution. In particular the great variation of data in a SERS experiment calls for robust data analysis tools. Approaches will be introduced that have been originally developed in the field of bioinformatics for the application to omics data and that show specific potential in the analysis of SERS data. They include the use of simulated data and machine learning tools that can yield chemical information beyond achieving spectral classification.

细胞或组织等生物材料的表面增强拉曼散射(SERS)光谱可用于从这些异质样品的纳米体积中获取生化信息。本教程综述讨论了决定复杂生物有机样品 SERS 实验结果的因素。这些因素涉及 SERS 过程本身、选择性探测样品中某些区域或成分的可能性,以及检索振动信息以识别分子及其相互作用。在介绍了生物兼容环境下 SERS 实验的基本方面之后,举例说明了典型显微镜环境下的光谱学,包括将 SERS 与其他线性和非线性显微镜工具相结合的可能性,以及利用提高横向和时间分辨率的方法。特别是 SERS 实验中数据的巨大差异需要强大的数据分析工具。我们将介绍最初在生物信息学领域开发的方法,这些方法适用于omics数据,并在SERS数据分析中显示出特殊的潜力。这些方法包括使用模拟数据和机器学习工具,这些工具不仅能实现光谱分类,还能产生化学信息。
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引用次数: 0
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