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Neural-network-based molecular dynamics simulations reveal that proton transport in water is doubly gated by sequential hydrogen-bond exchange 基于神经网络的分子动力学模拟揭示了质子在水中的迁移是由连续的氢键交换双重控制的
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-20 DOI: 10.1038/s41557-024-01593-y
Axel Gomez, Ward H. Thompson, Damien Laage
The transport of excess protons in water is central to acid–base chemistry, biochemistry and energy production. However, elucidating its mechanism has been challenging. Recent nonlinear vibrational spectroscopy experiments could not be explained by existing models. Here we use both vibrational spectroscopy calculations and neural-network-based molecular dynamics simulations that account for nuclear quantum effects for all atoms to determine the proton transport mechanism. Our simulations reveal an equilibrium between two stable proton-localized structures with distinct Eigen-like and Zundel-like hydrogen-bond motifs. Proton transport follows a three-step mechanism gated by two successive hydrogen-bond exchanges: the first reduces the proton-acceptor water coordination, leading to proton transfer, and the second, the rate-limiting step, prevents rapid back-transfer by increasing the proton-donor coordination. This sequential mechanism is consistent with experimental characterizations of proton diffusion, explaining the low activation energy and the prolonged intermediate lifetimes in vibrational spectroscopy. These results are crucial for understanding proton dynamics in biochemical and technological systems. Recent vibrational spectroscopy experiments suggested that excess proton transport in water is more complex than previously thought. Now the proton transport mechanism has been explored using neural-network-based simulations and related to experimental measurements through vibrational spectra calculations. It was observed to be a three-step process gated by two successive hydrogen-bond exchanges.
过量质子在水中的迁移是酸碱化学、生物化学和能源生产的核心。然而,阐明其机理一直是一项挑战。现有模型无法解释最近的非线性振动光谱实验。在这里,我们利用振动光谱计算和基于神经网络的分子动力学模拟(考虑到所有原子的核量子效应)来确定质子传输机制。我们的模拟揭示了两种稳定的质子定位结构之间的平衡,这两种结构具有不同的类 Eigen 和类 Zundel 氢键图案。质子迁移遵循一个由两次连续氢键交换驱动的三步机制:第一步降低质子受体水配位,导致质子转移;第二步,即限制速率的一步,通过增加质子供体配位防止快速反向转移。这种顺序机制与质子扩散的实验特征一致,解释了振动光谱中的低活化能和中间寿命延长的原因。这些结果对于理解生化和技术系统中的质子动力学至关重要。
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引用次数: 0
Machine learning trims the peptide drug design process to a sweet spot 机器学习将多肽药物设计过程缩减至最佳状态
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-16 DOI: 10.1038/s41557-024-01610-0
Chloe E. Markey, Daniel Reker
Drugs that target peptide hormone receptors are of great interest in the treatment of type 2 diabetes. In spite of limited data and vast design spaces, a bespoke computational pipeline has designed peptides that target two receptors with high potency.
靶向肽类激素受体的药物在治疗 2 型糖尿病方面具有重大意义。尽管数据有限,设计空间巨大,但一个定制的计算管道已经设计出了针对两种受体的高效力多肽。
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引用次数: 0
Sulfone cross-coupling outcompetes proton transfer 砜交叉偶联取代质子转移
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-15 DOI: 10.1038/s41557-024-01612-y
Chloe D. Wong, Elizabeth R. Jarvo
The development of enantiospecific sulfone reactions has been hindered by the inherent acidity of sulfones, which result in deleterious racemization. Now, the synthesis of enantioenriched diarylalkanes has been reported via sufficiently fast cross-coupling that circumvents racemization of the chiral sulfone.
砜的固有酸性会导致有害的消旋化,这阻碍了对映体特异性砜反应的发展。现在,有报告称,通过足够快的交叉偶联,可以避免手性砜的消旋化,从而合成对映体丰富的二芳基烷烃。
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引用次数: 0
A dynamic metal–organic framework photocatalyst 动态金属有机框架光催化剂
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-14 DOI: 10.1038/s41557-024-01607-9
Photocatalytic overall water splitting (OWS) is highly desirable for hydrogen production but challenging owing to rapid charge recombination. We demonstrate a dynamic metal–organic framework (MOF) photocatalyst that achieves OWS via one-step photoexcitation. Upon excitation by light, the MOF undergoes a structural twist that suppresses charge recombination and achieves OWS.
光催化整体水分离(OWS)对于制氢来说非常理想,但由于电荷的快速重组而具有挑战性。我们展示了一种动态金属有机框架(MOF)光催化剂,可通过一步光激发实现 OWS。在光的激发下,MOF 会发生结构扭曲,从而抑制电荷重组并实现 OWS。
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引用次数: 0
Discovery of the selenium-containing antioxidant ovoselenol derived from convergent evolution 从聚合进化中发现含硒抗氧化剂卵硒醇
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-14 DOI: 10.1038/s41557-024-01600-2
Chase M. Kayrouz, Kendra A. Ireland, Vanessa Y. Ying, Katherine M. Davis, Mohammad R. Seyedsayamdost
Selenium is an essential micronutrient, but its presence in biology has been limited to protein and nucleic acid biopolymers. The recent identification of a biosynthetic pathway for selenium-containing small molecules suggests that there is a larger family of selenometabolites that remains to be discovered. Here we identify a recently evolved branch of abundant and uncharacterized metalloenzymes that we predict are involved in selenometabolite biosynthesis using a bioinformatic search strategy that relies on the mapping of composite active site motifs. Biochemical studies confirm this prediction and show that these enzymes form an unusual C–Se bond onto histidine, thus giving rise to a distinct selenometabolite and potent antioxidant that we have termed ovoselenol. Aside from providing insights into the evolution of this enzyme class and the structural basis of C–Se bond formation, our work offers a blueprint for charting the microbial selenometabolome in the future. Although biosynthetic pathways of selenium-containing macromolecules have been known for decades, pathways for specific incorporation of selenium into small molecules have only recently begun to be uncovered. Now the selenometabolome is expanded further through the discovery and biosynthetic elucidation of ovoselenol, a selenium-containing antioxidant found in marine microorganisms.
硒是人体必需的微量元素,但它在生物学中的存在仅限于蛋白质和核酸生物聚合物。最近发现的含硒小分子生物合成途径表明,还有一个更大的硒代谢物家族有待发现。在这里,我们利用生物信息学搜索策略,通过绘制复合活性位点图案,发现了最近进化的、丰富的、未表征的金属酶分支,并预测它们参与了硒代谢物的生物合成。生化研究证实了这一预测,并表明这些酶在组氨酸上形成了不寻常的 C-Se键,从而产生了一种独特的硒代谢物和强效抗氧化剂,我们称之为卵硒醇。我们的工作不仅为了解这类酶的进化和 C-Se 键形成的结构基础提供了见解,还为未来绘制微生物硒代谢组提供了蓝图。
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引用次数: 0
Dynamic-to-static switch of hydrogen bonds induces a metal–insulator transition in an organic–inorganic superlattice 氢键的动静转换诱导有机-无机超晶格中的金属-绝缘体转变
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-14 DOI: 10.1038/s41557-024-01566-1
Zhenkai Xie, Rui Luo, Tianping Ying, Yurui Gao, Boqin Song, Tongxu Yu, Xu Chen, Munan Hao, Congcong Chai, Jiashu Yan, Zhiheng Huang, Zhiguo Chen, Luojun Du, Chongqin Zhu, Jiangang Guo, Xiaolong Chen
Hydrogen bonds profoundly influence the fundamental chemical, physical and biological properties of molecules and materials. Owing to their relatively weaker interactions compared to other chemical bonds, hydrogen bonds alone are generally insufficient to induce substantial changes in electrical properties, thus imposing severe constraints on their applications in related devices. Here we report a metal–insulator transition controlled by hydrogen bonds for an organic–inorganic (1,3-diaminopropane)0.5SnSe2 superlattice that exhibits a colossal on–off ratio of 107 in electrical resistivity. The key to inducing the transition is a change in the amino group’s hydrogen-bonding structure from dynamic to static. In the dynamic state, thermally activated free rotation continuously breaks and forms transient hydrogen bonds with adjacent Se anions. In the static state, the amino group forms three fixed-angle positions, each separated by 120°. Our findings contribute to the understanding of electrical phenomena in organic–inorganic hybrid materials and may be used for the design of future molecule-based electronic materials. Hydrogen bonds impact the chemical, physical and biological properties of molecular materials, but are rarely able to induce significant changes in electrical properties. Now a dynamic-to-static transition of hydrogen bonds in an organic–inorganic superlattice has been shown to yield a metal–insulator transition with an on–off ratio of 107 in electrical resistivity.
氢键深刻影响着分子和材料的基本化学、物理和生物特性。与其他化学键相比,氢键的相互作用相对较弱,因此仅靠氢键一般不足以引起电学性质的实质性变化,从而严重制约了氢键在相关设备中的应用。在这里,我们报告了由氢键控制的有机-无机(1,3-二氨基丙烷)0.5SnSe2 超晶格的金属-绝缘体转变,其电阻率的开关比高达 107。诱导这种转变的关键在于氨基的氢键结构从动态转变为静态。在动态状态下,热激活的自由旋转不断断裂并与相邻的硒阴离子形成瞬时氢键。在静态下,氨基形成三个固定角度位置,每个位置之间相隔 120°。我们的发现有助于理解有机-无机杂化材料中的电现象,并可用于设计未来的分子电子材料。
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引用次数: 0
Author Correction: Repurposing a plant peptide cyclase for targeted lysine acylation 作者更正:重新利用植物肽环化酶进行靶向赖氨酸酰化。
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-13 DOI: 10.1038/s41557-024-01625-7
Fabian B. H. Rehm, Tristan J. Tyler, Yan Zhou, Yen-Hua Huang, Conan K. Wang, Nicole Lawrence, David J. Craik, Thomas Durek
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引用次数: 0
Publisher Correction: Establishing the origin of Marcus-inverted-region behaviour in the excited-state dynamics of cobalt(III) polypyridyl complexes 出版商更正:确定钴(III)多吡啶络合物激发态动力学中马库斯-反区域行为的起源。
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-13 DOI: 10.1038/s41557-024-01615-9
Atanu Ghosh, Jonathan T. Yarranton, James K. McCusker
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引用次数: 0
Multi-tiered chemical proteomic maps of tryptoline acrylamide–protein interactions in cancer cells 癌细胞中色素丙烯酰胺与蛋白质相互作用的多层化学蛋白质组图谱
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-13 DOI: 10.1038/s41557-024-01601-1
Evert Njomen, Rachel E. Hayward, Kristen E. DeMeester, Daisuke Ogasawara, Melissa M. Dix, Tracey Nguyen, Paige Ashby, Gabriel M. Simon, Stuart L. Schreiber, Bruno Melillo, Benjamin F. Cravatt
Covalent chemistry is a versatile approach for expanding the ligandability of the human proteome. Activity-based protein profiling (ABPP) can infer the specific residues modified by electrophilic compounds through competition with broadly reactive probes. However, the extent to which such residue-directed platforms fully assess the protein targets of electrophilic compounds in cells remains unclear. Here we evaluate a complementary protein-directed ABPP method that identifies proteins showing stereoselective reactivity with alkynylated, chiral electrophilic compounds—termed stereoprobes. Integration of protein- and cysteine-directed data from cancer cells treated with tryptoline acrylamide stereoprobes revealed generally well-correlated ligandability maps and highlighted features, such as protein size and the proteotypicity of cysteine-containing peptides, that explain gaps in each ABPP platform. In total, we identified stereoprobe binding events for >300 structurally and functionally diverse proteins, including compounds that stereoselectively and site-specifically disrupt MAD2L1BP interactions with the spindle assembly checkpoint complex leading to delayed mitotic exit in cancer cells. The ligandability of the human proteome can be expanded using covalent chemistry. A multi-tiered chemical proteomic strategy now provides in-depth maps of tryptoline acrylamide–protein interactions in cancer cells. This platform afforded the discovery of stereoselective covalent ligands for hundreds of human proteins, including compounds that disrupt protein–protein interactions regulating the cell cycle.
共价化学是一种扩展人类蛋白质组配体的多功能方法。基于活性的蛋白质分析(ABPP)可以通过与广义反应探针的竞争来推断亲电化合物修饰的特定残基。然而,这种残基定向平台能在多大程度上全面评估亲电化合物在细胞中的蛋白质靶标仍不清楚。在这里,我们评估了一种互补的蛋白质定向 ABPP 方法,该方法可识别与炔化手性亲电化合物--立体探针--发生立体选择性反应的蛋白质。通过整合用色啉丙烯酰胺立体配体处理癌细胞的蛋白质和半胱氨酸定向数据,我们发现了大致相关的配体性图谱,并强调了蛋白质大小和含半胱氨酸肽的蛋白型等特征,这些特征解释了每个 ABPP 平台中存在的差距。我们总共鉴定了 300 种结构和功能各异的蛋白质的立体探针结合事件,其中包括立体选择性和位点特异性地破坏 MAD2L1BP 与纺锤体组装检查点复合物相互作用的化合物,这些化合物会导致癌细胞的有丝分裂退出延迟。
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引用次数: 0
Dynamic structural twist in metal–organic frameworks enhances solar overall water splitting 金属有机框架的动态结构扭曲增强了太阳能整体水分离能力
IF 19.2 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2024-08-12 DOI: 10.1038/s41557-024-01599-6
Kang Sun, Yan Huang, Fusai Sun, Qingyu Wang, Yujie Zhou, Jingxue Wang, Qun Zhang, Xusheng Zheng, Fengtao Fan, Yi Luo, Jun Jiang, Hai-Long Jiang
Photocatalytic overall water splitting holds great promise for solar-to-hydrogen conversion. Maintaining charge separation is a major challenge but is key to unlocking this potential. Here we discovered a metal–organic framework (MOF) that shows suppressed charge recombination. This MOF features electronically insulated Zn2+ nodes and two chemically equivalent, yet crystallographically independent, linkers. These linkers behave as an electron donor–acceptor pair with non-overlapping band edges. Upon photoexcitation, the MOF undergoes a dynamic excited-state structural twist, inducing orbital rearrangements that forbid radiative relaxation and thereby promote a long-lived charge-separated state. As a result, the MOF achieves visible-light photocatalytic overall water splitting, in the presence of co-catalysts, with an apparent quantum efficiency of 3.09 ± 0.32% at 365 nm and shows little activity loss in 100 h of consecutive runs. Furthermore, the dynamic excited-state structural twist is also successfully extended to other photocatalysts. This strategy for suppressing charge recombination will be applicable to diverse photochemical processes beyond overall water splitting. Solar water splitting holds great promise for hydrogen production but is significantly hindered by rapid recombination of photogenerated charges. Now a metal–organic framework photocatalyst has been shown to undergo, upon photoexcitation, a dynamic excited-state structural twist that greatly suppresses charge recombination to enable efficient photocatalytic overall water splitting.
光催化整体水分离为太阳能转化为氢气带来了巨大前景。保持电荷分离是一项重大挑战,但也是释放这一潜力的关键。在这里,我们发现了一种可抑制电荷重组的金属有机框架(MOF)。这种 MOF 具有电子绝缘的 Zn2+ 节点和两个化学等价但晶体学上独立的连接体。这些连接体作为一对电子供体-受体,具有不重叠的带边。光激发时,MOF 会发生动态激发态结构扭曲,诱发轨道重排,禁止辐射弛豫,从而促进长寿命的电荷分离态。因此,在助催化剂存在的情况下,MOF 实现了可见光光催化整体水分离,在 365 纳米波长下的表观量子效率为 3.09 ± 0.32%,并且在连续运行 100 小时后活性几乎没有下降。此外,动态激发态结构扭曲还成功地扩展到了其他光催化剂。这种抑制电荷重组的策略将适用于整体水分离以外的各种光化学过程。
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Nature chemistry
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