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Computational protein design and structure prediction—the 2024Nobel prize in chemistry

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Science China chemistry 2025年

作者： Peilong Lu Lei Liu School of Life Sciences and Research Center for Industries of the Future Westlake University Tsinghua-Peking Joint Center for Life Sciences Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Center for Synthetic and Systems Biology Department of Chemistry Tsinghua University

The 2024 Nobel prize in chemistry recognizes groundbreaking advancements in protein science, highlighting the power of artificial intelligence (AI) to decipher and design the molecular machinery of life. Half of the prize was awarded to David Baker for the computational design of proteins; the other to Demis Hassabis and John Jumper for their AI-driven predictions of protein structures. This article briefly reviews their achievements, and discusses the opportunities and directions that their work has enabled (Figure1).

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Identifying the dynamic behaviors in complete reconstruction of Co-based complex precatalysts during electrocatalytic oxygen evolution

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Journal of Energy chemistry 2025年第1期100卷 226-233页

作者： Jingfang Zhang Danyang Wu Linke Cai Youluan Lu Fanpeng Cheng Lijuan Shi Qun Yi Yao Liu Yi Huang Key laboratory of Green Chemical Engineering Process of Ministry of Education Engineering Research Center of Phosphorus Resources Development and Utilization of Ministry of Education Hubei Key Laboratory of Novel Reactor and Green Chemical Technology School of Chemical Engineering & Pharmacy Wuhan Institute of Technology Key laboratory of Pesticide & Chemical Biology of Ministry of Education Engineering Research Center of Photoenergy Utilization for Pollution Control and Carbon Reduction of Ministry of Education College of Chemistry Central China Normal University College of Materials Science and Engineering Fuzhou University

Transition metal-based nanomaterials have emerged as promising electrocatalysts for oxygen evolution reaction（OER）. Considerable research efforts have shown that self-reconstruction occurs on these nanomaterials under operating conditions of OER process. However, most of them undergo incomplete reconstruction with limited thickness of reconstruction layer, leading to low component utilization and arduous exploration of real catalytic mechanism. Herein, we identify the dynamic behaviors in complete reconstruction of Co-based complexes during OER. The hollow phytic acid（PA） cross-linked CoFe-based complex nanoboxes with porous nanowalls are designed because of their good electrolyte penetration and mass transport ability, in favor of the fast and complete reconstruction. A series of experiment characterizations demonstrate that the reconstruction process includes the fast substitution of PA by OH-to form Co（Fe）(OH)xand subsequent potential-driven oxidation to Co（Fe）OOH. The obtained CoFeOOH delivers a low overpotential of 290 mV at a current density of 10 mA cm-2and a long-term *** experiment results together with theory calculations reveal that the Fe incorporation can result in the electron rearrangement of reconstructed CoFeOOH and optimization of their electronic structure,accounting for the enhanced OER activity. The work provides new insights into complete reconstruction of metal-based complexes during OER and offers guidelines for rational design of high-performance electrocatalysts.

关键词： Oxygen evolution reaction

Facile Fabrication of Aggregation-induced Emission Based Red Fluorescent Organic Nanoparticles for Cell Imaging

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Chinese Journal of Polymer Science 2014年第7期32卷 871-879页

作者：张锡奇 Xiao-yong Zhang Bin Yang 危岩 Department of chemistry and Key laboratory of bioorganic phosphorus chemistry & Chemical Biology(Ministry of Education) Tsinghua University

A cyano-substituted diarylethlene derivative aggregation-induced emission （ALE） dye with two amino end-groups and 4,4＇-（hexafluoroisopropylidene）diphthalic anhydride were facilely incorporated into red fluorescent organic nanoparticles （FONs） via room temperature anhydride ring-opening polymerization under an air atmosphere. These obtained RO-HFDA FONs were characterized by a series of techniques including gel permeation chromatography, Fourier transform infrared spectroscopy, size distribution and zeta potential measurements, UV-Vis absorption spectrum, fluorescent spectroscopy and transmission electron microscopy. Biocompatibility evaluation and cell uptake behavior of RO-HFDA FONs were further investigated to explore their potential biomedical application. We demonstrated that such FONs showed high water dispersibility, stable uniform spherical morphology （150-200 nm）, broad excitation band （350-605 nm）, intense red fluorescence （627 nm） and excellent biocompatibility, making them promising for cell imaging applications.

关键词： Cyano-substituted diarylethlene derivative Aggregation-induced emission Anhydride ring-opening polymerization Red fluorescent organic nanoparticles Cell imaging.

Rearrangement mechanism of the sodium adducts of Fmoc protected amino acids

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Chinese Science Bulletin 2003年第21期48卷 2317-2319页

作者： DU Jintang, LI Yanmei, ZHU Zhentai, CHEN Yi & ZHAO Yufen laboratory of bioorganic phosphorus chemistry, Department of Chem-istry, Tsinghua University, Beijing 100084, China Correspondence should be addressed to Li Yanmei (e-mail: liym@mail. ***) laboratory for bioorganic phosphorus chemistry Department of Chemistry Tsinghua University China

The cationized 9-fluorenylmethoxycarbonyl (Fmoc) protected amino acids were analyzed by the electros-pray ionization tandem mass spectrometry (ESI-MS/MS). A rearrangement reaction leading to the C-terminal hydroxyl group transfer was observed. The sodium adducts of Fmoc-OH was formed. A possible rearrangement mechanism was proposed. The rearrangement reaction depended on the Fmoc group, metal ions and metal ion radius. It was shown that the Fmoc group has a strong affinity to the hydroxyl group in the gas phase.

关键词：氨基酸钠羟基重组机制金属离子

Synthesis and Crystal Structure of (1-Naphthyl){[3- (2,6-dibromo-4-methylphenylimino)methyl]-5-chloro- 2-hydroxy-benzaldehyde}(triphenylphosphine) Nickel(II) Triphenylphosphine

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Chinese Journal of Structural chemistry 2006年第1期25卷 73-77页

作者：江艳烽席婵娟阳香华 Key laboratory for bioorganic phosphorus chemistry of Ministry of Education Department of Chemistry Tsinghua University Beijing 100084 China

The crystal of the title compound, [Ni（C15HgBr2ClNO2）（C18H15P）（C10H7）]（C18H15P）, has been prepared and confirmed by X-ray diffraction. The crystal belongs to the triclinic system, space group PI with a = 9.991（3）, b = 15.250（4）, c = 18.542（5） A, α = 104.927（5）, β = 104.009（6）, γ = 94.422（6）°, V= 2619.2（11）A^3, Z = 2, Mr = 1140.91, Dc= 1.447 g/cm^3, F（000） = 1160 and μ（MoKα） = 2.053 mm^-1. The structure is refined to R = 0.0779 for 3773 observed reflections with I 〉 2σ（I） and wR = 0.1694 for 9026 unique reflections. The crystal （1-PPh3） is composed of neutral nickel（Ⅱ） complexes and co-crystallized PPh3 molecules. Intramolecular C-H...π interactions between C-H bond of the aldehyde group and phenyl ring of the coordinated PPh3 molecule in the nickel（Ⅱ） complex are observed, and intermolecular π-π interactions between neutral nickel（Ⅱ） complexes are also found in the crystal.

关键词： nickel(Ⅱ) complex PPh3 C-H...π interactions π-π interactions

Synthesis of Ras proteins and their application in biofunctional studies

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Chinese Chemical Letters 2018年第7期29卷 1043-1050页

作者： Jun Hu Pengcheng Zhu Yanmei Li Yongxiang Chen Key laboratory of bioorganic phosphorus chemistry and Chemical Biology(Ministry of Education) Department of ChemistryTsinghua University

Approximately 30% of human cancers are associated with RAS mutation. Ras proteins on the plasma membrane regulate a plenty of important cellular processes. The post-translational modifications(PTMs)of Ras proteins like lipidation and methylation are crucial for their correct cellular localization and biological function. Hence, obtaining Ras proteins with different kinds of modifications is the necessary prerequisite to investigate their biological properties at molecular level. In this review, we mainly summarize the developed strategies including chemical total synthesis, biosynthesis and semi-synthesis for producing Ras proteins with modifications and their application in biological studies.

关键词： Ras Lipopeptides Semi-synthesis Multi-PTMs Biophysical function

FABRICATION OF HIGHLY HYDROPHOBIC FILMS OF POLY(3-HEXADECYL PYRROLE) NANOPARTICLES BY LANGMUIR-BLODGETT TECHNIQUE

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Chinese Journal of Polymer Science 2006年第5期24卷 457-462页

作者：石高全 Department of chemistry and bioorganic phosphorus Lab Tsinghua University Beijing 100084 China

Thin films of poly（3-hexadecyl pyrrole）（P3HDP） nanoparticles have been fabricated by using Langmuir-Blodgett film deposition technique. The structures and morphology of the films were studied by using infrared spectroscopy, scanning and transmission microscopes. The experimental results demonstrated that the nanoparticles were formed by self-assembling P3HDP at air-water surface. The water contact angles of these films with different deposition layers were measured to be as high as 110°.

关键词： Poly(3-hexadecyl pyrrole) LB technique High hydrophobicity.

A microchip to analyze single crystal growth and size-controllability

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Science China chemistry 2009年第7期52卷 1014-1020页

作者： PANG YuanFeng LIU JiangJiang LI HaiFang LIN JinMing The Key laboratory of bioorganic phosphorus chemistry and Chemical Biology Department of ChemistryTsinghua UniversityBeijing 100084China

A microfluidic device to control single crystallization on the micron scale has been developed. The salt solution was stored in the nano-volume gaps between the arrays of protrudent circular plots in the microchip. The mixed organic solvent was injected into the chip as the counter diffusion phase for crystallization forming. This device provides a liquid-liquid interface through which only one phase flows while the other stays at the fixed plot. Therefore, it is possible to control the position of crystallization on the fixed plot. We can control the size and the uniformity of single crystals from 5 to 50 μm in length by adjusting the relative factors, such as interface lifetime, breeds of the mix-organic solvents and injecting velocities. The longer interface lifetime and lower organic solvent injecting velocities can bring up larger and more asymmetric crystals, which nearly shows the same trend compared with the macroscopic crystallization. Finally, the effect of the surfactant on the crystallization in the microdevice was studied. By adding the surfactant into the liquid-liquid interface, smaller sizes of crystals can be obtained without changing the crystal configuration.

关键词： microfluidic device single crystallization liquid-liquid interface size controllability

Stereoselective Synthesis and Crystal Structure Analysis of N-Naphthyl-2-deoxy-α-D-ribopyranosylamine

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Chinese Journal of Structural chemistry 2009年第6期28卷 761-765页

作者：尚培华成昌梅杨永冲王如骥赵玉芬 Key laboratory of bioorganic phosphorus chemistry & Chemical Biology (Ministry of Education) Department of Chemistry Tsinghua University

A new compound N-naphthyl-2-deoxy-α-D-ribopyranosylamine was synthesized and structurally determined. It crystallizes in the orthorhombic system, space group P212121 with a = 8.361（2）, b = 12.432（3）, c = 12.791（4） A^°, Z= 4, V= 1329.6（6） A^°^3, Dc= 1.295 g/cm^3, F（000） = 552, Cl5H17NO3 and Mr= 259.30. All the active hydrogen atoms are involved in the formation of hydrogen bonds in the molecule.

关键词： N-naphthyl-2-deoxy-α-D-ribopyranosylamine synthesis X-ray diffraction crystal structure