De-Xian Wang’s research while affiliated with Chinese Academy of Sciences and other places

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Publications (211)


Inherently chiral molecular barrels via directional cascade hooping
  • Article

June 2025

Chinese Chemical Letters

Hao Zhou

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Xu-Dong Wang

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Qi-Qiang Wang

Figure 1: (a, b) Crystal structure of B4aH (hydrogen atoms are omitted for clarity), and (c) the stacking structure of the crystal of B4aH (the blue dotted lines represent hydrogen bonds).
Figure 2: (a) The structures of host and guests, (b) 1 H NMR spectra (298 K, 400 MHz, CD 3 CN) of B4aH upon titration with C6 2− (c(B4aH) = 1 mM), (c) chemical shift changes of H a versus titration equivalents c(dicarboxylate)/c(B4aH), and (d) association constants of host and guests.
Scheme 1: Synthesis of ultracycles.
Dicarboxylate recognition based on ultracycle hosts through cooperative hydrogen bonding and anion–π interactions
  • Article
  • Full-text available

May 2025

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14 Reads

Beilstein Journal of Organic Chemistry

The efficient binding of dicarboxylates represents an important yet challenging issue in supramolecular chemistry. In this study, we designed functional ultracycles as hosts to accommodate large organic dicarboxylate anions. These ultracycles were synthesized via a one-pot strategy starting from macrocyclic precursors. Host–dicarboxylate binding was investigated using ¹ H NMR titrations, revealing that B4aH exhibits strong binding affinities toward a series of dicarboxylates, with association constants reaching up to 6896 M ⁻¹ . The selectivity for heptanedioate ( C7 ²⁻ ) was attributed to cooperative hydrogen bonding, anion–π interactions, and a size-matching effect, as supported by DFT optimizations.

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Barbiturate-containing macrocycles: synthesis, structure and anion recognition through anion-carbonyl interactions

April 2025

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10 Reads

Science China-Chemistry

Anion-carbonyl interaction is a newly developed non-covalent bond, and its application as a driving force in supramolecular chemistry deserves exploration. Herein, a series of barbiturate-containing macrocycles were synthesized using macrocycle-to-macrocycle transformation or one-pot macrocyclization. Various structural conformations arising from the interplay of non-aromatic barbiturate and benzene rings through N–C rotations in solution were revealed. The macrocycles featuring carbonyl donors and acceptors resulted in unique self-assembly structures and host-guest complexes in the crystalline state. The [3+3] macrocycle 7a was applied as a host molecule to investigate the complexation with anions by 13C nuclear magnetic resonance (NMR) titrations, which showed selective binding towards malonate with an association constant of Ka(1:1) = 13.2 ± 1.57 M−1. Multiple anion-carbonyl interactions between 7a and malonate were revealed by density functional theory (DFT) optimization of the complex.


C 3-symmetric aromatic triimides as useful building blocks for supramolecular chemistry and advanced materials

March 2025

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22 Reads

Chemical Society Reviews

C 3-symmetric aromatic triimides (ATIs) represent an interesting class of electron-deficient molecular backbones, characterized by π-conjugated aromatic cores symmetrically substituted with three imide groups. Their unique structural and electronic features, combined with exceptional stability and straightforward N-functionalization at three imide sites, make ATIs promising as versatile building blocks for applications in supramolecular chemistry and materials science. Despite their promising attributes, research on ATIs remains underexplored compared to the extensively studied aromatic imides and diimides, largely due to the synthetic challenges involved in constructing three imide groups on the aromatic frameworks. In recent years, advances in synthetic protocols have significantly propelled ATI-related chemistry, expanding their applications in the realm of functional materials. This review compiles advancements in the synthesis, structural and physicochemical properties, and applications of ATIs in supramolecular chemistry and advanced materials. We anticipate that this review will not only draw greater attention to ATIs but also serve as a valuable guide for future research into these molecular building blocks.




Workflow of machine learning-assisted amidase-catalytic enantioselectivity prediction and rational design of variants
This workflow includes several key steps: data collection and feature engineering, model training, virtual screening, and rational design of protein variants. Machine learning classifiers are labeled in blue color.
Comparison of model predictions with experimental measurements towards new substrates
Predicted and measured results of biocatalysis of substrates 1a (A) and 3 (B). The detailed experimental procedures are given in SI. Amide groups are labeled in blue and carboxylic acid ester groups are labeled in red.
ML prediction of biocatalytic enantioselectivity toward substrates 1a-l
Positive and negative results are represented in gray and white grids, respectively. The labels of para-substituented substrates are highlighted in italics. Substrates with predicted −ΔΔG≠\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-\Delta \Delta {G}^{\ne }$$\end{document} values < 1.86, between 1.86 and 2.40, between 2.40 and 3.00 are labeled in black, blue and red, respectively.
Molecular docking studies based on virtual screening results
Molecular docking of the substrate (R)−1a (A), (S)−1a (B) and (S)−1i (C) into the active site of amidase. protein in white cartoon, oxygen in red, nitrogen in blue, residues I198 and W328 in green, and carbon of substrates in cyan. The key interatomic distances are highlighted by red dashed lines with values. The figure was created using PyMOL⁶⁷.
Measured E values of biocatalysis toward substrate 1a by amidase variants
The E values are displayed above the bars, while the variants are labeled below. The detailed data was shown in Table S7.
Machine learning-assisted amidase-catalytic enantioselectivity prediction and rational design of variants for improving enantioselectivity

October 2024

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124 Reads

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5 Citations

Biocatalysis is an attractive approach for the synthesis of chiral pharmaceuticals and fine chemicals, but assessing and/or improving the enantioselectivity of biocatalyst towards target substrates is often time and resource intensive. Although machine learning has been used to reveal the underlying relationship between protein sequences and biocatalytic enantioselectivity, the establishment of substrate fitness space is usually disregarded by chemists and is still a challenge. Using 240 datasets collected in our previous works, we adopt chemistry and geometry descriptors and build random forest classification models for predicting the enantioselectivity of amidase towards new substrates. We further propose a heuristic strategy based on these models, by which the rational protein engineering can be efficiently performed to synthesize chiral compounds with higher ee values, and the optimized variant results in a 53-fold higher E-value comparing to the wild-type amidase. This data-driven methodology is expected to broaden the application of machine learning in biocatalysis research.


Spontaneous Transition between Multiple Conductance States and Rectifying Behaviors in an Artificial Single‐Molecule Funnel

August 2024

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4 Reads

Angewandte Chemie

It has long been an aspirational goal to create artificial channel structures that replicate the feat achieved by ion channel proteins. Biological ion channels occasionally demonstrate multiple conductance states (known as subconductance), remaining a challenging property to achieve in artificial channel molecules. We report a funnel‐shaped single‐molecule channel constructed by an electron‐deficient macrocycle and two electron‐deficient aromatic imide arms. Planar lipid bilayer measurements reveal distinct current recordings, including a closed state, two conducting states, and spontaneous transitions between the three states, resembling the events seen in biological ion channels. The transitions result from conformational changes induced by chloride transport in the channel molecule. Both opening states show a non‐linear and rectifying I–V relationship, indicating voltage‐dependent transport due to the asymmetrical channel structure. This work could enhance our understanding of ion permeation and channel opening mechanism.


(a) The structure of artificial ion channel 1 consisting of membrane anchor, selectivity filer and electron‐deficient arm. (b) Schematic illustration of chloride‐induced conformational changes (main state and substate) under the planar lipid bilayer measurement. Once ion channel 1 transported Cl⁻ predominantly and changed conformations, this transition resulted in a change of the conducting ionic current (L1 and L2) through the channel.
(a) ¹⁹F NMR spectra (1 : 9 D2O/H2O, 298 K) of 1 in different solutions including (i) 1 in buffer without the addition of EYPC‐LUVs suspension, (ii) EYPC‐LUVs suspension with 1 in pre‐loading way, and (iii) EYPC‐LUVs suspension with 1 in post‐loading way. Recorded frequency of 658 MHz for (i) and 470 MHz for (ii) and (iii); chemical shift referenced to KF at −125.3 ppm. (b) Cryo‐TEM image of molecule 1 embedded in the lipid bilayer. Left, full image; right, partially enlarged image. The yellow arrow points towards the projection image of a single molecule of 1. (c) Schematic diagram of the lucigenin fluorescence assay. (d) Dose‐response curves of 1 in mediating chloride influx into lucigenin⊂EYPC‐LUVs in KCl solutions.
(a) Current recordings from planar lipid bilayer with the incorporation of channel 1 under ±180 mV and ±100 mV in neutral symmetrical KCl solutions (cis/trans = 1.0 M/1.0 M). (b) Histogram showing the relative occurrence of three distinct states at different current levels under −100 mV in neutral symmetrical KCl solutions (cis/trans = 1.0 M/1.0 M). The histograms were fitted with Gaussian model.
(a, b) Current‐voltage plots for L1 and L2 exhibited a nonlinear exponential relationship in neutral symmetrical KCl solutions (cis/trans = 1.0 M/1.0 M), reflecting chloride flowed through (a) one single channel under positive potential (zg, L1: 0.21±0.02; L2: 0.18±0.03), and through (b) another single channel under negative potential (zg, L1: 0.21±0.02; L2: 0.16±0.03). Gating charges were determined using the exponential equation: I = Aexp(zgeV/kT) + const, where e = elementary charge, k = Boltzmann constant, T = temperature. (c) Current‐voltage plots for L1 and L2 in asymmetrical KCl solutions (cis/trans = 1.0 M/0.5 M), pH = 4.0. The inset is the enlarged region of the intersection of the curve on the x‐axis. Reversal potentials (Vrev) were +13.14 mV for L1 and +5.77 mV for L2 after correction by the differential chloride potential of −18 mV. Mean±standard deviations were shown.
Synthesis of channel molecule 1. Conditions: (i) DMF, 110 °C, 24 h, 29 %; (ii) TFA, DCM, rt, 0.5 h, 83 %; (iii) 6FDA, L‐Phenylalanine benzyl ester hydrochloride, Et3N, DMF, 130 °C, 30 h, 13 %; (iv) 1) EDCI, DMAP, rt, 1 h, 2) PPTS, EtOH, reflux, 3 h, 65 %; (v) K2CO3, CH3CN, reflux, 3.5 h, 39 %; (vi) Pd/C, H2, THF, rt, 24 h, 76 %.
Spontaneous Transition between Multiple Conductance States and Rectifying Behaviors in an Artificial Single‐Molecule Funnel

August 2024

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22 Reads

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4 Citations

It has long been an aspirational goal to create artificial channel structures that replicate the feat achieved by ion channel proteins. Biological ion channels occasionally demonstrate multiple conductance states (known as subconductance), remaining a challenging property to achieve in artificial channel molecules. We report a funnel‐shaped single‐molecule channel constructed by an electron‐deficient macrocycle and two electron‐deficient aromatic imide arms. Planar lipid bilayer measurements reveal distinct current recordings, including a closed state, two conducting states, and spontaneous transitions between the three states, resembling the events seen in biological ion channels. The transitions result from conformational changes induced by chloride transport in the channel molecule. Both opening states show a non‐linear and rectifying I–V relationship, indicating voltage‐dependent transport due to the asymmetrical channel structure. This work could enhance our understanding of ion permeation and channel opening mechanism.


Citations (71)


... Moreover, it was found that the catalytic activity of 3d metal ions, such as copper(II), can be improved by coordinating TEMPO molecules with the metal center [22,23]. These features are significant for the remediation process of aqueous pollutants, such as dye effluents from textile and paper industries, which require low-cost oxidants such as O 2 and H 2 O 2 . ...

Reference:

Synthesis, Structure, and Magnetic Properties of a Copper(II)‐Nitroxide Chain and Its Catalytic Activity Toward Congo Red Decolorization
Regulating Spin Density using TEMPOL Molecules for Enhanced CO2‐to‐Ethylene Conversion by HKUST‐1 Framework Derived Electrocatalysts

... Finally, we return now to the observation that many reported minerals in the Söhncke space groups do not even mention that the mineral is chiral (and should exist therefore in two forms). An example is the small but unique family of chiral silicate zeolite minerals, all of which belong to the 43 non-enantiomorphic space groups and none of which is described as chiral; these are as follows: Ignoring the chirality of zeolites is somewhat surprising because when it comes to synthetic zeolites, their chirality is a main issue in many applications, including enantioselective catalysis, enantiomers separation and more [41] (Huang et al., 2024). ...

Reference:

Chiral Minerals
Recent progress in chiral zeolites: Structure, synthesis, characterization and applications
  • Citing Article
  • March 2024

Chinese Chemical Letters

... [1][2][3][4] Macrocyclic hosts, with their well-defined cavities, serve as nanoreactors capable of encapsulating and preorganizing reactants. [5][6][7][8][9][10][11][12] Generally, macrocyclic hosts catalyze reactions through two pathways: (1) by increasing substrate local concentration within cavities, [13][14][15][16][17][18] or (2) by enabling preorganized substrate conformations. [19][20][21][22] These strategies present the importance of macrocyclic structures in providing steric hindrance or nanoconfinement effects. ...

Selective Alkane Desaturation Catalyzed by Molecular Cage Copper Complexes Under Mild Conditions
  • Citing Article
  • January 2024

CCS Chemistry

... To address this question, we designed a new molecular hourglass 3 (Figure 7) by modifying the original molecular hourglass 1 with electronrich arms. [29] The resulting new molecule showed both chloride and potassium binding ability, with a stronger affinity toward Cl À (K 1 = 1067.0 � 28.8 M À 1 , K 2 = 23.1 � 0.2 M À 1 ) than K + (K 1 = 242.9 ...

Reversing the ion transport selectivity through arm modification of artificial molecular hourglass

Chemical Communications

... Therefore, the recognition and detection of dicarboxylates are of great importance. Despite the development of a number of receptors for dicarboxylates [21,26,27], their recognition remains a challenging task due to their strong hydrophilicity (−400 kJ/mol) [28,29], dispersed negative charges at both ends, complex shapes, and flexible conformations. Moreover, the similar carbon skeletons of many dicarboxylates make selective recognition particularly difficult. ...

Ultracycles consisting of macrocycles
  • Citing Article
  • September 2023

Chinese Chemical Letters

... Intramolecular weak interactions (IWIs) that are intrinsically dynamic and flexible play a crucial role in biomolecules determining their functioning. [1] Following Nature, scientists have learned to use weak non-covalent interactions in various fields, such as materials chemistry, [2][3][4][5][6][7][8] catalysis, [9][10][11][12][13][14][15][16] supramolecular chemistry, [17][18][19][20][21][22][23] etc. Controllable weak interactions form a basis for creating molecular switches, logic gates, sensors and molecular recognition systems. [24][25][26][27][28][29] Weak interactions can be smartly tailored to endow stabilization of the intermediates containing atoms in unusual valence states and providing new properties. ...

Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis

... The AMPs studied here possess this feature. A recent study on an artificial Cl − channel indicated that an organic structure that is relatively simple compared with a channel protein could display Cl − selectivity 53 . ...

An Artificial Single Molecular Channel Showing High Chloride Transport Selectivity and pH‐Responsive Conductance
  • Citing Article
  • April 2023

Angewandte Chemie

... Among all xenon biosensors, cryptophanes [129][130][131][132][133][134][135][136][137] stand out as the most extensively studied host molecules. In the 1980s, Collet [138] made significant contributions by synthesizing a novel class of molecules known as cryptophanes. ...

Xenon Induces Its Own Preferred Heterochiral Host from Exclusive Homochiral Assembly
  • Citing Article
  • December 2022

Journal of the American Chemical Society

... [21] Although many researchers are currently committed to studying how to obtain single-chiral metalorganic cages, more research results still focus on the enantiomeric separation or asymmetric synthesis of discrete chiral cages. [13,[22][23][24][25] It presents a considerable obstacle to achieve the resolution of chiral metal-organic cages through the modulation of the crystallization process and employ such asymmetric units for constructing noncentrosymmetric materials. ...

Inherently Chiral Cages via Hierarchical Desymmetrization
  • Citing Article
  • September 2022

Journal of the American Chemical Society

... [24][25][26][27][28] As depicted in Figure 2b, the LUMO energy level of PeTI is lower than the first ionization energy (IE) of CoCp 2 , illustrating the electron transfer from CoCp 2 to PeTI will occur spontaneously under a certain condition. [29][30][31] Treatment of PeTI with CoCp 2 in chloroform at room temperature under nitrogen resulted in an obvious color change from green to brown within seconds, indicating the formation of electron transfer (ET) complex (PeTI-CoCp 2 ) ( Figure 2c, Scheme S5). ...

π-Pimer, π-Dimer, π-Trimer, and 1D π-Stacks in a Series of Benzene Triimide Radical Anions: Substituent-Modulated π Interactions and Physical Properties in Crystalline State
  • Citing Article
  • June 2022

CCS Chemistry