Rational Design Research Articles

Bridged Pt-OH-Mn Mediator in N-coordinated Mn Single Atoms and Pt Nanoparticles for Electrochemical Biomolecule Oxidation and Discrimination.

The rational design of efficient catalysts for uric acid (UA) electrooxidation, as well as the establishment of structure-activity relationships, remains a critical bottleneck in the field of electrochemical sensing. To address these challenges, herein, a hybrid catalyst that integrates carbon-supported Pt nanoparticles and nitrogen-coordinated Mn single atoms (PtNPs/MnNC) is developed. The metal-metal interaction during annealing affords the construction of metallic-bonded Pt-Mn pairs between PtNPs and Mn single atoms, facilitating the electron transfer from PtNPs to the support and thereby optimizing the electronic structure of catalysts. More importantly, experiments and theoretical calculations provide visual proof for the 'incipient hydrous oxide adatom mediator' mechanism for UA oxidation. The Pt-Mn pairs first adsorb OH* to construct the bridged Pt-OH-Mn mediators to serve as a highly active intermediate for N-H bond dissociation and proton transfer. Benefiting from the unique electronic and geometric structure of the catalytic center and reactive intermediates, PtNPs/MnNC exhibits superior electrooxidation performance. The electrochemical sensor based on PtNPs/MnNC enables sensitive detection and discrimination of UA and dopamine in serum samples. This work offers new insights into the construction of novel electrocatalysis for sensitive sensing platforms.

Valence can control the nonexponential viscoelastic relaxation of multivalent reversible gels.

Gels made of telechelic polymers connected by reversible cross-linkers are a versatile design platform for biocompatible viscoelastic materials. Their linear response to a step strain displays a fast, near-exponential relaxation when using low-valence cross-linkers, while larger supramolecular cross-linkers bring about much slower dynamics involving a wide distribution of timescales whose physical origin is still debated. Here, we propose a model where the relaxation of polymer gels in the dilute regime originates from elementary events in which the bonds connecting two neighboring cross-linkers all disconnect. Larger cross-linkers allow for a greater average number of bonds connecting them but also generate more heterogeneity. We characterize the resulting distribution of relaxation timescales analytically and accurately reproduce stress relaxation measurements on metal-coordinated hydrogels with a variety of cross-linker sizes including ions, metal-organic cages, and nanoparticles. Our approach is simple enough to be extended to any cross-linker size and could thus be harnessed for the rational design of complex viscoelastic materials.

Diamond-lattice photonic crystals assembled from DNA origami.

Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.

Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1.

Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains largely unknown. Here, we employed all-atom molecular dynamics simulations, coupled to steered and umbrella sampling techniques, to examine the thermodynamics governing the transport of glucose and two glycoconjugate drugs (i.e., 6-D-glucose-conjugated methane sulfonate and 6-D-glucose chlorambucil) by GLUT1. We characterized the specific interactions between GLUT1 and substrates at different transport stages, including substrate recognition, transport, and releasing, and identified the key residues involved in these procedures. Importantly, our results described, for the first time, the free energy profiles of GLUT1-transporting glycoconjugate drugs, and demonstrated that H160 and W388 served as important gates to regulate their transport via GLUT1. These findings provide novel atomic-scale insights for understanding the transport mechanism of GLUT1, facilitating the discovery and rational design of GLUT1-targeted anticancer drugs.

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST.

The fluorescent light-up aptamer RhoBAST, which binds and activates the fluorophore-quencher conjugate tetramethylrhodamine-dinitroaniline with high affinity, super high brightness, remarkable photostability, and fast exchange kinetics, exhibits excellent performance in super-resolution RNA imaging. Here we determine the co-crystal structure of RhoBAST in complex with tetramethylrhodamine-dinitroaniline to elucidate the molecular basis for ligand binding and fluorescence activation. The structure exhibits an asymmetric "A"-like architecture for RhoBAST with a semi-open binding pocket harboring the xanthene of tetramethylrhodamine at the tip, while the dinitroaniline quencher stacks over the phenyl of tetramethylrhodamine instead of being fully released. Molecular dynamics simulations show highly heterogeneous conformational ensembles with the contact-but-unstacked fluorophore-quencher conformation for both free and bound tetramethylrhodamine-dinitroaniline being predominant. The simulations also show that, upon RNA binding, the fraction of xanthene-dinitroaniline stacked conformation significantly decreases in free tetramethylrhodamine-dinitroaniline. This highlights the importance of releasing dinitroaniline from xanthene tetramethylrhodamine to unquench the RhoBAST-tetramethylrhodamine-dinitroaniline complex. Using SAXS and ITC, we characterized the magnesium dependency of the folding and binding mode of RhoBAST in solution and indicated its strong structural robustness. The structures and binding modes of relevant fluorescent light-up aptamers are compared, providing mechanistic insights for rational design and optimization of this important fluorescent light-up aptamer-ligand system.

Rational Design of an Optimal Al-substituted Layered Oxide Cathode for Na-ion Batteries

Layered oxide cathodes, a promising avenue for Na-ion batteries, hold the highest potential for commercialization. Herein, we delve into the structural and electrochemical properties of Al-substituted layered oxides in our quest to pinpoint the optimal cathode composition in the Na3/4(Mn-Al-Ni)O2 pseudo-ternary system. The cathode materials investigated were synthesized in three distinct phase configurations, which include two monophasic configurations with P3 and P2-type structures and a third biphasic cathode with equal proportions of P3 and P2 phases. The fractions of the P3 and P2 type phases in the cathode materials were manipulated by adjusting the calcination temperature. The varying concentration of Mn3+ and Mn4+, confirmed by X-ray photoelectron spectroscopy, was found to impact the cyclic stability of these materials significantly. During electrochemical testing, the P3 cathodes showed impressive rate performance and exhibited an excellent specific capacity of 195 mAh g−1 at 0.1C. Regarding cyclic performance, the biphasic cathodes consistently outperformed their monophasic counterparts, with P3/P2-Na0.75Mn0.50Ni0.25Al0.25O2 exhibiting 82% capacity retention after 300 cycles. Analysis of operando Synchrotron XRD data revealed an absence of P3 to O3 type phase transition in the cathodes even at low voltages where large structural variations to the unit cell structure were observed. The absence of P3 to O3 transformations and the superior electrochemical performance of Na0.75Mn0.50Ni0.25Al0.25O2 underlines the importance of Al substitution and P3/P2 biphasic structure in enhancing the electrochemical performance of layered oxides.

Bridged Pt–OH–Mn Mediator in N‐coordinated Mn Single Atoms and Pt Nanoparticles for Electrochemical Biomolecule Oxidation and Discrimination

The rational design of efficient catalysts for uric acid (UA) electrooxidation, as well as the establishment of structure‐activity relationships, remains a critical bottleneck in the field of electrochemical sensing. To address these challenges, herein, a hybrid catalyst that integrates carbon‐supported Pt nanoparticles and nitrogen‐coordinated Mn single atoms (PtNPs/MnNC) is developed. The metal‐metal interaction during annealing affords the construction of metallic‐bonded Pt−Mn pairs between PtNPs and Mn single atoms, facilitating the electron transfer from PtNPs to the support and thereby optimizing the electronic structure of catalysts. More importantly, experiments and theoretical calculations provide visual proof for the ‘incipient hydrous oxide adatom mediator’ mechanism for UA oxidation. The Pt−Mn pairs first adsorb OH* to construct the bridged Pt–OH–Mn mediators to serve as a highly active intermediate for N–H bond dissociation and proton transfer. Benefiting from the unique electronic and geometric structure of the catalytic center and reactive intermediates, PtNPs/MnNC exhibits superior electrooxidation performance. The electrochemical sensor based on PtNPs/MnNC enables sensitive detection and discrimination of UA and dopamine in serum samples. This work offers new insights into the construction of novel electrocatalysis for sensitive sensing platforms.

DCAF16-Based Covalent Handle for the Rational Design of Monovalent Degraders

DCAF16-Based Covalent Handle for the Rational Design of Monovalent Degraders

Rational Design of Coumarin-Based Hybridized Local and Charge-Transfer Blue Emitters for Solution-Processed Organic Light-Emitting Diodes.

Hybridized local and charge-transfer (HLCT) with the utilization of both singlet and triplet excitons through the "hot excitons" channel have great application potential in highly efficient blue organic light-emitting diodes (OLEDs). The proportion of charge-transfer (CT) and locally excited (LE) components in the relevant singlet and triplet states makes a big difference for the high-lying reverse intersystem crossing process. Herein, three novel donor (D)-acceptor (A) type HLCT materials, 7-([1,1'-biphenyl]-4-yl(9,9-dimethyl-9H-fluoren-2-yl)amino)-3-phenyl-1H-isochromen-1-one (pPh-7P), 7-([1,1'-biphenyl]-4-yl(9,9-dimethyl-9H-fluoren-2-yl)amino)-3-methyl-1H-isochromen-1-one (pPh-7M), and 6-([1,1'-biphenyl]-4-yl(9,9-dimethyl-9H-fluoren-2-yl)amino)-3-methyl-1H-isochromen-1-one (pPh-6M), were rationally designed and synthesized with diphenylamine derivative as donor and oxygen heterocyclic coumarin moiety as acceptors. The proportions of CT and LE components were fine controlled by changing the connection site of diphenylamine derivative at C6/C7-position and the substituent at C3-position of coumarin moiety. The HLCT characteristics of pPh-7P, pPh-7M, and pPh-6M were systematically demonstrated through photophysical properties and density functional theory calculations. The solution-processed doped OLEDs based on pPh-6M exhibited deep-blue electroluminescence with the maximum emission wavelength of 446 nm, maximum luminance of 8755 cd m-2, maximum current efficiency of 5.83 cd A-1, and maximum external quantum efficiency of 6.54%. The results reveal that pPh-6M with dominant 1LE and 3CT components has better OLED performance.

Cobalt-Catalyzed Domino Transformations via Enantioselective C-H Activation/Nucleophilic [3 + 2] Annulation toward Chiral Bridged Bicycles.

Selective synthesis of chiral bridged (hetero)bicyclic scaffolds via asymmetric C-H activation constitutes substantial challenges due to the multiple reactivities of strained bicyclic structures. Herein, we develop the domino transformations through an unprecedented cobalt-catalyzed enantioselective C-H activation/nucleophilic [3 + 2] annulation with symmetrical bicyclic alkenes. The methods offer straightforward access to a wide range of chiral molecules bearing [2.2.1]-bridged bicyclic cores with four and five consecutive stereocenters in a single step. Two elaborate salicyloxazoline (Salox) ligands were synthesized based on the rational design and mechanistic understanding. The well-defined chiral pockets generated from asymmetric coordination around the trivalent cobalt catalyst direct the orientation of bicyclic alkenes, leading to excellent enantioselectivity.

Prediction of Paratope-Epitope Pairs Using Convolutional Neural Networks.

Antibodies play a central role in the adaptive immune response of vertebrates through the specific recognition of exogenous or endogenous antigens. The rational design of antibodies has a wide range of biotechnological and medical applications, such as in disease diagnosis and treatment. However, there are currently no reliable methods for predicting the antibodies that recognize a specific antigen region (or epitope) and, conversely, epitopes that recognize the binding region of a given antibody (or paratope). To fill this gap, we developed ImaPEp, a machine learning-based tool for predicting the binding probability of paratope-epitope pairs, where the epitope and paratope patches were simplified into interacting two-dimensional patches, which were colored according to the values of selected features, and pixelated. The specific recognition of an epitope image by a paratope image was achieved by using a convolutional neural network-based model, which was trained on a set of two-dimensional paratope-epitope images derived from experimental structures of antibody-antigen complexes. Our method achieves good performances in terms of cross-validation with a balanced accuracy of 0.8. Finally, we showcase examples of application of ImaPep, including extensive screening of large libraries to identify paratope candidates that bind to a selected epitope, and rescoring and refining antibody-antigen docking poses.

Enzymatic Synthesis and Structural Modeling of Bio-Based Oligoesters as an Approach for the Fast Screening of Marine Biodegradation and Ecotoxicity.

Given the widespread use of esters and polyesters in products like cosmetics, fishing nets, lubricants and adhesives, whose specific application(s) may cause their dispersion in open environments, there is a critical need for stringent eco-design criteria based on biodegradability and ecotoxicity evidence. Our approach integrates experimental and computational methods based on short oligomers, offering a screening tool for the rapid identification of sustainable monomers and oligomers, with a special focus on bio-based alternates. We provide insights into the relationships between the chemical structure and properties of bio-based oligomers in terms of biodegradability in marine environments and toxicity in benchmark organisms. The experimental results reveal that the considered aromatic monomers (terephthalic acid and 2,5-furandicarboxylic acid) accumulate under the tested conditions (OECD 306), although some slight biodegradation is observable when the inoculum derives from sites affected by industrial and urban pollution, which suggests that ecosystems adapt to non-natural chemical pollutants. While clean seas are more susceptible to toxic chemical buildup, biotic catalytic activities offer promise for plastic pollution mitigation. Without prejudice to the fact that biodegradability inherently signifies a desirable trait in plastic products, nor that it automatically grants them a sustainable "license", this study is intended to facilitate the rational design of new polymers and materials on the basis of specific uses and applications.

Piezoelectric Polarization and Sulfur Vacancy Enhanced Photocatalytic Hydrogen Evolution Performance of Bi2S3/ZnSn(OH)6 Piezo-photocatalyst.

The combination of piezoelectric catalysis and photocatalysis could effectively enhance the carrier separation efficiency and further improve the hydrogen production activity. However, piezoelectric polarization always suffers from a low polarization strength, which severely restricts its actual applications. In this study, we successfully synthesized a novel sulfur vacancy-rich Bi2S3/ZnSn (OH)6 (BS-12/ZSH) piezo-photocatalyst for hydrogen evolution through water splitting. Notably, the piezo-photocatalytic hydrogen generation rate of the 8% BS-12/ZSH catalyst (336.21 μmol/g/h) was superior to that of pristine ZSH (29.71 μmol/g/h) and BS-12 (21.66 μmol/g/h). In addition, the hydrogen generation for 8% BS-12/ZSH (336.21 μmol/g/h) under ultrasonic coupling illumination was significantly higher than that under single illumination (52.09 μmol/g/h) and ultrasound (121.90 μmol/g/h), owing to the cooperative interaction of the sulfur vacancy and piezoelectric field. Various characterization analyses confirmed that (1) the introduction of sulfur vacancies in BS-12 provided more active sites, (2) BS-12 with sulfur vacancies acted as a co-catalyst to accelerate the hydrogen production rate, and (3) the piezoelectric field eliminated the electrostatic shielding and offered an additional driving force, which effectively promoted the separation of electron-hole pairs. This research clearly reveals the synergistic effect between piezocatalysis and photocatalysis as well as offers a promising sight for the rational design of high-efficiency piezo-photocatalysts.

Synthesis of myrcene using a hybrid cell-free reaction system

Myrcene is a typical monoterpene with applications as pharmaceutical product, biofuel, and so forth. However, only traces of myrcene accumulate in plants, and in vivo production of monoterpene in microbial cells also contains multiple restrictive factors. To alleviate this limitation, a hybrid cell-free metabolic engineering (CFME) system was developed in this study and a series of CFME strategies were employed for the engineering of myrcene synthase from glucose. First, a convenient CFME system was established, in which Pichia pastoris and Escherichia coli lysates enriched with MVA pathway and myrcene synthase respectively were used as “plug and play” modules and combined. After optimization, the myrcene titer was significantly improved by 119.26%. Second, rational design of myrcene synthase was performed by conserved residues modification and substrate tunnel engineering. Myrcene synthase variant N238S outperformed the wild-type enzyme in CFME system, and the myrcene titer value reached 56.80 mg/L. Molecular dynamics simulations provided significant mechanistic insights into the enhanced catalytic capability and myrcene production. This work highlights the feasibility of hybrid CFME system to connect tandem module and sustain complex metabolism for myrcene biomanufacturer. It also illustrates the value of the cell-free approach as a starting point for the rational engineering of monoterpene synthase.

Rational Design of Polymeric mRNA Delivery Vectors to Achieve Excellent Room-Temperature Storage Stability and Delivery Efficiency

Rational Design of Polymeric mRNA Delivery Vectors to Achieve Excellent Room-Temperature Storage Stability and Delivery Efficiency

Π‐Bridge Modulations in D–π–A Conjugated Microporous Polymers to Facilitate Charge Separation and Transfer Kinetics for Efficient Photocatalysis

AbstractThe burgeoning field of conjugated microporous polymers (CMPs) has generated widespread interest due to their potential as photocatalysts for hydrogen production from water. Nevertheless, their photocatalytic performance is sometimes hindered by inadequate charge separation and transfer, coupled with rapid charge recombination. Herein, a strategy to enhance photocatalytic performance via the customization of π‐bridges through the modulation of heteroatoms in a series of donor‐π‐acceptor (D‐π‐A) CMPs is proposed. This affords optimized energy levels and improved charge separation and transfer, thus boosting photocatalytic efficiency. Among various heteroatom substitutions, S‐doped CMP (10 mg) demonstrates the highest photocatalytic hydrogen evolution rate of 203 µmol h−1 (AQY450nm = 7.4%) under visible light irradiation. Subsequent experimental analysis reveals its superior photocatalytic performance can be largely related to its minimized exciton binding energy, facilitated charge transfer efficiency, and impeded charge recombination among these heteroatom‐doped D‐π‐A CMPs. This research paves the way for the rational design and modification of organic semiconductors for advanced solar‐driven photocatalysis by promoting charge separation and transfer.

Theoretical study on CO production mechanism from CO2 reduction on Cu–catalyst surface with different oxidation states

The rational design of copper (Cu)-based catalysts with different oxidation states is essential to achieve highly selective and efficient CO2 electroreduction. However, the effect of different oxide states of Cu-based catalysts has rarely been studied. Herein, the reaction mechanism of CO2 hydrogenation into CO on Cu-based catalysts with different oxidation states, such as Cu(111), Cu2O(111) and CuO(111), was studied using the density functional theory. The most favored pathway for CO production and the rate-controlling step on the three catalyst models were determined. The results show that, Cu2O (111) shows the best catalytic activity among the three catalysts due to the lowest activation barrier. The electronic structure analysis shows that Cu2O has the proper electronic structure to activate CO2 which is further reduced to CO. This work provides an important insight on the effect of oxidation state of Cu-based catalysts on the reduction of CO2 to CO.

Highly dispersed Pt nanoparticles onto dendritic silica as colorimetric probe for CO sensing in mainstream cigarette smokes

Carbon monoxide (CO) is a typical substance harmful to human body produced during cigarette smoking. Its content in cigarette smoke is one of the important indicators for evaluating its toxicity and the filtration effect of cigarette filter tips, which provides important guidance for its rational design. In this work, Pt nanoparticles with superior peroxidase catalytic ability were synthesized and loaded onto fibrous SiO2 nanoparticles as nanozymes to detect CO in cigarette smoke by taking advantage of the reduced catalytic performance of CO adsorption on the active sites of the nanozymes. The fibrous SiO2 not only provide abundant sites for the deposition and dispersion of Pt NPs, but also prevent their aggregation and thus maintain their high catalytic activity. Density functional theory calculations reveal that Pt nanoparticles exhibits superior peroxidase ability over Au and Pd nanoparticles, which can be significantly inhibited by CO. Accordingly, a nanozyme-inhibition based colorimetric method was developed for the detection of CO in cigarette smoke with the limit of detection of 0.15 mg/L. The applicability of this method was validated by analyzing the CO contents in 8 kinds of cigarette smoke with different types of filter tips. The concentrations of CO are in the range of 5.40–6.73 mg/branch, which are in good agreement with those of GC results, indicating the accuracy and reliability of our method. This assay is fast, convenient and sensitive for quantitatively assessing the CO content in cigarette smoke, and it lays the foundation for prompting the widespread use of nanozyme-inhibition in chemical sensing.

Crystal epitaxy-confined Pd, Ti-bimetallic sites in the MFI zeolite for benzylalcohol oxidation.

A general strategy for confining Pd, Ti-bimetallic sites in the MFI zeolite by crystal epitaxy was developed. The tailored spatial intimacy of the bimetallic sites demonstrated distinct catalytic performance for the oxidation of benzylalcohol. The related mechanism was clarified and afforded a valuable pathway for rational catalyst design.

Genetic Diversity and Natural Selection of Plasmodium vivax Merozoite Surface Protein 8 in Global Populations

Plasmodium vivax Merozoite Surface Protein 8 (PvMSP8) is a promising candidate target for the development of multi-component vaccines. Therefore, determining the genetic variation pattern of Pvmsp8 is essential in providing a reference for the rational design of the P. vivax malaria vaccines. This study delves into the genetic characteristics of the Pvmsp8 gene, specifically focusing on samples from the China-Myanmar border (CMB) region, and contrasts these findings with broader global patterns. The study uncovers that Pvmsp8 exhibits a notable level of conservation across different populations, with limited polymorphisms and relatively low nucleotide diversity (0.00023–0.00120). This conservation contrasts starkly with the high polymorphisms found in other P. vivax antigens such as Pvmsp1. A total of 25 haplotypes and 14 amino acid mutation sites were identified in the global populations, and all mutation sites were confined to non-functional regions. The study also notes that most CMB Pvmsp8 haplotypes are shared among Burmese, Cambodian, Thai, and Vietnamese populations, indicating less geographical variance, but differ notably from those found in Pacific island regions or the Panama. The findings underscore the importance of considering regional genetic diversity in P. vivax when developing targeted malaria vaccines. Non departure from neutral evolution were found by Tajima's D test, however, statistically significant differences were observed between the kn/ks rates. The study's findings are crucial in understanding the evolution and population structure of the Pvmsp8 gene, particularly during regional malaria elimination efforts. The highly conserved nature of Pvmsp8, combined with the lack of mutations in its functional domain, presents it as a promising candidate for developing a broad and effective P. vivax vaccine. This research thus lays a foundation for the rational development of multivalent malaria vaccines targeting this genetically stable antigen.