Rational Design Research Articles

Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation.

Odorant-binding proteins (OBPs) in insects are key to detection and recognition of external chemical signals associated with survival. OBP7 in Spodoptera frugiperda's larval stage (SfruOBP7) may search for host plants by sensing plant volatiles, which are important sources of pest attractants and repellents. However, the atomic-level basis of binding modes remains elusive. SfruOBP7 structure was constructed through homology modeling, and complex models of six plant volatiles ((E)-2-hexenol, α-pinene, (Z)-3-hexenyl acetate, lauric acid, O-cymene and 1-octanol) and SfruOBP7 were obtained through molecular docking. To study the detailed interactions between the six plant volatile molecules and SfruOBP7, we conducted three 300 ns molecular dynamics simulations for each study object. The correlation coefficients between binding free energy obtained by molecular mechanics/generalized Born surface area together with solvated interaction energy methods and experimental values are 0.90 and 0.88, respectively, showing a good correlation. By comparing binding free energy along with interaction patterns between SfruOBP7 and the six volatile molecules, hotspot residues of SfruOBP7 when binding with different volatile molecules were determined. Hydrophobic interactions stemming from van der Waals interactions play a significant role in SfruOBP7 and these plant volatile systems. The optimized three-dimensional structure of SfruOBP7 and its binding modes with six plant volatiles revealed their interactions, thus providing a means for estimating the binding energies of other plant volatiles. Our study will help to guide the rational design of effective and selective insect attractants. © 2024 Society of Chemical Industry.

Design of advanced steels by integrated computational materials engineering

AbstractThe integrated computational materials engineering (ICME) has achieved great success in accelerating the rational design and deployment of new materials. It is a new route of designing new materials and processes and highlighted by Materials Genome Initiative/Engineering that stresses the high‐throughput computation in addition to high‐throughput experimentation and materials informatics. This article presents a brief review on the basic theories and multi‐scale computational tools of ICME to design advanced steel grades, including the first‐principles calculations, the CALPHAD method (i.e., computational thermodynamics) fueled by dedicated databases, diffusion and phase‐field simulations, as well as finite analysis methods and machine learning. In the ICME scheme to deal with steels, the CALPHAD method is considered as the core to readily consider multi‐component systems and integrated to link the microscopic simulations (such as diffusion and phase field method to predict microstructure evolutions in response to external conditions) and macroscopic finite analysis method to deal with mechanical properties. Two applications are also presented to address the new routes to carry out materials design, especially for advanced steels.

Amine-Functionalized Metal-Free Nanocarbon to Boost Selective CO2 Electroreduction to CO in a Flow Cell.

Highly efficient electrochemical CO2-to-CO conversion is a promising approach for achieving carbon neutrality. While nonmetallic carbon electrocatalysts have shown potential for CO2-to-CO utilization in H-type cells, achieving efficient conversion in flow cells at an industrial scale remains challenging. In this study, we present a cost-effective synthesis strategy for preparing ultrathin 2D carbon nanosheet catalysts through simple amine functionalization. The optimized catalyst, NCNs-2.5, demonstrates exceptional CO selectivity with a maximum Faradaic efficiency of 98% and achieves a high current density of 55 mA cm-2 in a flow cell. Furthermore, the catalyst exhibits excellent long-term stability, operating continuously for 50 h while maintaining a CO selectivity above 90%. The superior catalytic activity of NCNs-2.5 is attributed to the presence of amine-N active sites within the carbon lattice structure. This work establishes a foundation for the rational design of cost-effective nonmetallic carbon catalysts as sustainable alternatives to metals in energy conversion systems.

Triply Interlocked [2]catenanes: Rational Synthesis, Reversible Conversion Studies and Unprecedented Application in Photothermal Responsive Elastomer

Triply interlocked [2]catenane complexes featuring two identical, mechanically interlocked units are extraordinarily rare chemical compounds, whose properties and applications remain open to detailed studies. Herein, we introduce the rational design of a new ligand precursor, L1, suitable for the synthesis of six triply interlocked [2]catenanes by coordination‐driven self‐assembly. The interlocked compounds can be reversibly converted into the corresponding simple triangular prism metallacage by addition of H2O or DMF solvents to their CH3OH solutions, thereby demonstrating the importance of π···π stacking and hydrogen bonding interactions in the formation of triply interlocked [2]catenanes. Moreover, extensive studies have been conducted to assess the remarkable photothermal conversion performance. Complex 6a, exhibiting outstanding photothermal conversion performance (conversion efficiency in solution : 31.82%), is used to prepare novel photoresponsive elastomer in combination with thermally activated liquid crystal elastomer. The resultant material displays robust response to near‐infrared (NIR) laser and the capability of completely reforming the shape and reversible actuation, paving the way for the application of half‐sandwich organometallic units in photo‐responsive smart materials.

Atomic Design of Copper Active Sites in Pristine Metal-Organic Coordination Compounds for Electrocatalytic Carbon Dioxide Reduction.

Electrocatalytic carbon dioxide reduction reaction (CO2RR) has emerged as a promising and sustainable approach to cut carbon emissions by converting greenhouse gas CO2 to value-added chemicals and fuels. Metal-organic coordination compounds, especially the copper (Cu)-based coordination compounds, which feature well-defined crystalline structures and designable metal active sites, have attracted much research attention in electrocatalytic CO2RR. Herein, the recent advances of electrochemical CO2RR on pristine Cu-based coordination compounds with different types of Cu active sites are reviewed. First, the general reaction pathways of electrocatalytic CO2RR on Cu-based coordination compounds are briefly introduced. Then the highly efficient conversion of CO2 on various kinds of Cu active sites (e.g., single-Cu site, dimeric-Cu site, multi-Cu site, and heterometallic site) is systematically discussed, along with the corresponding catalytic reaction mechanisms. Finally, some existing challenges and potential opportunities for this research direction are provided to guide the rational design of metal-organic coordination compounds for their practical application in electrochemical CO2RR.

Triply Interlocked [2]catenanes: Rational Synthesis, Reversible Conversion Studies and Unprecedented Application in Photothermal Responsive Elastomer.

Triply interlocked [2]catenane complexes featuring two identical, mechanically interlocked units are extraordinarily rare chemical compounds, whose properties and applications remain open to detailed studies. Herein, we introduce the rational design of a new ligand precursor, L1, suitable for the synthesis of six triply interlocked [2]catenanes by coordination-driven self-assembly. The interlocked compounds can be reversibly converted into the corresponding simple triangular prism metallacage by addition of H2O or DMF solvents to their CH3OHsolutions, thereby demonstrating the importance of π···πstacking and hydrogen bonding interactions in the formation of triply interlocked [2]catenanes. Moreover, extensive studies have been conducted to assess the remarkable photothermal conversion performance. Complex 6a, exhibiting outstanding photothermal conversion performance (conversion efficiency in solution : 31.82%), is used to prepare novel photoresponsive elastomer in combination with thermally activated liquid crystal elastomer. The resultant material displays robust response to near-infrared(NIR)laser and the capability of completely reforming the shape and reversible actuation, paving the way for the application of half-sandwich organometallic units in photo-responsive smart materials.

Developing Next-Generation Live Attenuated Vaccines for Porcine Epidemic Diarrhea Using Reverse Genetic Techniques.

Porcine epidemic diarrhea virus (PEDV) is the etiology of porcine epidemic diarrhea (PED), a highly contagious digestive disease in pigs and especially in neonatal piglets, in which a mortality rate of up to 100% will be induced. Immunizing pregnant sows remains the most promising and effective strategy for protecting their neonatal offspring from PEDV. Although half a century has passed since its first report in Europe and several prophylactic vaccines (inactivated or live attenuated) have been developed, PED still poses a significant economic concern to the swine industry worldwide. Hence, there is an urgent need for novel vaccines in clinical practice, especially live attenuated vaccines (LAVs) that can induce a strong protective lactogenic immune response in pregnant sows. Reverse genetic techniques provide a robust tool for virological research from the function of viral proteins to the generation of rationally designed vaccines. In this review, after systematically summarizing the research progress on virulence-related viral proteins, we reviewed reverse genetics techniques for PEDV and their application in the development of PED LAVs. Then, we probed into the potential methods for generating safe, effective, and genetically stable PED LAV candidates, aiming to provide new ideas for the rational design of PED LAVs.

Versatile separators toward advanced lithium-sulfur batteries: status, recent progress, challenges and perspective.

Lithium-sulfur batteries (LSBs) have recently gained extensive attention due to their high energy density, low cost, and environmental friendliness. However, serious shuttle effect and uncontrolled growth of lithium dendrites restrict them from further commercial applications. As "the third electrode", functional separators are of equal significance as both anodes and cathodes in LSBs. The challenges mentioned above are effectively addressed with rational design and optimization in separators, thereby enhancing their reversible capacities and cycle stability. The review discusses the status/operation mechanism of functional separators, then primarily focuses on recent research progress in versatile separators with purposeful modifications for LSBs, and summarizes the methods and characteristics of separator modification, including heterojunction engineering, single atoms, quantum dots, and defect engineering. From the perspective of the anodes, distinct methods to inhibit the growth of lithium dendrites by modifying the separator are discussed. Modifying the separators with flame retardant materials or choosing a solid electrolyte is expected to improve the safety of LSBs. Besides, in-situ techniques and theoretical simulation calculations are proposed to advance LSBs. Finally, future challenges and prospects of separator modifications for next-generation LSBs are highlighted. We believe that the review will be enormously essential to the practical development of advanced LSBs.

Steric Effects of Alcohols on the [Mn4O4] Cubane-Type Structures

[M4O4] (M = 3d transition metal) represents an interesting class of compounds featuring cubane-type molecular structures, and particularly, [Mn4O4] cubanes or their derivatives attract much attention by virtue of their potential applications as single-molecule magnets (SMMs) or catalysts. However, the rational design of desired cubane-related structures is still a challenging subject due to the lack of readily available methods to effectively tune the construction patterns of the molecule assembly. In this work, we report the employment of different alcohols to prepare three cubane-related molecules, Mn2(dhd)4(iPrOH)2 (1), Mn4(dhd)4(OEt)4(EtOH)4 (2) and Mn4(dhd)6(OMe)2(MeOH)2 (3) (dhd = 5,5-dimethyl-2,4-hexanedione). Interestingly, the bulkiest iPrOH leads to simple rhombic dimer molecule 1. It can be deemed a rudimentary structure oftetranuclear [Mn4O4] cubane 2, which can be realized by the use of less bulky EtOH. In addition, the least bulky MeOH promotes the assembly of the cubanes, eventually bringing about defective dicubane molecular cluster 3. The accurate crystal structures of 1–3 were modeled by single-crystal X-ray diffraction, and their electronic structures were investigated through absorption spectroscopy coupled with theoretical calculations. Overall, this work demonstrates a systematic study on controlling cubane-type structures of Mn-based compounds by applying different solvents, which provides a new means to design functional molecules for specific applications.

Development of Physiologically Based Biopharmaceutical Model (PBBM) for Felodipine Prolonged-Release Tablet as useful tool for prediction of formulation.

Physiologically Based Biopharmaceutical Models (PBBMs) are advanced tools that integrate physiological parameters with drug-specific properties to simulate drug behavior in vivo. In this study, we present the development of a PBBM specifically tailored for felodipine prolonged-release (PR) tablet formulations. Felodipine, a potent calcium channel blocker, is widely used for the treatment of hypertension and angina pectoris. Prolonged-release formulations aim to provide controlled drug release, ensuring sustained therapeutic effect with reduced dosing frequency and minimized adverse effects. Our PBBM incorporates key physiological processes such as gastrointestinal transit, drug dissolution, absorption, distribution, metabolism, and elimination. Data from in vitro dissolution studies, preclinical pharmacokinetics, and clinical observations are integrated to parameterize the model accurately. Special attention is given to the physicochemical properties of felodipine and the release characteristics of the PR tablet formulation. Validation of the PBBM is conducted against clinical pharmacokinetic data obtained from bioequivalence studies and population pharmacokinetic analyses of felodipine PR tablets. The model may demonstrate excellent predictive performance, accurately capturing plasma concentration-time profiles across different dosing regimens and patient populations. The developed PBBM provides valuable insights into the biopharmaceutical behavior of felodipine PR tablets, facilitating rational formulation design, dosage regimen optimization, and therapeutic individualization. It serves as a powerful tool for drug developers, regulatory agencies, and clinicians to enhance the efficiency and effectiveness of drug development and clinical pharmacotherapy

Musical protein: Mapping the time sequence of music onto the spatial architecture of proteins

Background and objectiveMusic, the ubiquitous language across human cultures, is traditionally considered as a form of art but has been linked to biomolecules in recent years. However, previous efforts have only been addressed on sonification of nucleic acids and proteins to produce so-called life music, the soundscape from the basic building blocks of life. In this study, we attempted to, for the first time, conduct a reverse operation of this process, i.e. conversion of music to protein (CoMtP). MethodsA novel notion termed musical protein (MP) –– the protein defined by music –– was proposed and, on this basis, we described a computational strategy to map the time sequence of music onto the spatial architecture of proteins, which considered that each note in the stave of a music (target) can be simply characterized by two acoustical quantities and that each residue in the primary sequence of a protein (hit) was represented by amino acid descriptors. ResultsA simulated annealing (SA) algorithm was applied to iteratively generate the best matched MP hit for a music target and structural bioinformatics was then used to model spatial advanced structure for the resulting MP. We also demonstrated that some small MPs derived from music segments may have potential biological functions, which, for example, can serve as antimicrobial peptides (AMPs) to inhibit clinical bacterial strains with moderate or high antibacterial potency. ConclusionsThis work may benefit many aspects; for example, it would open a door for the hearing-impaired persons to ‘listen’ music in a biological vision and could be a mean of exposing students to the concepts of biomolecules at an earlier age through the use of auditory characteristics. The CoMtP would also facilitate the rational design of proteins with biological and medicinal significance.

Enhancing in vivo cell and tissue targeting by modulation of polymer nanoparticles and macrophage decoys.

The in vivo efficacy of polymeric nanoparticles (NPs) is dependent on their pharmacokinetics, including time in circulation and tissue tropism. Here we explore the structure-function relationships guiding physiological fate of a library of poly(amine-co-ester) (PACE) NPs with different compositions and surface properties. We find that circulation half-life as well as tissue and cell-type tropism is dependent on polymer chemistry, vehicle characteristics, dosing, and strategic co-administration of distribution modifiers, suggesting that physiological fate can be optimized by adjusting these parameters. Our high-throughput quantitative microscopy-based platform to measure the concentration of nanomedicines in the blood combined with detailed biodistribution assessments and pharmacokinetic modeling provides valuable insight into the dynamic in vivo behavior of these polymer NPs. Our results suggest that PACE NPs-and perhaps other NPs-can be designed with tunable properties to achieve desired tissue tropism for the in vivo delivery of nucleic acid therapeutics. These findings can guide the rational design of more effective nucleic acid delivery vehicles for in vivo applications.

Hepatitis C Virus E1E2 Structure, Diversity, and Implications for Vaccine Development.

Hepatitis C virus (HCV) is a major medical health burden and the leading cause of chronic liver disease and cancer worldwide. More than 58 million people are chronically infected with HCV, with 1.5 million new infections occurring each year. An effective HCV vaccine is a major public health and medical need as recognized by the World Health Organization. However, due to the high variability of the virus and its ability to escape the immune response, HCV rapidly accumulates mutations, making vaccine development a formidable challenge. An effective vaccine must elicit broadly neutralizing antibodies (bnAbs) in a consistent fashion. After decades of studies from basic research through clinical development, the antigen of choice is considered the E1E2 envelope glycoprotein due to conserved, broadly neutralizing antigenic domains located in the constituent subunits of E1, E2, and the E1E2 heterodimeric complex itself. The challenge has been elicitation of robust humoral and cellular responses leading to broad virus neutralization due to the relatively low immunogenicity of this antigen. In view of this challenge, structure-based vaccine design approaches to stabilize key antigenic domains have been hampered due to the lack of E1E2 atomic-level resolution structures to guide them. Another challenge has been the development of a delivery platform in which a multivalent form of the antigen can be presented in order to elicit a more robust anti-HCV immune response. Recent nanoparticle vaccines are gaining prominence in the field due to their ability to facilitate a controlled multivalent presentation and trafficking to lymph nodes, where they can interact with both the cellular and humoral components of the immune system. This review focuses on recent advances in understanding the E1E2 heterodimeric structure to facilitate a rational design approach and the potential for development of a multivalent nanoparticle-based HCV E1E2 vaccine. Both aspects are considered important in the development of an effective HCV vaccine that can effectively address viral diversity and escape.

Rational Design of Droplet Microfluidic Reactors for Controllable Non-Newton Viscous Production of Functional Chitosan Microspheres

Rational Design of Droplet Microfluidic Reactors for Controllable Non-Newton Viscous Production of Functional Chitosan Microspheres

Facile Estimation of Surface Oxygen Vacancies in Co3O4 Catalysts with a Colorimetric Method.

Oxygen vacancy (Ov) is known to act as an active center of the metal oxide. Quantification of surface Ov is vital for understanding the quantitative structure-activity relationship. Facile quantification characterization of surface Ov is highly desirable but still challenging. In this study, we presented a simple colorimetric method for rapidly quantifying surface Ov. As an example of metal oxide nanoparticles, Co3O4 was used to catalyze the 3,3',5,5'-tetramethylbenzidine (TMB)-H2O2 colorimetric reaction. It was found that the absorbance of the TMB-H2O2 system was dependent on the surface Ov amount in Co3O4. The investigation of the mechanism showed that the Ov-dependent absorbance would be attributed to the activity of surface Ov to easily adsorb and dissociate H2O2 into a hydroxyl radical (•OH). The absorbance signal of the TMB-H2O2 system acted as a probe to estimate the surface Ov. This colorimetric measurement could be completed in less than 20 min. The Ov concentrations obtained by the proposed colorimetric method matched well with those obtained by X-ray photoelectron spectroscopy. This method does not require any complex operation and expensive equipment and can be performed in any ordinary chemical laboratory. So, this colorimetric method is expected to become an alternative approach for quantifying the surface Ov in metal oxide nanoparticles. This method will provide essential insights into the rational design and application of Ov.

Structure and Chemical Reactivity of Y-Stabilized ZrO2 Surfaces: Importance for the Water-Gas Shift Reaction.

The surface structure and chemical properties of Y-stabilized zirconia (YSZ) have been subjects of intense debate over the past three decades. However, a thorough understanding of chemical processes occurring at YSZ powders faces significant challenges due to the absence of reliable reference data acquired for well-controlled model systems. Here, we present results from polarization-resolved infrared reflection absorption spectroscopy (IRRAS) obtained for differently oriented, Y-doped ZrO2 single-crystal surfaces after exposure to CO and D2O. The IRRAS data reveal that the polar YSZ(100) surface undergoes reconstruction, characterized by an unusual, red-shifted CO band at 2132 cm-1. Density functional theory calculations allowed to relate this unexpected observation to under-coordinated Zr4+ cations in the vicinity of doping-induced O vacancies. This reconstruction leads to a strongly increased chemical reactivity and water spontaneously dissociates on YSZ(100). The latter, which is an important requirement for catalysing the water-gas-shift (WGS) reaction, is absent for YSZ(111), where only associative adsorption was observed. Together with a novel analysis scheme these reference data allowed for an operando characterisation of YSZ powders using DRIFTS (diffuse reflectance infrared Fourier transform spectroscopy). These findings facilitate rational design and tuning of YSZ-based powder materials for catalytic applications, in particular CO oxidation and the WGS reaction.

High Entropy Borides as Efficient Catalysts for Electrochemical Reduction of Nitrate to Ammonia

Electrochemical reduction of nitrate (NO3-RR) to ammonia has attracted great attention as a strategy for simultaneously achieving pollutant removal and economic product acquisition. To achieve high Faradaic efficiency of ammonia (FE) and ammonia selectivity, it is necessary to develop highly active catalysts with strong hydrogenation ability. In this work, we report high-entropy-borides (HEB) with tunable cation composition as high-performance catalysts for NO3-RR. Taking (TiVCrMo)B2 as the model material systems, we systematically investigate the effect of doping (Co, Fe and Ni) on the activity of NO3-RR. Electrochemical test results show that the HEB doped with Co element exhibited the optimal performance, with a FE reaching 97.9%. Combining several advanced spectroscopic techniques, we find that Co dopant can effectively facilitate the hydrogenation process of NO3-RR. This work demonstrates high-entropy ceramics as an excellent platform for rational design of highly active catalyst for energy and environmental applications.

Conformally reactive interphase enables excellent kinetics and cyclability in quasi-solid-state sodium metal battery

The rational design of flexible and robust anode-electrolyte interface is of great significance for extending the cycle life and improving the kinetics performance for sodium metal batteries (SMBs). Herein, a conformally reactive solid-electrolyte interphase (SEI) is constructed through a spontaneous absorption-oligomerization strategy in a quasi-solid-state polymer electrolyte (QSE-T). The polymeric network in the QSE-T system ensures a stable environment with high Na+ transfer number to suppress Na dendrite growth and chemical corrosion. Simultaneously, the reactive SEI is consisted of inorganic NaF and low crosslinked O-B-O and O-B-F segments derived from the 4-trifluoromethylphenylboronic acid (TFPBA) additive, which exhibits lower Na+ diffusion-barriers, and accommodates the ever-changing quasi-solid interface during cycling. Consequently, the NVP||QSE-T||Na cells exhibit ultra-stable cycling performance and high rate capability, with a high initial capacity of 95.1 mAh g−1 at a high rate of 5 C and a capacity retention rate of 86.6 % after 12,000 cycles.

A Review on Indole-triazole Molecular Hybrids as a Leading Edge in Drug Discovery: Current Landscape and Future Perspectives.

Molecular hybridization is a rational design strategy used to create new ligands or pro-totypes by identifying and combining specific pharmacophoric subunits from the molecular struc-tures of two or more known bioactive derivatives. Molecular hybridization is a valuable technique in drug discovery, enabling the modulation of unwanted side effects and the creation of potential dual-acting drugs that combine the effects of multiple therapeutic agents. Indole-triazole conju-gates have emerged as promising candidates for new drug development. The indole and triazole moieties can be linked through various synthetic strategies, such as click chemistry or other cou-pling reactions, to generate a library of diverse compounds for biological screening. The achieva-ble structural diversity with indole-triazole conjugates offers avenues to optimize their pharmaco-kinetic and pharmacodynamic attributes, amplifying their therapeutic efficacy. Researchers have extensively tailored both indole and triazole frameworks with diverse modifications to compre-hend their impact on the drug's pharmacokinetic and pharmacodynamic characteristics. The cur-rent review article endeavours to explore and discuss various research strategies to design indole-triazole hybrids and elucidate their significance in a variety of pathological conditions. The in-sights provided herein are anticipated to be beneficial for the researchers and will likely encour-age further exploration in this field.

Systematic metabolic engineering of Zymomonas mobilis for β-farnesene production

Zymomonas mobilis is an ethanologenic bacterium that can produce hopanoids using farnesyl pyrophosphate (FPP), which can be used as the precursor by β-farnesene synthase for β-farnesene production. To explore the possibility and bottlenecks of developing Z. mobilis for β-farnesene production, five heterologous β-farnesene synthases were selected and screened, and AaBFS from Artemisia annua had the highest β-farnesene titer. Recombinant strains with AaBFS driven by the strong constitutive promoter Pgap (Pgap–AaBFS) doubled its β-farnesene production to 25.73 ± 0.31 mg/L compared to the recombinant strain with AaBFS driven by Ptet (Ptet–AaBFS), which can be further improved by overexpressing the Pgap–AaBFS construct using the strategies of multiple plasmids (41.00 ± 0.40 mg/L) or genomic multi-locus integration (48.33 ± 3.40 mg/L). The effect of cofactor NADPH balancing on β-farnesene production was also investigated, which can be improved only in zwf-overexpressing strains but not in ppnK-overexpressing strains, indicating that cofactor balancing is important and sophisticated. Furthermore, the β-farnesene titer was improved to 73.30 ± 0.71 mg/L by overexpressing dxs, ispG, and ispH. Finally, the β-farnesene production was increased to 159.70 ± 7.21 mg/L by fermentation optimization, including the C/N ratio, flask working volume, and medium/dodecane ratio, which was nearly 13-fold improved from the parental strain. This work thus not only generated a recombinant β-farnesene production Z. mobilis strain but also unraveled the bottlenecks to engineer Z. mobilis for farnesene production, which will help guide the future rational design and construction of cell factories for terpenoid production in non-model industrial microorganisms.