Molecular Systems Design & Engineering最新文献

{"title":"Quantum chemical screening of eutectic solvent components for insights into CO2 complexation mechanisms†","authors":"Stephen P. Vicchio, Osasumwen J. Ikponmwosa and Rachel B. Getman","doi":"10.1039/D5ME00034C","DOIUrl":"https://doi.org/10.1039/D5ME00034C","url":null,"abstract":"<p >Developing new negative emission technologies (NETs) to capture atmospheric CO<small>₂</small> is necessary to limit global temperature rise below 1.5 °C by 2050. The technologies, such as direct air capture (DAC), rely on sorption materials to harvest trace amounts of CO<small>₂</small> from ambient air. Deep eutectic solvents (DESs) and eutectic solvents (ESs), a subset of ionic liquids (ILs), are all promising new CO<small>₂</small> sorption materials for DAC. However, the experimental design space for different DESs/ESs/ILs is vast, with the exact CO<small>₂</small> complexation pathways difficult to elucidate; this creates significant limitations in rationally designing new materials with targeted CO<small>₂</small> sorption energetics. Herein, the CO<small>₂</small> complexation pathways for a structural library of different DES/ES components are computed using quantum chemical calculations (<em>i.e.</em>, density functional theory). For the entire structure library, we report the energies of elementary CO<small>₂</small> binding and proton transfer reactions as these reactions are fundamental in DAC within DESs and ESs. These elementary reactions are combined to generate CO<small>₂</small> complexation pathways and calculate their free energies. The different elementary steps and reaction pathways demonstrate the range of CO<small>₂</small> complexation free energies and the significance between CO<small>₂</small> binding and proton transfer reactions. We also report the CO<small>₂</small> complexation free energies with different functional groups around the CO<small>₂</small> sorption site, supporting the concept of functionalization for tuning CO<small>₂</small> complexation thermodynamics. Additionally, our findings suggest potential descriptors, such as proton affinity or p<em>K</em><small>_a</small>, could be useful when identifying candidate species for ESs and predicting/rationalizing product distributions. Our work has implications for experimental synthesis, characterization, and performance evaluation of new DAC sorption materials.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 6","pages":" 447-458"},"PeriodicalIF":3.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d5me00034c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of ring sizes on the dynamic behaviors of [2]catenane","authors":"Rundong Li, Xiaohui Wen, Xinbiao Huang, Hai Li and Zhuling Jiang","doi":"10.1039/D5ME00025D","DOIUrl":"https://doi.org/10.1039/D5ME00025D","url":null,"abstract":"<p >A hybrid mesoscopic simulation approach combining multiple particle collision dynamics (MPCD) with molecular dynamics (MD) is employed to investigate the dynamic behaviors and conformational changes of semi-flexible [2]catenanes with varying ring sizes under steady shear flow conditions. Firstly, our study reveals an irregular linear relationship between the three-dimensional surface area of the rings and the shear rate, as evidenced by changes in the surface area of the semi-flexible [2]catenane. Through schematic observations, we find that the dynamic behaviors of [2]catenanes differ for varying ring sizes. Small rings exhibit tumbling motions, medium rings show slip-tumbling motions, while large rings undergo fold-slipping motions. Medium and large rings show shear thinning conformation changes. Secondly, we analyze the normal and diagonal angles of the two rings, demonstrating that the movements in both the shear direction and the gradient direction are complete but intermittent. Thirdly, we analyze how the relative displacement vector of the center of mass between the two rings in the [2]catenane changes over time. This analysis indication of the relative motion occurring between the two rings. We also find that within certain ranges of shear rate and ring size, the two rings of the [2]catenane twist into “8” shapes, rather than slip-tumbling and fold-slipping motions. These findings provide valuable insights for guiding the transport of catenane polymers in biological systems and for designing catenane polymeric materials for industrial applications.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 6","pages":" 483-493"},"PeriodicalIF":3.2,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward understanding biomolecular materials comprising intrinsically disordered proteins via simulation and experiment","authors":"Bin Wang, Tianren Zhang, Sirui Shen, Darrin J. Pochan, Jeffery G. Saven and Kristi L. Kiick","doi":"10.1039/D4ME00197D","DOIUrl":"10.1039/D4ME00197D","url":null,"abstract":"<p >Intrinsically disordered proteins (IDPs) yield solutions with tunable phase transition behavior and have been widely applied in designing stimuli-responsive materials. Understanding interactions between amino acid residues of the IDP sequence is critical to designing new IDP-based materials with selective phase behavior, assembly, and mechanical properties. The lack of defined structure for this class of proteins complicates accurate prediction of their molecular-scale behavior. In this review, recent progress is presented in the development and application of simulation methods to describe the behavior of IDPs. Results for elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs) are highlighted, focusing on studies that compare simulation results with experimental findings.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 7","pages":" 502-518"},"PeriodicalIF":3.2,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of vitrimer-based reusable prosthetic materials","authors":"Suraj W. Wajge, Ashutosh Bagde, Bhupesh Sarode and Chayan Das","doi":"10.1039/D4ME00173G","DOIUrl":"https://doi.org/10.1039/D4ME00173G","url":null,"abstract":"<p >This study presents a cross-linked bisphenol A propoxylate diglycidyl ether network (BP17) synthesised <em>via</em> a dynamic transesterification reaction. The reaction involves a linear long chain bisphenol A propoxylate diglycidyl ether terminated (BP), high molecular weight cross-linker <em>viz.</em>, Pripol 1017, and Zn(OAc)<small>₂</small> as a catalyst. The thermal dynamics of the BP17 network are investigated using creep recovery tests. BP17 shows appreciable resistance to solvents such as dimethyl sulfoxide (DMSO), even at 160 °C. Thermogravimetric analysis reveals its excellent thermal stability, with an onset degradation temperature of 290 °C. In addition, it could be reprocessed by hot-pressing at 160 °C, retaining its mechanical properties even after the third cycle. Moreover, the cytocompatibility test confirms the biocompatibility of BP17, making it a promising candidate for use in maxillofacial prosthetics. Thus, the thermoset-like properties of BP17, at relatively high temperature, make it very promising for biomedical and other advanced applications.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 6","pages":" 472-482"},"PeriodicalIF":3.2,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing a multi-epitope vaccine targeting UPF0721 of meningitis-causing Salmonella enterica serovar Typhimurium strain L-4126 by utilizing immuno-informatics and in silico approaches","authors":"Elham Mohammed Khatrawi, Syed Luqman Ali, Syed Yasir Ali, Aigul Abduldayeva and Alaa S. Alhegaili","doi":"10.1039/D5ME00027K","DOIUrl":"https://doi.org/10.1039/D5ME00027K","url":null,"abstract":"<p >Salmonellae, which pose a significant global health threat, cause a range of infections, including gastroenteritis and, in severe cases, meningitis, particularly in immunocompromised individuals. The emergence of multi-drug-resistant <em>Salmonella enterica</em> serovar Typhimurium underscores the urgent need for effective vaccine development. In this study, a chimeric vaccine was constructed, targeting UPF0721 transmembrane proteins of serovar Typhimurium strain L-4126, which are critical for its life cycle. Fifteen highly antigenic epitopes, including CTL, HTL, and B-cell epitopes, were recognised and assessed for their ability to elicit T-cell and IFN-γ-mediated immune-responses. Physiochemical analyses confirmed their safety profiles. The vaccine construct integrated these epitopes with linkers (EAAAK, GPGPG, AAY, and KK) and β-defensin adjuvants to enhance immunogenicity, stability, and molecular interactions. Molecular docking demonstrated robust binding affinity, particularly with TLR8, and highlighted the vaccine's structural stability and immunogenic potential. The eigenvalue analysis (9.728895) validated the vaccine's flexibility and favorable biophysical properties. Molecular dynamics simulations validated the energy minimization, molecular stability and flexibility assessments. Immune simulation results indicated strong immune responses, while the physicochemical analysis confirmed solubility and stability during recombinant peptide expression in <em>E. coli</em>. This study also explored mRNA vaccine constructs, emphasizing their potential in combating serovar Typhimurium infections such as meningitis. The vaccine construct showed high potential, demanding further investigation into their immune efficacy against serovar Typhimurium infections through experimental assays and medical trials.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 7","pages":" 549-566"},"PeriodicalIF":3.2,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First-principles study on electrocatalytic CO2 reduction by 2D TM3(HATNA)2: products and mechanism†","authors":"Xin Wang, Beibei An, Hui Zhao, Huali Jia, Like Wang, Jie Li, Yongliang Ban and Xiaoming Zhu","doi":"10.1039/D4ME00162A","DOIUrl":"https://doi.org/10.1039/D4ME00162A","url":null,"abstract":"<p >Single-atom catalysts (SACs) have attracted great attention due to their distinct advantages; however, their complicated synthesis procedures have impeded their large-scale application. Additionally, nano-particles or subnano-clusters generated during the synthesis can adversely affect the final performance of the catalysts. The appearance of two-dimensional metal–organic frameworks (2D-MOFs) has provided a new strategy to synthesize SACs. Moreover, highly ordered MOFs have high electrical conductivity and are conducive to electron transfer, which is crucial in improving the electrochemical activity of catalysts. A series of single-atom catalysts TM<small>₃</small>(HATNA)<small>₂</small> (where TM is one of ten different transition metals) based on 2D-MOFs has been designed using hexazine hetero-trinaphthalene (HATNA) as ligands. The mechanisms and routes of the carbon dioxide reduction reaction (CO<small>₂</small>RR) catalyzed by these materials have been studied using first-principles methods. The results testify that TM<small>₃</small>(HATNA)<small>₂</small> (TM = Cr, Ru and Rh) may serve as potential catalysts for the CO<small>₂</small>RR with good stability and catalytic activity. The reduction product of Cr<small>₃</small>(HATNA)<small>₂</small> is methane (CH<small>₄</small>), while that of both Ru<small>₃</small>(HATNA)<small>₂</small> and Rh<small>₃</small>(HATNA)<small>₂</small> is methanol (CH<small>₃</small>OH). This work provides a new substrate material for the development of single-atom catalysts with abundant and diverse catalytic products.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 6","pages":" 464-471"},"PeriodicalIF":3.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144206256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the role of charge transfer on semiconductor properties in a new donor–acceptor cocrystal 1,5-dihydroxynaphthalene : TCNQ†","authors":"Arkalekha Mandal, Chris Erik Mohn, Carl Henrik Görbitz, Melania Rogowska and Ola Nilsen","doi":"10.1039/D5ME00033E","DOIUrl":"https://doi.org/10.1039/D5ME00033E","url":null,"abstract":"<p >In this work, we have investigated the semiconducting properties of an unprecedented 1 : 1 π-stacked donor–acceptor cocrystal of 1,5-dihydroxynaphthalene (DHN) as the π-donor (D) with 7,7′,8,8′-tetracyanoquinodimethane (TCNQ) as the π-acceptor (A). Molecular semiconductors with electron dominant transport, narrow bandgap, solution processing ability, air-stability are highly sought-after for application in n-channel organic field effect transistors. The DHN : TCNQ cocrystal shows n-type semiconductor nature with a narrow bandgap of around 1 eV, and a low LUMO energy level (−3.8 eV) making it less prone to areal degradation. The electron dominant transport in this cocrystal is described by assuming that electron and hole hop <em>via</em> a super-exchange mechanism along the mixed ⋯D–A⋯ π-stack direction. The participation of bridging molecular orbitals other than donor HOMO make a significant contribution to the super-exchange electron transfer, thus resulting in electron hopping from acceptor to acceptor which is four times larger than the value of hole hopping from donor to donor. Detailed analysis of crystal packing and electronic properties demonstrate that the super-exchange charge carrier transport is facilitated by strong π⋯π stacking interaction between the donor and acceptor, and prominent charge transfer.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 7","pages":" 519-533"},"PeriodicalIF":3.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d5me00033e?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of an organic cage-based porous ionic liquid using an aminal tying strategy†","authors":"Aiting Kai, Austin Mroz, Kim E. Jelfs, Andrew I. Cooper, Marc A. Little and Rebecca L. Greenaway","doi":"10.1039/D5ME00004A","DOIUrl":"10.1039/D5ME00004A","url":null,"abstract":"<p >An aminal tying method was applied to post-synthetically modify a flexible organic cage, <strong>RCC1</strong>, to construct a porous ionic liquid (PIL)<small>.</small> The resulting PIL, [<strong>RCC1</strong>-IM][NTf<small>₂</small>]<small>₆</small>, displayed melting behaviour below 100 °C, a transition to a glass phase on melt-quenching, CO<small>₂</small> uptake, and its permanent porosity was confirmed using molecular dynamic simulations.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 6","pages":" 459-463"},"PeriodicalIF":3.2,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11979736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transfer learning accelerated discovery of conjugated oligomers for advanced organic photovoltaics†","authors":"Siyan Deng, Jing Xiang Ng and Shuzhou Li","doi":"10.1039/D4ME00188E","DOIUrl":"https://doi.org/10.1039/D4ME00188E","url":null,"abstract":"<p >Machine learning accelerates material discovery which includes selection of candidate small molecules and polymers for high-efficiency organic photovoltaic (OPV) materials. However, conventional machine learning models suffer from data scarcity for conjugated oligomers, crucial for OPV material production. To address this challenge, transfer learning within a graph neural network was introduced to reduce the data requirement while accurately predicting the electronic properties of the conjugated oligomers. By leveraging on transfer learning using original conjugated oligomer data and pre-trained models from the renowned PubChemQC dataset, the limitations posed by insufficient data were mitigated. The models in this study achieved a low mean absolute error, ranging from 0.46 to 0.74 eV, for the HOMO, LUMO, and HOMO–LUMO gap. An original candidate dataset of 3710 conjugated oligomers was constructed for materials discovery, and a high-throughput screening pipeline was developed by integrating the models with density functional theory. This pipeline effectively identified 46 promising conjugated oligomer candidates, showcasing its effectiveness in accelerating the discovery of advanced materials for organic photovoltaics. These results demonstrated the potential of the approach used in this study to overcome data scarcity while accelerating the discovery of new innovative materials in organic electronics.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 5","pages":" 413-423"},"PeriodicalIF":3.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d4me00188e?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143913723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stable n-type organic small-molecule conductor enabled by chemically doped ternary components†","authors":"Bohan Zhou, Ziting Zhong, Runshi Wu, Wenzhao Xiong, Huawei Hu, Anlian Pan, Dafei Yuan and Xiaozhang Zhu","doi":"10.1039/D4ME00192C","DOIUrl":"https://doi.org/10.1039/D4ME00192C","url":null,"abstract":"<p >Chemical doping is a versatile method for tuning the optoelectronic properties of organic semiconductors (OSCs). Compared to p-type doping, achieving stable and efficient n-type doping in OSCs, especially in small molecules, remains a significant challenge. The lack of a universal doping strategy, along with OSCs having deep lowest unoccupied molecular orbital (LUMO) energy levels and high electron mobility, limits the development of n-type doped OSCs. In this work, a ternary system containing the small-molecule OSC 2DQTT-o, with a deep LUMO level and high electron mobility, the n-type dopant N-DMBI, and the polar insulating polymer PEO was developed. With the introduction of PEO, the miscibility, doping level and doping stability were significantly improved. Notably, the ternary doped components showed excellent air stability, retaining 82% of the initial electrical conductivity after exposure to air for 240 h, representing a 32% improvement compared to the system without PEO. Furthermore, the ternary doped films exhibited good thermal stability, retaining 55% of the initial electrical conductivity after heating at 200 °C. In contrast, the two-component doped films decomposed and became insulating.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 5","pages":" 357-363"},"PeriodicalIF":3.2,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143913716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}