Molecular Systems Design & Engineering最新文献

{"title":"DynaMate: leveraging AI-agents for customized research workflows","authors":"Orlando A. Mendible-Barreto, Misael Díaz-Maldonado, Fernando J. Carmona Esteva, J. Emmanuel Torres, Ubaldo M. Córdova-Figueroa and Yamil J. Colón","doi":"10.1039/D5ME00062A","DOIUrl":"https://doi.org/10.1039/D5ME00062A","url":null,"abstract":"<p >Developments related to large language models (LLMs) have deeply impacted everyday activities and are even more significant in scientific applications. They range from simple chatbots that respond to a prompt to very complex agents that plan, conduct, and analyze experiments. As more models and algorithms continue to be developed at a rapid pace, the complexity involved in building this framework increases. Additionally, editing these algorithms for personalized applications has become increasingly challenging. To this end, we present a modular code template that allows easy implementation of custom Python code functions to enable a multi-agent framework capable of using these functions to perform complex tasks. We used the template to build DynaMate, a complex framework for generating, running, and analyzing molecular simulations. We performed various tests that included the simulation of solvents and metal–organic frameworks, calculation of radial distribution functions, and determination of free energy landscapes. The modularity of these templates allows for easy editing and the addition of custom tools, which enables rapid access to the many tools that can be involved in scientific workflows.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 7","pages":" 585-598"},"PeriodicalIF":3.2,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d5me00062a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519600","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":"Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments†","authors":"ByungUk Park and Reid C. Van Lehn","doi":"10.1039/D5ME00032G","DOIUrl":"https://doi.org/10.1039/D5ME00032G","url":null,"abstract":"<p >The orientation of integral membrane proteins (IMPs) with respect to the membrane is established during protein synthesis and insertion into the membrane. After synthesis, IMP orientation is thought to be fixed due to the thermodynamic barrier for “flipping” protein loops or helices across the hydrophobic core of the membrane in a process analogous to lipid flip-flop. A notable exception is EmrE, a homodimeric IMP with an N-terminal transmembrane helix that can flip across the membrane until flipping is arrested upon dimerization. Understanding the features of the EmrE sequence that permit this unusual flipping behavior would be valuable for guiding the design of synthetic materials capable of translocating or flipping charged groups across lipid membranes. To elucidate the molecular mechanisms underlying flipping in EmrE and derive bioinspired design rules, we employ atomistic molecular dynamics simulations and enhanced sampling techniques to systematically investigate the flipping of truncated segments of EmrE. Our results demonstrate that a membrane-exposed charged glutamate residue at the center of the N-terminal helix lowers the energetic barrier for flipping (from ∼12.1 kcal mol<small>⁻¹</small> to ∼5.4 kcal mol<small>⁻¹</small>) by stabilizing water defects and minimizing membrane perturbation. Comparative analysis reveals that the marginal hydrophobicity of this helix, rather than the marginal hydrophilicity of its loop, is the key determinant of flipping propensity. Our results further indicate that interhelical hydrogen bonding upon dimerization inhibits flipping. These findings establish several bioinspired design principles to govern flipping in related materials: (1) marginally hydrophobic helices with membrane-exposed charged groups promote flipping, (2) modulating protonation states of membrane-exposed groups tunes flipping efficiency, and (3) interhelical hydrogen bonding can be leveraged to arrest flipping. These insights provide a foundation for engineering synthetic peptides, engineered proteins, and biomimetic nanomaterials with controlled flipping or translocation behavior for applications in intracellular drug delivery and membrane protein design.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 7","pages":" 567-584"},"PeriodicalIF":3.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144519604","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":"Flame growth of nickel-based cocatalyst for efficient solar water splitting of BiVO4 photoanode†","authors":"Haohua Wang, Youyi Su, Xiangui Pang, Ming Zhang, Wufang Wang, Pingping Yang, Xinxin Lu and Jiale Xie","doi":"10.1039/D5ME00006H","DOIUrl":"https://doi.org/10.1039/D5ME00006H","url":null,"abstract":"<p >The low charge separation efficiency and slow water oxidation kinetics of bismuth vanadate (BiVO<small>₄</small>, BVO) limit its performance for solar water splitting. Here, a flame growth method has been developed to rapidly grow a nickel-based cocatalyst (NiO<small>_<em>x</em></small>) on the surface of the worm-like BVO films. After 20 s flame growth, the NiO<small>_<em>x</em></small> cocatalyst, which is comprised of Ni, NiO, and NiOOH, can be uniformly and rapidly synthesized. The NiO<small>_<em>x</em></small>/BVO composite photoanode achieves a photocurrent density of 3.80 mA cm<small>⁻²</small> at 1.23 V <em>vs.</em> RHE in a neutral electrolyte, which is 6.67 times higher than that of the pristine BiVO<small>₄</small>. Under the assistance of polyacrylamide hydrogel coating, the photocurrent of the NiO<small>_<em>x</em></small>/BVO photoanode can be well maintained at 62.26% after a 24 h long-term stability test. The performance improvement can be mainly attributed to the fact that the NiO<small>_<em>x</em></small> layer reduces the resistance of the charge transfer and the energy barrier of the oxygen evolution reactions, and introduces a large number of oxygen vacancies. This research confirms that the flame growth of cocatalysts is an efficient method for preparing the cocatalytic layer on the nanostructure photoelectrode, which can well maintain the nanostructures.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 8","pages":" 675-681"},"PeriodicalIF":3.2,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144716438","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":"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}