Molecular Systems Design & Engineering最新文献

{"title":"Mesoscale artificial synthesis of conjugated microporous polymers†","authors":"Catherine Mollart, Bartosz Ciborowski and Abbie Trewin","doi":"10.1039/D3ME00130J","DOIUrl":"10.1039/D3ME00130J","url":null,"abstract":"<p >This work reports the mesoscale artificial synthesis of a conjugated microporous polymer, CMP-1, using a hybrid coarse-grained methodology. Whilst using a coarse grain approach does give a lower density and surface area when compared to the all-atom equivalent, this allowed a simulation cell volume scale-up of up to 64 times, and an overall speed-up factor of 44% when compared to the all-atom equivalent.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/me/d3me00130j?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136304050","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":"Dehydration induced selective ion trapping by topology constrained atomically thin graphene-crown membranes†","authors":"Pooja Sahu and Sk. Musharaf Ali","doi":"10.1039/D3ME00118K","DOIUrl":"10.1039/D3ME00118K","url":null,"abstract":"<p >Inspired by the host–guest recognition of crown ethers, the current era is evolving around the graphene-crown-based atomically thin membranes that will profoundly impact diverse fields of science and engineering. Using extensive MD simulations and DFT calculations, we investigate the binding affinities of graphene-embedded 18-crown-6, 16-crown-5, and 14-crown-4 for Li<small>⁺</small>, Na<small>⁺</small>, K<small>⁺</small>, Mg<small>²⁺</small>, and Ca<small>²⁺</small> metal ions. We highlight that the binding preference of these membranes depends not only on the size of the crown ether cavity but also on the stability of the hydration shell of binding ions, as demonstrated by the hydration-induced energy transfer barrier. The diverse transport behavior of these membranes is attributed to ion transport over a free energy barrier raised from ionic dehydration. Results designate that the deformation of the hydration shell is a necessary condition for the adsorption of metal ions within crown ether pores, which controls the selectivity of the membrane for particular metal ions. The findings from microstructure analysis about the ion location and pore occupancy reveal how sub-nanopores of graphene-crown membranes are capable of distinguishing ions of similar characteristics. The observed ion dehydration and kinetic behavior are sensitive to pore size and the chemical environment lining the pore, similar to those observed with biological ion channels.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136208461","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":"In silico identification of novel PqsD inhibitors: promising molecules for quorum sensing interference in Pseudomonas aeruginosa†","authors":"Tatiana F. Vieira, Nuno M. F. S. A. Cerqueira, Manuel Simões and Sérgio F. Sousa","doi":"10.1039/D3ME00107E","DOIUrl":"10.1039/D3ME00107E","url":null,"abstract":"<p >PqsD is an anthraniloyl-CoA anthraniloyltransferase involved in the synthesis of the secondary metabolites essential to the formation of <em>Pseudomonas</em> quinolone signal (PQS) inducer molecules. Its main substrate is anthraniloyl-coenzyme A (ACoA) but it can accept malonyl-CoA as secondary substrate. Suppression of PqsD activity has been connected to the inhibition of biofilm formation and can also be a good target for dual inhibition, when combined with PqsR inhibition. Here we describe the validation and application of an <em>in silico</em> methodology to find new compounds to inhibit PqsD. Using molecular docking and structure-based virtual screening protocols, five databases of compounds were screened (FDA approved subset of the ZINC database, Chimiothèque Nationale, Mu.Ta.Lig. Virtual Chemotheca, Interbioscreen (IBS), and Comprehensive Marine Natural Products Database (CMNPD)), representing a total of 221 146 molecules. The top five compounds of each database were selected to be further analysed using molecular dynamics simulations. Binding affinity was validated using free energy calculations, enabling the selection and characterization of eight compounds for future studies aiming to develop new quorum sensing inhibitors.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135700467","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":"Early detection of SARS-CoV-2 with functionalized gold and molecularly imprinted polymeric nanoparticles: a mini review","authors":"Pankaj Singla, Harpreet Kaur, Saweta Garg, Navalpreet Kaur, Francesco Canfarotta, Rakesh Kumar Mahajan and Marloes Peeters","doi":"10.1039/D3ME00131H","DOIUrl":"https://doi.org/10.1039/D3ME00131H","url":null,"abstract":"<p >The novel coronavirus COVID-19 was first reported in Wuhan, China, in December 2019 and rapidly spread to the rest of the world, with the WHO declaring a global pandemic in March 2020. Rapid mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have challenged its diagnosis and treatments. Reverse transcription-polymerase chain reaction (RT-PCR) tests are widely used for the diagnosis of COVID-19; however, they present several drawbacks including high cost, long turnaround time, and need for sophisticated lab infrastructure and trained technical personnel. Lateral flow tests based on antigen sensing are an interesting alternative since they offer rapid (15–30 min) and low-cost analysis, although their low sensitivity has led to several adopted tests being withdrawn from the market. Henceforth, the development of detection methods which are fast, robust, reliable, cost-effective, easy to use and portable is indispensable to prevent community transmission of COVID-19. We have reviewed two different emerging colloidal-based methodologies, (a) functionalized gold nanoparticles (functionalized AuNPs) and (b) molecularly imprinted polymers (MIPs), for fast, highly specific, and reliable identification of SARS-CoV-2. Different modifications of AuNPs with antibodies, antigens and nucleoproteins and their various assays including colorimetric, electrochemical, localized surface plasmon resonance (LSPR) and lateral flow immunoassays are discussed. In contrast, with MIP-based sensors, various antigen proteins and virus particles can be imprinted within the polymeric nanoplatform and hence can be detected with various readout techniques. The operating characteristics of these two emerging diagnostic platforms were critically reviewed and compared against each other.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71907781","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":"Bio-inspired dry adhesive pads using multi-walled carbon nanotube/polydimethylsiloxane composites for efficient wafer transfer robot arms in smart factories†","authors":"Bom Lee, Young Chun Ko, Simon Kim, Su Eon Lee, Ho Jun Jin, Dong Joon Chang, Min-Ho Park and Bong Hoon Kim","doi":"10.1039/D3ME00126A","DOIUrl":"10.1039/D3ME00126A","url":null,"abstract":"<p >The development of dry adhesive pads (DAPs) is essential to prevent wafer detachment from high-speed wafer-transfer robot arms. However, polydimethylsiloxane (PDMS)-based DAPs, which are insulating elastomers, generate residual charges inside DAPs. These cause charge accumulation and electrostatic interactions between the DAP and the wafer interface. Furthermore, at a high processing temperature of &gt;300 °C, the adhesive and mechanical strengths of conventional DAPs are degraded because of their low thermal and mechanical stability. In this study, we developed bio-inspired DAPs (BDAPs) with various shapes (hole, cylinder, and line patterns) and different contact areas (20, 40, and 60%) through systematic investigations to determine optimized patterns and shapes for different motions. Additionally, we fabricated a multi-walled carbon nanotube (MWCNT)/PDMS composite-based BDAP (c-BDAP), which exhibited high heat resistance and high electrical conductivity. The conductivity of c-BDAP was 6.16 × 10<small>⁻³</small> S m<small>⁻¹</small>, and it had a weight loss of ∼4% at 300 °C after 1 h. Our findings can inspire the development of low-cost and high-performance c-BDAPs, which are reliable for various robot arm movements.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135445785","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":"Factors influencing the catalytic activity of metal-dependent histidine-rich peptides: sequence, conformation, stereochemistry, self-assembly or their interplay?†","authors":"Patrizia Janković, Marko Babić, Marko Perčić, Ana S. Pina and Daniela Kalafatovic","doi":"10.1039/D3ME00117B","DOIUrl":"https://doi.org/10.1039/D3ME00117B","url":null,"abstract":"<p >The sequence-to-function relationship of peptide-based catalysts remains a challenge, as even subtle modifications at the sequence level can alternate their catalytic activity. A set of linear and cyclic histidine-rich peptides was synthesized to assess the impact of amino acid disposition, cyclization, and incorporation of <small>D</small>-amino acids on their ability to self-assemble, coordinate Zn<small>²⁺</small> ions, and show intrinsic hydrolase-like activity. Self-assembly into β-sheets was confirmed for both linear peptides and one cyclic analogue (cy-hh) by FTIR, ThT binding, CD, and AFM. Interestingly, only peptide A demonstrated efficient ester hydrolysis of <em>p</em>-NPA, <em>p</em>-NPB and <em>p</em>-NPO substrates, indicative of its effective Zn<small>²⁺</small> coordination. Our findings highlight that increased rigidity of the peptide can hinder metal ion coordination by limiting the necessary conformational adjustments for optimal Zn<small>²⁺</small> binding. These insights into the structural changes underlying the function of short peptides offer valuable knowledge for the design of metal-dependent peptide-based catalysts.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71907766","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":"Steric effects stabilize reverse micelle domains in supercritical CO2 by determined conformation: restrictions of water and cations†","authors":"Huiwen Sun, Meng Wang, Pan Wang and Muhan Wang","doi":"10.1039/D3ME00115F","DOIUrl":"10.1039/D3ME00115F","url":null,"abstract":"<p >Previous research into designing CO<small>₂</small>-philic surfactants has certain limitations, necessitating the exploration of effective design concepts for hydrocarbon surfactants, which are far less expensive and less toxic than fluorocarbon surfactants. In this study, molecular simulations were employed to extensively investigate preassembled models of four representative surfactants and elucidate the structure of water-in-carbon dioxide (W/C) microemulsions. Innovative strategies for evaluating the stability of surfactant microemulsions and designing CO<small>₂</small>-philic surfactants were developed. Thorough investigations into the microemulsion structure revealed that fluorocarbon surfactants formed stable micelles due to the steric effect arising from the determined conformation, which is restricted by hydrogen bonds. Fluorination at the terminal end of the surfactant tail will lead to a more restrictive structure, acting as a steric hindrance. Investigation into a hydrocarbon surfactant also determined that the group at the surfactant tail terminal formed hydrogen bonds with water molecules, restricting the conformation of the surfactant. This is a feasible method <em>via</em> fluorine substitution. This work reveals that steric effects arising from water molecules and cation restrictions can guide surfactant synthesis strategies or stabilize reverse micelles in scCO<small>₂</small> systems. With the development of these basic design principles, the synthesis of efficient hydrocarbon surfactants will be achieved in the foreseeable future.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135400598","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":"Combined computational and experimental approach for bio-sourced monomers to design green pressure-sensitive adhesives†","authors":"Manjinder Singh, Sushanta K. Sahoo and Gaurav Manik","doi":"10.1039/D3ME00080J","DOIUrl":"10.1039/D3ME00080J","url":null,"abstract":"<p >The food packaging and healthcare industries have extensively demanded eco-friendly pressure-sensitive adhesives (PSAs) owing to their inherent renewability, sustainability and adhesion properties. In the present research, linseed oil derivatives have been used to synthesize bio-based PSAs by replacing petro-based low <em>T</em><small>_g</small> monomers. A dual approach consisting of computational and experimental studies has been conducted to explore the potential of acrylated epoxidized linseed oil (AELO) and acrylated epoxidized methyl ester (AEME) as low <em>T</em><small>_g</small> resins to develop bio-based PSAs. The thermal studies revealed that poly (AELO) and poly (AEME) are thermally stable up to 610 K and 577 K, respectively. The rheology of these resins suggests that AEME would be easily processable, while the addition of diluents to AELO can improve its processing significantly. The <em>T</em><small>_g</small> values from DSC thermograms and simulation studies for poly (AELO) and poly (AEME) were in close proximity and met the prerequisite of low <em>T</em><small>_g</small> monomers, thereby verifying the simulation protocol adopted. Further, surface energy and interaction energy with three different substrates were estimated to understand and compare the adhesion behavior of the synthesized resins. The potential applications of these bio-resins in healthcare and food packaging industries have been explored by estimating the binding strength with human skin and polypropylene (PP), respectively. An increment of ∼37% and ∼809% was observed in the interaction energy of poly (AELO) with human skin and PP as compared with the conventional poly (2-ethylhexyl acrylate (2-EHA))-based systems, respectively. The adhesion strength was found to be 38.2 and 31.5 N m<small>⁻¹</small> for cured samples of poly (AELO) and poly (AEME), respectively, which are comparable to various commercially available PSAs. This research provides a path for exploring the potential of linseed oil derived AELO and AEME to formulate PSAs with desirable properties for healthcare and food packaging industries.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135360673","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":"Evaluating the CO2 capture performance of a “phase-change” metal–organic framework in a pressure-vacuum swing adsorption process†","authors":"David Danaci, Elena Pulidori, Luca Bernazzani, Camille Petit and Marco Taddei","doi":"10.1039/D3ME00098B","DOIUrl":"10.1039/D3ME00098B","url":null,"abstract":"<p >Metal–organic frameworks (MOFs) that display step-shaped adsorption isotherms, <em>i.e.</em>, “phase-change” MOFs, represent a relatively small subset of all known MOFs. Yet, they are rapidly emerging as promising sorbents to achieve excellent gas separation performances with little energy demand. In this work, we assessed F4_MIL-140A(Ce), a recently discovered “phase-change” MOF adsorbent, for CO<small>₂</small> capture in two scenarios using a pressure-vacuum swing adsorption process, namely a coal-fired power plant flue gas (12.5%<small>_mol</small> CO<small>₂</small>), and a steel plant flue gas (25.5%<small>_mol</small> CO<small>₂</small>). Four CO<small>₂</small> and three N<small>₂</small> adsorption isotherms were collected on F4_MIL-140A(Ce) over a range of temperatures and modelled using a bespoke equation for step-shaped isotherms. We accurately measured the heat capacity of F4_MIL-140A(Ce), a key thermodynamic property for a sorbent, using a method based on differential scanning calorimetry that overcomes the issues associated with the poor thermal conductivity of MOF powders. We then used these experimental data as input in a process optimisation framework and we compared the CO<small>₂</small> capture performance of F4_MIL-140A(Ce) to that of other “canonical” sorbents, including, zeolite 13X, activated carbon and three MOFs (<em>i.e.</em>, HKUST-1, UTSA-16 and CALF-20). We found that F4_MIL-140A(Ce) has the potential to perform better than other sorbents, in terms of recovery and purity, under most of the simulated process conditions. We attribute such promising performance to the non-hysteretic step-shaped isotherm, the low uptake capacity for N<small>₂</small> and the mild heat of CO<small>₂</small> adsorption displayed by F4_MIL-140A(Ce).</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2023/me/d3me00098b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122553264","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":"Chiral self-organization of the TPPS4 porphyrin assisted by molecular rotations†","authors":"Gioacchino Schifino, Mariagrazia Fortino, Luigi Monsù Scolaro and Adriana Pietropaolo","doi":"10.1039/D3ME00072A","DOIUrl":"10.1039/D3ME00072A","url":null,"abstract":"<p >Self-assembly strategies are attracting considerable interest for the development and design of advanced chiral materials from the nano- up to the macroscale. In particular, the spontaneous chiral self-organization of achiral π-conjugated molecules has gained significant attention due to their versatile optical and electronic properties. The 5,10,15,20-tetrakis(4-sulphonatophenyl)porphyrin (TPPS<small>₄</small>) has shown an interesting ability to self-assemble into chiral supramolecular structures. Understanding the fundamental principles behind the generation of chirality can guide rational fabrication and control of the chiral assembly mechanism of the TPPS<small>₄</small> scaffold. Axial chirality due to the side chain rotations of the sulphonato-phenyl groups may propagate chiral information through specific interactions along the whole supramolecular structure during the non-covalent self-assembly interactions. Therefore, starting from the atropisomers of TPPS<small>₄</small> in its diacid form (H<small>₄</small>TPPS<small>₄</small><small>²⁻</small>), enhanced sampling simulations have been performed on this species considering its monomeric, dimeric, trimeric and tetrameric aggregates. The free-energy profiles have been reconstructed for all the porphyrin aggregates as a function of the pyrrole improper torsions of the porphyrin ring, allowing evaluation of how the symmetry or the asymmetry of the H<small>₄</small>TPPS<small>₄</small><small>²⁻</small> supramolecular system can be selectively affected by increasing the aggregate size. The formation of a specific twisted arrangement has been detected during the self-assembly process depending on the odd (destabilizer of a twisted arrangement) or even (stabilizer of a twisted arrangement) number of structural units forming the aggregate. The results in this study could help to create accurate predictive models for the generation of chiral supramolecular structures.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115265156","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}