Molecular Systems Design & Engineering最新文献

Molecular design of protein-based materials – state of the art, opportunities and challenges at the interface between materials engineering and synthetic biology 基于蛋白质的材料的分子设计--材料工程与合成生物学界面的技术现状、机遇与挑战

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-19 DOI: 10.1039/d4me00122b

Ebony Shire, André A. B. Coimbra, Carlos Barba Ostria, Leonardo Rios-Solis, Diego López Barreiro

{"title":"Molecular design of protein-based materials – state of the art, opportunities and challenges at the interface between materials engineering and synthetic biology","authors":"Ebony Shire, André A. B. Coimbra, Carlos Barba Ostria, Leonardo Rios-Solis, Diego López Barreiro","doi":"10.1039/d4me00122b","DOIUrl":"https://doi.org/10.1039/d4me00122b","url":null,"abstract":"Structural proteins like silk, squid ring teeth, elastin, collagen, or resilin, among others, are inspiring the development of new sustainable biopolymeric materials for applications including healthcare, food, soft robotics, or textiles. Furthermore, advances in the fields of soft materials and synthetic biology have a joint great potential to guide the design of novel structural proteins, despite both fields progressing mostly in a separate fashion so far. Using recombinant DNA technologies and microbial fermentations, we can design new structural proteins with monomer-level sequence control and a dispersity of ca. 1.0, based on permutations of tandem repeats derived from natural structural proteins. However, the molecular design of recombinant and repetitive structural proteins is a nontrivial task that is generally approached using low-throughput trial-and-error experimentation. Here, we review recent progress in this area, in terms of structure–function relationships and DNA synthesis technologies. We also discuss experimental and computational advances towards the establishment of rapid prototyping pipelines for this family of biopolymers. Finally, we highlight future challenges to make protein-based materials a commercially viable alternative to current fossil-based polymers.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269140","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}

引用次数: 0

Multi-site esterification: a tunable, reversible strategy to tailor therapeutic peptides for delivery 多位点酯化：定制治疗肽递送的可调、可逆策略

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-13 DOI: 10.1039/d4me00072b

Mark S. Bannon, Jeffrey F. Ellena, Aditi S. Gourishankar, Spencer R. Marsh, Dilza Trevisan-Silva, Nicholas E. Sherman, L. Jane Jourdan, Robert G. Gourdie, Rachel A. Letteri

{"title":"Multi-site esterification: a tunable, reversible strategy to tailor therapeutic peptides for delivery","authors":"Mark S. Bannon, Jeffrey F. Ellena, Aditi S. Gourishankar, Spencer R. Marsh, Dilza Trevisan-Silva, Nicholas E. Sherman, L. Jane Jourdan, Robert G. Gourdie, Rachel A. Letteri","doi":"10.1039/d4me00072b","DOIUrl":"https://doi.org/10.1039/d4me00072b","url":null,"abstract":"Peptides are naturally potent and selective therapeutics with massive potential; however, low cell membrane permeability limits their clinical implementation, particularly for hydrophilic, anionic peptides with intracellular targets. To overcome this limitation, esterification of anionic carboxylic acids on therapeutic peptides can simultaneously increase hydrophobicity and net charge to facilitate cell internalization, whereafter installed esters can be cleaved hydrolytically to restore activity. To date, however, most esterified therapeutics contain either a single esterification site or multiple esters randomly incorporated on multiple sites. This investigation provides molecular engineering insight into how the number and position of esters installed onto the therapeutic peptide α carboxyl terminus 11 (αCT11, RPRPDDLEI) with 4 esterification sites affect hydrophobicity and the hydrolysis process that reverts the peptide to its original form. After installing methyl esters onto αCT11 using Fischer esterification, we isolated 5 distinct products and used 2D nuclear magnetic resonance spectroscopy, reverse-phase high performance liquid chromatography, and mass spectrometry to determine which residues were esterified in each and the resulting increase in hydrophobicity. We found esterifying the C-terminal isoleucine to impart the largest increase in hydrophobicity. Monitoring ester hydrolysis showed the C-terminal isoleucine ester to be the most hydrolytically stable, followed by the glutamic acid, whereas esters on aspartic acids hydrolyze rapidly. LC-MS revealed the formation of transient intramolecular aspartimides prior to hydrolysis to carboxylic acids. In vitro proof-of-concept experiments showed esterifying αCT11 to increase cell migration into a scratch, highlighting the potential of multi-site esterification as a tunable, reversible strategy to enable the delivery of therapeutic peptides.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209494","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}

引用次数: 0

Controlling the Photochromism of Zirconium Pyromellitic Diimide-Based Metal-Organic Frameworks through Coordinating Solvents 通过配位溶剂控制吡咯并二亚胺锆基金属有机框架的光致变色性

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-12 DOI: 10.1039/d4me00104d

Youcong Li, Jiahao Dong, Yue Zhao, Lei Gao, Yu-Hao Gu, Shuai Yuan

{"title":"Controlling the Photochromism of Zirconium Pyromellitic Diimide-Based Metal-Organic Frameworks through Coordinating Solvents","authors":"Youcong Li, Jiahao Dong, Yue Zhao, Lei Gao, Yu-Hao Gu, Shuai Yuan","doi":"10.1039/d4me00104d","DOIUrl":"https://doi.org/10.1039/d4me00104d","url":null,"abstract":"Metal–organic frameworks (MOFs) are promising platforms for designing photoresponsive materials due to their structural versatility and tunable properties. However, challenges remain in fine-tuning the photoresponsive behavior while maintaining the high stability of MOFs. In this study, we synthesized a MOF containing redox-active pyromellitic diimide (PMDI) groups and unsaturated Zr6 clusters (named Zr-PMDI-DMF) and fine-tuned its photochromic properties by exchanging the coordination solvent molecules on the Zr sites. Unlike traditional Zr6 clusters with bidentate carboxylate coordination, Zr-PMDI-DMF features monodentate carboxylate coordination with the exposed Zr sites occupied by solvent molecules. We post-synthetically exchanged the coordinated N, N-dimethylformamide (DMF) solvent molecules with 2-(dimethylamino)ethanol (DMAE), N-methyltetrahydropyrrole (NMP), and dimethyl sulfoxide (DMSO), and determined the structures of the coordinated solvent molecules using single-crystal X-ray diffraction. Through photochromic and bleaching cycle experiments, electron paramagnetic resonance spectroscopy, and density functional theory calculations, we found that the coordinated solvents act as electron donors. In contrast, the PMDI ligands act as electron acceptors, causing the intra-framework electron transfer and the photochromism. The rate of the photochromic response correlated with the electron-donating ability of the solvents, following the trend of DMAE > NMP > DMSO > DMF.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209522","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}

引用次数: 0

On the design of optimal computer experiments to model solvent effects on reaction kinetics 关于设计最佳计算机实验来模拟溶剂对反应动力学的影响

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-06 DOI: 10.1039/d4me00074a

Lingfeng Gui, Alan Armstrong, Amparo Galindo, Fareed Bhasha Sayyed, Stanley P Kolis, Claire Adjiman

{"title":"On the design of optimal computer experiments to model solvent effects on reaction kinetics","authors":"Lingfeng Gui, Alan Armstrong, Amparo Galindo, Fareed Bhasha Sayyed, Stanley P Kolis, Claire Adjiman","doi":"10.1039/d4me00074a","DOIUrl":"https://doi.org/10.1039/d4me00074a","url":null,"abstract":"Developing an accurate predictive model of solvent effects on reaction kinetics is a challenging task, yet it can play an important role in process development. While first-principles or machine learning models are often compute- or data-intensive, simple surrogate models, such as multivariate linear or quadratic regression models, are useful when computational resources and data are scarce. The judicious choice of a small set of training data, i.e., a set of solvents in which quantum mechanical (QM) calculations of liquid-phase rate constants are to be performed is critical to obtaining a reliable model. This is, however, made especially challenging by the highly irregular shape of the discrete space of possible experiments (solvent choices). In this work, we demonstrate that when choosing a set of computer experiments to generate training data, the D-optimality criterion value of the chosen set correlates well with the likelihood of achieving good model performance. With the Menschutkin reaction of pyridine and phenacyl bromide as a case study, this finding is further verified via the evaluation of the surrogate models regressed using D-optimal solvent sets generated from four distinct selection spaces. We also find that incorporating quadratic terms in the surrogate model and choosing the D-optimal solvent set from a selection space similar to the test set can significantly improve the accuracy of reaction rate constant predictions while using a small training dataset. Our approach holds promise for the use of statistical optimality criteria for other types of computer experiments, supporting the construction of surrogate models with reduced resource and data requirements.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209520","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}

引用次数: 0

Selective mineralization at hydrogel interface induced by fusion between peptide hydrogels 多肽水凝胶之间的融合诱导水凝胶界面的选择性矿化

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-03 DOI: 10.1039/d4me00112e

Yongbaek Kim, Hiroto Isobe, Keishi Nishio, Kazuki Murai

引用次数: 0

Construction of amide-bonded supramolecular multifunctional fillers towards boosted self-healing, thermal conductivity and dielectric properties 构建酰胺键超分子多功能填料，提高自愈性、导热性和介电性能

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-09-01 DOI: 10.1039/d4me00114a

Junlong Yao, Zongqiang Fu, Huan Yang, Lin Gao, Xueliang Jiang, Wei Nie, Zhengguang Sun, Haolan Lu, Meiyun Lin, Jinglou Xu

{"title":"Construction of amide-bonded supramolecular multifunctional fillers towards boosted self-healing, thermal conductivity and dielectric properties","authors":"Junlong Yao, Zongqiang Fu, Huan Yang, Lin Gao, Xueliang Jiang, Wei Nie, Zhengguang Sun, Haolan Lu, Meiyun Lin, Jinglou Xu","doi":"10.1039/d4me00114a","DOIUrl":"https://doi.org/10.1039/d4me00114a","url":null,"abstract":"Multifunctional composites with rapid self-healing performance have been widely applied in various fields. However, different types of fillers result in decreased self-healing efficiency and present agglomeration and poor compatibility especially at high filler contents. Here, based on the different surface modifications of barium titanate (BT) and silicon carbide (SiC) and the amide-bond synergistic effects between these fillers, self-healing supramolecular composites with high filler contents (up to 30%) are reported, and exhibit high strength, dielectric and thermal-conduction properties. Modification significantly improves the dispersion of these fillers, and greatly enhances the coexistence and synergy between these fillers. This three-phase amide-bonded supramolecular composite exhibits a high tensile strength of 3.22 MPa compared to other self-healing materials such as self-healing hydrogels, a high dielectric constant of 23, a high thermal conductivity of 0.36 W m−1 K−1 and a superior self-healing efficiency of above 94%. These performances are ascribed to the formation of amide bonds between the amino groups in 3-aminopropyltriethoxysilane (KH550)-modified silicon carbide (SiC-NH2) and the carboxyl groups in tartaric acid (TA)-modified barium titanate (BT-TA), which can provide efficient supramolecular interactions between different fillers, as well as more reversible hydrogen bonding for the matrix. This three-phase amide-bonded supramolecular composite provides an effective strategy to improve the self-healing properties of multifunctional composites, and will bring pioneering functions to electronic packaging materials, dielectric energy storage materials, environmental energy and other fields, which can open up broad application prospects.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209515","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}

引用次数: 0

Self-supervised graph neural networks for polymer property prediction 用于聚合物性能预测的自监督图神经网络

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-29 DOI: 10.1039/d4me00088a

Qinghe Gao, Tammo Dukker, Artur M. Schweidtmann, Jana M. Weber

{"title":"Self-supervised graph neural networks for polymer property prediction","authors":"Qinghe Gao, Tammo Dukker, Artur M. Schweidtmann, Jana M. Weber","doi":"10.1039/d4me00088a","DOIUrl":"https://doi.org/10.1039/d4me00088a","url":null,"abstract":"The estimation of polymer properties is of crucial importance in many domains such as energy, healthcare, and packaging. Recently, graph neural networks (GNNs) have shown promising results for the prediction of polymer properties based on supervised learning. However, the training of GNNs in a supervised learning task demands a huge amount of polymer property data that is time-consuming and computationally/experimentally expensive to obtain. Self-supervised learning offers great potential to reduce this data demand through pre-training the GNNs on polymer structure data only. These pre-trained GNNs can then be fine-tuned on the supervised property prediction task using a much smaller labeled dataset. We propose to leverage self-supervised learning techniques in GNNs for the prediction of polymer properties. We employ a recent polymer graph representation that includes essential features of polymers, such as monomer combinations, stochastic chain architecture, and monomer stoichiometry, and process the polymer graphs through a tailored GNN architecture. We investigate three self-supervised learning setups: (i) node- and edge-level pre-training, (ii) graph-level pre-training, and (iii) ensembled node-, edge- & graph-level pre-training. We additionally explore three different transfer strategies of fully connected layers with the GNN architecture. Our results indicate that the ensemble node-, edge- & graph-level self-supervised learning with all layers transferred depicts the best performance across dataset size. In scarce data scenarios, it decreases the root mean square errors by 28.39% and 19.09% for the prediction of electron affinity and ionization potential compared to supervised learning without the pre-training task.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209518","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}

引用次数: 0

Computational-assisted molecular design, synthesis and application of benzobisthiadiazole-based near-infrared dye in electrowetting displays 基于苯并二噻二唑的近红外染料在电润湿显示器中的计算辅助分子设计、合成和应用

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-22 DOI: 10.1039/d4me00115j

Junheng Chen, Haoteng Lin, Xintong Wang, Dinggui He, Baoyi Luo, Yuanyuan Guo, Wangqiao Chen, Guofu Zhou

{"title":"Computational-assisted molecular design, synthesis and application of benzobisthiadiazole-based near-infrared dye in electrowetting displays","authors":"Junheng Chen, Haoteng Lin, Xintong Wang, Dinggui He, Baoyi Luo, Yuanyuan Guo, Wangqiao Chen, Guofu Zhou","doi":"10.1039/d4me00115j","DOIUrl":"https://doi.org/10.1039/d4me00115j","url":null,"abstract":"Electrowetting display (EWD) technology is among the most promising reflective display technologies due to its full-color capabilities and fast video-speed performance. The colored EWD inks are typically prepared by dissolving soluble organic dyes in non-polar solvents, which significantly influence the color performance, electro-optical behaviour, and longevity of EWD devices. In this study, density functional theory (DFT) at the PBE1PBE/6-31G* level and time-dependent density functional theory (TD-DFT) at the M06-2X/6-31G* level were utilized to calculate a series of benzobisthiadiazole-based donor–acceptor–donor (D–A–D) type near-infrared organic dyes for EWDs, providing structural and spectral data to aid in spectral assignment. The quantum chemical calculations' results align with our experimental synthesis data, showing molecular colors spanning blue, green, and cyan. Detailed investigations into the properties of these dyes, including absorption, electro-optical response, and photo-stability, were conducted. The experimental outcomes indicate that these organic dyes are excellent candidates for EWD applications.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209521","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}

引用次数: 0

Design strategy and molecular level understanding: hole transport materials with suitable transition dipole orientation for OLEDs 设计策略和分子层面的理解：具有合适过渡偶极取向的空穴传输材料，适用于有机发光二极管

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-22 DOI: 10.1039/d3me00127j

Krishan Kumar, Sunil Kumar, Anirban Karmakar, Dipanshu Sharma, Feng-Rong Chen, Mangey Ram Nagar, Jwo-Huei Jou, Subrata Banik, Subrata Ghosh

{"title":"Design strategy and molecular level understanding: hole transport materials with suitable transition dipole orientation for OLEDs","authors":"Krishan Kumar, Sunil Kumar, Anirban Karmakar, Dipanshu Sharma, Feng-Rong Chen, Mangey Ram Nagar, Jwo-Huei Jou, Subrata Banik, Subrata Ghosh","doi":"10.1039/d3me00127j","DOIUrl":"https://doi.org/10.1039/d3me00127j","url":null,"abstract":"The development of hole transport materials with desirable properties is important for the fabrication of efficient organic light-emitting diodes (OLEDs). The present work demonstrates an approach for developing a library of phenothiazine-based hole transport materials (HTMs) for OLED application with considerably good triplet energy (theoretical). Furthermore, the single-crystal structure analysis at the molecular level for some of the developed molecules reveals the possibility of poor electronic communications between the corresponding units. Theoretical studies on transition dipole orientation revealed that all the present phenothiazine-based molecules have appreciable transition dipole orientation. Hence, the objective of the current work has been to assess the impact of chemical structures on certain features of a group of phenothiazine-based functional molecular HTMs with donor–acceptor characteristics. Finally, the hole-only devices (HODs) were fabricated with the synthesized materials as HTMs, and these showed an enhancement in current density with the increase in operating voltage from ∼2–8 V. All these theoretical and experimental outcomes suggested that the present set of molecules could be used as possible efficient HTMs for OLED applications.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209516","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}

引用次数: 0

Crafting porous nanoscaled architecture as a potential frontier for drug delivery 将多孔纳米结构作为药物输送的潜在前沿领域

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-22 DOI: 10.1039/d4me00098f

Koyeli Girigoswami, Pragya Pallavi, Agnishwar Girigoswami

引用次数: 0