Molecular Systems Design & Engineering最新文献

{"title":"Retraction: Heteroatoms chemical tailoring of aluminum nitrite nanotubes as biosensors for 5-hydroxyindole acetic acid (a biomarker for carcinoid tumors): insights from a computational study","authors":"Chioma B. Ubah, Martilda U. Akem, Innocent Benjamin, Henry O. Edet, Adedapo S. Adeyinka and Hitler Louis","doi":"10.1039/D5ME90004B","DOIUrl":"https://doi.org/10.1039/D5ME90004B","url":null,"abstract":"<p >Retraction of ‘Heteroatoms chemical tailoring of aluminum nitrite nanotubes as biosensors for 5-hydroxyindole acetic acid (a biomarker for carcinoid tumors): insights from a computational study’ by Chioma B. Ubah <em>et al.</em>, <em>Mol. Syst. Des. Eng.</em>, 2024, <strong>9</strong>, 832–846, https://doi.org/10.1039/D4ME00019F.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 167-167"},"PeriodicalIF":3.2,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d5me90004b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107591","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":"Process-based screening of porous materials for vacuum swing adsorption based on 1D classical density functional theory and PC-SAFT.","authors":"Fabian Mayer, Benedikt Buhk, Johannes Schilling, Philipp Rehner, Joachim Gross, André Bardow","doi":"10.1039/d4me00127c","DOIUrl":"https://doi.org/10.1039/d4me00127c","url":null,"abstract":"<p><p>Adsorption-based processes are showing substantial potential for carbon capture. Due to the vast space of potential solid adsorbents and their influence on the process performance, the choice of the material is not trivial but requires systematic approaches. In particular, the material choice should be based on the performance of the resulting process. In this work, we present a method for the process-based screening of porous materials for pressure and vacuum swing adsorption. The method is based on an equilibrium process model that incorporates one-dimensional classical density functional theory (1D-DFT) and the PC-SAFT equation of state. Thereby, the presented method can efficiently screen databases of potential adsorbents and identify the best-performing materials as well as the corresponding optimized process conditions for a specific carbon capture application. We apply our method to a point-source carbon capture application at a cement plant. The results show that the process model is crucial to evaluating the performance of adsorbents instead of relying solely on material heuristics. Furthermore, we enhance our approach through multi-objective optimization and demonstrate for materials with high performance that our method is able to capture the trade-offs between two process objectives, such as specific work and purity. The presented method thus provides an efficient screening tool for adsorbents to maximize process performance.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142941624","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":"Accelerating multicomponent phase-coexistence calculations with physics-informed neural networks†","authors":"Satyen Dhamankar, Shengli Jiang and Michael A. Webb","doi":"10.1039/D4ME00168K","DOIUrl":"https://doi.org/10.1039/D4ME00168K","url":null,"abstract":"<p >Phase separation in multicomponent mixtures is of significant interest in both fundamental research and technology. Although the thermodynamic principles governing phase equilibria are straightforward, practical determination of equilibrium phases and constituent compositions for multicomponent systems is often laborious and computationally intensive. Here, we present a machine-learning workflow that simplifies and accelerates phase-coexistence calculations. We specifically analyze capabilities of neural networks to predict the number, composition, and relative abundance of equilibrium phases of systems described by Flory–Huggins theory. We find that incorporating physics-informed material constraints into the neural network architecture enhances the prediction of equilibrium compositions compared to standard neural networks with minor errors along the boundaries of the stable region. However, introducing additional physics-informed losses does not lead to significant further improvement. These errors can be virtually eliminated by using machine-learning predictions as a warm-start for a subsequent optimization routine. This work provides a promising pathway to efficiently characterize multicomponent phase coexistence.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 89-101"},"PeriodicalIF":3.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d4me00168k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107592","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":"Is DFT enough? Towards accurate high-throughput computational screening of azobenzenes for molecular solar thermal applications†","authors":"Flavia Aleotti, Lorenzo Soprani, Lucas F. Rodríguez-Almeida, Francesco Calcagno, Fabio Loprete, Ivan Rivalta, Silvia Orlandi, Elisabetta Canè, Marco Garavelli, Irene Conti and Luca Muccioli","doi":"10.1039/D4ME00183D","DOIUrl":"https://doi.org/10.1039/D4ME00183D","url":null,"abstract":"<p >An efficient screening of azobenzene (AB) derivatives for Molecular Solar Thermal (MOST) applications based on ground state properties (energy stored per molecule and <em>Z</em> isomer stability) could be performed with quasi-CASPT2 accuracy. In this work, we show how wavefunction and electron density based methods can be efficiently combined in a computational protocol that yields accurate potential energy profiles with a significant reduction in computational cost compared to that of a fully-CASPT2 characterization. Our results on prototypical electron donor/withdrawing AB derivatives clearly identify pull–pull substitution as the most promising, allowing to draw guidelines for the chemical design of promising azo-MOST candidates.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 13-18"},"PeriodicalIF":3.2,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d4me00183d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142912704","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":"Extrapolative machine learning models for copolymers","authors":"Israrul H. Hashmi, Himanshu, Rahul Karmakar and Tarak K. Patra","doi":"10.1039/D4ME00123K","DOIUrl":"https://doi.org/10.1039/D4ME00123K","url":null,"abstract":"<p >Machine learning models have been progressively used for predicting materials' properties. These models can be built using pre-existing data and are useful for rapidly screening the physicochemical space of a material, which is astronomically large. However, ML models are inherently interpolative, and their efficacy for searching candidates outside a material's known range of properties is unresolved. Moreover, the performance of an ML model is intricately connected to its learning strategy and the volume of training data. Here, we determine the relationship between the extrapolation ability of an ML model, the size and range of its training dataset, and its learning approach. We focus on a canonical problem of predicting the properties of a copolymer as a function of the sequence of its monomers. Tree search algorithms, which learn the similarities between polymer structures, are found to be inefficient for extrapolation. Conversely, the extrapolation capability of neural networks and XGBoost models, which attempt to learn the underlying functional correlation between the structure and properties of polymers, shows strong correlations with the volume and range of training data. These findings have important implications on ML-based new material development.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 158-166"},"PeriodicalIF":3.2,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107590","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":"Supramolecular charge transfer adducts of rare earth 3,5-dinitrobenzoates and diaminodurene: a new approach to increasing spin density in lanthanide complexes†","authors":"Pavel S. Koroteev, Andrey B. Ilyukhin, Vadim V. Minin, Zhanna V. Dobrokhotova, Natalia N. Breslavskaya, Elena N. Timokhina, Elena A. Ugolkova, Amgalanbaatar Baldansuren, Floriana Tuna and Nikolay N. Efimov","doi":"10.1039/D4ME00124A","DOIUrl":"https://doi.org/10.1039/D4ME00124A","url":null,"abstract":"<p >Seven isostructural supramolecular adducts, [Ln<small>₂</small>(O<small>₂</small>CC<small>₆</small>H<small>₃</small>(NO<small>₂</small>)<small>₂</small>)<small>₆</small>(DMSO)<small>₄</small>]·4(1,4-(H<small>₂</small>N)<small>₂</small>C<small>₆</small>Me<small>₄</small>) (Ln = Sm (<strong>1</strong>), Gd (<strong>2</strong>), Tb (<strong>3</strong>), Dy (<strong>4</strong>), Ho (<strong>5</strong>), Er (<strong>6</strong>), Y (<strong>7</strong>)), were synthesized by reacting LnCl<small>₃</small>·6H<small>₂</small>O with potassium 3,5-dinitrobenzoate in acetonitrile in the presence of 2,3,5,6-tetramethyl-1,4-phenylenediamine (DAD) and DMSO, and characterized by X-ray diffraction analysis. The charge transfer (CT) between DAD molecules and binuclear 3,5-dinitrobenzoate fragments gives rise to stacking interactions, which determine the supramolecular structures of complexes <strong>1–7</strong>. Optical spectroscopy of complexes <strong>1–7</strong> corroborates the occurrence of significant CT, whereas magnetic studies substantiate the presence of a paramagnetic ion-radical structure which contributes to the magnetic moment of all the complexes and determines the paramagnetism of the yttrium compound <strong>7</strong>. In the case of the latter complex, the value of the paramagnetic contribution resulting from CT was determined directly by magnetic measurement. It was demonstrated that this contribution decreases with the lowering of temperature, reflecting the depopulation of the triplet state of the CT complex, the ion-radical pair. A comprehensive EPR study of complex <strong>7</strong> was carried out by means of both continuous-wave (CW) and pulsed EPR spectroscopy in X- and Q-bands. The magnetic properties of complexes <strong>2–6</strong> indicate the prevalence of weak antiferromagnetic interactions within the binuclear fragments. The Dy complex exhibits field-induced single-molecule magnet (SMM) behaviour. The CT in the complex structures was modelled using DFT calculations.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 143-157"},"PeriodicalIF":3.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107589","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":"Dual-labelled polymeric micelles for singlet oxygen reporting in biological systems†","authors":"Yasuhiro Nakagawa, Hayato Laurence Mizuno, Yuta Ushimaru, Jumpei Norimatsu, Kazunori Igarashi, Keita Masuda, Madoka Takai, Yasutaka Anraku and Horacio Cabral","doi":"10.1039/D4ME00105B","DOIUrl":"https://doi.org/10.1039/D4ME00105B","url":null,"abstract":"<p >Visualizing singlet oxygen (<small>¹</small>O<small>₂</small>) in biological systems could greatly enhance our understanding of its biological roles and offer new diagnostics and therapeutics. However, <small>¹</small>O<small>₂</small> is unstable and highly reactive, making its detection in living systems a significant challenge. To address this, we have developed dually-labelled polymeric micelles designed to trace both the location and levels of <small>¹</small>O<small>₂</small>.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 1","pages":" 7-12"},"PeriodicalIF":3.2,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d4me00105b?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142912710","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":"Unveiling the influence of oxidation state and heavy atom effects in chalcogen group on boron centered D(X)BNA core: a computational study on RTP versus TADF†","authors":"Ramalingam Mahaan, Murugesan Panneerselvam, Luciano T. Costa and Aruljothy John Bosco","doi":"10.1039/D4ME00131A","DOIUrl":"https://doi.org/10.1039/D4ME00131A","url":null,"abstract":"<p >The endeavor of utilizing non-radiative triplet excitons in RTP and TADF molecules has garnered significant interest in recent studies, presenting a highly desirable yet challenging pursuit. In this investigation, we utilized DFT and TD-DFT computational approaches to anticipate the photophysical characteristics of multifunctional materials, uncovering their significant reliance on the oxidation state and heavy atom influences of the chalcogen group on boron centered D(X)BNA cores, along with substitutions of weak phenylcarbazole (P-CBZ) and strong phenyldimethylacridine (P-DMAC) donors. The calculations demonstrated that both heavy atom (X = O, S, Se, Te) and oxidation (S, SO, SO<small>₂</small>, and Se, SeO) effects caused a decrease in singlet (S<small>₁</small>) and triplet (T<small>₁</small>) energies. Unexpectedly, the first singlet-triplet energy difference (Δ<em>E</em><small>_ST</small>) values exhibit a systematic decrease with weak donor-based molecules, while they increase with strong donor unit-based molecules with the heavy atom effects. Moreover, the Δ<em>E</em><small>_ST</small> values decrease systematically with the oxidation effect in both types of donor unit-based molecules. Conversely, the magnitudes of spin–orbit coupling (SOC) increase with heavy atom effects due to the orbital mixing and screening effects of lone pair electrons and decrease with oxidation effects because of their decreased lone pair electrons in both the S<small>₁</small>–T<small>₁</small> and T<small>₁</small>–S<small>₀</small> pathways. The elevated SOC and intersystem crossing (ISC) rates in heavy atom-based molecules, and low Δ<em>E</em><small>_ST</small> and high reverse intersystem crossing (RISC) in oxidation-based molecules, meet the criteria for multifunctional RTP and TADF molecules, respectively.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 102-114"},"PeriodicalIF":3.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107630","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":"DORA-XGB: an improved enzymatic reaction feasibility classifier trained using a novel synthetic data approach†","authors":"Yash Chainani, Zhuofu Ni, Kevin M. Shebek, Linda J. Broadbelt and Keith E. J. Tyo","doi":"10.1039/D4ME00118D","DOIUrl":"https://doi.org/10.1039/D4ME00118D","url":null,"abstract":"<p >Retrobiosynthesis tools harness the inherent promiscuities of enzymes for the <em>de novo</em> design of novel biosynthetic pathways to key small molecules. Many existing pathway search algorithms rely on exhaustively enumerating the space of all possible enzymatic reactions using generalized rules, followed by an extensive analysis of the ensuing reaction network to extract candidate pathways for experimental validation. While this approach is comprehensive, many false positive reactions are often generated given the permissiveness of such reaction rules. Here, we have developed DORA-XGB, a enzymatic reaction feasibility classifier. DORA-XGB can be used within our DORAnet framework to assess whether newly enumerated enzymatic reactions and pathways would be feasible. To curate a training dataset for our model, we extracted enzymatic reactions from public databases and screened them for their general thermodynamic feasibility. We then considered alternate reaction centers on known substrates to strategically generate infeasible reactions with high confidence, thereby circumventing the lack of negative data in the literature. In training our model, we also experimented with various molecular fingerprinting techniques and configurations for assembling reaction fingerprints, taking into account not just primary substrate and primary product structures, but cofactor structures as well. Our model's utility is demonstrated through favorable benchmarking against a previously published classifier, the successful recovery of newly published reactions, and the ranking of previously predicted pathways for the biosynthesis of propionic acid from pyruvate.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 129-142"},"PeriodicalIF":3.2,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2025/me/d4me00118d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107588","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 xanthan gum-based solid desiccants for the extraction of water vapors from humid air†","authors":"Hemant Mittal, Ali Al Alili, Saeed M. Alhassan, Naved I. Malek and Md. Didarul Islam","doi":"10.1039/D4ME00134F","DOIUrl":"https://doi.org/10.1039/D4ME00134F","url":null,"abstract":"<p >This research paper reports the synthesis of a super-porous hydrogel of xanthan gum with acrylamide (<em>i.e.</em>, XG-SPH) with highly dense interconnected capillary channels and its application as a desiccant material to capture water vapors from humid air. For the generation of the porous structure with interconnected capillary channels, the polymer desiccant was synthesized <em>via</em> gas blowing, foaming and polymerization. The presence of interconnected capillary channels was observed in the scanning electron microscopy (SEM) images. The synthesized desiccant exhibited 0.27 g g<small>⁻¹</small> adsorption capacity at 50% relative humidity and 25 °C which drastically increased to 1.38 g g<small>⁻¹</small> at 25 °C and 90% relative humidity which suggested that the hydrophilic nature or the desiccant performance of the synthesized polymer desiccant increased with increasing relative humidity. The main driving force behind this high-water vapor adsorption capacity was the capillary condensation process which facilitated the adsorption or accommodation of more incoming water molecules at higher pressures. The adsorption of water molecules by the capillary condensation mechanism was further supported by the applicability of the type-III adsorption isotherm and the experimental data fitted well with the GAB adsorption isotherm. Moreover, the experimental kinetics data correlated well with the driving force model and indicated that water diffusion within the polymer structure followed a type II diffusion mechanism. The desorption kinetics indicated that the desorption occurred rapidly in the initial desorption stages, and most of the captured water was released within the first hour. Moreover, regenerating XG-SPH was energy efficient as it could be successfully regenerated at 50 °C and used for twenty adsorption–desorption cycles. The desiccant was able to retain almost 70% of its original adsorption capacity in the twentieth adsorption cycle. This suggests that gum polysaccharide-based super-porous hydrogels can extract or capture a considerable amount of water from the atmosphere without using any hygroscopic salt.</p>","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":" 2","pages":" 115-128"},"PeriodicalIF":3.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143107631","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}