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Integrating chemical Information into Reinforcement Learning for Enhanced Molecular Geometry Optimization

Journal of chemical theory and computation 2023年第23期19卷 8598-8609页

作者： Yu-Cheng Chang Yi-Pei Li Department of Chemical Engineering National Taiwan University No. 1 Sect. 4 Roosevelt Road Taipei 10617 Taiwan. Taiwan International Graduate Program on Sustainable Chemical Science and Technology (TIGP-SCST) Academia Sinica No. 128 Sec. 2 Academia Road Taipei 11529 Taiwan.

Geometry optimization is a crucial step in computational chemistry, and the efficiency of optimization algorithms plays a pivotal role in reducing computational costs. In this study, we introduce a novel reinforcement-learning-based optimizer that surpasses traditional methods in terms of efficiency. What sets our model apart is its ability to incorporate chemical information into the optimization process. By exploring different state representations that integrate gradients, displacements, primitive type labels, and additional chemical information from the SchNet model, our reinforcement learning optimizer achieves exceptional results. It demonstrates an average reduction of about 50% or more in optimization steps compared to the conventional optimization algorithms that we examined when dealing with challenging initial geometries. Moreover, the reinforcement learning optimizer exhibits promising transferability across various levels of theory, emphasizing its versatility and potential for enhancing molecular geometry optimization. This research highlights the significance of leveraging reinforcement learning algorithms to harness chemical knowledge, paving the way for future advancements in computational chemistry.

关键词： Algorithms Geometry optimization Mathematical methods Molecules Optimization

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Two-Dimensional Metal-Organic Frameworks/Epoxy Composite Coatings with Superior O2/H2O Resistance for Anticorrosion Applications

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ACS applied materials & interfaces 2024年第31期16卷 41421-41434页

作者： Hao-Hsuan Hsia You-Liang Chen Yu-Ting Tai Hong-Kang Tian Chung-Wei Kung Wei-Ren Liu Department of Chemical Engineering R&D Center for Membrane Technology Research Center for Circular Economy Chung Yuan Christian University Taoyuan 32023 Taiwan. Department of Graduate Institude of Applied Science and Technology National Taiwan University of Science and Technology Taipei City 106335 Taiwan. Department of Chemical Engineering National Cheng Kung University Tainan City 70101 Taiwan. Program on Smart and Sustainable Manufacturing Academy of Innovative Semiconductor and Sustainable Manufacturing National Cheng Kung University Tainan 70101 Taiwan. Hierarchical Green-Energy Materials (Hi-GEM) Research Center National Cheng Kung University Tainan 70101 Taiwan.

Corrosion protection technology plays a crucial role in preserving infrastructure, ensuring safety and reliability, and promoting long-term sustainability. In this study, we combined experiments and various analyses to investigate the mechanism of corrosion occurring on the epoxy-based anticorrosive coating containing the additive of two-dimensional (2D) and water-stable zirconium-based metalorganic frameworks (Zr-MOFs). By using benzoic acid as the modulator for the growth of the MOF, a 2D MOF constructed from hexazirconium clusters and BTB linkers (BTB = 1,3,5-tri(4-carboxyphenyl)benzene) with coordinated benzoate (BA-ZrBTB) can be synthesized. By coating the BA-ZrBTB/epoxy composite film (BA-ZrBTB/EP) on the surface of cold-rolled steel (CRS), we found the lowest coating roughness (RMS) of BA-ZrBTB/EP is 2.83 nm with the highest water contact angle as 99.8°, which represents the hydrophobic coating surface. Notably, the corrosion rate of the BA-ZrBTB/EP coating is 2.28 × 10 mpy, which is 4 orders of magnitude lower than that of the CRS substrate. Moreover, the energy barrier for oxygen diffusion through BA-ZrBTB/EP coating is larger than that for epoxy coating (EP), indicating improved oxygen resistance for adding 2D Zr-MOFs as the additive. These results underscore the high efficiency and potential of BA-ZrBTB as a highly promising agent for corrosion prevention in various commercial applications. Furthermore, this study represents the first instance of applying 2D Zr-MOF materials in anticorrosion applications, opening up new possibilities for advanced corrosion-resistant coatings.

关键词： 2D structure Zr-based MOFs anticorrosion density functional theory epoxy hydrophobic

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Electroactive Carbazole-Based Polycyclic Aromatic Hydrocarbons: Synthesis, Photophysical Properties, and Computational Studies

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ACS omega 2024年第27期9卷 29379-29390页

作者： Hui Qi Wong Ting-Hsuan Lin Jian-Ming Liao Septia Kholimatussadiah Febri Baskoro Hui-Hsu Gavin Tsai Hung-Ju Yen Institute of Chemistry Academia Sinica 128 Academia Road Section 2 Nankang Taipei 11529 Taiwan. Sustainable Chemical Science and Technology Program Taiwan International Graduate Program (TIGP) Academia Sinica and National Taiwan University Taipei 11529 Taiwan. Department of Chemical Engineering National Taiwan University Taipei 10617 Taiwan. Department of Chemical Engineering National Taiwan University of Science and Technology Taipei 10607 Taiwan. Department of Chemistry National Central University No. 300 Zhongda Rd. Zhongli District Taoyuan City 32001 Taiwan. Nano Science and Technology Program TIGP Academia Sinica and National Taiwan University Taipei 11529 Taiwan. Research Center of New Generation Light Driven Photovoltaic Module National Central University No. 300 Zhongda Road Zhongli District Taoyuan City 32001 Taiwan.

Herein, we explored the oxidative coupling reactions of carbazole-based polycyclic aromatic hydrocarbons using traditional Scholl reactions and electrochemical oxidation. Our findings indicate that the oxidation predominantly occurs at the carbazole functional group. The underlying reaction mechanisms were also clarified through theoretical investigations, highlighting that the primary oxidation pathway involves the 3,6-positions of the carbazole moiety, which is attributable to its high electron density.

关键词： Aromatic compounds Cations Show More

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Adhesion, infection, and therapeutic treatment of Helicobacter pylori: a review on current aspects and future promise

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Discover Applied sciences 2024年第6期6卷 323页

作者： Ong, Lih-Lih Lin, Chun-Hung Institute of Biological Chemistry Academia Sinica No.128 Academia Road Section 2 Nan-Kang Taipei11529 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University 1001 University Road Eastern District HsinChu Taiwan Institute of Chemistry Academia Sinica No. 128 Academia Road Section 2 Nan-Kang Taipei11529 Taiwan Sustainable Chemical Science and Technology Taiwan International Graduate Program Academia Sinica No. 128 Academia Road Section 2 Nan-Kang Taipei11529 Taiwan Department of Chemistry and Institute of Biochemical Sciences National Taiwan University Taipei Taiwan

Background: Helicobacter pylori is a Gram-negative bacterium infecting over half of the human population worldwide. In addition to causing chronic gastritis, the bacterial infection often progresses to gastrointestinal pathologies at various degrees, including gastric carcinoma. World Health Organization announced in 1994 that H. pylori is Group 1 carcinogen. Although antibiotics-based treatment is mostly effective, the alarming rise in drug resistance have resulted in a serious concern for the health. Main body: This review covers the aspects of bacterial infection, epidemiology and therapy of H. pylori. An additional emphasis is placed on the bacterial adhesion and anti-adhesion because the attachment of H. pylori to gastric epithelial cells is crucial for the pathogenesis. We review several anti-adhesion agents that have been shown to interfere with the bacterial adhesion. These agents can either function as receptor and adhesin analogs or foster preventive probiotics. Furthermore, cholesteryl 6′-O-acyl-α-d-glucopyranoside (CAG), exclusively produced in H. pylori by the unique biosynthetic pathway, has been shown critical for the bacterial virulence. Studies are reviewed to show how CAG influences bacterial adhesion by affecting membrane features, including lipid rafts clustering. Conclusion: Owing to the emerging threat of multiple drug resistance, current therapy is not always effective to H. pylori infection, demonstrating the necessity to develop other alternatives. The approaches of anti-adhesion appear to be attractive since they blockade the initial step of bacterial pathogenesis. This in-depth review of anti-adhesive agents and corresponding mechanisms showcases their potential for future development of therapeutic intervention. © The Author(s) 2024.

关键词： Antibiotics

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Two-Step Machine Learning Approach for Charge-Transfer Coupling with Structurally Diverse Data

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Journal of Physical Chemistry A 2024年第1期128卷 271-280页

作者： Lin, Hung-Hsuan Wang, Chun-I Yang, Chou-Hsun Secario, Muhammad Khari Hsu, Chao-Ping Institute of Chemistry Academia Sinica 128 Section 2 Academia Road Nankang Taipei115 Taiwan Taiwan International Graduate Program on Sustainable Chemical Science & Technology Academia Sinica Institute of Chemistry 128 Academia Road Sec.2 Nankang Taipei115 Taiwan Department of Applied Chemistry National Yang Ming Chiao Tung University 1001 University Road Hsinchu300 Taiwan Division of Physics National Center for Theoretical Sciences 1 Section 4 Roosevelt Road Taipei106 Taiwan Molecular Science and Digital Innovation Center Genetics Generation Advancement Corp No. 28 Ln. 36 Xinhu First Rd. Neihu Taipei114 Taiwan Department of Chemistry University of Illinois at Urbana-Champaign UrbanaIL61801 United States

Electronic coupling is important in determining charge-transfer rates and dynamics. Coupling strength is sensitive to both intermolecular, e.g., orientation or distance, and intramolecular degrees of freedom. Hence, it is challenging to build an accurate machine learning model to predict electronic coupling of molecular pairs, especially for those derived from the amorphous phase, for which intermolecular configurations are much more diverse than those derived from crystals. In this work, we devise a new prediction algorithm that employs two consecutive KRR models. The first model predicts molecular orbitals (MOs) from structural variation for each fragment, and coupling is further predicted by using the overlap integral included in a second model. With our two-step procedure, we achieved mean absolute errors of 0.27 meV for an ethylene dimer and 1.99 meV for a naphthalene pair, much improved accuracy amounting to 14-fold and 3-fold error reductions, respectively. In addition, MOs from the first model can also be the starting point to obtain other quantum chemical properties from atomistic structures. This approach is also compatible with a MO predictor with sufficient accuracy. © 2023 American chemical Society.

关键词： Molecular orbitals

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Low-temperature sintering of Li0.33La0.55TiO3 electrolyte for all-solid-state Li batteries

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Journal of the European Ceramic Society 2023年第16期43卷 7543-7552页

作者： Lin, Che-an Ihrig, Martin Kung, Kuan-chen Chen, Hsiang-ching Scheld, Walter Sebastian Ye, Ruijie Finsterbusch, Martin Guillon, Olivier Lin, Shih-kang Department of Materials Science and Engineering National Cheng Kung University Tainan70101 Taiwan Institute of Energy and Climate Research – Materials Synthesis and Processing Forschungszentrum Jülich GmbH Jülich52425 Germany Department of Chemical Engineering National Taiwan University of Science and Technology No. 43 Keelung Rd. Section 4 Da'an Dist Taipei City106 Taiwan Helmholtz Institute Münster: Ionics in Energy Storage Corrensstr. 46 Münster48149 Germany Research Center National Cheng Kung University Tainan70101 Taiwan Program on Smart and Sustainable Manufacturing Academy of Innovative Semiconductor and Sustainable Manufacturing National Cheng Kung University Tainan70101 Taiwan Core Facility Center National Cheng Kung University Tainan70101 Taiwan

Ceramic solid-state Li batteries have promising electrochemical properties. However, their device integration is hampered by the required high sintering temperature step to obtain good ionic conductivity. The sintering temperature often leads to thermal decomposition of the cathode active material. Advanced sintering techniques, such as field-assisted sintering technology/spark plasma sintering (FAST/SPS), utilizing applied mechanical pressure to achieve a lower sintering temperature and shorter dwell time, are helpful in overcoming thermal stability challenges. While thermal stability issues are overcome by a lower sintering temperature, new challenges in the form of surface impurities arise. Low-temperature sintering does not thermally decompose surface impurities which causes low grain boundary conductivity and thus low total ionic conductivity. In this work, a cleaning method and a low-temperature sintering process is exemplarily developed for Li0.33La0.55TiO3 (LLTO) and the impact of applied mechanical pressure during FAST/SPS on the total ionic conductivity and the phase stability of LLTO is revealed. © 2023 Elsevier Ltd

关键词： Spark plasma sintering

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Effects of carbon dioxide concentration and swine wastewater on the cultivation of Chlorella vulgaris FSP-E and bioethanol production from microalgae biomass

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Applied Energy 2024年 369卷

作者： Condor, Billriz E. de Luna, Mark Daniel G. Lacson, Carl Francis Z. Acebu, Paula Isabel G. Abarca, Ralf Ruffel M. Nagarajan, Dillirani Lee, Duu-Jong Chang, Jo-Shu Energy Engineering Program National Graduate School of Engineering University of the Philippines Diliman Quezon City Philippines Quezon City1101 Philippines Department of Chemical Engineering University of the Philippines Diliman Quezon City1101 Philippines Center of Excellence in Environmental Catalysis and Adsorption Thammasat University Pathum Thani12121 Thailand Department of Chemical Engineering and Technology Mindanao State University-Iligan Institute of Technology Iligan City9200 Philippines College of Hydrosphere Science Institute of Aquatic Science and Technology National Kaohsiung University of Science and Technology Kaohsiung City811532 Taiwan Department of Mechanical Engineering City University of Hong Kong Kowloon Tang Hong Kong Department of Chemical and Materials Engineering Tunghai University 407 Taiwan Research Center for Smart Sustainable Circular Economy Tunghai University Taichung407 Taiwan Department of Chemical Engineering National Cheng Kung University Tainan701 Taiwan Department of Chemical Engineering and Materials Science Yuan Ze University Chung-Li Taiwan

The study investigated the potential of wastewater-derived microalgae as a cost-effective feedstock for bioethanol production. The influence of CO2 loading, use of swine wastewater as a nutrient source, effect of micronutrients in the cultivation media, and scale-up of Chlorella vulgaris FSP-E was conducted. Results showed that 2% CO2, 25% swine wastewater, 500 mg/L sodium nitrate, 40 mg/L K2HPO4, 75 mg/L MgSO4, and 6 mg/L citric acid were optimal for maximal biomass production, nitrate removal, and carbohydrate accumulation in BG-11 medium. The maximum biomass and carbohydrate content obtained in this study were 35-fold and 60%, respectively. Scaling up to 5 L volume was challenging due to illumination, aeration, and mixing issues. The obtained carbohydrate-rich biomass was subjected to mild sulfuric acid hydrolysis and subsequently used for bioethanol fermentation. The hydrolysate was composed solely of glucose and galactose and was converted into bioethanol within 8 h by Saccharomyces cerevisiae with an ethanol yield of 0.22 ± 0.01 g ethanol per g biomass. Further exploration of effective lighting and mixing strategies are recommended to realize economically viable microalgal biofuels. © 2024 Elsevier Ltd

关键词： Biomass

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Optimizing cultivation strategies and scaling up for fucoxanthin production using Pavlova sp.

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Bioresource technology 2024年 399卷 130609页

作者： Chen, Chun-Yen Liu, Ping-Yung Chang, Yu-Han Nagarajan, Dillirani Latagan, Mary Joy D. de Luna, Mark Daniel G. Chen, Jih-Heng Chang, Jo-Shu University Center for Bioscience and Biotechnology National Cheng Kung University Tainan Taiwan Department of Biotechnology and Bioindustry Sciences National Cheng Kung University Tainan701 Taiwan Department of Chemical Engineering National Cheng Kung University Tainan Taiwan Institute of Aquatic Science and Technology College of Hydrosphere Science National Kaohsiung University of Science and Technology Nanzih Campus Kaohsiung City Taiwan Energy Engineering Program National Graduate School of Engineering University of the Philippines Diliman Quezon City1101 Philippines Environmental Engineering Program National Graduate School of Engineering University of the Philippines Quezon City Diliman1101 Philippines Department of Chemical Engineering University of the Philippines Diliman Quezon City1101 Philippines Department of Chemical and Materials Engineering National Kaohsiung University of Science and Technology Kaohsiung807 Taiwan Department of Chemical and Materials Engineering Tunghai University Taichung407 Taiwan Research Center for Smart Sustainable Circular Economy Tunghai University Taichung407 Taiwan Department of Chemical Engineering and Materials Science Yuan Ze University Chung-Li Taiwan

The microalgal-based production of fucoxanthin has emerged as an imperative research endeavor due to its antioxidant, and anticancer properties. In this study, three brown marine microalgae, namely Skeletonema costatum, Chaetoceros gracilis, and Pavlova sp., were screened for fucoxanthin production. All strains displayed promising results, with Pavlova sp. exhibiting the highest fucoxanthin content (27.91 mg/g) and productivity (1.16 mg/L·day). Moreover, the influence of various cultivation parameters, such as culture media, salinity, sodium nitrate concentration, inoculum size, light intensity, and iron concentration, were investigated and optimized, resulting in a maximum fucoxanthin productivity of 7.89 mg/L·day. The investigation was further expanded to large-scale outdoor cultivation using 50 L tubular photobioreactors, illustrating the potential of Pavlova sp. and the cultivation process for future commercialization. The biomass and fucoxanthin productivity for the large-scale cultivation were 70.7 mg/L·day and 4.78 mg/L·day, respectively. Overall, the findings demonstrated considerable opportunities for fucoxanthin synthesis via microalgae cultivation and processing. © 2024 Elsevier Ltd

关键词： Microalgae

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Ph-Controlled Release Feature of Chitosan Assembled Silica Nanoparticles Containing Nano-Formulated Curcumin Over in Vitro Gastric and Physiological Condition

SSRN

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SSRN 2023年

作者： Saputra, Ozi Adi Safitriono, Wahyu Nur Maharani, Dyah Elyawati Kusumaningtyas Febiana, Amalia Wibowo, Fajar Rakhman Sustainable Chemical Science and Technology Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan Institute of Chemistry Academia Sinica Taipei11529 Taiwan Department of Chemical Engineering Collage of Engineering National Taiwan University Taipei10617 Taiwan Master Program of Chemistry Universitas Sebelas Maret Surakarta57126 Indonesia Department of Chemistry Faculty of Mathematic and Natural Science Universitas Sebelas Maret Surakarta57126 Indonesia

Low water solubility leading to poor bioavailability has an impact on the decreasing of curcumin uptake in the body, resulting in a deficiency of its medicinal benefits. This study aims to overcome the limitations of curcumin by formulating a nano-emulsion called curcumin emulsion (CE). Furthermore, in order to improve the physicochemical properties and drug release features, the CE was encapsulated within chitosan-assembled mesoporous silica nanoparticles (Chi@SiO2@CE). This material was prepared using a one-pot method and was characterized by ATR-FTIR, PSA, TGA, N2 adsorption-desorption, SEM, and TEM. Additionally, antioxidant activity and in vitro drug release were also conducted. The study demonstrated that CE has strong antioxidant activity (IC50 = 14.14 µM) compared to curcumin alone. Additionally, the Chi@SiO2@CE exhibited pH-controlled release behavior, with less than 20% release of curcumin under an artificial gastric environment and 50% release under pH 7.4 conditions within 24 hours. Therefore, this research suggest that Chi@SiO2@CE material has potential as a pH-responsive drug delivery material. © 2023, The Authors. All rights reserved.

关键词： Chitosan

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MOF-Derived Bimetal-Embedded Carbon with Etched Morphologies as an Efficient Activator of Peroxymonosulfate for Eliminate Emerging Contaminants

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Korean Journal of chemical Engineering 2024年第6期41卷 1815-1831页

作者： Chen, Yi-Chun Jiang, Xin-Yu Lin, Jia-Yin Thanh, Bui Xuan Wang, Haitao Huang, Chao-Wei Ghotekar, Suresh Huang, Chih-Feng Lin, Kun-Yi Andrew Department of Biotechnology National Formosa University Yunlin63208 Taiwan Department of Environmental Engineering & amp Innovation and Development Center of Sustainable Agriculture National Chung Hsing University Taichung Taiwan Semiconductor and Green Technology Program National Chung Hsing University 250 Kuo-Kuang Road Taichung Taiwan Ho Chi Minh City Viet Nam Ho Chi Minh City700000 Viet Nam Key Laboratory of Pollution Processes and Environmental Criteria College of Environmental Science and Engineering Nankai University Tianjin300071 China Department of Engineering Science National Cheng Kung University Tainan70101 Taiwan Centre for Herbal Pharmacology and Environmental Sustainability Chettinad Hospital and Research Institute Chettinad Academy of Research and Education Kelambakkam Tamil Nadu Chennai603103 India Department of Chemical Engineering National Chung Hsing University Taichung Taiwan Institute of Analytical and Environmental Sciences National Tsing Hua University Hsinchu Taiwan Department of Civil Engineering National Taipei University of Technology Taipei City Taiwan

As bis(4-hydroxyphenyl)methanone (BHP) is one of the most common UV light stabilizers (UVLS), but exhibits endocrine disrupting toxicity, this study aims to develop useful sulfate radical-based techniques to eliminate BHP from water by activating peroxymonosulfate (PMS). Hence, while cobalt (Co) exhibits efficacy as a transition metal for the activation of PMS, the utilization of manganese/cobalt (Mn/Co) bimetallic oxides presents an even more encouraging prospect as heterogeneous catalysts for PMS activation. In this study, we have successfully produced N-doped carbon-supported Mn/Co nanoparticles (NCMC) with a distinctive hollow-engineered nanostructure. The synthesis involved the utilization of Co-MOF as a precursor, followed by easy etching and Mn doping to achieve the desired composition of Mn/Co bimetallic oxide nanoparticles. The inclusion of Mn dopant facilitates the integration of Mn/Co nanoparticles into the hollow-structured N-doped carbon matrix. NCMC demonstrates much higher activity compared to NCC and the benchmark catalyst, Co3O4 NP, in terms of PMS activation for the degradation of BHP. The findings of the eco-toxicity study indicate that the degradation of BHP by NCMC + PMS does not yield hazardous or extremely toxic byproducts, so establishing NCMC as a potentially effective heterogeneous catalyst for activating PMS in the degradation of BHP. © The Author(s), under exclusive licence to Korean Institute of chemical Engineers, Seoul, Korea 2024.

关键词： Transition metals

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