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Teaching Green chemistry Through Student-Generated Open Educational Resources

Journal of College Science Teaching 2023年第4期52卷 3-5页

作者： Grieger, Krystal Leontyev, Alexey Department of Chemistry and Biochemistry North Dakota State University in Fargo ND United States Department of Chemistry and Biochemistry and Discipline-Based Education Research PhD Program North Dakota State University Fargo ND United States

This article describes the implementation of a student-generated open educational resource project into a majors ’ organic chemistry laboratory. This scaffolded semester-long project was organized into six phases and designed to promote the goals of teaching students about both green chemistry and real-life applications of the reactions covered in the course while simultaneously creating open educational resources for future students. A project-based learning approach was utilized to promote student engagement, especially during remote instruction. To further promote engagement, multiple opportunities for peer feedback were provided using web-based software that supports anonymous feedback. The effect of the project on cognitive learning gains and student perceptions was assessed and is reported. Overall, positive learning gains on green chemistry knowledge and skills were observed, and most students viewed the project favorably. © 2023 National Science Teaching Association.

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Kinetics of primary mechanochemical covalent-bond-forming reactions

RSC Mechanochemistry

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RSC Mechanochemistry 2024年第1期1卷 11-32页

作者： Yerzhan S. Zholdassov Ryan W. Kwok Milan A. Shlain Monil Patel Mateusz Marianski Adam B. Braunschweig Advanced Science Research Center at the Graduate Center of the City University of New York 85 St Nicholas Terrace New York NY 10031 USA abraunschweig@gc.cuny.edu Department of Chemistry Hunter College 695 Park Ave New York NY 10065 USA PhD Program in Chemistry Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA PhD Program in Biochemistry Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA

Mechanical activation of reactions can reduce significantly the amounts of solvent and energy required to form covalent organic bonds. Despite growing interest in the field of mechanochemistry and increasing reports of mechanochemical synthesis of organic molecules, the fundamental question of how stresses activate covalent-bond-forming (CBF) reactions remains unresolved. This question remains unresolved because of the difficulties involved in measuring the applied forces and the reaction times in mechanochemical reactors, and the challenges related to deconvoluting microscopic (primary) and macroscopic (secondary) processes in the analysis of reaction kinetics. Here we discuss the use nanoscopic probe-microscope tips to explore the kinetics of CBF reactions. Because these experiments examine reactions on monolayers, surfaces, or nanoscopic particles, they circumvent secondary processes to isolate how stress affects the rates of the primary, CBF events. The major result of these studies is an emerging consensus that stress accelerates reactions by distorting organic molecules and in doing so, lowers reaction activation energies and alters reaction trajectories. This new understanding of how stresses activate reactions can be used to predict the outcomes of CBF mechanochemical reactions, which will lead to the wider adoption of sustainable mechanochemical processes by the synthetic community.

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Synthetic investigations of the diisocyanide-bridged Cp*-cobalt rectangles

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Journal of the Chinese Chemical Society 2024年第4期71卷 376-384页

作者： Huang, Cheng-Chang Chu, Yu-Ting Huang, Yen-Chung Chang, Yu-Lun Ding, Shangwu Hsu, Sodio C. N. Department of Medicinal and Applied Chemistry Kaohsiung Medical University Kaohsiung Taiwan Department of Chemistry National Sun Yat-Sen University Kaohsiung Taiwan International PhD Program for Science National Sun Yat-Sen University Kaohsiung Taiwan

This study explores the utilization of 1,4-diisocyanobenzene as a linear bridging ligand for the assembly of organometallic CpCo or Cp*Co complexes. Overcoming solubility challenges, the synthesis of organometallic Cp* cobalt complexes incorporating bridging 1,4-diisocyanobenzene ligands was successfully achieved, while similar CpCo complexes were not attainable. The presented approach encompasses investigations into both stepwise and self-assembly synthetic pathways, leading to the construction of a rectangular tetranuclear complex [(Cp*CoI)₄(μ-1,4-CNC₆H₄NC)₄](OTf)₄ (3). Through single-crystal x-ray diffraction and spectroscopic techniques such as infrared, nuclear magnetic resonance, and electrospray ionization-mass spectrometry, the cobalt-isocyanides complexes were characterized. © 2024 The Chemical Society Located in Taipei & Wiley-VCH GmbH.

关键词： 1,4-diisocyanobenzene cobalt Cp* cyclic voltammetry self-assembly

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Potential Vibrational Modes Tied to Diffuse Interstellar Bands

arXiv

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arXiv 2025年

作者： Majaess, Daniel Seuret, Halis Harriott, Tina A. Morera-Boado, Cercis Sullivan, Ailish Massa, Lou Matta, Chérif F. Department of Chemistry and Physics Mount Saint Vincent University HalifaxNSB3M2J6 Canada Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Department of Mathematics and Statistics Mount Saint Vincent University HalifaxNSB3M2J6 Canada IXM-Cátedra Conahcyt Centro de Investigaciones Químicas IICBA Universidad Autónoma del Estado de Morelos Morelos Cuernavaca62209 Mexico Hunter College PhD Program of the Graduate Center City University of New York New York United States Department of Chemistry Saint Mary’s University HalifaxNSB3H3C3 Canada Département de Chimie Université Laval QuébecG1V0A6 Canada Department of Chemistry Dalhousie University HalifaxNSB3H4J3 Canada

Potential vibrational modes associated with diffuse interstellar bands (DIBs) could be discerned by examining energy differences between correlated DIBs. Consequently, ≈ 103 higher correlated DIB pairs (r − σr ≥ 0.8, ≥ 12 sightlines) were extracted from the Apache Point Observatory DIB catalog, and their energy spacings computed. In this first macro exploratory step, a histogram possibly reveals chemical bond signatures of C≡C, C≡N, S−H, C−O, C=O, Si−H, N−H, C−H (aliphatic), C...C (in-ring), and aromatics (C−H stretch, C...C in-ring, oop C−H bending, and overtones). Continued research is required to (in)validate the histogram approach, mitigate noise, scrutinize maxima, break degeneracies, and converge upon an optimal framework. © 2025, CC BY.

关键词： Bond strength (chemical)

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Self-assembling protein nanoparticles for cytosolic delivery of nucleic acids and proteins

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Nature Biotechnology 2025年 1-14页

作者： Eweje, Feyisayo Ibrahim, Vanessa Shajii, Aram Walsh, Michelle L. Ahmad, Kiran Alrefai, Assma Miyasato, Dominie Davis, Jessie R. Ham, Hyunok Li, Kaicheng Roehrl, Michael Haller, Carolyn A. Liu, David R. Chen, Jiaxuan Chaikof, Elliot L. Department of Surgery Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States Harvard and MIT Division of Health Science and Technology Massachusetts Institute of Technology CambridgeMA United States Harvard/MIT MD–PhD Program BostonMA United States Wyss Institute of Biologically Inspired Engineering Harvard University BostonMA United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA United States Howard Hughes Medical Institute Harvard University CambridgeMA United States Merkin Institute of Transformative Technologies in Healthcare Broad Institute of MIT and Harvard CambridgeMA United States Department of Pathology Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States

Intracellular delivery of biomacromolecules is hampered by low efficiency and cytotoxicity. Here we report the development of elastin-based nanoparticles for therapeutic delivery (ENTER), a recombinant elastin-like polypeptide (ELP)-based delivery system for effective cytosolic delivery of biomacromolecules in vitro and in vivo. Through iterative design, we developed fourth-generation ELPs fused to cationic endosomal escape peptides (EEPs) that self-assemble into pH-responsive micellar nanoparticles and enable cytosolic entry of cargo following endocytic uptake. In silico screening of α-helical peptide libraries led to the discovery of an EEP (EEP13) with 48% improved protein delivery efficiency versus a benchmark peptide. Our lead ELP–EEP13 showed similar or superior performance compared to lipid-based transfection reagents in the delivery of mRNA-encoded, DNA-encoded and protein-form Cre recombinase and CRISPR gene editors as well as short interfering RNAs to multiple cell lines and primary cell types. Intranasal administration of ELP–EEP13 combined with Cre protein achieved efficient editing of lung epithelial cells in reporter mice. © The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.

关键词： Glycoproteins

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Professional Perspectives: The Good Old Days Are Now

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Lab Medicine 2000年第3期31卷 131-133页

作者： Cathcart, Polly Steindel, Steven J. Polly Cathcart MMSc MT(ASCP)SC is chemistry supervisor at Piedmont Hospital Atlanta. Steven J. Steindel PhD is a supervisor health scientist in the Division of Laboratory Systems Public Health Practice Program Office Centers for Disease Control and Prevention Atlanta.

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Overcoming Cytosolic Delivery Barriers of Proteins Using Denatured Protein-Conjugated Mesoporous Silica Nanoparticles

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ACS Applied Materials and Interfaces 2023年第1期15卷 432-451页

作者： Dembélé, Julien Liao, Jou-Hsuan Liu, Tsang-Pai Chen, Yi-Ping Graduate Institute of Biomedical Materials & Tissue Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan Laboratory of Toxicology Environment and Health Doctorate School of Health University Joseph Ki-Zerbo Ouaga03 BP 7021 Burkina Faso Department of Chemistry National Taiwan University Taipei10617 Taiwan Department of Surgery Mackay Memorial Hospital Taipei10449 Taiwan Graduate Institute of Nanomedicine and Medical Engineering Taipei Medical University Taipei11031 Taiwan International PhD Program in Biomedical Engineering College of Biomedical Engineering Taipei Medical University Taipei11031 Taiwan

Intracellular delivery of therapeutic proteins has increased advantages over current small-molecule drugs and gene therapies, especially in therapeutic efficacies for a broad spectrum of diseases. Hence, developing the protein therapeutics approach provides a needed alternative. Here, we designed a mesoporous silica nanoparticle (MSN)-mediated protein delivery approach and demonstrated effective intracellular delivery of the denatured superoxide dismutase (SOD) protein, overcoming the delivery challenges and achieving higher enzymatic activity than native SOD-conjugated MSNs. The denatured SOD-conjugated MSN delivery strategy provides benefits of reduced size and steric hindrance, increased protein flexibility without distorting its secondary structure, exposure of the cell-penetrating peptide transactivator of transcription for enhanced efficient delivery, and a change in the corona protein composition, enabling cytosolic delivery. After delivery, SOD displayed a specific activity around threefold higher than in our previous reports. Furthermore, the in vivo biosafety and therapeutic potential for neuron therapy were evaluated, demonstrating the biocompatibility and the effective antioxidant effect in Neuro-2a cells that protected neurite outgrowth from paraquat-induced reactive oxygen species attack. This study offers an opportunity to realize the druggable possibility of cytosolic proteins using MSNs. © 2022 American Chemical Society.

关键词： Peptides

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Photoswitchable positive allosteric modulators of metabotropic glutamate receptor 4 to improve selectivity

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iScience 2024年第6期27卷 110123页

作者： Panarello, Silvia González-Díez, Aleix Berizzi, Alice E. Malhaire, Fanny Borràs-Tudurí, Roser Rovira, Xavier Serra, Carme Prézeau, Laurent Pin, Jean-Philippe Goudet, Cyril Llebaria, Amadeu Gómez-Santacana, Xavier MCS Institute for Advanced Chemistry of Catalonia – CSIC Barcelona Spain PhD Program in Organic Chemistry of the University of Barcelona Barcelona Spain Institut de Génomique Fonctionnelle Université de Montpellier UMR 5203 CNRS and U 1191 INSERM Montpellier France

Metabotropic glutamate receptors (mGlu) regulate multiple functions in the nervous systems and are involved in several neurological disorders. However, selectively targeting individual mGlu subtypes with spatiotemporal precision is still an unmet need. Photopharmacology can address this concern through the utilization of photoswitchable compounds such as optogluram, which is a positive allosteric modulator (PAM) of mGlu₄ that enables the precise control of physiological responses using light but does not have an optimal selectivity profile. Optogluram analogs were developed to obtain photoswitchable PAMs of mGlu₄ receptor with an improved selectivity. Among them, optogluram-2 emerged as a photoswitchable ligand for mGlu₄ receptor with activity as both PAM and allosteric agonists. It presents a higher selectivity and offers improved photoswitching of mGlu₄ activity. These improved properties make optogluram-2 an excellent candidate to study the role of mGlu₄ with a high spatiotemporal precision in systems where mGlu₄ can be co-expressed with other mGlu receptors. © 2024 The Author(s)

关键词： Biochemistry biological sciences molecular biology natural sciences pharmacology

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Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials

arXiv

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arXiv 2024年

作者： Zariquiey, Francesc Sabanés Galvelis, Raimondas Gallicchio, Emilio Chodera, John D. Markland, Thomas E. De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York NY11210 United States Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Department of Chemistry Stanford University 337 Campus Drive StanfordCA94305 United States Passeig Lluis Companys 23 Barcelona08010 Spain

This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology (NNP/MM). We compute relative binding free energies (RBFE) with the Alchemical Transfer Method (ATM) and validate its performance against established benchmarks and find significant enhancements compared to conventional MM force fields like GAFF2. Copyright © 2024, The Authors. All rights reserved.

关键词： Molecular dynamics

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Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series

arXiv

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arXiv 2023年

作者： Zariquiey, Francesc Sabanés Pérez, Adrià Majewski, Maciej Gallicchio, Emilio De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York United States Acellera Devonshire House 582 Honeypot Lane Stanmore Middlesex HA7 1JS United Kingdom Passeig Lluis Companys 23 Barcelona08010 Spain

The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary depending on the methodology. In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function. Copyright © 2023, The Authors. All rights reserved.

关键词： Ligands

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