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1. A Protocol for Custom Biomineralization of Enzymes in Metal–Organic Frameworks (MOFs)

   https://doi.org/10.21769/BioProtoc.4930  

   Armstrong, Zoe; Jordahl, Drew; MacRae, Austin; Li, Qiaobi; Lenertz, Mary; Shen, Patrick; Botserovska, Anastasiia; Feng, Li; Ugrinov, Angel; Yang, Zhongyu (January 2024, BIO-PROTOCOL)

   Enzyme immobilization offers a number of advantages that improve biocatalysis; however, finding a proper way to immobilize enzymes is often a challenging task. Implanting enzymes in metal–organic frameworks (MOFs) via co-crystallization, also known as biomineralization, provides enhanced reusability and stability with minimal perturbation and substrate selectivity to the enzyme. Currently, there are limited metal–ligand combinations with a proper protocol guiding the experimental procedures. We have recently explored 10 combinations that allow custom immobilization of enzymes according to enzyme stability and activity in different metals/ligands. Here, as a follow-up of that work, we present a protocol for how to carry out custom immobilization of enzymes using the available combinations of metal ions and ligands. Detailed procedures to prepare metal ions, ligands, and enzymes for their co-crystallization, together with characterization and assessment, are discussed. Precautions for each experimental step and result analysis are highlighted as well. This protocol is important for enzyme immobilization in various research and industrial fields. 

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2. Connecting the dots for fundamental understanding of structure–photophysics–property relationships of COFs, MOFs, and perovskites using a Multiparticle Holstein Formalism

   https://doi.org/10.1039/D2SC03793A  

   Ghosh, Raja; Paesani, Francesco (February 2023, Chemical Science)

   Photoactive organic and hybrid organic–inorganic materials such as conjugated polymers, covalent organic frameworks (COFs), metal–organic frameworks (MOFs), and layered perovskites, display intriguing photophysical signatures upon interaction with light. Elucidating structure–photophysics–property relationships across a broad range of functional materials is nontrivial and requires our fundamental understanding of the intricate interplay among excitons (electron–hole pair), polarons (charges), bipolarons, phonons (vibrations), inter-layer stacking interactions, and different forms of structural and conformational defects. In parallel with electronic structure modeling and data-driven science that are actively pursued to successfully accelerate materials discovery, an accurate, computationally inexpensive, and physically-motivated theoretical model, which consistently makes quantitative connections with conceptually complicated experimental observations, is equally important. Within this context, the first part of this perspective highlights a unified theoretical framework in which the electronic coupling as well as the local coupling between the electronic and nuclear degrees of freedom can be efficiently described for a broad range of quasiparticles with similarly structured Holstein-style vibronic Hamiltonians. The second part of this perspective discusses excitonic and polaronic photophysical signatures in polymers, COFs, MOFs, and perovskites, and attempts to bridge the gap between different research fields using a common theoretical construct – the Multiparticle Holstein Formalism. We envision that the synergistic integration of state-of-the-art computational approaches with the Multiparticle Holstein Formalism will help identify and establish new, transformative design strategies that will guide the synthesis and characterization of next-generation energy materials optimized for a broad range of optoelectronic, spintronic, and photonic applications. 

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3. Crystalline Porous Frameworks via Hierarchical Dynamic Covalent Assembly

   https://doi.org/10.1021/acs.accounts.5c00393  

   Ge, Yanqing; Huang, Shaofeng; Yuan, Zhehao; Zhang, Wei (August 2025, Accounts of Chemical Research)

   Crystalline porous frameworks, such as covalent organic frameworks (COFs), metal–organic frameworks (MOFs), and hydrogen-bonded organic frameworks (HOFs), have demonstrated exceptional potential in diverse applications, including gas adsorption/separation, catalysis, sensing, electronic devices, etc. However, the building blocks for constructing ordered frameworks are typically limited to multisubstituted aromatic small molecules, and uncontrolled interpenetration has remained a long-standing challenge in the field. Shape-persistent macrocycles and molecular cages have garnered significant attention in supramolecular chemistry and materials science due to their unique structures and novel properties. Using such preporous shape-persistent 2D macrocycles or 3D cages as building blocks to construct extended networks is particularly appealing. This macrocycle-to-framework/cage-to-framework hierarchical assembly approach not only mitigates the issue of interpenetration but also enables the integration of diverse properties in an emergent fashion. Since our demonstration of the first organic cage framework (OCF) in 2011 and the first macrocycle-based ionic COFs (ICOFs) in 2015, substantial advancements have been made over the past decade. In this Account, we will summarize our contributions to the development of crystalline porous frameworks, consisting of shape-persistent macrocycles and molecular cages as preporous building blocks, via hierarchical dynamic covalent assembly. We will begin by reviewing representative design strategies and the synthesis of shape-persistent macrocycles and molecular cages from small molecule-based primary building blocks, emphasizing the critical role of dynamic covalent chemistry (DCvC). Next, we will discuss the further assembly of preporous macrocycle/cage-based secondary building blocks into extended frameworks, followed by an overview of their properties and applications. Finally, we will highlight the current challenges and future directions for this hierarchical assembly approach in the synthesis of crystalline porous frameworks. This Account offers valuable insights into the design and synthesis of functional porous frameworks, contributing to the advancement of this important field. 

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4. Expanding the “library” of Metal-Organic Frameworks (MOFs) for enzyme biomineralization

   Jordahl, Drew Jordahl; Armstrong, Zoe; Li, Qiaobin; Gao, Runxiang; Liu, Wei; Johnson, Kelley; Brown, William; Scheiwiller, Allison; Feng, Li; Ugrinov, Angel; et al (October 2022, ACS applied materials interfaces)

   Farha, Omar (Ed.)

   Metal-Organic Frameworks (MOFs) are advanced platforms for enzyme immobilization. Enzymes can be entrapped via either diffusion (into pre-formed MOFs) or co-crystallization. Enzyme co-crystallization with specific metals/ligands in the aqueous phase, also known as biomineralization, minimizes the enzyme loss as compared to organic phase co-crystallization, removes the size limitation on enzymes and substrates, and can potentially broaden the application of enzyme@MOF composites. However, not all enzymes are stable/functional in the presence of excess metal ions and/or ligands currently available for co-crystallization. Furthermore, most current biomineralization-based MOFs have limited (acid-) pH stability, making it necessary to explore other metal-ligand combinations that can also immobilize enzymes. Here, we report our discovery on the combination of five metal ions and two ligands that can form biocomposites with two model enzymes differing in size and hydrophobicity in the aqueous phase under ambient conditions. Surprisingly, most of the formed composites are single- or multi- phase crystals even though the reaction phase is aqueous, with the rest as amorphous powders. All 20 enzyme@MOF composites showed good to excellent reusability, and were stable under weakly acidic pHs. The stability under weakly basic conditions depended on the selection of enzyme and metal-ligand combinations, yet for both enzymes, 3-4 MOFs offered decent stability under basic conditions. This work initiates the expansion of the current “library” of metal-ligand selection for encapsulating/biomineralizing large enzymes/enzyme clusters, leading to customized encapsulation of enzymes according to enzymes stability, functionality, and optimal pH. 

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5. Synthesis, Postsynthetic Modifications, and Applications of the First Quinoxaline-Based Covalent Organic Framework

   https://doi.org/https://doi.org/10.1021/acsami.1c08854  

   Valerie A. Kuehl, Phuoc H. (January 2021, ACS applied materials interfaces)

   We report a new synthetic protocol for preparing highly ordered two-dimensional nanoporous covalent organic frameworks (2D-COFs) based on a quinoxaline backbone. The quinoxaline framework represents a new type of COF that enables postsynthetic modification by placing two different chemical functionalities within the nanopores including layer-to-layer cross-linking. We also demonstrate that membranes fabricated using this new 2D-COF perform highly selective separations resulting in dramatic performance enhancement post cross-linking. 

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