Automated Rational Design of Metal–Organic PolyhedraClick to copy article linkArticle link copied!
- Aleksandar KondinskiAleksandar KondinskiDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.More by Aleksandar Kondinski
- Angiras MenonAngiras MenonDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.More by Angiras Menon
- Daniel NurkowskiDaniel NurkowskiCMCL Innovations, Sheraton House, Castle Park, Cambridge CB3 0AX, U.K.More by Daniel Nurkowski
- Feroz FaraziFeroz FaraziDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.More by Feroz Farazi
- Sebastian MosbachSebastian MosbachDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.More by Sebastian Mosbach
- Jethro AkroydJethro AkroydDepartment of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.More by Jethro Akroyd
- Markus Kraft*Markus Kraft*[email protected]Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.CARES, Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, Singapore 138602CMCL Innovations, Sheraton House, Castle Park, Cambridge CB3 0AX, U.K.School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459The Alan Turing Institute, 2QR, John Dodson House, 96 Euston Road, London NW1 2DB, U.K.More by Markus Kraft
Abstract
Metal–organic polyhedra (MOPs) are hybrid organic–inorganic nanomolecules, whose rational design depends on harmonious consideration of chemical complementarity and spatial compatibility between two or more types of chemical building units (CBUs). In this work, we apply knowledge engineering technology to automate the derivation of MOP formulations based on existing knowledge. For this purpose we have (i) curated relevant MOP and CBU data; (ii) developed an assembly model concept that embeds rules in the MOP construction; (iii) developed an OntoMOPs ontology that defines MOPs and their key properties; (iv) input agents that populate The World Avatar (TWA) knowledge graph; and (v) input agents that, using information from TWA, derive a list of new constructible MOPs. Our result provides rapid and automated instantiation of MOPs in TWA and unveils the immediate chemical space of known MOPs, thus shedding light on new MOP targets for future investigations.
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License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.
License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
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Introduction
Methodology
Immediate Chemical Space and Its Uncertainties
Assembly Models
Polyhedra Modeling during Early Cognitive Development
Chemical Complementarity
Topological Compatibility
Driving Forces in MOP Self-Assembly
Derivation of Assembly Models
The World Avatar: OntoMOPs
MOP Discovery as Part of a Digital Ecosystem
Ontological Modeling
List all MOPs having a particular CBU.
List all MOPs having a particular AM.
What type of AMs have been constructed using a particular CBU?
Show all MOPs having tetrahedral shape.
Show all GBUs required to form a particular shape/AM.
Show the substituting functionality of a particular CBU.
What is the associated modularity of a particular species acting as a CBU in MOPs?
MOP Information and Geometry Data Curation
Population of the KG
Algorithms and Implementation
Results and Discussion
Prediction of New MOPs Structures: Algorithmic Output
Summary and Outlook
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.2c03402.
Summary of algorithmic output, description Logic, list of chemical building units, illustration of the CBU sharing phenomenon, comments, algorithmic Output II and visual construction of new MOPs based on Algorithmic Output II (PDF)
Supporting Video S1 (MP4)
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgments
This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore under its Campus for Research Excellence and Technological Enterprise (CREATE) program. The authors are grateful to the UK Engineering and Physical Sciences Research Council (EPSRC, Grant Number: EP/R029369/1) and ARCHER for financial and computational support as a part of their funding to the UK Consortium on Turbulent Reacting Flows (www.ukctrf.com). AK and MK thank the Humboldt Foundation (Berlin, Germany) and the Isaac Newtwon Trust (Cambridge, UK) for the Feodor Lynen Fellowship. Mr. Jiaru Bai is thanked for discussions and feedback.
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- 15Li, H.; Eddaoudi, M.; O’Keeffe, M.; Yaghi, O. M. Design and synthesis of an exceptionally stable and highly porous metal-organic framework. Nature 1999, 402, 276– 279, DOI: 10.1038/46248Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXnvFSiuro%253D&md5=68f27e20a7e4e15ea2c2f49a2a61e98aDesign and synthesis of an exceptionally stable and highly porous metal-organic frameworkLi, Hailian; Eddaoudi, Mohamed; O'Keeffe, M.; Yaghi, M.Nature (London) (1999), 402 (6759), 276-279CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)Open metal-org. frameworks are widely regarded as promising materials for applications in catalysis, sepn., gas storage and mol. recognition. Compared to conventionally used microporous inorg. materials such as zeolites, these org. structures have the potential for more flexible rational design, through control of the architecture and functionalization of the pores. So far, the inability of these open frameworks to support permanent porosity and to avoid collapsing in the absence of guest mols., such as solvents, has hindered further progress in the field. The authors report the synthesis of a metal-org. framework, Zn4O(BDC)3.(DMF)8.(PhCl) (named MOF-5, where BDC = 1,4-benzenedicarboxylate), which remains cryst., as evidenced by x-ray single-crystal analyses, and stable when fully desolvated and when heated up to 300°. This synthesis is achieved by borrowing ideas from metal carboxylate cluster chem., where an org. dicarboxylate linker was used in a reaction that gives supertetrahedron clusters when capped with monocarboxylates. The rigid and divergent character of the added linker allows the articulation of the clusters into a three-dimensional framework resulting in a structure with higher apparent surface area and pore vol. than most porous cryst. zeolites. This simple and potentially universal design strategy is currently being pursued in the synthesis of new phases and composites, and for gas-storage applications.
- 16Vardhan, H.; Yusubov, M.; Verpoort, F. Self-assembled metal–organic polyhedra: An overview of various applications. Coord. Chem. Rev. 2016, 306, 171– 194, DOI: 10.1016/j.ccr.2015.05.016Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1Onu7vL&md5=5dfe403e624b2797e829f81ca8cfa3b4Self-assembled metal-organic polyhedra: An overview of various applicationsVardhan, Harsh; Yusubov, Mekhman; Verpoort, FrancisCoordination Chemistry Reviews (2016), 306 (Part_1), 171-194CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)A review. Self-assembly is a potent synthetic tool that allowed chemists to design numerous complex structures, supramols. of various shapes from relatively simple starting materials. Metal-org. polyhedra are a rising and promising member of the self-assembled supramol. family possessing fascinating structures and functionalities directly deriving from the precursor units. During the last two decades, research in this field was briskly progressed and it is now objective to exemplify various applications such as biomedical, catalysis, mol. sensing, gas adsorption and sepn., and synthesis of metal-org. frameworks from polyhedra. This review will be focus on each and every application with various unprecedented examples and highlight few challenges still need to be address.
- 17Guillerm, V.; Kim, D.; Eubank, J. F.; Luebke, R.; Liu, X.; Adil, K.; Lah, M. S.; Eddaoudi, M. A supermolecular building approach for the design and construction of metal–organic frameworks. Chem. Soc. Rev. 2014, 43, 6141– 6172, DOI: 10.1039/C4CS00135DGoogle Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFehsbvO&md5=97bf12cb969bfc7f409f5f06facd593bA supermolecular building approach for the design and construction of metal-organic frameworksGuillerm, Vincent; Kim, Dongwook; Eubank, Jarrod F.; Luebke, Ryan; Liu, Xinfang; Adil, Karim; Lah, Myoung Soo; Eddaoudi, MohamedChemical Society Reviews (2014), 43 (16), 6141-6172CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. In this review, the authors describe two recently implemented conceptual approaches facilitating the design and deliberate construction of metal-org. frameworks (MOFs), supermol. building block (SBB) and supermol. building layer (SBL) approaches. The authors' main objective is to offer an appropriate means to assist/aid chemists and material designers alike to rationally construct desired functional MOF materials, made-to-order MOFs. The authors introduce the concept of net-coded building units (net-cBUs), where precise embedded geometrical information codes uniquely and matchlessly a selected net, as a compelling route for the rational design of MOFs. This concept is based on employing pre-selected 0-periodic metal-org. polyhedra or 2-periodic metal-org. layers, SBBs or SBLs, resp., as a pathway to access the requisite net-cBUs. In this review, inspired by the authors' success with the original rht-MOF, the authors extrapolated the authors' strategy to other known MOFs via their deconstruction into more elaborate building units (polyhedra or layers) to (i) elucidate the unique relation between edge-transitive polyhedra or layers and minimal edge-transitive 3-periodic nets, and (ii) illustrate the potential of the SBB and SBL approaches as a rational pathway for the design and construction of 3-periodic MOFs. Using this design strategy, the authors have also identified several new hypothetical MOFs which are synthetically targetable.
- 18Mallick, A.; Garai, B.; Díaz, D. D.; Banerjee, R. Hydrolytic conversion of a metal–organic polyhedron into a metal–organic framework. Angew. Chem., Int. Ed. 2013, 52, 13755– 13759, DOI: 10.1002/anie.201307486Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslCqs73K&md5=2c2cd9ec27001bbbd003c18cde5cb80fHydrolytic Conversion of a Metal-Organic Polyhedron into a Metal-Organic FrameworkMallick, Arijit; Garai, Bikash; Diaz, David Diaz; Banerjee, RahulAngewandte Chemie, International Edition (2013), 52 (51), 13755-13759CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A metal-org. polyhedron (MOP), [Cu24L24(H2O)24] [H2L = 5-(propynyloxy)isophthalic acid] was prepd. and structurally characterized. Heating in water results in transformation of the polyhedron into a metal-org. framework. The release of encapsulated caffeine from the polyhedron can be driven by this transformation.
- 19Perry, I. J. J.; Perman, J. A.; Zaworotko, M. J. Design and synthesis of metal–organic frameworks using metal–organic polyhedra as supermolecular building blocks. Chem. Soc. Rev. 2009, 38, 1400– 1417, DOI: 10.1039/b807086pGoogle Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvValsr4%253D&md5=296a7ae534acdc37203ce097b2013d18Design and synthesis of metal-organic frameworks using metal-organic polyhedra as supermolecular building blocksPerry, John J., IV; Perman, Jason A.; Zaworotko, Michael J.Chemical Society Reviews (2009), 38 (5), 1400-1417CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)This crit. review highlights supermol. building blocks (SBBs) in the context of their impact upon the design, synthesis, and structure of metal-org. materials (MOMs). MOMs, also known as coordination polymers, hybrid inorg.-org. materials, and metal-org. frameworks, represent an emerging class of materials that have attracted the imagination of solid-state chemists because MOMs combine unprecedented levels of porosity with a range of other functional properties that occur through the metal moiety and/or the org. ligand. First generation MOMs exploited the geometry of metal ions or secondary building units (SBUs), small metal clusters that mimic polygons, for the generation of MOMs. In this crit. review we examine the recent (<5 years) adoption of much larger scale metal-org. polyhedra (MOPs) as SBBs for the construction of MOMs by highlighting how the large size and high symmetry of such SBBs can afford improved control over the topol. of the resulting MOM and a new level of scale to the resulting framework (204 refs.).
- 20Pilgrim, B.; Champness, N. R. Metal-Organic Frameworks and Metal-Organic Cages–A Perspective. ChemPlusChem. 2020, 85, 1842– 1856, DOI: 10.1002/cplu.202000408Google Scholar20https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhslWqurnE&md5=fc03763d1c4b87c0e8ade9914ab64362Metal-Organic Frameworks and Metal-Organic Cages - A PerspectivePilgrim, Ben S.; Champness, Neil R.ChemPlusChem (2020), 85 (8), 1842-1856CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)The fields of metal-org. cages (MOCs) and metal-org. frameworks (MOFs) are both highly topical and continue to develop at a rapid pace. Despite clear synergies between the two fields, overlap is rarely obsd. This article discusses the peculiarities and similarities of MOCs and MOFs in terms of synthetic strategies and approaches to system characterization. The stability of both classes of material is compared, particularly in relation to their applications in guest storage and catalysis. Lastly, suggestions are made for opportunities for each field to learn and develop in partnership with the other.
- 21Li, X.-X.; Zhao, D.; Zheng, S.-T. Recent advances in POM-organic frameworks and POM-organic polyhedra. Coord. Chem. Rev. 2019, 397, 220– 240, DOI: 10.1016/j.ccr.2019.07.005Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVWhtbvI&md5=8fbf28181c1b2cc4ac7b0bdb2639bad7Recent advances in POM-organic frameworks and POM-organic polyhedraLi, Xin-Xiong; Zhao, Dan; Zheng, Shou-TianCoordination Chemistry Reviews (2019), 397 (), 220-240CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)During the past two decades, the search of strategies to introduce polyoxometalate (POM) clusters as secondary building units (SBUs) to construct porous extended POM-org. frameworks (POMOFs) and discrete POM-org. polyhedra (POMOPs) have attracted sustained interests because such materials not only integrate the advantages of both POMs and framework/polyhedra structures, but also exhibit good prospects in photo-/electro-catalysis, sepn., mol. recognition, host-guest chem. and so on. In this review, the recent advancements of POMOFs and POMOPs, including their assembly methodologies, classification and related applications are summarized. Moreover, the current challenges in the design and fabrication of POMOFs and POMOPs as well as the great potential in these two areas are also discussed.
- 22Zhang, D.; Ronson, T. K.; Zou, Y.-Q.; Nitschke, J. R. Metal–organic cages for molecular separations. Nat. Rev. Chem. 2021, 5, 168– 182, DOI: 10.1038/s41570-020-00246-1Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXosFersr0%253D&md5=52aa58c2690363dda8b4b703142f3426Metal-organic cages for molecular separationsZhang, Dawei; Ronson, Tanya K.; Zou, You-Quan; Nitschke, Jonathan R.Nature Reviews Chemistry (2021), 5 (3), 168-182CODEN: NRCAF7; ISSN:2397-3358. (Nature Research)A review. Sepn. technol. is central to industries as diverse as petroleum, pharmaceuticals, mining and life sciences. Metal-org. cages, a class of mol. containers formed via coordination-driven self-assembly, show great promise as sepn. agents. Precise control of the shape, size and functionalization of cage cavities enables them to selectively bind and distinguish a wide scope of physicochem. similar substances in soln. Extensive research has, thus, been performed involving sepns. of high-value targets using coordination cages, ranging from gases and liqs. to compds. dissolved in soln. Enantiopure capsules also show great potential for the sepn. of chiral mols. The use of cryst. cages as absorbents, or the incorporation of cages into polymer membranes, could increase the selectivity and efficiency of sepn. processes. This Review covers recent progress in using metal-org. cages to achieve sepns., with discussion of the many methods of using them in this context. Challenges and potential future developments are also discussed.
- 23Sudik, A. C.; Millward, A. R.; Ockwig, N. W.; Côté, A. P.; Kim, J.; Yaghi, O. M. Design, synthesis, structure, and gas (N2, Ar, CO2, CH4, and H2) sorption properties of porous metal-organic tetrahedral and heterocuboidal polyhedra. J. Am. Chem. Soc. 2005, 127, 7110– 7118, DOI: 10.1021/ja042802qGoogle Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtl2ntLg%253D&md5=654522c7c7f2351595cea3091c172cb1Design, Synthesis, Structure, and Gas (N2, Ar, CO2, CH4, and H2) Sorption Properties of Porous Metal-Organic Tetrahedral and Heterocuboidal PolyhedraSudik, Andrea C.; Millward, Andrew R.; Ockwig, Nathan W.; Cote, Adrien P.; Kim, Jaheon; Yaghi, Omar M.Journal of the American Chemical Society (2005), 127 (19), 7110-7118CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A strategy based on assembling metal ions and org. carboxylate links was applied for the design and synthesis of a new class of porous, truncated tetrahedral and heterocuboidal polyhedra, whose pore size and functionality can be systematically varied. The synthesis of this series of metal-org. polyhedra (MOPs) employs sulfate-capped O-centered Fe-carboxylate trimers, Fe3O(CO2)3(SO4)3, as rigid nodes sepd. by linear (Ph, biphenyl, terphenyl, and tetrahydropyrene) or trigonal (benzenetriphenyl) links to yield five highly cryst. polyhedra [NH2Me2]8[Fe12O4(SO4)12(link)x(py)12]·G (x = 6 for linear or 4 for trigonal, py = pyridine, G = guests). In this series, the size of each polyhedron was varied from 20.0 to 28.5 Å (on edge), and the corresponding pore diam. from 7.3 to 13.3 Å. Gas sorption isotherms were measured for three members of this series to reveal significant uptake of gases (N2, Ar, CO2, H2, CH4) and benzene and exhibit Type I sorption behavior that is indicative of permanent porosity. The apparent surface areas for these compds. range from 387 to 480 m2/g. Magnetic susceptibility studies indicate antiferromagnetic interactions between iron centers, and long-range coupling between clusters is assumed to be negligible.
- 24Xing, W.-H.; Li, H.-Y.; Dong, X.-Y.; Zang, S.-Q. Robust multifunctional Zr-based metal-organic polyhedra for high proton conductivity and selective CO2 capture. J. Mater. Chem. A 2018, 6, 7724– 7730, DOI: 10.1039/C8TA00858BGoogle Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXlslSksbw%253D&md5=92283c1532c6ab5cf84b48ff9e3505caRobust multifunctional Zr-based metal-organic polyhedra for high proton conductivity and selective CO2 captureXing, Wen-Hao; Li, Hai-Yang; Dong, Xi-Yan; Zang, Shuang-QuanJournal of Materials Chemistry A: Materials for Energy and Sustainability (2018), 6 (17), 7724-7730CODEN: JMCAET; ISSN:2050-7496. (Royal Society of Chemistry)New stable Zr-based metal-org. polyhedra (MOPs) have been designed and constructed through the self-assembly of a designed flexible sulfonate-carboxylate ligand, 1,2-bis(sodium-2-sulfonate-4-carboxyphenoxy)ethane (NaH2L), and the secondary building units (SBUs) of Cp3Zr3(μ3-O)(μ2-OH)3, (Cp = η5-C5H5). The MOPs feature candy-like cages and the anionic sulfonic groups on the org. ligand strengthened the stability of the MOPs (thermal stability and acid and alkali resistance) by forming strong multiple charge-assisted hydrogen bonds with the cationic SBUs. The unique cavities of this 3D porous framework endowed the MOPs with highly selective CO2 capture. The 2D H-bond networks obtained by the connection of coordinated water mols. and free water mols. between the discrete MOPs enabled a high proton cond. of 1.41 × 10-3 S cm-1 at 30 °C, 98% relative humidity (RH) and a low activation energy of 0.225 eV for the proton transfer.
- 25Tan, C.; Jiao, J.; Li, Z.; Liu, Y.; Han, X.; Cui, Y. Design and Assembly of a Chiral Metallosalen-Based Octahedral Coordination Cage for Supramolecular Asymmetric Catalysis. Angew. Chem., Int. Ed. 2018, 57, 2085– 2090, DOI: 10.1002/anie.201711310Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsl2nu7g%253D&md5=d5ac64201de9fca4ab6cc16cfb247348Design and Assembly of a Chiral Metallosalen-Based Octahedral Coordination Cage for Supramolecular Asymmetric CatalysisTan, Chunxia; Jiao, Jingjing; Li, Zijian; Liu, Yan; Han, Xing; Cui, YongAngewandte Chemie, International Edition (2018), 57 (8), 2085-2090CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Supramol. containers featuring both high catalytic activity and high enantioselectivity represent a design challenge of practical importance. Herein, a chiral octahedral coordination cage can be constructed by using twelve enantiopure Mn(salen)-derived dicarboxylic acids as linear linkers and six Zn4-p-tert-butylsulfonylcalix[4]arene clusters as tetravalent four-connected vertexes. The porous cage features a large hydrophobic cavity (≈3944 Å3) decorated with catalytically active metallosalen species and is an efficient and recyclable asym. catalyst for the oxidative kinetic resoln. of racemic secondary alcs. and the epoxidn. of olefins with up to >99% enantiomeric excess. The cage architecture not only prevents intermol. deactivation and stabilizes the Mn(salen) catalysts but also encapsulates substrates and concs. reactants in the cavity, resulting in enhanced reactivity and enantioselectivity relative to the free metallosalen catalyst.
- 26Jiao, J.; Tan, C.; Li, Z.; Liu, Y.; Han, X.; Cui, Y. Design and assembly of chiral coordination cages for asymmetric sequential reactions. J. Am. Chem. Soc. 2018, 140, 2251– 2259, DOI: 10.1021/jacs.7b11679Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1Ggtro%253D&md5=04061c0ce8bb3236f4d596b8f68d3d25Design and Assembly of Chiral Coordination Cages for Asymmetric Sequential ReactionsJiao, Jingjing; Tan, Chunxia; Li, Zijian; Liu, Yan; Han, Xing; Cui, YongJournal of the American Chemical Society (2018), 140 (6), 2251-2259CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Supramol. nanoreactors featuring multiple catalytically active sites are of great importance, esp. for asym. catalysis, and are yet challenging to construct. Here we report the design and assembly of five chiral single- and mixed-linker tetrahedral coordination cages using six dicarboxylate ligands derived-from enantiopure Mn(salen), Cr(salen) and/or Fe(salen) as linear linkers and four Cp3Zr3 clusters as three-connected vertices. The formation of these cages was confirmed by a variety of techniques including single-crystal and powder X-ray diffraction, inductively coupled plasma optical emission spectrometer, quadrupole-time-of-flight mass spectrometry and energy dispersive X-ray spectrometry. The cages feature a nanoscale hydrophobic cavity decorated with the same or different catalytically active sites, and the mixed-linker cage bearing Mn(salen) and Cr(salen) species is shown to be an efficient supramol. catalyst for sequential asym. alkene epoxidn./epoxide ring-opening reactions with up to 99.9% ee. The cage catalyst demonstrates improved activity and enantioselectivity over the free catalysts owing to stabilization of catalytically active metallosalen units and concn. of reactants within the cavity. Manipulation of catalytic org. linkers in cages can control the activities and selectivities, which may provide new opportunities for the design and assembly of novel functional supramol. architectures.
- 27Vardhan, H.; Verpoort, F. Metal-Organic Polyhedra: Catalysis and Reactive Intermediates. Adv. Synth. Catal 2015, 357, 1351– 1368, DOI: 10.1002/adsc.201400778Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtlSksrg%253D&md5=448498e450135fddccb8d20b6671b7e0Metal-Organic Polyhedra: Catalysis and Reactive IntermediatesVardhan, Harsh; Verpoort, FrancisAdvanced Synthesis & Catalysis (2015), 357 (7), 1351-1368CODEN: ASCAF7; ISSN:1615-4150. (Wiley-VCH Verlag GmbH & Co. KGaA)A review; the catalytic nature of self-assembled metal-org. polyhedra gives an entirely new dimension to the reactivity and properties of mols. within a well-defined confined space. Encapsulation of a range of guests brings about not only host-guest interactions but also gives rise to unusual reactivities with selectivity and stabilization of various reactive intermediates. This review briefly covers the synthesis of self-assembled metal-org. polyhedra and elaborates their influence in different chem. reactions as well as in the stabilization of unstable chem. species.
- 28Hosono, N.; Kitagawa, S. Modular design of porous soft materials via self-organization of metal–organic cages. Acc. Chem. Res. 2018, 51, 2437– 2446, DOI: 10.1021/acs.accounts.8b00361Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhslOgtrfP&md5=1e7a0ca54e9c2b7025550d8f76e598f8Modular Design of Porous Soft Materials via Self-Organization of Metal-Organic CagesHosono, Nobuhiko; Kitagawa, SusumuAccounts of Chemical Research (2018), 51 (10), 2437-2446CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The authors describe recent progress in bottom-up "modular" approaches for the synthesis of porous, processable MOF-based materials, wherein metal-org. cages (MOCs), alternatively called metal-org. polyhedra (MOPs), are used as "modular cavities" to build porous soft materials. The outer periphery of a MOP is decorated with polymeric and dendritic side chains to obtain a polymer-grafted MOP, imparting both soln. and thermal processability to the MOP cages, which have an inherent nanocavity along with high tailorability analogous to MOFs. Well-ordered MOP assemblies can be designed to obtain phases ranging from crystals to liq. crystals, allowing the fabrication of flexible free-standing sheets with preservation of the long-range ordering of MOPs. Furthermore, future prospects of the modular design for porous soft materials are provided with the anticipation that the bottom-up design will combine porous materials and soft matter sciences, leading to the discovery and development of many unexplored new materials and devices such as MOF-based self-healing membranes possessing well-defined nanochannels. The macroscopic alignment of channels can be controlled by external factors, including elec. and magnetic fields, external forces, and modified surfaces (templating and patterning), which are conventionally used for engineering of soft materials.
- 29Gosselin, A. J.; Antonio, A. M.; Korman, K. J.; Deegan, M. M.; Yap, G. P.; Bloch, E. D. Elaboration of Porous Salts. J. Am. Chem. Soc. 2021, 143, 14956– 14961, DOI: 10.1021/jacs.1c05613Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFKrtr%252FN&md5=7584aac9ba5280aa33180fe3c0b08748Elaboration of Porous SaltsGosselin, Aeri J.; Antonio, Alexandra M.; Korman, Kyle J.; Deegan, Meaghan M.; Yap, Glenn P. A.; Bloch, Eric D.Journal of the American Chemical Society (2021), 143 (37), 14956-14961CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A large library of novel porous salts based on charged coordination cages was synthesized via straightforward salt metathesis reactions. For these, solns. of salts of oppositely charged coordination cages are mixed to ppt. MOF-like permanently porous products where metal identity, pore size, ligand functional groups, and surface area are highly tunable. For most of these materials, the constituent cages combine in the ratios expected based on their charge. Addnl. studies focused on the rate of salt metathesis or reaction stoichiometry as variables to tune particle size or product compn., resp. It is expected that the design principles outlined here will be widely applicable for the synthesis of new porous salts based on a variety of charged porous mol. precursors.
- 30Kitano, H. Nobel Turing Challenge: creating the engine for scientific discovery. NPJ Syst. Biol. Appl. 2021, 7, 1– 12, DOI: 10.1038/s41540-021-00189-3Google ScholarThere is no corresponding record for this reference.
- 31Bai, J.; Cao, L.; Mosbach, S.; Akroyd, J.; Lapkin, A. A.; Kraft, M. From Platform to Knowledge Graph: Evolution of Laboratory Automation. JACS Au 2022, 2, 292– 309, DOI: 10.1021/jacsau.1c00438Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XltlKgug%253D%253D&md5=2209bca32f8d212982179327e09a079dFrom Platform to Knowledge Graph: Evolution of Laboratory AutomationBai, Jiaru; Cao, Liwei; Mosbach, Sebastian; Akroyd, Jethro; Lapkin, Alexei A.; Kraft, MarkusJACS Au (2022), 2 (2), 292-309CODEN: JAAUCR; ISSN:2691-3704. (American Chemical Society)A review. High-fidelity computer-aided experimentation is becoming more accessible with the development of computing power and artificial intelligence tools. The advancement of exptl. hardware also empowers researchers to reach a level of accuracy that was not possible in the past. Marching toward the next generation of self-driving labs., the orchestration of both resources lies at the focal point of autonomous discovery in chem. science. To achieve such a goal, algorithmically accessible data representations and standardized communication protocols are indispensable. In this perspective, we recategorize the recently introduced approach based on Materials Acceleration Platforms into five functional components and discuss recent case studies that focus on the data representation and exchange scheme between different components. Emerging technologies for interoperable data representation and multiagent systems are also discussed with their recent applications in chem. automation. We hypothesize that knowledge graph technol., orchestrating semantic web technologies and multiagent systems will be the driving force to bring data to knowledge, evolving our way of automating lab.
- 32Inderwildi, O., Kraft, M., Eds.; Intelligent Decarbonisation, 1st ed.; Lecture Notes in Energy; Springer International Publishing, 2022.Google ScholarThere is no corresponding record for this reference.
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- 34Menon, A.; Krdzavac, N. B.; Kraft, M. From database to knowledge graph─using data in chemistry. Curr. Opin. Chem. Eng. 2019, 26, 33– 37, DOI: 10.1016/j.coche.2019.08.004Google ScholarThere is no corresponding record for this reference.
- 35Frey, J. G.; Bird, C. L. Cheminformatics and the semantic web: adding value with linked data and enhanced provenance. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2013, 3, 465– 481, DOI: 10.1002/wcms.1127Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFKlsL3K&md5=ff829207ef6b4477b9adab4a49b3513aCheminformatics and the semantic web: adding value with linked data and enhanced provenanceFrey, Jeremy G.; Bird, Colin L.Wiley Interdisciplinary Reviews: Computational Molecular Science (2013), 3 (5), 465-481CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)Cheminformatics is evolving from being a field of study assocd. primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chem. data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chem., biochem., biol., and medical information. These developments depend on a range of factors: the principles of chem. identifiers and their role in relationships between chem. and biol. entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration.
- 36Bird, C. L.; Willoughby, C.; Frey, J. G. Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences. Chem. Soc. Rev. 2013, 42, 8157– 8175, DOI: 10.1039/c3cs60122fGoogle Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVyrtbnI&md5=58abff9515441c27ec6f2e9923fed604Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciencesBird, Colin L.; Willoughby, Cerys; Frey, Jeremy G.Chemical Society Reviews (2013), 42 (20), 8157-8175CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions. Their medium was paper, but despite the quality of their notebooks, we cannot turn the clock back. Our primary purpose is to review the influences of the digital era on scientific record keeping. We examine the foundations of the emerging opportunities for preserving and curating electronic records focussing on electronic lab. notebooks (ELNs), with an emphasis on their characteristics and usability.
- 37Degtyarenko, K.; De Matos, P.; Ennis, M.; Hastings, J.; Zbinden, M.; McNaught, A.; Alcántara, R.; Darsow, M.; Guedj, M.; Ashburner, M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2007, 36, D344– D350, DOI: 10.1093/nar/gkm791Google ScholarThere is no corresponding record for this reference.
- 38Cohen, S.; Hershcovitch, M.; Taraz, M.; Kißig, O.; Wood, A.; Waddington, D.; Chin, P.; Friedrich, T. Complex Networks & Their Applications X; Springer, 2021; pp 742– 753.Google ScholarThere is no corresponding record for this reference.
- 39Kanza, S.; Frey, J. G. A new wave of innovation in Semantic web tools for drug discovery. Expert. Opin. Drug. Discovery 2019, 14, 433– 444, DOI: 10.1080/17460441.2019.1586880Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXltFyitbg%253D&md5=e095f935975ddb15aa82b4ab2d65b17fA new wave of innovation in Semantic web tools for drug discoveryKanza, Samantha; Frey, Jeremy GrahamExpert Opinion on Drug Discovery (2019), 14 (5), 433-444CODEN: EODDBX; ISSN:1746-0441. (Taylor & Francis Ltd.)A review. : The use of semantic web technologies to aid drug discovery has gained momentum over recent years. Researchers in this domain have realized that semantic web technologies are key to dealing with the high levels of data for drug discovery. These technologies enable us to represent the data in a formal, structured, interoperable and comparable way, and to tease out undiscovered links between drug data (be it identifying new drug-targets or relevant compds., or links between specific drugs and diseases).: This review focuses on explaining how semantic web technologies are being used to aid advances in drug discovery. The main types of semantic web technologies are explained, outlining how they work and how they can be used in the drug discovery process, with a consideration of how the use of these technologies has progressed from their initial usage.: The increased availability of shared semantic resources (tools, data and importantly the communities) have enabled the application of semantic web technologies to facilitate semantic (context dependent) search across multiple data sources, which can be used by machine learning to produce better predictions by exploiting the semantic links in knowledge graphs and linked datasets.
- 40Kraft, M.; Eibeck, A. J-Park Simulator: Knowledge Graph for Industry 4.0. Chem. Ing. Technol. 2020, 92, 967– 977, DOI: 10.1002/cite.202000002Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovFymtr0%253D&md5=3d3e483534a09a0dec8338544eff9458J-Park Simulator: Knowledge Graph for Industry 4.0Kraft, Markus; Eibeck, AndreasChemie Ingenieur Technik (2020), 92 (7), 967-977CODEN: CITEAH; ISSN:0009-286X. (Wiley-VCH Verlag GmbH & Co. KGaA)This article introduces ontologies, Knowledge Graphs, agents and their role in the context of Industry 4.0. The importance of interoperability of agents in cross-domain scenarios using the J-Park Simulator (JPS), which is part of the Knowledge Graph () is shown. The dispersion of air pollutants from a power plant situated in Berlin is investigated with the help of JPS. The article describes how interoperability between agents in cross-domain scenarios can be achieved and discusses related open problems.
- 41Akroyd, J.; Mosbach, S.; Bhave, A.; Kraft, M. Universal Digital Twin – A Dynamic Knowledge Graph. Data-centric Eng. 2021, 2, e14 DOI: 10.1017/dce.2021.10Google ScholarThere is no corresponding record for this reference.
- 42Eibeck, A.; Lim, M. Q.; Kraft, M. J-Park Simulator: An ontology-based platform for cross-domain scenarios in process industry. Comput. Chem. Eng. 2019, 131, 106586, DOI: 10.1016/j.compchemeng.2019.106586Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFyhu7zE&md5=c9b82998ac83d5665b40676198e488e7J-Park Simulator: An ontology-based platform for cross-domain scenarios in process industryEibeck, Andreas; Lim, Mei Qi; Kraft, MarkusComputers & Chemical Engineering (2019), 131 (), 106586CODEN: CCENDW; ISSN:0098-1354. (Elsevier B.V.)The J-Park Simulator (JPS) acts as a continuously growing platform for integrating real-time data, knowledge, models, and tools related to process industry. It aims at simulation and optimization in cross-domain and multi-level scenarios and relies heavily on ontologies and semantic technologies. In this paper, we demonstrate the interoperability between different applications in JPS, introduce new domain ontologies into the JPS, and integrate live data. For this, we utilize a knowledge graph to store and link semantically described data and models and create agents wrapping the applications and updating the data in the knowledge graph dynamically. We present a comprehensive industrial air pollution scenario, which has been implemented as part of the JPS, to show how knowledge graphs and modular domain ontologies support the interoperability between agents. We show that the architecture of JPS increases the interoperability and flexibility in cross-domain scenarios and conclude that the potential of ontologies outweighs addnl. wrapping efforts.
- 43Farazi, F.; Krdzavac, N. B.; Akroyd, J.; Mosbach, S.; Menon, A.; Nurkowski, D.; Kraft, M. Linking reaction mechanisms and quantum chemistry: An ontological approach. Comput. Chem. Eng. 2020, 137, 106813, DOI: 10.1016/j.compchemeng.2020.106813Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXms12it70%253D&md5=566bddc2a113cc005cbb510977141b08Linking reaction mechanisms and quantum chemistry: An ontological approachFarazi, Feroz; Krdzavac, Nenad B.; Akroyd, Jethro; Mosbach, Sebastian; Menon, Angiras; Nurkowski, Daniel; Kraft, MarkusComputers & Chemical Engineering (2020), 137 (), 106813CODEN: CCENDW; ISSN:0098-1354. (Elsevier B.V.)In this paper, a linked-data framework for connecting species in chem. kinetic reaction mechanisms with quantum calcns. is presented. A mechanism can be constructed from thermodn., reaction rate, and transport data that has been obtained either exptl., computationally, or by a combination of both. This process in practice requires multiple sources of data, which raises, inter alia, species naming and data inconsistency issues. A linked data-centric knowledge-graph approach is taken in this work to address these challenges. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chem. kinetic reaction mechanisms, and OntoCompChem, for representing quantum chem. calcns., are extended. In addn., a new ontol., which we call OntoSpecies, is developed for uniquely representing chem. species. The framework also includes agents to populate and link knowledge-bases created through the instantiation of these ontologies. In addn., the developed knowledge-graph and agents naturally form a part of the J-Park Simulator (JPS) - an Industry 4.0 platform which combines linked data and an eco-system of autonomous agents for cross-domain applications. The functionality of the framework is demonstrated via a use-case based on a hydrogen combustion mechanism.
- 44Farazi, F.; Akroyd, J.; Mosbach, S.; Buerger, P.; Nurkowski, D.; Salamanca, M.; Kraft, M. OntoKin: An ontology for chemical kinetic reaction mechanisms. J. Chem. Inf. Model. 2020, 60, 108– 120, DOI: 10.1021/acs.jcim.9b00960Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVWlt7nO&md5=d79229952eb19b43e70ac54722050743OntoKin: An Ontology for Chemical Kinetic Reaction MechanismsFarazi, Feroz; Akroyd, Jethro; Mosbach, Sebastian; Buerger, Philipp; Nurkowski, Daniel; Salamanca, Maurin; Kraft, MarkusJournal of Chemical Information and Modeling (2020), 60 (1), 108-120CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)An ontol. for capturing both data and the semantics of chem. kinetic reaction mechanisms has been developed. Such mechanisms can be applied to simulate and understand the behavior of chem. processes, for example, the emission of pollutants from internal combustion engines. An ontol. development methodol. was used to produce the semantic model of the mechanisms, and a tool was developed to automate the assertion process. As part of the development methodol., the ontol. is formally represented using a web ontol. language (OWL), assessed by domain experts, and validated by applying a reasoning tool. The resulting ontol., termed OntoKin, has been used to represent example mechanisms from the literature. OntoKin and its instantiations are integrated to create a knowledge base (KB), which is deployed using the RDF4J triple store. The use of the OntoKin ontol. and the KB is demonstrated for three use cases-querying across mechanisms, modeling atm. pollution dispersion, and as a mechanism browser tool. As part of the query use case, the OntoKin tools have been applied by a chemist to identify variations in the rate of a prompt NOx formation reaction in the combustion of ammonia as represented by four mechanisms in the literature.
- 45Bai, J.; Geeson, R.; Farazi, F.; Mosbach, S.; Akroyd, J.; Bringley, E. J.; Kraft, M. Automated Calibration of a Poly (oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph Technology. J. Chem. Inf. Model. 2021, 61, 1701– 1717, DOI: 10.1021/acs.jcim.0c01322Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXotVOktrw%253D&md5=b12ffe5a93ae6e634d9ece130db746b6Automated Calibration of a Poly(oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph TechnologyBai, Jiaru; Geeson, Rory; Farazi, Feroz; Mosbach, Sebastian; Akroyd, Jethro; Bringley, Eric J.; Kraft, MarkusJournal of Chemical Information and Modeling (2021), 61 (4), 1701-1717CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)In this paper, we develop a knowledge graph-based framework for the automated calibration of combustion reaction mechanisms and demonstrate its effectiveness on a case study of poly(oxymethylene)dimethyl ether (PODEn, where n = 3) oxidn. We develop an ontol. representation for combustion expts., OntoChemExp, that allows for the semantic enrichment of expts. within the J-Park simulator (JPS, theworldavatar.com), an existing cross-domain knowledge graph. OntoChemExp is fully capable of supporting exptl. results in the Process Informatics Model (PrIMe) database. Following this, a set of software agents are developed to perform exptl. result retrieval, sensitivity anal., and calibration tasks. The sensitivity anal. agent is used for both generic sensitivity analyses and reaction selection for subsequent calibration. The calibration process is performed as a sampling task, followed by an optimization task. The agents are designed for use with generic models but are demonstrated with ignition delay time and laminar flame speed simulations. We find that calibration times are reduced, while accuracy is increased compared to manual calibration, achieving a 79% decrease in the objective function value, as defined in this study. Further, we demonstrate how this workflow is implemented as an extension of the JPS.
- 46Krdzavac, N.; Mosbach, S.; Nurkowski, D.; Buerger, P.; Akroyd, J.; Martin, J.; Menon, A.; Kraft, M. An ontology and semantic web service for quantum chemistry calculations. J. Chem. Inf. Model. 2019, 59, 3154– 3165, DOI: 10.1021/acs.jcim.9b00227Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtVyjsLzN&md5=c51fb379d9ac835e7e1bf41d0d6ce9dbAn Ontology and Semantic Web Service for Quantum Chemistry CalculationsKrdzavac, Nenad; Mosbach, Sebastian; Nurkowski, Daniel; Buerger, Philipp; Akroyd, Jethro; Martin, Jacob; Menon, Angiras; Kraft, MarkusJournal of Chemical Information and Modeling (2019), 59 (7), 3154-3165CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)The purpose of this article is to present an ontol., termed OntoCompChem, for quantum chem. calcns. as performed by the Gaussian quantum chem. software, as well as a semantic web service named MolHub. The OntoCompChem ontol. has been developed based on the semantics of concepts specified in the CompChem convention of Chem. Markup Language (CML) and by extending the Gainesville Core (GNVC) ontol. MolHub is developed in order to establish semantic interoperability between different tools used in quantum chem. and thermochem. calcns., and as such is integrated into the J-Park Simulator (JPS)-a multidomain interactive simulation platform and expert system. It uses the OntoCompChem ontol. and implements a formal language based on propositional logic as a part of its query engine, which verifies satisfiability through reasoning. This paper also presents a NASA polynomial use-case scenario to demonstrate semantic interoperability between Gaussian and a tool for thermodn. data calcns. within MolHub.
- 47Zhang, Y.; Gan, H.; Qin, C.; Wang, X.; Su, Z.; Zaworotko, M. J. Self-Assembly of Goldberg Polyhedra from a Concave [WV5O11(RCO2)5(SO4)] 3–Building Block with 5-Fold Symmetry. J. Am. Chem. Soc. 2018, 140, 17365– 17368, DOI: 10.1021/jacs.8b10866Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXit1Cit7bK&md5=3d5ae0b4e8c567cf2e55d37d812f039aSelf-Assembly of Goldberg Polyhedra from a Concave [WV5O11(RCO2)5(SO4)]3- Building Block with 5-Fold SymmetryZhang, Yuteng; Gan, Hongmei; Qin, Chao; Wang, Xinlong; Su, Zhongmin; Zaworotko, Michael J.Journal of the American Chemical Society (2018), 140 (50), 17365-17368CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Nanoscale regular polyhedra with icosahedral symmetry exist naturally as exemplified by virus capsids and fullerenes. Nevertheless, their generation by supramol. chem. through the linking of 5-fold symmetry vertices remains unmet because of the absence of 5-fold symmetry building blocks with the requisite geometric features. This situation contrasts with that of tetrahedral and octahedral symmetry metal-org. polyhedra (MOPs), for which appropriate triangular and square mol. building blocks (MBBs) that can serve as vertices or faces are readily available. Herein, authors report isolation of a pentagonal [WV5O11(SO4)6]8- cluster and reveal its utility to afford the first four examples of nanoscale Goldberg MOPs, based upon 5-fold MBBs. Two 32-faced Gv(1,1) MOPs and two 42-faced Gv(2,0) MOPs were formed using linear or triangular org. ligands, resp. The largest Goldberg MOP-4, exhibits a diam. of 4.3 nm, can trap fullerene C60 mols. in its interstitial cavities.
- 48Lyu, H.; Ji, Z.; Wuttke, S.; Yaghi, O. M. Digital reticular chemistry. Chem. 2020, 6, 2219– 2241, DOI: 10.1016/j.chempr.2020.08.008Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVeqsbrJ&md5=47893e5b08ace46ebeecaced7b36c9e9Digital Reticular ChemistryLyu, Hao; Ji, Zhe; Wuttke, Stefan; Yaghi, Omar M.Chem (2020), 6 (9), 2219-2241CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)A review. Reticular chem. operates in an infinite space of compns., structures, properties, and applications. Although great progress has been made in exploring this space through the development of metal-org. frameworks and covalent org. frameworks, there remains a gap between what we foresee as being possible and what can actually be accomplished with the current tools and methods. The establishment of digital reticular chem., where digital tools are deployed, in particular lab. robotics and artificial intelligence, will fundamentally change the current workflow to enable discovery of this untapped chem. space and to go beyond the limits of human capacity. In so doing, long-standing challenges in reticular chem. can finally be addressed faster and better, and more significantly, new questions, unimagined before digitization, can be articulated. The interface between human and "machine" is an integral part of this endeavor and one whose quality is crit. to uncovering science transcending intellectual and phys. borders.
- 49Tranchemontagne, D. J.; Mendoza-Cortés, J. L.; O’Keeffe, M.; Yaghi, O. M. Secondary building units, nets and bonding in the chemistry of metal–organic frameworks. Chem. Soc. Rev. 2009, 38, 1257– 1283, DOI: 10.1039/b817735jGoogle Scholar49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvValsr8%253D&md5=3e03c5e2c057b36eb590c1904aa5e5a1Secondary building units, nets and bonding in the chemistry of metal-organic frameworksTranchemontagne, David J.; Mendoza-Cortes, Jose L.; O'Keeffe, Michael; Yaghi, Omar M.Chemical Society Reviews (2009), 38 (5), 1257-1283CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)This crit. review presents a comprehensive study of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) towards construction and synthesis of metal-org. frameworks (MOFs). We describe the geometries of 131 SBUs, their connectivity and compn. This contribution presents a comprehensive list of the wide variety of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) in the construction and synthesis of metal-org. frameworks. The SBUs discussed here were obtained from a search of mols. and extended structures archived in the Cambridge Structure Database (CSD, version 5.28, Jan. 2007) which included only crystals contg. metal carboxylate linkages (241 refs.).
- 50Evans, J. D.; Jelfs, K. E.; Day, G. M.; Doonan, C. J. Application of computational methods to the design and characterisation of porous molecular materials. Chem. Soc. Rev. 2017, 46, 3286– 3301, DOI: 10.1039/C7CS00084GGoogle Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXntlWhsLs%253D&md5=65b0f66e14f0114dd08f01e5b63835ffApplication of computational methods to the design and characterisation of porous molecular materialsEvans, Jack D.; Jelfs, Kim E.; Day, Graeme M.; Doonan, Christian J.Chemical Society Reviews (2017), 46 (11), 3286-3301CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)Composed from discrete units, porous mol. materials (PMMs) possess unique properties not obsd. for conventional, extended, solids, such as soln. processibility and permanent porosity in the liq. phase. However, identifying the origin of porosity is not a trivial process, esp. for amorphous or liq. phases. Furthermore, the assembly of mol. components is typically governed by a subtle balance of weak intermol. forces that makes structure prediction challenging. Accordingly, in this review we canvass the crucial role of mol. simulations in the characterization and design of PMMs. We will outline strategies for modeling porosity in cryst., amorphous and liq. phases and also describe the state-of-the-art methods used for high-throughput screening of large datasets to identify materials that exhibit novel performance characteristics.
- 51Poole, D. A.; Bobylev, E. O.; Mathew, S.; Reek, J. N. Topological prediction of palladium coordination cages. Chem. Sci. 2020, 11, 12350– 12357, DOI: 10.1039/D0SC03992FGoogle Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVyhsL%252FO&md5=bf181f858ca6d0818ab5ca6b8f575a40Topological prediction of palladium coordination cagesPoole, David A.; Bobylev, Eduard O.; Mathew, Simon; Reek, Joost N. H.Chemical Science (2020), 11 (45), 12350-12357CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)The prepn. of functionalized, heteroleptic PdxL2x coordination cages is desirable for catalytic and optoelectronic applications. Current rational design of these cages uses the angle between metal-binding (∠B) sites of the di(pyridyl)arene linker to predict the topol. of homoleptic cages obtained via non-covalent chem. However, this model neglects the contributions of steric bulk between the pyridyl residues-a prerequisite for endohedrally functionalized cages, and fails to rationalize heteroleptic cages. We describe a classical mechanics (CM) approach to predict the topol. outcomes of PdxL2x coordination cage formation with arbitrary linker combinations, accounting for the electronic effects of coordination and steric effects of linker structure. Initial validation of our CM method with reported homoleptic Pd12LFu24 (LFu = 2,5-bis(pyridyl)furan) assembly suggested the formation of a minor topol. Pd15LFu30, identified exptl. by mass spectrometry. Application to heteroleptic cage systems employing mixts. of LFu (∠B = 127°) and its thiophene congener LTh (∠B = 149° ∠Bexp = 152.4°) enabled prediction of Pd12L24 and Pd24L48 coordination cages formation, reliably emulating exptl. data. Finally, the topol. outcome for exohedrally (LEx) and endohedrally (LEn) functionalized heteroleptic PdxL2x coordination cages were predicted to assess the effect of steric bulk on both topol. outcomes and coordination cage yields, with comparisons drawn to exptl. data.
- 52Jiang, Y.; Tan, P.; Qi, S.-C.; Gu, C.; Peng, S.-S.; Wu, F.; Liu, X.-Q.; Sun, L.-B. Breathing metal–organic polyhedra controlled by light for carbon dioxide capture and liberation. CCS Chemistry 2021, 3, 1659– 1668, DOI: 10.31635/ccschem.020.202000314Google Scholar52https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXit1Smt7jL&md5=2b51ad5e227e7d57bb87c5a10fab2719Breathing metal-organic polyhedra controlled by light for carbon dioxide capture and liberationJiang, Yao; Tan, Peng; Qi, Shi-Chao; Gu, Chen; Peng, Song-Song; Wu, Fan; Liu, Xiao-Qin; Sun, Lin-BingCCS Chemistry (2021), 3 (6), 1659-1668CODEN: CCCHB2 ISSN:. (Chinese Chemical Society)Metal-org. polyhedra (MOPs) have emerged as versatile platforms for artificial models of biol. systems due to their discrete structure and modular nature. However, the design and fabrication of MOPs with special functionality for mimicking biol. processes are challenging. Inspired by the breathing mechanism of lungs, we developed a new type of MOP (a breathing MOP, denoted as NUT-101) by directly using azobenzene units as the pillars of the polyhedra to coordinate with Zr-based metal clusters. In addn. to considerable thermal and chem. stability, the obtained MOP exhibits photocontrollable breathing behavior. Upon irradn. with visible or UV light, the configuration of azobenzene units transforms, leading to reversible expansion or contraction of the cages and, correspondingly, capture or liberation of CO2 mols. Such a breathing behavior of NUT-101 is further confirmed by d. functional theory (DFT) calcn. This system might establish an avenue for the construction of new materials with particular functionality that mimic biol. processes.
- 53Hoffmann, R.; Schleyer, P.; Schaefer, H., III Predicting Molecules—More Realism, Please. Angew. Chem., Int. Ed. 2008, 47, 7164– 7167, DOI: 10.1002/anie.200801206Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD1crpt12jsw%253D%253D&md5=5c7b8656a39374a82114630bbb1bcdf1Predicting molecules--more realism, please!Hoffmann Roald; Schleyer Paul von Rague; Schaefer Henry F 3rdAngewandte Chemie (International ed. in English) (2008), 47 (38), 7164-7 ISSN:.There is no expanded citation for this reference.
- 54Heine, T. Grand challenges in computational materials science: from description to prediction at all scales. Front. Mater. 2014, 1, 7, DOI: 10.3389/fmats.2014.00007Google ScholarThere is no corresponding record for this reference.
- 55Dumontheil, I. Development of abstract thinking during childhood and adolescence: The role of rostrolateral prefrontal cortex. Dev. Cogn. Neurosci. 2014, 10, 57– 76, DOI: 10.1016/j.dcn.2014.07.009Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2M%252Fms1yisQ%253D%253D&md5=73d8f03c182c96836b3466c32d44492bDevelopment of abstract thinking during childhood and adolescence: the role of rostrolateral prefrontal cortexDumontheil IroiseDevelopmental cognitive neuroscience (2014), 10 (), 57-76 ISSN:.Rostral prefrontal cortex (RPFC) has increased in size and changed in terms of its cellular organisation during primate evolution. In parallel emerged the ability to detach oneself from the immediate environment to process abstract thoughts and solve problems and to understand other individuals' thoughts and intentions. Rostrolateral prefrontal cortex (RLPFC) is thought to play an important role in supporting the integration of abstract, often self-generated, thoughts. Thoughts can be temporally abstract and relate to long term goals, or past or future events, or relationally abstract and focus on the relationships between representations rather than simple stimulus features. Behavioural studies have provided evidence of a prolonged development of the cognitive functions associated with RLPFC, in particular logical and relational reasoning, but also episodic memory retrieval and prospective memory. Functional and structural neuroimaging studies provide further support for a prolonged development of RLPFC during adolescence, with some evidence of increased specialisation of RLPFC activation for relational integration and aspects of episodic memory retrieval. Topics for future research will be discussed, such as the role of medial RPFC in processing abstract thoughts in the social domain, the possibility of training abstract thinking in the domain of reasoning, and links to education.
- 56Kondinski, A.; Parac-Vogt, T. N. Programmable interlocking disks: bottom-up modular assembly of chemically relevant polyhedral and reticular structural models. J. Chem. Educ. 2019, 96, 601– 605, DOI: 10.1021/acs.jchemed.8b00769Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXis1KjtL8%253D&md5=3ebdc5b076261b07ba431c213e7da3d4Programmable Interlocking Disks: Bottom-Up Modular Assembly of Chemically Relevant Polyhedral and Reticular Structural ModelsKondinski, Aleksandar; Parac-Vogt, Tatjana N.Journal of Chemical Education (2019), 96 (3), 601-605CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)Single-type, 8-fold-grooved, com. accessible interlocking disks (ILDs) have been used for modeling of complex polyhedral and reticular topologies with relevance to inorg. and hybrid materials. The assembly of complex topologies relies on the prepn. of secondary building units (SBUs), which exhibit different connectivity than that of the primary ILDs. All ILD-based models are light, scalable, programmable, and suitable for discovery-based learning and classroom demonstrations of stereochem. and complex chem. concepts.
- 57Kondinski, A.; Moons, J.; Zhang, Y.; Bussé, J.; De Borggraeve, W.; Nies, E.; Parac-Vogt, T. N. Modeling of Nanomolecular and Reticular Architectures with 6-fold Grooved, Programmable Interlocking Disks. J. Chem. Educ. 2020, 97, 289– 294, DOI: 10.1021/acs.jchemed.9b00739Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitVCktbrI&md5=e9dbd99956ec602fedbaa3deb5492de5Modeling of Nanomolecular and Reticular Architectures with 6-fold Grooved, Programmable Interlocking DisksKondinski, Aleksandar; Moons, Jens; Zhang, Yujie; Busse, Jakob; De Borggraeve, Wim; Nies, Erik; Parac-Vogt, Tatjana N.Journal of Chemical Education (2020), 97 (1), 289-294CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)Single-type, 6-fold sym. grooved, and com. accessible interlocking disks (ILDs) have been used for modeling of sp2 hybridized carbon-based nanoarchitectures and complex polyhedral and reticular material models. In the case of the carbon-based nanoarchitectures, we showcase that the primary ILDs can be directly used for representing individual atoms and bonds. Further on, the spatial connectivity of the primary ILDs can be extended by assembly of sym. secondary building units (SBUs). The constructed (deci)meter scale models are robust, light, scalable, and suitable for classroom demonstrations. The ILD technique is also suitable for use in workshops for facile discovery-based learning of nanomol. structure, showing promise for wider use in the chem. curriculum.
- 58Castilla, A. M.; Ramsay, W. J.; Nitschke, J. R. Stereochemistry in subcomponent self-assembly. Acc. Chem. Res. 2014, 47, 2063– 2073, DOI: 10.1021/ar5000924Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXntlSktb8%253D&md5=873d21bb2346217d47e23ca5ae78db04Stereochemistry in Subcomponent Self-AssemblyCastilla, Ana M.; Ramsay, William J.; Nitschke, Jonathan R.Accounts of Chemical Research (2014), 47 (7), 2063-2073CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. As Pasteur noted >150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt 1-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomol. structure is clear: the single-handed forms of bio(macro)mols. interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramol. structures, provided a means to study the mechanisms of transmission and amplification of stereochem. information, which are key processes to understand in the context of the origins and functions of biol. homochirality. Control over stereochem. information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and sepn., asym. catalysis, and mol. devices. In this Account, the authors explore different aspects of stereochem. encountered during the use of subcomponent self-assembly, whereby complex structures were prepd. through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N=C) bonds. This technique provides a useful method to study stereochem. information transfer processes within metal-org. assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. The authors start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the org. ligands of mononuclear coordination complexes and communicate stereochem. information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then incorporated in self-assembly reactions to control the stereochem. of increasingly complex architectures. This strategy has also allowed exploration of the degree to which stereochem. information is propagated through tetrahedral frameworks cooperatively, leading to the observation of stereochem. coupling across >2 nm between metal stereocenters and the enantioselective synthesis of a face-capped tetrahedron contg. no carbon stereocenters via a stereochem. memory effect. Several studies on the communication of stereochem. between the configurationally flexible metal centers in tetrahedral metal-org. cages have shed light on the factors governing this process, allowing the synthesis of an asym. cage, obtained in racemic form, in which all symmetry elements were broken. Finally, how stereochem. diversity leads to structural complexity in the structures prepd. through subcomponent self-assembly are discussed. Initial use of octahedral metal templates with facial stereochem. in subcomponent self-assembly, which predictably gave rise to structures of tetrahedral symmetry, was extended to meridional metal centers. These lower-symmetry linkages have allowed the assembly of increasingly intricate 3D architectures of varying functionality. The knowledge gained from investigating different aspects of the stereochem. of metal-templated assemblies thus not only leads to new means of structural control but also opens pathways toward functions such as stereoselective guest binding and transformation.
- 59Harris, K.; Sun, Q.-F.; Sato, S.; Fujita, M. M12L24 spheres with endo and exo coordination sites: scaffolds for non-covalent functionalization. J. Am. Chem. Soc. 2013, 135, 12497– 12499, DOI: 10.1021/ja4043609Google Scholar59https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1CltLnL&md5=2738eebbd8e277e0730348a747cbd6bfM12L24 Spheres with Endo and Exo Coordination Sites: Scaffolds for Non-Covalent FunctionalizationHarris, Kate; Sun, Qing-Fu; Sato, Sota; Fujita, MakotoJournal of the American Chemical Society (2013), 135 (34), 12497-12499CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Palladium M12L24 spherical complexes incorporating 24 free pyridine rings on their interior or exterior surfaces were synthesized via the self-assembly of tridentate tris(pyridine) ligands with Pd2+ ions. Coordination of secondary metal ions in the interior of the spherical framework was achieved through interactions of 24 Ag+ ions with the free endo pyridine rings.
- 60Müller, A.; Krickemeyer, E.; Bögge, H.; Schmidtmann, M.; Peters, F. Organizational forms of matter: an inorganic super fullerene and keplerate based on molybdenum oxide. Angew. Chem., Int. Ed. 1998, 37, 3359– 3363, DOI: 10.1002/(SICI)1521-3773(19981231)37:24<3359::AID-ANIE3359>3.0.CO;2-JGoogle Scholar60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1Mjot1ygtw%253D%253D&md5=0106c893ea55a061725c7ffb9e351105Organizational Forms of Matter: An Inorganic Super Fullerene and Keplerate Based on Molybdenum OxideMuller Achim; Krickemeyer Erich; Bogge Hartmut; Schmidtmann Marc; Peters FrankAngewandte Chemie (International ed. in English) (1998), 37 (24), 3359-3363 ISSN:.Plato and Kepler would have been pleased. Despite the large number of atoms present the cluster anion 1 resembles an icosahedral-type structure. This represents definitively an unprecedented event in chemistry! The structure is made up of 12 {Mo11 } fragments such that the fivefold symmetry axes are retained in the resulting spherical object. As an inscribed icosahedron can be recognized in the spherical shell of 1 (see picture), similarities with Kepler's famous shell model of the cosmos can be seen.
- 61Yaghi, O. M.; Kalmutzki, M. J.; Diercks, C. S. Introduction to Reticular Chemistry; John Wiley and Sons, 2019; Chapter 19, pp 453– 462.Google ScholarThere is no corresponding record for this reference.
- 62He, S.; Zhang, M.; Xue, B.; Lai, Y.; Li, M.; Yin, P. Surface Functionality-Regulated and Entropy-Driven Thermodynamics of the Formation of Coordination Nanocages. J. Phys. Chem. B. 2021, 125, 13229– 13234, DOI: 10.1021/acs.jpcb.1c06690Google Scholar62https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisFars7vF&md5=df38aa48c917b5a6d7171dededa64391Surface Functionality-Regulated and Entropy-Driven Thermodynamics of the Formation of Coordination NanocagesHe, Shuqian; Zhang, Mingxin; Xue, Binghui; Lai, Yuyan; Li, Mu; Yin, PanchaoJournal of Physical Chemistry B (2021), 125 (48), 13229-13234CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)Coordination nanocages (CNCs) are under intense research in nanoscience and supramol. chem. for their enriched surface functionalities and micro-porosity; however, the understanding of their formation mechanism is still poor due to the difficulty in probing their soln. structures. Herein, the CNC formation process from the coordination complexation of the macromol. isophthalic acid (IPA) ligand and Cu2+ is studied via isothermal titrn. calorimetry, and its entropy-driven feature is revealed to be originated from the collapse of solvation layers of the assembly units. The CNC formation is thermodynamically less favored with smaller binding consts. when the sizes of macromol. IPA ligands are larger, which originated from the space crowding of macromols. of the ligands on CNC surfaces and the resulting entropy loss of polymer chain conformations. Meanwhile, the chem. equil. of CNC formation can be tuned upon altering the Cu2+/IPA ratio, and the yield of CNCs, suggested from size exclusion chromatog. studies, decreases when excessive Cu2+ is applied, providing guidelines for CNC design and synthesis.
- 63Piskorz, T. K.; Martí-Centelles, V.; Young, T. A.; Lusby, P. J.; Duarte, F. Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities. ACS Catal. 2022, 12, 5806– 5826, DOI: 10.1021/acscatal.2c00837Google Scholar63https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XhtFCqs7vK&md5=02201ef10653b8eb66db651ebb51aa11Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and OpportunitiesPiskorz, Tomasz K.; Marti-Centelles, Vicente; Young, Tom A.; Lusby, Paul J.; Duarte, FernandaACS Catalysis (2022), 12 (10), 5806-5826CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)A review. Self-assembled metallo-org. cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive exptl. work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-org. cages are scarce, not least due to the challenges assocd. with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, the authors discuss key mol. principles governing the design of functional metallo-org. cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. The authors will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing exptl. observable and to guide synthetic efforts. To illustrate this point, the authors present several examples where modeling has helped to elucidate fundamental principles behind mol. recognition and reactivity. The authors highlight the importance of combining computational and exptl. efforts to speed up supramol. catalyst design while reducing time and resources.
- 64Cheetham, A. K.; Kieslich, G.; Yeung, H.-M. Thermodynamic and kinetic effects in the crystallization of metal–organic frameworks. Acc. Chem. Res. 2018, 51, 659– 667, DOI: 10.1021/acs.accounts.7b00497Google Scholar64https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXivVSlu7o%253D&md5=7d4d54f0debf7feedbb23a922815d9e1Thermodynamic and Kinetic Effects in the Crystallization of Metal-Organic FrameworksCheetham, Anthony K.; Kieslich, G.; Yeung, H. H.-M.Accounts of Chemical Research (2018), 51 (3), 659-667CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The evolution of metal-org. frameworks (MOFs) has been one of the most exciting aspects of materials chem. over the last 20 years. In this Account, we discuss the development during this period in our understanding of the factors that control the crystn. of MOFs from soln. Both classical porous MOFs and dense MOF phases are considered. This is an opportune time at which to examine this complex area because the exptl. tools now available to interrogate crystn. processes have matured significantly in the last 5 years, particularly with the use of in situ synchrotron X-ray diffraction. There have also been impressive developments in the use of d. functional theory (DFT) to treat not only the energies of very complex structures but also their entropies. This is particularly important in MOF frameworks because of their much greater flexibility compared with inorg. structures such as zeolites. The first section of the Account describes how early empirical observations on the crystn. of dense MOFs pointed to a strong degree of thermodn. control, with both enthalpic and entropic factors playing important roles. For example, reactions at higher temps. tend to lead to denser structures with higher degrees of framework connectivity and lower levels of solvation, and polymorphs tend to form according to their thermodn. stabilities. In the case of metal tartrates, these trends have been validated by calorimetric studies. It has been clear for more than a decade, however, that certain phases crystallize under kinetic control, esp. when a change in conformation of the ligand or coordination around a metal center might be necessary to form the thermodynamically preferred product. We describe how this can lead to time-dependent crystn. processes that evolve according to the Ostwald rule of stages and can be obsd. by in situ methods. We then consider the crystn. of porous MOFs, which presents addnl. challenges because of solvation effects. In spite of these problems, much has been learned about the energetics of the underlying frameworks, where the relationship between porosity and stability initially seemed to mirror the behavior of zeolites, with more porous structures being less stable. Recently, however, this simple relationship has had to be reconsidered with the emergence of some very flexible structures wherein the open structures are more stable than their denser analogs at finite temps. because of their large vibrational entropies. In the final section we describe how the concepts developed in the MOF work have been extended into the closely related area of hybrid org.-inorg. perovskites. We describe recent studies on polymorphism in hybrid perovskites, which is amenable to total free energy calcns. using a combination of DFT and lattice dynamics methods.
- 65Piccinno, F.; Hischier, R.; Seeger, S.; Som, C. From laboratory to industrial scale: a scale-up framework for chemical processes in life cycle assessment studies. J. Clean. Prod 2016, 135, 1085– 1097, DOI: 10.1016/j.jclepro.2016.06.164Google ScholarThere is no corresponding record for this reference.
- 66Eibeck, A.; Chadzynski, A.; Lim, M. Q.; Aditya, K.; Ong, L.; Devanand, A.; Karmakar, G.; Mosbach, S.; Lau, R.; Karimi, I. A.; Foo, E. Y. S.; Kraft, M. A parallel world framework for scenario analysis in knowledge graphs. Data-centric Eng. 2020, 1, e6 DOI: 10.1017/dce.2020.6Google ScholarThere is no corresponding record for this reference.
- 67Berners-Lee, T.; Hendler, J.; Lassila, O. The semantic web. Sci. Am. 2001, 284, 34– 43, DOI: 10.1038/scientificamerican0501-34Google ScholarThere is no corresponding record for this reference.
- 68Wilkinson, M. D. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 2016, 3, 1– 9, DOI: 10.1038/sdata.2016.18Google ScholarThere is no corresponding record for this reference.
- 69Mosbach, S.; Menon, A.; Farazi, F.; Krdzavac, N.; Zhou, X.; Akroyd, J.; Kraft, M. Multiscale cross-domain thermochemical knowledge-graph. J. Chem. Inf. Model. 2020, 60, 6155– 6166, DOI: 10.1021/acs.jcim.0c01145Google Scholar69https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVGrurbK&md5=7cf31a486b5a094351f90909617fe4ccMultiscale Cross-Domain Thermochemical Knowledge-GraphMosbach, Sebastian; Menon, Angiras; Farazi, Feroz; Krdzavac, Nenad; Zhou, Xiaochi; Akroyd, Jethro; Kraft, MarkusJournal of Chemical Information and Modeling (2020), 60 (12), 6155-6166CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)In this paper, we develop a set of software agents which improve a knowledge-graph contg. thermodn. data of chem. species by means of quantum chem. calcns. and error-canceling balanced reactions. The knowledge-graph represents species-assocd. information by making use of the principles of linked data, as employed in the Semantic Web, where concepts correspond to vertices and relationships between the concepts correspond to edges of the graph. We implement this representation by means of ontologies, which formalize the definition of concepts and their relationships, as a crit. step to achieve interoperability between heterogeneous data formats and software. The agents, which conduct quantum chem. calcns. and derive the ests. of std. enthalpies of formation, update the knowledge-graph with newly obtained results, improving data values, and adding nodes and connections between them. A key distinguishing feature of our approach is that it extends an existing, general-purpose knowledge-graph, called J-Park Simulator (http://theworldavatar.com), and its ecosystem of autonomous agents, thus enabling seamless cross-domain applications in wider contexts. To this end, we demonstrate how quantum calcns. can directly affect the atm. dispersion of pollutants in an industrial emission use-case.
- 70Czaja, A. U.; Trukhan, N.; Müller, U. Industrial applications of metal–organic frameworks. Chem. Soc. Rev. 2009, 38, 1284– 1293, DOI: 10.1039/b804680hGoogle Scholar70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvVamu7o%253D&md5=63295ce7e2fb393c1abecd7623bc9c58Industrial applications of metal-organic frameworksCzaja, Alexander U.; Trukhan, Natalia; Muller, UlrichChemical Society Reviews (2009), 38 (5), 1284-1293CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. New materials are prerequisite for major breakthrough applications affecting the daily life, and therefore are pivotal for the chem. industry. Metal-org. frameworks (MOFs) constitute an emerging class of materials useful in gas storage, gas purifn., and sepn. applications as well as heterogeneous catalysis. They not only offer higher surface areas and the potential for enhanced activity than currently used materials like base metal oxides, but also provide shape/size selectivity which is important both for sepns. and catalysis. In this crit. review an overview of the potential applications of MOFs in the chem. industry is presented. Furthermore, the synthesis and characterization of the materials are briefly discussed from the industrial perspective.
- 71Grüninger, M.; Fox, M. S. Methodology for the design and evaluation of ontologies. In International Joint Conferences on Artificial Intelligence (IJCAI), Workshop on Basic Ontological Issues in Knowledge Sharing, Montreal, Canada, 1995.Google ScholarThere is no corresponding record for this reference.
- 72Uschold, M.; King, M. Towards a Methodology for Building Ontologies; Citeseer, 1995.Google ScholarThere is no corresponding record for this reference.
- 73Noy, N. F.; McGuinness, D. L. Ontology Development 101: A Guide to Creating Your First Ontology; Stanford University, 2001.Google ScholarThere is no corresponding record for this reference.
- 74Pinto, H. S.; Martins, J. P. Ontologies: How can they be built?. Knowledge and information systems 2004, 6, 441– 464, DOI: 10.1007/s10115-003-0138-1Google ScholarThere is no corresponding record for this reference.
- 75Giunchiglia, F.; Dutta, B.; Maltese, V.; Farazi, F. A facet-based methodology for the construction of a large-scale geospatial ontology. J. Data Semant 2012, 1, 57– 73, DOI: 10.1007/s13740-012-0005-xGoogle ScholarThere is no corresponding record for this reference.
- 76Giunchiglia, F.; Dutta, B.; Maltese, V. From knowledge organization to knowledge representation. Knowl. Organ. 2014, 41, 44– 56, DOI: 10.5771/0943-7444-2014-1-44Google ScholarThere is no corresponding record for this reference.
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- 78Allen, F. H.; Bellard, S.; Brice, M. D.; Cartwright, B. A.; Doubleday, A.; Higgs, H.; Hummelink, T.; Hummelink-Peters, B. G.; Kennard, O.; Motherwell, W. D. S.; Rodgers, J. R.; Watson, D. G. The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Crystallogr. B 1979, 35, 2331– 2339, DOI: 10.1107/S0567740879009249Google ScholarThere is no corresponding record for this reference.
- 79O’Keeffe, M.; Peskov, M. A.; Ramsden, S. J.; Yaghi, O. M. The reticular chemistry structure resource (RCSR) database of, and symbols for, crystal nets. Acc. Chem. Res. 2008, 41, 1782– 1789, DOI: 10.1021/ar800124uGoogle Scholar79https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXht1SgsrjF&md5=392c624f403dd8457460a7649aa496f3The Reticular Chemistry Structure Resource (RCSR) database of, and symbols for, crystal netsO'Keeffe, Michael; Peskov, Maxim A.; Ramsden, Stuart J.; Yaghi, Omar M.Accounts of Chemical Research (2008), 41 (12), 1782-1789CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)During the past decade, interest has grown tremendously in the design and synthesis of cryst. materials constructed from mol. clusters linked by extended groups of atoms. Most notable are metal-org. frameworks (MOFs), in which polyat. inorg. metal-contg. clusters are joined by polytopic linkers. (Although these materials are sometimes referred to as coordination polymers, we prefer to differentiate them, because MOFs are based on strong linkages that yield robust frameworks.) The realization that MOFs could be designed and synthesized in a rational way from mol. building blocks led to the emergence of a discipline that we call reticular chem.MOFs can be represented as a special kind of graph called a periodic net. Such descriptions date back to the earliest crystallog. studies but have become much more common recently because thousands of new structures and hundreds of underlying nets have been reported. In the simplest cases (e.g., the structure of diamond), the atoms in the crystal become the vertices of the net, and bonds are the links (edges) that connect them. In the case of MOFs, polyat. groups act as the vertices and edges of the net.Because of the explosive growth in this area, a need has arisen for a universal system of nomenclature, classification, identification, and retrieval of these topol. structures. We have developed a system of symbols for the identification of three periodic nets of interest, and this system is now in wide use. In this Account, we explain the underlying methodol. of assigning symbols and describe the Reticular Chem. Structure Resource (RCSR), in which about 1600 such nets are collected and illustrated in a database that can be searched by symbol, name, keywords, and attributes. The resource also contains searchable data for polyhedra and layers.The database entries come from systematic enumerations or from known chem. compds. or both. In the latter case, refs. to occurrences are provided. We describe some crystallog., topol., and other attributes of nets and explain how they are reported in the database. We also describe how the database can be used as a tool for the design and structural anal. of new materials. Assocd. with each net is a natural tiling, which is a natural partition of space into space-filling tiles. The database allows export of data that can be used to analyze and illustrate such tilings.
- 80Glimm, B.; Horrocks, I.; Motik, B.; Stoilos, G.; Wang, Z. HermiT: an OWL 2 reasoner. J. Automat. Reason. 2014, 53, 245– 269, DOI: 10.1007/s10817-014-9305-1Google ScholarThere is no corresponding record for this reference.
- 81Motik, B.; Shearer, R.; Horrocks, I. Hypertableau reasoning for description logics. J. Artif. Intell. Res. 2009, 36, 165– 228, DOI: 10.1613/jair.2811Google ScholarThere is no corresponding record for this reference.
- 82López, X.; Carbó, J. J.; Bo, C.; Poblet, J. M. Structure, properties and reactivity of polyoxometalates: a theoretical perspective. Chem. Soc. Rev. 2012, 41, 7537– 7571, DOI: 10.1039/c2cs35168dGoogle Scholar82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsFGqurnP&md5=e030c2995f5e45094c0388033bb96607Structure, properties and reactivity of polyoxometalates: A theoretical perspectiveLopez, Xavier; Carbo, Jorge J.; Bo, Carles; Poblet, Josep M.Chemical Society Reviews (2012), 41 (22), 7537-7571CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)In the thematic review dedicated to polyoxometalate (POM) chem. published in Chem. Reviews in 1998, no contribution was devoted to theory. This is not surprising because computational modeling of mol. metal-oxide clusters was in its infancy at that time. Nowadays, the situation has completely changed and modern computational methods have been successfully applied to study the structure, electronic properties, spectroscopy and reactivity of POM clusters. Indeed, the progress achieved during the past decade has been spectacular and herein we critically review the most important papers to provide the reader with an almost complete perspective of the field.
- 83Kondinski, A. Chemical Modelling; RSC, 2021; pp 39– 71.Google ScholarThere is no corresponding record for this reference.
- 84Hoffmann, R. Qualitative thinking in the age of modern computational chemistry─or what Lionel Salem knows. J. Mol. Struct. Theochem 1998, 424, 1– 6, DOI: 10.1016/S0166-1280(97)00219-4Google Scholar84https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhtFygu7w%253D&md5=8ff2b9bc495e45e14f431c48e0c0ef10Qualitative thinking in the age of modern computational chemistry or what Lionel Salem knowsHoffmann, RoaldJournal of Molecular Structure: THEOCHEM (1998), 424 (1-2), 1-6CODEN: THEODJ; ISSN:0166-1280. (Elsevier Science B.V.)A personal assessment is given of the present state of computational chem., and in particular of the persistent need for qual. orbital thinking at a time when exceedingly accurate calcns. are possible. The need for the qual. view arises, it is claimed, from the inherent difference between predictability and understanding, from certain potential impediments to chem. understanding intrinsic to human-computer interactions, from the peculiar yet productive way that expt. and theory interact in chem., and lastly from some special features of theory in science in general.
- 85Chung, Y. G.; Haldoupis, E.; Bucior, B. J.; Haranczyk, M.; Lee, S.; Zhang, H.; Vogiatzis, K. D.; Milisavljevic, M.; Ling, S.; Camp, J. S.; Slater, B.; Siepmann, J. I.; Sholl, D. S.; Snurr, R. Q. Advances, updates, and analytics for the computation-ready, experimental metal–organic framework database: CoRE MOF 2019. J. Chem. Eng. Data 2019, 64, 5985– 5998, DOI: 10.1021/acs.jced.9b00835Google Scholar85https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitVOmtrrL&md5=51670c93eb8cb43309395afaaf620253Advances, Updates, and Analytics for the Computation-Ready, Experimental Metal-Organic Framework Database: CoRE MOF 2019Chung, Yongchul G.; Haldoupis, Emmanuel; Bucior, Benjamin J.; Haranczyk, Maciej; Lee, Seulchan; Zhang, Hongda; Vogiatzis, Konstantinos D.; Milisavljevic, Marija; Ling, Sanliang; Camp, Jeffrey S.; Slater, Ben; Siepmann, J. Ilja; Sholl, David S.; Snurr, Randall Q.Journal of Chemical & Engineering Data (2019), 64 (12), 5985-5998CODEN: JCEAAX; ISSN:0021-9568. (American Chemical Society)Over 14 000 porous, three-dimensional metal-org. framework structures are compiled and analyzed as a part of an update to the Computation-Ready, Exptl. Metal-Org. Framework Database (CoRE MOF Database). The updated database includes addnl. structures that were contributed by CoRE MOF users, obtained from updates of the Cambridge Structural Database and a Web of Science search, and derived through semiautomated reconstruction of disordered structures using a topol.-based crystal generator. In addn., value is added to the CoRE MOF database through new analyses that can speed up future nanoporous materials discovery activities, including open metal site detection and duplicate searches. Crystal structures (only for the subset that underwent significant changes during curation), pore analytics, and phys. property data are included with the publicly available CoRE MOF 2019 database.
- 86Te Velde, G. t.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; van Gisbergen, S. J.; Snijders, J. G.; Ziegler, T. Chemistry with ADF. J. Comput. Chem. 2001, 22, 931– 967, DOI: 10.1002/jcc.1056Google Scholar86https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjtlGntrw%253D&md5=314e7e942de9b28e664afc5adb2f574fChemistry with ADFTe Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T.Journal of Computational Chemistry (2001), 22 (9), 931-967CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)A review with 241 refs. We present the theor. and tech. foundations of the Amsterdam D. Functional (ADF) program with a survey of the characteristics of the code (numerical integration, d. fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chem. shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, at. VDD charges). In the Applications section we discuss the phys. model of the electronic structure and the chem. bond, i.e., the Kohn-Sham MO (MO) theory, and illustrate the power of the Kohn-Sham MO model in conjunction with the ADF-typical fragment approach to quant. understand and predict chem. phenomena. We review the "Activation-strain TS interaction" (ATS) model of chem. reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in org. chem. or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochem. (structure and bonding of DNA) and of time-dependent d. functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the anal. of chem. phenomena.
- 87Rappé, A. K.; Casewit, C. J.; Colwell, K.; Goddard, W. A., III; Skiff, W. M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024– 10035, DOI: 10.1021/ja00051a040Google Scholar87https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38Xmtl2qur8%253D&md5=cf41e8bb9ad299fd5d79f070d690afe1UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulationsRappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M.Journal of the American Chemical Society (1992), 114 (25), 10024-35CODEN: JACSAT; ISSN:0002-7863.A new mol. mechanics force field, the Universal force field (UFF), is described wherein the force field parameters are estd. using general rules based only on the element, its hybridization and its connectivity. The force field functional forms, parameters, and generating formulas for the full periodic table are presented.
- 88Albalad, J.; Carné-Sánchez, A.; Grancha, T.; Hernández-López, L.; Maspoch, D. Protection strategies for directionally-controlled synthesis of previously inaccessible metal–organic polyhedra (MOPs): the cases of carboxylate-and amino-functionalised Rh (ii)-MOPs. Chem. Commun. 2019, 55, 12785– 12788, DOI: 10.1039/C9CC07083DGoogle Scholar88https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvV2ms7fI&md5=10a527781a41f305bb5447fd7c6470c7Protection strategies for directionally-controlled synthesis of previously inaccessible metal-organic polyhedra (MOPs): the cases of carboxylate- and amino-functionalised Rh(II)-MOPsAlbalad, Jorge; Carne-Sanchez, Arnau; Grancha, Thais; Hernandez-Lopez, Laura; Maspoch, DanielChemical Communications (Cambridge, United Kingdom) (2019), 55 (85), 12785-12788CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Herein the authors report that strategic use of protecting groups in coordination reactions enables directional inhibition that gives highly functionalized metal-org. polyhedra (MOPs), rather than of the extended coordination networks. Using this approach, the authors functionalized two new porous cuboctahedral Rh(II) benzenedicarboxylate-based MOPs with 24 peripheral carboxylic acid groups or 24 peripheral amino groups.
- 89Zhang, Z.; Wojtas, L.; Zaworotko, M. J. Organic–inorganic hybrid polyhedra that can serve as supermolecular building blocks. Chem. Sci. 2014, 5, 927– 931, DOI: 10.1039/C3SC53099JGoogle Scholar89https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1Oru7g%253D&md5=45d48f2b26bf68b42bf2157802a37872Organic-inorganic hybrid polyhedra that can serve as supermolecular building blocksZhang, Zhenjie; Wojtas, Lukasz; Zaworotko, Michael J.Chemical Science (2014), 5 (3), 927-931CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)[V4O8X(COO)4]z- or [V5O9X(COO)4]2- polyoxometalate anions can function as 4-connected nodes that assemble with 3-connected org. nodes (1,3,5-benzentricarboxylate) to afford small cubicuboctahedral hybrid nanoballs (hyball-3, -4, -5) in high yield. The resulting polyhedral cages exhibit 550 Å3 internal vols. and gas sorption measurements reveal that solid forms of the hyballs are permanently porous. The exterior surfaces of the hyballs are suited for further self-assembly and hyball-3 can serve as an octahedral supermol. building block for the generation of primitive cubic (pcu) nets via two types of linkage: H bonds or coordination bonds.
- 90Gan, H.; Xu, N.; Qin, C.; Sun, C.; Wang, X.; Su, Z. Equi–size nesting of Platonic and Archimedean metal–organic polyhedra into a twin capsid. Nat. Commun. 2020, 11, 1– 8, DOI: 10.1038/s41467-020-17989-6Google ScholarThere is no corresponding record for this reference.
- 91Simms, C.; Kondinski, A.; Parac-Vogt, T. N. Metal-Addenda Substitution in Plenary Polyoxometalates and in Their Modular Transition Metal Analogues. Eur. J. Inorg. Chem. 2020, 2020, 2559– 2572, DOI: 10.1002/ejic.202000254Google Scholar91https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVSgsbfE&md5=666fe63addf20d55c3ca0a2c898d7738Metal-Addenda Substitution in Plenary Polyoxometalates and in their Modular Transition Metal AnaloguesSimms, Charlotte; Kondinski, Aleksandar; Parac-Vogt, Tatjana N.European Journal of Inorganic Chemistry (2020), 2020 (27), 2559-2572CODEN: EJICFO; ISSN:1434-1948. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. For decades, the formal metal addenda substitution in the matrix of bulk metal oxides has been a prolific strategy to develop numerous (non-)stoichiometric all-inorg. compds. with tunable electronic and magnetic properties, and broad technol. applications. In contrast to bulk mixed-metal oxides, the formal metal-addenda substitution in their mol. equiv. typically leads to stoichiometrically precise mixed-metal cluster formulations which retain the overall structural topol. of the monometallic archetype, but exhibit pronounced differences in terms of reactivity and spectroscopic properties. These mixed-metal mol. metal oxides often show complex configurational isomerism that has been the subject of many exptl. and theor. studies. The mixed-addenda metal-oxo clusters are most prominent among the classical plenary (that contain no vacant metal sites) polyoxometalate (POMs) archetypes, which have emerging applications in homogeneous catalysis and material science (e.g. formation of open frameworks), and have also been explored in heterogeneous metal org. framework (MOF) catalysts. Therefore, this article provides comprehensive theor. and exptl. insights into the isomer problem of mixed-addenda mol. metal oxides and their applications.
- 92Kondinski, A.; Rasmussen, M.; Mangelsen, S.; Pienack, N.; Simjanoski, V.; Nather, C.; Stares, D. L.; Schalley, C. A.; Bensch, W. Composition-driven Archetype Dynamics in Polyoxovanadates. Chem. Sci. 2022, 13, 6397, DOI: 10.1039/D2SC01004FGoogle Scholar92https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xht1yks7fI&md5=6757382fdcf1819e8e5003c89c1c52eeComposition-driven archetype dynamics in polyoxovanadatesKondinski, Aleksandar; Rasmussen, Maren; Mangelsen, Sebastian; Pienack, Nicole; Simjanoski, Viktor; Nather, Christian; Stares, Daniel L.; Schalley, Christoph A.; Bensch, WolfgangChemical Science (2022), 13 (21), 6397-6412CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Mol. metal oxides often adopt common structural frameworks (i.e. archetypes), many of them boasting impressive structural robustness and stability. However, the ability to adapt and to undergo transformations between different structural archetypes is a desirable material design feature offering applicability in different environments. Using systems thinking approach that integrates synthetic, anal. and computational techniques, we explore the transformations governing the chem. of polyoxovanadates (POVs) constructed of arsenate and vanadate building units. The water-sol. salt of the low nuclearity polyanion [V6As8O26]4- can be effectively used for the synthesis of the larger spherical (i.e. kegginoidal) mixed-valent [V12As8O40]4- ppt., while the novel [V10As12O40]8- POVs having tubular cyclic structures are another, well sol. product. Surprisingly, in contrast to the common observation that high-nuclearity polyoxometalate (POM) clusters are fragmented to form smaller moieties in soln., the low nuclearity [V6As8O26]4- anion is in situ transformed into the higher nuclearity cluster anions. The obtained products support a conceptually new model that is outlined in this article and that describes a continuous evolution between spherical and cyclic POV assemblies. This new model represents a milestone on the way to rational and designable POV self-assemblies.
- 93Segler, M. H.; Waller, M. P. Modelling chemical reasoning to predict and invent reactions. Chem. Eur. J. 2017, 23, 6118– 6128, DOI: 10.1002/chem.201604556Google Scholar93https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXislersw%253D%253D&md5=ac3b304ec62b8d90110b7722305e2b3dModelling Chemical Reasoning to Predict and Invent ReactionsSegler, Marwin H. S.; Waller, Mark P.Chemistry - A European Journal (2017), 23 (25), 6118-6128CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)The ability to reason beyond established knowledge allows org. chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chem. reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph contg. 14.4 million mols. and 8.2 million binary reactions, which represents the bulk of all chem. reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalyzed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery.
- 94Mellot-Draznieks, C.; Dutour, J.; Férey, G. Hybrid organic–inorganic frameworks: routes for computational design and structure prediction. Angew. Chem., Int. Ed. 2004, 116, 6450– 6456, DOI: 10.1002/ange.200454251Google ScholarThere is no corresponding record for this reference.
- 95Addicoat, M. A.; Coupry, D. E.; Heine, T. AuToGraFS: automatic topological generator for framework structures. J. Phys. Chem. A 2014, 118, 9607– 9614, DOI: 10.1021/jp507643vGoogle Scholar95https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsFamsL%252FF&md5=4e07c2795b0f7e6d386c3ad5bc3ce488AuToGraFS: Automatic Topological Generator for Framework StructuresAddicoat, Matthew A.; Coupry, Damien E.; Heine, ThomasJournal of Physical Chemistry A (2014), 118 (40), 9607-9614CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Metal-org. frameworks (MOFs) and covalent org. frameworks (COFs) are recently notable examples of highly porous polymer frameworks with a raft of potential applications. Synthesis of these compds. is modular, with "connectors" and "linkers" able to be replaced almost at will in the fabrication of isoreticular frameworks (frameworks with the same underlying topol.). The range of components available to form such framework structures is vast, leading to a "combinatorial explosion" problem in predicting which framework compds. might have a set of desired properties. Computational investigations can be used in both predictive and explanatory roles in this research but rely on accurate structural models. In this work, we present our software, AuToGraFS, Automated Topol. Generator for Framework Structures, and show some of its advanced functionality in "computational reticular chem.". AuToGraFS is linked to a fully featured force field to produce fully optimized structures of arbitrary frameworks. AuToGraFS, including a graphical user interface, is publicly available for download.
- 96Wahiduzzaman, M.; Wang, S.; Sikora, B. J.; Serre, C.; Maurin, G. Computational structure determination of novel metal–organic frameworks. Chem. Commun. 2018, 54, 10812– 10815, DOI: 10.1039/C8CC05455JGoogle Scholar96https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsVWhtb7E&md5=8bcdaca8037f3538971461e64c18b109Computational structure determination of novel metal-organic frameworksWahiduzzaman, Mohammad; Wang, Sujing; Sikora, Benjamin J.; Serre, Christian; Maurin, GuillaumeChemical Communications (Cambridge, United Kingdom) (2018), 54 (77), 10812-10815CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A structure prediction tool has been developed to guide the discovery of MOF materials. This computational strategy has been trained over a series of existing MOFs and further successfully applied in tandem with an exptl. effort to produce novel Zr MOFs based on naturally occurring carboxylic acids.
- 97Turcani, L.; Tarzia, A.; Szczypiński, F. T.; Jelfs, K. E. stk: An extendable Python framework for automated molecular and supramolecular structure assembly and discovery. J. Chem. Phys. 2021, 154, 214102, DOI: 10.1063/5.0049708Google Scholar97https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXht1aqu73N&md5=f4de0edc1440cc685fe00b03571be80fstk: An extendable Python framework for automated molecular and supramolecular structure assembly and discoveryTurcani, Lukas; Tarzia, Andrew; Szczypinski, Filip T.; Jelfs, Kim E.Journal of Chemical Physics (2021), 154 (21), 214102CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Computational software workflows are emerging as all-in-one solns. to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, mol. and supramol. materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramol. toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)mol. structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-contg. structures and rotaxanes as well as general implementation and interface improvements. Addnl., this version includes built-in tools for exploring chem. space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk. (c) 2021 American Institute of Physics.
- 98Young, T. A.; Gheorghe, R.; Duarte, F. cgbind: A Python Module and Web App for Automated Metallocage Construction and Host–Guest Characterization. J. Chem. Inf. Model. 2020, 60, 3546– 3557, DOI: 10.1021/acs.jcim.0c00519Google Scholar98https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXht1CltLjN&md5=ce1a2502ad771f176d1caad1df1eee28cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest CharacterizationYoung, Tom A.; Gheorghe, Razvan; Duarte, FernandaJournal of Chemical Information and Modeling (2020), 60 (7), 3546-3557CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)Metallocages offer a diverse and underexplored region of chem. space in which to search for novel catalysts and substrate hosts. However, the ability to tailor such structures toward applications in binding and catalysis is a challenging task. Here, we present an open-source computational toolkit, cgbind, that facilitates the construction, characterization, and prediction of functional metallocages. It employs known structural scaffolds as starting points and computationally efficient approaches for property evaluation. We demonstrate the ability of cgbind to construct libraries of cages with varied topologies and linker functionalities, generate accurate geometries (RMSD < 1.5 Å to crystal structures), and predict substrate binding with accuracy on par with semiempirical QM, all in seconds. The cgbind code presented here is freely available at github.com/duartegroup/cgbind and also via a web-based graphical user interface at cgbind.chem.ox.ac.uk. The protocol described here paves the way for high-throughput virtual screening of potential supramol. structures, accelerating the search for new hosts and catalysts.
- 99Zhou, X.; Nurkowski, D.; Mosbach, S.; Akroyd, J.; Kraft, M. Question answering system for chemistry. J. Chem. Inf. Model. 2021, 61, 3868– 3880, DOI: 10.1021/acs.jcim.1c00275Google Scholar99https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1Kru7vJ&md5=7984547eaed72640f808bbf30ba9b749Question Answering System for ChemistryZhou, Xiaochi; Nurkowski, Daniel; Mosbach, Sebastian; Akroyd, Jethro; Kraft, MarkusJournal of Chemical Information and Modeling (2021), 61 (8), 3868-3880CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)This paper describes the implementation and evaluation of a proof-of-concept Question Answering (QA) system for accessing chem. data from knowledge graphs (KGs) which offer data from chem. kinetics to the chem. and phys. properties of species. We trained the question classification and named the entity recognition models that specialize in interpreting chem. questions. The system has a novel design which applies a topic model to identify the question-to-ontol. affiliation to handle ontologies with different structures. The topic model also helps the system to provide answers with a higher quality. Moreover, a new method that automatically generates training questions from ontologies is also implemented. The question set generated for training contains 432,989 questions under 11 types. Such a training set has been proven to be effective for training both the question classification model and the named entity recognition model. We evaluated the system using other KGQA systems as baselines. The system outperforms the chosen KGQA system answering chem.-related questions. The QA system is also compared to the Google search engine and the WolframAlpha engine. It shows that the QA system can answer certain types of questions better than the search engines.
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- 2Drexler, K. E. Molecular engineering: An approach to the development of general capabilities for molecular manipulation. Proc. Natl. Acad. Sci. U.S.A 1981, 78, 5275– 5278, DOI: 10.1073/pnas.78.9.52752https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL3MXmtFKnsLw%253D&md5=7446965e92130b007b703bfc953bc418Molecular engineering: An approach to the development of general capabilities for molecular manipulationDrexler, K. EricProceedings of the National Academy of Sciences of the United States of America (1981), 78 (9), 5275-8CODEN: PNASA6; ISSN:0027-8424.A review with 17 refs., on the development of the ability to design protein mols. with ref. to org. chem. and genetic engineering procedures.
- 3Whitesides, G. M.; Mathias, J. P.; Seto, C. T. Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures. Science 1991, 254, 1312– 1319, DOI: 10.1126/science.19621913https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38XktVGntA%253D%253D&md5=29bdb8706dafad3a83eba7a3c7266448Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructuresWhitesides, George M.; Mathias, John P.; Seto, Christopher T.Science (Washington, DC, United States) (1991), 254 (5036), 1312-19CODEN: SCIEAS; ISSN:0036-8075.A review with 68 refs.
- 4Balzani, V.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Artificial molecular machines. Angew. Chem., Int. Ed. 2000, 39, 3348– 3391, DOI: 10.1002/1521-3773(20001002)39:19<3348::AID-ANIE3348>3.0.CO;2-X4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXpslGgug%253D%253D&md5=a320e773ae60305a52d0f42784273046Artificial molecular machinesBalzani, Vincenzo; Credi, Alberto; Raymo, Francisco M.; Stoddart, J. FraserAngewandte Chemie, International Edition (2000), 39 (19), 3348-3391CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH)A review with 208 refs. The miniaturization of components used in the construction of working devices is being pursued currently by the large-downward (Top-down) fabrication. This approach, however, which obliges solid-state physicists and electronic engineers to manipulate progressively smaller and smaller pieces of matter, has its intrinsic limitations. An alternative approach is a small-upward (bottom-up) one, starting from the smallest compns. of matter that have distinct shapes and unique properties - namely mols. In the context of this particular challenge, chemists have been extending the concept of a macroscopic machine to the mol. level. A mol.-level machine can be defined as an assembly of a distinct no. of mol. components that are designed to perform machinelike movements (output) as a result of an appropriate external stimulation (input). In common with their macroscopic counterparts, a mol. machine is characterized by (1) the kind of energy input supplied to make it work, (2) the nature of the movements of its component parts, (3) the way in which its operation can be monitored and controlled, (4) the ability to make it repeat its operation in a cyclic fashion, (5) the timescale needed to complete a full cycle of movements and (6) the purpose of its operation. Undoubtedly, the best energy inputs to make mol. machines work are photons or electrons. Indeed, with appropriately chosen photochem. and electrochem. driven reactions, it is possible to design and synthesize mol. machines that do work. Moreover, the dramatic increase in our fundamental understanding of self-assembly and self-organizational processes in chem. synthesis has aided and abetted the construction of artificial mol. machines through the development of new methods of noncovalent synthesis and the emergence of supramol. assistance to covalent synthesis as a uniquely powerful synthetic tool. The aim of this review is to present a unified view of the field of mol. machines by focusing on past achievements, present limitations, and future perspectives. After analyzing a few important examples of natural mol. machines, the most significant developments in the field of artificial mol. machines are highlighted. The systems reviewed include (1) chem. rotors, (2) photochem. and electrochem. induced mol. (conformational) rearrangements, and (3) chem., photochem., and electrochem. controllable (co-conformational) motions in interlocked mols. (catenanes and rotaxanes) as well as in coordination and supramol. complexes, including pseudorotaxanes. Artificial mol. machines based on biomols. and interfacing artificial mol. machines with surfaces and solid supports are among some of the cutting-edge topics featured in this review. The extension of the concept of a machine to the mol. level is of interest not only for the sake of basic research, but also for the growth of nanoscience and the subsequent development of nanotechnol.
- 5Kido, J.; Kimura, M.; Nagai, K. Multilayer white light-emitting organic electroluminescent device. Science 1995, 267, 1332– 1334, DOI: 10.1126/science.267.5202.13325https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK2MXktF2itr0%253D&md5=72b10005dd42a8e78979f1e40aee4522Multilayer white light-emitting organic electroluminescent deviceKido, Junji; Kimura, Masato; Nagai, KatsutoshiScience (Washington, D. C.) (1995), 267 (5202), 1332-4CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)Org. electroluminescent devices are light-emitting diodes in which the active materials consist entirely of org. materials. Here, the fabrication of a white light-emitting org. electroluminescent device made from vacuum-deposited org. thin films in reported. In this device, three emitter layers with different carrier transport properties, each emitting blue, green, or red light, are used to generate white light. Bright white light, over 2000 candelas per square meter, nearly as bright as a fluorescent lamp, was successfully obtained at low drive voltages such as 15 to 16 V. The applications of such a device include paper-thin sources, which are particularly useful for places that require lightweight illumination devices, such as in aircraft and space shuttles. Other uses are a backlight for liq. crystal display as well as full color displays, achieved by combining the emitters with micropatterned color filters.
- 6Kim, S.; Lee, J. K.; Kang, S. O.; Ko, J.; Yum, J.-H.; Fantacci, S.; De Angelis, F.; Di Censo, D.; Nazeeruddin, M. K.; Grätzel, M. Molecular engineering of organic sensitizers for solar cell applications. J. Am. Chem. Soc. 2006, 128, 16701– 16707, DOI: 10.1021/ja066376f6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28Xht1yrtrjL&md5=693077d2a2d12b6bfb07e0e60a9c51f6Molecular Engineering of Organic Sensitizers for Solar Cell ApplicationsKim, Sanghoon; Lee, Jae Kwan; Kang, Sang Ook; Ko, Jaejung; Yum, J.-H.; Fantacci, Simona; De Angelis, Filippo; Di Censo, D.; Nazeeruddin, Md. K.; Graetzel, MichaelJournal of the American Chemical Society (2006), 128 (51), 16701-16707CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Novel org. sensitizers comprising donor, electron-conducting, and anchoring groups were engineered at mol. level and synthesized. The functionalized unsym. org. sensitizers 3-{5-[N,N-bis(9,9-dimethylfluorene-2-yl)aminophenyl]-thiophene-2-yl}-2-cyano-acrylic acid (JK-1) and 3-{5'-[N,N-bis(9,9-dimethylfluorene-2-yl)aminophenyl]-2,2'-bisthiophene-5-yl}-2-cyano-acrylic acid (JK-2), upon anchoring onto TiO2 film, exhibit unprecedented incident photon to current conversion efficiency of 91%. The photovoltaic data using an electrolyte having compn. of 0.6M M-methyl-N-Bu imidazolium iodide, 0.04M iodine, 0.025M LiI, 0.05M guanidinium thiocyanate, and 0.28M tert-butylpyridine in a 15/85 (vol./vol.) mixt. of valeronitrile and acetonitrile revealed a short circuit photocurrent d. of 14.0 ± 0.2 mA/cm2, an open circuit voltage of 753 ± 10 mV, and a fill factor of 0.76 ± 0.02, corresponding to an overall conversion efficiency of 8.01% under std. AM 1.5 sunlight. DFT/TDDFT calcns. were performed on the two org. sensitizers to gain insight into their structural, electronic, and optical properties. The cyanoacrylic acid groups are essentially coplanar with respect to the thiophene units, reflecting the strong conjugation across the thiophene-cyanoacrylic groups. MOs anal. confirmed the exptl. assignment of redox potentials, while TDDFT calcns. allowed assignment of the visible absorption bands.
- 7Steed, J. W.; Atwood, J. L. Supramolecular Chemistry; John Wiley & Sons, 2022.There is no corresponding record for this reference.
- 8Lehn, J.-M. Supramolecular chemistry. Science 1993, 260, 1762– 1764, DOI: 10.1126/science.85115828https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK3sXlsFCjt7g%253D&md5=dbfe1c6c9ab190cb3fb1b4dba0ebff12Supramolecular chemistryLehn, Jean MarieScience (Washington, DC, United States) (1993), 260 (5115), 1762-3CODEN: SCIEAS; ISSN:0036-8075.A review with 11 refs. Recognition, reactivity and transport are basic functional features in supramol. species.
- 9Anyushin, A. V.; Kondinski, A.; Parac-Vogt, T. N. Hybrid polyoxometalates as post-functionalization platforms: from fundamentals to emerging applications. Chem. Soc. Rev. 2020, 49, 382– 432, DOI: 10.1039/C8CS00854J9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1OrsbvF&md5=686af031f63606d42c230a45a9b8a68aHybrid polyoxometalates as post-functionalization platforms: from fundamentals to emerging applicationsAnyushin, Alexander V.; Kondinski, Aleksandar; Parac-Vogt, Tatjana N.Chemical Society Reviews (2020), 49 (2), 382-432CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)Polyoxometalates (POMs) represent an important group of metal-oxo nanoclusters, typically comprised of early transition metals in high oxidn. states (mainly V, Mo and W). Many plenary POMs exhibit good pH, solvent, thermal and redox stability, which makes them attractive components for the design of covalently integrated hybrid org.-inorg. mols., herein referred to as hybrid-POMs. Until now, thousands of org. hybrid-POMs have been reported; however, only a small fraction can be further functionalized using other org. mols. or metal cations. This emerging class of 'post-functionalizable' hybrid-POMs constitute a valuable modular platform that permits coupling of POM properties with different org. and metal cation functionalities, thereby expanding the key physicochem. properties that are relevant for application in (photo)catalysis, bioinorg. chem. and materials science. The post-functionalizable hybrid-POM platforms offer an opportunity to covalently link multi-electron redox responsive POM cores with virtually any (bio)org. mol. or metal cation, generating a wide range of materials with tailored properties. Over the past few years, these materials have been showcased in the prepn. of framework materials, functional surfaces, surfactants, homogeneous and heterogeneous catalysts and light harvesting materials, among others. This review article provides an overview on the state of the art in POM post-functionalization and highlights the key design and structural features that permit the discovery of new hybrid-POM platforms. In doing so, we aim to make the subject more comprehensible, both for chemists and for scientists with different materials science backgrounds interested in the applications of hybrid (POM) materials. The review article goes beyond the realms of polyoxometalate chem. and encompasses emerging research domains such as reticular materials, surfactants, surface functionalization, light harvesting materials, non-linear optics, charge storing materials, and homogeneous acid-base catalysis among others.
- 10Kondinski, A. Metal–metal bonds in polyoxometalate chemistry. Nanoscale 2021, 13, 13574– 13592, DOI: 10.1039/D1NR02357H10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhsV2qtbbO&md5=ac37dbbae1da5abe7d835fe85346ec4fMetal-metal bonds in polyoxometalate chemistryKondinski, AleksandarNanoscale (2021), 13 (32), 13574-13592CODEN: NANOHL; ISSN:2040-3372. (Royal Society of Chemistry)Half a century ago, F. Albert Cotton emphasized the relevance of metal-metal bonding in the constitution of cluster materials. Based on his description, nanoscale polyoxometalates (POMs) normally would not be regarded as cluster materials. One reason is that metal-metal bonding is typically assocd. with inorg. systems featuring metal centers in low oxidn. states, a feature that is not common for POMs. However, over the past decades, there have been increasing reports on POMs integrating different types of metal-metal bonding. This article conceptualises and reviews the area of metal-metal bonded POMs, and their prepn. and physicochem. properties. Attention is given to the changes in the electronic structure of POMs, the emergence of covalent dynamics and its impact on the development of applications in catalysis, nanoswitches, donor-acceptor systems, electron storage materials and nanoelectronics (i.e., "POMtronics").
- 11Tranchemontagne, D. J.; Ni, Z.; O’Keeffe, M.; Yaghi, O. M. Reticular chemistry of metal–organic polyhedra. Angew. Chem., Int. Ed. 2008, 47, 5136– 5147, DOI: 10.1002/anie.20070500811https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXos1Gkurs%253D&md5=40306252f38fbf10274de523547dc44fReticular chemistry of metal-organic polyhedraTranchemontagne, David J.; Ni, Zheng; O'Keeffe, Michael; Yaghi, Omar M.Angewandte Chemie, International Edition (2008), 47 (28), 5136-5147CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. Metal-org. polyhedra (MOPs), are discrete metal-org. mol. assemblies. They are useful as host mols. that can provide tailorable internal vol. in terms of metrics, functionality, and active metal sites. As a result, these materials are potentially useful for a variety of applications such as highly selective guest inclusion and gas storage, and as nanoscale reaction vessels. This review identifies the nine most important polyhedra, and describes the design principles for the five polyhedra most likely to result from the assembly of secondary building units, and provides examples of these shapes that are known as metal-org. crystals.
- 12Lee, S.; Jeong, H.; Nam, D.; Lah, M. S.; Choe, W. The rise of metal–organic polyhedra. Chem. Soc. Rev. 2021, 50, 528– 555, DOI: 10.1039/D0CS00443J12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXit1Onur3M&md5=df68be70e6a64dcd8db4623342fcaa3dThe rise of metal-organic polyhedraLee, Soochan; Jeong, Hyein; Nam, Dongsik; Lah, Myoung Soo; Choe, WonyoungChemical Society Reviews (2021), 50 (1), 528-555CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)Metal-org. polyhedra are a member of metal-org. materials, and are together with metal-org. frameworks utilized as emerging porous platforms for numerous applications in energy- and bio-related sciences. However, metal-org. polyhedra have been significantly underexplored, unlike their metal-org. framework counterparts. In this review, we will cover the topologies and the classification of metal-org. polyhedra and share several suggestions, which might be useful to synthetic chemists regarding the future directions in this rapid-growing field.
- 13Gosselin, A. J.; Rowland, C. A.; Bloch, E. D. Permanently microporous metal–organic polyhedra. Chem. Rev. 2020, 120, 8987– 9014, DOI: 10.1021/acs.chemrev.9b0080313https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtFSrt7jN&md5=7077c68de8dc057eeef76e3ce4b45860Permanently Microporous Metal-Organic PolyhedraGosselin, Aeri J.; Rowland, Casey A.; Bloch, Eric D.Chemical Reviews (Washington, DC, United States) (2020), 120 (16), 8987-9014CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)A review. As compared to porous network solids, including metal-org. frameworks, covalent-org. frameworks, porous arom. frameworks, and zeolites, porous mol. materials are relatively unexplored. Addnl., within porous mol. space, porous org. cages (POCs) have been the most widely reported over the past decade. Relatively recently, however, porous hybrid metal-org. mol. complexes have received considerable attention with a large fraction of surface areas for these coordination cages reported over the past three years. This review focuses on advances in this area. We highlight the recent work with permanently microporous metal-org. polyhedra (MOPs). Analogous to early work in the area of MOFs, the vast majority of MOPs for which surface areas have been reported have been based on paddlewheel building units and carboxylate ligands. We describe the synthesis of porous cages and highlight those based on monometallic, bimetallic, trimetallic, tetrametallic, and higher nuclearity clusters. Finally, we showcase work wherein the porosity of MOPs has been leveraged for applications related to the storage and sepn. of small mols. and the incorporation of these porous and potentially porous cages into membranes.
- 14Long, J. R.; Yaghi, O. M. The pervasive chemistry of metal–organic frameworks. Chem. Soc. Rev. 2009, 38, 1213– 1214, DOI: 10.1039/b903811f14https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvValsrw%253D&md5=6764928147334cafac2213ad3d66e382The pervasive chemistry of metal-organic frameworksLong, Jeffrey R.; Yaghi, Omar M.Chemical Society Reviews (2009), 38 (5), 1213-1214CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)There is no expanded citation for this reference.
- 15Li, H.; Eddaoudi, M.; O’Keeffe, M.; Yaghi, O. M. Design and synthesis of an exceptionally stable and highly porous metal-organic framework. Nature 1999, 402, 276– 279, DOI: 10.1038/4624815https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1MXnvFSiuro%253D&md5=68f27e20a7e4e15ea2c2f49a2a61e98aDesign and synthesis of an exceptionally stable and highly porous metal-organic frameworkLi, Hailian; Eddaoudi, Mohamed; O'Keeffe, M.; Yaghi, M.Nature (London) (1999), 402 (6759), 276-279CODEN: NATUAS; ISSN:0028-0836. (Macmillan Magazines)Open metal-org. frameworks are widely regarded as promising materials for applications in catalysis, sepn., gas storage and mol. recognition. Compared to conventionally used microporous inorg. materials such as zeolites, these org. structures have the potential for more flexible rational design, through control of the architecture and functionalization of the pores. So far, the inability of these open frameworks to support permanent porosity and to avoid collapsing in the absence of guest mols., such as solvents, has hindered further progress in the field. The authors report the synthesis of a metal-org. framework, Zn4O(BDC)3.(DMF)8.(PhCl) (named MOF-5, where BDC = 1,4-benzenedicarboxylate), which remains cryst., as evidenced by x-ray single-crystal analyses, and stable when fully desolvated and when heated up to 300°. This synthesis is achieved by borrowing ideas from metal carboxylate cluster chem., where an org. dicarboxylate linker was used in a reaction that gives supertetrahedron clusters when capped with monocarboxylates. The rigid and divergent character of the added linker allows the articulation of the clusters into a three-dimensional framework resulting in a structure with higher apparent surface area and pore vol. than most porous cryst. zeolites. This simple and potentially universal design strategy is currently being pursued in the synthesis of new phases and composites, and for gas-storage applications.
- 16Vardhan, H.; Yusubov, M.; Verpoort, F. Self-assembled metal–organic polyhedra: An overview of various applications. Coord. Chem. Rev. 2016, 306, 171– 194, DOI: 10.1016/j.ccr.2015.05.01616https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1Onu7vL&md5=5dfe403e624b2797e829f81ca8cfa3b4Self-assembled metal-organic polyhedra: An overview of various applicationsVardhan, Harsh; Yusubov, Mekhman; Verpoort, FrancisCoordination Chemistry Reviews (2016), 306 (Part_1), 171-194CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)A review. Self-assembly is a potent synthetic tool that allowed chemists to design numerous complex structures, supramols. of various shapes from relatively simple starting materials. Metal-org. polyhedra are a rising and promising member of the self-assembled supramol. family possessing fascinating structures and functionalities directly deriving from the precursor units. During the last two decades, research in this field was briskly progressed and it is now objective to exemplify various applications such as biomedical, catalysis, mol. sensing, gas adsorption and sepn., and synthesis of metal-org. frameworks from polyhedra. This review will be focus on each and every application with various unprecedented examples and highlight few challenges still need to be address.
- 17Guillerm, V.; Kim, D.; Eubank, J. F.; Luebke, R.; Liu, X.; Adil, K.; Lah, M. S.; Eddaoudi, M. A supermolecular building approach for the design and construction of metal–organic frameworks. Chem. Soc. Rev. 2014, 43, 6141– 6172, DOI: 10.1039/C4CS00135D17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtFehsbvO&md5=97bf12cb969bfc7f409f5f06facd593bA supermolecular building approach for the design and construction of metal-organic frameworksGuillerm, Vincent; Kim, Dongwook; Eubank, Jarrod F.; Luebke, Ryan; Liu, Xinfang; Adil, Karim; Lah, Myoung Soo; Eddaoudi, MohamedChemical Society Reviews (2014), 43 (16), 6141-6172CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. In this review, the authors describe two recently implemented conceptual approaches facilitating the design and deliberate construction of metal-org. frameworks (MOFs), supermol. building block (SBB) and supermol. building layer (SBL) approaches. The authors' main objective is to offer an appropriate means to assist/aid chemists and material designers alike to rationally construct desired functional MOF materials, made-to-order MOFs. The authors introduce the concept of net-coded building units (net-cBUs), where precise embedded geometrical information codes uniquely and matchlessly a selected net, as a compelling route for the rational design of MOFs. This concept is based on employing pre-selected 0-periodic metal-org. polyhedra or 2-periodic metal-org. layers, SBBs or SBLs, resp., as a pathway to access the requisite net-cBUs. In this review, inspired by the authors' success with the original rht-MOF, the authors extrapolated the authors' strategy to other known MOFs via their deconstruction into more elaborate building units (polyhedra or layers) to (i) elucidate the unique relation between edge-transitive polyhedra or layers and minimal edge-transitive 3-periodic nets, and (ii) illustrate the potential of the SBB and SBL approaches as a rational pathway for the design and construction of 3-periodic MOFs. Using this design strategy, the authors have also identified several new hypothetical MOFs which are synthetically targetable.
- 18Mallick, A.; Garai, B.; Díaz, D. D.; Banerjee, R. Hydrolytic conversion of a metal–organic polyhedron into a metal–organic framework. Angew. Chem., Int. Ed. 2013, 52, 13755– 13759, DOI: 10.1002/anie.20130748618https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhslCqs73K&md5=2c2cd9ec27001bbbd003c18cde5cb80fHydrolytic Conversion of a Metal-Organic Polyhedron into a Metal-Organic FrameworkMallick, Arijit; Garai, Bikash; Diaz, David Diaz; Banerjee, RahulAngewandte Chemie, International Edition (2013), 52 (51), 13755-13759CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A metal-org. polyhedron (MOP), [Cu24L24(H2O)24] [H2L = 5-(propynyloxy)isophthalic acid] was prepd. and structurally characterized. Heating in water results in transformation of the polyhedron into a metal-org. framework. The release of encapsulated caffeine from the polyhedron can be driven by this transformation.
- 19Perry, I. J. J.; Perman, J. A.; Zaworotko, M. J. Design and synthesis of metal–organic frameworks using metal–organic polyhedra as supermolecular building blocks. Chem. Soc. Rev. 2009, 38, 1400– 1417, DOI: 10.1039/b807086p19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvValsr4%253D&md5=296a7ae534acdc37203ce097b2013d18Design and synthesis of metal-organic frameworks using metal-organic polyhedra as supermolecular building blocksPerry, John J., IV; Perman, Jason A.; Zaworotko, Michael J.Chemical Society Reviews (2009), 38 (5), 1400-1417CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)This crit. review highlights supermol. building blocks (SBBs) in the context of their impact upon the design, synthesis, and structure of metal-org. materials (MOMs). MOMs, also known as coordination polymers, hybrid inorg.-org. materials, and metal-org. frameworks, represent an emerging class of materials that have attracted the imagination of solid-state chemists because MOMs combine unprecedented levels of porosity with a range of other functional properties that occur through the metal moiety and/or the org. ligand. First generation MOMs exploited the geometry of metal ions or secondary building units (SBUs), small metal clusters that mimic polygons, for the generation of MOMs. In this crit. review we examine the recent (<5 years) adoption of much larger scale metal-org. polyhedra (MOPs) as SBBs for the construction of MOMs by highlighting how the large size and high symmetry of such SBBs can afford improved control over the topol. of the resulting MOM and a new level of scale to the resulting framework (204 refs.).
- 20Pilgrim, B.; Champness, N. R. Metal-Organic Frameworks and Metal-Organic Cages–A Perspective. ChemPlusChem. 2020, 85, 1842– 1856, DOI: 10.1002/cplu.20200040820https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhslWqurnE&md5=fc03763d1c4b87c0e8ade9914ab64362Metal-Organic Frameworks and Metal-Organic Cages - A PerspectivePilgrim, Ben S.; Champness, Neil R.ChemPlusChem (2020), 85 (8), 1842-1856CODEN: CHEMM5; ISSN:2192-6506. (Wiley-VCH Verlag GmbH & Co. KGaA)The fields of metal-org. cages (MOCs) and metal-org. frameworks (MOFs) are both highly topical and continue to develop at a rapid pace. Despite clear synergies between the two fields, overlap is rarely obsd. This article discusses the peculiarities and similarities of MOCs and MOFs in terms of synthetic strategies and approaches to system characterization. The stability of both classes of material is compared, particularly in relation to their applications in guest storage and catalysis. Lastly, suggestions are made for opportunities for each field to learn and develop in partnership with the other.
- 21Li, X.-X.; Zhao, D.; Zheng, S.-T. Recent advances in POM-organic frameworks and POM-organic polyhedra. Coord. Chem. Rev. 2019, 397, 220– 240, DOI: 10.1016/j.ccr.2019.07.00521https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsVWhtbvI&md5=8fbf28181c1b2cc4ac7b0bdb2639bad7Recent advances in POM-organic frameworks and POM-organic polyhedraLi, Xin-Xiong; Zhao, Dan; Zheng, Shou-TianCoordination Chemistry Reviews (2019), 397 (), 220-240CODEN: CCHRAM; ISSN:0010-8545. (Elsevier B.V.)During the past two decades, the search of strategies to introduce polyoxometalate (POM) clusters as secondary building units (SBUs) to construct porous extended POM-org. frameworks (POMOFs) and discrete POM-org. polyhedra (POMOPs) have attracted sustained interests because such materials not only integrate the advantages of both POMs and framework/polyhedra structures, but also exhibit good prospects in photo-/electro-catalysis, sepn., mol. recognition, host-guest chem. and so on. In this review, the recent advancements of POMOFs and POMOPs, including their assembly methodologies, classification and related applications are summarized. Moreover, the current challenges in the design and fabrication of POMOFs and POMOPs as well as the great potential in these two areas are also discussed.
- 22Zhang, D.; Ronson, T. K.; Zou, Y.-Q.; Nitschke, J. R. Metal–organic cages for molecular separations. Nat. Rev. Chem. 2021, 5, 168– 182, DOI: 10.1038/s41570-020-00246-122https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXosFersr0%253D&md5=52aa58c2690363dda8b4b703142f3426Metal-organic cages for molecular separationsZhang, Dawei; Ronson, Tanya K.; Zou, You-Quan; Nitschke, Jonathan R.Nature Reviews Chemistry (2021), 5 (3), 168-182CODEN: NRCAF7; ISSN:2397-3358. (Nature Research)A review. Sepn. technol. is central to industries as diverse as petroleum, pharmaceuticals, mining and life sciences. Metal-org. cages, a class of mol. containers formed via coordination-driven self-assembly, show great promise as sepn. agents. Precise control of the shape, size and functionalization of cage cavities enables them to selectively bind and distinguish a wide scope of physicochem. similar substances in soln. Extensive research has, thus, been performed involving sepns. of high-value targets using coordination cages, ranging from gases and liqs. to compds. dissolved in soln. Enantiopure capsules also show great potential for the sepn. of chiral mols. The use of cryst. cages as absorbents, or the incorporation of cages into polymer membranes, could increase the selectivity and efficiency of sepn. processes. This Review covers recent progress in using metal-org. cages to achieve sepns., with discussion of the many methods of using them in this context. Challenges and potential future developments are also discussed.
- 23Sudik, A. C.; Millward, A. R.; Ockwig, N. W.; Côté, A. P.; Kim, J.; Yaghi, O. M. Design, synthesis, structure, and gas (N2, Ar, CO2, CH4, and H2) sorption properties of porous metal-organic tetrahedral and heterocuboidal polyhedra. J. Am. Chem. Soc. 2005, 127, 7110– 7118, DOI: 10.1021/ja042802q23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXjtl2ntLg%253D&md5=654522c7c7f2351595cea3091c172cb1Design, Synthesis, Structure, and Gas (N2, Ar, CO2, CH4, and H2) Sorption Properties of Porous Metal-Organic Tetrahedral and Heterocuboidal PolyhedraSudik, Andrea C.; Millward, Andrew R.; Ockwig, Nathan W.; Cote, Adrien P.; Kim, Jaheon; Yaghi, Omar M.Journal of the American Chemical Society (2005), 127 (19), 7110-7118CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A strategy based on assembling metal ions and org. carboxylate links was applied for the design and synthesis of a new class of porous, truncated tetrahedral and heterocuboidal polyhedra, whose pore size and functionality can be systematically varied. The synthesis of this series of metal-org. polyhedra (MOPs) employs sulfate-capped O-centered Fe-carboxylate trimers, Fe3O(CO2)3(SO4)3, as rigid nodes sepd. by linear (Ph, biphenyl, terphenyl, and tetrahydropyrene) or trigonal (benzenetriphenyl) links to yield five highly cryst. polyhedra [NH2Me2]8[Fe12O4(SO4)12(link)x(py)12]·G (x = 6 for linear or 4 for trigonal, py = pyridine, G = guests). In this series, the size of each polyhedron was varied from 20.0 to 28.5 Å (on edge), and the corresponding pore diam. from 7.3 to 13.3 Å. Gas sorption isotherms were measured for three members of this series to reveal significant uptake of gases (N2, Ar, CO2, H2, CH4) and benzene and exhibit Type I sorption behavior that is indicative of permanent porosity. The apparent surface areas for these compds. range from 387 to 480 m2/g. Magnetic susceptibility studies indicate antiferromagnetic interactions between iron centers, and long-range coupling between clusters is assumed to be negligible.
- 24Xing, W.-H.; Li, H.-Y.; Dong, X.-Y.; Zang, S.-Q. Robust multifunctional Zr-based metal-organic polyhedra for high proton conductivity and selective CO2 capture. J. Mater. Chem. A 2018, 6, 7724– 7730, DOI: 10.1039/C8TA00858B24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXlslSksbw%253D&md5=92283c1532c6ab5cf84b48ff9e3505caRobust multifunctional Zr-based metal-organic polyhedra for high proton conductivity and selective CO2 captureXing, Wen-Hao; Li, Hai-Yang; Dong, Xi-Yan; Zang, Shuang-QuanJournal of Materials Chemistry A: Materials for Energy and Sustainability (2018), 6 (17), 7724-7730CODEN: JMCAET; ISSN:2050-7496. (Royal Society of Chemistry)New stable Zr-based metal-org. polyhedra (MOPs) have been designed and constructed through the self-assembly of a designed flexible sulfonate-carboxylate ligand, 1,2-bis(sodium-2-sulfonate-4-carboxyphenoxy)ethane (NaH2L), and the secondary building units (SBUs) of Cp3Zr3(μ3-O)(μ2-OH)3, (Cp = η5-C5H5). The MOPs feature candy-like cages and the anionic sulfonic groups on the org. ligand strengthened the stability of the MOPs (thermal stability and acid and alkali resistance) by forming strong multiple charge-assisted hydrogen bonds with the cationic SBUs. The unique cavities of this 3D porous framework endowed the MOPs with highly selective CO2 capture. The 2D H-bond networks obtained by the connection of coordinated water mols. and free water mols. between the discrete MOPs enabled a high proton cond. of 1.41 × 10-3 S cm-1 at 30 °C, 98% relative humidity (RH) and a low activation energy of 0.225 eV for the proton transfer.
- 25Tan, C.; Jiao, J.; Li, Z.; Liu, Y.; Han, X.; Cui, Y. Design and Assembly of a Chiral Metallosalen-Based Octahedral Coordination Cage for Supramolecular Asymmetric Catalysis. Angew. Chem., Int. Ed. 2018, 57, 2085– 2090, DOI: 10.1002/anie.20171131025https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsl2nu7g%253D&md5=d5ac64201de9fca4ab6cc16cfb247348Design and Assembly of a Chiral Metallosalen-Based Octahedral Coordination Cage for Supramolecular Asymmetric CatalysisTan, Chunxia; Jiao, Jingjing; Li, Zijian; Liu, Yan; Han, Xing; Cui, YongAngewandte Chemie, International Edition (2018), 57 (8), 2085-2090CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Supramol. containers featuring both high catalytic activity and high enantioselectivity represent a design challenge of practical importance. Herein, a chiral octahedral coordination cage can be constructed by using twelve enantiopure Mn(salen)-derived dicarboxylic acids as linear linkers and six Zn4-p-tert-butylsulfonylcalix[4]arene clusters as tetravalent four-connected vertexes. The porous cage features a large hydrophobic cavity (≈3944 Å3) decorated with catalytically active metallosalen species and is an efficient and recyclable asym. catalyst for the oxidative kinetic resoln. of racemic secondary alcs. and the epoxidn. of olefins with up to >99% enantiomeric excess. The cage architecture not only prevents intermol. deactivation and stabilizes the Mn(salen) catalysts but also encapsulates substrates and concs. reactants in the cavity, resulting in enhanced reactivity and enantioselectivity relative to the free metallosalen catalyst.
- 26Jiao, J.; Tan, C.; Li, Z.; Liu, Y.; Han, X.; Cui, Y. Design and assembly of chiral coordination cages for asymmetric sequential reactions. J. Am. Chem. Soc. 2018, 140, 2251– 2259, DOI: 10.1021/jacs.7b1167926https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXht1Ggtro%253D&md5=04061c0ce8bb3236f4d596b8f68d3d25Design and Assembly of Chiral Coordination Cages for Asymmetric Sequential ReactionsJiao, Jingjing; Tan, Chunxia; Li, Zijian; Liu, Yan; Han, Xing; Cui, YongJournal of the American Chemical Society (2018), 140 (6), 2251-2259CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Supramol. nanoreactors featuring multiple catalytically active sites are of great importance, esp. for asym. catalysis, and are yet challenging to construct. Here we report the design and assembly of five chiral single- and mixed-linker tetrahedral coordination cages using six dicarboxylate ligands derived-from enantiopure Mn(salen), Cr(salen) and/or Fe(salen) as linear linkers and four Cp3Zr3 clusters as three-connected vertices. The formation of these cages was confirmed by a variety of techniques including single-crystal and powder X-ray diffraction, inductively coupled plasma optical emission spectrometer, quadrupole-time-of-flight mass spectrometry and energy dispersive X-ray spectrometry. The cages feature a nanoscale hydrophobic cavity decorated with the same or different catalytically active sites, and the mixed-linker cage bearing Mn(salen) and Cr(salen) species is shown to be an efficient supramol. catalyst for sequential asym. alkene epoxidn./epoxide ring-opening reactions with up to 99.9% ee. The cage catalyst demonstrates improved activity and enantioselectivity over the free catalysts owing to stabilization of catalytically active metallosalen units and concn. of reactants within the cavity. Manipulation of catalytic org. linkers in cages can control the activities and selectivities, which may provide new opportunities for the design and assembly of novel functional supramol. architectures.
- 27Vardhan, H.; Verpoort, F. Metal-Organic Polyhedra: Catalysis and Reactive Intermediates. Adv. Synth. Catal 2015, 357, 1351– 1368, DOI: 10.1002/adsc.20140077827https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXhtlSksrg%253D&md5=448498e450135fddccb8d20b6671b7e0Metal-Organic Polyhedra: Catalysis and Reactive IntermediatesVardhan, Harsh; Verpoort, FrancisAdvanced Synthesis & Catalysis (2015), 357 (7), 1351-1368CODEN: ASCAF7; ISSN:1615-4150. (Wiley-VCH Verlag GmbH & Co. KGaA)A review; the catalytic nature of self-assembled metal-org. polyhedra gives an entirely new dimension to the reactivity and properties of mols. within a well-defined confined space. Encapsulation of a range of guests brings about not only host-guest interactions but also gives rise to unusual reactivities with selectivity and stabilization of various reactive intermediates. This review briefly covers the synthesis of self-assembled metal-org. polyhedra and elaborates their influence in different chem. reactions as well as in the stabilization of unstable chem. species.
- 28Hosono, N.; Kitagawa, S. Modular design of porous soft materials via self-organization of metal–organic cages. Acc. Chem. Res. 2018, 51, 2437– 2446, DOI: 10.1021/acs.accounts.8b0036128https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhslOgtrfP&md5=1e7a0ca54e9c2b7025550d8f76e598f8Modular Design of Porous Soft Materials via Self-Organization of Metal-Organic CagesHosono, Nobuhiko; Kitagawa, SusumuAccounts of Chemical Research (2018), 51 (10), 2437-2446CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The authors describe recent progress in bottom-up "modular" approaches for the synthesis of porous, processable MOF-based materials, wherein metal-org. cages (MOCs), alternatively called metal-org. polyhedra (MOPs), are used as "modular cavities" to build porous soft materials. The outer periphery of a MOP is decorated with polymeric and dendritic side chains to obtain a polymer-grafted MOP, imparting both soln. and thermal processability to the MOP cages, which have an inherent nanocavity along with high tailorability analogous to MOFs. Well-ordered MOP assemblies can be designed to obtain phases ranging from crystals to liq. crystals, allowing the fabrication of flexible free-standing sheets with preservation of the long-range ordering of MOPs. Furthermore, future prospects of the modular design for porous soft materials are provided with the anticipation that the bottom-up design will combine porous materials and soft matter sciences, leading to the discovery and development of many unexplored new materials and devices such as MOF-based self-healing membranes possessing well-defined nanochannels. The macroscopic alignment of channels can be controlled by external factors, including elec. and magnetic fields, external forces, and modified surfaces (templating and patterning), which are conventionally used for engineering of soft materials.
- 29Gosselin, A. J.; Antonio, A. M.; Korman, K. J.; Deegan, M. M.; Yap, G. P.; Bloch, E. D. Elaboration of Porous Salts. J. Am. Chem. Soc. 2021, 143, 14956– 14961, DOI: 10.1021/jacs.1c0561329https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhvFKrtr%252FN&md5=7584aac9ba5280aa33180fe3c0b08748Elaboration of Porous SaltsGosselin, Aeri J.; Antonio, Alexandra M.; Korman, Kyle J.; Deegan, Meaghan M.; Yap, Glenn P. A.; Bloch, Eric D.Journal of the American Chemical Society (2021), 143 (37), 14956-14961CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)A large library of novel porous salts based on charged coordination cages was synthesized via straightforward salt metathesis reactions. For these, solns. of salts of oppositely charged coordination cages are mixed to ppt. MOF-like permanently porous products where metal identity, pore size, ligand functional groups, and surface area are highly tunable. For most of these materials, the constituent cages combine in the ratios expected based on their charge. Addnl. studies focused on the rate of salt metathesis or reaction stoichiometry as variables to tune particle size or product compn., resp. It is expected that the design principles outlined here will be widely applicable for the synthesis of new porous salts based on a variety of charged porous mol. precursors.
- 30Kitano, H. Nobel Turing Challenge: creating the engine for scientific discovery. NPJ Syst. Biol. Appl. 2021, 7, 1– 12, DOI: 10.1038/s41540-021-00189-3There is no corresponding record for this reference.
- 31Bai, J.; Cao, L.; Mosbach, S.; Akroyd, J.; Lapkin, A. A.; Kraft, M. From Platform to Knowledge Graph: Evolution of Laboratory Automation. JACS Au 2022, 2, 292– 309, DOI: 10.1021/jacsau.1c0043831https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XltlKgug%253D%253D&md5=2209bca32f8d212982179327e09a079dFrom Platform to Knowledge Graph: Evolution of Laboratory AutomationBai, Jiaru; Cao, Liwei; Mosbach, Sebastian; Akroyd, Jethro; Lapkin, Alexei A.; Kraft, MarkusJACS Au (2022), 2 (2), 292-309CODEN: JAAUCR; ISSN:2691-3704. (American Chemical Society)A review. High-fidelity computer-aided experimentation is becoming more accessible with the development of computing power and artificial intelligence tools. The advancement of exptl. hardware also empowers researchers to reach a level of accuracy that was not possible in the past. Marching toward the next generation of self-driving labs., the orchestration of both resources lies at the focal point of autonomous discovery in chem. science. To achieve such a goal, algorithmically accessible data representations and standardized communication protocols are indispensable. In this perspective, we recategorize the recently introduced approach based on Materials Acceleration Platforms into five functional components and discuss recent case studies that focus on the data representation and exchange scheme between different components. Emerging technologies for interoperable data representation and multiagent systems are also discussed with their recent applications in chem. automation. We hypothesize that knowledge graph technol., orchestrating semantic web technologies and multiagent systems will be the driving force to bring data to knowledge, evolving our way of automating lab.
- 32Inderwildi, O., Kraft, M., Eds.; Intelligent Decarbonisation, 1st ed.; Lecture Notes in Energy; Springer International Publishing, 2022.There is no corresponding record for this reference.
- 33Tecuci, G.; Marcu, D.; Boicu, M.; Schum, D. A. Knowledge Engineering: Building Cognitive Assistants for Evidence-Based Reasoning; Cambridge University Press, 2016.There is no corresponding record for this reference.
- 34Menon, A.; Krdzavac, N. B.; Kraft, M. From database to knowledge graph─using data in chemistry. Curr. Opin. Chem. Eng. 2019, 26, 33– 37, DOI: 10.1016/j.coche.2019.08.004There is no corresponding record for this reference.
- 35Frey, J. G.; Bird, C. L. Cheminformatics and the semantic web: adding value with linked data and enhanced provenance. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2013, 3, 465– 481, DOI: 10.1002/wcms.112735https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsFKlsL3K&md5=ff829207ef6b4477b9adab4a49b3513aCheminformatics and the semantic web: adding value with linked data and enhanced provenanceFrey, Jeremy G.; Bird, Colin L.Wiley Interdisciplinary Reviews: Computational Molecular Science (2013), 3 (5), 465-481CODEN: WIRCAH; ISSN:1759-0884. (Wiley-Blackwell)Cheminformatics is evolving from being a field of study assocd. primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chem. data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chem., biochem., biol., and medical information. These developments depend on a range of factors: the principles of chem. identifiers and their role in relationships between chem. and biol. entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration.
- 36Bird, C. L.; Willoughby, C.; Frey, J. G. Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences. Chem. Soc. Rev. 2013, 42, 8157– 8175, DOI: 10.1039/c3cs60122f36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhsVyrtbnI&md5=58abff9515441c27ec6f2e9923fed604Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciencesBird, Colin L.; Willoughby, Cerys; Frey, Jeremy G.Chemical Society Reviews (2013), 42 (20), 8157-8175CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions. Their medium was paper, but despite the quality of their notebooks, we cannot turn the clock back. Our primary purpose is to review the influences of the digital era on scientific record keeping. We examine the foundations of the emerging opportunities for preserving and curating electronic records focussing on electronic lab. notebooks (ELNs), with an emphasis on their characteristics and usability.
- 37Degtyarenko, K.; De Matos, P.; Ennis, M.; Hastings, J.; Zbinden, M.; McNaught, A.; Alcántara, R.; Darsow, M.; Guedj, M.; Ashburner, M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2007, 36, D344– D350, DOI: 10.1093/nar/gkm791There is no corresponding record for this reference.
- 38Cohen, S.; Hershcovitch, M.; Taraz, M.; Kißig, O.; Wood, A.; Waddington, D.; Chin, P.; Friedrich, T. Complex Networks & Their Applications X; Springer, 2021; pp 742– 753.There is no corresponding record for this reference.
- 39Kanza, S.; Frey, J. G. A new wave of innovation in Semantic web tools for drug discovery. Expert. Opin. Drug. Discovery 2019, 14, 433– 444, DOI: 10.1080/17460441.2019.158688039https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXltFyitbg%253D&md5=e095f935975ddb15aa82b4ab2d65b17fA new wave of innovation in Semantic web tools for drug discoveryKanza, Samantha; Frey, Jeremy GrahamExpert Opinion on Drug Discovery (2019), 14 (5), 433-444CODEN: EODDBX; ISSN:1746-0441. (Taylor & Francis Ltd.)A review. : The use of semantic web technologies to aid drug discovery has gained momentum over recent years. Researchers in this domain have realized that semantic web technologies are key to dealing with the high levels of data for drug discovery. These technologies enable us to represent the data in a formal, structured, interoperable and comparable way, and to tease out undiscovered links between drug data (be it identifying new drug-targets or relevant compds., or links between specific drugs and diseases).: This review focuses on explaining how semantic web technologies are being used to aid advances in drug discovery. The main types of semantic web technologies are explained, outlining how they work and how they can be used in the drug discovery process, with a consideration of how the use of these technologies has progressed from their initial usage.: The increased availability of shared semantic resources (tools, data and importantly the communities) have enabled the application of semantic web technologies to facilitate semantic (context dependent) search across multiple data sources, which can be used by machine learning to produce better predictions by exploiting the semantic links in knowledge graphs and linked datasets.
- 40Kraft, M.; Eibeck, A. J-Park Simulator: Knowledge Graph for Industry 4.0. Chem. Ing. Technol. 2020, 92, 967– 977, DOI: 10.1002/cite.20200000240https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXovFymtr0%253D&md5=3d3e483534a09a0dec8338544eff9458J-Park Simulator: Knowledge Graph for Industry 4.0Kraft, Markus; Eibeck, AndreasChemie Ingenieur Technik (2020), 92 (7), 967-977CODEN: CITEAH; ISSN:0009-286X. (Wiley-VCH Verlag GmbH & Co. KGaA)This article introduces ontologies, Knowledge Graphs, agents and their role in the context of Industry 4.0. The importance of interoperability of agents in cross-domain scenarios using the J-Park Simulator (JPS), which is part of the Knowledge Graph () is shown. The dispersion of air pollutants from a power plant situated in Berlin is investigated with the help of JPS. The article describes how interoperability between agents in cross-domain scenarios can be achieved and discusses related open problems.
- 41Akroyd, J.; Mosbach, S.; Bhave, A.; Kraft, M. Universal Digital Twin – A Dynamic Knowledge Graph. Data-centric Eng. 2021, 2, e14 DOI: 10.1017/dce.2021.10There is no corresponding record for this reference.
- 42Eibeck, A.; Lim, M. Q.; Kraft, M. J-Park Simulator: An ontology-based platform for cross-domain scenarios in process industry. Comput. Chem. Eng. 2019, 131, 106586, DOI: 10.1016/j.compchemeng.2019.10658642https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFyhu7zE&md5=c9b82998ac83d5665b40676198e488e7J-Park Simulator: An ontology-based platform for cross-domain scenarios in process industryEibeck, Andreas; Lim, Mei Qi; Kraft, MarkusComputers & Chemical Engineering (2019), 131 (), 106586CODEN: CCENDW; ISSN:0098-1354. (Elsevier B.V.)The J-Park Simulator (JPS) acts as a continuously growing platform for integrating real-time data, knowledge, models, and tools related to process industry. It aims at simulation and optimization in cross-domain and multi-level scenarios and relies heavily on ontologies and semantic technologies. In this paper, we demonstrate the interoperability between different applications in JPS, introduce new domain ontologies into the JPS, and integrate live data. For this, we utilize a knowledge graph to store and link semantically described data and models and create agents wrapping the applications and updating the data in the knowledge graph dynamically. We present a comprehensive industrial air pollution scenario, which has been implemented as part of the JPS, to show how knowledge graphs and modular domain ontologies support the interoperability between agents. We show that the architecture of JPS increases the interoperability and flexibility in cross-domain scenarios and conclude that the potential of ontologies outweighs addnl. wrapping efforts.
- 43Farazi, F.; Krdzavac, N. B.; Akroyd, J.; Mosbach, S.; Menon, A.; Nurkowski, D.; Kraft, M. Linking reaction mechanisms and quantum chemistry: An ontological approach. Comput. Chem. Eng. 2020, 137, 106813, DOI: 10.1016/j.compchemeng.2020.10681343https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXms12it70%253D&md5=566bddc2a113cc005cbb510977141b08Linking reaction mechanisms and quantum chemistry: An ontological approachFarazi, Feroz; Krdzavac, Nenad B.; Akroyd, Jethro; Mosbach, Sebastian; Menon, Angiras; Nurkowski, Daniel; Kraft, MarkusComputers & Chemical Engineering (2020), 137 (), 106813CODEN: CCENDW; ISSN:0098-1354. (Elsevier B.V.)In this paper, a linked-data framework for connecting species in chem. kinetic reaction mechanisms with quantum calcns. is presented. A mechanism can be constructed from thermodn., reaction rate, and transport data that has been obtained either exptl., computationally, or by a combination of both. This process in practice requires multiple sources of data, which raises, inter alia, species naming and data inconsistency issues. A linked data-centric knowledge-graph approach is taken in this work to address these challenges. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chem. kinetic reaction mechanisms, and OntoCompChem, for representing quantum chem. calcns., are extended. In addn., a new ontol., which we call OntoSpecies, is developed for uniquely representing chem. species. The framework also includes agents to populate and link knowledge-bases created through the instantiation of these ontologies. In addn., the developed knowledge-graph and agents naturally form a part of the J-Park Simulator (JPS) - an Industry 4.0 platform which combines linked data and an eco-system of autonomous agents for cross-domain applications. The functionality of the framework is demonstrated via a use-case based on a hydrogen combustion mechanism.
- 44Farazi, F.; Akroyd, J.; Mosbach, S.; Buerger, P.; Nurkowski, D.; Salamanca, M.; Kraft, M. OntoKin: An ontology for chemical kinetic reaction mechanisms. J. Chem. Inf. Model. 2020, 60, 108– 120, DOI: 10.1021/acs.jcim.9b0096044https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVWlt7nO&md5=d79229952eb19b43e70ac54722050743OntoKin: An Ontology for Chemical Kinetic Reaction MechanismsFarazi, Feroz; Akroyd, Jethro; Mosbach, Sebastian; Buerger, Philipp; Nurkowski, Daniel; Salamanca, Maurin; Kraft, MarkusJournal of Chemical Information and Modeling (2020), 60 (1), 108-120CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)An ontol. for capturing both data and the semantics of chem. kinetic reaction mechanisms has been developed. Such mechanisms can be applied to simulate and understand the behavior of chem. processes, for example, the emission of pollutants from internal combustion engines. An ontol. development methodol. was used to produce the semantic model of the mechanisms, and a tool was developed to automate the assertion process. As part of the development methodol., the ontol. is formally represented using a web ontol. language (OWL), assessed by domain experts, and validated by applying a reasoning tool. The resulting ontol., termed OntoKin, has been used to represent example mechanisms from the literature. OntoKin and its instantiations are integrated to create a knowledge base (KB), which is deployed using the RDF4J triple store. The use of the OntoKin ontol. and the KB is demonstrated for three use cases-querying across mechanisms, modeling atm. pollution dispersion, and as a mechanism browser tool. As part of the query use case, the OntoKin tools have been applied by a chemist to identify variations in the rate of a prompt NOx formation reaction in the combustion of ammonia as represented by four mechanisms in the literature.
- 45Bai, J.; Geeson, R.; Farazi, F.; Mosbach, S.; Akroyd, J.; Bringley, E. J.; Kraft, M. Automated Calibration of a Poly (oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph Technology. J. Chem. Inf. Model. 2021, 61, 1701– 1717, DOI: 10.1021/acs.jcim.0c0132245https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXotVOktrw%253D&md5=b12ffe5a93ae6e634d9ece130db746b6Automated Calibration of a Poly(oxymethylene) Dimethyl Ether Oxidation Mechanism Using the Knowledge Graph TechnologyBai, Jiaru; Geeson, Rory; Farazi, Feroz; Mosbach, Sebastian; Akroyd, Jethro; Bringley, Eric J.; Kraft, MarkusJournal of Chemical Information and Modeling (2021), 61 (4), 1701-1717CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)In this paper, we develop a knowledge graph-based framework for the automated calibration of combustion reaction mechanisms and demonstrate its effectiveness on a case study of poly(oxymethylene)dimethyl ether (PODEn, where n = 3) oxidn. We develop an ontol. representation for combustion expts., OntoChemExp, that allows for the semantic enrichment of expts. within the J-Park simulator (JPS, theworldavatar.com), an existing cross-domain knowledge graph. OntoChemExp is fully capable of supporting exptl. results in the Process Informatics Model (PrIMe) database. Following this, a set of software agents are developed to perform exptl. result retrieval, sensitivity anal., and calibration tasks. The sensitivity anal. agent is used for both generic sensitivity analyses and reaction selection for subsequent calibration. The calibration process is performed as a sampling task, followed by an optimization task. The agents are designed for use with generic models but are demonstrated with ignition delay time and laminar flame speed simulations. We find that calibration times are reduced, while accuracy is increased compared to manual calibration, achieving a 79% decrease in the objective function value, as defined in this study. Further, we demonstrate how this workflow is implemented as an extension of the JPS.
- 46Krdzavac, N.; Mosbach, S.; Nurkowski, D.; Buerger, P.; Akroyd, J.; Martin, J.; Menon, A.; Kraft, M. An ontology and semantic web service for quantum chemistry calculations. J. Chem. Inf. Model. 2019, 59, 3154– 3165, DOI: 10.1021/acs.jcim.9b0022746https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhtVyjsLzN&md5=c51fb379d9ac835e7e1bf41d0d6ce9dbAn Ontology and Semantic Web Service for Quantum Chemistry CalculationsKrdzavac, Nenad; Mosbach, Sebastian; Nurkowski, Daniel; Buerger, Philipp; Akroyd, Jethro; Martin, Jacob; Menon, Angiras; Kraft, MarkusJournal of Chemical Information and Modeling (2019), 59 (7), 3154-3165CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)The purpose of this article is to present an ontol., termed OntoCompChem, for quantum chem. calcns. as performed by the Gaussian quantum chem. software, as well as a semantic web service named MolHub. The OntoCompChem ontol. has been developed based on the semantics of concepts specified in the CompChem convention of Chem. Markup Language (CML) and by extending the Gainesville Core (GNVC) ontol. MolHub is developed in order to establish semantic interoperability between different tools used in quantum chem. and thermochem. calcns., and as such is integrated into the J-Park Simulator (JPS)-a multidomain interactive simulation platform and expert system. It uses the OntoCompChem ontol. and implements a formal language based on propositional logic as a part of its query engine, which verifies satisfiability through reasoning. This paper also presents a NASA polynomial use-case scenario to demonstrate semantic interoperability between Gaussian and a tool for thermodn. data calcns. within MolHub.
- 47Zhang, Y.; Gan, H.; Qin, C.; Wang, X.; Su, Z.; Zaworotko, M. J. Self-Assembly of Goldberg Polyhedra from a Concave [WV5O11(RCO2)5(SO4)] 3–Building Block with 5-Fold Symmetry. J. Am. Chem. Soc. 2018, 140, 17365– 17368, DOI: 10.1021/jacs.8b1086647https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXit1Cit7bK&md5=3d5ae0b4e8c567cf2e55d37d812f039aSelf-Assembly of Goldberg Polyhedra from a Concave [WV5O11(RCO2)5(SO4)]3- Building Block with 5-Fold SymmetryZhang, Yuteng; Gan, Hongmei; Qin, Chao; Wang, Xinlong; Su, Zhongmin; Zaworotko, Michael J.Journal of the American Chemical Society (2018), 140 (50), 17365-17368CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Nanoscale regular polyhedra with icosahedral symmetry exist naturally as exemplified by virus capsids and fullerenes. Nevertheless, their generation by supramol. chem. through the linking of 5-fold symmetry vertices remains unmet because of the absence of 5-fold symmetry building blocks with the requisite geometric features. This situation contrasts with that of tetrahedral and octahedral symmetry metal-org. polyhedra (MOPs), for which appropriate triangular and square mol. building blocks (MBBs) that can serve as vertices or faces are readily available. Herein, authors report isolation of a pentagonal [WV5O11(SO4)6]8- cluster and reveal its utility to afford the first four examples of nanoscale Goldberg MOPs, based upon 5-fold MBBs. Two 32-faced Gv(1,1) MOPs and two 42-faced Gv(2,0) MOPs were formed using linear or triangular org. ligands, resp. The largest Goldberg MOP-4, exhibits a diam. of 4.3 nm, can trap fullerene C60 mols. in its interstitial cavities.
- 48Lyu, H.; Ji, Z.; Wuttke, S.; Yaghi, O. M. Digital reticular chemistry. Chem. 2020, 6, 2219– 2241, DOI: 10.1016/j.chempr.2020.08.00848https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhvVeqsbrJ&md5=47893e5b08ace46ebeecaced7b36c9e9Digital Reticular ChemistryLyu, Hao; Ji, Zhe; Wuttke, Stefan; Yaghi, Omar M.Chem (2020), 6 (9), 2219-2241CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)A review. Reticular chem. operates in an infinite space of compns., structures, properties, and applications. Although great progress has been made in exploring this space through the development of metal-org. frameworks and covalent org. frameworks, there remains a gap between what we foresee as being possible and what can actually be accomplished with the current tools and methods. The establishment of digital reticular chem., where digital tools are deployed, in particular lab. robotics and artificial intelligence, will fundamentally change the current workflow to enable discovery of this untapped chem. space and to go beyond the limits of human capacity. In so doing, long-standing challenges in reticular chem. can finally be addressed faster and better, and more significantly, new questions, unimagined before digitization, can be articulated. The interface between human and "machine" is an integral part of this endeavor and one whose quality is crit. to uncovering science transcending intellectual and phys. borders.
- 49Tranchemontagne, D. J.; Mendoza-Cortés, J. L.; O’Keeffe, M.; Yaghi, O. M. Secondary building units, nets and bonding in the chemistry of metal–organic frameworks. Chem. Soc. Rev. 2009, 38, 1257– 1283, DOI: 10.1039/b817735j49https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvValsr8%253D&md5=3e03c5e2c057b36eb590c1904aa5e5a1Secondary building units, nets and bonding in the chemistry of metal-organic frameworksTranchemontagne, David J.; Mendoza-Cortes, Jose L.; O'Keeffe, Michael; Yaghi, Omar M.Chemical Society Reviews (2009), 38 (5), 1257-1283CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)This crit. review presents a comprehensive study of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) towards construction and synthesis of metal-org. frameworks (MOFs). We describe the geometries of 131 SBUs, their connectivity and compn. This contribution presents a comprehensive list of the wide variety of transition-metal carboxylate clusters which may serve as secondary building units (SBUs) in the construction and synthesis of metal-org. frameworks. The SBUs discussed here were obtained from a search of mols. and extended structures archived in the Cambridge Structure Database (CSD, version 5.28, Jan. 2007) which included only crystals contg. metal carboxylate linkages (241 refs.).
- 50Evans, J. D.; Jelfs, K. E.; Day, G. M.; Doonan, C. J. Application of computational methods to the design and characterisation of porous molecular materials. Chem. Soc. Rev. 2017, 46, 3286– 3301, DOI: 10.1039/C7CS00084G50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXntlWhsLs%253D&md5=65b0f66e14f0114dd08f01e5b63835ffApplication of computational methods to the design and characterisation of porous molecular materialsEvans, Jack D.; Jelfs, Kim E.; Day, Graeme M.; Doonan, Christian J.Chemical Society Reviews (2017), 46 (11), 3286-3301CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)Composed from discrete units, porous mol. materials (PMMs) possess unique properties not obsd. for conventional, extended, solids, such as soln. processibility and permanent porosity in the liq. phase. However, identifying the origin of porosity is not a trivial process, esp. for amorphous or liq. phases. Furthermore, the assembly of mol. components is typically governed by a subtle balance of weak intermol. forces that makes structure prediction challenging. Accordingly, in this review we canvass the crucial role of mol. simulations in the characterization and design of PMMs. We will outline strategies for modeling porosity in cryst., amorphous and liq. phases and also describe the state-of-the-art methods used for high-throughput screening of large datasets to identify materials that exhibit novel performance characteristics.
- 51Poole, D. A.; Bobylev, E. O.; Mathew, S.; Reek, J. N. Topological prediction of palladium coordination cages. Chem. Sci. 2020, 11, 12350– 12357, DOI: 10.1039/D0SC03992F51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitVyhsL%252FO&md5=bf181f858ca6d0818ab5ca6b8f575a40Topological prediction of palladium coordination cagesPoole, David A.; Bobylev, Eduard O.; Mathew, Simon; Reek, Joost N. H.Chemical Science (2020), 11 (45), 12350-12357CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)The prepn. of functionalized, heteroleptic PdxL2x coordination cages is desirable for catalytic and optoelectronic applications. Current rational design of these cages uses the angle between metal-binding (∠B) sites of the di(pyridyl)arene linker to predict the topol. of homoleptic cages obtained via non-covalent chem. However, this model neglects the contributions of steric bulk between the pyridyl residues-a prerequisite for endohedrally functionalized cages, and fails to rationalize heteroleptic cages. We describe a classical mechanics (CM) approach to predict the topol. outcomes of PdxL2x coordination cage formation with arbitrary linker combinations, accounting for the electronic effects of coordination and steric effects of linker structure. Initial validation of our CM method with reported homoleptic Pd12LFu24 (LFu = 2,5-bis(pyridyl)furan) assembly suggested the formation of a minor topol. Pd15LFu30, identified exptl. by mass spectrometry. Application to heteroleptic cage systems employing mixts. of LFu (∠B = 127°) and its thiophene congener LTh (∠B = 149° ∠Bexp = 152.4°) enabled prediction of Pd12L24 and Pd24L48 coordination cages formation, reliably emulating exptl. data. Finally, the topol. outcome for exohedrally (LEx) and endohedrally (LEn) functionalized heteroleptic PdxL2x coordination cages were predicted to assess the effect of steric bulk on both topol. outcomes and coordination cage yields, with comparisons drawn to exptl. data.
- 52Jiang, Y.; Tan, P.; Qi, S.-C.; Gu, C.; Peng, S.-S.; Wu, F.; Liu, X.-Q.; Sun, L.-B. Breathing metal–organic polyhedra controlled by light for carbon dioxide capture and liberation. CCS Chemistry 2021, 3, 1659– 1668, DOI: 10.31635/ccschem.020.20200031452https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXit1Smt7jL&md5=2b51ad5e227e7d57bb87c5a10fab2719Breathing metal-organic polyhedra controlled by light for carbon dioxide capture and liberationJiang, Yao; Tan, Peng; Qi, Shi-Chao; Gu, Chen; Peng, Song-Song; Wu, Fan; Liu, Xiao-Qin; Sun, Lin-BingCCS Chemistry (2021), 3 (6), 1659-1668CODEN: CCCHB2 ISSN:. (Chinese Chemical Society)Metal-org. polyhedra (MOPs) have emerged as versatile platforms for artificial models of biol. systems due to their discrete structure and modular nature. However, the design and fabrication of MOPs with special functionality for mimicking biol. processes are challenging. Inspired by the breathing mechanism of lungs, we developed a new type of MOP (a breathing MOP, denoted as NUT-101) by directly using azobenzene units as the pillars of the polyhedra to coordinate with Zr-based metal clusters. In addn. to considerable thermal and chem. stability, the obtained MOP exhibits photocontrollable breathing behavior. Upon irradn. with visible or UV light, the configuration of azobenzene units transforms, leading to reversible expansion or contraction of the cages and, correspondingly, capture or liberation of CO2 mols. Such a breathing behavior of NUT-101 is further confirmed by d. functional theory (DFT) calcn. This system might establish an avenue for the construction of new materials with particular functionality that mimic biol. processes.
- 53Hoffmann, R.; Schleyer, P.; Schaefer, H., III Predicting Molecules—More Realism, Please. Angew. Chem., Int. Ed. 2008, 47, 7164– 7167, DOI: 10.1002/anie.20080120653https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BD1crpt12jsw%253D%253D&md5=5c7b8656a39374a82114630bbb1bcdf1Predicting molecules--more realism, please!Hoffmann Roald; Schleyer Paul von Rague; Schaefer Henry F 3rdAngewandte Chemie (International ed. in English) (2008), 47 (38), 7164-7 ISSN:.There is no expanded citation for this reference.
- 54Heine, T. Grand challenges in computational materials science: from description to prediction at all scales. Front. Mater. 2014, 1, 7, DOI: 10.3389/fmats.2014.00007There is no corresponding record for this reference.
- 55Dumontheil, I. Development of abstract thinking during childhood and adolescence: The role of rostrolateral prefrontal cortex. Dev. Cogn. Neurosci. 2014, 10, 57– 76, DOI: 10.1016/j.dcn.2014.07.00955https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC2M%252Fms1yisQ%253D%253D&md5=73d8f03c182c96836b3466c32d44492bDevelopment of abstract thinking during childhood and adolescence: the role of rostrolateral prefrontal cortexDumontheil IroiseDevelopmental cognitive neuroscience (2014), 10 (), 57-76 ISSN:.Rostral prefrontal cortex (RPFC) has increased in size and changed in terms of its cellular organisation during primate evolution. In parallel emerged the ability to detach oneself from the immediate environment to process abstract thoughts and solve problems and to understand other individuals' thoughts and intentions. Rostrolateral prefrontal cortex (RLPFC) is thought to play an important role in supporting the integration of abstract, often self-generated, thoughts. Thoughts can be temporally abstract and relate to long term goals, or past or future events, or relationally abstract and focus on the relationships between representations rather than simple stimulus features. Behavioural studies have provided evidence of a prolonged development of the cognitive functions associated with RLPFC, in particular logical and relational reasoning, but also episodic memory retrieval and prospective memory. Functional and structural neuroimaging studies provide further support for a prolonged development of RLPFC during adolescence, with some evidence of increased specialisation of RLPFC activation for relational integration and aspects of episodic memory retrieval. Topics for future research will be discussed, such as the role of medial RPFC in processing abstract thoughts in the social domain, the possibility of training abstract thinking in the domain of reasoning, and links to education.
- 56Kondinski, A.; Parac-Vogt, T. N. Programmable interlocking disks: bottom-up modular assembly of chemically relevant polyhedral and reticular structural models. J. Chem. Educ. 2019, 96, 601– 605, DOI: 10.1021/acs.jchemed.8b0076956https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXis1KjtL8%253D&md5=3ebdc5b076261b07ba431c213e7da3d4Programmable Interlocking Disks: Bottom-Up Modular Assembly of Chemically Relevant Polyhedral and Reticular Structural ModelsKondinski, Aleksandar; Parac-Vogt, Tatjana N.Journal of Chemical Education (2019), 96 (3), 601-605CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)Single-type, 8-fold-grooved, com. accessible interlocking disks (ILDs) have been used for modeling of complex polyhedral and reticular topologies with relevance to inorg. and hybrid materials. The assembly of complex topologies relies on the prepn. of secondary building units (SBUs), which exhibit different connectivity than that of the primary ILDs. All ILD-based models are light, scalable, programmable, and suitable for discovery-based learning and classroom demonstrations of stereochem. and complex chem. concepts.
- 57Kondinski, A.; Moons, J.; Zhang, Y.; Bussé, J.; De Borggraeve, W.; Nies, E.; Parac-Vogt, T. N. Modeling of Nanomolecular and Reticular Architectures with 6-fold Grooved, Programmable Interlocking Disks. J. Chem. Educ. 2020, 97, 289– 294, DOI: 10.1021/acs.jchemed.9b0073957https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitVCktbrI&md5=e9dbd99956ec602fedbaa3deb5492de5Modeling of Nanomolecular and Reticular Architectures with 6-fold Grooved, Programmable Interlocking DisksKondinski, Aleksandar; Moons, Jens; Zhang, Yujie; Busse, Jakob; De Borggraeve, Wim; Nies, Erik; Parac-Vogt, Tatjana N.Journal of Chemical Education (2020), 97 (1), 289-294CODEN: JCEDA8; ISSN:0021-9584. (American Chemical Society and Division of Chemical Education, Inc.)Single-type, 6-fold sym. grooved, and com. accessible interlocking disks (ILDs) have been used for modeling of sp2 hybridized carbon-based nanoarchitectures and complex polyhedral and reticular material models. In the case of the carbon-based nanoarchitectures, we showcase that the primary ILDs can be directly used for representing individual atoms and bonds. Further on, the spatial connectivity of the primary ILDs can be extended by assembly of sym. secondary building units (SBUs). The constructed (deci)meter scale models are robust, light, scalable, and suitable for classroom demonstrations. The ILD technique is also suitable for use in workshops for facile discovery-based learning of nanomol. structure, showing promise for wider use in the chem. curriculum.
- 58Castilla, A. M.; Ramsay, W. J.; Nitschke, J. R. Stereochemistry in subcomponent self-assembly. Acc. Chem. Res. 2014, 47, 2063– 2073, DOI: 10.1021/ar500092458https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXntlSktb8%253D&md5=873d21bb2346217d47e23ca5ae78db04Stereochemistry in Subcomponent Self-AssemblyCastilla, Ana M.; Ramsay, William J.; Nitschke, Jonathan R.Accounts of Chemical Research (2014), 47 (7), 2063-2073CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. As Pasteur noted >150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt 1-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomol. structure is clear: the single-handed forms of bio(macro)mols. interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramol. structures, provided a means to study the mechanisms of transmission and amplification of stereochem. information, which are key processes to understand in the context of the origins and functions of biol. homochirality. Control over stereochem. information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and sepn., asym. catalysis, and mol. devices. In this Account, the authors explore different aspects of stereochem. encountered during the use of subcomponent self-assembly, whereby complex structures were prepd. through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N=C) bonds. This technique provides a useful method to study stereochem. information transfer processes within metal-org. assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. The authors start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the org. ligands of mononuclear coordination complexes and communicate stereochem. information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then incorporated in self-assembly reactions to control the stereochem. of increasingly complex architectures. This strategy has also allowed exploration of the degree to which stereochem. information is propagated through tetrahedral frameworks cooperatively, leading to the observation of stereochem. coupling across >2 nm between metal stereocenters and the enantioselective synthesis of a face-capped tetrahedron contg. no carbon stereocenters via a stereochem. memory effect. Several studies on the communication of stereochem. between the configurationally flexible metal centers in tetrahedral metal-org. cages have shed light on the factors governing this process, allowing the synthesis of an asym. cage, obtained in racemic form, in which all symmetry elements were broken. Finally, how stereochem. diversity leads to structural complexity in the structures prepd. through subcomponent self-assembly are discussed. Initial use of octahedral metal templates with facial stereochem. in subcomponent self-assembly, which predictably gave rise to structures of tetrahedral symmetry, was extended to meridional metal centers. These lower-symmetry linkages have allowed the assembly of increasingly intricate 3D architectures of varying functionality. The knowledge gained from investigating different aspects of the stereochem. of metal-templated assemblies thus not only leads to new means of structural control but also opens pathways toward functions such as stereoselective guest binding and transformation.
- 59Harris, K.; Sun, Q.-F.; Sato, S.; Fujita, M. M12L24 spheres with endo and exo coordination sites: scaffolds for non-covalent functionalization. J. Am. Chem. Soc. 2013, 135, 12497– 12499, DOI: 10.1021/ja404360959https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXht1CltLnL&md5=2738eebbd8e277e0730348a747cbd6bfM12L24 Spheres with Endo and Exo Coordination Sites: Scaffolds for Non-Covalent FunctionalizationHarris, Kate; Sun, Qing-Fu; Sato, Sota; Fujita, MakotoJournal of the American Chemical Society (2013), 135 (34), 12497-12499CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Palladium M12L24 spherical complexes incorporating 24 free pyridine rings on their interior or exterior surfaces were synthesized via the self-assembly of tridentate tris(pyridine) ligands with Pd2+ ions. Coordination of secondary metal ions in the interior of the spherical framework was achieved through interactions of 24 Ag+ ions with the free endo pyridine rings.
- 60Müller, A.; Krickemeyer, E.; Bögge, H.; Schmidtmann, M.; Peters, F. Organizational forms of matter: an inorganic super fullerene and keplerate based on molybdenum oxide. Angew. Chem., Int. Ed. 1998, 37, 3359– 3363, DOI: 10.1002/(SICI)1521-3773(19981231)37:24<3359::AID-ANIE3359>3.0.CO;2-J60https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A280%3ADC%252BC1Mjot1ygtw%253D%253D&md5=0106c893ea55a061725c7ffb9e351105Organizational Forms of Matter: An Inorganic Super Fullerene and Keplerate Based on Molybdenum OxideMuller Achim; Krickemeyer Erich; Bogge Hartmut; Schmidtmann Marc; Peters FrankAngewandte Chemie (International ed. in English) (1998), 37 (24), 3359-3363 ISSN:.Plato and Kepler would have been pleased. Despite the large number of atoms present the cluster anion 1 resembles an icosahedral-type structure. This represents definitively an unprecedented event in chemistry! The structure is made up of 12 {Mo11 } fragments such that the fivefold symmetry axes are retained in the resulting spherical object. As an inscribed icosahedron can be recognized in the spherical shell of 1 (see picture), similarities with Kepler's famous shell model of the cosmos can be seen.
- 61Yaghi, O. M.; Kalmutzki, M. J.; Diercks, C. S. Introduction to Reticular Chemistry; John Wiley and Sons, 2019; Chapter 19, pp 453– 462.There is no corresponding record for this reference.
- 62He, S.; Zhang, M.; Xue, B.; Lai, Y.; Li, M.; Yin, P. Surface Functionality-Regulated and Entropy-Driven Thermodynamics of the Formation of Coordination Nanocages. J. Phys. Chem. B. 2021, 125, 13229– 13234, DOI: 10.1021/acs.jpcb.1c0669062https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXisFars7vF&md5=df38aa48c917b5a6d7171dededa64391Surface Functionality-Regulated and Entropy-Driven Thermodynamics of the Formation of Coordination NanocagesHe, Shuqian; Zhang, Mingxin; Xue, Binghui; Lai, Yuyan; Li, Mu; Yin, PanchaoJournal of Physical Chemistry B (2021), 125 (48), 13229-13234CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)Coordination nanocages (CNCs) are under intense research in nanoscience and supramol. chem. for their enriched surface functionalities and micro-porosity; however, the understanding of their formation mechanism is still poor due to the difficulty in probing their soln. structures. Herein, the CNC formation process from the coordination complexation of the macromol. isophthalic acid (IPA) ligand and Cu2+ is studied via isothermal titrn. calorimetry, and its entropy-driven feature is revealed to be originated from the collapse of solvation layers of the assembly units. The CNC formation is thermodynamically less favored with smaller binding consts. when the sizes of macromol. IPA ligands are larger, which originated from the space crowding of macromols. of the ligands on CNC surfaces and the resulting entropy loss of polymer chain conformations. Meanwhile, the chem. equil. of CNC formation can be tuned upon altering the Cu2+/IPA ratio, and the yield of CNCs, suggested from size exclusion chromatog. studies, decreases when excessive Cu2+ is applied, providing guidelines for CNC design and synthesis.
- 63Piskorz, T. K.; Martí-Centelles, V.; Young, T. A.; Lusby, P. J.; Duarte, F. Computational Modeling of Supramolecular Metallo-organic Cages–Challenges and Opportunities. ACS Catal. 2022, 12, 5806– 5826, DOI: 10.1021/acscatal.2c0083763https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XhtFCqs7vK&md5=02201ef10653b8eb66db651ebb51aa11Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and OpportunitiesPiskorz, Tomasz K.; Marti-Centelles, Vicente; Young, Tom A.; Lusby, Paul J.; Duarte, FernandaACS Catalysis (2022), 12 (10), 5806-5826CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)A review. Self-assembled metallo-org. cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive exptl. work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-org. cages are scarce, not least due to the challenges assocd. with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, the authors discuss key mol. principles governing the design of functional metallo-org. cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. The authors will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing exptl. observable and to guide synthetic efforts. To illustrate this point, the authors present several examples where modeling has helped to elucidate fundamental principles behind mol. recognition and reactivity. The authors highlight the importance of combining computational and exptl. efforts to speed up supramol. catalyst design while reducing time and resources.
- 64Cheetham, A. K.; Kieslich, G.; Yeung, H.-M. Thermodynamic and kinetic effects in the crystallization of metal–organic frameworks. Acc. Chem. Res. 2018, 51, 659– 667, DOI: 10.1021/acs.accounts.7b0049764https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXivVSlu7o%253D&md5=7d4d54f0debf7feedbb23a922815d9e1Thermodynamic and Kinetic Effects in the Crystallization of Metal-Organic FrameworksCheetham, Anthony K.; Kieslich, G.; Yeung, H. H.-M.Accounts of Chemical Research (2018), 51 (3), 659-667CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)A review. The evolution of metal-org. frameworks (MOFs) has been one of the most exciting aspects of materials chem. over the last 20 years. In this Account, we discuss the development during this period in our understanding of the factors that control the crystn. of MOFs from soln. Both classical porous MOFs and dense MOF phases are considered. This is an opportune time at which to examine this complex area because the exptl. tools now available to interrogate crystn. processes have matured significantly in the last 5 years, particularly with the use of in situ synchrotron X-ray diffraction. There have also been impressive developments in the use of d. functional theory (DFT) to treat not only the energies of very complex structures but also their entropies. This is particularly important in MOF frameworks because of their much greater flexibility compared with inorg. structures such as zeolites. The first section of the Account describes how early empirical observations on the crystn. of dense MOFs pointed to a strong degree of thermodn. control, with both enthalpic and entropic factors playing important roles. For example, reactions at higher temps. tend to lead to denser structures with higher degrees of framework connectivity and lower levels of solvation, and polymorphs tend to form according to their thermodn. stabilities. In the case of metal tartrates, these trends have been validated by calorimetric studies. It has been clear for more than a decade, however, that certain phases crystallize under kinetic control, esp. when a change in conformation of the ligand or coordination around a metal center might be necessary to form the thermodynamically preferred product. We describe how this can lead to time-dependent crystn. processes that evolve according to the Ostwald rule of stages and can be obsd. by in situ methods. We then consider the crystn. of porous MOFs, which presents addnl. challenges because of solvation effects. In spite of these problems, much has been learned about the energetics of the underlying frameworks, where the relationship between porosity and stability initially seemed to mirror the behavior of zeolites, with more porous structures being less stable. Recently, however, this simple relationship has had to be reconsidered with the emergence of some very flexible structures wherein the open structures are more stable than their denser analogs at finite temps. because of their large vibrational entropies. In the final section we describe how the concepts developed in the MOF work have been extended into the closely related area of hybrid org.-inorg. perovskites. We describe recent studies on polymorphism in hybrid perovskites, which is amenable to total free energy calcns. using a combination of DFT and lattice dynamics methods.
- 65Piccinno, F.; Hischier, R.; Seeger, S.; Som, C. From laboratory to industrial scale: a scale-up framework for chemical processes in life cycle assessment studies. J. Clean. Prod 2016, 135, 1085– 1097, DOI: 10.1016/j.jclepro.2016.06.164There is no corresponding record for this reference.
- 66Eibeck, A.; Chadzynski, A.; Lim, M. Q.; Aditya, K.; Ong, L.; Devanand, A.; Karmakar, G.; Mosbach, S.; Lau, R.; Karimi, I. A.; Foo, E. Y. S.; Kraft, M. A parallel world framework for scenario analysis in knowledge graphs. Data-centric Eng. 2020, 1, e6 DOI: 10.1017/dce.2020.6There is no corresponding record for this reference.
- 67Berners-Lee, T.; Hendler, J.; Lassila, O. The semantic web. Sci. Am. 2001, 284, 34– 43, DOI: 10.1038/scientificamerican0501-34There is no corresponding record for this reference.
- 68Wilkinson, M. D. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 2016, 3, 1– 9, DOI: 10.1038/sdata.2016.18There is no corresponding record for this reference.
- 69Mosbach, S.; Menon, A.; Farazi, F.; Krdzavac, N.; Zhou, X.; Akroyd, J.; Kraft, M. Multiscale cross-domain thermochemical knowledge-graph. J. Chem. Inf. Model. 2020, 60, 6155– 6166, DOI: 10.1021/acs.jcim.0c0114569https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXisVGrurbK&md5=7cf31a486b5a094351f90909617fe4ccMultiscale Cross-Domain Thermochemical Knowledge-GraphMosbach, Sebastian; Menon, Angiras; Farazi, Feroz; Krdzavac, Nenad; Zhou, Xiaochi; Akroyd, Jethro; Kraft, MarkusJournal of Chemical Information and Modeling (2020), 60 (12), 6155-6166CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)In this paper, we develop a set of software agents which improve a knowledge-graph contg. thermodn. data of chem. species by means of quantum chem. calcns. and error-canceling balanced reactions. The knowledge-graph represents species-assocd. information by making use of the principles of linked data, as employed in the Semantic Web, where concepts correspond to vertices and relationships between the concepts correspond to edges of the graph. We implement this representation by means of ontologies, which formalize the definition of concepts and their relationships, as a crit. step to achieve interoperability between heterogeneous data formats and software. The agents, which conduct quantum chem. calcns. and derive the ests. of std. enthalpies of formation, update the knowledge-graph with newly obtained results, improving data values, and adding nodes and connections between them. A key distinguishing feature of our approach is that it extends an existing, general-purpose knowledge-graph, called J-Park Simulator (http://theworldavatar.com), and its ecosystem of autonomous agents, thus enabling seamless cross-domain applications in wider contexts. To this end, we demonstrate how quantum calcns. can directly affect the atm. dispersion of pollutants in an industrial emission use-case.
- 70Czaja, A. U.; Trukhan, N.; Müller, U. Industrial applications of metal–organic frameworks. Chem. Soc. Rev. 2009, 38, 1284– 1293, DOI: 10.1039/b804680h70https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXkvVamu7o%253D&md5=63295ce7e2fb393c1abecd7623bc9c58Industrial applications of metal-organic frameworksCzaja, Alexander U.; Trukhan, Natalia; Muller, UlrichChemical Society Reviews (2009), 38 (5), 1284-1293CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)A review. New materials are prerequisite for major breakthrough applications affecting the daily life, and therefore are pivotal for the chem. industry. Metal-org. frameworks (MOFs) constitute an emerging class of materials useful in gas storage, gas purifn., and sepn. applications as well as heterogeneous catalysis. They not only offer higher surface areas and the potential for enhanced activity than currently used materials like base metal oxides, but also provide shape/size selectivity which is important both for sepns. and catalysis. In this crit. review an overview of the potential applications of MOFs in the chem. industry is presented. Furthermore, the synthesis and characterization of the materials are briefly discussed from the industrial perspective.
- 71Grüninger, M.; Fox, M. S. Methodology for the design and evaluation of ontologies. In International Joint Conferences on Artificial Intelligence (IJCAI), Workshop on Basic Ontological Issues in Knowledge Sharing, Montreal, Canada, 1995.There is no corresponding record for this reference.
- 72Uschold, M.; King, M. Towards a Methodology for Building Ontologies; Citeseer, 1995.There is no corresponding record for this reference.
- 73Noy, N. F.; McGuinness, D. L. Ontology Development 101: A Guide to Creating Your First Ontology; Stanford University, 2001.There is no corresponding record for this reference.
- 74Pinto, H. S.; Martins, J. P. Ontologies: How can they be built?. Knowledge and information systems 2004, 6, 441– 464, DOI: 10.1007/s10115-003-0138-1There is no corresponding record for this reference.
- 75Giunchiglia, F.; Dutta, B.; Maltese, V.; Farazi, F. A facet-based methodology for the construction of a large-scale geospatial ontology. J. Data Semant 2012, 1, 57– 73, DOI: 10.1007/s13740-012-0005-xThere is no corresponding record for this reference.
- 76Giunchiglia, F.; Dutta, B.; Maltese, V. From knowledge organization to knowledge representation. Knowl. Organ. 2014, 41, 44– 56, DOI: 10.5771/0943-7444-2014-1-44There is no corresponding record for this reference.
- 77Fernández-López, M.; Gómez-Pérez, A.; Juristo, N. Methontology: from ontological art towards ontological engineering. Proceedings of the Ontological Engineering AAAI-97 Spring Symposium Series ; 1997.There is no corresponding record for this reference.
- 78Allen, F. H.; Bellard, S.; Brice, M. D.; Cartwright, B. A.; Doubleday, A.; Higgs, H.; Hummelink, T.; Hummelink-Peters, B. G.; Kennard, O.; Motherwell, W. D. S.; Rodgers, J. R.; Watson, D. G. The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information. Acta Crystallogr. B 1979, 35, 2331– 2339, DOI: 10.1107/S0567740879009249There is no corresponding record for this reference.
- 79O’Keeffe, M.; Peskov, M. A.; Ramsden, S. J.; Yaghi, O. M. The reticular chemistry structure resource (RCSR) database of, and symbols for, crystal nets. Acc. Chem. Res. 2008, 41, 1782– 1789, DOI: 10.1021/ar800124u79https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXht1SgsrjF&md5=392c624f403dd8457460a7649aa496f3The Reticular Chemistry Structure Resource (RCSR) database of, and symbols for, crystal netsO'Keeffe, Michael; Peskov, Maxim A.; Ramsden, Stuart J.; Yaghi, Omar M.Accounts of Chemical Research (2008), 41 (12), 1782-1789CODEN: ACHRE4; ISSN:0001-4842. (American Chemical Society)During the past decade, interest has grown tremendously in the design and synthesis of cryst. materials constructed from mol. clusters linked by extended groups of atoms. Most notable are metal-org. frameworks (MOFs), in which polyat. inorg. metal-contg. clusters are joined by polytopic linkers. (Although these materials are sometimes referred to as coordination polymers, we prefer to differentiate them, because MOFs are based on strong linkages that yield robust frameworks.) The realization that MOFs could be designed and synthesized in a rational way from mol. building blocks led to the emergence of a discipline that we call reticular chem.MOFs can be represented as a special kind of graph called a periodic net. Such descriptions date back to the earliest crystallog. studies but have become much more common recently because thousands of new structures and hundreds of underlying nets have been reported. In the simplest cases (e.g., the structure of diamond), the atoms in the crystal become the vertices of the net, and bonds are the links (edges) that connect them. In the case of MOFs, polyat. groups act as the vertices and edges of the net.Because of the explosive growth in this area, a need has arisen for a universal system of nomenclature, classification, identification, and retrieval of these topol. structures. We have developed a system of symbols for the identification of three periodic nets of interest, and this system is now in wide use. In this Account, we explain the underlying methodol. of assigning symbols and describe the Reticular Chem. Structure Resource (RCSR), in which about 1600 such nets are collected and illustrated in a database that can be searched by symbol, name, keywords, and attributes. The resource also contains searchable data for polyhedra and layers.The database entries come from systematic enumerations or from known chem. compds. or both. In the latter case, refs. to occurrences are provided. We describe some crystallog., topol., and other attributes of nets and explain how they are reported in the database. We also describe how the database can be used as a tool for the design and structural anal. of new materials. Assocd. with each net is a natural tiling, which is a natural partition of space into space-filling tiles. The database allows export of data that can be used to analyze and illustrate such tilings.
- 80Glimm, B.; Horrocks, I.; Motik, B.; Stoilos, G.; Wang, Z. HermiT: an OWL 2 reasoner. J. Automat. Reason. 2014, 53, 245– 269, DOI: 10.1007/s10817-014-9305-1There is no corresponding record for this reference.
- 81Motik, B.; Shearer, R.; Horrocks, I. Hypertableau reasoning for description logics. J. Artif. Intell. Res. 2009, 36, 165– 228, DOI: 10.1613/jair.2811There is no corresponding record for this reference.
- 82López, X.; Carbó, J. J.; Bo, C.; Poblet, J. M. Structure, properties and reactivity of polyoxometalates: a theoretical perspective. Chem. Soc. Rev. 2012, 41, 7537– 7571, DOI: 10.1039/c2cs35168d82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhsFGqurnP&md5=e030c2995f5e45094c0388033bb96607Structure, properties and reactivity of polyoxometalates: A theoretical perspectiveLopez, Xavier; Carbo, Jorge J.; Bo, Carles; Poblet, Josep M.Chemical Society Reviews (2012), 41 (22), 7537-7571CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)In the thematic review dedicated to polyoxometalate (POM) chem. published in Chem. Reviews in 1998, no contribution was devoted to theory. This is not surprising because computational modeling of mol. metal-oxide clusters was in its infancy at that time. Nowadays, the situation has completely changed and modern computational methods have been successfully applied to study the structure, electronic properties, spectroscopy and reactivity of POM clusters. Indeed, the progress achieved during the past decade has been spectacular and herein we critically review the most important papers to provide the reader with an almost complete perspective of the field.
- 83Kondinski, A. Chemical Modelling; RSC, 2021; pp 39– 71.There is no corresponding record for this reference.
- 84Hoffmann, R. Qualitative thinking in the age of modern computational chemistry─or what Lionel Salem knows. J. Mol. Struct. Theochem 1998, 424, 1– 6, DOI: 10.1016/S0166-1280(97)00219-484https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK1cXhtFygu7w%253D&md5=8ff2b9bc495e45e14f431c48e0c0ef10Qualitative thinking in the age of modern computational chemistry or what Lionel Salem knowsHoffmann, RoaldJournal of Molecular Structure: THEOCHEM (1998), 424 (1-2), 1-6CODEN: THEODJ; ISSN:0166-1280. (Elsevier Science B.V.)A personal assessment is given of the present state of computational chem., and in particular of the persistent need for qual. orbital thinking at a time when exceedingly accurate calcns. are possible. The need for the qual. view arises, it is claimed, from the inherent difference between predictability and understanding, from certain potential impediments to chem. understanding intrinsic to human-computer interactions, from the peculiar yet productive way that expt. and theory interact in chem., and lastly from some special features of theory in science in general.
- 85Chung, Y. G.; Haldoupis, E.; Bucior, B. J.; Haranczyk, M.; Lee, S.; Zhang, H.; Vogiatzis, K. D.; Milisavljevic, M.; Ling, S.; Camp, J. S.; Slater, B.; Siepmann, J. I.; Sholl, D. S.; Snurr, R. Q. Advances, updates, and analytics for the computation-ready, experimental metal–organic framework database: CoRE MOF 2019. J. Chem. Eng. Data 2019, 64, 5985– 5998, DOI: 10.1021/acs.jced.9b0083585https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitVOmtrrL&md5=51670c93eb8cb43309395afaaf620253Advances, Updates, and Analytics for the Computation-Ready, Experimental Metal-Organic Framework Database: CoRE MOF 2019Chung, Yongchul G.; Haldoupis, Emmanuel; Bucior, Benjamin J.; Haranczyk, Maciej; Lee, Seulchan; Zhang, Hongda; Vogiatzis, Konstantinos D.; Milisavljevic, Marija; Ling, Sanliang; Camp, Jeffrey S.; Slater, Ben; Siepmann, J. Ilja; Sholl, David S.; Snurr, Randall Q.Journal of Chemical & Engineering Data (2019), 64 (12), 5985-5998CODEN: JCEAAX; ISSN:0021-9568. (American Chemical Society)Over 14 000 porous, three-dimensional metal-org. framework structures are compiled and analyzed as a part of an update to the Computation-Ready, Exptl. Metal-Org. Framework Database (CoRE MOF Database). The updated database includes addnl. structures that were contributed by CoRE MOF users, obtained from updates of the Cambridge Structural Database and a Web of Science search, and derived through semiautomated reconstruction of disordered structures using a topol.-based crystal generator. In addn., value is added to the CoRE MOF database through new analyses that can speed up future nanoporous materials discovery activities, including open metal site detection and duplicate searches. Crystal structures (only for the subset that underwent significant changes during curation), pore analytics, and phys. property data are included with the publicly available CoRE MOF 2019 database.
- 86Te Velde, G. t.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; van Gisbergen, S. J.; Snijders, J. G.; Ziegler, T. Chemistry with ADF. J. Comput. Chem. 2001, 22, 931– 967, DOI: 10.1002/jcc.105686https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD3MXjtlGntrw%253D&md5=314e7e942de9b28e664afc5adb2f574fChemistry with ADFTe Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Fonseca Guerra, C.; Van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T.Journal of Computational Chemistry (2001), 22 (9), 931-967CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)A review with 241 refs. We present the theor. and tech. foundations of the Amsterdam D. Functional (ADF) program with a survey of the characteristics of the code (numerical integration, d. fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chem. shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, at. VDD charges). In the Applications section we discuss the phys. model of the electronic structure and the chem. bond, i.e., the Kohn-Sham MO (MO) theory, and illustrate the power of the Kohn-Sham MO model in conjunction with the ADF-typical fragment approach to quant. understand and predict chem. phenomena. We review the "Activation-strain TS interaction" (ATS) model of chem. reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in org. chem. or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochem. (structure and bonding of DNA) and of time-dependent d. functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the anal. of chem. phenomena.
- 87Rappé, A. K.; Casewit, C. J.; Colwell, K.; Goddard, W. A., III; Skiff, W. M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024– 10035, DOI: 10.1021/ja00051a04087https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaK38Xmtl2qur8%253D&md5=cf41e8bb9ad299fd5d79f070d690afe1UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulationsRappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M.Journal of the American Chemical Society (1992), 114 (25), 10024-35CODEN: JACSAT; ISSN:0002-7863.A new mol. mechanics force field, the Universal force field (UFF), is described wherein the force field parameters are estd. using general rules based only on the element, its hybridization and its connectivity. The force field functional forms, parameters, and generating formulas for the full periodic table are presented.
- 88Albalad, J.; Carné-Sánchez, A.; Grancha, T.; Hernández-López, L.; Maspoch, D. Protection strategies for directionally-controlled synthesis of previously inaccessible metal–organic polyhedra (MOPs): the cases of carboxylate-and amino-functionalised Rh (ii)-MOPs. Chem. Commun. 2019, 55, 12785– 12788, DOI: 10.1039/C9CC07083D88https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvV2ms7fI&md5=10a527781a41f305bb5447fd7c6470c7Protection strategies for directionally-controlled synthesis of previously inaccessible metal-organic polyhedra (MOPs): the cases of carboxylate- and amino-functionalised Rh(II)-MOPsAlbalad, Jorge; Carne-Sanchez, Arnau; Grancha, Thais; Hernandez-Lopez, Laura; Maspoch, DanielChemical Communications (Cambridge, United Kingdom) (2019), 55 (85), 12785-12788CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)Herein the authors report that strategic use of protecting groups in coordination reactions enables directional inhibition that gives highly functionalized metal-org. polyhedra (MOPs), rather than of the extended coordination networks. Using this approach, the authors functionalized two new porous cuboctahedral Rh(II) benzenedicarboxylate-based MOPs with 24 peripheral carboxylic acid groups or 24 peripheral amino groups.
- 89Zhang, Z.; Wojtas, L.; Zaworotko, M. J. Organic–inorganic hybrid polyhedra that can serve as supermolecular building blocks. Chem. Sci. 2014, 5, 927– 931, DOI: 10.1039/C3SC53099J89https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhs1Oru7g%253D&md5=45d48f2b26bf68b42bf2157802a37872Organic-inorganic hybrid polyhedra that can serve as supermolecular building blocksZhang, Zhenjie; Wojtas, Lukasz; Zaworotko, Michael J.Chemical Science (2014), 5 (3), 927-931CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)[V4O8X(COO)4]z- or [V5O9X(COO)4]2- polyoxometalate anions can function as 4-connected nodes that assemble with 3-connected org. nodes (1,3,5-benzentricarboxylate) to afford small cubicuboctahedral hybrid nanoballs (hyball-3, -4, -5) in high yield. The resulting polyhedral cages exhibit 550 Å3 internal vols. and gas sorption measurements reveal that solid forms of the hyballs are permanently porous. The exterior surfaces of the hyballs are suited for further self-assembly and hyball-3 can serve as an octahedral supermol. building block for the generation of primitive cubic (pcu) nets via two types of linkage: H bonds or coordination bonds.
- 90Gan, H.; Xu, N.; Qin, C.; Sun, C.; Wang, X.; Su, Z. Equi–size nesting of Platonic and Archimedean metal–organic polyhedra into a twin capsid. Nat. Commun. 2020, 11, 1– 8, DOI: 10.1038/s41467-020-17989-6There is no corresponding record for this reference.
- 91Simms, C.; Kondinski, A.; Parac-Vogt, T. N. Metal-Addenda Substitution in Plenary Polyoxometalates and in Their Modular Transition Metal Analogues. Eur. J. Inorg. Chem. 2020, 2020, 2559– 2572, DOI: 10.1002/ejic.20200025491https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhtVSgsbfE&md5=666fe63addf20d55c3ca0a2c898d7738Metal-Addenda Substitution in Plenary Polyoxometalates and in their Modular Transition Metal AnaloguesSimms, Charlotte; Kondinski, Aleksandar; Parac-Vogt, Tatjana N.European Journal of Inorganic Chemistry (2020), 2020 (27), 2559-2572CODEN: EJICFO; ISSN:1434-1948. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. For decades, the formal metal addenda substitution in the matrix of bulk metal oxides has been a prolific strategy to develop numerous (non-)stoichiometric all-inorg. compds. with tunable electronic and magnetic properties, and broad technol. applications. In contrast to bulk mixed-metal oxides, the formal metal-addenda substitution in their mol. equiv. typically leads to stoichiometrically precise mixed-metal cluster formulations which retain the overall structural topol. of the monometallic archetype, but exhibit pronounced differences in terms of reactivity and spectroscopic properties. These mixed-metal mol. metal oxides often show complex configurational isomerism that has been the subject of many exptl. and theor. studies. The mixed-addenda metal-oxo clusters are most prominent among the classical plenary (that contain no vacant metal sites) polyoxometalate (POMs) archetypes, which have emerging applications in homogeneous catalysis and material science (e.g. formation of open frameworks), and have also been explored in heterogeneous metal org. framework (MOF) catalysts. Therefore, this article provides comprehensive theor. and exptl. insights into the isomer problem of mixed-addenda mol. metal oxides and their applications.
- 92Kondinski, A.; Rasmussen, M.; Mangelsen, S.; Pienack, N.; Simjanoski, V.; Nather, C.; Stares, D. L.; Schalley, C. A.; Bensch, W. Composition-driven Archetype Dynamics in Polyoxovanadates. Chem. Sci. 2022, 13, 6397, DOI: 10.1039/D2SC01004F92https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xht1yks7fI&md5=6757382fdcf1819e8e5003c89c1c52eeComposition-driven archetype dynamics in polyoxovanadatesKondinski, Aleksandar; Rasmussen, Maren; Mangelsen, Sebastian; Pienack, Nicole; Simjanoski, Viktor; Nather, Christian; Stares, Daniel L.; Schalley, Christoph A.; Bensch, WolfgangChemical Science (2022), 13 (21), 6397-6412CODEN: CSHCCN; ISSN:2041-6520. (Royal Society of Chemistry)Mol. metal oxides often adopt common structural frameworks (i.e. archetypes), many of them boasting impressive structural robustness and stability. However, the ability to adapt and to undergo transformations between different structural archetypes is a desirable material design feature offering applicability in different environments. Using systems thinking approach that integrates synthetic, anal. and computational techniques, we explore the transformations governing the chem. of polyoxovanadates (POVs) constructed of arsenate and vanadate building units. The water-sol. salt of the low nuclearity polyanion [V6As8O26]4- can be effectively used for the synthesis of the larger spherical (i.e. kegginoidal) mixed-valent [V12As8O40]4- ppt., while the novel [V10As12O40]8- POVs having tubular cyclic structures are another, well sol. product. Surprisingly, in contrast to the common observation that high-nuclearity polyoxometalate (POM) clusters are fragmented to form smaller moieties in soln., the low nuclearity [V6As8O26]4- anion is in situ transformed into the higher nuclearity cluster anions. The obtained products support a conceptually new model that is outlined in this article and that describes a continuous evolution between spherical and cyclic POV assemblies. This new model represents a milestone on the way to rational and designable POV self-assemblies.
- 93Segler, M. H.; Waller, M. P. Modelling chemical reasoning to predict and invent reactions. Chem. Eur. J. 2017, 23, 6118– 6128, DOI: 10.1002/chem.20160455693https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXislersw%253D%253D&md5=ac3b304ec62b8d90110b7722305e2b3dModelling Chemical Reasoning to Predict and Invent ReactionsSegler, Marwin H. S.; Waller, Mark P.Chemistry - A European Journal (2017), 23 (25), 6118-6128CODEN: CEUJED; ISSN:0947-6539. (Wiley-VCH Verlag GmbH & Co. KGaA)The ability to reason beyond established knowledge allows org. chemists to solve synthetic problems and invent novel transformations. Herein, we propose a model that mimics chem. reasoning, and formalises reaction prediction as finding missing links in a knowledge graph. We have constructed a knowledge graph contg. 14.4 million mols. and 8.2 million binary reactions, which represents the bulk of all chem. reactions ever published in the scientific literature. Our model outperforms a rule-based expert system in the reaction prediction task for 180 000 randomly selected binary reactions. The data-driven model generalises even beyond known reaction types, and is thus capable of effectively (re-)discovering novel transformations (even including transition metal-catalyzed reactions). Our model enables computers to infer hypotheses about reactivity and reactions by only considering the intrinsic local structure of the graph and because each single reaction prediction is typically achieved in a sub-second time frame, the model can be used as a high-throughput generator of reaction hypotheses for reaction discovery.
- 94Mellot-Draznieks, C.; Dutour, J.; Férey, G. Hybrid organic–inorganic frameworks: routes for computational design and structure prediction. Angew. Chem., Int. Ed. 2004, 116, 6450– 6456, DOI: 10.1002/ange.200454251There is no corresponding record for this reference.
- 95Addicoat, M. A.; Coupry, D. E.; Heine, T. AuToGraFS: automatic topological generator for framework structures. J. Phys. Chem. A 2014, 118, 9607– 9614, DOI: 10.1021/jp507643v95https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhsFamsL%252FF&md5=4e07c2795b0f7e6d386c3ad5bc3ce488AuToGraFS: Automatic Topological Generator for Framework StructuresAddicoat, Matthew A.; Coupry, Damien E.; Heine, ThomasJournal of Physical Chemistry A (2014), 118 (40), 9607-9614CODEN: JPCAFH; ISSN:1089-5639. (American Chemical Society)Metal-org. frameworks (MOFs) and covalent org. frameworks (COFs) are recently notable examples of highly porous polymer frameworks with a raft of potential applications. Synthesis of these compds. is modular, with "connectors" and "linkers" able to be replaced almost at will in the fabrication of isoreticular frameworks (frameworks with the same underlying topol.). The range of components available to form such framework structures is vast, leading to a "combinatorial explosion" problem in predicting which framework compds. might have a set of desired properties. Computational investigations can be used in both predictive and explanatory roles in this research but rely on accurate structural models. In this work, we present our software, AuToGraFS, Automated Topol. Generator for Framework Structures, and show some of its advanced functionality in "computational reticular chem.". AuToGraFS is linked to a fully featured force field to produce fully optimized structures of arbitrary frameworks. AuToGraFS, including a graphical user interface, is publicly available for download.
- 96Wahiduzzaman, M.; Wang, S.; Sikora, B. J.; Serre, C.; Maurin, G. Computational structure determination of novel metal–organic frameworks. Chem. Commun. 2018, 54, 10812– 10815, DOI: 10.1039/C8CC05455J96https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhsVWhtb7E&md5=8bcdaca8037f3538971461e64c18b109Computational structure determination of novel metal-organic frameworksWahiduzzaman, Mohammad; Wang, Sujing; Sikora, Benjamin J.; Serre, Christian; Maurin, GuillaumeChemical Communications (Cambridge, United Kingdom) (2018), 54 (77), 10812-10815CODEN: CHCOFS; ISSN:1359-7345. (Royal Society of Chemistry)A structure prediction tool has been developed to guide the discovery of MOF materials. This computational strategy has been trained over a series of existing MOFs and further successfully applied in tandem with an exptl. effort to produce novel Zr MOFs based on naturally occurring carboxylic acids.
- 97Turcani, L.; Tarzia, A.; Szczypiński, F. T.; Jelfs, K. E. stk: An extendable Python framework for automated molecular and supramolecular structure assembly and discovery. J. Chem. Phys. 2021, 154, 214102, DOI: 10.1063/5.004970897https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXht1aqu73N&md5=f4de0edc1440cc685fe00b03571be80fstk: An extendable Python framework for automated molecular and supramolecular structure assembly and discoveryTurcani, Lukas; Tarzia, Andrew; Szczypinski, Filip T.; Jelfs, Kim E.Journal of Chemical Physics (2021), 154 (21), 214102CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)Computational software workflows are emerging as all-in-one solns. to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, mol. and supramol. materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramol. toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)mol. structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-contg. structures and rotaxanes as well as general implementation and interface improvements. Addnl., this version includes built-in tools for exploring chem. space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk. (c) 2021 American Institute of Physics.
- 98Young, T. A.; Gheorghe, R.; Duarte, F. cgbind: A Python Module and Web App for Automated Metallocage Construction and Host–Guest Characterization. J. Chem. Inf. Model. 2020, 60, 3546– 3557, DOI: 10.1021/acs.jcim.0c0051998https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXht1CltLjN&md5=ce1a2502ad771f176d1caad1df1eee28cgbind: A Python Module and Web App for Automated Metallocage Construction and Host-Guest CharacterizationYoung, Tom A.; Gheorghe, Razvan; Duarte, FernandaJournal of Chemical Information and Modeling (2020), 60 (7), 3546-3557CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)Metallocages offer a diverse and underexplored region of chem. space in which to search for novel catalysts and substrate hosts. However, the ability to tailor such structures toward applications in binding and catalysis is a challenging task. Here, we present an open-source computational toolkit, cgbind, that facilitates the construction, characterization, and prediction of functional metallocages. It employs known structural scaffolds as starting points and computationally efficient approaches for property evaluation. We demonstrate the ability of cgbind to construct libraries of cages with varied topologies and linker functionalities, generate accurate geometries (RMSD < 1.5 Å to crystal structures), and predict substrate binding with accuracy on par with semiempirical QM, all in seconds. The cgbind code presented here is freely available at github.com/duartegroup/cgbind and also via a web-based graphical user interface at cgbind.chem.ox.ac.uk. The protocol described here paves the way for high-throughput virtual screening of potential supramol. structures, accelerating the search for new hosts and catalysts.
- 99Zhou, X.; Nurkowski, D.; Mosbach, S.; Akroyd, J.; Kraft, M. Question answering system for chemistry. J. Chem. Inf. Model. 2021, 61, 3868– 3880, DOI: 10.1021/acs.jcim.1c0027599https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1Kru7vJ&md5=7984547eaed72640f808bbf30ba9b749Question Answering System for ChemistryZhou, Xiaochi; Nurkowski, Daniel; Mosbach, Sebastian; Akroyd, Jethro; Kraft, MarkusJournal of Chemical Information and Modeling (2021), 61 (8), 3868-3880CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)This paper describes the implementation and evaluation of a proof-of-concept Question Answering (QA) system for accessing chem. data from knowledge graphs (KGs) which offer data from chem. kinetics to the chem. and phys. properties of species. We trained the question classification and named the entity recognition models that specialize in interpreting chem. questions. The system has a novel design which applies a topic model to identify the question-to-ontol. affiliation to handle ontologies with different structures. The topic model also helps the system to provide answers with a higher quality. Moreover, a new method that automatically generates training questions from ontologies is also implemented. The question set generated for training contains 432,989 questions under 11 types. Such a training set has been proven to be effective for training both the question classification model and the named entity recognition model. We evaluated the system using other KGQA systems as baselines. The system outperforms the chosen KGQA system answering chem.-related questions. The QA system is also compared to the Google search engine and the WolframAlpha engine. It shows that the QA system can answer certain types of questions better than the search engines.
Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.2c03402.
Summary of algorithmic output, description Logic, list of chemical building units, illustration of the CBU sharing phenomenon, comments, algorithmic Output II and visual construction of new MOPs based on Algorithmic Output II (PDF)
Supporting Video S1 (MP4)
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