Identi fi cation Schemes for Metal − Organic Frameworks To Enable Rapid Search and Cheminformatics Analysis

: The modular nature of metal − organic frameworks (MOFs) leads to a very large number of possible structures. High-throughput computational screening has led to a rapid increase in property data that has enabled several potential applications for MOFs, including gas storage, separations, catalysis

[1]  Robin Taylor,et al.  A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. , 2019, Chemical reviews.

[2]  Alán Aspuru-Guzik,et al.  SELFIES: a robust representation of semantically constrained graphs with an example application in chemistry , 2019, ArXiv.

[3]  Randall Q. Snurr,et al.  Identifying promising metal–organic frameworks for heterogeneous catalysis via high‐throughput periodic density functional theory , 2019, J. Comput. Chem..

[4]  Alán Aspuru-Guzik,et al.  Autonomous Molecular Design: Then and Now. , 2019, ACS applied materials & interfaces.

[5]  Daniel C. Elton,et al.  Deep learning for molecular generation and optimization - a review of the state of the art , 2019, Molecular Systems Design & Engineering.

[6]  Diego A. Gómez-Gualdrón,et al.  Increasing topological diversity during computational “synthesis” of porous crystals: how and why , 2019, CrystEngComm.

[7]  D. Adams,et al.  Chemical control of structure and guest uptake by a conformationally mobile porous material , 2019, Nature.

[8]  Rochus Schmid,et al.  TopoFF: MOF structure prediction using specifically optimized blueprints. , 2018, Faraday discussions.

[9]  O. Yaghi,et al.  Secondary building units as the turning point in the development of the reticular chemistry of MOFs , 2018, Science Advances.

[10]  P. Nachtigall,et al.  Towards operando computational modeling in heterogeneous catalysis , 2018, Chemical Society reviews.

[11]  M. Zaworotko,et al.  A dynamic and multi-responsive porous flexible metal–organic material , 2018, Nature Communications.

[12]  Anand Chandrasekaran,et al.  Polymer Genome: A Data-Powered Polymer Informatics Platform for Property Predictions , 2018, The Journal of Physical Chemistry C.

[13]  M. O'keeffe,et al.  Enriching the Reticular Chemistry Repertoire: Merged Nets Approach for the Rational Design of Intricate Mixed-Linker Metal-Organic Framework Platforms. , 2018, Journal of the American Chemical Society.

[14]  O. Yaghi,et al.  The geometry of periodic knots, polycatenanes and weaving from a chemical perspective: a library for reticular chemistry. , 2018, Chemical Society reviews.

[15]  Andrius Merkys,et al.  Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database , 2018, Journal of Cheminformatics.

[16]  Christina T. Lollar,et al.  Interior Decoration of Stable Metal-Organic Frameworks. , 2018, Langmuir : the ACS journal of surfaces and colloids.

[17]  Michael O'Keeffe,et al.  Deconstruction of Crystalline Networks into Underlying Nets: Relevance for Terminology Guidelines and Crystallographic Databases , 2018 .

[18]  Regina Barzilay,et al.  Junction Tree Variational Autoencoder for Molecular Graph Generation , 2018, ICML.

[19]  Senja Barthel,et al.  Distinguishing Metal–Organic Frameworks , 2018, Crystal growth & design.

[20]  Thierry Kogej,et al.  Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks , 2017, ACS central science.

[21]  Christina T. Lollar,et al.  PCN-250 under Pressure: Sequential Phase Transformation and the Implications for MOF Densification , 2017 .

[22]  David S. Sholl,et al.  How Reproducible Are Isotherm Measurements in Metal–Organic Frameworks? , 2017 .

[23]  Jihan Kim,et al.  Text Mining Metal-Organic Framework Papers , 2017, J. Chem. Inf. Model..

[24]  Maciej Haranczyk,et al.  Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization , 2017, Front. Mater..

[25]  Diego A. Gómez-Gualdrón,et al.  Elucidating the Nanoparticle–Metal Organic Framework Interface of Pt@ZIF-8 Catalysts , 2017 .

[26]  Diego A. Gómez-Gualdrón,et al.  Topologically Guided, Automated Construction of Metal–Organic Frameworks and Their Evaluation for Energy-Related Applications , 2017 .

[27]  Luciano A. Abriata,et al.  Web Apps Come of Age for Molecular Sciences , 2017, Informatics.

[28]  A. Karmakar,et al.  Recent advances on supramolecular isomerism in metal organic frameworks , 2017 .

[29]  K. Lillerud,et al.  Pitfalls in metal-organic framework crystallography: towards more accurate crystal structures. , 2017, Chemical Society reviews.

[30]  T. Uemura,et al.  Hybridization of MOFs and polymers. , 2017, Chemical Society reviews.

[31]  Adam H. Steeves,et al.  Leveraging Cheminformatics Strategies for Inorganic Discovery: Application to Redox Potential Design , 2017 .

[32]  S. Kaskel,et al.  “The Chemistry of Metal-Organic Frameworks: Synthesis, Characterization, and Applications” , 2017 .

[33]  Peyman Z. Moghadam,et al.  Development of a Cambridge Structural Database Subset: A Collection of Metal-Organic Frameworks for Past, Present, and Future , 2017 .

[34]  Jeffrey S. Camp,et al.  Large-Scale Refinement of Metal−Organic Framework Structures Using Density Functional Theory , 2017 .

[35]  O. Yaghi,et al.  The atom, the molecule, and the covalent organic framework , 2017, Science.

[36]  M. O'keeffe,et al.  Crystal structures as periodic graphs: the topological genome and graph databases , 2017, Structural Chemistry.

[37]  J. Hupp,et al.  Room-Temperature Synthesis of UiO-66 and Thermal Modulation of Densities of Defect Sites , 2017 .

[38]  Andrey Kazennov,et al.  The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology , 2016, Oncotarget.

[39]  M. Weiss,et al.  Topological control of 3,4-connected frameworks based on the Cu-2-paddle-wheel node: tbo or pto, and why? , 2016 .

[40]  Alán Aspuru-Guzik,et al.  Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules , 2016, ACS central science.

[41]  Diego A. Gómez-Gualdrón,et al.  Evaluating topologically diverse metal–organic frameworks for cryo-adsorbed hydrogen storage , 2016 .

[42]  Fengqi You,et al.  In silico discovery of metal-organic frameworks for precombustion CO2 capture using a genetic algorithm , 2016, Science Advances.

[43]  Heather J. Kulik,et al.  molSimplify: A toolkit for automating discovery in inorganic chemistry , 2016, J. Comput. Chem..

[44]  Kyriakos C. Stylianou,et al.  In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis , 2016, Chemical science.

[45]  Svetlana Artemova,et al.  Automatic molecular structure perception for the universal force field , 2016, J. Comput. Chem..

[46]  B. Meredig,et al.  Materials science with large-scale data and informatics: Unlocking new opportunities , 2016 .

[47]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[48]  Ryan Arlitt,et al.  Automated design of flexible linkers. , 2016, Dalton transactions.

[49]  M. A. van der Veen,et al.  Controlled partial interpenetration in metal–organic frameworks , 2016, Nature Chemistry.

[50]  Jeffrey S. Camp,et al.  A Comprehensive Set of High-Quality Point Charges for Simulations of Metal–Organic Frameworks , 2016 .

[51]  Roger A. Sayle,et al.  Get Your Atoms in Order - An Open-Source Implementation of a Novel and Robust Molecular Canonicalization Algorithm , 2015, J. Chem. Inf. Model..

[52]  Gang Fu,et al.  PubChem Substance and Compound databases , 2015, Nucleic Acids Res..

[53]  Ryan P. Lively,et al.  Defects in Metal-Organic Frameworks: Challenge or Opportunity? , 2015, The journal of physical chemistry letters.

[54]  Wendy A. Warr,et al.  Many InChIs and quite some feat , 2015, Journal of Computer-Aided Molecular Design.

[55]  Kwang‐Hwi Cho,et al.  Identification of Isomers of Organometallic Compounds , 2015 .

[56]  Stephen R. Heller,et al.  InChI, the IUPAC International Chemical Identifier , 2015, Journal of Cheminformatics.

[57]  Richard L. Martin,et al.  In silico prediction of MOFs with high deliverable capacity or internal surface area. , 2015, Physical chemistry chemical physics : PCCP.

[58]  Dongwook Kim,et al.  Topology analysis of metal–organic frameworks based on metal–organic polyhedra as secondary or tertiary building units , 2015 .

[59]  Maciej Haranczyk,et al.  In Silico Discovery of High Deliverable Capacity Metal–Organic Frameworks , 2015 .

[60]  Maciej Haranczyk,et al.  Computation-Ready, Experimental Metal–Organic Frameworks: A Tool To Enable High-Throughput Screening of Nanoporous Crystals , 2014 .

[61]  Joshua Borycz,et al.  Defining the Proton Topology of the Zr6-Based Metal-Organic Framework NU-1000. , 2014, The journal of physical chemistry letters.

[62]  Diego A. Gómez-Gualdrón,et al.  Computational Design of Metal–Organic Frameworks Based on Stable Zirconium Building Units for Storage and Delivery of Methane , 2014 .

[63]  Diego A. Gómez-Gualdrón,et al.  Water-stable zirconium-based metal-organic framework material with high-surface area and gas-storage capacities. , 2014, Chemistry.

[64]  Omar K Farha,et al.  Beyond post-synthesis modification: evolution of metal-organic frameworks via building block replacement. , 2014, Chemical Society reviews.

[65]  Vishwesh Venkatraman,et al.  Automated Building of Organometallic Complexes from 3D Fragments , 2014, J. Chem. Inf. Model..

[66]  A. P. Shevchenko,et al.  Applied Topological Analysis of Crystal Structures with the Program Package ToposPro , 2014 .

[67]  Matthew J. Lennox,et al.  Polymorphism of metal-organic frameworks: direct comparison of structures and theoretical N₂-uptake of topological pto- and tbo-isomers. , 2014, Chemical communications.

[68]  M. Fröba,et al.  Two Metal–Organic Frameworks with a Tetratopic Linker: Solvent-Dependent Polymorphism and Postsynthetic Bromination , 2014 .

[69]  Michael O'Keeffe,et al.  Topological analysis of metal-organic frameworks with polytopic linkers and/or multiple building units and the minimal transitivity principle. , 2014, Chemical reviews.

[70]  Michael O’Keeffe,et al.  The Chemistry and Applications of Metal-Organic Frameworks , 2013, Science.

[71]  Lars Öhrström,et al.  Terminology of metal–organic frameworks and coordination polymers (IUPAC Recommendations 2013) , 2013 .

[72]  Li-Chiang Lin,et al.  Mail-Order Metal–Organic Frameworks (MOFs): Designing Isoreticular MOF-5 Analogues Comprising Commercially Available Organic Molecules , 2013 .

[73]  Christopher Southan,et al.  InChI in the wild: an assessment of InChIKey searching in Google , 2013, Journal of Cheminformatics.

[74]  R. Schmid,et al.  Hypothetical 3D-periodic covalent organic frameworks: exploring the possibilities by a first principles derived force field , 2013 .

[75]  Giovanni Garberoglio,et al.  OBGMX: A web‐based generator of GROMACS topologies for molecular and periodic systems using the universal force field , 2012, J. Comput. Chem..

[76]  Zhangwen Wei,et al.  Zirconium-metalloporphyrin PCN-222: mesoporous metal-organic frameworks with ultrahigh stability as biomimetic catalysts. , 2012, Angewandte Chemie.

[77]  Hongli Li,et al.  HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation , 2012, J. Chem. Inf. Model..

[78]  Noel M. O'Boyle Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI , 2012, Journal of Cheminformatics.

[79]  Seth M. Cohen,et al.  Functional group effects on metal-organic framework topology. , 2012, Chemical communications.

[80]  D. Cascio,et al.  Synthesis, structure, and metalation of two new highly porous zirconium metal-organic frameworks. , 2012, Inorganic chemistry.

[81]  V. V. Speybroeck,et al.  Synthesis, Structural Characterization, and Catalytic Performance of a Vanadium-Based Metal–Organic Framework (COMOC-3) , 2012 .

[82]  Lars Öhrström,et al.  Coordination polymers, metal-organic frameworks and the need for terminology guidelines , 2012 .

[83]  Michael O'Keeffe,et al.  Deconstructing the crystal structures of metal-organic frameworks and related materials into their underlying nets. , 2012, Chemical reviews.

[84]  C. Wilmer,et al.  Large-scale screening of hypothetical metal-organic frameworks. , 2012, Nature chemistry.

[85]  A. Clark Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting , 2011, J. Chem. Inf. Model..

[86]  Peter Moeck,et al.  Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration , 2011, Nucleic Acids Res..

[87]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[88]  C. Knobler,et al.  Metal-organic frameworks of vanadium as catalysts for conversion of methane to acetic acid. , 2011, Inorganic chemistry.

[89]  I. Bruno,et al.  Deducing chemical structure from crystallographically determined atomic coordinates , 2011, Acta crystallographica. Section B, Structural science.

[90]  Wendy A. Warr,et al.  Representation of chemical structures , 2011 .

[91]  Hong-Cai Zhou,et al.  Isomerism in Metal-Organic Frameworks: "Framework Isomers". , 2011, The journal of physical chemistry letters.

[92]  V. Blatov,et al.  Underlying nets in three-periodic coordination polymers: topology, taxonomy and prediction from a computer-aided analysis of the Cambridge Structural Database , 2011 .

[93]  M. Hirscher,et al.  Elucidating gating effects for hydrogen sorption in MFU-4-type triazolate-based metal-organic frameworks featuring different pore sizes. , 2011, Chemistry.

[94]  Axel Drefahl,et al.  CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures , 2011, J. Cheminformatics.

[95]  Michael O'Keeffe,et al.  Secondary building units, nets and bonding in the chemistry of metal-organic frameworks. , 2009, Chemical Society reviews.

[96]  Nicholas E. Day,et al.  Automated analysis and validation of open chemical data , 2009 .

[97]  O. Yaghi,et al.  The Reticular Chemistry Structure Resource (RCSR) database of, and symbols for, crystal nets. , 2008, Accounts of chemical research.

[98]  Saeed Amirjalayer,et al.  Conformational Isomerism in the Isoreticular Metal Organic Framework Family: A Force Field Investigation , 2008 .

[99]  Beatriz Cordero,et al.  Covalent radii revisited. , 2008, Dalton transactions.

[100]  Peter Murray-Rust,et al.  Engineering Polymer Informatics: Towards The Computer-Aided Design of Polymers , 2008 .

[101]  Chris Morley,et al.  Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit , 2008, Chemistry Central journal.

[102]  A. J. Blake,et al.  High H2 adsorption by coordination-framework materials. , 2006, Angewandte Chemie.

[103]  Michael O'Keeffe,et al.  Porous, Crystalline, Covalent Organic Frameworks , 2005, Science.

[104]  Michael O'Keeffe,et al.  Reticular chemistry: occurrence and taxonomy of nets and grammar for the design of frameworks. , 2005, Accounts of chemical research.

[105]  Vladislav A. Blatov,et al.  Interpenetrating metal–organic and inorganic 3D networks: a computer-aided systematic investigation. Part I. Analysis of the Cambridge structural database , 2004 .

[106]  Davide M. Proserpio,et al.  POLYCATENATION, POLYTHREADING AND POLYKNOTTING IN COORDINATION NETWORK CHEMISTRY , 2003 .

[107]  Michael O'Keeffe,et al.  Identification of and symmetry computation for crystal nets. , 2003, Acta crystallographica. Section A, Foundations of crystallography.

[108]  Michael O'Keeffe,et al.  Reticular synthesis and the design of new materials , 2003, Nature.

[109]  Robin Taylor,et al.  New software for searching the Cambridge Structural Database and visualizing crystal structures. , 2002, Acta crystallographica. Section B, Structural science.

[110]  M. Eddaoudi,et al.  Metal–organic frameworks constructed from pentagonal antiprismatic and cuboctahedral secondary building units , 2001 .

[111]  T. Reineke,et al.  Assembly of metal-organic frameworks from large organic and inorganic secondary building units: new examples and simplifying principles for complex structures. , 2001, Journal of the American Chemical Society.

[112]  David Weininger,et al.  SMILES. 2. Algorithm for generation of unique SMILES notation , 1989, J. Chem. Inf. Comput. Sci..

[113]  David Weininger,et al.  SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules , 1988, J. Chem. Inf. Comput. Sci..

[114]  Donald D. Chamberlin,et al.  SEQUEL: A structured English query language , 1974, SIGFIDET '74.

[115]  T. Heine,et al.  Extension of the Universal Force Field for Metal-Organic Frameworks. , 2016, Journal of chemical theory and computation.

[116]  Maik Moeller An Introduction To Chemoinformatics , 2016 .

[117]  R. Fischer,et al.  Metal–organic frameworks as hosts for nanoparticles , 2015 .

[118]  Jarad A. Mason Metal-Organic Frameworks for Gas Storage and Separation , 2015 .

[119]  N. Null How Many Miles Have We Gone, InChI by InChI? , 2012 .

[120]  Banglin Chen,et al.  High H2 adsorption in a microporous metal-organic framework with open metal sites. , 2005, Angewandte Chemie.

[121]  C. Serre,et al.  Very large breathing effect in the first nanoporous chromium(III)-based solids: MIL-53 or Cr(III)(OH) x [O(2)C-C(6)H(4)-CO(2)] x [HO(2)C-C(6)H(4)-CO(2)H](x) x H(2)O(y). , 2002, Journal of the American Chemical Society.

[122]  Murray Gm A whole greater than the sum of its parts. , 1992, Computers in healthcare.

[123]  L. G. Donaruma,et al.  Nomenclature for regular single-strand and quasi single-strand inorganic and coordination polymers (Recommendations 1984): International Union of Pure and Applied Chemistry (IUPAC) Macromolecular Division, Commission on Macromolecular Nomenclature Inorganic Chemistry Division, Commission on Nomencla , 1986 .