A New Kind of Atlas of Zeolite Building Blocks

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{
  "revision": 1, 
  "id": "260", 
  "created": "2020-05-12T13:53:27.575483+00:00", 
  "metadata": {
    "doi": "10.24435/materialscloud:2019.0079/v1", 
    "status": "published", 
    "title": "A New Kind of Atlas of Zeolite Building Blocks", 
    "mcid": "2019.0079/v1", 
    "license_addendum": "", 
    "_files": [
      {
        "description": "Description of file contents", 
        "key": "README.txt", 
        "size": 3597, 
        "checksum": "md5:935d4d59674d16d8c64bbe96ffa70a6b"
      }, 
      {
        "description": "Silicon-centered environment descriptors and properties used in the corresponding study. The structures used to generate the descriptors are a subset of those found in the DEEM SLC PCOD database (http://www.hypotheticalzeolites.net/DATABASE/DEEM/)", 
        "key": "archive.tar.gz", 
        "size": 925699568, 
        "checksum": "md5:3c1ecfacaae2b13830b408133d9f1dcb"
      }
    ], 
    "owner": 28, 
    "_oai": {
      "id": "oai:materialscloud.org:260"
    }, 
    "keywords": [
      "MARVEL", 
      "Machine Learning", 
      "ERC", 
      "SCCER", 
      "Zeolites"
    ], 
    "conceptrecid": "259", 
    "is_last": true, 
    "references": [
      {
        "type": "Journal reference", 
        "doi": "10.1063/1.5119751", 
        "url": "", 
        "comment": "Paper for which the dataset was generated", 
        "citation": "B. A. Helfrecht, R. Semino, G. Pireddu, S. M. Auerbach, M. Ceriotti, J. Chem. Phys. 151, 154112 (2019)."
      }, 
      {
        "type": "Journal reference", 
        "doi": "10.1039/c0cp02255a", 
        "url": "", 
        "comment": "Paper in which the Deem database was originally created, described, and used", 
        "citation": "R. Pophale, P. A. Cheeseman, M. W. Deem, Phys. Chem. Chem. Phys. 13, 12407-12412 (2011)"
      }
    ], 
    "publication_date": "Nov 06, 2019, 00:00:00", 
    "license": "Creative Commons Attribution 4.0 International", 
    "id": "260", 
    "description": "We have analyzed structural motifs in the Deem database of hypothetical zeolites to investigate whether the structural diversity found in this database can be well-represented by classical descriptors, such as distances, angles, and ring sizes, or whether a more general representation of the atomic structure, furnished by the smooth overlap of atomic position (SOAP) method, is required to capture accurately structure\u2013property relations. We assessed the quality of each descriptor by machine-learning the molar energy and volume for each hypothetical framework in the dataset. We have found that a SOAP representation with a cutoff length of 6 \u00c5, which goes beyond near-neighbor tetrahedra, best describes the structural diversity in the Deem database by capturing relevant interatomic correlations. Kernel principal component analysis shows that SOAP maintains its superior performance even when reducing its dimensionality to those of the classical descriptors and that the first three kernel principal components capture the main variability in the dataset, allowing a 3D point cloud visualization of local environments in the Deem database. This \u201ccloud atlas\u201d of local environments was found to show good correlations with the contribution of a given motif to the density and stability of its parent framework. Local volume and energy maps constructed from the SOAP/machine learning analyses provide new images of zeolites that reveal smooth variations of local volumes and energies across a given framework and correlations between the contributions to volume and energy associated with each atom-centered environment.", 
    "version": 1, 
    "contributors": [
      {
        "email": "benjamin.helfrecht@epfl.ch", 
        "affiliations": [
          "Institut des Mat\u00e9riaux, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland"
        ], 
        "familyname": "Helfrecht", 
        "givennames": "Benjamin A."
      }, 
      {
        "affiliations": [
          "Institut des Mat\u00e9riaux, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland and Institut Charles Gerhardt Montpellier UMR 5253 CNRS, Universit\u00e9 de Montpellier, Place E. Bataillon, 34095 Montpellier Cedex 05, France"
        ], 
        "familyname": "Semino", 
        "givennames": "Rocio"
      }, 
      {
        "affiliations": [
          "Institut des Mat\u00e9riaux, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland and Dipartimento di Chimica e Farmacia, Unversit\u00e0 degli Studi di Sassari, Via Vienna 2, 01700 Sassari, Italy"
        ], 
        "familyname": "Pireddu", 
        "givennames": "Giovanni"
      }, 
      {
        "affiliations": [
          "Department of Chemistry and Department of Chemical Engineering, University of Massachusetts, Amherst, Amherst, Massachusetts 01003, USA"
        ], 
        "familyname": "Auerbach", 
        "givennames": "Scott M."
      }, 
      {
        "email": "michele.ceriotti@epfl.ch", 
        "affiliations": [
          "Institut des Mat\u00e9riaux, \u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne, 1015 Lausanne, Switzerland"
        ], 
        "familyname": "Ceriotti", 
        "givennames": "Michele"
      }
    ], 
    "edited_by": 98
  }, 
  "updated": "2019-11-06T00:00:00+00:00"
}