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Title: Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

Abstract

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..

Authors:
ORCiD logo [1];  [1];  [2]; ORCiD logo [3]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States). Deconstruction Division; Sandia National Lab. (SNL-CA), Livermore, CA (United States). Biomass Science and Conversion Technology Dept.
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States). Deconstruction Division; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems and Engineering Division
  3. Univ. of Manchester (United Kingdom). Manchester Institute of Biotechnology (MIB), and School of Chemistry
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1377950
Alternate Identifier(s):
OSTI ID: 1398064; OSTI ID: 1416934
Grant/Contract Number:  
AC02-05CH11231; EP/K005472
Resource Type:
Journal Article: Published Article
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Volume: 38; Journal Issue: 29; Journal ID: ISSN 0192-8651
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING; quantum chemical topology; quantum theory of atoms in molecules; blender; molecular graphics; visualization

Citation Formats

Mills, Matthew J. L., Sale, Kenneth L., Simmons, Blake A., and Popelier, Paul L. A. Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. United States: N. p., 2017. Web. doi:10.1002/jcc.25054.
Mills, Matthew J. L., Sale, Kenneth L., Simmons, Blake A., & Popelier, Paul L. A. Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. United States. doi:10.1002/jcc.25054.
Mills, Matthew J. L., Sale, Kenneth L., Simmons, Blake A., and Popelier, Paul L. A. Thu . "Rhorix: An interface between quantum chemical topology and the 3D graphics program blender". United States. doi:10.1002/jcc.25054.
@article{osti_1377950,
title = {Rhorix: An interface between quantum chemical topology and the 3D graphics program blender},
author = {Mills, Matthew J. L. and Sale, Kenneth L. and Simmons, Blake A. and Popelier, Paul L. A.},
abstractNote = {Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..},
doi = {10.1002/jcc.25054},
journal = {Journal of Computational Chemistry},
number = 29,
volume = 38,
place = {United States},
year = {Thu Aug 31 00:00:00 EDT 2017},
month = {Thu Aug 31 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1002/jcc.25054

Citation Metrics:
Cited by: 1 work
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