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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. Deconstruction Division, Joint BioEnergy Institute, Emeryville California, Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore Califonia
  2. Deconstruction Division, Joint BioEnergy Institute, Emeryville California, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley Califonia
  3. Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester and School of Chemistry, University of Manchester, Oxford Road, Manchester Great Britain
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:
Published Article
Journal Name:
Journal of Computational Chemistry
Additional Journal Information:
Journal Name: Journal of Computational Chemistry; 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 = ,
volume = ,
place = {United States},
year = {2017},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1002/jcc.25054

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Cited by: 2 works
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