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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
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. 2017. "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 = 2017,
month = 8
}

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

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  • 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 ofmore » 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..« less
  • Solutions of the system HCl-HNO/sub 3/-H/sub 2/O are often used for the structural etching and polishing of cadmium telluride, but there is no information in the literature on the rate and mechanism of the reaction of CdTe with these solutions. These investigations show that the solution of cadmium telluride in aqueous solutions of HCl-HNO/sub 3/ mixtures is determined by the concentration of hydrochloric acid retarding the process. In the concentration triangle for HCl-HNO/sub 3/-H/sub 2/O three regions were distinguished, differing with respect to the CdTe solution mechanism. It was shown that in each of these regions the CdTe surface ismore » coated with a film consisting of tellurium and its oxidation products. The thickness of the film also is determined by the hydrochloric acid concentration.« less
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