DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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 Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
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. https://doi.org/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. https://doi.org/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 = {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. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.},
doi = {10.1002/jcc.25054},
journal = {Journal of Computational Chemistry},
number = ,
volume = ,
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
https://doi.org/10.1002/jcc.25054

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Visualization and integration of quantum topological atoms by spatial discretization into finite elements
journal, January 2007

  • Rafat, M.; Popelier, P. L. A.
  • Journal of Computational Chemistry, Vol. 28, Issue 16
  • DOI: 10.1002/jcc.20767

Generating Efficient Quantum Chemistry Codes for Novel Architectures
journal, November 2012

  • Titov, Alexey V.; Ufimtsev, Ivan S.; Luehr, Nathan
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 1
  • DOI: 10.1021/ct300321a

Accelerating self-consistent field convergence with the augmented Roothaan–Hall energy function
journal, February 2010

  • Hu, Xiangqian; Yang, Weitao
  • The Journal of Chemical Physics, Vol. 132, Issue 5
  • DOI: 10.1063/1.3304922

Quantisierung als Eigenwertproblem
journal, January 1926


Zur Quantentheorie der hom�opolaren Valenzzahlen
journal, July 1928


A physical basis for the VSEPR model of molecular geometry
journal, October 1988

  • Bader, Richard F. W.; Gillespie, Ronald J.; MacDougall, Preston J.
  • Journal of the American Chemical Society, Vol. 110, Issue 22
  • DOI: 10.1021/ja00230a009

Characterization of a Dihydrogen Bond on the Basis of the Electron Density
journal, March 1998

  • Popelier, P. L. A.
  • The Journal of Physical Chemistry A, Vol. 102, Issue 10
  • DOI: 10.1021/jp9805048

The role of OH…O and CH…O hydrogen bonds and H…H interactions in ethanol/methanol–water heterohexamers
journal, July 2016

  • Mejía, Sol M.; Espinal, Juan F.; Mills, Matthew J. L.
  • Journal of Molecular Modeling, Vol. 22, Issue 8
  • DOI: 10.1007/s00894-016-3050-9

A fast algorithm to compute atomic charges based on the topology of the electron density
journal, April 2001

  • Popelier, P. L. A.
  • Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 105, Issue 4-5
  • DOI: 10.1007/s002140000224

Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis
journal, August 1980

  • Vosko, S. H.; Wilk, L.; Nusair, M.
  • Canadian Journal of Physics, Vol. 58, Issue 8
  • DOI: 10.1139/p80-159

The Architecture of Molecules
journal, May 1964

  • Pauling, L.
  • Proceedings of the National Academy of Sciences, Vol. 51, Issue 5
  • DOI: 10.1073/pnas.51.5.977

Computer-generated schematic diagrams of protein structures
journal, April 1982


Molecular simulation by knowledgeable quantum atoms
journal, February 2016


Extension of Gaussian-2 (G2) theory to molecules containing third-row atoms K and Ca
journal, October 1997

  • Blaudeau, Jean-Philippe; McGrath, Mark P.; Curtiss, Larry A.
  • The Journal of Chemical Physics, Vol. 107, Issue 13
  • DOI: 10.1063/1.474865

Representation in Chemistry
journal, January 1991

  • Hoffmann, Roald; Laszlo, Pierre
  • Angewandte Chemie International Edition in English, Vol. 30, Issue 1
  • DOI: 10.1002/anie.199100013

Six questions on topology in theoretical chemistry
journal, February 2015


Virial Field Relationship for Molecular Charge Distributions and the Spatial Partitioning of Molecular Properties
journal, April 1972

  • Bader, R. F. W.; Beddall, P. M.
  • The Journal of Chemical Physics, Vol. 56, Issue 7
  • DOI: 10.1063/1.1677699

Structure of aryl O -demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism
journal, April 2017

  • Kohler, Amanda C.; Mills, Matthew J. L.; Adams, Paul D.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 16
  • DOI: 10.1073/pnas.1619263114

The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain
journal, April 1951

  • Pauling, L.; Corey, R. B.; Branson, H. R.
  • Proceedings of the National Academy of Sciences, Vol. 37, Issue 4, p. 205-211
  • DOI: 10.1073/pnas.37.4.205

Atom–atom partitioning of intramolecular and intermolecular Coulomb energy
journal, April 2001

  • Popelier, P. L. A.; Kosov, D. S.
  • The Journal of Chemical Physics, Vol. 114, Issue 15
  • DOI: 10.1063/1.1356013

Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions
journal, January 1980

  • Krishnan, R.; Binkley, J. S.; Seeger, R.
  • The Journal of Chemical Physics, Vol. 72, Issue 1
  • DOI: 10.1063/1.438955

On the differential geometry of interatomic surfaces
journal, June 1996

  • Popelier, Paul L. A.
  • Canadian Journal of Chemistry, Vol. 74, Issue 6
  • DOI: 10.1139/v96-092

Molecular Models of Amino Acids, Peptides, and Proteins
journal, August 1953

  • Corey, Robert B.; Pauling, Linus
  • Review of Scientific Instruments, Vol. 24, Issue 8
  • DOI: 10.1063/1.1770803

Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids
journal, April 1953

  • Wilkins, M. H. F.; Stokes, A. R.; Wilson, H. R.
  • Nature, Vol. 171, Issue 4356
  • DOI: 10.1038/171738a0

Two-Angstrom Crystal Structure of Oxidized Chromatium High Potential Iron Protein
journal, July 1974


Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements
journal, October 1982

  • Francl, Michelle M.; Pietro, William J.; Hehre, Warren J.
  • The Journal of Chemical Physics, Vol. 77, Issue 7, p. 3654-3665
  • DOI: 10.1063/1.444267

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
journal, October 1991


Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets
journal, November 1951

  • Pauling, L.; Corey, R. B.
  • Proceedings of the National Academy of Sciences, Vol. 37, Issue 11
  • DOI: 10.1073/pnas.37.11.729

Integration of atoms in molecules: a critical examination
journal, April 1996


On the full topology of the Laplacian of the electron density
journal, February 2000


A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010

  • Grimme, Stefan; Antony, Jens; Ehrlich, Stephan
  • The Journal of Chemical Physics, Vol. 132, Issue 15
  • DOI: 10.1063/1.3382344

An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY
journal, February 2003

  • Malcolm, Nathaniel O. J.; Popelier, Paul L. A.
  • Journal of Computational Chemistry, Vol. 24, Issue 4
  • DOI: 10.1002/jcc.10203

Fully Analytical Integration Over the 3D Volume Bounded by the β Sphere in Topological Atoms
journal, November 2011

  • Popelier, Paul L. A.
  • The Journal of Physical Chemistry A, Vol. 115, Issue 45
  • DOI: 10.1021/jp206223g

Effect of the damping function in dispersion corrected density functional theory
journal, March 2011

  • Grimme, Stefan; Ehrlich, Stephan; Goerigk, Lars
  • Journal of Computational Chemistry, Vol. 32, Issue 7
  • DOI: 10.1002/jcc.21759

Density‐functional thermochemistry. III. The role of exact exchange
journal, April 1993

  • Becke, Axel D.
  • The Journal of Chemical Physics, Vol. 98, Issue 7, p. 5648-5652
  • DOI: 10.1063/1.464913

Macromolecular shape and surface maps by solvent exclusion.
journal, January 1978

  • Greer, J.; Bush, B. L.
  • Proceedings of the National Academy of Sciences, Vol. 75, Issue 1
  • DOI: 10.1073/pnas.75.1.303

MORPHY, a program for an automated “atoms in molecules” analysis
journal, February 1996


Efficient and Flexible Sampling with Blue Noise Properties of Triangular Meshes
journal, June 2012

  • Corsini, M.; Cignoni, P.; Scopigno, R.
  • IEEE Transactions on Visualization and Computer Graphics, Vol. 18, Issue 6
  • DOI: 10.1109/TVCG.2012.34

DL-FIND: An Open-Source Geometry Optimizer for Atomistic Simulations
journal, October 2009

  • Kästner, Johannes; Carr, Joanne M.; Keal, Thomas W.
  • The Journal of Physical Chemistry A, Vol. 113, Issue 43
  • DOI: 10.1021/jp9028968

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988


The influence of polarization functions on molecular orbital hydrogenation energies
journal, January 1973

  • Hariharan, P. C.; Pople, J. A.
  • Theoretica Chimica Acta, Vol. 28, Issue 3
  • DOI: 10.1007/BF00533485

A simple measure of electron localization in atomic and molecular systems
journal, May 1990

  • Becke, A. D.; Edgecombe, K. E.
  • The Journal of Chemical Physics, Vol. 92, Issue 9
  • DOI: 10.1063/1.458517

Molecular Configuration in Sodium Thymonucleate
journal, April 1953

  • Franklin, Rosalind E.; Gosling, R. G.
  • Nature, Vol. 171, Issue 4356
  • DOI: 10.1038/171740a0

ImprovedSCF convergence acceleration
journal, January 1982


Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics
journal, August 2009

  • Ufimtsev, Ivan S.; Martinez, Todd J.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 10
  • DOI: 10.1021/ct9003004

Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18
journal, May 1980

  • McLean, A. D.; Chandler, G. S.
  • The Journal of Chemical Physics, Vol. 72, Issue 10, p. 5639-5648
  • DOI: 10.1063/1.438980

Atomic Properties of Amino Acids: Computed Atom Types as a Guide for Future Force-Field Design
journal, August 2003


Appreciation. Jane S. Richardson
journal, November 1992


Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
journal, April 1953

  • Watson, J. D.; Crick, F. H. C.
  • Nature, Vol. 171, Issue 4356
  • DOI: 10.1038/171737a0

The Three-Dimensional Structure of a Protein Molecule
journal, December 1961


The performance of the Becke—Lee—Yang—Parr (B—LYP) density functional theory with various basis sets
journal, September 1992


RASMOL: biomolecular graphics for all
journal, September 1995


A method to integrate an atom in a molecule without explicit representation of the interatomic surface
journal, February 1998


Atomic Partitioning of Molecular Electrostatic Potentials
journal, August 2000

  • Kosov, D. S.; Popelier, P. L. A.
  • The Journal of Physical Chemistry A, Vol. 104, Issue 31
  • DOI: 10.1021/jp0003407

XLIV.— On the Theory of Isomeric Compounds
journal, January 1864


Avogadro: an advanced semantic chemical editor, visualization, and analysis platform
journal, August 2012

  • Hanwell, Marcus D.; Curtis, Donald E.; Lonie, David C.
  • Journal of Cheminformatics, Vol. 4, Issue 1
  • DOI: 10.1186/1758-2946-4-17

Bonded and nonbonded charge concentrations and their relation to molecular geometry and reactivity
journal, March 1984

  • Bader, R. F. W.; MacDougall, P. J.; Lau, C. D. H.
  • Journal of the American Chemical Society, Vol. 106, Issue 6
  • DOI: 10.1021/ja00318a009

Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
journal, November 1994

  • Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.
  • The Journal of Physical Chemistry, Vol. 98, Issue 45, p. 11623-11627
  • DOI: 10.1021/j100096a001

Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F
journal, October 1983

  • Clark, Timothy; Chandrasekhar, Jayaraman; Spitznagel, G�nther W.
  • Journal of Computational Chemistry, Vol. 4, Issue 3
  • DOI: 10.1002/jcc.540040303

The cytotoxic Staphylococcus aureus PSMα3 reveals a cross-α amyloid-like fibril
journal, February 2017

  • Tayeb-Fligelman, Einav; Tabachnikov, Orly; Moshe, Asher
  • Science, Vol. 355, Issue 6327
  • DOI: 10.1126/science.aaf4901

Bond Paths Are Not Chemical Bonds
journal, September 2009

  • Bader, Richard F. W.
  • The Journal of Physical Chemistry A, Vol. 113, Issue 38
  • DOI: 10.1021/jp906341r

Ueber die Configuration des Traubenzuckers und seiner Isomeren
journal, January 1891


VMD: Visual molecular dynamics
journal, February 1996


Characterization of an agostic bond on the basis of the electron density
journal, March 1998