Using Constraint Programming to Generate Benzenoid Structures in Theoretical Chemistry

Benzenoids are a subfamily of hydrocarbons (molecules that are only made of hydrogen and carbon atoms) whose carbon atoms form hexagons. These molecules are widely studied in theoretical chemistry and have a lot of concrete applications. Therefore, generating benzenoids which have certain structural properties (e.g. having a given number of hexagons or having a particular structure from a graph viewpoint) is an interesting and important problem. It constitutes a preliminary step for studying their chemical properties. In this paper, we show that modeling this problem in Choco Solver and just letting its search engine generate the solutions is a fast enough and very flexible approach. It can allow to generate many different kinds of benzenoids with predefined structural properties by posting new constraints, saving the efforts of developing bespoke algorithmic methods for each kind of benzenoids.

[1]  Christine Wei Wu.  Modelling Chemical Reactions Using Constraint Programming and Molecular Graphs , 2004, CP.

[2]  Pierre Hansen,et al.  A constructive enumeration of fusenes and benzenoids , 2001, J. Algorithms.

[3]  Rolf Backofen,et al.  Atom mapping with constraint programming , 2014, Algorithms for Molecular Biology.

[4]  A. Luch.  The Carcinogenic Effects of Polycyclic Aromatic Hydrocarbons , 2005 .

[5]  Thomas Schiex,et al.  Guaranteed Discrete Energy Optimization on Large Protein Design Problems. , 2015, Journal of chemical theory and computation.

[6]  Woo Youn Kim,et al.  Efficient prediction of reaction paths through molecular graph and reaction network analysis† †Electronic supplementary information (ESI) available: Detailed information on reaction networks and pathways for two example reactions, Cartesian coordinates of molecules in the reaction networks obtained , 2017, Chemical science.

[7]  Pierre Hansen,et al.  Enumeration of Polyhex Hydrocarbons to h = 21 , 1997, J. Chem. Inf. Comput. Sci..

[8]  E. Peeters,et al.  The Infrared Spectra of Very Large, Compact, Highly Symmetric, Polycyclic Aromatic Hydrocarbons (PAHs) , 2008, 0802.1071.

[9]  G. Trinquier,et al.  Predicting the Open-Shell Character of Polycyclic Hydrocarbons in Terms of Clar Sextets. , 2017, The journal of physical chemistry. A.

[10]  Wojciech Pisula,et al.  Graphenes as potential material for electronics. , 2007, Chemical reviews.

[11]  S. Sandford,et al.  Modeling the Unidentified Infrared Emission with Combinations of Polycyclic Aromatic Hydrocarbons , 1999, The Astrophysical journal.

[12]  C. Pignedoli,et al.  Large-Cavity Coronoids with Different Inner and Outer Edge Structures , 2020, Journal of the American Chemical Society.

[13]  E. Clar.  The aromatic sextet , 1972 .

[14]  Sven J. Cyvin,et al.  Search for concealed non-Kekulean benzenoids and coronoids , 1989, J. Chem. Inf. Comput. Sci..

[15]  C. Bauschlicher,et al.  THE INFRARED SPECTROSCOPY OF COMPACT POLYCYCLIC AROMATIC HYDROCARBONS CONTAINING UP TO 384 CARBONS , 2012 .

[16]  Jean‐François Morin,et al.  Polycyclic Aromatic Hydrocarbons as Potential Building Blocks for Organic Solar Cells. , 2019, Chemical record.

[17]  C. Pignedoli,et al.  Synthesis and Characterization of π-Extended Triangulene. , 2019, Journal of the American Chemical Society.

[18]  K. Müllen,et al.  A C216-Nanographene Molecule with Defined Cavity as Extended Coronoid. , 2016, Journal of the American Chemical Society.

[19]  K. Müllen,et al.  New advances in nanographene chemistry. , 2015, Chemical Society reviews.

[20]  Jerry Ray Dias.  Structure and electronic characteristics of coronoid polycyclic aromatic hydrocarbons as potential models of graphite layers with hole defects. , 2008, The journal of physical chemistry. A.

[21]  Scott Habershon,et al.  Automatic Proposal of Multistep Reaction Mechanisms using a Graph-Driven Search. , 2019, The journal of physical chemistry. A.

[22]  B. Draine.  Astronomical Models of PAHs and Dust , 2011, PAHs and the Universe.

[23]  Maurice Bruynooghe,et al.  Improved Static Symmetry Breaking for SAT , 2016, SAT.

[24]  Forever young: polycyclic aromatic hydrocarbons as model cases for structural and optical studies , 2010 .

[25]  E. Peeters,et al.  Polycyclic Aromatic Hydrocarbons with Armchair Edges: Potential Emitters in Class B Sources , 2019, The Astrophysical Journal.

[26]  Erika R. Bérczi-Kovács,et al.  The complexity of the Clar number problem and an exact algorithm , 2015, Journal of Mathematical Chemistry.