Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis
This paper reviews some of our developments in algorithmic graph theory, with some applications in physical chemistry and catalysis. Two levels of granularity in the topological graphs have been developed: atomistic 2D-MolGraphs and coarse-grained polygraphs of H-bonded cycles. These graphs have bee...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Académie des sciences
2024-11-01
|
| Series: | Comptes Rendus. Chimie |
| Subjects: | |
| Online Access: | https://comptes-rendus.academie-sciences.fr/chimie/articles/10.5802/crchim.317/ |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1825206101920972800 |
|---|---|
| author | Bougueroua, Sana Aboulfath, Ylène Cimas, Alvaro Hashemi, Ali Pidko, Evgeny A. Barth, Dominique Gaigeot, Marie-Pierre |
| author_facet | Bougueroua, Sana Aboulfath, Ylène Cimas, Alvaro Hashemi, Ali Pidko, Evgeny A. Barth, Dominique Gaigeot, Marie-Pierre |
| author_sort | Bougueroua, Sana |
| collection | DOAJ |
| description | This paper reviews some of our developments in algorithmic graph theory, with some applications in physical chemistry and catalysis. Two levels of granularity in the topological graphs have been developed: atomistic 2D-MolGraphs and coarse-grained polygraphs of H-bonded cycles. These graphs have been implemented with the key algorithms of isomorphism and polymorphism, in order to analyze molecular dynamics simulations of complex molecular systems. These topological graphs are transferable without modification from “simple” gas molecules, to liquids, to more complex inhomogeneous interfaces between solid and liquid for instance. We show hereby that the use of algorithmic graph theory provides a direct and fast approach to identify the actual conformations sampled over time in a trajectory. Graphs of transitions can also be extracted, showing at first glance all the interconversions over time between these conformations. H-bond networks in condensed matter molecular systems such as aqueous interfaces are shown to be easily captured through the topological graphs. We also show how the 2D-MolGraphs can easily be included in automated high-throughput in silico reactivity workflows, and how essential they are in some of the decisive steps to be taken in these workflows. The coarse-grained polygraphs of H-bonded cycles are shown to be essential topological graphs to analyze the dynamics of flexible molecules such as a hexapeptide in gas phase. |
| format | Article |
| id | doaj-art-a961302483414df986633f4033f053e6 |
| institution | Kabale University |
| issn | 1878-1543 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Académie des sciences |
| record_format | Article |
| series | Comptes Rendus. Chimie |
| spelling | doaj-art-a961302483414df986633f4033f053e62025-02-07T13:41:22ZengAcadémie des sciencesComptes Rendus. Chimie1878-15432024-11-0112310.5802/crchim.31710.5802/crchim.317Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysisBougueroua, Sana0https://orcid.org/0000-0002-0642-5275Aboulfath, Ylène1Cimas, Alvaro2https://orcid.org/0000-0001-8095-2279Hashemi, Ali3 Pidko, Evgeny A.4https://orcid.org/0000-0001-9242-9901Barth, Dominique5Gaigeot, Marie-Pierre6https://orcid.org/0000-0002-3409-5824Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, FranceUniversité Paris-Saclay, Univ Versailles Saint Quentin, DAVID, 78035 Versailles, FranceUniversité Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, FranceInorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, 2629 HZ Delft, The NetherlandsInorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, 2629 HZ Delft, The NetherlandsUniversité Paris-Saclay, Univ Versailles Saint Quentin, DAVID, 78035 Versailles, FranceInstitut Universitaire de France (IUF), 75005 Paris, France; Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, FranceThis paper reviews some of our developments in algorithmic graph theory, with some applications in physical chemistry and catalysis. Two levels of granularity in the topological graphs have been developed: atomistic 2D-MolGraphs and coarse-grained polygraphs of H-bonded cycles. These graphs have been implemented with the key algorithms of isomorphism and polymorphism, in order to analyze molecular dynamics simulations of complex molecular systems. These topological graphs are transferable without modification from “simple” gas molecules, to liquids, to more complex inhomogeneous interfaces between solid and liquid for instance. We show hereby that the use of algorithmic graph theory provides a direct and fast approach to identify the actual conformations sampled over time in a trajectory. Graphs of transitions can also be extracted, showing at first glance all the interconversions over time between these conformations. H-bond networks in condensed matter molecular systems such as aqueous interfaces are shown to be easily captured through the topological graphs. We also show how the 2D-MolGraphs can easily be included in automated high-throughput in silico reactivity workflows, and how essential they are in some of the decisive steps to be taken in these workflows. The coarse-grained polygraphs of H-bonded cycles are shown to be essential topological graphs to analyze the dynamics of flexible molecules such as a hexapeptide in gas phase.https://comptes-rendus.academie-sciences.fr/chimie/articles/10.5802/crchim.317/Algorithmic graph theoryConformational searchMolecular dynamicsIdentification of conformersPathwaysReaction network |
| spellingShingle | Bougueroua, Sana Aboulfath, Ylène Cimas, Alvaro Hashemi, Ali Pidko, Evgeny A. Barth, Dominique Gaigeot, Marie-Pierre Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis Comptes Rendus. Chimie Algorithmic graph theory Conformational search Molecular dynamics Identification of conformers Pathways Reaction network |
| title | Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| title_full | Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| title_fullStr | Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| title_full_unstemmed | Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| title_short | Topological graphs: a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| title_sort | topological graphs a review of some of our achievements and perspectives in physical chemistry and homogeneous catalysis |
| topic | Algorithmic graph theory Conformational search Molecular dynamics Identification of conformers Pathways Reaction network |
| url | https://comptes-rendus.academie-sciences.fr/chimie/articles/10.5802/crchim.317/ |
| work_keys_str_mv | AT bouguerouasana topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT aboulfathylene topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT cimasalvaro topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT hashemiali topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT pidkoevgenya topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT barthdominique topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis AT gaigeotmariepierre topologicalgraphsareviewofsomeofourachievementsandperspectivesinphysicalchemistryandhomogeneouscatalysis |