M3C: A Computational Approach To Describe Statistical Fragmentation of Excited Molecules and ClustersClick to copy article linkArticle link copied!
Abstract

The Microcanonical Metropolis Monte Carlo method, based on a random sampling of the density of states, is revisited for the study of molecular fragmentation in the gas phase (isolated molecules, atomic and molecular clusters, complex biomolecules, etc.). A random walk or uniform random sampling in the configurational space (atomic positions) and a uniform random sampling of the relative orientation, vibrational energy, and chemical composition of the fragments is used to estimate the density of states of the system, which is continuously updated as the random sampling populates individual states. The validity and usefulness of the method is demonstrated by applying it to evaluate the caloric curve of a weakly bound rare gas cluster (Ar13), to interpret the fragmentation of highly excited small neutral and singly positively charged carbon clusters (Cn, n = 5,7,9 and Cn+, n = 4,5) and to simulate the mass spectrum of the acetylene molecule (C2H2).
Cited By
Smart citations by scite.ai include citation statements extracted from the full text of the citing article. The number of the statements may be higher than the number of citations provided by ACS Publications if one paper cites another multiple times or lower if scite has not yet processed some of the citing articles.
This article is cited by 22 publications.
- Lejin Xu, Wuyang Li, Pierre Désesquelles, Nguyen-Thi Van-Oanh, Sébastien Thomas, Jun Yang. A Statistical Model and DFT Study of the Fragmentation Mechanisms of Metronidazole by Advanced Oxidation Processes. The Journal of Physical Chemistry A 2019, 123
(4)
, 933-942. https://doi.org/10.1021/acs.jpca.8b10554
- Marie-Anne Hervé du Penhoat, Nely Rodrı́guez Moraga, Marie-Pierre Gaigeot, Rodolphe Vuilleumier, Ivano Tavernelli, Marie-Fraņcoise Politis. Proton Collision on Deoxyribose Originating from Doubly Ionized Water Molecule Dissociation. The Journal of Physical Chemistry A 2018, 122
(24)
, 5311-5320. https://doi.org/10.1021/acs.jpca.8b04787
- Ewa Erdmann, Marta Łabuda, Néstor F. Aguirre, Sergio Díaz-Tendero, Manuel Alcamí. Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations. The Journal of Physical Chemistry A 2018, 122
(16)
, 4153-4166. https://doi.org/10.1021/acs.jpca.8b00881
- Marco Parriani, Emelie Olsson, Veronica Daver Ideböhn, Måns Wallner, Richard J. Squibb, Gunnar Nyman, Stefano Falcinelli, John H. D. Eland, Majdi Hochlaf, Raimund Feifel. Characterization of the electronic structure and fate of doubly ionized carbon diselenide. Scientific Reports 2025, 15
(1)
https://doi.org/10.1038/s41598-025-90637-5
- Laura Carlini, Anna Rita Casavola, Jacopo Chiarinelli, Francesco Porcelli, Elena Molteni, Giuseppe Mattioli, Paola Bolognesi, Davide Sangalli, Federico Vismarra, Yingxuan Wu, Rocio Borrego-Varillas, Mauro Nisoli, Manjot Singh, Mohammadhassan Valadan, Carlo Altucci, Robert Richter, Lorenzo Avaldi. Fragmentation and charge transfer in cyclic dipeptides with an aromatic side chain induced by VUV radiation. Journal of Physics B: Atomic, Molecular and Optical Physics 2024, 57
(10)
, 105401. https://doi.org/10.1088/1361-6455/ad3c00
- Xiang Meng, Pierre Désesquelles, Lejin Xu. Decomposition mechanisms of nuclear-grade cationic exchange resin by advanced oxidation processes: Statistical molecular fragmentation model and DFT calculations. Journal of Environmental Sciences 2024, 135 , 433-448. https://doi.org/10.1016/j.jes.2023.01.024
- Pierre Désesquelles, Dominik Domin, Lejin Xu, Nguyen‐Thi Van‐Oanh. Competition between Loss of H
2
versus H+H in the Fragmentation of the Fluorene Cation. ChemPhysChem 2023, 75 https://doi.org/10.1002/cphc.202300241
- Lukas Tiefenthaler, Paul Scheier, Ewa Erdmann, Néstor F. Aguirre, Sergio Díaz-Tendero, Thomas F. M. Luxford, Jaroslav Kočišek. Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations. Physical Chemistry Chemical Physics 2023, 25
(7)
, 5361-5371. https://doi.org/10.1039/D2CP04172C
- Emilio Martínez‐Núñez, George L. Barnes, David R. Glowacki, Sabine Kopec, Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez‐Fernández, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces, Saulo A. Vazquez. AutoMeKin2021
: An open‐source program for automated reaction discovery. Journal of Computational Chemistry 2021, 42
(28)
, 2036-2048. https://doi.org/10.1002/jcc.26734
- Henning Zettergren, Alicja Domaracka, Thomas Schlathölter, Paola Bolognesi, Sergio Díaz-Tendero, Marta Łabuda, Sanja Tosic, Sylvain Maclot, Per Johnsson, Amanda Steber, Denis Tikhonov, Mattea Carmen Castrovilli, Lorenzo Avaldi, Sadia Bari, Aleksandar R. Milosavljević, Alicia Palacios, Shirin Faraji, Dariusz G. Piekarski, Patrick Rousseau, Daniela Ascenzi, Claire Romanzin, Ewa Erdmann, Manuel Alcamí, Janina Kopyra, Paulo Limão-Vieira, Jaroslav Kočišek, Juraj Fedor, Simon Albertini, Michael Gatchell, Henrik Cederquist, Henning T. Schmidt, Elisabeth Gruber, Lars H. Andersen, Oded Heber, Yoni Toker, Klavs Hansen, Jennifer A. Noble, Christophe Jouvet, Christina Kjær, Steen Brøndsted Nielsen, Eduardo Carrascosa, James Bull, Alessandra Candian, Annemieke Petrignani. Roadmap on dynamics of molecules and clusters in the gas phase. The European Physical Journal D 2021, 75
(5)
https://doi.org/10.1140/epjd/s10053-021-00155-y
- Pierre Désesquelles, Nguyen-Thi Van-Oanh, Lejin Xu, Yining Luo, Tam V.-T. Mai, Lam K. Huynh, Dominik Domin. Multiple dehydrogenation of fluorene cation and neutral fluorene using the statistical molecular fragmentation model. Physical Chemistry Chemical Physics 2021, 23
(16)
, 9900-9910. https://doi.org/10.1039/D0CP06100J
- Néstor F. Aguirre, Sergio Díaz-Tendero, Paul-Antoine Hervieux, Manuel Alcamí, Marin Chabot, Karine Béroff, Fernando Martín. Charge and energy sharing in the fragmentation of astrophysically relevant carbon clusters. Theoretical Chemistry Accounts 2021, 140
(3)
https://doi.org/10.1007/s00214-020-02702-z
- Ewa Erdmann, Néstor F. Aguirre, Suvasthika Indrajith, Jacopo Chiarinelli, Alicja Domaracka, Patrick Rousseau, Bernd A. Huber, Paola Bolognesi, Robert Richter, Lorenzo Avaldi, Sergio Díaz-Tendero, Manuel Alcamí, Marta Łabuda. A general approach to study molecular fragmentation and energy redistribution after an ionizing event. Physical Chemistry Chemical Physics 2021, 23
(3)
, 1859-1867. https://doi.org/10.1039/D0CP04890A
- Sylvain Maclot, Jan Lahl, Jasper Peschel, Hampus Wikmark, Piotr Rudawski, Fabian Brunner, Hélène Coudert-Alteirac, Suvasthika Indrajith, Bernd A. Huber, Sergio Díaz-Tendero, Néstor F. Aguirre, Patrick Rousseau, Per Johnsson. Dissociation dynamics of the diamondoid adamantane upon photoionization by XUV femtosecond pulses. Scientific Reports 2020, 10
(1)
https://doi.org/10.1038/s41598-020-59649-1
- Néstor F. Aguirre, Julie Jung, Ping Yang. Unraveling the structural stability and the electronic structure of ThO
2
clusters. Physical Chemistry Chemical Physics 2020, 22
(33)
, 18614-18621. https://doi.org/10.1039/D0CP00478B
- Pierre Désesquelles, Nguyen-Thi Van-Oanh, Sébastien Thomas, Dominik Domin. Statistical molecular fragmentation: which parameters influence the branching ratios?. Physical Chemistry Chemical Physics 2020, 22
(6)
, 3160-3172. https://doi.org/10.1039/C9CP05095G
- S Indrajith, E Erdmann, J Chiarinelli, A Domaracka, M Łabuda, L Avaldi, M Alcami, N F Aguirre, S Díaz-Tendero, P Bolognesi, P Rousseau, B A Huber. Determination of energy-transfer distributions in ionizing ion-molecule collisions. Journal of Physics: Conference Series 2020, 1412
(15)
, 152085. https://doi.org/10.1088/1742-6596/1412/15/152085
- Néstor F. Aguirre, Sergio Díaz-Tendero, Tijani IdBarkach, Marin Chabot, Karine Béroff, Manuel Alcamí, Fernando Martín. Fully versus constrained statistical fragmentation of carbon clusters and their heteronuclear derivatives. The Journal of Chemical Physics 2019, 150
(14)
https://doi.org/10.1063/1.5083864
- Tijani IdBarkach, Thejus Mahajan, Marin Chabot, Karine Béroff, Néstor F. Aguirre, Sergio Diaz-Tendero, Thibaut Launoy, Arnaud Le Padellec, Luc Perrot, Maëlle A. Bonnin, Kim Cuong Le, Florian Geslin, Nicolas de Séréville, Fairouz Hammache, Aurélie Jallat, Anne Meyer, Emeline Charon, Thomas Pino, Thibault Hamelin, Valentine Wakelam. Semiempirical breakdown curves of C2N(+) and C3N(+) molecules; application to products branching ratios predictions of physical and chemical processes involving these adducts. Molecular Astrophysics 2018, 12 , 25-32. https://doi.org/10.1016/j.molap.2018.06.003
- Khidhir Alhameedi, Björn Bohman, Amir Karton, Dylan Jayatilaka. Predicting the primary fragments in mass spectrometry using
ab initio
Roby–Gould bond indices. International Journal of Quantum Chemistry 2018, 118
(15)
https://doi.org/10.1002/qua.25603
- Ivana Blaženović, Tobias Kind, Jian Ji, Oliver Fiehn. Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites 2018, 8
(2)
, 31. https://doi.org/10.3390/metabo8020031
- Michael Gatchell, Rudy Delaunay, Giovanna D'Angelo, Arkadiusz Mika, Kostiantyn Kulyk, Alicja Domaracka, Patrick Rousseau, Henning Zettergren, Bernd A. Huber, Henrik Cederquist. Ion-induced molecular growth in clusters of small hydrocarbon chains. Physical Chemistry Chemical Physics 2017, 19
(30)
, 19665-19672. https://doi.org/10.1039/C7CP02090B
Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.
Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.
The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.