Enhanced flexibility of the O2 + N2 interaction and Its effect on collisional vibrational energy exchange

12 págs.; 8 figs.; 1 app. This article is part of the Piergiorgio Casavecchia and Antonio Lagana Festschrift special issue.Prompted by a comparison of measured and computed rate coefficients of Vibration-to-Vibration and Vibration-to-Translation energy transfer in O2 + N2 nonreactive collisions, extended semiclassical calculations of the related cross sections were performed to rationalize the role played by attractive and repulsive components of the interaction on two different potential energy surfaces. By exploiting the distributed concurrent scheme of the Grid Empowered Molecular Simulator we extended the computational work to quasiclassical techniques, investigated in this way more in detail the underlying microscopic mechanisms, singled out the interaction components facilitating the energy transfer, improved the formulation of the potential, and performed additional calculations that confirmed the effectiveness of the improvement introduced.The authors acknowledge financial support from the Phys4entry FP7/2007-2013 project (Contract No. 242311), ARPA Umbria, INSTM, the EGI-Inspire project (Contract No. 261323), MIUR PRIN 2008 (2008KJX4SN 003) and 2010/2011 (2010ERFKXL_002), the ESA-ESTEC Contract No. 21790/ 08/NL/HE and the Spanish CTQ2012-37404 and FIS2013- 48275-C2-1-P projects. Computations have been supported by the use of Grid resources and services provided by the European Grid Infrastructure (EGI) and the Italian Grid Infrastructure (IGI) through the COMPCHEM Virtual Organization. Thanks are also due to the COST CMST European Cooperative Project CHEMGRID (Action D37) EGI Inspire.Peer reviewe

Efficiency of Collisional O2 + N2 Vibrational Energy Exchange

10 pags.; 6 figs.; 5 tabs. In press.By following the scheme of the Grid Empowered Molecular Simulator (GEMS), a new O2 + N2 intermolecular potential, built on ab initio calculations and experimental (scattering and second virial coefficient) data, has been coupled with an appropriate intramolecular one. On the resulting potential energy surface detailed rate coefficients for collision induced vibrational energy exchanges have been computed using a semiclassical method. A cross comparison of the computed rate coefficients with the outcomes of previous semiclassical calculations and kinetic experiments has provided a foundation for characterizing the main features of the vibrational energy transfer processes of the title system as well as a critical reading of the trajectory outcomes and kinetic data. On the implemented procedures massive trajectory runs for the proper interval of initial conditions have singled out structures of the vibrational distributions useful to formulate scaling relationships for complex molecular simulations.The authors acknowledge financial support from the Phys4- entry FP7/2007-2013 project (Contract 242311), ARPA Umbria, INSTM, the EGI-Inspire project (Contract 261323), MIUR PRIN 2008 (2008KJX4SN 003) and 2010/2011 (2010ERFKXL_002), the ESA-ESTEC contract 21790/08/ NL/HE, and the Spanish CTQ2012-37404 and FIS2013- 48275-C2-1-P projects. Computations have been supported by the use of Grid resources and services provided by the European Grid Infrastructure (EGI) and the Italian Grid Infrastructure (IGI) through the COMPCHEM Virtual Organization. Thanks are also due to the COST CMST European Cooperative Project CHEMGRID (Action D37) EGI Inspire.Peer reviewe

Full Dimensional Potential Energy Function and Calculation of State-Specific Properties of the CO+N2 Inelastic Processes Within an Open Molecular Science Cloud Perspective

A full dimensional Potential Energy Surface (PES) of the CO + N2 system has been generated by extending an approach already reported in the literature and applied to N2-N2 (Cappelletti et al., 2008), CO2-CO2 (Bartolomei et al., 2012), and CO2-N2 (Lombardi et al., 2016b) systems. The generation procedure leverages at the same time experimental measurements and high-level ab initio electronic structure calculations. The procedure adopts an analytic formulation of the PES accounting for the dependence of the electrostatic and non-electrostatic components of the intermolecular interaction on the deformation of the monomers. In particular, the CO and N2 molecular multipole moments and electronic polarizabilities, the basic physical properties controlling the behavior at intermediate and long-range distances of the interaction components, were made to depend on relevant internal coordinates. The formulated PES exhibits substantial advantages when used for structural and dynamical calculations. This makes it also well suited for reuse in Open Molecular Science Cloud services

Cooperative modelling and design on the computing grid: Data, flux and knowledge interoperability

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Atomic and molecular data for spacecraft re-entry plasmas

The modeling of atmospheric gas, interacting with the space vehicles in re-entry conditions in planetary exploration missions, requires a large set of scattering data for all those elementary processes occurring in the system. A fundamental aspect of re-entry problems is represented by the strong non-equilibrium conditions met in the atmospheric plasma close to the surface of the thermal shield, where numerous interconnected relaxation processes determine the evolution of the gaseous system towards equilibrium conditions. A central role is played by the vibrational exchanges of energy, so that collisional processes involving vibrationally excited molecules assume a particular importance. In the present paper, theoretical calculations of complete sets of vibrationally state-resolved cross sections and rate coefficients are reviewed, focusing on the relevant classes of collisional processes: resonant and non-resonant electron-impact excitation of molecules, atom-diatom and molecule-molecule collisions as well as gas-surface interaction. In particular, collisional processes involving atomic and molecular species, relevant to Earth (N2, O2, NO), Mars (CO2, CO, N2) and Jupiter (H2, He) atmospheres are considered

Atomic and molecular data for spacecraft re-entry plasmas

The modeling of atmospheric gas, interacting with the space vehicles in re-entry conditions in planetary exploration missions, requires a large set of scattering data for all those elementary processes occurring in the system. A fundamental aspect of re-entry problems is represented by the strong non-equilibrium conditions met in the atmospheric plasma close to the surface of the thermal shield, where numerous interconnected relaxation processes determine the evolution of the gaseous system towards equilibrium conditions. A central role is played by the vibrational exchanges of energy, so that collisional processes involving vibrationally excited molecules assume a particular importance. In the present paper, theoretical calculations of complete sets of vibrationally state-resolved cross sections and rate coefficients are reviewed, focusing on the relevant classes of collisional processes: resonant and non-resonant electron-impact excitation of molecules, atom-diatom and molecule-molecule collisions as well as gas-surface interaction. In particular, collisional processes involving atomic and molecular species, relevant to Earth (N-2, O-2, NO), Mars (CO2, CO, N-2) and Jupiter (H-2, He) atmospheres are considered

Gas-phase formation and isomerization reactions of cyanoacetaldehyde, a prebiotic molecule of astrochemical interest

Cyanoacetaldehyde (NC-CH2CH=O) is considered, together with guanidine and urea, as a precursor of the pyrimidine bases cytosine and uracil. Although it has not yet been detected in the interstellar medium (ISM), several hypotheses have been put forward about its synthesis in solution and in the gas phase. In this paper, we present a gas-phase model of the barrierless reaction between formyl (HCO) and cyanomethyl (CH2CN) radicals leading to cyanoacetaldehyde and focus on its evolution through isomerization and dissociation pathways. The potential-energy surface for all reactions has been explored by DFT calculations employing double-hybrid functionals and further refined through the "Cheap" composite scheme. Our results indicate that the direct association of the two reacting radicals (HCO and CH2CN) is strongly exothermic and thus thermodynamically favored under the harsh conditions of the ISM. Microcanonical rate constants computed with the help of the StarRate program for energies up to 6 kJ mol(-)(1) above the dissociation limit show that the most abundant products are the two conformers of cyanoacetaldehyde (nitrile and carbonyl groups in a cis or trans configuration) which, despite having comparable stability, are obtained with a cis/trans ratio of 0.35:0.65. The formation of other products with relative abundances not exceeding 10% is also discussed

Molecular simulations as test beds for bridging high throughput and high performance computing

La forte connotation de la chimie computationnelle en termes de technologies informatiques est en même temps la force et la faiblesse des simulations moléculaires. En effet, dans le but de réaliser des études de ce type(même pour les systèmes contenant un petit nombre d'atomes), il faut d'abord procéder à des calculs de structure électronique de haut niveau. Ces calculs nécessitent généralement des nœuds (ou clusters de nœuds) équipés de mémoires de grande taille (de l'ordre de plusieurs Go), et de processeurs performants au niveau de plusieurs Gigaflops. Celà parce que la surface d'énergie potentielle ensemble (PES) qui régît le mouvement nucléaire doit être élaborée préalablement. Sur des plate-formes High Performance Computing (HPC) avec des capacités parallèles améliorées nous pouvons exécuter simultanément, sur plusieurs single (ou clusters de) processeurs multicœurs, le calculs requis par le grand nombre des valeurs d'énergie potentielles nécessaires pour décrire les PES explorés par une processus de réactivité chimique. Le véritable goulot d'étranglement dans la réalisation des calculs nécessaires, en effet, est représentée par la disponibilité d'une plate-forme informatique ayant des exigences informatiques appropriées en matière de temps de calcul et de mémoire physique. Les capacités de calcul (limitée) en général accessibles à la communauté scientifique, en fait, a toujours fixé des limites sévères à l'élaboration d'un système informatique complet de simulation a priori des processus moléculaires. Heureusement, des technologies informatiques innovantes, alliant la concurrence et la mise en réseau (tels que l'informatique distribuée, les laboratoires virtuels, le calcul intensif, le "Grid computing") ouvrent des perspectives nouvelles à la possibilité de réaliser d'importants débits de calcul et, par conséquent, de développer des simulations moléculaires a priori des systèmes réels. Les fondements théoriques et les paradigmes informatiques utilisés pour l'assemblage des composants du "Grid Empowered Molecular Simulator" (GEMS) sont décrits dans le Chapitre 1. Dans ce chapitre, nous illustrons le développement de workflows basés sur la grille, qui permettent l'évaluation ab initio des propriétés observables des systèmes chimiques petits à partir du calcul des propriétés électroniques. Dans le chapitre 2 nous abordons la question de l'interopérabilité entre codes de calcul à travers les différentes étapes du flux de travail (workflow). Ce chapitre propose les formats Q5cost et D5cost comme modèles "standard de facto" pour les calculs de chimie quantique. Le Chapitre 3 porte sur les résultats de calculs ab initio autonomes effectués sur des différents systèmes chimiques (petits clusters X_4 (X=Li,Na,K,Cu) ainsi que le dimère BeH-). Le chapitre traite des liaisons chimiques particulières et intéressantes présentes dans ces systèmes, qui nécessitent de méthodes quantiques de haut niveau à fin d'une possible rationalisation. Enfin, les chapitre 4 et 5 concernent respectivement les résultats de notre travail sur deux problèmes de combustion et la chimie atmosphérique (l'isomérisation CH3CH2OO• et la réaction N2+N2). Ils visent tous les deux à la construction des PES pour un processus réactif. Une fois la PES générée, les données cinétiques et dynamiques doivent être calculées pour un grand nombre de conditions initiales, et cela peut être fait sur des plateformes HTC. L'assemblage des workflows informatiques pour l'utilisation couplée des systèmes HPC et HTC est également traitée dans cette thèse.The strong connotation of computational chemistry in terms of computer technologies is at the same time the strength and the weakness of molecular simulations. As a matter of fact, in order to perform such studies (even for few-atom systems) we first need to carry out high-level electronic structure calculations. These calculations typically require nodes (or clusters of nodes) equipped with large (of the order of many GB) memories and processors performing at the level of several Gigaflops. This is because the whole Potential Energy Surface (PES) governing the nuclear motion needs to be worked out first. On the High Performance Computing (HPC) platforms with enhanced parallel capabilities we can run concurrently, on several single multicore (or clusters of) processors, the calculations required by the (large number of) potential energy values necessary to describe the PES explored by a reactive chemical process. The real bottleneck in carrying out related computational campaigns, indeed, is represented by the availability of a computing platform having the proper computational requirements in terms of computing time and physical memory. The (limited) computing capabilities in general available to the scientific community, in fact, still set severe limitations to the development of full a priori computational simulations of molecular processes. Fortunately, innovative computing technologies combining concurrency and networking (such as distributed computing, virtual laboratories, supercomputing, Grid computing) are opening new prospects to the possibility of achieving significant computational throughputs and, therefore, of developing a priori molecular simulations of real systems. The theoretical foundations and the computing paradigms employed for the assemblage of the components of the Grid Empowered Molecular Simulator GEMS are described in Chapter 1. In that chapter the development of grid based workflows allowing the ab initio evaluation of the observable properties of small chemical systems starting from the calculation of the electronic properties is illustrated. In Chapter 2 the issue of the of interoperability between computational codes across different stages of the workflow is faced. The Chapter proposes Q5cost and D5cost common data models as de facto standard formats for quantum chemistry calculations. Chapter 3 relates to the results of standalone ab initio calculations performed on different small chemical systems (X4 clusters and BeH- dimer). The Chapter discusses particular and interesting chemical bonds requiring high-level quantum methods to the end of being rationalized. Finally Chapter 4 and Chapter 5 report the results of our work on two combustion and atmospheric chemistry problems (CH3CH2OO• isomerization and N2+N2 reaction) respectively. They both aim at constructing the PES for a reactive process. Once a PES is generated, the kinetic and dynamical data need to be calculated for a large number of initial conditions, and can be computed on HTC platforms. The assemblage of the computational workflows for the coupled use of HPC and HTC systems is also dealt there

Computational development of models and tools for the kinetic study of astrochemical gas-phase reactions

This PhD thesis focuses on the application and development of computational tools and methodologies for the modeling of the kinetics of gas-phase reactions of astrophysical interest in the interstellar medium (ISM). The complexity related to the investigation of chemical reactivity in space is mostly due to the extreme physical conditions of temperature, pressure and exposure to high-energy radiation, which in turn also lead to the formation of exotic species, like radicals and ions. Nevertheless, there is still much to be understood about the formation of molecules, the major issue being the lack of sufficient laboratory (experimental and computational) studies. A more detailed and accurate study of all the chemical processes occurring in the ISM will allow us to obtain the data necessary to simulate the chemical evolution of an interstellar cloud over time using kinetic models including thousands of reactions that involve hundreds of species. The collection of the kinetic parameters required for the relevant reactions has led to the growth of different astrochemical databases, such as KIDA and UMIST. However, the data gathered in these catalogues are incomplete, and rely extensively on crude estimations and extrapolations. These rates are of paramount importance to get a better comprehension of the relative abundances of the chemical compounds extrapolated by the astronomers from the spectral data recorded through the radio telescopes and the in-orbit devices, like the satellites. Accurate state-of-the-art computational approaches play a fundamental role in analyzing feasible reaction mechanisms and in accurately predicting the associated kinetics. Such approaches usually rely on chemical intuition where a by-hand search of the most likely pathways is performed. Unfortunately, thisprocedure can lead to overlook significant mechanisms, especially when large molecular systems are investigated. Increasing the size of a molecule can also increase the number of its possible conformers which can show a different chemical reactivity with respect to the same chemical partner. This brings to get very complex chemical reaction networks in which hundreds of chemical species are involved and thousands of chemical reactions can occur.During the last decades, a lot of effort has been done to develop computational techniques able to perform extensive and thorough investigations of complex reaction mechanisms. Such approaches rely on automated computational protocols which drastically decrease the risk of making blunders during the search for significant reaction pathways.Furthermore, the accurate characterization of the potential energy surfaces (PESs) critical points, like reactants, intermediates, transition states and products involved in the reaction mechanism, is crucial in order to carry out a reliable kinetic investigation. The kinetic analysis of an erroneous potential energy surface, would lead to gross errors in the estimation of the rate constants of the chemical species involved in the reaction.In order to avoid such errors, the combination of high-level electronic structure calculations via composite scheme can be helpful to get a more precise estimation of the energy barriers involved in the reaction mechanism. It has been proven that "cheap"[1] composite schemes can achieve subchemical accuracy without any empirical parameters and with convenient computation times, making them perfect for the purpose of this thesis.In recent decades, many efforts have been made to develop theoretical and computational methodologies to perform accurate numerical simulations of the kinetics of such complex reaction mechanisms in a wide range of thermodynamic conditions that mimic extreme reaction environmentsas for combustion systems, the atmosphere and the ISM. Such methodologies are based on the ab initio-transition-state-theory-based master equation approach, which allows the determination of rate coefficients and branching ratios of chemical species involved in complex chemical reactions. This methodology allows to make accurate predictions of the relative abundances of the reaction products for complex reactions even under conditions of temperature and pressure not experimentally accessible, such as those that characterize the ISM. Based on these premises, this dissertation has been focused on the application of a computational protocol for the ab initio-based computational modeling and kinetic investigation of gas-phase reactions which can occur in the ISM.This protocol is based on the application of validated methodologies for the automated discovery of complex reaction mechanisms by means of the AutoMeKin[2] program, the accurate calculation of the energetic of the potential energy surfaces (PESs) through the junChS and junChS-F12a "cheap" composite schemes and the kinetic investigation using the StarRate computer program specifically designed to study gas-phase reactions of astrochemical interest in conjunction with the MESS program. Furthermore, this dissertation has been also focused on the development and implementation of StarRate, a computer program for the accurate calculation of kinetics through a chemical master equation approach of multi-step chemical reactions. StarRate is an object-based program written in the so-called F language. It is structured in three main modules, namely molecules, steps and reactions, which extract the properties needed to calculate the kinetics for the single-step reactions partecipating in the overall reaction. Another module, in_out, handles program’s input and output operations. The main program,starrate, controls the sequences of the calling of the procedures contained in each of the three main modules.Through these modular structure, StarRate[3] can compute canonical and microcanonical rate coefficients taking into account for the tunneling effect and the energy-dependent and time-dependent evolution of the species concentrations involved in the reaction mechanism. Such protocol has been applied to investigate the formation reaction mechanisms of some complex interstellar polyatomic molecules, named interstellar complex organic molecules (iCOMs). More specifically, the formation of prebiotic iCOMs in space has raised considerable interest in the scientific community, because they are considered as precursors of more complex biological systems involved in the origin of life in the Universe. Debate on the origins of these biomolecular building blocks has been further stimulated by the discovery of nucleobases and amino acids in meteorites and other extraterrestrial sources. However, few insights on the chemistry which brings to the formation of such compounds is known.  References: [1] Jacopo Lupi,Silvia Alessandrini,Cristina Puzzarini,and Vincenzo Barone.junchs and junchs-F12 models:Parameter-free efficient yet accurate compositeschemes for energies and structures of noncovalent complexes. Journal of Chem-ical Theory and Computation, 17(11):6974–6992, 2021. PMID: 34677974.[2] Emilio Martínez-Núñez, George L. Barnes, David R. Glowacki, Sabine Kopec,Daniel Peláez, Aurelio Rodríguez, Roberto Rodríguez-Fernández, Robin J. Shan-non, James J. P. Stewart, Pablo G. Tahoces, and Saulo A. Vazquez.Au-tomekin2021: An open-source program for automated reaction discovery. Journalof Computational Chemistry, 42(28):2036–2048, 2021.[3] Surajit Nandi, Bernardo Ballotta, Sergio Rampino, and Vincenzo Barone.Ageneral user-friendly tool for kinetic calculations of multi-step reactions withinthe virtual multifrequency spectrometer project. Applied Sciences, 10(5), 2020