Computational and Theoretical Chemistry

Input and output files for CMOEDA analysis of rotational barriers in amides and thioamides.

Results of MRCI computations on electronic states of the dicationic diphoshoros

The outcomes and input of Gaussian 09

Molecular structures and data analysis for generalized energy decomposition analysis (gEDA) of static polarizability for thiophene

The file contains the starting structure of the molecule, the spectrogram file and the image, etc.

The structures (PDB files) and coordinates ( PFS files) were generated from topologies and initial force field parameters obtained from the Protein Data Bank (RCSB)[11] for L-Trp used in all simulations and the pyrrole monomer used in simulation A. For the (Py)n oligomers in simulations B, C, and D, the structures, topologies, and force field parameters were obtained from the Swiss Institute of Bioinformatics[12] The initial orientation was attained with Swiss.pdb Viewer. CHARMM force fields were used all throughout [13–16]

It has been proposed recently based on molecular dynamics simulations that electron irradiation of graphene nanoribbons of alternating width can lead to creation of 1D hybrid nanoobjects composed of alternating double carbon chains and polycyclic hydrocarbon regions [1]. We have performed density functional theory calculations of such 1D hybrid nanoobjects using Quantum ESPRESSO [2]. Semi-local exchange and correlation functional of Perdew, Burke and Ernzerhof [3] and screened exchange hybrid density functional of Heyd, Scuseria and Ernzerhof [4] were used. The dependences of structure, magnetic and electronic properies on the length of chains and type of the polycyclic hydrocarbon region were studied. I.V.L acknowledges the IKUR HPC project "First-principles simulations of complex condensed matter in exascale computers" funded by MCIN and by the European Union NextGenerationEU/PRTR-C17.I1, as well as by the Department of Education of the Basque Government through the collaboration agreement with nanoGUNE within the framework of the IKUR Strategy, computer resources at MareNostrum and the technical support provided by Barcelona Supercomputing Center (RES grant nos. FI-2022-1-0023, FI-2022-2-0035, FI-2022-3-0048 and FI-2023-1-0037). A.M.P., and Y.E.L. acknowledge the support by the Russian Science Foundation grant No. 23-42-10010, https://rscf.ru/en/project/23-42-10010/. S.A.V. and N.A.P. acknowledge support by the Belarusian Republican Foundation for Fundamental Research (Grant No. F23RNF-049) and by the Belarusian National Research Program "Convergence-2025". [1] A. S. Sinitsa, I. V. Lebedeva, Y. G. Polynskaya, D. G. de Oteyza, S. V. Ratkevich, A. A. Knizhnik, A. M. Popov, N. A. Poklonski, and Y. E. Lozovik, “Transformation of a graphene nanoribbon into a hybrid 1D nanoobject with alternating double chains and polycyclic regions,” Phys. Chem. Chem. Phys. 23, 425–441 (2021). [2] P. Giannozzi et al., “Advanced capabilities for materials modelling with Quantum ESPRESSO,” J. Phys.: Condens. Matter 29, 465901 (2017). [3] J. P. Perdew, K. Burke, and M. Ernzerhof, “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 3865–3868 (1996). [4] J. Heyd, G. E. Scuseria, and M. Ernzerhof, “Hybrid functionals based on a screened Coulomb potential,” J. Chem. Phys. 118, 8207–8215 (2003).

The rate constant for the CF3O + NO reaction has been studied with the variable reaction coordinate transitionstate theory and multichannel RRKM calculation based on the potential energy surface obtained by the G3B3//UB3LYP/6-311 + G(3df) level of theory. The total rate constant was found to exhibit weak negative temperature dependence, in line with most experimental results. The formation of FNO + CF2O is dominant at ambient temperature. The branching ratio of FNO + CF2O accounts for 0.922-0.618 at T = 150-3000 K peaking around 400 K. When temperature rises, the FON + CF2O channel becomes more and more appreciable, the branching ratio of FON + CF2O accounts for 0.001-0.382 at T = 150-3000 K increasing with temperature. At room temperature, the total rate constant is almost independent of the pressure, in agreement with previous experimental result.

Related Article: Alexey Yu. Fedorov, Tatiana N. Drebushchak, Christian Tantardini|2019|Comp.Theo.Chem.|1157|47|doi:10.1016/j.comptc.2019.04.012