Protonation-Induced Structural and Spectroscopic Variations in Molecular Species: A Computational Study on N2, H2, CO, CS, and PH3

Authors

  • John Pual Shinggu Federal University Wukari
  • Emmanuel E. Etim Federal University Wukari
  • Alfred I. Onen Federal University Wukari

Keywords:

Proton affinity, Spectroscopic properties, Computational methods, Bond lengths, Bond angles

Abstract

Communication in Physical Sciences, 2023, 9(4): 408-433

Authors: John Pual Shinggu, Emmanuel E. Etim* and Alfred I. Onen

Received: 23 April 2023/Accepted 02 August 2023

This research presents computational studies on the influence of protonation on the structural and spectroscopic properties of molecules, with a focus on N2, CO, H2, CS, and PH3. Computational calculations were performed using various methods and levels of theories, including G4, MP2/6-311*, MP2/CC-pvdz, CCSD/CC-pvdz, and W2U. Calculations of thethe proton affinity (PA) and the examination of the effects of protonation on the bond lengths, bond angles, vibrational frequencies, dipole moment, and rotational constants of various molecules were also performed. The results of the calculation displayed a significant variation in molecular geometries, vibrational frequencies, dipole moments, and proton affinity protonation. Protonation was observed to be a precursor to the e formation of charged species and therefore highlighted, their potential as reactive intermediates in chemical reactions. The computational methods employed in this study clearly show that adopted methods can effectively be employed to describe the protonation-induced structural and spectroscopic variations in the molecules. These findings contribute to a better understanding of protonation processes in diatomic molecules and have implications for various fields, including chemistry, spectroscopy, and theoretical studies.

Downloads

Download data is not yet available.

Author Biographies

John Pual Shinggu, Federal University Wukari

Department of Chemical Sciences

Emmanuel E. Etim, Federal University Wukari

Department of Chemical Sciences

Alfred I. Onen, Federal University Wukari

Department of Chemical Sciences

References

Agúndez, M., Cernicharo, J., De Vicente, P., Marcelino, N., Roueff, E., Fuente, A., ... & Tercero, F. (2015). Probing non-polar interstellar molecules through their protonated form: Detection of protonated cyanogen (NCCNH+ ). Astronomy & Astrophysics, 579, L10.

Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. H., Corcelli, S. A., ... & Zanni, M. T. (2020). Vibrational spectroscopic map, vibrational spectroscopy, and intermolecular interaction. Chemical reviews, 120, 15, pp. 7152-7218.18.

Benkyi, I., Tapavicza, E., Fliegl, H., & Sundholm, D. (2019). Calculation of vibrationally resolved absorption spectra of acenes and pyrene. Physical Chemistry Chemical Physics, 21, 37, pp. 21094-21103.

Ben-Shimon, A., Shalev, D. E., & Niv, M. Y. (2013). Protonation States in molecular dynamics simulations of peptide folding and binding. Current pharmaceutical design, 19, 23, pp. 4173-4181.

Bodenstein, T., & Kvaal, S. (2020). A state-specific multireference coupled-cluster method based on the bivariational principle. The Journal of Chemical Physics, 153(2).

Cabezas, C., Agúndez, M., Marcelino, N., Tercero, B., Fuentetaja, R., de Vicente, P., & Cernicharo, J. (2022). Discovery of a new molecular ion, HC7NH+ , in TMC-1. Astronomy & Astrophysics, 659, L8.

Caselli, P., Sipilä, O., & Harju, J. (2019). Deuterated forms of H3+ and their importance in astrochemistry. Philosophical Transactions of the Royal Society A, 377(2154), 20180401.

Chen, B. W., Xu, L., & Mavrikakis, M. (2020). Computational methods in heterogeneous catalysis. Chemical Reviews, 121(2), 1007-1048. Baiz, C. R., Błasiak, B., Bredenbeck, J., Cho, M., Choi, J. H., Corcelli, S. A., ... & Zanni, M. T. (2020).

Chen, J., Zhang, S., Wang, W., Sun, H., Zhang, Q., & Liu, X. (2021). Binding of inhibitors to BACE1 affected by pH-dependent protonation: An exploration from multiple replica Gaussian accelerated molecular dynamics and MM-GBSA calculations. ACS Chemical Neuroscience, 12(14), 2591-2607.

Chester, S. M. (2019). Weizmann lectures on the numerical conformal bootstrap. arXiv preprint arXiv:1907.05147.

Cramer, C. J. (2013). Essentials of computational chemistry: theories and models. John Wiley & Sons.

DeFrees, D. J., & McLean, A. D. (1986). Ab initio determination of the proton affinities of small neutral and anionic molecules. Journal of computational chemistry, 7(3), 321-333.

Eddy, N. O. & Ita, B. I. (2011). Experimental and theoretical studies on the inhibition potentials of some derivatives of cyclopenta-1,3-diene. International Journal of Quantum Chemistry 111, 14, pp. 3456-3473. DOI:10.1002/qua

Eddy, N. O. & Ita, B. I. (2011). Theoretical and experimental studies on the inhibition potentials of aromatic oxaldehydes for the corrosion of mild steel in 0.1 M HCl. Journal of Molecular Modeling 17, pp. 633-647. DOI:10.1007/s00894-010-0749

Etim, E. E., & Arunan, E. (2016). Interstellar isomeric species: Energy, stability and abundance relationship. The European Physical Journal Plus, 131, pp. 1-10.

Etim, E. E., Gorai, P., Das, A., & Arunan, E. (2017). Interstellar protonated molecular species. Advances in Space Research, 60(3), 709-721.

Etim, E. E., & Oko Emmanuel, G. (2020). Protonation in Heteronuclear Diatomic Molecules: Same Molecule, Different Proton Affinities. Communication in Physical Sciences, 6(2).

Gaussian09, R. A. (2009). 1, mj frisch, gw trucks, hb schlegel, ge scuseria, ma robb, jr cheeseman, g. Scalmani, v. Barone, b. Mennucci, ga petersson et al., gaussian. Inc., Wallingford CT, 121, 150-166.

Herbst, E. (2017). The synthesis of large interstellar molecules. International Reviews in Physical Chemistry, 36, 2, pp. 287-331.

Keith, J. A., Vassilev-Galindo, V., Cheng, B., Chmiela, S., Gastegger, M., Müller, K. R., & Tkatchenko, A. (2021). Combining machine learning and computational chemistry for predictive insights into chemical systems. Chemical reviews, 121, 16, pp. 9816-9872.

Knauth, D. C., Andersson, B. G., McCandliss, S. R., & Warren Moos, H. (2004). The interstellar N2 abundance towards HD 124314 from far-ultraviolet observations. Nature, 429(6992), 636-638.

Krynski, M., & Rossi, M. (2021). Efficient Gaussian process regression for prediction of molecular crystals harmonic free energies. npj Computational Materials, 7, 1, pp. 169.

Larsson, M., McCall, B. J., & Orel, A. E. (2008). The dissociative recombination of H3+ –a saga coming to an end?. Chemical Physics Letters, 462, 4-6, pp. 145-151.

Mata, R. A. (2010). Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes. Physical Chemistry Chemical Physics, 12, 19, pp. 5041-5052.

Montes de Oca-Estevez, M. J., & Prosmiti, R. (2021). Computational Characterization of Astrophysical Species: The Case of Noble Gas Hydride Cations. Frontiers in Chemistry, 9, 664693.

Nair, A. S., & Pathak, B. (2021). Computational strategies to address the catalytic activity of nanoclusters. Wiley Interdisciplinary Reviews: Computational Molecular Science, 11, 4, , e1508.

Nguyen, Q. T., Tran, P., Ngo, T. D., Tran, P. A., & Mendis, P. (2014). Experimental and computational investigations on fire resistance of GFRP composite for building façade. Composites Part B: Engineering, 62, pp. 218-229.

Noble, J., Dedonder-Lardeux, C., & Jouvet, C. (2019). Excited States Processes in Protonated Molecules Studied by Frequency-Domain pectroscopy. Physical Chemistry of Cold Gas-Phase Functional Molecules and Clusters, 337-365.

Noble, J., Dedonder-Lardeux, C., & Jouvet, C. (2019). Excited States Processes in Protonated Molecules Studied by Frequency-Domain pectroscopy. Physical Chemistry of Cold Gas-Phase Functional Molecules and Clusters, 337-365.

Re, S., Watabe, S., Nishima, W., Muneyuki, E., Yamaguchi, Y., MacKerell Jr, A. D., & Sugita, Y. (2018). Characterization of conformational ensembles of protonated N-glycans in the gas-phase. Scientific Reports, 8, 1, pp. (1), 1644.

Thaddeus, P., Guélin, M., & Linke, R. A. (1981).Three new'nonterrestrial'molecules. The Astrophysical Journal, 246, pp. L41-L45.

Turner, A. M., Koutsogiannis, A. S., Kleimeier, N. F., Bergantini, A., Zhu, C., Fortenberry, R. C., & Kaiser, R.I. (2020). An experimental and theoretical investigation into the formation of ketene (H2CCO) and ethynol (HCCHO) in interstellar analog ices. The Astrophysical Journal, 896, 1, pp. 88.

Wang, S., Kind, T., Tantillo, D. J., & Fiehn, O. (2020). Predicting in silico electron ionization mass spectra using quantum chemistry. Journal of cheminformatics, 12, 1, pp. 1-11.

Downloads

Published

2023-04-08