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Kinetics and Dynamics pp 77–106Cite as

Formamide as the Model Compound for Photodissociation Studies of the Peptide Bond

Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH,volume 12)

Abstract

Dynamics simulations are an essential step in exploring ultrafast phenomena in photochemistry and photobiology. In this chapter we present results of photodynamics studies for some model compounds for the peptide bond using the on-the-fly surface hopping method. The mechanism of photodissociation of formamide, its protonated forms and methyl substituted derivatives in their lowest singlet excited states in the gas phase is discussed in detail. Merits and demerits of using these simple molecules as models in exploring photochemical and photophysical properties of more complex systems, like peptides and proteins, are emphasized. It is found that in all examined model molecules the major deactivation process after excitation to the S1 state is dissociation of the peptide C–N bond. The same holds for the deactivation path from the S2 state, with exception of the O- protonated formamide in which C–O dissociation becomes the major deactivation process. Furthermore, it is shown that substitution by the methyl group(s), as well as protonation, strongly influence the lifetime of both excited states. In the last section application of the newly developed hybrid nonadiabatic photodynamics QM/MM approach in calculating photodissociation of formamide in argon matrix is illustrated.

Keywords

  • Excited state
  • Peptide bond
  • Photodissociation
  • Nonadiabatic dynamics
  • Formamide
  • Substituted formamides
  • Surface hopping
  • Environmental effects
  • QM/MM

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Acknowledgements

This work has been supported by the Ministry of Science, Education and Sport of Croatia through the project. No. 098-0982933-2920 (Mirjana Eckert-Maksić, Ivana Antol, and Mario Vazdar) and by the Austrian Science Fund within the framework of the Special Research Program F16 (Advanced Light Sources) and Project P18411-N19 (Hans Lischka and Mario Barbatti). H.L. acknowledges support by the grant from the Ministry of Education of the Czech Republic (Center for Biomolecules and Complex Molecular Systems, LC512) and by the Praemium Academiae of the Academy of Sciences of the Czech Republic, awarded to Pavel Hobza in 2007 and by the research project Z40550506 of the Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic. The support by the COST D37 action, WG0001-06 and WTZ treaty between Austria and Croatia (Project No. HR17/2008) are also acknowledged. The authors especially acknowledge the technical support and computer time at the Linux PC cluster Schrödinger III of the computer center of the University of Vienna. Zagreb group (Mirjana Eckert-Maksić, Ivana Antol, and Mario Vazdar) also thanks allocation of computation time on the ISABELLA cluster at the University Computing Center in Zagreb.

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Authors and Affiliations

  1. Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, 10002, Zagreb, Croatia

    Mirjana Eckert-Maksić, Ivana Antol & Mario Vazdar

  2. Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A1090, Vienna, Austria

    Mario Barbatti & Hans Lischka

  3. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic

    Hans Lischka

Authors
  1. Mirjana Eckert-Maksić
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  2. Ivana Antol
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  3. Mario Vazdar
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  4. Mario Barbatti
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  5. Hans Lischka
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Correspondence to Mirjana Eckert-Maksić .

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Editors and Affiliations

  1. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Piotr Paneth

  2. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Agnieszka Dybala-Defratyka

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Eckert-Maksić, M., Antol, I., Vazdar, M., Barbatti, M., Lischka, H. (2010). Formamide as the Model Compound for Photodissociation Studies of the Peptide Bond. In: Paneth, P., Dybala-Defratyka, A. (eds) Kinetics and Dynamics. Challenges and Advances in Computational Chemistry and Physics, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3034-4_3

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