Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides
Abstract
:1. Introduction
2. Results and Discussion
2.1. Anodic Reaction of Amino Acids
2.2. Anodic Reaction of Peptides
3. Methods
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Holleman, A.F.; Wiberg, E. Lehrbuch der Anorganischen Chemie, 101st ed.; De Gruyter: Berlin, Germany, 1749. [Google Scholar]
- Sternberg, A.; Bardow, A. Power-to-What?–Environmental assessment of energy storage systems. Energy Environ. Sci. 2015, 8, 389–400. [Google Scholar] [CrossRef]
- Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory. Phys. Rev. Lett. 1985, 55, 2471–2474. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hohenberg, P.; Kohn, W. Inhomogeneous electron gas. Phys. Rev. 1964, 136, 864–871. [Google Scholar] [CrossRef] [Green Version]
- Kohn, W.; Sham, L.J. Self-consistent equations including exchange and correlation effects. Phys. Rev. 1965, 140, 1133–1138. [Google Scholar] [CrossRef] [Green Version]
- Becke, A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. 1988, 38, 3098–3100. [Google Scholar] [CrossRef]
- Marx, D.; Hutter, J. Modern Methods and Algorithms of Quantum Chemistry. In Ab Initio Molecular Dynamics: Theory and Implementation; Grotendorst, J., Ed.; John von Neumann Institute for Computing: New York, NY, USA, 2000; Volume 1, pp. 301–449. [Google Scholar]
- Van Duin, A.C.T.; Dasgupta, S.; Lorant, F.; Iii, W.A.G. ReaxFF: A Reactive Force Field for Hydrocarbons. J. Phys. Chem. 2001, 105, 9396–9409. [Google Scholar] [CrossRef] [Green Version]
- Chenoweth, K.; Van Duin, A.C.T.; Goddard, W.A. ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation. J. Phys. Chem. A 2008, 112, 1040–1053. [Google Scholar] [CrossRef] [Green Version]
- Alonso, J.L.; Andrade, X.; Echenique, P.; Falceto, F.; Prada-Gracia, D.; Rubio, A. Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density funtional theory. Chem. Phys. Lett. 2008, 101, 1–6. [Google Scholar]
- Parrinello, M. From silicon to RNA: The coming of age of ab initio molecular dynamics. Solid State Commun. 1997, 102, 107–120. [Google Scholar] [CrossRef]
- Fois, E.; Gamba, A.; Tabacchi, G. First-principles simulation of the intracage oxidation of nitrite to nitrate sodalite. Chem. Phys. Lett. 2000, 329, 1–6. [Google Scholar] [CrossRef]
- Boero, M.; Parrinello, M.; Terakura, K. First Principles Molecular Dynamics Study of Ziegler−Natta Heterogeneous Catalysis. J. Am. Chem. Soc. 1998, 120, 2746–2752. [Google Scholar] [CrossRef]
- Frank, I.; Parrinello, M.; Klamt, A. Insight into Chemical Reactions from First-Principles Simulations: The Mechanism of the Gas-Phase Reaction of OH Radicals with Ketones. J. Phys. Chem. 1998, 102, 3614–3617. [Google Scholar] [CrossRef]
- Reinhardt, S.; Marian, C.; Frank, I. The influence of excess ammonia on the mechanism of the reaction of boron trichloride with ammonia–An ab initio molecular dynamics study. Angew. Chem. 2001, 113, 3683–3685. [Google Scholar] [CrossRef]
- Nonnenberg, C.; Frank, I. Formation and decay of tetrazane derivates–a Car-Parrinello molecular dynamics study. Phys. Chem. Chem. Phys. 2008, 10, 4383–4392. [Google Scholar] [CrossRef] [PubMed]
- Hofbauer, F.; Frank, I. Electrolysis of Water in the Diffusion Layer: First-Principles Molecular Dynamics Simulation. Chem. A Eur. J. 2011, 18, 277–282. [Google Scholar] [CrossRef]
- Frank, I. Ab-Initio Molecular Dynamics Simulation of the Electrolysis of Waste Water. ChemistrySelect 2019, 4, 4376–4381. [Google Scholar] [CrossRef]
- Blumberger, J.; Bernasconi, L.; Tavernelli, I.; Vuilleumier, R.; Sprik, M. Electronic structure and solvation of copper and silver ions: A theoretical picture of a model aqueous redox reaction. J. Am. Chem. Soc. 2004, 126, 3928–3938. [Google Scholar] [CrossRef]
- Blumberger, J.; Tateyama, Y.; Sprik, M. Ab initio molecular dynamics simulation of redox reactions in solution. Comput. Phys. Commun. 2005, 169, 256–261. [Google Scholar] [CrossRef]
- Zhang, C.; Sayer, T.; Hutter, J.; Sprik, M. Modelling electrochemical systems with finite field molecular dynamics. J. Phys. Energy 2020, 2, 032005. [Google Scholar] [CrossRef]
- Tomilov, A.P.; Fioshin, M.Y. Free radical reactions in the electrolysis of organic compounds. Russ. Chem. Rev. 1963, 32, 30–44. [Google Scholar] [CrossRef]
- Wiebe, A.; Gieshoff, T.; Möhle, S.; Rodrigo, E.; Zirbes, M.; Waldvogel, S.R. Electrifying organic synthesis. Angew. Chem. Int. Ed. 2018, 57, 5594–5619. [Google Scholar] [CrossRef] [PubMed]
- CPMD. Copyright IBM Corp, 1990–2008; Copyright MPI für Festkörperforshung Stuttgart 1997–2001. Available online: http://www.cpmd.org/ (accessed on 16 January 2012).
- Grimme, S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006, 27, 1787–1799. [Google Scholar] [CrossRef] [PubMed]
- Troullier, N.; Martins, J.L. Efficient pseudopotentials for plane-wave calculations. Phys. Rev. B 1991, 43, 1993–2006. [Google Scholar] [CrossRef] [PubMed]
- Boero, M.; Parrinello, M.; Terakura, K.; Weiss, H. Car—Parrinello study of Ziegler—Natta heterogeneous catalysis: Stability and destabilization problems of the active site models. Mol. Phys. 2002, 100, 2935–2940. [Google Scholar] [CrossRef]
- Gunnarsson, O.; Lundqvist, B.I. Exchange and correlation in atoms, molecules, and solids by the spin-density-functional formalism. Phys. Rev. B 1976, 13, 4274–4298. [Google Scholar] [CrossRef]
- Harada, K.; Suzuki, S.; Harada, S.S.K. Formation of amino acids from elemental carbon by contact glow discharge electrolysis. Nat. Cell Biol. 1977, 266, 275–276. [Google Scholar] [CrossRef]
- Harada, K.; Nomoto, M.M.; Gunji, H. Formation of amino acids from aliphatic amines by contact glow discharge electrolysis. Tetrahedron Lett. 1981, 22, 769–772. [Google Scholar] [CrossRef]
- Gupta, S.K.S. Contact Glow Discharge Electrolysis: A Novel Tool for Manifold Applications. Plasma Chem. Plasma Process. 2017, 37, 897–945. [Google Scholar] [CrossRef]
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Kiakojouri, A.; Nadimi, E.; Frank, I. Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides. Molecules 2020, 25, 5415. https://doi.org/10.3390/molecules25225415
Kiakojouri A, Nadimi E, Frank I. Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides. Molecules. 2020; 25(22):5415. https://doi.org/10.3390/molecules25225415
Chicago/Turabian StyleKiakojouri, Ali, Ebrahim Nadimi, and Irmgard Frank. 2020. "Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides" Molecules 25, no. 22: 5415. https://doi.org/10.3390/molecules25225415