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Suchan J, Janoš J, Slavíček P. Pragmatic Approach to Photodynamics: Mixed Landau–Zener Surface Hopping with Intersystem Crossing. J Chem Theory Comput 2020; 16:5809-5820. [DOI: 10.1021/acs.jctc.0c00512] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jiří Suchan
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Jiří Janoš
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 16628 Prague, Czech Republic
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Herlem G, Alhedabi T, Picaud F. From Anodic Oxidation of Aliphatic α-Amino Acids to Polypeptides by Quantum Electrochemistry Approach: Beyond Miller-Urey Experiments. J Am Chem Soc 2019; 141:14230-14238. [PMID: 31429556 DOI: 10.1021/jacs.9b05910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For years, polypeptide formation has fascinated the scientific world because its understanding could lead to one of the possible explanations for the origin of life. Anodic oxidation of aliphatic α-amino acids in aqueous electrolytes can result either in their decomposition or in their polymerization into polypeptide. This behavior depends experimentally on both amino acid concentration and pH. The elucidation of the involved mechanisms remains a challenge because of the multitude of products which can be obtained. In this context, the electrochemical behavior of glycine and alanine on a biased platinum surface was examined at the nanoscale by quantum electrochemistry via the effective screening medium method. Several electrochemical systems with different concentrations and pH values have been explored. Simulations of the anodic oxidation of the amino acids have not only confirmed their electropolymerization and decomposition at high and low concentrations, respectively, but also have revealed unsuspected mechanisms at the origin of polypeptide formation. This sheds new light on electrochemistry of α-amino acids, on occurrence of polypeptides, and more generally on organic electrochemistry.
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Affiliation(s)
- Guillaume Herlem
- Nanomedicine Laboratory EA4662, Bat. E , University of Bourgogne Franche-Comté, UFR Sciences & Techniques , 16 route de Gray , 25030 Besançon Cedex , France
| | - Taleb Alhedabi
- Nanomedicine Laboratory EA4662, Bat. E , University of Bourgogne Franche-Comté, UFR Sciences & Techniques , 16 route de Gray , 25030 Besançon Cedex , France.,Department of Chemistry, College of Science , University of Sumer , Rifai , Thi-Qar , Iraq
| | - Fabien Picaud
- Nanomedicine Laboratory EA4662, Bat. E , University of Bourgogne Franche-Comté, UFR Sciences & Techniques , 16 route de Gray , 25030 Besançon Cedex , France
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Wagner JP, Giles SM, Duncan MA. Gas phase infrared spectroscopy of the H2C NH2+ methaniminium cation. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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QUAPP WOLFGANG. REDUCED GRADIENT METHODS AND THEIR RELATION TO REACTION PATHS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633603000604] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reaction path is an important concept in theoretical chemistry. We discuss different definitions, their merits as well as their drawbacks: IRC (steepest descent from saddle), reduced gradient following (RGF), gradient extremals, and some others. Many properties and problems are explained by two-dimensional figures. This paper is both a review and a pointer to future research. The branching points of RGF curves are valley-ridge inflection (VRI) points of the potential energy surface. These points may serve as indicators for bifurcations of the reaction path. The VRI points are calculated with the help of Branin's method. All the important features of the potential energy surface are independent of the coordinate system. Besides the theoretical definitions, we also discuss the numerical use of the methods.
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Affiliation(s)
- WOLFGANG QUAPP
- Mathematical Institute, University of Leipzig, Augustus-Platz, D-04109 Leipzig, Germany
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Gichuhi WK, Mebel AM, Suits AG. UV Photodissociation of Ethylamine Cation: A Combined Experimental and Theoretical Investigation. J Phys Chem A 2010; 114:13296-302. [DOI: 10.1021/jp107913p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wilson K. Gichuhi
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States, and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - A. M. Mebel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States, and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Arthur G. Suits
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States, and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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Barbatti M, Granucci G, Persico M, Ruckenbauer M, Vazdar M, Eckert-Maksić M, Lischka H. The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2006.12.008] [Citation(s) in RCA: 380] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Barbatti M, Aquino AJA, Lischka H. Ultrafast two-step process in the non-adiabatic relaxation of the CH2 molecule. Mol Phys 2007. [DOI: 10.1080/00268970500417945] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mario Barbatti
- a Institute for Theoretical Chemistry , University of Vienna , Whringerstrasse 17, A-1090 Vienna, Austria
| | - Adélia J. A. Aquino
- a Institute for Theoretical Chemistry , University of Vienna , Whringerstrasse 17, A-1090 Vienna, Austria
| | - Hans Lischka
- a Institute for Theoretical Chemistry , University of Vienna , Whringerstrasse 17, A-1090 Vienna, Austria
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Gridelet E, Dehareng D, Locht R, Lorquet AJ, Lorquet JC, Leyh B. Ground and Excited State Dissociation Dynamics of Ionized 1,1-Difluoroethene. J Phys Chem A 2005; 109:8225-35. [PMID: 16834209 DOI: 10.1021/jp051542b] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The kinetic energy release distributions (KERDs) for the fluorine atom loss from the 1,1-difluoroethene cation have been recorded with two spectrometers in two different energy ranges. A first experiment uses dissociative photoionization with the He(I) and Ne(I) resonance lines, providing the ions with a broad internal energy range, up to 7 eV above the dissociation threshold. The second experiment samples the metastable range, and the average ion internal energy is limited to about 0.2 eV above the threshold. In both energy domains, KERDs are found to be bimodal. Each component has been analyzed by the maximum entropy method. The narrow, low kinetic energy components display for both experiments the characteristics of a statistical, simple bond cleavage reaction: constraint equal to the square root of the fragment kinetic energy and ergodicity index higher than 90%. Furthermore, this component is satisfactorily accounted for in the metastable time scale by the orbiting transition state theory. Potential energy surfaces corresponding to the five lowest electronic states of the dissociating 1,1-C2H2F2+ ion have been investigated by ab initio calculations at various levels. The equilibrium geometry of these states, their dissociation energies, and their vibrational wavenumbers have been calculated, and a few conical intersections between these surfaces have been identified. It comes out that the ionic ground state X2B1 is adiabatically correlated with the lowest dissociation asymptote. Its potential energy curve increases in a monotonic way along the reaction coordinate, giving rise to the narrow KERD component. Two states embedded in the third photoelectron band (B2A1 at 15.95 eV and C2B2 at 16.17 eV) also correlate with the lowest asymptote at 14.24 eV. We suggest that their repulsive behavior along the reaction coordinate be responsible for the KERD high kinetic energy contribution.
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Affiliation(s)
- E Gridelet
- Department of Chemistry, Molecular Dynamics Laboratory, Building B6c, and Centre for Protein Engineering, Building B6a, University of Liège, B-4000 SART-TILMAN, Belgium
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Roithová J, Schröder D, Schwarz H. Unimolecular Fragmentation of CH3NH2: Towards a Mechanistic Description of HCN Formation. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fati D, Lorquet AJ, Locht R, Lorquet JC, Leyh B. Kinetic Energy Release Distributions for Tropylium and Benzylium Ion Formation from the Toluene Cation. J Phys Chem A 2004. [DOI: 10.1021/jp048058d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- D. Fati
- Department of Chemistry, University of Liège, Sart-Tilman, Building B6c, B-4000 Liège 1, Belgium
| | - A. J. Lorquet
- Department of Chemistry, University of Liège, Sart-Tilman, Building B6c, B-4000 Liège 1, Belgium
| | - R. Locht
- Department of Chemistry, University of Liège, Sart-Tilman, Building B6c, B-4000 Liège 1, Belgium
| | - J. C. Lorquet
- Department of Chemistry, University of Liège, Sart-Tilman, Building B6c, B-4000 Liège 1, Belgium
| | - B. Leyh
- Department of Chemistry, University of Liège, Sart-Tilman, Building B6c, B-4000 Liège 1, Belgium
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Fati D, Leyh B. Charge exchange in tandem mass spectrometry: dissociative single electron capture by doubly-charged toluene cations. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2003; 9:223-235. [PMID: 12939475 DOI: 10.1255/ejms.546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Single electron capture by doubly-charged toluene cations upon collision with various target gases has been investigated by sector tandem mass spectrometry. Both non-dissociative and dissociative charge transfer reactions leading to C(7)H(7)(+) + H and to C(5)H(5)(+) + [C(2),H(3)] are detected. Seven atomic or molecular target gases have been used with ionisation energies ranging from 8.8 eV to 14 eV. The branching ratios between the different non-dissociative and dissociative exit channels have been determined as well as the translational energy release on the dissociation products. The experimental data are compared to the predictions of a two-state semi-classical theoretical model that takes into account the non-adiabatic transition responsible for the charge transfer reaction. A wide reaction window shows up but the internal energies of the C(7)H(8)(+) cations produced by single electron capture are observed to be larger than expected. We assign this effect partly to the influence of the large density of vibrational states and to the multichannel nature of the process. Excited states of the dication are also most probably involved in the charge exchange reaction.
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Affiliation(s)
- Dorina Fati
- Département de Chimie, Bâtiment B6c, Université de Liège, B-4000 Sart-Tilman, Belgium
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