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Zhou J, Jia S, Xue X, Skitnevskaya AD, Wang E, Wang X, Hao X, Zeng Q, Kuleff AI, Dorn A, Ren X. Revealing the Role of N Heteroatoms in Noncovalent Aromatic Interactions by Ultrafast Intermolecular Coulombic Decay. J Phys Chem Lett 2024; 15:1529-1538. [PMID: 38299504 DOI: 10.1021/acs.jpclett.3c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Despite the widely recognized importance of noncovalent interactions involving aromatic rings in many fields, our understanding of the underlying forces and structural patterns, especially the impact of heteroaromaticity, is still incomplete. Here, we investigate the relaxation processes that follow inner-valence ionization in a range of molecular dimers involving various combinations of benzene, pyridine, and pyrimidine, which initiate an ultrafast intermolecular Coulombic decay process. Multiparticle coincidence momentum spectroscopy, combined with ab initio calculations, enables us to explore the principal orientations of these fundamental dimers and, thus, to elucidate the influence of N heteroatoms on the relative preference of the aromatic π-stacking, H-bonding, and CH-π interactions and their dependence on the number of nitrogen atoms in the rings. Our studies reveal a sensitive tool for the structural imaging of molecular complexes and provide a more complete understanding of the effects of N heteroatoms on the noncovalent aromatic interactions at the molecular level.
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Affiliation(s)
- Jiaqi Zhou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shaokui Jia
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaorui Xue
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Anna D Skitnevskaya
- Laboratory of Quantum Chemistry, Irkutsk State University, Irkutsk 664003, Russia
| | - Enliang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xing Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xintai Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qingrui Zeng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Alexander I Kuleff
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander Dorn
- Max-Planck-Institut für Kernphysik, Heidelberg 69117, Germany
| | - Xueguang Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
- Max-Planck-Institut für Kernphysik, Heidelberg 69117, Germany
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2
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Sajeev Y. Prebiotic chemical origin of biomolecular complementarity. Commun Chem 2023; 6:259. [PMID: 38012323 PMCID: PMC10681984 DOI: 10.1038/s42004-023-01060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
The early Earth, devoid of the protective stratospheric ozone layer, must have sustained an ambient prebiotic physicochemical medium intensified by the co-existence of shortwave UV photons and very low energy electrons (vLEEs). Consequently, only intrinsically stable molecules against these two co-existing molecular destructors must have proliferated and thereby chemically evolved into the advanced molecules of life. Based on this view, we examined the stability inherent in nucleobases and their complementary pairs as resistance to the molecular damaging effects of shortwave UV photons and vLEEs. This leads to the conclusion that nucleobases could only proliferated as their complementary pairs under the unfavorable prebiotic conditions on early Earth. The complementary base pairing not only enhances but consolidates the intrinsic stability of nucleobases against short-range UV photons, vLEEs, and possibly many as-yet-unknown deleterious agents co-existed in the prebiotic conditions of the early Earth. In short, complementary base pairing is a manifestation of chemical evolution in the unfavorable prebiotic medium created by the absence of the stratospheric ozone layer.
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Affiliation(s)
- Y Sajeev
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
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3
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Bejoy NB, Singh RK, Singh NK, Pananghat B, Patwari GN. Dynamics of Hydrogen Bond Breaking Induced by Outer-Valence Intermolecular Coulombic Decay. J Phys Chem Lett 2023:5718-5726. [PMID: 37318228 DOI: 10.1021/acs.jpclett.3c01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The photoexcitation of weakly bound complexes can lead to several decay pathways, depending on the nature of the potential energy surfaces. Upon excitation of a chromophore in a weakly bound complex, ionization of its neighbor upon energy transfer can occur due to a unique relaxation process known as intermolecular Coulombic decay (ICD), a phenomenon of renewed focus owing to its relevance in biological systems. Herein, we report the evidence for outer-valence ICD induced by multiphoton excitation by near-ultraviolet radiation of 4.4 eV photons, hitherto unknown in molecular systems. In the binary complexes of 2,6-difluorophenylacetylene with aliphatic amines, a resonant two-photon excitation localized on the 2,6-difluorophenylacetylene chromophore results in the formation of an amine cation following an outer-valence ICD process. The unique trends in experimentally observed translational energy distribution profiles of the amine cations following hydrogen bond dissociation, analyzed with the help of electronic structure and ab initio molecular dynamics calculations, revealed the presence of a delicate interplay of roaming dynamics, methyl-rotor dynamics, and binding energy.
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Affiliation(s)
- Namitha Brijit Bejoy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Reman Kumar Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nitin K Singh
- Indian Institute of Science Education and Research (IISER) Mohali, S. A. S Nagar, Mohali 140306, India
| | - Balanarayan Pananghat
- Indian Institute of Science Education and Research (IISER) Mohali, S. A. S Nagar, Mohali 140306, India
| | - G Naresh Patwari
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Zhou J, Jia S, Hu X, Wang E, Xue X, Wu Y, Wang J, Dorn A, Ren X. Intermolecular Charge Transfer Induced Fragmentation of Formic Acid Dimers. PHYSICAL REVIEW LETTERS 2023; 130:233001. [PMID: 37354420 DOI: 10.1103/physrevlett.130.233001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/19/2023] [Accepted: 04/20/2023] [Indexed: 06/26/2023]
Abstract
We investigate the intermolecular nonradiative charge transfer process in a double hydrogen-bonded formic acid (FA) dimer, initiated by electron-collision induced double ionization of one FA molecule. Through fragment ions and electron coincident momentum measurements and ab initio calculations, we obtain direct evidence that electron transfer from the neighboring FA molecule to fill one of the two vacancies occurs by a potential energy curve crossing of FA^{++}+FA with FA^{+}+FA^{+*} curves, forming an electronic excited state of dicationic dimers. This process causes the breaking of two hydrogen bonds and subsequently the cleavage of C─H and C─O covalent bonds in the dimers, which is expected to be a general phenomenon occurring in molecular complexes and can have important implications for radiation damage to biological matter.
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Affiliation(s)
- Jiaqi Zhou
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shaokui Jia
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaoqing Hu
- Institute of Applied Physics and Computational Mathematics, Beijing 100088, China
| | - Enliang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China, Hefei 230026, China
| | - Xiaorui Xue
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yong Wu
- Institute of Applied Physics and Computational Mathematics, Beijing 100088, China
| | - Jianguo Wang
- Institute of Applied Physics and Computational Mathematics, Beijing 100088, China
| | - Alexander Dorn
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - Xueguang Ren
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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Skitnevskaya AD, Gokhberg K, Trofimov AB, Grigoricheva EK, Kuleff AI, Cederbaum LS. Two-Sided Impact of Water on the Relaxation of Inner-Valence Vacancies of Biologically Relevant Molecules. J Phys Chem Lett 2023; 14:1418-1426. [PMID: 36731025 DOI: 10.1021/acs.jpclett.2c03654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
After ionization of an inner-valence electron of molecules, the resulting cation-radicals store substantial internal energy which, if sufficient, can trigger ejection of an additional electron in an Auger decay usually followed by molecule fragmentation. In the environment, intermolecular Coulombic decay (ICD) and electron-transfer mediated decay (ETMD) are also operative, resulting in one or two electrons being ejected from a neighbor, thus preventing the fragmentation of the initially ionized molecule. These relaxation processes are investigated theoretically for prototypical heterocycle-water complexes of imidazole, pyrrole, and pyridine. It is found that the hydrogen-bonding site of the water molecule critically influences the nature and energetics of the electronic states involved, opening or closing certain relaxation processes of the inner-valence ionized system. Our results indicate that the relaxation mechanisms of biologically relevant systems with inner-valence vacancies on their carbon atoms can strongly depend on the presence of the electron-density donating or accepting neighbor, either water or another biomolecule.
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Affiliation(s)
- Anna D Skitnevskaya
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
| | - Kirill Gokhberg
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Alexander B Trofimov
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
- Favorsky's Institute of Chemistry, SB RAS, Favorsky Str. 1, 664033 Irkutsk, Russia
| | - Emma K Grigoricheva
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
- Laboratory of Quantum Chemical Modeling of Molecular Systems, Irkutsk State University, Karl Marx Str. 1, 664003 Irkutsk, Russia
| | - Alexander I Kuleff
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
| | - Lorenz S Cederbaum
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg 69120, Germany
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Zhou J, Jia S, Xue X, Hao X, Zeng Q, Wang X, Ren X. Structural and dynamical studies of CH- πbonded CH 4-C 6H 6dimer by ultrafast intermolecular Coulombic decay. NANOTECHNOLOGY 2023; 34:165102. [PMID: 36645904 DOI: 10.1088/1361-6528/acb358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The inner-valence ionization and fragmentation dynamics of CH4-C6H6dimer induced by 200 eV electron impact is studied utilizing a multi-particle coincidence momentum spectroscopy. The three-dimensional momentum vectors and kinetic energy release (KER) of the CH4++C6H6+ion pairs are obtained by coincident momentum measurement. Our analysis on the absolute cross sections indicates that the intermediate dication CH4+-C6H6+is preferentially produced by the removal of an inner-valence electron from CH4or C6H6and subsequent relaxation of ultrafast intermolecular Coulombic decay followed by two-body Coulomb explosion. Combining withab initiomolecular dynamics (AIMD) simulations, the real-time fragmentation dynamics including translational, vibrational and rotational motions are presented as a function of propagation time. The revealed fragmentation dynamics are expected to have a potential implication for crystal structure imaging with various radiation sources.
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Affiliation(s)
- Jiaqi Zhou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Shaokui Jia
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xiaorui Xue
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xintai Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Qingrui Zeng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xing Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
| | - Xueguang Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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Charlieux F, Abdoul-Carime H. Processes Induced by Electrons at Sub-Ionization Energies Studied by the Correlated Ions-(Ions/Neutrals) Mass Spectrometry. Chemphyschem 2022; 24:e202200722. [PMID: 36562329 DOI: 10.1002/cphc.202200722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Sub-ionization energy electrons play a substantial role in the early time of (radiation/photo-) chemistry by generating reactive ions and neutral radicals. As the ions can be easily identified by mass spectrometry methods, information on the neutral species produced in correlation relies mainly on theoretical calculations. Here we show that coupling a double counter-propagative electron beams with a dual (+/-) time-of-flight mass spectrometer is probably the most versatile instrument for studying processes induced by low energy electrons, by providing correlated information between (ion and ion) and (ion and neutral) species. We demonstrate the feasibility of this technique for the prototypical case of carbon tetrachloride, but this method is generally applicable as shown for nitromethane.
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Affiliation(s)
- Florence Charlieux
- Université de Lyon, Université Lyon 1, Institut de Physique des 2 Infinis, CNRS/IN2P3, UMR5822, 69003, Lyon, France
| | - Hassan Abdoul-Carime
- Université de Lyon, Université Lyon 1, Institut de Physique des 2 Infinis, CNRS/IN2P3, UMR5822, 69003, Lyon, France
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Zhou J, Belina M, Jia S, Xue X, Hao X, Ren X, Slavíček P. Ultrafast Charge and Proton Transfer in Doubly Ionized Ammonia Dimers. J Phys Chem Lett 2022; 13:10603-10611. [PMID: 36350084 DOI: 10.1021/acs.jpclett.2c02560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We investigate the ultrafast energy and charge transfer processes between ammonia molecules following ionization reactions initiated by electron impact. Exploring ionization-induced processes in molecular clusters provides us with a detailed insight into the dynamics using experiments in the energy domain. We ionize the ammonia dimer with 200 eV electrons and apply the fragment ions coincident momentum spectroscopy and nonadiabatic molecular dynamics simulations. We identify two mechanisms leading to the doubly charged ammonia dimer. In the first one, a single molecule is ionized. This initiates an ultrafast proton transfer process, leading to the formation of the NH2+ + NH4+ pair. Alternatively, a dimer with a delocalized charge is formed dominantly via the intermolecular Coulombic decay, forming the NH3+·NH3+ dication. This dication further dissociates into two NH3+ cations. The ab initio calculations have reproduced the measured kinetic energy release of the ion pairs and revealed the dynamical processes following the double ionization.
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Affiliation(s)
- Jiaqi Zhou
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Michal Belina
- Department of Physical Chemistry, University of Chemistry and Technology,Technická 5, 16628Prague 6, Czech Republic
| | - Shaokui Jia
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xiaorui Xue
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xintai Hao
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xueguang Ren
- School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology,Technická 5, 16628Prague 6, Czech Republic
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