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Zawadzki M, Luxford TFM, Kočišek J. Carboxylation Enhances Fragmentation of Furan upon Resonant Electron Attachment. J Phys Chem A 2020; 124:9427-9435. [PMID: 33125242 PMCID: PMC7667636 DOI: 10.1021/acs.jpca.0c07283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/17/2020] [Indexed: 01/18/2023]
Abstract
We report a dissociative electron attachment study to 2-furoic acid (C5H4O3) isolated in a gas phase, which is a model molecule consisting of a carboxylic group and a furan ring. Dissociation of furan by low energy electrons is accessible only via electronic excited Feshbach resonances at energies of incident electrons above 5 eV. On the other hand, carboxylic acids are well-known to dissociate via attachment of electrons at subexcitation energies. Here we elucidate how the electron and proton transfer reactions induced by carboxylation influence stability of the furan ring. Overlap of the furan and carboxyl π orbitals results in transformation of the nondissociative π2 resonance of the furan ring to a dissociative resonance. The interpretation of hydrogen transfer reactions is supported by experimental studies of 3-methyl-2-furoic and 5-methyl-2-furoic acids (C6H6O3) and density functional theory (DFT) calculations.
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Affiliation(s)
- Mateusz Zawadzki
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, Dolejškova 3, 18223 Prague, Czech Republic
- Atomic
Physics Division, Department of Atomic, Molecular and Optical Physics,
Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Thomas F. M. Luxford
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of
Sciences, Dolejškova 3, 18223 Prague, Czech Republic
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2
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Hänninen V, Murdachaew G, Nathanson GM, Gerber RB, Halonen L. Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water. Phys Chem Chem Phys 2018; 20:23717-23725. [PMID: 30191926 DOI: 10.1039/c8cp03857k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory. The two energetically lowest FA dimer isomers were collided with a water slab at thermal and high kinetic energies up to 68kBT. Our simulations agree with recent experimental observations of nearly a complete uptake of gas-phase FA dimer: the calculated average kinetic energy of the dimers immediately after collision is 5 ± 4% of the incoming kinetic energy, which compares well with the experimental value of 10%. Simulations support the experimental observation of no delayed desorption of FA dimers following initial adsorption. Our analysis shows that the FA dimer forms hydrogen bonds with surface water molecules, where the hydrogen bond order depends on the dimer structure, such that the most stable isomer possesses fewer FA-water hydrogen bonds than the higher energy isomer. Nevertheless, even the most stable isomer can attach to the surface through one hydrogen bond despite its reduced hydrophilicity. Our simulations further show that the probability of FA dimer dissociation is increased by high collision energies, the dimer undergoes isomerization from the higher energy to the lowest energy isomer, and concerted double-proton transfer occurs between the FA monomers. Interestingly, proton transfer appears to be driven by the release of energy arising from such isomerization, which stimulates those internal vibrational degrees of freedom that overcome the barrier of a proton transfer.
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Affiliation(s)
- Vesa Hänninen
- Department of Chemistry, University of Helsinki, P. O. Box 55 (A.I. Virtasen aukio 1), FI-00014, Finland.
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3
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Zawadzki M, Ranković M, Kočišek J, Fedor J. Dissociative electron attachment and anion-induced dimerization in pyruvic acid. Phys Chem Chem Phys 2018; 20:6838-6844. [PMID: 29350234 DOI: 10.1039/c7cp07472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report partial cross sections for the dissociative electron attachment to pyruvic acid. A rich fragmentation dynamics is observed. Electronic structure calculations facilitate the identification of complex rearrangement reactions that occur during the dissociation. Furthermore, a number of fragment anions produced at electron energies close to 0 eV are observed, that cannot originate from single electron-molecule collisions. We ascribe their production to secondary reactions of the transient anions with neutral molecules. Such reactions turn out to be unusually efficient; the most probable reason for this is that they proceed via the formation of a double-hydrogen-bonded complex followed by an ultrafast proton transfer between the reaction partners.
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Affiliation(s)
- M Zawadzki
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic.
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4
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Keolopile ZG, Ryder MR, Calzada B, Gutowski M, Buytendyk AM, Graham JD, Bowen KH. Electrophilicity of oxalic acid monomer is enhanced in the dimer by intermolecular proton transfer. Phys Chem Chem Phys 2017; 19:29760-29766. [PMID: 29105713 DOI: 10.1039/c7cp00474e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have analyzed the effect of excess electron attachment on the network of hydrogen bonds in the oxalic acid dimer (OA)2. The most stable anionic structures may be viewed as complexes of a neutral hydrogenated moiety HOA˙ coordinated to an anionic deprotonated moiety (OA-H)-. HOA˙ acts as a double proton donor and (OA-H)- as a double proton acceptor. Thus the excess electron attachment drives intermolecular proton transfer. We have identified several cyclic hydrogen bonded structures of (OA)2-. Their stability has been analyzed in terms of the stability of the involved conformers, the energetic penalty for deformation of these conformers to the geometry of the dimer, and the two-body interaction energy between the deformed HOA˙ and (OA-H)-. There are at least seven isomers of (OA)2- with stabilization energies in the range of 1.26-1.39 eV. These energies are dominated by attractive two-body interaction energies. The anions are vertically bound electronically by 3.0-3.4 eV and adiabatically bound by at least 1.6 eV. The computational predictions are consistent with the anion photoelectron spectrum of (OA)2-. The spectrum consists of a broad feature, with an onset of 2.5 eV and spanning to 4.3 eV. The electron vertical detachment energy (VDE) is assigned to be 3.3 eV.
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Affiliation(s)
- Zibo G Keolopile
- Institute of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, UK.
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Keolopile ZG, Gutowski M, Buonaugurio A, Collins E, Zhang X, Erb J, Lectka T, Bowen KH, Allan M. Importance of Time Scale and Local Environment in Electron-Driven Proton Transfer. The Anion of Acetoacetic Acid. J Am Chem Soc 2015; 137:14329-40. [DOI: 10.1021/jacs.5b08134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zibo G. Keolopile
- Department
of Physics, University of Botswana, Private Bag 0022, Gaborone, Botswana
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Maciej Gutowski
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Angela Buonaugurio
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Evan Collins
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Xinxing Zhang
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeremy Erb
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kit H. Bowen
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael Allan
- Department
of Chemistry, University of Fribourg, chemin du Musée 9, Fribourg 1700, Switzerland
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6
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Keolopile ZG, Ryder MR, Gutowski M. Intermolecular Interactions between Molecules in Various Conformational States: The Dimer of Oxalic Acid. J Phys Chem A 2014; 118:7385-91. [DOI: 10.1021/jp4125638] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zibo G. Keolopile
- Institute
of Chemical Sciences,
School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, United Kingdom
| | - Matthew R. Ryder
- Institute
of Chemical Sciences,
School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, United Kingdom
| | - Maciej Gutowski
- Institute
of Chemical Sciences,
School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, United Kingdom
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Houplin J, Amiaud L, Humblot V, Martin I, Matar E, Azria R, Pradier CM, Lafosse A. Selective terminal function modification of SAMs driven by low-energy electrons (0-15 eV). Phys Chem Chem Phys 2013; 15:7220-7. [PMID: 23558312 DOI: 10.1039/c3cp43750g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Low-energy electron induced degradation of a model self-assembled monolayer (SAM) of acid terminated alkanethiol was studied under ultra-high vacuum (UHV) conditions at room and low (~40 K) temperatures. Low-energy electron induced chemical modifications of 11-mercaptoundecanoic acid (MUA, HS-(CH2)10-COOH) SAMs deposited on gold were probed in situ as a function of the irradiation energy (<11 eV) by combining two complementary techniques: High Resolution Electron Energy Loss Spectroscopy (HREELS), a surface sensitive vibrational spectroscopy technique, and Electron Stimulated Desorption (ESD) analysis of neutral fragments. The SAM's terminal functions were observed to be selectively damaged at around 1 eV by a resonant electron attachment mechanism, observed to decay by CO, CO2 and H2O formation and desorption. CO2 and H2O were also directly identified at low temperature by vibrational analysis of the irradiated SAMs. At higher irradiation energy, both terminal functions and spacer alkyl chains are damaged upon electron irradiation, by resonant and non-resonant processes.
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Affiliation(s)
- J Houplin
- Université Paris-Sud, Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, Orsay, France
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Gerardi HK, DeBlase AF, Leavitt CM, Su X, Jordan KD, McCoy AB, Johnson MA. Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2−, with vibrational and photoelectron spectroscopies. J Chem Phys 2012; 136:134318. [DOI: 10.1063/1.3693271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Dong L, Wang J. The degree of proton transfer for XH⋯NH3 (X=F, Br, HS, and HCOO) heterodimers upon attachment of an excess electron. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Eustis SN, Radisic D, Bowen KH, Bachorz RA, Haranczyk M, Schenter GK, Gutowski M. Electron-Driven Acid-Base Chemistry: Proton Transfer from Hydrogen Chloride to Ammonia. Science 2008; 319:936-9. [DOI: 10.1126/science.1151614] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Stable Valence Anions of Nucleic Acid Bases and DNA Strand Breaks Induced by Low Energy Electrons. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8184-2_21] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Allan M. Electron collisions with formic acid monomer and dimer. PHYSICAL REVIEW LETTERS 2007; 98:123201. [PMID: 17501119 DOI: 10.1103/physrevlett.98.123201] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Indexed: 05/11/2023]
Abstract
Processes induced by the attachment of slow electrons to formic acid and its hydrogen-bonded dimer were studied. The elastic cross section and the cross section for the excitation of low quanta of discrete vibrations were found to be of a similar magnitude for both targets. A dramatic difference was found in the excitation of a vibrational quasicontinuum in the 1-2 eV range with the ejection of very slow electrons (E<0.1 eV), which was about 20x more intense in the dimer. The association of two formic acid molecules to form a dimer thus dramatically increases the power to quasithermalize electrons arriving with energies in the 1-2 eV energy range. Rapid electron-driven intracluster proton transfer is invoked to explain the observation.
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Affiliation(s)
- Michael Allan
- Department of Chemistry, University of Fribourg, Switzerland
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Mazurkiewicz K, Harańczyk M, Gutowski M, Rak J, Radisic D, Eustis SN, Wang D, Bowen KH. Valence Anions in Complexes of Adenine and 9-Methyladenine with Formic Acid: Stabilization by Intermolecular Proton Transfer. J Am Chem Soc 2007; 129:1216-24. [PMID: 17263404 DOI: 10.1021/ja066229h] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Photoelectron spectra of adenine-formic acid (AFA(-)) and 9-methyladenine-formic acid (MAFA(-)) anionic complexes have been recorded with 2.540 eV photons. These spectra reveal broad features with maxima at 1.5-1.4 eV that indicate formation of stable valence anions in the gas phase. The neutral and anionic complexes of adenine/9-methyladenine and formic acid were also studied computationally at the B3LYP, second-order Møller-Plesset, and coupled-cluster levels of theory with the 6-31++G** and aug-cc-pVDZ basis sets. The neutral complexes form cyclic hydrogen bonds, and the most stable dimers are bound by 17.7 and 16.0 kcal/mol for AFA and MAFA, respectively. The theoretical results indicate that the excess electron in both AFA(-) and MAFA(-) occupies a pi* orbital localized on adenine/9-methyladenine, and the adiabatic stability of the most stable anions amounts to 0.67 and 0.54 eV for AFA(-) and MAFA(-), respectively. The attachment of the excess electron to the complexes induces a barrier-free proton transfer (BFPT) from the carboxylic group of formic acid to a N atom of adenine or 9-methyladenine. As a result, the most stable structures of the anionic complexes can be characterized as neutral radicals of hydrogenated adenine (9-methyladenine) solvated by a deprotonated formic acid. The BFPT to the N atoms of adenine may be biologically relevant because some of these sites are not involved in the Watson-Crick pairing scheme and are easily accessible in the cellular environment. We suggest that valence anions of purines might be as important as those of pyrimidines in the process of DNA damage by low-energy electrons.
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Affiliation(s)
- Kamil Mazurkiewicz
- Department of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Mazurkiewicz K, Bachorz RA, Gutowski M, Rak J. On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study. J Phys Chem B 2006; 110:24696-707. [PMID: 17134233 DOI: 10.1021/jp065666f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).
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Affiliation(s)
- Kamil Mazurkiewicz
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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Harańczyk M, Rak J, Gutowski M. Stabilization of very rare tautomers of 1-methylcytosine by an excess electron. J Phys Chem A 2006; 109:11495-503. [PMID: 16354040 DOI: 10.1021/jp0535590] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized valence anionic states of 1-methylcytosine using various electronic structure methods. We found that the most stable valence anion is related to neither the canonical amino-oxo nor a rare imino-oxo tautomer, in which a proton is transferred from the N4 to N3 atom. Instead, it is related to an imino-oxo tautomer, in which the C5 atom is protonated. This anion is characterized by an electron vertical detachment energy (VDE) of 2.12 eV and it is more stable than the anion based on the canonical tautomer by 1.0 kcal/mol. The latter is characterized by a VDE of 0.31 eV. Another unusual low-lying imino-oxo tautomer with a VDE of 3.60 eV has the C6 atom protonated and is 3.6 kcal/mol less stable than the anion of the canonical tautomer. All these anionic states are adiabatically unbound with respect to the canonical amino-oxo neutral, with the instability of 5.8 kcal/mol for the most stable valence anion. The mechanism of formation of anionic tautomers with carbon atoms protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to the C5 or C6 atom. The six-member ring structure of anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Indeed the neutral systems collapse without a barrier to a linear or a bicyclo structure, which might be viewed as lesions to DNA or RNA. Within the PCM hydration model, the anions become adiabatically bound with respect to the corresponding neutrals, and the two most stable tautomers have a carbon atom protonated.
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Affiliation(s)
- Maciej Harańczyk
- Chemical Sciences Division, Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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