| 1. |
- Abid, Abdul Rahman, et al.
(författare)
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Forming Bonds While Breaking Old Ones : Isomer-Dependent Formation of H3O+ from Aminobenzoic Acid During X-ray-Induced Fragmentation
- 2023
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:6, s. 1395-1401
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Tidskriftsartikel (refereegranskat)abstract
- Intramolecular hydrogen transfer, a reaction where donor and acceptor sites of a hydrogen atom are part of the same molecule, is a ubiquitous reaction in biochemistry and organic synthesis. In this work, we report hydronium ion (H3O+) production from aminobenzoic acid (ABA) after core-level ionization with soft X-ray synchrotron radiation. The formation of H3O+ during the fragmentation requires that at least two hydrogen atoms migrate to one of the oxygen atoms within the molecule. The comparison of two structural isomers, ortho- and meta-ABA, revealed that the production of H3O+ depends strongly on the structure of the molecule, the ortho-isomer being much more prone to produce H3O+. The isomer-dependency suggests that the amine group acts as a donor in the hydrogen transfer process. In the case of ortho-ABA, detailed H3O+ production pathways were investigated using photoelectron-photoion-photoion coincidence (PEPIPICO) spectroscopy. It was found that H3O+ can result from a direct two-body dissociation but also from sequential fragmentation processes.
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| 2. |
- Ablyasova, Olesya S., et al.
(författare)
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Electronic Structure of the Complete Series of Gas-Phase Manganese Acetylacetonates by X-ray Absorption Spectroscopy
- 2023
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:34, s. 7121-7131
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Tidskriftsartikel (refereegranskat)abstract
- Metal centers in transition metal–ligand complexes occur in a variety of oxidation states causing their redox activity and therefore making them relevant for applications in physics and chemistry. The electronic state of these complexes can be studied by X-ray absorption spectroscopy, which is, however, due to the complex spectral signature not always straightforward. Here, we study the electronic structure of gas-phase cationic manganese acetylacetonate complexes Mn(acac)1–3+ using X-ray absorption spectroscopy at the metal center and ligand constituents. The spectra are well reproduced by multiconfigurational wave function theory, time-dependent density functional theory as well as parameterized crystal field and charge transfer multiplet simulations. This enables us to get detailed insights into the electronic structure of ground-state Mn(acac)1–3+ and extract empirical parameters such as crystal field strength and exchange coupling from X-ray excitation at both the metal and ligand sites. By comparison to X-ray absorption spectra of neutral, solvated Mn(acac)2,3 complexes, we also show that the effect of coordination on the L3 excitation energy, routinely used to identify oxidation states, can contribute about 40–50% to the observed shift, which for the current study is 1.9 eV per oxidation state.
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| 3. |
- Andersen, J., et al.
(författare)
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Far-Infrared Investigation of the Benzene-Water Complex : The Identification of Large-Amplitude Motion and Tunneling Pathways
- 2020
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:3, s. 513-519
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Tidskriftsartikel (refereegranskat)abstract
- The far-infrared spectrum of the weakly OH···πhydrogen-bonded benzene-water complex has been studied in neon and argon matrices, below 30 K. The in-plane water libration has been observed in both neon and argon for H2O and D2O complexed with C6H6 and C6D6 but not for the corresponding complexes involving HDO. Both H2O and D2O can tunnel between the two possible hydrogen bonds. This is not possible for HDO. The reported far-infrared observations have implications for the interpretation of the previously obtained molecular beam microwave spectrum of the benzene-water complex.
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| 4. |
- Andersson, Åke, et al.
(författare)
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Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:4, s. 938-45
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.
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| 5. |
- Andersson, Åke, et al.
(författare)
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IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase
- 2021
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:34, s. 7449-7456
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Tidskriftsartikel (refereegranskat)abstract
- We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multi-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm(-1). Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.
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| 6. |
- Andersson, Åke, et al.
(författare)
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Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations
- 2020
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:12, s. 2408-2415
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Tidskriftsartikel (refereegranskat)abstract
- The structures of three proton-bound dimers (Met(2)H(+), MetTrpH(+), and Trp(2)H(+)) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600-1850 cm(-1) are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYPGD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500-1700 cm(-1) are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp(2)H(+) is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom. 2016, 30, 24-28). In addition, gas-phase Met(2)H(+) and MetTrpH(+) have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met(2)H(+), however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.
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| 7. |
- Apriliyanto, Yusuf Bramastya, et al.
(författare)
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Toward a Generalized Hückel Rule : The Electronic Structure of Carbon Nanocones
- 2021
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:45, s. 9819-9825
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we investigate a particular class of carbon nanocones, which we name graphannulenes, and present a generalized Hückel rule (GHR) that predicts the character of their ground state based on simply the three topological indices that uniquely define them. Importantly, this rule applies to both flat and curved systems, encompassing a wide variety of known structures that do not satisfy the “classic” 4n + 2 rule such as coronene, corannulene, and Kekulene. We test this rule at the Hückel level of theory for a large number of systems, including structures that are convex and flat, with a saddle-like geometry, and at the CASSCF level of theory for a selected representative subset. All the performed calculations support the GHR that we propose in this work.
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| 8. |
- Ashworth, Eleanor K., et al.
(författare)
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Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:7, s. 1158-1167
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Tidskriftsartikel (refereegranskat)abstract
- The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion–betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion–zwitterion complexes.
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| 9. |
- Ashworth, Eleanor K., et al.
(författare)
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Cryogenic Fluorescence Spectroscopy of Ionic Fluorones in Gaseous and Condensed Phases : New Light on Their Intrinsic Photophysics
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:51, s. 9553-9563
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Tidskriftsartikel (refereegranskat)abstract
- Fluorescence spectroscopy of gas-phase ions generated through electrospray ionization is an emerging technique able to probe intrinsic molecular photophysics directly without perturbations from solvent interactions. While there is ample scope for the ongoing development of gas-phase fluorescence techniques, the recent expansion into low-temperature operating conditions accesses a wealth of data on intrinsic fluorophore photophysics, offering enhanced spectral resolution compared with room-temperature measurements, without matrix effects hindering the excited-state dynamics. This perspective reviews current progress on understanding the photophysics of anionic fluorone dyes, which exhibit an unusually large Stokes shift in the gas phase, and discusses how comparison of gas- and condensed-phase fluorescence spectra can fingerprint structural dynamics. The capacity for temperature-dependent measurements of both fluorescence emission and excitation spectra helps establish the foundation for the use of fluorone dyes as fluorescent tags in macromolecular structure determination. We suggest ideas for technique development.
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| 10. |
- Ayub, Rabia, et al.
(författare)
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Triplet State Baird Aromaticity in Macrocycles : Scope, Limitations, and Complications
- 2021
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society. - 1089-5639 .- 1520-5215. ; 125:2, s. 570-584
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Tidskriftsartikel (refereegranskat)abstract
- The aromaticity of cyclic 4nπ-electron molecules in their first ππ∗ triplet state (T1), labeled Baird aromaticity, has gained growing attention in the past decade. Here we explore computationally the limitations of T1 state Baird aromaticity in macrocyclic compounds, [n]CM's, which are cyclic oligomers of four different monocycles (M = p-phenylene (PP), 2,5-linked furan (FU), 1,4-linked cyclohexa-1,3-diene (CHD), and 1,4-linked cyclopentadiene (CPD)). We strive for conclusions that are general for various DFT functionals, although for macrocycles with up to 20 π-electrons in their main conjugation paths we find that for their T1 states single-point energies at both canonical UCCSD(T) and approximative DLPNO-UCCSD(T) levels are lowest when based on UB3LYP over UM06-2X and UCAM-B3LYP geometries. This finding is in contrast to what has earlier been observed for the electronic ground state of expanded porphyrins. Yet, irrespective of functional, macrocycles with 2,5-linked furans ([n]CFU's) retain Baird aromaticity until larger n than those composed of the other three monocycles. Also, when based on geometric, electronic and energetic aspects of aromaticity, a 3[n]CFU with a specific n is more strongly Baird-aromatic than the analogous 3[n]CPP while the magnetic indices tell the opposite. To construct large T1 state Baird-aromatic [n]CM's, the design should be such that the T1 state Baird aromaticity of the macrocyclic perimeter dominates over a situation with local closed-shell Hückel aromaticity of one or a few monocycles and semilocalized triplet diradical character. Monomers with lower Hückel aromaticity in S0 than benzene (e.g., furan) that do not impose steric congestion are preferred. Structural confinement imposed by, e.g., methylene bridges is also an approach to larger Baird-aromatic macrocycles. Finally, by using the Zilberg-Haas description of T1 state aromaticity, we reveal the analogy to the Hückel aromaticity of the corresponding closed-shell dications yet observe stronger Hückel aromaticity in the macrocyclic dications than Baird aromaticity in the T1 states of the neutral macrocycles. © 2021 The Authors.
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