| 1. |
- Abid, Abdul Rahman, et al.
(författare)
-
Forming Bonds While Breaking Old Ones : Isomer-Dependent Formation of H3O+ from Aminobenzoic Acid During X-ray-Induced Fragmentation
- 2023
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:6, s. 1395-1401
-
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.
|
|
| 2. |
- Ablyasova, Olesya S., et al.
(författare)
-
Electronic Structure of the Complete Series of Gas-Phase Manganese Acetylacetonates by X-ray Absorption Spectroscopy
- 2023
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:34, s. 7121-7131
-
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.
|
|
| 3. |
- Abrahamsson, Erik, 1974, et al.
(författare)
-
Dynamics of the O + CN Reaction and N + CO Scattering on Two Coupled Surfaces
- 2009
-
Ingår i: J. Phys. Chem. A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 113:52, s. 14824-14830
-
Tidskriftsartikel (refereegranskat)abstract
- Spin−orbit coupling between the two collinear 2Π and 4Σ− potential energy surfaces for the NCO system are calculated using the RASSI method with CASSCF wave functions as basis set. The GDVR method has been used to interpolate a spin−orbit coupling surface. Wave packet and quasi-classical trajectory surface hopping calculations have been performed and compared for both the O(3P) + CN(X2Σ+) → N(4S) + CO(X1Σ+) reaction and for electronically inelastic scattering in the N + CO channels. The O + CN nonadiabatic reaction probabilities are small. The wavepacket study gives a resonance structure. Also for the N + CO electronically inelastic scattering the wave packet calculations give a distinct resonance structure with peak transition probabilities up to around 10%, which is somewhat lower than the trajectory surface hopping results.
|
|
| 4. |
- Abu-samha, M., et al.
(författare)
-
What Can C1s Photoelectron Spectroscopy Tell about Structure and Bonding in Clusters of Methanol and Methyl Chloride?
- 2007
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 111:37, s. 8903-8909
-
Tidskriftsartikel (refereegranskat)abstract
- Single-component clusters of methanol and methyl chloride have been produced by adiabatic expansion, and their carbon Is photoelectron spectra were recorded using synchrotron radiation and a high-resolution electron analyzer. The experimental spectra are interpreted by means of theoretical models based on molecular dynamics simulations. The data are used to explore to what extent core-level photoelectron spectra may provide information on the bonding mechanism and the geometric structure of clusters of polar molecules. The results indicate that the cluster-to-monomer shift in ionization energy and also the width of the cluster peak may be used to distinguish between hydrogen bonding and weaker electrostatic interactions. Moreover, the larger width of the cluster peak in methanol clusters as compared to methyl chloride clusters is partly due to the structured surface of methanol clusters. Theoretical modeling greatly facilitates the analysis of core-level photoelectron spectra of molecular clusters.
|
|
| 5. |
- Adams, Christopher, et al.
(författare)
-
Vibrational Autodetachment from Anionic Nitroalkane Chains - From Molecular Signatures to Thermionic Emission
- 2019
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 123:40, s. 8562-8570
-
Tidskriftsartikel (refereegranskat)abstract
- We report the kinetic energy distributions in electron autodetachment from nitroethane, 1-nitropropane, and 1-nitrobutane anions upon laser excitation of CH stretching modes measured using velocity map electron imaging. In striking contrast to the case of nitromethane, the kinetic energy distributions show almost no distinct vibrational features, and they can be described by thermionic emission, relating the shape of the distributions to the electron capture cross section of the neutral molecule. The data suggest that a classical description is warranted above ca. 20 meV electron kinetic energy. At lower energies, quantum effects suppress the attachment cross section.
|
|
| 6. |
- Ahlstrand, Emma, et al.
(författare)
-
Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations
- 2017
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:13, s. 2643-2654
-
Tidskriftsartikel (refereegranskat)abstract
- Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.
|
|
| 7. |
- Aidas, Kestutis, et al.
(författare)
-
Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
- 2007
-
Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 111:20, s. 4199-4210
-
Tidskriftsartikel (refereegranskat)abstract
- The gas-to-aqueous solution shifts of the O-17 and C-13 NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.
|
|
| 8. |
- Al-Saidi, W. A., et al.
(författare)
-
Resonance raman spectra of TNT and RDX using vibronic theory, excited-state gradient, and complex polarizability approximations
- 2012
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 116:30, s. 7862-7872
-
Tidskriftsartikel (refereegranskat)abstract
- Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO 2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO 2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.
|
|
| 9. |
- Albinsson, Bo, 1963, et al.
(författare)
-
Conformers of n-Si5Me12: A comparison of ab initio and molecular mechanics methods
- 1999
-
Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 103:14, s. 2184-2196
-
Tidskriftsartikel (refereegranskat)abstract
- Optimized geometries of the conformers of permethylated linear pentasilane, n-Si5Me12, were calculated by the HF/3-21G*, MM3, MM2, and MM+ methods, which predict eight, nine, six, and six energetically distinct enantiomeric conformer pairs, respectively, at geometries representing various combinations of the anti (similar to 165 degrees), ortho (similar to 90 degrees), and gauche (similar to 55 degrees) SiSiSiSi dihedral angles in the backbone. The results of the MM2 and MM+ methods, based on the same force field, differ insignificantly. The barriers between conformers appear to be exaggerated by the molecular mechanics methods, particularly MM2. Contour maps showing the groundstate energy as a function of the full range of two backbone SiSiSiSi dihedral angles, with all other geometrical variables optimized, computed by each of the methods (only a limited range of angles near the anti,anti geometry in the case of HF/3-21G*) are compared with each other and with analogous results for a model compound, Si4Me10. Conformer interconversion paths are discussed, and two meso transition states for enantiomer interconversion have been located at the HF/3-21G* level of calculation. At the eight HF/3-21G* optimized geometries, single-point energies (HF/6-31G* and MP2/6-31G*) and vibrational frequencies (HF/3-21G*) were computed. The predicted IR and Raman spectra suggest that about half of the expected conformers will be identifiable by vibrational spectroscopy under conditions of matrix isolation. Relative conformer energies calculated by the MM2 and HF methods are similar and favor the anti dihedral angles over gauche and ortho, in agreement with results of solution experiments. Those calculated by the hIM3 and HF methods are similar to each other and favor both anti and gauche dihedral angles nearly equally over ortho, in agreement with indications provided by gas-phase experiments. A rationalization of these solvent effects is proposed. The energies of the conformers of Si4Me10 and Si3Me12 were used to set up a system of additive increments at the MM2, MM3, HF/3-21G*, HF/6-31G*, and MP2/6-31G* levels of calculation, which can be used to predict conformational energies of longer permethylated oligosilanes. An intrinsic energy value is assigned to each of the a, o, and g dihedral angles, and interaction energy values are assigned to each combination of two dihedral angles. The interaction values follow the expected rules in that equal twist sense is favored for adjacent aa, ag, oo, and gg pairs, whereas opposite twist sense is generally favored for adjacent so and go pairs. The MM3-derived set of increments has been tested against results computed for Si6Me14 and found to perform well.
|
|
| 10. |
- Andersen, Christina, et al.
(författare)
-
Atmospheric Chemistry of Tetrahydrofuran, 2-Methyltetrahydrofuran, and 2,5-Dimethyltetrahydrofuran : Kinetics of Reactions with Chlorine Atoms, OD Radicals, and Ozone
- 2016
-
Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1089-5639. ; 120:37, s. 7320-7326
-
Tidskriftsartikel (refereegranskat)abstract
- FTIR smog chamber techniques were used to study the kinetics of the gas-phase reactions of Cl atoms, OD radicals, and O3 with the five-membered ring-structured compounds tetrahydrofuran (C4H8O, THF), 2-methyltetrahydrofuran (CH3C4H7O, 2-MTHF), 2,5-dimethyltetrahydrofuran ((CH3)2C4H5O, 2,5-DMTHF), and furan (C4H4O). The rate coefficients determined using relative rate methods were kTHF+Cl = (1.96 ± 0.24) × 10-10, kTHF+OD = (1.81 ± 0.27) × 10-11, kTHF+O3 = (6.41 ± 2.90) × 10-21, k2-MTHF+Cl = (2.65 ± 0.43) × 10-10, k2-MTHF+OD = (2.41 ± 0.51) × 10-11, k2-MTHF+O3 = (1.87 ± 0.82) × 10-20, k2,5-DMTHF+OD = (4.56 ± 0.68) × 10-11, k2,5-DMTHF+Cl = (2.84 ± 0.34) × 10-10, k2,5-DMTHF+O3 = (4.58 ± 2.18), kfuran+Cl = (2.39 ± 0.27) × 10-10, and kfuran+O3 = (2.60 ± 0.31) × 10-18 molecules cm-3 s-1. Rate coefficients of the reactions with ozone were also determined using the absolute rate method under pseudo-first-order conditions. OD radicals, in place of OH radicals, were produced from CD3ONO to avoid spectral overlap of isopropyl and methyl nitrite with the reactants. The kinetics of OD radical reactions are expected to resemble the kinetics of OH radical reactions, and the rate coefficients of the reactions with OD radicals were used to calculate the atmospheric lifetimes with respect to reactions with OH radicals. The lifetimes of THF, 2-MTHF, and 2,5-DMTHF are approximately 15, 12, and 6 h, respectively.
|
|
