1. |
- Malysheva, Lyuba, et al.
(författare)
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Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling
- 2005
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106 .- 1520-5207. ; 109:34, s. 7788-7796
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Tidskriftsartikel (refereegranskat)abstract
- The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O)6H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.
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2. |
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3. |
- 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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4. |
- 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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5. |
- Abrahamsson, Erik, 1974, et al.
(författare)
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Dynamics of the O + CN Reaction and N + CO Scattering on Two Coupled Surfaces
- 2009
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Ingår i: J. Phys. Chem. A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 113:52, s. 14824-14830
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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.
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6. |
- Abu-samha, M., et al.
(författare)
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What Can C1s Photoelectron Spectroscopy Tell about Structure and Bonding in Clusters of Methanol and Methyl Chloride?
- 2007
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 111:37, s. 8903-8909
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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.
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7. |
- Adams, Christopher, et al.
(författare)
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Vibrational Autodetachment from Anionic Nitroalkane Chains - From Molecular Signatures to Thermionic Emission
- 2019
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 123:40, s. 8562-8570
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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.
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8. |
- Ahlstrand, Emma, et al.
(författare)
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Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations
- 2017
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:13, s. 2643-2654
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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.
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9. |
- Aidas, Kestutis, et al.
(författare)
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Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches
- 2007
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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
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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.
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10. |
- Al-Saidi, W. A., et al.
(författare)
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Resonance raman spectra of TNT and RDX using vibronic theory, excited-state gradient, and complex polarizability approximations
- 2012
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 116:30, s. 7862-7872
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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.
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11. |
- Albinsson, Bo, 1963, et al.
(författare)
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Conformers of n-Si5Me12: A comparison of ab initio and molecular mechanics methods
- 1999
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Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 103:14, s. 2184-2196
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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.
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12. |
- Andersen, Christina, et al.
(författare)
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Atmospheric Chemistry of Tetrahydrofuran, 2-Methyltetrahydrofuran, and 2,5-Dimethyltetrahydrofuran : Kinetics of Reactions with Chlorine Atoms, OD Radicals, and Ozone
- 2016
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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
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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.
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13. |
- 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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14. |
- Andersson, Markus, 1981, et al.
(författare)
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Coordination of Imidazoles by Cu(II) and Zn(II) as Studied by NMR Relaxometry, EPR, far-FTIR Vibrational Spectroscopy and Ab Initio Calculations: Effect of Methyl Substitution
- 2010
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 114:50, s. 13146-13153
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Tidskriftsartikel (refereegranskat)abstract
- Synthetic imidazole ligands are typically substituted at the N-1 ((1)-Im) position while natural imidazole ligands are substituted at the C-4 ((4)-Im) position. To outline the difference in coordination properties, the methyl-substituted imidazoles Me(4)-Im and Me(1)-Im were complexed with CuCl2 and ZnCl2 and investigated by NMR relaxometry, electron paramagnetic resonance, far-Fourier transform IR vibrational spectroscopy, and ab initio calculations. Me(4)-Im, Me(1)-Im, and Im in excess form the usual tetragonal D-4h [CuL4X2] complexes with CuCl2 whereas the methylated imidazoles form pseudotetrahedral C-2v, complexes instead of the usual octahedral O-h [ZnIm(6)](2+) complex. All imidazoles display a high degree of covalence in the M-L sigma- and pi-bonds and the pi-interaction strength affects the relative energies of complexation. Opportunities to tailor complexes by the chemical properties of the substituents are envisaged due to the role of the inductive and hyperconjugative effects, rather than position.
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15. |
- Andersson, M P, et al.
(författare)
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New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-xi basis set 6-311+G(d,p)
- 2005
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 109:12, s. 2937-2941
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Tidskriftsartikel (refereegranskat)abstract
- We have calculated optimal frequency scaling factors for the B3LYP/ 6-311+G(d,p) method for fundamental vibrational frequencies on the basis of a set of 125 molecules. Using the new scaling factor, the vibrational frequencies calculated with the triple-zeta basis set 6-311+G(d,p) give significantly better accuracy than those calculated with the double-zeta 6-31G(d) basis set. Scale factors were also determined for low-frequency vibrations using the molecular set of 125 molecules and for zero-point energies using a smaller set of 40 molecules. We have studied the effect on the calculated vibrational frequencies for various combinations of diffuse and polarization functions added to the triple-zeta 6-311G basis set. The 6-311+G(d,p) basis set is found to give almost converged frequencies for most molecules, and we conclude that our optimum scaling factors are valid for the basis sets 6-311 G(d,p) to 6-311++G(3df,3pd). The new scale factors are 0.9679 for vibrational frequencies, 1.0100 for low-frequency vibrations, and 0.9877 for zero-point vibrational energies.
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16. |
- Andersson, Patrik U, 1970, et al.
(författare)
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Carbon dioxide interactions with crystalline and amorphous ice surfaces
- 2004
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:21, s. 4627-4631
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Tidskriftsartikel (refereegranskat)abstract
- Carbon dioxide interactions with crystalline and amorphous water ice have been studied by time-resolved molecular beam techniques. CO2 collisions at thermal kinetic energies with ice in the temperature range 100-160 K result in efficient trapping on the ice surface followed by desorption. The desorption kinetics on crystalline ice at 100-125 K are well described by the Arrhenius equation with an activation energy of 0.22 +/- 0.02 eV and a preexponential factor of 10(13.32+/-0.57) s(-1). Below 120 K, CO2 populates strongly bonded sites on amorphous ice, resulting in surface residence times on the order of minutes at 100 K, and the desorption data can in this case not be explained by a simple first-order process. The results are compared to previous studies of gas-ice interactions, and the implications for heterogeneous processes in the terrestrial atmosphere are discussed.
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17. |
- Andersson, Stefan, 1973, et al.
(författare)
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Comparison of quantum dynamics and quantum transition state theory estimates of the H + CH4 reaction rate.
- 2009
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Ingår i: The journal of physical chemistry. A. - : American Chemical Society (ACS). - 1520-5215 .- 1089-5639. ; 113:16, s. 4468-78
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Tidskriftsartikel (refereegranskat)abstract
- Thermal rate constants are calculated for the H + CH(4) --> CH(3) + H(2) reaction employing the potential energy surface of Espinosa-Garcia (Espinosa-Garcia, J. J. Chem. Phys. 2002, 116, 10664). Two theoretical approaches are used. First, we employ the multiconfigurational time-dependent Hartree method combined with flux correlation functions. In this way rate constants in the range 225-400 K are obtained and compared with previous results using the same theoretical method but the potential energy surface of Wu et al. (Wu, T.; Werner, H.-J.; Manthe, U. Science 2004, 306, 2227). It is found that the Espinosa-Garcia surface results in larger rate constants. Second, a harmonic quantum transition state theory (HQTST) implementation of instanton theory is used to obtain rate constants in a temperature interval from 20 K up to the crossover temperature at 296 K. The HQTST estimates are larger than MCTDH ones by a factor of about three in the common temperature range. Comparison is also made with various tunneling corrections to transition state theory and quantum instanton theory.
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18. |
- Andersson, Stefan, 1973, et al.
(författare)
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Computational studies of the kinetics of the C+NO and O+CN reactions
- 2003
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 107:28, s. 5439-5447
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Tidskriftsartikel (refereegranskat)abstract
- Thermal rate coefficients for the reactions C(3P) + NO(X2Π) → CN(X2Σ+) + O(3P), C(3P) + NO(X2Π) → CO(X1Σ+) + N(2D), and O(3P) + CN(X2Σ+) → CO(X1Σ+) + N(2D) in the temperature range from 5 to 5000 K have been obtained using quasiclassical trajectory calculations. Results are reported for two ab initio potential energy surfaces corresponding to states of 2A‘ and 2A‘ ‘ symmetry. Good agreement between calculated and experimental rate coefficients are obtained for the C + NO reactions for all temperatures, whereas the rate coefficient for the O + CN reaction at room temperature is larger than that found experimentally. The dynamics is considerably different on the two potential energy surfaces with the 2A‘ ‘ giving rate coefficients in better agreement with experiments. The quality of the potential energy surfaces are discussed in the light of new electronic structure calculations including spin−orbit coupling.
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19. |
- 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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20. |
- 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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21. |
- 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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22. |
- Andreasson, Joakim, 1973, et al.
(författare)
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Efficient non-radiative deactivation and conformational flexibility of meso-diaryloctaalkylporphyrins in the excited triplet state
- 2000
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Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 104:41, s. 9307-9314
-
Tidskriftsartikel (refereegranskat)abstract
- The excited triplet state deactivation of zinc(II) meso-diaryloctaalkylporphyrins (ZnDAOAP) has been studied over a wide temperature range using transient triplet-triplet absorption spectroscopy together with steady-state and time-resolved phosphorescence techniques, The results from transient absorption measurements show that the depopulation of the initially formed triplet state (T-1A state) is unusually fast at temperatures above 150 K. The efficiency of the deactivation originates from a spin allowed transition to a second tripler state (T-1B state), The transformation process T-1A-->T-1B is therefore the dominating deactivation channel of the T-1A state in this temperature range, and direct intersystem crossing T-1A-->S-0 makes negligible contribution. The subsequent ground-state recovery T-1B-->S-0 is also very efficient in comparison to many other porphyrins. Due to the substantial activation energy found for the transformation process, it most likely involves a conformational distortion of the porphyrin macrocycle. At low temperature, however, the relaxation of the T-1A State occurs by direct intersystem crossing to the ground state.
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23. |
- Andreasson, Joakim, 1973, et al.
(författare)
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Photoinduced hole transfer from the triplet state in a porphyrin-based donor-bridge-acceptor system
- 2003
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 107:42, s. 8825-8833
-
Tidskriftsartikel (refereegranskat)abstract
- The triplet excited-state deactivation of a gold porphyrin (AuP) in porphyrin-based donor-bridge-acceptor (D-B-A) systems has been studied. The results from room temperature and 80 K measurements are presented. The primary objectives have been to investigate whether electrons/electron holes or excitation energy could be transferred from (AuP)-Au-3 to the appended zinc porphyrin (ZnP) in the dimers. As the bridging chromophores in our D-B-A systems separate the ZnP and AuP moieties by 19 A edge-to-edge, we do not expect a significant contribution to either electron or energy transfer from a direct (through space) exchange mechanism. This gives us the opportunity to scrutinize how the bridging chromophores influence the transfer reactions. The results show that quenching of (AuP)-Au-3 occurs with high efficiency in the dimers that are connected by fully conjugated bridging chromophores, whereas no quenching is observed when the conjugation of the bridge is broken. We also observed that the decay of (AuP)-Au-3 is complex at temperatures below 110 K. In addition to the two previously published lifetimes on the order of some 10-100 mus, we have found a third lifetime on the nanosecond time scale.
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24. |
- Apriliyanto, Yusuf Bramastya, et al.
(författare)
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Toward a Generalized Hückel Rule : The Electronic Structure of Carbon Nanocones
- 2021
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:45, s. 9819-9825
-
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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25. |
- Ashworth, Eleanor K., et al.
(författare)
-
Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects
- 2022
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:7, s. 1158-1167
-
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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26. |
- 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
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:51, s. 9553-9563
-
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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27. |
- Ausmeel, S., et al.
(författare)
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Reactions of Three Lactones with Cl, OD, and O3 : Atmospheric Impact and Trends in Furan Reactivity
- 2017
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:21, s. 4123-4131
-
Tidskriftsartikel (refereegranskat)abstract
- Lactones, cyclic esters of hydroxycarboxylic acids, are interesting biofuel candidates as they can be made from cellulosic biomass and have favorable physical and chemical properties for distribution and use. The reactions of γ-valerolactone (GVL), γ-crotonolactone (2(5H)-F), and α-methyl-γ-crotonolactone (3M-2(5H)-F) with Cl, OD, and O3 were investigated in a static chamber at 700 Torr and 298 ± 2 K. The relative rate method was used to determine kGVL+Cl = (4.56 ± 0.51) × 10-11, kGVL+OD = (2.94 ± 0.41) × 10-11, k2(5H)-F+Cl = (2.94 ± 0.41) × 10-11, k2(5H)-F+OD = (4.06 ± 0.073) × 10-12, k3M-2(5H)-F+Cl = (16.1 ± 1.8) × 10-11, and k3M-2(5H)-F+OD = (12.6 ± 0.52) × 10-12, all rate coefficients in units of cm3 molecule-1 s-1. An absolute rate method was used to determine k2(5H)-F+O3 = (6.73 ± 0.18) × 10-20 and k3M-2(5H)-F+O3 = (5.42 ± 1.23) × 10-19 in units of cm3 molecule-1 s-1. Products were identified for reactions of the lactones with Cl. In the presence of O2 the products are formic acid (HCOOH), formyl chloride (CHClO), and phosgene (CCl2O), and also maleic anhydride (C2H2(CO)2O) for 2(5H)-F. In addition both reactions produced a number of unidentified products that likely belong to molecules with the ring-structure intact. A review of literature data for reactions of other furans show that the reactivity of the lactones are generally lower compared to that of corresponding compounds without the carbonyl group.
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28. |
- Ayub, Rabia, et al.
(författare)
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Triplet State Baird Aromaticity in Macrocycles : Scope, Limitations, and Complications
- 2021
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society. - 1089-5639 .- 1520-5215. ; 125:2, s. 570-584
-
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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29. |
- Aziz, Emad F., et al.
(författare)
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Photoinduced formation of N-2 molecules in ammonium compounds
- 2007
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 111:39, s. 9662-9669
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Tidskriftsartikel (refereegranskat)abstract
- Via fluorescence yield (FY) and resonant inelastic scattering spectroscopy in the soft X-ray range we find that soft X-rays induce formation of N-2 molecules in solid NH4Cl and in related compounds. The nitrogen molecules form weak bonds in NH4Cl, so that a substantial fraction of the molecules remains in the sample. From measurements of the FY as a function of exposure and temperature, the rates for the photochemical processes are estimated. At elevated temperatures (363 K), several nitrogen atoms are removed from the sample per incoming photon. At lower temperatures (233 K), the rate is reduced to around 0.02 nitrogen atoms for each incoming photon. Virtually all these atoms form N-2 molecules which are bound in the sample. The generality and implications of these results are briefly discussed.
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30. |
- Bacskay, G. B., et al.
(författare)
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Covalent Bonding in the Hydrogen Molecule
- 2017
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:48, s. 9330-9345
-
Tidskriftsartikel (refereegranskat)abstract
- This work addresses the continuing disagreement between two schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, covalent bonding is a quantum mechanical phenomenon whereby lowering of the kinetic energy associated with electron sharing, i.e., delocalization, is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Following our study of H-2(+) we present an analogous detailed study of H-2 where bonding involves an electron pair with repulsion and correlation playing a significant role in its properties. We use a range of different computational approaches to study and reveal the relevant contributions to bonding as seen in the electron density and corresponding kinetic and potential energy distributions. The energetics associated with the more complex electronic structure of H-2, when examined in detail, clearly agrees with the analysis of Ruedenberg; i.e., covalent bonding is due to a decrease in the interatomic kinetic energy resulting from electronic delocalization. Our results support the view that covalent bonding is a quantum dynamical phenomenon requiring a properly quantized kinetic energy to be used in its description.
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31. |
- Bacskay, G. B., et al.
(författare)
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Covalent Bonding: The Fundamental Role of the Kinetic Energy
- 2013
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 117:33, s. 7946-7958
-
Tidskriftsartikel (refereegranskat)abstract
- This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H-2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H-2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.
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32. |
- Bacskay, G. B., et al.
(författare)
-
The Virial Theorem and Covalent Bonding
- 2018
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 122:39, s. 7880-7893
-
Tidskriftsartikel (refereegranskat)
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33. |
- Baeuml, Lena, et al.
(författare)
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Following the Nonadiabatic Ultrafast Dynamics of Uracil via Simulated X-ray Absorption Spectra
- 2023
-
Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 127:46, s. 9787-9796
-
Tidskriftsartikel (refereegranskat)abstract
- The nucleobase uracil exhibits high photostability due to ultrafast relaxation processes mediated by conical intersections (CoIns), where the interplay between nuclear and electron dynamics becomes crucial. In our previous study, we observed seemingly long-lived traces of electronic coherence for the relaxation process through the S-2/S-1 CoIn by applying our ansatz for coupled nuclear and electron dynamics in molecules (NEMol). In this work, we theoretically investigate how time-dependent transient X-ray absorption spectroscopy can be used to observe this ultrafast dynamics. Therefore, we calculated X-ray absorption spectra (XAS) for the oxygen K-edge, using a multireference protocol in combination with NEMol dynamics. Thus, we have access to both the transient XAS based on the nuclear wavepacket dynamics and the modulation of the signals caused by the electronic coherence induced by the excitation process and the presence of a CoIn seam. In both cases, we were able to qualitatively predict its influence on the resulting XAS.
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34. |
- Baev, Alexander, et al.
(författare)
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Optical limiting properties of Zinc- and Platinum-based organometallic compounds
- 2004
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:36, s. 7406-7416
-
Tidskriftsartikel (refereegranskat)abstract
- Optical power limiting is theoretically studied using an approach that combines quantum electronic structure calculations of multiphoton excitations and classical calculations of dynamical wave propagation. We illustrate the capability of such a combined approach by presenting results for a couple of organometallic compounds; basic metal-base porphyrins, vinylphenylamine porhyrin, and the so-called type IVc platinum compound. A comparative analysis of their electronic properties related to nonlinear absorption of electromagnetic radiation and their optical limiting capability has been performed based on dynamical simulations of the nonlinear pulse propagation taking account of resonant as well as off-resonant effects. Several key features and rate-limiting steps in the transmission have been examined in relation to various characteristics of the pulse. It is found that the resonant vs off-resonant conditions, the saturation conditions and the dephasing play critical roles for the nonlinear transmission. The saturation effects are sensitive to the pulse duration, the inter-system crossing rate and the quenching of the higher triplet state. The inter-system crossing rate has to be comparable with the inverse pulse duration in order to boost the stepwise two-photon channel associated with singlet-singlet followed by triplet-triplet transitions. It is illustrated that structure-to-property relations of the rate-limiting steps serve as important criteria for choices of compounds suitable for the application of interest.
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35. |
- Baev, Alexander, et al.
(författare)
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Theoretical Simulations of clamping levels in optical power limiting
- 2006
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207 .- 1520-5215. ; 110:42, s. 20912-20916
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Tidskriftsartikel (refereegranskat)abstract
- Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol-gel glass matrix. A clamping level of 2.5 mu J is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.
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36. |
- Baranets, Sviatoslav, et al.
(författare)
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Structural Uniqueness of the [Nb(As5)2]5– Cluster in the Zintl Phase Cs5NbAs10
- 2021
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:20, s. 4323-4333
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Tidskriftsartikel (refereegranskat)abstract
- The structure of the novel Zintl phase, Cs5NbAs10, is reported for the first time. This compound crystallizes in the monoclinic P21/c space group (no. 14) with eight formula units per cell. The structure represents a unique atomic arrangement, constituting a new structure type with Wyckoff sequence e32. The most important structural element is the unprecedented [Nb(As5)2]5– cluster anion, formed by a Nb atom enclosed between two As5 rings. These nonaromatic cyclic species, formally [As5]5–, adopt an envelope conformation similar to that of cyclopentane. To date, it is only the second example of an [As5]5– ring with this conformation, reported in an inorganic solid-state compound. The bonding characteristics of the [Nb(As5)2]5– cluster and the [As5]5– rings are thoroughly investigated using first-principles methods and discussed. Electronic band structure calculations on Cs5NbAs10 suggest that this compound is a semiconductor with an estimated band gap of ca. 1.4 eV.
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37. |
- Barinovs, G, et al.
(författare)
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Propagation of 3D wave packets for nonzero total angular momentum using the split operator method
- 2001
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 105:31, s. 7441-7445
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Tidskriftsartikel (refereegranskat)abstract
- Three-dimensional wave packet calculations for total angular momentum quantum number J ≥ 0 have been performed in Jacobi coordinates. To be able to use the split operator propagator together with the fast Fourier transform method, the wave function is transformed and a modified Hamiltonian obtained. The filter diagonalization method has been used to determine a few rovibrational eigenstates of the H2O molecule on the lowest potential energy surface. Good agreement with previous work is obtained.
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38. |
- Barone, Giampaolo, et al.
(författare)
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Nuclear quadrupole moment of Sn-119
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:7, s. 1666-1672
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Tidskriftsartikel (refereegranskat)abstract
- Second-order scalar-relativistic Douglas-Kroll-Hess density functional calculations of the electric field gradient, including an analytic correction of the picture change error, were performed for 34 tin compounds of which molecular structures and Sn-119 Mossbauer spectroscopy parameters are experimentally known. The components of the diagonalized electric field gradient tensor, V-xx,V-yy, V-zz, were used to determine the quantity V, which is proportional to the nuclear quadrupole splitting parameter Delta E. The slope of the linear correlation plot of the experimentally determined Delta E parameter versus the corresponding calculated V data allowed us to obtain an absolute value of the nuclear quadrupole moment Q of Sn-119 equal to Q = 13.2 +/- 0.1 fm(2). This is about 11% larger than the picture-change-error-affected value and in good agreement with previous estimates of the picture change error in compounds of similar atomic charge. Moreover, despite the variety of the tin compounds considered in this study, the new result is in excellent agreement with the previously determined most accurate value of Q for Sn-119 of Q = 12.8 +/- 0.7 fm(2), but with a noticeably narrower error bar. The reliability of the calibration method in the calculation of the Delta E parameter of tin compounds is within a margin of +/- 0.3 mm s(-1) when compared to experimental data and does not depend on the inclusion of the picture change correction in the density functional calculations but is essentially determined by the use of an atomic natural orbital relativistic core-correlated basis set for the description of the core electron density. The results obtained suggest that the present picture-change-corrected Douglas-Kroll-Hess approach provides reliable electric field gradients in the case of closed-shell metal compounds involving elements up to the fifth row of the periodic table for which spin-orbit coupling is negligible.
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39. |
- Baryshnikov, Glib, et al.
(författare)
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Odd-Number Cyclo[n]Carbons Sustaining Alternating Aromaticity
- 2022
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:16, s. 2445-2452
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Tidskriftsartikel (refereegranskat)abstract
- Cyclo[n]carbons (n = 5, 7, 9,..., 29) composed from an odd number of carbon atoms are studied computationally at density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) levels of theory to get insight into their electronic structure and aromaticity. DFT calculations predict a strongly delocalized carbene structure of the cyclo[n]carbons and an aromatic character for all of them. In contrast, calculations at the CASSCF level yield geometrically bent and electronically localized carbene structures leading to an alternating double aromaticity of the odd-number cyclo[n]carbons. CASSCF calculations yield a singlet electronic ground state for the studied cyclo[n]carbons except for C25, whereas at the DFT level the energy difference between the lowest singlet and triplet states depends on the employed functional. The BHandHLYP functional predicts a triplet ground state of the larger odd-number cyclo[n]carbons starting from n = 13. Current-density calculations at the BHandHLYP level using the CASSCFoptimized molecular structures show that there is a through-space delocalization in the cyclo[n]carbons. The current density avoids the carbene carbon atom, leading to an alternating double aromaticity of the oddnumber cyclo[n]carbons satisfying the antiaromatic [4k+1] and aromatic [4k+3] rules. C11, C15, and C19 are aromatic and can be prioritized in future synthesis. We predict a bond-shift phenomenon for the triplet state of the cyclo[n]carbons leading to resonance structures that have different reactivity toward dimerization.
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40. |
- Baryshnikov, Glib, V., et al.
(författare)
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Aromaticity of Even-Number Cyclo[n]carbons (n=6-100)
- 2020
-
Ingår i: Journal of Physical Chemistry A. - : AMER CHEMICAL SOC. - 1089-5639 .- 1520-5215. ; 124:51, s. 10849-10855
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Tidskriftsartikel (refereegranskat)abstract
- The recently synthesized cyclo[18]carbon molecule has been characterized in a number of studies by calculating electronic, spectroscopic, and mechanical properties. However, cyclo[18] carbon is only one member of the class of cyclo[n]carbons-standalone carbon allotrope representatives. Many of the larger members of this class of molecules have not been thoroughly investigated. In this work, we calculate the magnetically induced current density of cyclo[n]carbons in order to elucidate how electron delocalization and aromatic properties change with the size of the molecular ring (n), where n is an even number between 6 and 100. We find that the Hiickel rules for aromaticity (4k + 2) and antiaromaticity (4k) become degenerate for large C-n rings (n > 50), which can be understood as a transition from a delocalized electronic structure to a nonaromatic structure with localized current density fluxes in the triple bonds. Actually, the calculations suggest that cyclo[n]carbons with n > 50 are nonaromatic cyclic polyalkynes. The influence of the amount of nonlocal exchange and the asymptotic behavior of the exchange-correlation potential of the employed density functionals on the strength of the magnetically induced ring current and the aromatic character of the large cyclo[n]carbons is also discussed.
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41. |
- Bauschlicher, C.W., et al.
(författare)
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A further study of the products of scandium and dioxygen reactions
- 1999
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Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 103:28, s. 5463-5467
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Tidskriftsartikel (refereegranskat)abstract
- The products of the reaction of Sc and dioxygen have been reinvestigated. By adding the electron-trapping molecule CCl4 additional information about the IR spectra has been obtained, as well as the observation of new bands. New ab initio calculations are also performed on possible products of the Sc plus O-2 reaction. The previously observed band at 722.5 cm(-1) is assigned as the b(2) mode of ScO2-. Bands arising from ScO+, Sc(O-2)(+), and(O-2)ScO are also assigned. We are still unable to assign any bands to OScO. The problems associated with the computational study of ScO2 are discussed.
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42. |
- Becker, Hans-Christian, 1971, et al.
(författare)
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Ground- and excited-state properties of molecular complexes between adenine and 2,7-diazapyrene and its N-methylated cations
- 1997
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 101:47, s. 8853-8860
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Tidskriftsartikel (refereegranskat)abstract
- It has recently been found that 2,7-diazapyrenes upon interaction with nucleic acids form stacked (''intercalation'') complexes, which for the methylated derivatives exhibit new absorption features assigned as charge-transfer (CT) transitions.' To better understand the basis of these interactions and associated optical properties, the geometries and electronic spectra of complexes of adenine (A) with 2,7-diazapyrene (DAP), N-methyl-2,7-diazapyrenium (MDAP(+)), and N,N-dimethyl-2,7-diazapyrenium (DMDAP(2+)) have been modeled using semiempirical AM1 and PM3 geometry optimizations, ab initio (vacuum and Onsager model) energy calculations, and ZINDO/S calculations. In addition, absorption spectra, fluorescence quenching, and H-1 NMR spectra for the complexes in aqueous solution have been measured. For the A-DAP complex, a coplanar, hydrogen-bonded complex is predicted by the calculations, while A-MDAP(+) and A-DMDAP(2+) complexes should have edge-to-face geometry. The association is predicted to be of electrostatic nature, mainly between the pyridinium nitrogen (MDAP(+), DMDAP(2+)) and N-1/NH2 of adenine. There seems to be a preference (6 kcal/mol) for the hydrogen-bonded A-DAP complex, and the energetic difference between face-to-face and edge-to-face A-MDAP(+) and A-DMDAP(2+) complexes is 3 and 8 kcal/mol, respectively (Onsager ab initio, epsilon = 79.5). By contrast, the H-1 NMR data and experimental absorption spectra in conjunction with calculated spectra instead indicate that all three adenine-diazapyrene complexes assume face-to-face arrangement in water because of hydrophobic effects. In agreement with the putative CT absorption of diazapyrenium-DNA complexes, absorption tails are also observed for A-DMDAP(2+) and A-MDAP(+), however not for the A-DAP complex. Most satisfactorily, charge-transfer transitions are predicted by the calculations to occur in the correct wavelength region for A-DMDAP(2+) (strongest) and A-MDAP(+), while A-DAP is predicted not to have any CT transitions. Correspondingly, the observation of quenching of fluorescence of MDAP(+) and DMDAP(2+) (but not DAP) by adenine can explained by charge transfer from adenine to the diazapyrenium.
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43. |
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44. |
- Benetis, Nikolas P., et al.
(författare)
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Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra
- 2015
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 119:35, s. 9385-9404
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Tidskriftsartikel (refereegranskat)abstract
- A simple first-principles electronic structure computation, further qc (quantum chemistry) computation, of the methyl radical gives three equal hf (hyperfine) couplings for the three protons with the unpaired electron. The corresponding dipolar tensors were notably rhombic and had different orientations and regular magnitude components, as they should, but what the overall A-tensor was seen by the electron spin is a different story! The final g = (2.002993, 2.002993, 2.002231) tensor and the hf coupling results obtained in vacuum, at the B3LYP/EPRIII level of theory clearly indicate that in particular the above A = (-65.19, -65.19, 62.54) MHz tensor was axial to a first approximation without considering any rotational dynamics for the CH3. This approximation was not applicable, however, for the trifluoromethyl CF3 radical, a heavier and nonplanar rotor with very anisotropic hf coupling, used here for comparison. Finally, a derivation is presented explaining why there is actually no need for the CH3 radicals to consider additional rotational dynamics in order for the electron to obtain an axially symmetric hf (hyperfine) tensor by considering the simultaneous dipolar couplings of the three protons. An additional consequence is an almost isotropic A-tensor for the electron spin of the CH3 radical. To the best of our knowledge, this point has not been discussed in the literature before. The unexpected isotropy of the EPR parameters of CH3 was solely attributed to the rotational dynamics and was not clearly separated from the overall symmetry of the species. The present theoretical results allowed a first explanation of the forbidden satellite lines in the CH3 EPR spectrum. The satellites are a fingerprint of the radical rotation, helping thus in distinguishing the CH3 reorientation from quantum rotation at very low temperatures.
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45. |
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46. |
- Berglund-Baudin, Helena, et al.
(författare)
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Intramolecular Electron Transfer from Manganese(II) Coordinatively Linked to a Photogenerated Ru(III)-Polypyridine Complex: A Kinetic Analysis
- 1998
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Ingår i: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 102:15, s. 2512-2518
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Tidskriftsartikel (refereegranskat)abstract
- For further investigations in the field of artificial photosynthesis, a model compound, 1, has been developed to mimic the electron-transfer steps from the manganese cluster to P680+ in photosystem II. In this model compound the photosensitizer ruthenium(II)-trisbipyridyl was linked to a manganese(II) ion through a bridging ligand. Photoexcitation of 1 in the presence of the electron acceptor methyl viologen (MV2+) lead to electron transfer from the Ru moiety to MV2+. Laser flash photolysis experiments at different concentrations of 1 were performed in order to follow the subsequent reduction of the photooxidized Ru(III) species. A kinetic model, taking different parallel reactions into account, could explain the experimental data. It was shown that the major part of the photooxidized Ru(III) created was reduced again by intramolecular electron transfer from the attached Mn(II), with a rate constant of 1.8 × 105 s-1. However, Mn(II) was partially dissociated from 1, giving a fraction of Ru(III) without Mn(II) attached. In these complexes electron transfer could occur only after a rate-limiting reassociation of Mn(II), with a rate constant 2.9 × 109 M-1 s-1. In the analysis of the data, the fraction of dissociated Mn(II) could be determined independently at each concentration of 1, utilizing the fact that bound Mn(II) quenched the excited state, probably by energy transfer.
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47. |
- Bergson, Göran, et al.
(författare)
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Is a Proposed Reaction Mechanism Free from Unnecessary Assumptions? : Occam's Razor Applied in a Mathematical Way To Complex First-Order Reaction Systems
- 2008
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Ingår i: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; :112, s. 4235-4240
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Tidskriftsartikel (refereegranskat)abstract
- Following Occam's principle, a proposed reaction mechanism should not contain assumptions about the existence of reactive intermediates and reaction paths that are unnecessary for a full description and interpretation of the available facts. A mechanism refers, in this paper, to a proposed reaction scheme or network that represents the reactions supposed to be going on in a complex reaction system with observable species as well as unobservable reactive intermediates. The scope is limited here to (pseudo) first-order reactions and the steady-state approximation is invoked in order to relate unknown mechanistic rate constants to experimentally determined ones, and, when available, theoretically calculated quantities. When the resulting, nonlinear system of equations admits a unique solution within a physically reasonable domain, it is concluded that the reaction mechanism fulfills Occam's principle. Otherwise, there are many or no solutions. No subjective or qualitative arguments enter the procedure and the outcome is not negotiable.
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48. |
- Bermúdez, Eduardo, et al.
(författare)
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Mechanism of the organocatalyzed decarboxylative Knoevenagel-Doebner reaction. A theoretical study.
- 2010
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 114:50, s. 13086-92
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated important intermediates and key transition states of the organocatalyzed Knoevenagel condensation using density functional theory and two different basis sets (6-31 G(d,p) and 6-311++G(2df,2pd)), both in gas phase and simulating the bulk solvent (pyridine) using the PCM method. Calculated structures for reactants, intermediates, and key transition states suggest that the secondary amine catalyst is essential, both for activating the aldehyde for nucleophilic attack, and in the possible decarboxylation pathways. The calculated results are shown to agree with available experimental information. On the basis of the results obtained, the studied mechanism may be important in the understanding of vinylphenol production during malting and brewing of wheat and barley grains.
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49. |
- Bickelhaupt, F Matthias, et al.
(författare)
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Role of s-p orbital mixing in the bonding and properties of second-period diatomic molecules.
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:11, s. 2437-46
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Tidskriftsartikel (refereegranskat)abstract
- Qualitative molecular orbital theory is widely used as a conceptual tool to understand chemical bonding. Symmetry-allowed orbital mixing between atomic or fragment orbitals of different energies can greatly complicate such qualitative interpretations of chemical bonding. We use high-level Amsterdam Density Functional calculations to examine the issue of whether orbital mixing for some familiar second-row homonuclear and heteronuclear diatomic molecules results in net bonding or antibonding character for a given molecular orbital. Our results support the use of slopes of molecular orbital energy versus bond distance plots (designated radial orbital-energy slope: ROS) as the most useful criterion for making this determination. Calculated atomic charges and frontier orbital properties of these molecules allow their acid-base chemistry, including their reactivities as ligands in coordination chemistry, to be better understood within the context of the Klopman interpretation of hard and soft acid-base theory. Such an approach can be extended to any molecular species.
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50. |
- Billes, Ferenc, et al.
(författare)
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Vibrational spectroscopic and conformational analysis of pinosylvin
- 2002
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 106:26, s. 6232-6241
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Tidskriftsartikel (refereegranskat)abstract
- Infrared and Raman spectra of pinosylvin were recorded and the vibrational frequencies with the corresponding infrared intensities were compared with the results of ab initio calculations utilizing the DFT method with the Becke3P86 functional and the 6-31G(d) basis set. Normal coordinate analysis was carried out. The effect of the conformation of the OH groups on the distribution of net charges, molecular energy and vibrational fundamentals were analyzed. One of the OH-cis-OH-trans conformers has the lowest energy. The conformation has a strong effect on the aforementioned properties, e.g., the cis-to-trans transition generates electron repulsion toward the vinylidene group between the two benzene rings. The changes in the different properties are in good accordance with each other. For comparison, the vibrational spectra were also recorded and calculated for the parent compound, trans-stilbene.
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