| 1. |
- Baev, Alexander, et al.
(författare)
-
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
-
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.
|
|
| 2. |
- Malysheva, Lyuba, et al.
(författare)
-
Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling
- 2005
-
Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106 .- 1520-5207. ; 109:34, s. 7788-7796
-
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.
|
|
| 3. |
|
|
| 4. |
- 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.
|
|
| 5. |
- 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.
|
|
| 6. |
- 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.
|
|
| 7. |
- 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.
|
|
| 8. |
- 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.
|
|
| 9. |
- 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.
|
|
| 10. |
- 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.
|
|
