Biomedical subjects

Michael Odelius

Publications and source records attributed to Michael Odelius.

9 recordsLinked to original sources

PubMed2006

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.

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PubMed2006

The local structure of protonated water from x-ray absorption and density functional theory.

We present a combined x-ray absorption spectroscopy/computational study of water in hydrochloric acid (HCl) solutions of varying concentration to address the structure and bonding of excess protons and their effect on the hydrogen bonding network in liquid water. Intensity variations and energy shifts indicate changes in the hydrogen bonding structure in water as well as the local structure of the protonated complex as a function of the concentration of protons. In particular, in highly acidic solutions we find a dominance of the Eigen form, H(3)O(+), while the proton is less localized to a specific water under less acidic conditions.

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PubMed2006

Theoretical study of ion desorption from poly-(methyl methacrylate) and poly-(isopropenyl acetate) thin films through core excitation.

Site-specific chemical reactions following core excitation of poly-(methyl methacrylate) (PMMA) and poly-(isopropenyl acetate) (PiPAc) thin films were investigated. New x-ray absorption spectra of PMMA and PiPAc at the C and O K edges and theoretical spectra within the framework of density functional theory using model molecules were reported, and some new peak assignments were proposed for these spectra. Core-hole excited state molecular dynamics simulations were performed to discuss dissociation dynamics for the target systems, and some specific reaction mechanisms were discussed and explained theoretically; for example, the amount of CH3 ion fragments for PMMA was enhanced at the C and O K edges through the existence of the repulsive sigma*(O-CH3) excited state.

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PubMed2006

Auger decay calculations with core-hole excited-state molecular-dynamics simulations of water.

We report a new theoretical procedure for calculating Auger decay transition rates including effects of core-hole excited-state dynamics. Our procedure was applied to the normal and first resonant Auger processes of gas-phase water and compared to high-resolution experiments. In the normal Auger decay, calculated Auger spectra were found to be insensitive to the dynamics, while the repulsive character of the first resonant core-excited state makes the first resonantly excited Auger decay spectra depend strongly on the dynamics. The ultrafast dissociation of water upon O(1s)-->4a(1) excitation was analyzed and found to be very sensitive to initial vibrational distortions in the ground state which furthermore affect the excitation energy. Our calculated spectra reproduce the experimental Auger spectra except for the Franck-Condon vibrational structure which is not included in the procedure. We found that the Auger decay of OH and O fragments contributes to the total intensity, and that the contribution from these fragments increases with increasing excitation energy.

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PubMed2005

Half or full core hole in density functional theory X-ray absorption spectrum calculations of water?

We analyze the performance of two different core-hole potentials in the theoretical modeling of XAS of ice, liquid and gas phase water; the use of a full core-hole (FCH) in the calculations, as suggested by Hetenyi et al. [B. Hetenyi, F. De Angelis, P. Giamozzi and R. Car, J. Chem. Phys., 2004, 120(18), 8632], gives poor agreement with experiment in terms of intensity distribution as well as transition energies, while the half core hole (HCH) potential, in the case of water, provides a better compromise between initial and final state effects, leading to good agreement with the experimental data.

Gases↗

PubMed2005

Ultrafast core-hole-induced dynamics in water probed by x-ray emission spectroscopy.

The isotope effect and excitation-energy dependence have been measured in the oxygen K-edge x-ray emission spectrum (XES). The use of XES to monitor core decay processes provides information about molecular dynamics (MD) on an ultrafast time scale through the O1s lifetime of a few femtoseconds. Different nuclear masses give rise to differences in the dynamics and the observed isotope effect in XES is direct evidence of the importance of such processes. MD simulations show that even the excitation-energy dependence in the XES is mainly related to differences in core-excited-state dynamics.

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PubMed2004

X-ray absorption spectra of water within a plane-wave Car-Parrinello molecular dynamics framework.

We describe the implementation of a simple technique to simulate core-level spectra within the Car-Parrinello plane-waves molecular dynamics framework. The x-ray absorption (XA) spectra are generated using the transition potential technique with the effect of the core hole included through a specifically developed pseudopotential for the core-excited atom. Despite the lack of 1s core orbitals in the pseudopotential treatment, the required transition moments are accurately calculated without reconstruction of the all-electron orbitals. The method is applied to the oxygen XA spectra of water in its various aggregation states, but it is transferable to any first-row element. The computed spectra are compared favorably with the results from all-electron cluster calculations, as well as with experimental data. The periodicity of the plane-wave technique improves the description of condensed phases. The molecular dynamics simulation enables in principle a proper treatment of thermal effects and dynamical averaging in complex systems.

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PubMed2004

Photodissociation of diiodomethane in acetonitrile solution and fragment recombination into iso-diiodomethane studied with ab initio molecular dynamics simulations.

Photodissociation of diiodomethane (CH2I2) in acetonitrile solution has been studied with ab initio molecular dynamics simulations, which show how the iso-diiodomethane photoproduct (CH2I-I) can be formed. The first excited state, described by the "restricted open-shell Kohn-Sham" density functional method, is dissociative and photoexcitation of diiodomethane induces a breaking of one of the C-I bonds. In the simulations, we observe that energy dissipation to the surrounding solvent is essential in the formation of a stable iso-diiodomethane molecule. The caging effect of the solvent results in a recombination of the CH2I and I fragments into iso-diiodomethane on a picosecond time scale. The molecular dynamics simulations enable us to study the cage effect as well as the relaxation of intermediates and the distribution of energy. The CH2I fragment is formed vibrationally excited along the C-I stretching mode. After recombination of the CH2I and I fragments, iso-diiodomethane shows a strong vibration excitation in the CH2 group, which could be used as a fingerprint of the proposed mechanism.

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PubMed2002

Experimental evidence for sub-3-fs charge transfer from an aromatic adsorbate to a semiconductor.

The ultrafast timescale of electron transfer processes is crucial to their role in many biological systems and technological devices. In dye-sensitized solar cells, the electron transfer from photo-excited dye molecules to nanostructured semiconductor substrates needs to be sufficiently fast to compete effectively against loss processes and thus achieve high solar energy conversion efficiencies. Time-resolved laser techniques indicate an upper limit of 20 to 100 femtoseconds for the time needed to inject an electron from a dye into a semiconductor, which corresponds to the timescale on which competing processes such as charge redistribution and intramolecular thermalization of excited states occur. Here we use resonant photoemission spectroscopy, which has previously been used to monitor electron transfer in simple systems with an order-of-magnitude improvement in time resolution, to show that electron transfer from an aromatic adsorbate to a TiO(2) semiconductor surface can occur in less than 3 fs. These results directly confirm that electronic coupling of the aromatic molecule to its substrate is sufficiently strong to suppress competing processes.

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