Biomedical subjects

Lars G M Pettersson

Publications and source records attributed to Lars G M Pettersson.

10 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

CO2 sorption on MgO and CaO surfaces: a comparative quantum chemical cluster study.

A comparative quantum chemical study of CO2 adsorption on MgO and CaO has been carried out. Theoretical infrared (IR) frequencies are calculated and compared with IR experiments from the literature. The results show that CO2 adsorbs as monodentate on edge sites and bidentate on corner sites on MgO. The former assignment contradicts the common assumption of adsorption of CO2 in a bidentate configuration. On CaO, CO2 adsorbs as monodentate on both edge and corner sites, which is a reinterpretation of earlier experimental work. On terrace (100) sites, none of the adsorption modes on MgO or CaO possess calculated frequencies in agreement with the experimental IR spectra. These experimental bands were tentatively assigned to some slightly perturbed double negatively charged carbonate ions at the surface, rather than the monodentate structure suggested in the literature.

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PubMed2005

X-ray absorption spectroscopy study of the hydrogen bond network in the bulk water of aqueous solutions.

We utilized X-ray absorption spectroscopy (XAS) and X-ray Raman scattering (XRS) in order to study the ion solvation effect on the bulk hydrogen bonding structure of water. The fine structures in the X-ray absorption spectra are sensitive to the local environment of the probed water molecule related to the hydrogen bond length and angles. By varying the concentration of ions, we can distinguish between contributions from water in the bulk and in the first solvation sphere. We show that the hydrogen bond network in bulk water, in terms of forming and breaking hydrogen bonds as detected by XAS/XRS, remains unchanged, and only the water molecules in the close vicinity to the ions are affected.

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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

Functional dependence of core-excitation energies.

We examine in depth the functional dependence of computed core-electron binding and excitation energies based on a total-energy difference approach within Kohn-Sham density functional theory. Twenty-seven functional combinations were studied using a database of reliable experimental data on 18 molecules. The computed core-electron binding energies are largely dependent on the choice of exchange functional. The term value of the first resonant excited state and energy differences between the lowest core-excited states are, however, quite insensitive to the choice of functionals since the errors due to the core-region cancel out. Using these results we define a different exchange functional, which mixes two functionals designed by Perdew and Wang (PD86 and PD91), with the best results for both excitation and binding energies obtained for a mixing ratio 60:40 between these. We also reexamine the relativistic corrections for inner-shell excitations.

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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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