M. Kaukonen

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We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic(More)
Catalytic metal sites in enzymes frequently have second-sphere carboxylate groups that neutralize the charge of the site and share protons with first-sphere ligands. This gives rise to an ambiguity concerning the position of this proton, which has turned out to be hard to settle with experimental, as well as theoretical, methods. We study three such(More)
We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving(More)
X-ray photoelectron spectroscopy (XPS) is a widely used tool for studying the chemical composition of materials and it is a standard technique in surface science and technology. XPS is particularly useful for characterizing nanostructures such as carbon nanomaterials due to their reduced dimensionality. In order to assign the measured binding energies to(More)
Carbon vacuum arc was used to deposit 5–25 nm thick carbon coatings on single-walled carbon nanotube (SWCNT) networks. The SWCNT bundles thus embedded in conformal coatings maintained their optical transparency and electrical conductivity. Sheet resistances of the networks were measured during the vacuum arc deposition, revealing initially a 100-fold(More)
The catalytic cycle of cytochrome c oxidase has been simulated by means of quantum mechanical calculations. The experimental energetics of the catalytic cycle is nearly reproduced. The atomic structures of the intermediates are suggested. In particular, the structures of nonactive "resting" intermediates are proposed.
Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for(More)
Nature's recipe: A theoretical study analyzes how the environment of the [FeFe] hydrogenase's catalytic cofactor affects its chemical properties, particularly the relative stability of complexes with bridging and terminal hydride ligands (see picture; Fe teal, S yellow, C green, N blue, O red, H gray). The results help to elucidate key rules for the design(More)
The electronic transport properties of crossed carbon nanotube junctions are investigated using ab initio methods. The optimal atomic structures and the intertube distances of the junctions are obtained using van der Waals corrected density functional theory. The effect of gating on the intertube conductance of the junctions is explored, showing the charge(More)
Rights: © 1999 American Physical Society (APS). This is the accepted version of the following article: Kaukonen, M. & Nieminen, Risto M. & Pöykkö, S. & Seitsonen, Ari P. 1999. Nitrogen Doping of Amorphous Carbon Surfaces. Physical Review Letters. Volume 83, Issue 25. 5346-5349. ISSN 0031-9007 (printed). DOI: 10.1103/physrevlett.83.5346, which has been(More)