M. Kaukonen

A molecular dynamics study of N-incorporation into carbon systems: Doping, diamond growth and nitride formation

Abstract An ab-initio-based tight-binding molecular-dynamics method is used to describe the behaviour of a variety of carbon-nitrogen systems, ranging from doping in CVD diamond and the effect of N on CVD diamond growth to that of the possible fabrication of super-hard C3N4 crystals. We describe why N does not dope in CVD diamond though it is incorporated predominantly on-site. This also has consequences for growth processes, in particular the (100) Harris growth mechanism. Towards higher N densities, we observe clear trends counteracting the formation of a low-compressibility crystalline phase: (1) N-incorporation strongly catalyses C-under-coordination, which, in turn; (2) causes the nitrogens to develop in a paracyanogen-like manner (CN-double and -triple) bonding; and (3) the most favourable densities for a-CN appear to be much lower than the desired hard crystalline ones. Finally, we investigate the possibility that an admixture of Si catalyses sp3 carbon formation, thus favouring increased network connectivity and crystallinity.

QM/MM-PBSA method to estimate free energies for reactions in proteins

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 part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.

Growth of (110) diamond using pure dicarbon

We use a density-functional based tight-binding method to study diamond growth steps by depositing dicarbon species onto a hydrogen-free diamond (110) surface. Subsequent C_2 molecules are deposited on an initially clean surface, in the vicinity of a growing adsorbate cluster, and finally, near vacancies just before completion of a full new monolayer. The preferred growth stages arise from C_2n clusters in near ideal lattice positions forming zigzag chains running along the [-110] direction parallel to the surface. The adsorption energies are consistently exothermic by 8--10 eV per C_2, depending on the size of the cluster. The deposition barriers for these processes are in the range of 0.0--0.6 eV. For deposition sites above C_2n clusters the adsorption energies are smaller by 3 eV, but diffusion to more stable positions is feasible. We also perform simulations of the diffusion of C_2 molecules on the surface in the vicinity of existing adsorbate clusters using an augmented Lagrangian penalty method. We find migration barriers in excess of 3 eV on the clean surface, and 0.6--1.0 eV on top of graphene-like adsorbates. The barrier heights and pathways indicate that the growth from gaseous dicarbons proceeds either by direct adsorption onto clean sites or after migration on top of the existing C_2n chains.

Dynamic relaxation of the elastic properties of hard carbon films

The effect of enhanced atomic mobility on the growth of hard carbon films was examined. Tetrahedrally bonded amorphous carbon films were deposited by condensing energetic carbon ions using an arc-discharge deposition method. The deposition temperature varied between 50 and 400 °C. The dependence of elastic properties on deposition temperature was examined by determining the frequency-dependent propagation velocity of ultrasonic surface acoustic waves induced by a laser. A remarkable decrease in elastic coefficient was revealed above the deposition temperature of 300 °C and complete relaxation was obtained at 400 °C. This observation was analyzed by using a simple model which was in turn supported by molecular dynamics simulations. The relaxation turns out to be a thermally activated, dynamic process with an activation energy of 0.57 eV. Possible relaxation mechanisms associated with the migration of atoms or defects on a growing surface are discussed.

Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations.

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 proton-transfer reactions in two proteins and show that, in [Ni,Fe] hydrogenase, the bridging Cys-546 ligand is deprotonated by His-79, whereas in oxidized copper nitrite reductase, the His-100 ligand is neutral and the copper-bound water molecule is deprotonated by Asp-98. We show that these reactions strongly depend on the electrostatic interactions with the surrounding protein and solvent, because there is a large change in the dipole moment of the active site (2-6 D). Neither vacuum quantum mechanical (QM) calculations with large models, a continuum solvent, or a Poisson-Boltzmann treatment of the surroundings, nor combined QM and molecular mechanics (QM/MM) optimizations give reliable estimates of the proton-transfer energies (mean absolute deviations of over 20 kJ/mol). Instead, QM/MM free-energy perturbations are needed to obtain reliable estimates of the reaction energies. These calculations also indicate what interactions and residues are important for the energy, showing how the quantum system may be systematically enlarged. With such a procedure, results with an uncertainty of ∼10 kJ/mol can be obtained, provided that a proper QM method is used.

Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods.

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 the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.

Lennard‐Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations

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 CNT–water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ‐potential.

Possible n-type dopants in diamond and amorphous carbon

Abstract It has been extremely difficult to produce n-type conducting diamond, whereas it seems that n-type conducting tetrahedrally bonded amorphous carbon (ta-C) can be obtained using phosphorous or nitrogen as dopant. In this work we have studied substitutional group V–VII impurities (N, O and Cl) in diamond and ta-C using first-principles electronic structure methods. Electronic structure calculations reveal the differences between ta-C and diamond in the microscopic level and ease, therefore, the experimental search for producing n-type conducting diamond-like materials.

Molecular-dynamics simulation of the growth of diamond-like films

Abstract The growth of diamond-like thin films on substrates was investigated under different physical conditions by molecular dynamics simulation. A classical potential proposed by Tersoff [1] was used. An optimal energy region of the deposited atoms for most diamond-like films was found between 10–100 eV. Decreasing the substrate temperature and increasing the thermal conductivity at high deposition energies were found to favour diamond-like properties.

Effect of gating and pressure on the electronic transport properties of crossed nanotube junctions: formation of a Schottky barrier

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 accumulation to the nanotube contact and the charge depletion region at the metal-semiconductor Schottky contact. Finally, it is shown how the conductance of the junctions under the gate voltage is affected by pressure applied to the nanotube film.