Critical comparison of electrode models in density functional theory based quantum transport calculations

We study the performance of two different electrode models in quantum transport calculations based on density functional theory: parametrized Bethe lattices and quasi-one-dimensional wires or nanowires. A detailed account of implementation details in both the cases is given. From the systematic study of nanocontacts made of representative metallic elements, we can conclude that the parametrized electrode models represent an excellent compromise between computational cost and electronic structure definition as long as the aim is to compare with experiments where the precise atomic structure of the electrodes is not relevant or defined with precision. The results obtained using parametrized Bethe lattices are essentially similar to the ones obtained with quasi-one-dimensional electrodes for large enough cross-sections of these, adding a natural smearing to the transmission curves that mimics the true nature of polycrystalline electrodes. The latter are more demanding from the computational point of view, but present the advantage of expanding the range of applicability of transport calculations to situations where the electrodes have a well-defined atomic structure, as is the case for carbon nanotubes, graphene nanoribbons, or semiconducting nanowires. All the analysis is done with the help of codes developed by the authors which can be found in the quantum transport toolbox ALACANT and are publicly available.     

Benchmark density functional theory calculations for nanoscale conductance

We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code in combination with maximally localized Wannier functions and the norm-conserving pseudopotential code SIESTA which applies an atomic orbital basis set. All calculations have been converged with respect to the supercell size and the number of k|| points in the surface plane. For all systems we find that the SIESTA transmission functions converge toward the plane-wave result as the SIESTA basis is enlarged. Overall, we find that an atomic basis with double zeta and polarization is sufficient (and in some cases, even necessary) to ensure quantitative agreement with the plane-wave calculation. We observe a systematic downshift of the SIESTA transmission functions relative to the plane-wave results. The effect diminishes as the atomic orbital basis is enlarged; however, the convergence can be rather slow.     

Prediction of formation constants of metal-ammonia complexes in aqueous solution using density functional theory calculations

Density functional theory calculation of gas-phase Delta G of replacement of a water molecule by NH(3) on [M(H(2)O)(6)](n+)(g) for 19 different metal ions correlates well with Delta G of formation of mono NH(3) complexes of these ions in water, suggesting this approach will permit prediction of formation constants in aqueous solution, and produce insights into theories of metal complex formation reactions.     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

Studies of iridium nanoparticles using density functional theory calculations

The energetics and the electronic and magnetic properties of iridium nanoparticles in the range of 2-64 atoms were investigated using density functional theory calculations. A variety of different geometric configurations were studied, including planar, three-dimensional, nanowire, and single-walled nanotube. The binding energy per atom increases with size and dimensionality from 2.53 eV/atom for the iridium dimer to 6.09 eV/atom for the 64-atom cluster. The most stable geometry is planar until four atoms are reached and three-dimensional thereafter. The simple cubic structure is the most stable geometric building block until a strikingly large 48-atom cluster, when the most stable geometry transitions to face-centered cubic, as found in the bulk metal. The strong preference for cubic structure among small clusters demonstrates their rigidity. This result indicates that iridium nanoparticles intrinsically do not favor the coalescence process. Nanowires formed from linear atomic chains of up to 4-atom rings were studied, and the wires formed from 4-atom rings were extremely stable. Single-walled nanotubes were also studied. These nanotubes were formed by stacking 5- and 6-atom rings to form a tube. The ring stacking with each atom directly above the previous atom is more stable than if the alternate rings are rotated.     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Lithium adsorption on graphite from density functional theory calculations

The structural, energetic, and electronic properties of the Li/graphite system are studied through density functional theory (DFT) calculations using both the local spin density approximation (LSDA), and the gradient-corrected Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation energy. The calculations were performed using plane waves basis, and the electron-core interactions are described using pseudopotentials. We consider a disperse phase of the adsorbate comprising one Li atom for each 16 graphite surface cells, in a slab geometry. The close contact between the Li nucleus and the graphene plane results in a relatively large binding energy (larger than 1.1 eV). A detailed analysis of the electronic charge distribution, density difference distribution, and band structures indicates that one valence electron is entirely transferred from the atom to the surface, which gives rise to a strong interaction between the resulting lithium ion and the cloud of pi electrons in the substrate. We show that it is possible to explain the differences in the binding of Li, Na, and K adatoms on graphite considering the properties of the corresponding cation/aromatic complexes.     

Spectral analysis of acetylcholine halides by density functional theory calculations

The optimized molecular structures, vibrational frequencies and ¹H and ¹³C NMR chemical shifts of acetylcholine halides (F, Cl, and Br) have been investigated using density functional theory (B3LYP) method with 6-311G(d) basis set. The comparison of their experimental and calculated IR, R and NMR spectra of the compounds has indicated that the spectra of three optimized minimum energy conformers can simultaneously exist in one experimental spectrum. Thus, it was concluded that the compounds simultaneously exist in three conformations in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles), vibrational frequencies and NMR chemical shifts for the minimum energy conformers were seen to be in a good agreement with the corresponding experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program.     

Water chain encapsulated in carbon nanotube revealed by density functional theory

The noncovalent interactions between encapsulated water chains and single‐walled carbon nanotube (SWCNT) are studied using a self‐consistent charge density functional tight binding method with dispersion correction. The most interesting and important feature we observe is the diameter shrinking of CNTs when water chains are confined inside SWCNT. The diameter shrinking of CNTs can be suggested to the original of the van der Waals and H‐π interaction between water chains and CNTs. The calculated Raman spectra show the interactions between SWCNTs and water chains probably give rise to a kind of “mode hardening effect,” which agrees with the diameter shrinking of CNTs when water chains are confined inside SWCNT. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011.     

Time-dependent density functional theory calculations of the photoabsorption of fluorinated alkanes

Time-dependent density functional theory (TD-DFT) calculations of the transition energies and oscillator strengths of fluorinated alkanes have been performed. The TD-DFT method with the non-local B3LYP potential yields transition energies for the methanes, which are smaller by about 10% as compared to the experimental values. An empirical linear correlation was found between the calculated and experimental transition energies both at the B3LYP/DZ+Ryd(C, F) and B3LYP/cc-pVTZ+Ryd(C, F, H) levels for a total of 19 transitions of the fluorinated methanes with linear correlation coefficients of 0.987 for the former and 0.988 for the latter. This empirical correlation for fluorinated methane molecules is found to agree well with the previously obtained empirical correlations between calculated and experimental values for non-fluorinated molecules. The results show that a single empirical-correlation relationship can be used for both non-fluorinated and fluorinated molecules to predict transition energies. This linear relationship is then used to predict the photoabsorption spectra of ethane, propane, butane, and partially and fully fluorinated derivatives. A key result of these calculations is the dominance of Rydberg transitions in the spectral region of interest.     

Robust acceleration of self consistent field calculations for density functional theory

We show that the type 2 Broyden secant method is a robust general purpose mixer for self consistent field problems in density functional theory. The Broyden method gives reliable convergence for a large class of problems and parameter choices. We directly mix the approximation of the electronic density to provide a basis independent mixing scheme. In particular, we show that a single set of parameters can be chosen that give good results for a large range of problems. We also introduce a spin transformation to simplify treatment of spin polarized problems. The spin transformation allows us to treat these systems with the same formalism as regular fixed point iterations.     

Matrix infrared spectra and density functional theory calculations of molybdenum hydrides

Laser-ablated Mo atoms react with H2 upon condensation in excess argon, neon, and hydrogen. The molybdenum hydrides MoH, MoH2, MoH4, and MoH6 are identified by isotopic substitution (H2, D2, HD, H2 + D2) and by comparison with vibrational frequencies calculated by density functional theory. The MoH2 molecule is bent, MoH4 is tetrahedral, and MoH6 appears to have the distorted trigonal prism structure.     

Basis set dependence of phosphate frequencies in density functional theory calculations

The addition of extravalence, polarization and diffuse functions, were studied in order to conclude how they affect the P? O stretching frequencies of several biological relevant phosphate molecules. The results show that the polarization and the diffuse functions have opposite effects on the frequencies: the polarization functions downshift while the diffuse functions upshift the frequencies. The effect of the valence functions was more difficult to interpret. The effect of the conductor‐like screening model (CPCM)‐continuum model was also studied. The results show that the CPCM‐continuum model has a substantial effect on the frequencies for these small molecules. The continuum model's efficiency is mainly due to its effect on the geometries and not on the frequencies. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Basis set convergence of explicitly correlated double-hybrid density functional theory calculations

The basis set convergence of explicitly correlated double-hybrid density functional theory (DFT) is investigated using the B2GP-PLYP functional. As reference values, we use basis set limit B2GP-PLYP-F12 reaction energies extrapolated from the aug(')-cc-pV(Q+d)Z and aug(')-cc-pV(5+d)Z basis sets. Explicitly correlated double-hybrid DFT calculations converge significantly faster to the basis set limit than conventional calculations done with basis sets saturated up to the same angular momentum (typically, one "gains" one angular momentum in the explicitly correlated calculations). In explicitly correlated F12 calculations the VnZ-F12 basis sets converge faster than the orbital A(')VnZ basis sets. Furthermore, basis set convergence of the MP2-F12 component is apparently faster than that of the underlying Kohn-Sham calculation. Therefore, the most cost-effective approach consists of combining the MP2-F12 correlation energy from a comparatively small basis set such as VDZ-F12 with a DFT energy from a larger basis set such as aug(')-cc-pV(T+d)Z.     

Ab initio density functional theory investigation of Li-intercalated zinc oxide nanotube bundles

We have investigated the energetic, and geometric and electronic structure of Li-intercalated (5,5) zinc oxide nanotube (ZnONT) bundles via density functional theory as implemented in the code WIEN2k. Our results showed that the most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the ZnONTs. All the Li-intercalated (5,5) ZnONT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial spaces are susceptible for intercalation. The present calculations suggest that the single-walled zinc oxide nanotube (SwZnONT) bundle is a promising candidate for the anode material in battery applications.     

Projected gradient algorithms for Hartree-Fock and density matrix functional theory calculations

We present projected gradient algorithms designed for optimizing various functionals defined on the set of N-representable one-electron reduced density matrices. We show that projected gradient algorithms are efficient in minimizing the Hartree-Fock or the Muller-Buijse-Baerends functional. On the other hand, they converge very slowly when applied to the recently proposed BBk (k=1,2,3) functionals [O. Gritsenko et al., J. Chem. Phys. 122, 204102 (2005)]. This is due to the fact that the BBk functionals are not proper functionals of the density matrix.     

Condensed phase ionic polarizabilities from plane wave density functional theory calculations

A method is presented to allow the calculation of the dipole polarizabilities of ions and molecules in a condensed-phase coordination environment. These values will be useful for understanding the optical properties of materials and for developing simulation potentials which incorporate polarization effects. The reported values are derived from plane wave density functional theory calculations, though the method itself will apply to first-principles calculations on periodic systems more generally. After reporting results of test calculations on atoms to validate the procedure, values for the polarizabilities of the oxide ion and various cations in a range of materials are reported and compared with experimental information as well as previous theoretical results.     

Periodic Hartree-Fock and density functional theory calculations for Li-doped polyacetylene chains

We have performed periodic restricted Hartree-Fock/6-31G** and B3LYP6-31G** density functional theory calculations on Li-doped trans-polyacetylene at various dopant concentrations, using C(2m)H(2m)Li2 unit cells (m = 7-14). Except for maintaining P1 rod symmetry the geometry was completely optimized for both uniform and nonuniform doping structures. In addition to geometry we obtain atomic charges, along with soliton formation and dopant binding energies, as well as band structures and densities of states. A thorough analysis of the band structure and density of states, as a function of dopant concentration, is presented. We also characterize the complex nature of the binding interaction between Li and the polyacetylene chain.     

Critical examination of the supermolecule density functional theory calculations of intermolecular interactions

The results of calculations employing twelve different combinations of exchange and correlation functionals are compared with results of ab initio calculations for two different configurations of the water dimer and three different configurations of the thymine-adenine complex. None of the density functional theory (DFT) treatments could properly reproduce the results of coupled-cluster calculations for all configurations examined. The DFT approaches perform well when the interaction energy is dominated by the electrostatic component and the dispersion energy is less important. Two mechanisms that compensate for the missing dispersion component were identified. The first one is the decrease of the magnitude of the intermolecular exchange-repulsion and the second one is the increase of the magnitude of the attractive deformation energy. For some functionals both effects are observed together, but for some other ones only the second effect occurs. The three correlation functionals that were examined were found to make only very small contributions to the deformation energy. The examination of angular and distance dependence of the interactions shows that the currently available DFT approaches are not suitable for developing intermolecular potential energy surfaces. They could however be used to find global minima on potential energy surfaces governed by intermolecular electrostatic interactions. Additional single point ab initio calculations are recommended as the means of validating optimized structures.