Comparison Of Density Functional Theory Calculations Research Articles

2D Vanadium Sulfides: Synthesis, Atomic Structure Engineering, and Charge Density Waves.

Two ultimately thin vanadium-rich 2D materials based on VS2 are created via molecular beam epitaxy and investigated using scanning tunneling microscopy, X-ray photoemission spectroscopy, and density functional theory (DFT) calculations. The controlled synthesis of stoichiometric single-layer VS2 or either of the two vanadium-rich materials is achieved by varying the sample coverage and sulfur pressure during annealing. Through annealing of small stoichiometric single-layer VS2 islands without S pressure, S-vacancies spontaneously order in 1D arrays, giving rise to patterned adsorption. Via the comparison of DFT calculations with scanning tunneling microscopy data, the atomic structure of the S-depleted phase, with a stoichiometry of V4S7, is determined. By depositing larger amounts of vanadium and sulfur, which are subsequently annealed in a S-rich atmosphere, self-intercalated ultimately thin V5S8-derived layers are obtained, which host 2 × 2 V-layers between sheets of VS2. We provide atomic models for the thinnest V5S8-derived structures. Finally, we use scanning tunneling spectroscopy to investigate the charge density wave observed in the 2D V5S8-derived islands.

First-principles study of structural, electronic, magnetic and thermoelectric properties of the cubic mono-pnictides of thorium ThPn (Pn = Sb and Bi)

This study presents the density-functional-theory (DFT) calculations of B1-phase cubic mono-pnictides of thorium, i.e., ThSb and ThBi regarding their structural, electronic, magnetic and thermoelectric properties. We calculated lattice constant, bulk moduli and their pressure derivative, and ground-state energy by the full-potential linearized augmented plane wave (FPLAPW) method. We employed local-density approximation (LDA), with and without spin-polarization effect, and generalized-gradient approximations (GGA) as the exchange-correlation functionals for structural properties. Further comparison of DFT calculations is made with Perdew-Burke-Ernzerh (PBE) and Wu-Cohen (WC) corrections. For the comparative study of magnetic and electronic properties, DFT+U (Hubbard parameter) model is implemented. In addition, we used semiclassical Boltzman theory to explore the thermoelectric properties such as electrical conductivity, Seebeck coefficient, power factor, and figure of merit which present ThSb and ThBi as promising thermoelectric and thermonuclear materials and potential candidates for practical uses in nuclear power and thermoelectric devices.

Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations.

In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.

Electronic Spectroscopy and Computational Studies of Glutathionylco(III)balamin

We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.

Static Influence of Ligands: Comparison of DFT Calculations with Experimental Data

The possibility of reproducing regularities of static mutual influence of ligands in complexes of Period V and VI elements of the Periodic Table (Pd, Sn, Sb, Pt, Pb) using the density functional theory (DFT) calculations is studied. Relativistic effects are taken into account by means of the Dirac equation approximation (zero-order regular approximation, ZORA). The calculations reproduced trans-influence in Pt complexes and trans-shortening and cis-elongation in the nontransition metal complexes. At the same time, Pb chloride complexes and Sn iodide complexes exhibit substantial differences between experimental and calculation bond lengths. When solvation was accounted for by COSMO method, DFT calculations reproduce the relative stability of the cis- and trans-Pt(NH3)2X2 complexes (X is halogen) and of the sulfur-containing Ni and Pd chelate complexes. The calculated geometry of the cis-Pt(NH3)2X2 molecule noticeably differs from the experimental geometry due to the overestimated strength of intramolecular N-H···X hydrogen bonds.

Theoretical studies of unimolecular reactions of C2–C5 alkoxy radicals. Part I. Ab initio molecular orbital calculations

Structures, vibrational frequencies and barrier heights characterising the unimolecular reactions of primary and secondary alkoxy radicals up to pentoxy have been determined by means of quantum chemical calculations. Several additive model chemistries such as CBS-4, CBS-q, CBS-Q and G2(MP2,SVP) have been applied to obtain information on the reactive potential energy surfaces and to test their applicability to transition state structures. In addition, density functional theory calculations (DFT) using the B3LYP hybrid-functional have been performed. A comparison of DFT and classical ab initio results shows that only G2(MP2,SVP) theory yields critical energy barriers of nearly chemical accuracy. Consistently, the energy barriers obtained from the CBS-4, CBS-q and B3LYP calculations are too low. The CBS-4 and CBS-q energetics suffer from the UHF/3-21G* geometry optimisation. This can only partly be improved by the use of MP2(Full)/6-31G(d) geometries. Improvements to G2(MP2,SVP) theory are proposed to better account for the characteristics of transition states. Simultaneously, the importance of reliable zero point and thermal energy contributions is emphasised. The results obtained from the present calculations have been used in statistical kinetic rate theories (Somnitz and Zellner, Phys. Chem. Chem. Phys., 2000, 2, 1907).