IJMS: Physical Chemistry, Theoretical and Computational Chemistry: Applications of Density Functional Theory

IJMS, Vol. 10, Pages 5104-5114: Formation Energies of Antiphase Boundaries in GaAs and GaP: An ab Initio Study

Oleg Rubel — Wed, 25 Nov 2009 00:00:00 CET

Electronic and structural properties of antiphase boundaries in group III-V semiconductor compounds have been receiving increased attention due to the potential to integration of optically-active III-V heterostructures on silicon or germanium substrates. The formation energies of {110}, {111}, {112}, and {113} antiphase boundaries in GaAs and GaP were studied theoretically using a full-potential linearized augmented plane-wave density-functional approach. Results of the study reveal that the stoichiometric {110} boundaries are the most energetically favorable in both compounds. The specific formation energy γ of the remaining antiphase boundaries increases in the order of γf113g ≈ γf112g < γf111g, which suggests {113} and {112} as possible planes for faceting and annihilation of antiphase boundaries in GaAs and GaP.

IJMS, Vol. 10, Pages 4816-4940: Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems

Mihai V. Putz — Tue, 10 Nov 2009 00:00:00 CET

The density matrix theory, the ancestor of density functional theory, provides the immediate framework for Path Integral (PI) development, allowing the canonical density be extended for the many-electronic systems through the density functional closure relationship. Yet, the use of path integral formalism for electronic density prescription presents several advantages: assures the inner quantum mechanical description of the system by parameterized paths; averages the quantum fluctuations; behaves as the propagator for time-space evolution of quantum information; resembles Schrödinger equation; allows quantum statistical description of the system through partition function computing. In this framework, four levels of path integral formalism were presented: the Feynman quantum mechanical, the semiclassical, the Feynman-Kleinert effective classical, and the Fokker-Planck non-equilibrium ones. In each case the density matrix or/and the canonical density were rigorously defined and presented. The practical specializations for quantum free and harmonic motions, for statistical high and low temperature limits, the smearing justification for the Bohr’s quantum stability postulate with the paradigmatic Hydrogen atomic excursion, along the quantum chemical calculation of semiclassical electronegativity and hardness, of chemical action and Mulliken electronegativity, as well as by the Markovian generalizations of Becke-Edgecombe electronic focalization functions – all advocate for the reliability of assuming PI formalism of quantum mechanics as a versatile one, suited for analytically and/or computationally modeling of a variety of fundamental physical and chemical reactivity concepts characterizing the (density driving) many-electronic systems.

IJMS, Vol. 10, Pages 4342-4351: First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum

Shigeaki Ono — Fri, 09 Oct 2009 00:00:00 CEST

The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state.

IJMS, Vol. 10, Pages 4310-4329: Modelling Catalyst Surfaces Using DFT Cluster Calculations

Izabela Czekaj — Wed, 30 Sep 2009 00:00:00 CEST

We review our recent theoretical DFT cluster studies of a variety of industrially relevant catalysts such as TiO2, γ-Al2O3, V2O5-WO3-TiO2 and Ni/Al2O3. Aspects of the metal oxide surface structure and the stability and structure of metal clusters on the support are discussed as well as the reactivity of surfaces, including their behaviour upon poisoning. It is exemplarily demonstrated how such theoretical considerations can be combined with DRIFT and XPS results from experimental studies.

IJMS, Vol. 10, Pages 4284-4289: Theoretical Study on Reactions of Triplet Excited State Thioxanthone with Indole

Liang Shen — Wed, 30 Sep 2009 00:00:00 CEST

In the present work, a theoretical study on the deactivation of triplet excited (T1) state thioxanthone (TX) by indole (INH) was performed, based on density functional theory calculations. Three feasible pathways, namely direct electron transfer from INH to T1 state TX, electron transfer followed by proton transfer from INH·+ to TX·– , and H-atom transfer from nitrogen of INH to keto oxygen of T1 state TX, were proposed theoretically to be involved in T1 state TX deactivation by INH.

IJMS, Vol. 10, Pages 3918-3930: A Proline-Based Neuraminidase Inhibitor: DFT Studies on the Zwitterion Conformation, Stability and Formation

Zhi-Wei Yang — Mon, 07 Sep 2009 00:00:00 CEST

The designs of potent neuraminidase (NA) inhibitors are an efficient way to deal with the recent “2009 H1N1” influenza epidemic. In this work, density functional calculations were employed to study the conformation, stability and formation of the zwitterions of 5-[(1R,2S)-1-(acetylamino)-2-methoxy-2-methylpentyl]-4-[(1Z)-1-propenyl]-(4S,5R)-D-proline (BL), a proline-based NA inhibitor. Compared to proline, the zwitterion stability of BL is enhanced by 1.76 kcal mol-1 due to the introduction of functional groups. However, the zwitterion of BL will not represent a local minimum on the potential energy surface until the number of water molecules increases up to two (n = 2). With the addition of two and three water molecules, the energy differences between the zwitterions and corresponding canonical isomers were calculated at 3.13 and -1.54 kcal mol-1, respectively. The zwitterions of BL are mainly stabilized by the H-bonds with the water molecules, especially in the case of three water molecules where the carboxyl-O atoms are largely coordination-saturated by three H-bonds of medium strengths, causing the zwitterion stability even superior to the canonical isomer. With the presence of two and three water molecules, the energy barriers for the conversion processes from the canonical isomers to the zwitterions are equal to 4.96 and 3.13 kcal mol-1, respectively. It indicated that the zwitterion formation is facile to take place with addition of two molecules and further facilitated by more water molecules. Besides, the zwitterion formation of BL is finished in a single step, different from other NA inhibitors. Owing to the above advantages, BL is a good NA inhibitor candidate and more attention should be paid to explorations of BL-based drugs.

IJMS, Vol. 10, Pages 3502-3516: Theoretical Study for High-Energy-Density Compounds Derived from Cyclophosphazene. IV. DFT Studies on 1,1-Diamino-3,3,5,5,7,7-hexaazidocyclotetraphosphazene and Its Isomers

Jianguo Zhang — Thu, 06 Aug 2009 00:00:00 CEST

In the present study, a theoretical study of 1,1-diaminohexaazidocyclo-tetraphophazene (DAHA) and its isomers has been performed, using quantum computational density functional theory (B3LYP and B3PW91 methods) with 6-31G* and 6-31G** basis sets implemented in Gaussian 03 program suite. Molecular structure and bonding, vibrational frequencies, Milliken population analysis, and natural bond orbit (NBO) have been studied. The heats of formation from atomization energies have also been calculated based on the optimized geometry. The obtained heats of formation data are compared with their homologous cyclophosphazene in order to demonstrate the accuracy of the methods, which indicate that the studied compounds might be potentially used as high energetic materials. In addition, the relative stability of five isomers have been deduced based on the total energy and the gap of frontier orbital energies.

IJMS, Vol. 10, Pages 3488-3501: Conformational Analysis of Thioether Musks Using Density Functional Theory

William N. Setzer — Tue, 04 Aug 2009 00:00:00 CEST

A conformational analysis of nine macrocyclic thioether musks has been carried out using molecular mechanics (MMFF), density functional theory (DFT) using both B3LYP and M06 functionals, as well as Hartree-Fock and post-Hartree-Fock (MP2) ab initio methods. 6-Thia-, 10-thia- and 4-methyl-5-thia-14-tetradecananolide, 4-thia-, 7-thia-, 11-thia- and 12-thia-15-pentadecanolide and 6-thia- and 12-thia-16-hexadecanolide were modeled. Unfortunately, there was little agreement between the computational methods at the levels of theory used in this study.

IJMS, Vol. 10, Pages 3186-3193: A TD-DFT Study on the Photo-Physicochemical Properties of Chrysophanol from Rheum

Xue Zhao — Mon, 13 Jul 2009 00:00:00 CEST

As a naturally occurring anthraquinone pigment, chrysophanol (MHAQ) has attracted considerable attention in recent years owing to its efficient photosensitivity under the solar spectrum. Considering the successful use of time-dependent density functional theory (TD-DFT) in investigating the photo-physicochemical behaviors of dyes and pigments, we performed a study by means of TD-DFT calculations, which provided us with various excited state properties of chrysophanol, including absorption spectrum, lowest triplet excited-state energy, vertical electron affinity and vertical ionization potential. On the basis of the calculated results, the photosensitive mechanisms of chrysophanol were discussed and some deeper insights were gained. First, we indicated that the experimentally observed chrysophanol’s photo-damage to DNA in oxygen-free media is more likely to arise from MHAQ •+ rather than from T1 state chrysophanol. Second, we revealed that it is the MHAQ •− that is responsible for the O2•− generation in solvents. Based on the photosensitive activities, chrysophanol may be potentially used as the photodynamic medicine for clinical therapy of the diseases occurring on the shallow surface and vascular capillary diseases.

IJMS, Vol. 10, Pages 3128-3148: Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-

Liangfa Gong — Wed, 08 Jul 2009 00:00:00 CEST

The structures, electron affinities and bond dissociation energies of BrO4F/BrO4F− species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O2…O2 complexes possess 3A' electronic state for neutral molecule and 4A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). The EAad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies De (BrO4F → BrO4-mF + Om) (m = 1-4) and De- (BrO4F- → BrO4-mF- + Om and BrO4F- → BrO4-mF + Om-) are predicted. The adiabatic electron affinities (EAad) were predicted to be 4.52 eV for F-Br…O2…O2 (3A'← 4A') (B3LYP method).

IJMS, Vol. 10, Pages 1601-1608: Probing the Structure, Stability and Hydrogen Adsorption of Lithium Functionalized Isoreticular MOF-5 (Fe, Cu, Co, Ni and Zn) by Density Functional Theory

Natarajan Sathiyamoorthy Venkataramanan — Tue, 14 Apr 2009 00:00:00 CEST

Li adsorption on isoreticular MOFs with metal Fe, Cu, Co, Ni and Zn was studied using density function theory. Li functionalization shows a considerable structural change associated with a volume change in isoreticular MOF-5 except for the Zn metal center. Hydrogen binding energies on Li functionalized MOFs are seen to be in the range of 0.2 eV, which is the desired value for an ideal reversible storage system. This study has clearly shown that Li doping is possible only in Zn-based MOF-5, which would be better candidate to reversibly store hydrogen.