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Applications of Density Functional Theory
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Applications of Density Functional Theory

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 July 2009) | Viewed by 167323

Special Issue Editor

Dr. Abhijit Chatterjee

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Guest Editor
BIOVIA Materials Science Principal Scientist, Dassault Systems Biovia K.K., ThinkPark Tower 21F, 2-1-1 Osaki, Shinagawa-ku, Tokyo 141-6020, Japan
Interests: density functional theory; material designing; computational chemistry; inorganic catalytic material; catalytic reactions; inorganic membrane;  transition state calculation; atomistic simulation; ab initio first principle calculation; reactivity index
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Special Issue Information

Dear Colleagues,

Rapid advances are taking place in the application of density functional theory (DFT) to describe complex chemical reactions. Researchers in different fields working in the domain of quantum chemistry tend to have different perspectives and to use different computational approaches. DFT owes its popularity to recent developments in predictive powers for physical and chemical properties, and its ability to accurately treat large systems. Both theoretical content and computational methodology are developing at a pace which offers scientists working in diverse fields of quantum chemistry, cluster science and solid state physics, new opportunities. A major goal of this special issue is to draw together contributors from different fields to spread knowledge of current capabilities and new possibilities, and to stimulate the exchange of information between apparently disparate disciplines. The current issue aims to extract the current scenario of application of DFT to rationalize the physics behind and even down to understanding the chemical process.

Guest Editor
Abhijit Chatterjee, Ph.D.

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Keywords

  • Density Functional Theory (DFT)

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Published Papers (11 papers)

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Research

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11 pages, 1441 KB  
Article
Formation Energies of Antiphase Boundaries in GaAs and GaP: An ab Initio Study
by Oleg Rubel and Sergei D. Baranovskii
Int. J. Mol. Sci. 2009, 10(12), 5104-5114; https://doi.org/10.3390/ijms10125104 - 25 Nov 2009
Cited by 46 | Viewed by 14286
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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10 pages, 165 KB  
Article
First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum
by Shigeaki Ono
Int. J. Mol. Sci. 2009, 10(10), 4342-4351; https://doi.org/10.3390/ijms10104342 - 9 Oct 2009
Cited by 23 | Viewed by 10759
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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6 pages, 99 KB  
Article
Theoretical Study on Reactions of Triplet Excited State Thioxanthone with Indole
by Liang Shen and Hong-Fang Ji
Int. J. Mol. Sci. 2009, 10(10), 4284-4289; https://doi.org/10.3390/ijms10104284 - 30 Sep 2009
Cited by 9 | Viewed by 11494
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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13 pages, 469 KB  
Article
A Proline-Based Neuraminidase Inhibitor: DFT Studies on the Zwitterion Conformation, Stability and Formation
by Zhi-Wei Yang, Xiao-Min Wu, Li-Jun Zhou and Gang Yang
Int. J. Mol. Sci. 2009, 10(9), 3918-3930; https://doi.org/10.3390/ijms10093918 - 7 Sep 2009
Cited by 12 | Viewed by 15261
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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15 pages, 350 KB  
Article
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
by Jianguo Zhang, Huihui Zheng, Tonglai Zhang and Man Wu
Int. J. Mol. Sci. 2009, 10(8), 3502-3516; https://doi.org/10.3390/ijms10083502 - 6 Aug 2009
Cited by 5 | Viewed by 12237
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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14 pages, 2021 KB  
Article
Conformational Analysis of Thioether Musks Using Density Functional Theory
by William N. Setzer
Int. J. Mol. Sci. 2009, 10(8), 3488-3501; https://doi.org/10.3390/ijms10083488 - 4 Aug 2009
Cited by 6 | Viewed by 13647
Abstract
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- [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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8 pages, 188 KB  
Article
A TD-DFT Study on the Photo-Physicochemical Properties of Chrysophanol from Rheum
by Xue Zhao, Zebao Zheng, Shuai Feng, Zhiqiang Shi and Dezhan Chen
Int. J. Mol. Sci. 2009, 10(7), 3186-3193; https://doi.org/10.3390/ijms10073186 - 13 Jul 2009
Cited by 10 | Viewed by 14231
Abstract
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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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21 pages, 383 KB  
Article
Density Functional Study of Structures and Electron Affinities of BrO4F/BrO4F-
by Liangfa Gong, Jieming Xiong, Xinmin Wu, Chuansong Qi, Wei Li and Wenli Guo
Int. J. Mol. Sci. 2009, 10(7), 3128-3148; https://doi.org/10.3390/ijms10073128 - 8 Jul 2009
Cited by 1 | Viewed by 26467
Abstract
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 [...] Read more.
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). Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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8 pages, 241 KB  
Article
Probing the Structure, Stability and Hydrogen Adsorption of Lithium Functionalized Isoreticular MOF-5 (Fe, Cu, Co, Ni and Zn) by Density Functional Theory
by Natarajan Sathiyamoorthy Venkataramanan, Ryoji Sahara, Hiroshi Mizuseki and Yoshiyuki Kawazoe
Int. J. Mol. Sci. 2009, 10(4), 1601-1608; https://doi.org/10.3390/ijms10041601 - 14 Apr 2009
Cited by 32 | Viewed by 15656
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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Review

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125 pages, 887 KB  
Review
Path Integrals for Electronic Densities, Reactivity Indices, and Localization Functions in Quantum Systems
by Mihai V. Putz
Int. J. Mol. Sci. 2009, 10(11), 4816-4940; https://doi.org/10.3390/ijms10114816 - 10 Nov 2009
Cited by 30 | Viewed by 14444
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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20 pages, 460 KB  
Review
Modelling Catalyst Surfaces Using DFT Cluster Calculations
by Izabela Czekaj, Jörg Wambach and Oliver Kröcher
Int. J. Mol. Sci. 2009, 10(10), 4310-4329; https://doi.org/10.3390/ijms10104310 - 30 Sep 2009
Cited by 34 | Viewed by 16836
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applications of Density Functional Theory)
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