Combining ab initio and density functional theories with semiempirical methods

2002 ◽  
Vol 117 (12) ◽  
pp. 5617-5631 ◽  
Author(s):  
Qiang Cui ◽  
Hong Guo ◽  
Martin Karplus
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Semiempirical Methods

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

2003 ◽  
Vol 68 (12) ◽  
pp. 2231-2282 ◽  
Author(s):  
Jiří Šponer ◽  
Pavel Hobza
Keyword(s):  
Nucleic Acids ◽  
Ab Initio ◽  
Molecular Interactions ◽  
Quantum Chemical ◽  
Density Functional ◽  
Large Scale ◽  
Semiempirical Methods ◽  
Base Stacking ◽  
Dna And Rna ◽  
Dynamics Simulations

Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.

A Combined ab initio and Density Functional Study of the Electronic Structure of Thymine and 2-Thiothymine Radicals

2003 ◽  
Vol 68 (12) ◽  
pp. 2322-2334 ◽  
Author(s):  
Robert Vianello ◽  
Zvonimir B. Maksić
Keyword(s):  
Ab Initio ◽  
Spin Density ◽  
Density Functional ◽  
Radical Cations ◽  
Functional Study ◽  
Theory Approach ◽  
Functional Theory ◽  
Adiabatic Ionization Potential ◽  
Highest Occupied Molecular Orbital ◽  
Positively Charged

The electronic and energetic properties of thymine (1) and 2-thiothymine (2) and their neutral and positively charged radicals are considered by a combined ab initio and density functional theory approach. It is conclusively shown that ionization of 1 and 2 greatly facilitates deprotonation of the formed radical cations thus making the proton transfer between charged and neutral precursor species thermodynamically favourable. The adiabatic ionization potential of 1 and 2 are analysed. It appears that ADIP(1) is larger than ADIP(2) by 10 kcal/mol, because of greater stability of the highest occupied molecular orbital (HOMO) of the former. It is also shown beyond any doubt that the spin density in neutral and cationic radical of 2 is almost exclusively placed on the σ-3p AO of sulfur implying that these two systems represent rather rare sigma-radicals. In contrast, the spin density of radicals of 1 is distributed over their π-network.

scholarly journals Phonons in Short-Period GaN/AlN Superlattices: Group-Theoretical Analysis, Ab initio Calculations, and Raman Spectra

Nanomaterials ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 286
Author(s):  
Valery Davydov ◽  
Evgenii Roginskii ◽  
Yuri Kitaev ◽  
Alexander Smirnov ◽  
Ilya Eliseyev ◽  
...  
Keyword(s):  
Theoretical Analysis ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Raman Spectra ◽  
Density Functional ◽  
Structural Characteristics ◽  
Vibrational Modes ◽  
Phonon Modes ◽  
Short Period ◽  
Group Theoretical Analysis

We report the results of experimental and theoretical studies of phonon modes in GaN/AlN superlattices (SLs) with a period of several atomic layers, grown by submonolayer digital plasma-assisted molecular-beam epitaxy, which have a great potential for use in quantum and stress engineering. Using detailed group-theoretical analysis, the genesis of the SL vibrational modes from the modes of bulk AlN and GaN crystals is established. Ab initio calculations in the framework of the density functional theory, aimed at studying the phonon states, are performed for SLs with both equal and unequal layer thicknesses. The frequencies of the vibrational modes are calculated, and atomic displacement patterns are obtained. Raman spectra are calculated and compared with the experimental ones. The results of the ab initio calculations are in good agreement with the experimental Raman spectra and the results of the group-theoretical analysis. As a result of comprehensive studies, the correlations between the parameters of acoustic and optical phonons and the structure of SLs are obtained. This opens up new possibilities for the analysis of the structural characteristics of short-period GaN/AlN SLs using Raman spectroscopy. The results obtained can be used to optimize the growth technologies aimed to form structurally perfect short-period GaN/AlN SLs.

Ab Initio Calculation of Mechanical Properties of Stacking Fault in 3C-SiC: Effect of Stress and Doping

2012 ◽  
Vol 717-720 ◽  
pp. 415-418
Author(s):  
Yoshitaka Umeno ◽  
Kuniaki Yagi ◽  
Hiroyuki Nagasawa
Keyword(s):  
Mechanical Properties ◽  
Ab Initio ◽  
Density Functional ◽  
Stacking Faults ◽  
Single Layer ◽  
Local Strain ◽  
Density Functional Theory Calculations ◽  
Stacking Fault ◽  
Functional Theory ◽  
N Doping

We carry out ab initio density functional theory calculations to investigate the fundamental mechanical properties of stacking faults in 3C-SiC, including the effect of stress and doping atoms (substitution of C by N or Si). Stress induced by stacking fault (SF) formation is quantitatively evaluated. Extrinsic SFs containing double and triple SiC layers are found to be slightly more stable than the single-layer extrinsic SF, supporting experimental observation. Effect of tensile or compressive stress on SF energies is found to be marginal. Neglecting the effect of local strain induced by doping, N doping around an SF obviously increase the SF formation energy, while SFs seem to be easily formed in Si-rich SiC.

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

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