B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks

Szekeres, Zs.; Bogár, Ferenc; Ladik, J.

doi:10.1002/qua.20394

Cited by 21 publications

(6 citation statements)

References 30 publications

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“…The obtained fitting results (R 2 ) were showed in Table 7. Clearly, the calculation result for bond order using B3LYP/6-31G* [54,55] is better than others. Therefore, this combination of functional and basis set was chosen.…”

Section: Calculation Methods For the Parametersmentioning

confidence: 84%

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Yang

et al. 2017

Catalysts

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Quantitative structure-thermostability relationship was carried out for four series of bis(imino)pyridine iron (cobalt) complexes and α-diimine nickel complexes systems in ethylene oligo/polymerization. Three structural parameters were correlated with thermal stability, including bond order of metal-nitrogen (B), minimum distance (D) between central metal and ortho-carbon atoms on the aryl moiety and dihedral angle (α) of a central five-membered ring. The variation degree of catalytic activities between optimum and room temperatures (A T ) was calculated to describe the thermal stability of the complex. By multiple linear regression analysis (MLRA), the thermal stability presents good correlation with three structural parameters with the correlation coefficients (R 2 ) over 0.95. Furthermore, the contributions of each parameter were evaluated. Through this work, it is expected to help the design of a late transition metal complex with thermal stability at the molecular level.

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Section: Calculation Methods For the Parametersmentioning

confidence: 84%

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Yang

et al. 2017

Catalysts

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“…The functions of generalized gradient approximation (GGA) (Mani-Biswas and Cagin, 2012; Szekeres et al, 2005) and correlation method of BLYP (Baei et al, 2011;Bogar et al, 2003) were widely applied into the quantum chemistry field (Yuan et al, 2011). Alexiadis and Kassinos (2010) found that calculations based on the BLYP functional resulted in a stable -C 2 H 3 group, while other functionals (e.g., OLYP, XLYP, PBE, and BP) did not converge.…”

Section: Choice Of Calculation Methodsmentioning

confidence: 99%

Mechanisms Study of NH₃Formation in the Reaction Between H₂and Char Edge Models Containing 2-Pyridone

Jing

Sun

Zhu

et al. 2014

Combustion Science and Technology

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Molecular modeling research based on transition state theory and density functional theory was performed to clarify the mechanisms for NH 3 evolution during the reaction of H 2 with char edge models containing 2-pyridone in zigzag and armchair configurations. The thermal chemical activation energy and enthalpy change were calculated in the overall process of NH 3 formation. The results indicate that formation of −NH 2 radicals is possible for both char edge models containing 2-pyridone in the zigzag and armchair configurations. Then, NH 3 can be produced through homogeneous hydrogen abstraction. It is found that the reaction of releasing NH 3 can be completed relatively easily with the char edge model containing 2-pyridone in the armchair configuration. Most pathways for NH 3 evolution appear to involve endothermic reactions for both configurations. These results provide a reference and basis for controlling the emission of nitrogen oxide.

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“…The expected advantages of applying DNA molecules for electronic devices are: (1) possibility to synthesize any DNA oligomers with various sizes ($nm-mm) and sequences of four bases, adenine (A), thymine (T), guanine (G), and cytosine (C), to create nanoscale shapes and patterns [3], (2) flexible design of electronic structures by controlling the size and sequence to obtain useful electronic properties such as one-dimensional electron transports and superlattice structures as can be seen in the semiconductor microelectronic devices obtained by band engineering technologies, and (3) possibility to develop a new microscopic technique for the determination of the sequence in DNA strands. The calculated energy levels of the four bases A, T, G, and C [4,5] are compared with the experimental spectra obtained by ultraviolet photoelectron spectroscopy (UPS) measurements. We also show the preliminary results of controlling the alignment of relatively large DNA molecules by using one-dimensional lattices formed on Si(1 0 0) substrates.…”

Section: Introductionmentioning

confidence: 99%

Electronic structures of DNA molecules and their alignment control on Si(100) substrates with one–dimensional lattices

Motooka

Ueda

Harada

et al. 2006

Science and Technology of Advanced Materials

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We have carried out molecular-orbital calculations of the four bases of DNA, adenine (A), thymine (T), guanine (G), and cytosine (C), and the dimer dApA formed from a deoxyadenosine by using a phosphate and terminating at the sites of 5 0 and 3 0 . The calculated results for A, T, G, and C are compared with the UPS spectra obtained by using a He II lamp with irradiation at 40.8 eV, and the experimental spectra are found to be generally reproduced by the calculations. We have also examined the alignment of 1.5-mm-length ring-shaped pBR322DNA composed of 4361 bp on Si(1 0 0) substrates with one-dimensional lattices. It is found that pBR322DNA can be observed only in the bottom parts of the one-dimensional lattice, while no appreciable DNA can be observed on the top parts of the lattice. These results suggest that DNA alignment can be controlled by one-dimensional lattices on Si(1 0 0) substrates through capillary action. r

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B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks

Cited by 21 publications

References 30 publications

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Mechanisms Study of NH₃Formation in the Reaction Between H₂and Char Edge Models Containing 2-Pyridone

Electronic structures of DNA molecules and their alignment control on Si(100) substrates with one–dimensional lattices

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B3LYP, BLYP and PBE DFT band structures of the nucleotide base stacks

Cited by 21 publications

References 30 publications

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

Mechanisms Study of NH3Formation in the Reaction Between H2and Char Edge Models Containing 2-Pyridone

Electronic structures of DNA molecules and their alignment control on Si(100) substrates with one–dimensional lattices

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Mechanisms Study of NH₃Formation in the Reaction Between H₂and Char Edge Models Containing 2-Pyridone