Biomedical subjects

Yan Alexander Wang

Publications and source records attributed to Yan Alexander Wang.

10 recordsLinked to original sources

PubMed2006

Search for suitable approximation methods for fullerene structure and relative stability studies: case study with C50.

Local density approximation (LDA), several popular general gradient approximation (GGA), hybrid module based density functional theoretical methods: SVWN, BLYP, PBE, HCTH, B3LYP, PBE1PBE, B1LYP, and BHandHLYP, and some nonstandard hybrid methods are applied in geometry prediction for C60 and C70. HCTH with 3-21G basis set is found to be one of the best methods for fullerene structural prediction. In the predictions of relative stability of C50 isomers, PM3 is an efficient method in the first step for sorting out the most stable isomers. HCTH with 3-21G predicts very good geometries for C50, similar to the performance of B3LYP6-31G(d). The gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital from the predictions of all the density functional theory methods has the following descending order: E(gap)(half-and-half hybrid)>E(gap)(B3LYP)>E(gap)(HCTH)(GGA)>E(gap)(SVWN)(LDA).

Journal Article↗

PubMed2006

Ozonization at the vacancy defect site of the single-walled carbon nanotube.

The ozonization at the vacancy defect site of the single-walled carbon nanotube has been studied by static quantum mechanics and atom-centered density matrix propagation based ab initio molecular dynamics within a two-layered ONIOM approach. Among five different reaction pathways at the vacancy defect, the reaction involving the unsaturated active carbon atom is the most probable pathway, where ozone undergoes fast dissociation at the active carbon atom at 300 K. Complementary to the experiments, our work provides a microscopic understanding of the ozonization at the vacancy defect site of the single-walled carbon nanotube.

Journal Article↗

PubMed2006

Electronic properties and reactivity of Pt-doped carbon nanotubes.

The structures of the (5,5) single-walled carbon nanotube (SWCNT) segments with hemispheric carbon cages capped at the ends (SWCNT rod) and the Pt-doped SWCNT rods have been studied within density functional theory. Our theoretical studies find that the hemispheric cages introduce localized states on the caps. The cap-Pt-doped SWCNT rods can be utilized as sensors because of the sensitivity of the doped Pt atom. The Pt-doped SWCNT rods can also be used as catalysts, where the doped Pt atom serves as the enhanced and localized active center on the SWCNT. The adsorptions of C(2)H(4) and H(2) on the Pt atom in the Pt-doped SWCNT rods reveal different adsorption characteristics. The adsorption of C(2)H(4) on the Pt atom in all of the three Pt-doped SWCNT rods studied (cap-end-doped, cap-doped, and wall-doped) is physisorption with the strongest interaction occurring in the middle of the sidewall of the SWCNT. On the other hand, the adsorption of H(2) on the Pt atom at the sidewall of the SWCNT is chemisorption resulting in the decomposition of H(2), and the adsorption of H(2) at the hemispheric caps is physisorption.

Adsorption↗

PubMed2006

Vibrational assignment and structure of trifluorobenzoylacetone. A density functional theoretical study.

Molecular structure and vibrational frequencies of 4,4,4-trifluoro-1-phenyl-1,3-butanedione, known as trifluorobenzoylacetone (TFBA), have been investigated by means of density functional theory (DFT) calculations. The results were compared with those of benzoylacetone (BA), acetylacetone (AA), and trifluoroacetylacetone (TFAA). Comparing the calculated and experimental band frequencies and intensities suggests coexisting of both stable cis-enol conformers in comparable proportions in the sample. The energy difference between the two stable chelated enol forms is negligible, 0.96 kcal/mol, calculated at B3LYP/6-311++G** level of theory. The molecular stability and the hydrogen bond strength were investigated by applying the natural bond orbital (NBO) theory and geometry calculations. The theoretical calculations and spectroscopic results indicate that the hydrogen bond strength of TFBA is between those of TFAA and AA, considerably weaker than that of BA.

Butanones↗

PubMed2006

Orbital-corrected orbital-free density functional theory.

A new implementation of density functional theory (DFT), namely orbital-corrected orbital-free (OO) DFT, has been developed. With at most two non-self-consistent iterations, OO-DFT accomplishes the accuracy comparable to fully self-consistent Kohn-Sham DFT as demonstrated by its application on the cubic-diamond Si and the face-centered-cubic Ag systems. Our work provides a new impetus to further improve orbital-free DFT method and presents a robust means to significantly lower the cost associated with general applications of linear-scaling Kohn-Sham DFT methods on large systems of thousands of atoms within different chemical bonding environment.

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PubMed2006

Chemical reaction of nitric oxides with the 5-1DB defect of the single-walled carbon nanotube.

In this work, we applied a two-layered ONIOM (B3LYP/6-31G(d):UFF) method to study the reaction of nitric oxides with a 5-1DB defect on the sidewall of the single-walled carbon nanotube (SWCNT). We have chosen a suitable ONIOM model for the calculation of the SWCNT based on the analyses of the frontier molecular orbitals, local density of states, and natural bond orbitals. Our calculations clearly indicate that the 5-1DB defect is the chemically active center of the SWCNT. In the reaction of nitric oxides with the defected SWCNT, the 5-1DB defect site can capture a nitrogen atom from nitric oxides, yielding the N-substitutionally doped SWCNT. We have explored the reaction pathway in detail. Our work verifies the chemical reactivity of the 5-1DB defects of the SWCNTs, indicates that the 5-1DB defect is a possible site for the functionalization of the SWCNTs, and demonstrates a possible way to fabricate position controllable substitutionally doped SWCNTs with a low doping concentration under mild conditions via some simple chemical reactions.

Journal Article↗

PubMed2005

Structure, bonding, and reactivity of Ti and Zr amidate complexes: DFT and X-ray crystallographic studies.

Easily prepared and highly modular organic amide proligands have been used to synthesize a series of new bis(amidate)-bis(amido) Ti and Zr complexes via protonolysis. These complexes have been structurally characterized by NMR spectroscopy and X-ray crystallography. The solid-state molecular structures of these complexes indicate that the amidate ligands bind to the metal centers in an exclusively bidentate fashion, resulting in discrete monomeric species. Geometric isomerism in these species is highly dependent upon the steric characteristics of the proligands utilized in the synthesis. In solution, these complexes are observed to isomerize on the NMR time scale, with one isomer being predominant. Bonding in the bis(amidate)-bis(amido) complexes was investigated by DFT calculations. The geometric isomers predicted by theory matched the experimentally observed results, within experimental error. The orbitals associated with amidate-metal bonding are energetically well below the frontier orbitals. The HOMO in these complexes is a pi orbital associated with amido ligand-to-metal bonding character, while the LUMO in all cases is a vacant d orbital on the metal center.

Journal Article↗

PubMed2005

Synthesis, structure, and computational studies of soluble conjugated multidentate macrocycles.

[Chemical reaction: See text] Conjugated, shape-persistent macrocycles based on [3 + 3] Schiff-base condensation are of interest for supramolecular materials. In an effort to develop new discotic liquid crystals based on these compounds, a series of macrocycles with peripheral alkoxy groups of varying length have been prepared. The synthesis and mechanism of formation have been probed by isolation of oligomeric intermediates. A single-crystal X-ray diffraction study of one macrocycle revealed a nonplanar, strongly hydrogen-bonded structure. To our surprise, even with very long substituents, the macrocycles were not liquid crystalline. This has been rationalized by ab initio calculations that indicate the macrocycles are undergoing rotation of the dihydroxydiiminobenzene rings that may not allow a stable discotic liquid crystalline phase. These results provide new insight into the formation and properties of these large macrocycles and may provide guidance to developing stable liquid crystalline materials in the future.

Journal Article↗

PubMed2005

Theoretical studies of alkyl radicals in the NaY and HY zeolites.

Interplay of quantum mechanical calculations and experimental data on hyperfine coupling constants of ethyl radical in zeolites at several temperatures was engaged to study the geometries and binding energies and to predict the temperature dependence of hyperfine splitting of a series of alkyl radicals in zeolites for the first time. The main focus is on the hyperfine interaction of alkyl radicals in the NaY and HY zeolites. The hyperfine splitting for neutral free radicals and free radical cations is predicted for different zeolite environments. This information can be used to establish the nature of the muoniated alkyl radicals in the NaY and HY zeolites via muSR experiments. The muon hyperfine coupling constants of the ethane radical cation in these zeolites are very large with relatively little dependence on temperature. It was found that the intramolecular dynamics of alkyl free radicals are only weakly affected by their strong binding to zeolites. In contrast, the substrate binding has a significant effect on their intermolecular dynamics.

Journal Article↗

PubMed2004

Mechanisms of Staudinger reactions within density functional theory.

The Staudinger reactions of substituted phosphanes and azides have been investigated by using density functional theory. Four different initial reaction mechanisms have been found. All systems studied go through a cis-transition state rather than a trans-transition state or a one-step transition state. The one-step pathway of the phosphorus atom attacking the substituted nitrogen atom is always unfavorable energetically. Depending on the substituents on the azide and the phosphane, the reaction mechanism with the lowest initial reaction barrier can be classified into three categories: (1). like the parent reaction, PH(3) + N(3)H, the reaction goes through a cis-transition state, approaches a cis-intermediate, overcomes a PN-bond-shifting transition state, reaches a four-membered ring intermediate, dissociates N(2) by overcoming a small barrier, and results in the final products: N(2) and a phosphazene; (2). once reaching the cis-intermediate, the reaction goes through the N(2)-eliminating transition state and produces the final products; (3). the reaction has a concerted initial cis-transition state, in which the phosphorus atom attacks the first and the third nitrogen atoms of the azide simultaneously and reaches an intermediate, and then the reaction goes through similar steps of the first reaction mechanism. In contrast to the previous predictions on the relative stability of the unsubstituted cis-configured phosphazide intermediate and the unsubstituted trans-configured phosphazide intermediate, the total energy of the substituted trans-configured phosphazide intermediate is close to that of the substituted cis-configured phosphazide intermediate. The preference of the initial cis-transition state reaction pathway is thoroughly discussed. The relative stability of the cis- and the trans-intermediates is explored and analyzed with the aid of molecular orbitals. The effects of substituents and solvent effects on the reaction mechanisms of the Staudinger reactions are discussed in detail.

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