[Show abstract][Hide abstract] ABSTRACT: We studied the mechanism of the water–gas shift reaction (WGSR; CO + H2O → CO2 + H2) catalyzed by Co6@Au32 core–shell nanoalloy using density-functional theory (DFT) calculations to investigate the bimetallic effects on the catalytic activation. The molecular structures and adsorbate/substrate interaction energies were predicted, along with the potential energy surface constructed using the nudged elastic band (NEB) method. Our results indicated that the energetic barriers of the two hydrogen dissociation reactions are lower on the core–shell nanoalloy than on Au38. Furthermore, all of the related chemical species of the WGSR can adsorb stably on Co6@Au32 to allow the reactions to take place under ambient pressure. To gain insight into the synergistic effect in the catalytic activity of the Co6@Au32 nanoalloy, the nature of the interaction between the adsorbate and substrate was analyzed by detailed electronic local densities of states (LDOS) as well as molecular structures.
The Journal of Physical Chemistry C 12/2013; 118(1):298–309. DOI:10.1021/jp408517m · 4.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Protein backbone oxidation was investigated by studying the α-H abstraction reaction in a ß-hairpin peptide, called Chignolin (PDB ID 1UAO), with density functional theory calculation at the B3LYP/6-31G(d,p) without any constraint. In order to stabilize the zwitterionic form of Chignolin with the salt bridges, the effects of aqueous solution were implemented by using microsolvation combined with a conductor-like polarizable continuum model (CPCM). Comparison between three glycine residues located at three different sites in Chignolin was used to examine the possible site specificity of this backbone oxidation. To construct the reaction profile of these α-H abstraction reactions, the pre- and post-reactive complexes along with their associated transition states were located and verified with the intrinsic reaction coordinate (IRC) method. The bond dissociation energy and reaction rates of these OH α-H abstraction reactions were calculated with transition state theory. The differences in this abstraction reaction between the neutral and zwitterionic forms of Chignolin were also compared. A molecular dynamics simulation was implemented to study the explicit solvation effect on the abstracted Chignolin structure. The range of the simulation time scale covers from fs to υs, i.e., from onset of the abstraction to the abstracted products reaching thermal equilibrium. Our results show that there are three kinds of site-specificity in this abstraction reaction. The reactivity and stability of the abstraction products and their abstraction modes are all dependent on the location where OH attacks. Furthermore the free energy landscapes of these abstraction products are distinctively different. This may imply the pathological disorders or diseases caused by this type of radicals are also dependent on the abstraction location.
The Journal of Physical Chemistry B 12/2012; 117(3). DOI:10.1021/jp308879r · 3.30 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We have studied the mechanism of the water–gas shift reaction (WGS, CO + H2O → CO2 + H2) catalyzed by nanosized gold particles by using density functional theory calculations. The molecular structures and adsorbate/substrate interaction energies of H2O/Au38, CO/Au38, HO/Au38, and H/Au38 configurations were predicted. Several adsorption sites on the Au38 nanoparticle were considered in this study and characterized as top, bridge, hollow, and hcp sites. A potential energy surface for WGS reaction on the Au38 nanoparticle has been constructed using the nudged elastic band method. It was found that water dissociation (H2O → H + OH) is the rate-limiting step, with an energy barrier of 31.41 kcal/mol. The overall reaction CO + H2O + Au38 → CO2 + H2 + Au38 is exothermic by 16.18 kcal/mol. To gain insights into the high catalytic activity of the gold nanoparticles, the nature of the interaction between adsorbate and substrate is also analyzed by the detailed electronic local density of states.
The Journal of Physical Chemistry C 01/2012; 116(1):336–342. DOI:10.1021/jp209172w · 4.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α-H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor-like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α-H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α-H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction.
[Show abstract][Hide abstract] ABSTRACT: Our calculations with spin-polarized density functional theory were carried out to characterize the adsorption and dissociation of the NH3 molecule on the Fe(111) surface. The molecular structures and adsorbate/substrate interaction energies of NH3/Fe(111), NH2/Fe(111), NH/Fe(111), N/Fe(111), and H/Fe(111) configurations were predicted. In these calculations, four adsorption sites, such as top (T), bridge (B), 3-fold-shallow (S), and 3-fold-deep (D) sites, of the Fe(111) surface, were considered. It was shown that the barriers for the stepwise NH3 dissociation reaction, NH3(g) → N(a) + 3H(a), are 28.32 kcal/mol (for H2N−H bond activation), 28.49 kcal/mol (for HN−H bond activation), and 25.34 kcal/mol (for N−H bond activation), and the entire process is 20.08 kcal/mol exothermic. To gain insight into the catalytic activity of the Fe(111) surface for the dehydrogenation of NH3, the interaction nature between adsorbate and substrate is also analyzed by the detailed electronic analysis.
The Journal of Physical Chemistry C 12/2010; 115(2):521–528. DOI:10.1021/jp1089883 · 4.77 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The variation in reaction dynamics of OH hydrogen abstraction from glycine between HF, MP2, CCSD(T), M05-2X, BHandHLYP, and B3LYP levels was demonstrated. The abstraction mode shows distinct patterns between these five levels and determines the barrier height, and the spin density transfer between OH radical and glycine. These differences are mainly resulted from the spin density distribution and geometry of the alpha carbon during the abstraction. The captodative effect which is commonly believed as one of the major factors to stabilize the caron-centered radical can only be observed in DFT levels but not in HF and MP2 levels. Difference in the abstraction energy were found in these calculation levels, by using the result of CCSD(T) as reference, B3LYP, BHandHLYP, and M05-2X underestimated the reaction barrier about 5.1, 0.1, and 2.4 kcal mol(-1), while HF and MP2 overestimated 19.1 kcal mol(-1) and 1.6 kcal mol(-1), respectively. These differences can be characterized by the vibration mode of imaginary frequency of transition states, which indicates the topology around transition states and determines reaction barrier height. In this model system, BHandHLYP provides the best prediction of the energy barrier among those tested methods.
[Show abstract][Hide abstract] ABSTRACT: A naturally occurring beta-hairpin peptide (PDB ID 1UAO) was used as a model to study the backbone oxidation of a protein with ab initio calculation at the B3LYB/6-31G(d) without any constraints. The (alpha)C--H bond dissociation energy of three different glycyl radicals located at different sites on the beta-hairpin peptide was calculated to evaluate the site specificity of backbone oxidation. The molecular and electronic structures of these glycyl radicals were analyzed to rationalize this site specificity. The overall molecular structure of the alpha-H abstracted beta-hairpin peptide remained almost unchanged with the exception of the local conformation of the attacked residue. However, the (alpha)C--H bond strength varied dramatically among these different sites.
[Show abstract][Hide abstract] ABSTRACT: The variation in potential energy surface of OH hydrogen abstraction from glycine between HF, MP2, BHandHLYP and B3LYP levels was demonstrated. The abstraction mode shows distinct patterns between these four levels and determines the barrier height, and the spin density transfer between OH radical and glycine. These differences are mainly resulted from the spin density distribution and geometry of the alpha carbon during the abstraction. There are different computational errors in these four levels, the BHandHLYP slightly overestimated reaction barrier about 0.4 kcal/mol; the HF and MP2 overestimated 18.9 kcal/mol and 1.4 kcal/mol, respectively. The B3LYP method underestimated about 5.3 kcal/mol. This study figures out the different vibration mode of imaginary frequency of TS influences the reaction barrier height. In this model system, the BHandHLYP method provides good accurate prediction.