Density Functional Theory Study on the Cleavage Mechanism of the Carbonyl Bond in Amides on Flat and Stepped Ru Surfaces: Hydrogen-Induced or Direct C-O Bond Breaking?

We have performed density functional theory (DFT) calculations to investigate the reaction mechanism of the cleavage of the carbonyl bond in amides on both flat and stepped Ru surfaces. The simplest amide molecule, N,N-dimethylacetamide (DMA), was used as the exemplar model molecule. Through the calculations, the most stable transition states (TSs) in all the pathways on both flat and stepped Ru surfaces are identified. Comparing the energy profiles of different reaction pathways, we find that a direct cleavage mechanism is always energetically favored as compared with an alternative hydrogen-induced mechanism on either the flat or stepped Ru surface. It is easier for the dissociation process to occur on the stepped surface than on the flat surface. However, as compared with the terrace, the superiority of step sites boosting the C-O bond dissociation is not as evident as that on CO dissociation.

Time-dependent density functional theory study of charge transfer in collisions

We study the charge transfer between colliding ions, atoms, or molecules, within time-dependent density functional theory. Two particular cases are presented, the collision between a proton and a Helium atom, and between a gold atom and a butane molecule. In the first case, proton kinetic energies between 16 keV and 1.2 MeV are considered, with impact parameters between 0.31 and 1.9 angstrom. The partial transfer of charge is monitored with time. The total cross-section is obtained as a function of the proton kinetic energy. In the second case, we analyze one trajectory and discuss spin-dependent charge transfer between the different fragments.

Macroscopic limit of time-dependent density-functional theory for adiabatic local approximations of the exchange-correlation kernel

Time-dependent density-functional theory is a rather accurate and efficient way to compute electronic excitations for finite systems. However, in the macroscopic limit (systems of increasing size), for the usual adiabatic random-phase, local-density, or generalized-gradient approximations, one recovers the Kohn-Sham independent-particle picture, and thus the incorrect band gap. To clarify this trend, we investigate the macroscopic limit of the exchange-correlation kernel in such approximations by means of an algebraical analysis complemented with numerical studies of a one-dimensional tight-binding model. We link the failure to shift the Kohn-Sham spectrum of these approximate kernels to the fact that the corresponding operators in the transition space act only on a finite subspace.

Effect of spatial nonlocality on the density functional band gap

We show that for a large class of exchange-correlation functionals the local exchange-correlation potential obtained within an optimized effective potential severely underestimates the band gap. On the other hand, the corresponding nonlocal potential obtained from a generalized Kohn-Sham scheme provides a much better description of the band gap, in good agreement with experiments. These results strongly indicate that a local exchange-correlation potential, however good the exchange-correlation approximation, cannot capture the delicate interplay between correlation effects and spatial localization in the KS band structure, unless the (cumbersome) contribution from the derivative discontinuity of the exchange-correlation energy functional is considered.

Density Functional study of the photoactive yellow protein's chromophore

We have investigated the structural and electronic properties of p-coumaric acid, the chromophore of the photoactive yellow protein (PYP), by means of first-principles molecular dynamics based on density functional theory (DFT). We have studied the chromophore both in the vacuum and in an extended model which includes the nearest residues in the binding pocket of PYP, as derived from crystallographic data. We have characterized the ground state of the isolated chromophore in its protonated and deprotonated forms and computed the energy barrier involved in the trans to cis isomerization process around the carbon-carbon double bond. A comparison of the optimized structures of the chromophore in the vacuum and in the extended protein model, both in the trans (ground state of PYP in the dark) and cis (first light-activated intermediate) configuration, shows how the protein environment affects the chromophore in the first step of the photocycle. Our model gives an energy storage of 25 kcal/mol associated with the trans-to-cia photoisomerization. Finally, we have elucidated the nature of the electronic excitation relevant for the photochemistry of PYP by means of time-dependent DFT calculations.

Density functional study of the C atom adsorption on the α-Fe 2O3 (001) surface

The adsorption of C atoms on the α-Fe₂O₃ (001) surface was studied based on density function theory (DFT), in which the exchange-correlation potential was chosen as the PBE (Perdew, Burke and Ernzerhof) generalized gradient approximation (GGA) with a plane wave basis set. Upon the optimization on different adsorption sites with coverage of 1/20 and 1/5 ML, it was found that the adsorption of C atoms on the α-Fe ₂O₃ (001) surface was chemical adsorption. The coverage can affect the adsorption behavior greatly. Under low coverage, the most stable adsorption geometry lied on the bridged site with the adsorption energy of about 3.22 eV; however, under high coverage, it located at the top site with the energy change of 8.79 eV. Strong chemical reaction has occurred between the C and O atoms at this site. The density of states and population analysis showed that the s, p orbitals of C and p orbital of O give the most contribution to the adsorption bonding. During the adsorption process, O atom shares the electrons with C, and C can only affect the outermost and subsurface layers of α-Fe₂O₃; the third layer can not be affected obviously. Copyright © 2008 Chinese Journal of Structural Chemistry.

Density Functional Study on Reaction Activity of Steam Decomposition Products Adsorbed on Carbonaceous Surface

A systematic theoretical study on the adsorption of steam and its thermal decomposition products on carbon both zigzag and armchair surface was performed to provide molecular-level understanding of the reaction activity of all these reactants in biomass steam gasification process. All the calculations were carried out using density functional theory (DFT) at the B3LYP/6-31+g(d,p) level. The structures of carbonaceous surfaces, all reactants and surface complexes were optimized and characterized. Based on the value of adsorption heat been obtained from the calculation, the activity of all reactants can be ordered as: O > O2 >H2 >H >OH >H2O for both zigzag and armchair surface, and the adsorption style is physisorption to water molecule and chemisorption to the other dissociated components.

Identifying the distinct features of geometric structures for hole trapping to generate radicals on rutile TiO2(110) in photooxidation using density functional theory calculations with hybrid functional

Using density functional theory calculations with HSE 06 functional, we obtained the structures of spin-polarized radicals on rutile TiO2(110), which is crucial to understand the photooxidation at the atomic level, and further calculate the thermodynamic stabilities of these radicals. By analyzing the results, we identify the structural features for hole trapping in the system, and reveal the mutual effects among the geometric structures, the energy levels of trapped hole states and their hole trapping capacities. Furthermore, the results from HSE 06 functional are compared to those from DFT + U and the stability trend of radicals against the number of slabs is tested. The effect of trapped holes on two important steps of the oxygen evolution reaction, i.e. water dissociation and the oxygen removal, is investigated and discussed.

Density functional theory study of mixed-phase TiO2: heterostructures and electronic properties

In this work, density functional theory calculations have been performed to study the geometric, electronic, and energetic properties of two-phase TiO2 composites built by joining two single-phase TiO2 slabs, aiming at verifying possible improvement of the photo-activities of the composites through phase separation of excitons. We find that such desired electronic properties can be determined by several factors. When both the HOMO and LUMO levels of one of the two single-phase TiO2 slabs are higher than the corresponding ones of the other, the composite may have native electronic structures with phase-separated HOMO-LUMO states, especially when the two slabs exhibit highly matched surface lattices. For those pairs of TiO2 slabs with the HOMO and LUMO levels of one phase being within the range of those of the other, though the energetically favored composite give HOMO-LUMO states within one phase, one may still be able to separate them and move the HOMO state to the interface region by destabilizing the interactions between the two slabs.

Density functional theory study on the activation of molecular oxygen on a stepped gold surface in an aqueous environment: a new approach for simulating reactions in solution

The activation of oxygen molecules is an important issue in the gold-catalyzed partial oxidation of alcohols in aqueous solution. The complexity of the solution arising from a large number of solvent molecules makes it difficult to study the reaction in the system. In this work, O-2 activation on an Au catalyst is investigated using an effective approach to estimate the reaction barriers in the presence of solvent. Our calculations show that O-2 can be activated, undergoing OOH* in the presence of water molecules. The OOH* can readily be formed on Au(211) via four possible pathways with almost equivalent free energy barriers at the aqueous-solid interface: the direct or indirect activation of O-2 by surface hydrogen or the hydrolysis of O-2 following a Langmuir-Hinshelwood mechanism or an Eley-Rideal mechanism. Among them, the Eley-Rideal mechanism may be slightly more favorable due to the restriction of the low coverage of surface H on Au(211) in the other mechanisms. The results shed light on the importance of water molecules on the activation of oxygen in gold-catalyzed systems. Solvent is found to facilitate the oxygen activation process mainly by offering extra electrons and stabilizing the transition states. A correlation between the energy barrier and the negative charge of the reaction center is found. The activation barrier is substantially reduced by the aqueous environment, in which the first solvation shell plays the most important role in the barrier reduction. Our approach may be useful for estimating the reaction barriers in aqueous systems.

Mn ion dissolution from MnS:a density functional theory study

The dissolution of MnS inclusions could induce pitting corrosion in stainless steels, but its dissolution mechanism is poorly understood at the atomic scale. With the help of ab initio molecular dynamics calculations, one inevitable step in the dissolution of MnS is studied by simulating the process of one Mn ion leaving the surface. The reaction mechanism is determined to contain three steps with two large barriers and a small one, leading to two slow steps in the Mn ion dissolution. Comparing to the Na ion dissolution from NaCl, the barriers of the Mn ion dissolution are much larger, which is a reflection of their different electronic structures.

Density Functional Theory Studies of Ethanol Decomposition on Rh(211)

Density functional theory calculations were carried out to examine the mechanism of ethanol decomposition on the Rh(211) surface. We found that there are two possible decomposition pathways: (1) CH(3)CH(2)OH -> CH(3)CHOH -> CH(3)COH -> CH(3)CO -> CH(3) + CO -> CH(2) + CO -> CH + CO -> C + CO and (2) CH(3)CH(2)OH -> CH(3)CHOH -> CH(3)COH -> CH(2)COH -> CHCOH -> CHCO -> CH + CO -> C + CO. Both pathways have a common intermediate of CH(3)COH, and the key step is the formation of CH(3)CHOH species. According to our calculations, the mechanism of ethanol decomposition on Rh(211) is totally different from that on Rh(111): the reaction proceeds via CH(3)COH rather than an oxametallacycle species (-CH(2)CH(2)O- for Rh( 111)), which implies that the decomposition process is structure sensitive. Further analyses on electronic structures revealed that the preference of the initial C(alpha)-H path is mainly due to the significant reduction of d-electron energy in the presence of the transition state (TS) complex, which may stabilize the TS-surface system. The present work first provides a clear picture for ethanol decomposition on stepped Rh(211), which is an important first step to completely understand the more complicated reactions, like ethanol steam reforming and electrooxidation.

Some Understanding of Fischer-Tropsch Synthesis from Density Functional Theory Calculations

The combination of density functional theory (DFT) calculations and kinetic analyses is a very useful approach to study surface reactions in heterogeneous catalysis. The present paper reviews some recent work applying this approach to Fischer-Tropsch (FT) synthesis. Emphasis is placed on the following fundamental issues in FT synthesis: (i) reactive sites for both hydrogenation and C-C coupling reactions; (ii) reaction mechanisms including carbene mechanism, CO-insertion mechanism and hydroxyl-carbene mechanism; (iii) selectivity with a focus on CH(4) selectivity, alpha-olefin selectivity and chain growth probability; and (iv) activity.

Density Functional Theory Study of Iron and Cobalt Carbides for Fischer-Tropsch Synthesis

Carbides are important phases in heterogeneous catalysis. However, the understanding of carbide phases is inadequate: Fe and Co are the two commercial catalysts for Fischer-Tropsch (FT) synthesis, and experimental work showed that Fe carbide is the active phase in FT synthesis, whereas the appearance of Co carbide is considered as a possible deactivation cause, TO understand very different catalytic roles of carbides, all the key elementary steps in FT synthesis, that is, CO dissociation, C(1) hydrogenation, and C(1)+C(1) coupling, are extensively investigated on both carbide surfaces using first principles calculations. In particular, the most important issues in FT synthesis, the activity and methane selectivity, on the carbide surfaces are quantitatively determined and analyzed. They are also discussed together with metallic Fe and Co surfaces. It is found that (i) Fe carbide is more active than metallic Fe and has similar methane selectivity to Fe, being consistent with the experiments; and (ii) Co carbide is less active than Co and has higher methane selectivity, providing evidence on the molecular level to support the suggestion that the formation of Co carbide is a cause of relatively high methane selectivity and deactivation on Co catalysts.