Density functional theory study of enantiospecific adsorption at chiral surfaces

Density functional theory calculations are carried out for the adsorption of a chiral molecule, (S)- and (R)-HSCH(2)CHNH(2)CH(2)P(CH(3))(2), on a chiral surface, Au(17 11 9)(S)(). The S-enantiomer is found to bind more strongly than the R-enantiomer by 8.8 kJ/mol, evidencing that the chiral nature of the kink sites at the Au(17 11 9) surface leads to enantiospecific binding. The adsorption of two related chiral molecules, HSCH(2)CHNH(2)COOH ("cysteine") and HSCH(2)CHNH(2)CH(2)NH(2), does not, however, lead to enantiospecific binding. The results of the density functional calculations are broken down into a local binding model in which each of the chiral molecule's three contact points with the surface provides a contribution to the overall adsorption bond strength. The enantiospecific binding is demonstrated to originate from the simultaneous optimization of these three local bonds. In the model, the deformation energy costs of both the molecule and the surface are further included. The model reveals that the molecule may undergo large deformations in the attempt to optimize the three bonds, while the surface deforms to a lesser extent. The most favorable binding configurations of each enantiomer are, however, characterized by small deformation energies only, justifying a local binding picture.     

Inaccessibility of beta-hydride elimination from -OH functional groups in Wacker-type oxidation

Quantum mechanics calculations (B3LYP and MPW1K density functional theory) on mechanisms relevant to the Wacker process for dehydrogenation of alcohol to ketone show that the commonly accepted mechanism for product formation (beta-hydride elimination (BHE) leading to Pd-H formation) is not energetically feasible (36.2 kcal/mol). An alterative pathway involving a five-bodied reductive elimination (RE) leads to an activation enthalpy of 18.8 kcal/mol, which is just half that of the BHE from the -OH group usually assumed for the Wacker process. We find that a water molecule catalyzes both processes, reducing the barrier to 17.2 for RE and 25.0 for BHE, but will not change the relative ordering of the two mechanisms. This suggests that assumptions of BHE mechanisms should be reexamined for cases in which the beta atom is not an alkyl group.     

Atomic, molecular and cluster dynamics on flat and stepped surfaces

Surface diffusion is responsible for transport of atoms at the surface. It is therefore essential for understanding many surface phenomena where transport of atoms and molecules are involved. Using the field ion microscope and scanning tunneling microscope, we have directly observed many elementary surface atomic and molecular processes at terraces and steps and have measured the activation barrier heights of these processes, and have also studied their atomic mechanisms in detail. For Si(111) surface, transport of atoms above 450°C appears to be achieved by magic clusters of about 10–15 atoms in size, and their diffusion behavior is very different from those of individual atoms and molecules. We discuss how atom dynamics affects the growth behavior, island shape transitions, and growth modes in the growth of crystals and epitaxial films.     

Density functional theory study of p‐chloroaniline adsorption on Pd surfaces and clusters

The adsorption mode of aromatic molecules on transition metal surfaces plays a key role in their catalytic transformation. In this study, by means of density functional theory calculations, we systematically investigate the adsorption of p‐chloroaniline on a series of Pd surfaces, including stepped surfaces, flat surfaces, and clusters. The adsorption energies of p‐chloroaniline on these substrates [Pd(221), Pd(211), Pd(111), Pd(100), Pd₁₃‐icosahedral, Pd₁₃‐cubo‐octahedron, Pd₅₅] are ?1.90, ?2.13, ?1.70, ?2.11, ?2.53, ?2.65, ?2.23 eV, respectively. Benzene ring is adsorpted on catalyst rather than amine group in p‐chloroaniline molecular. A very good linear relationship is further found between the adsorption energies of p‐chloroaniline and the d‐band center of both Pd surfaces and clusters. The lower of d‐band center of Pd models, the stronger adsorption of p‐chloroaniline on catalysts. In addition, the frontier molecular orbital and density of states analysis explain the adsorption energy sequence: cluster Pd₁₃ > stepped Pd(221) surface > flat Pd(111) surface. © 2014 Wiley Periodicals, Inc.     

Density functional theory study of the brookite surfaces and phase transitions between natural titania polymorphs

The present study is concerned with the structural and electronic properties of the low-index surfaces of the brookite form of titanium dioxide. A theoretical investigation is carried out using the density functional formalism under the nonlocal B3LYP approximation to calculate surface energies, band energy values, and to interpret the response to hydrostatic pressure of the bulk and surfaces of the brookite structure. In addition, phase transformations with pressure are predicted from the anatase and the rutile to the brookite polymorph at about 3.8 and 6.2 GPa, respectively. The orthorhombic structure and the fractional coordinates of brookite vary isotropically with the rise in pressure. The calculated band gap energy is 3.78 eV for the bulk brookite. The brookite surface stabilities follow the sequence (010) < (110) < (100), and the minimum gap energy value is found for the (110) surface.     

磷化镍晶体结构的密度泛函理论研究

运用密度泛函理论系统地研究了已知的磷化镍晶体如Ni3P、 Ni12P5、 Ni2P、 Ni5P4、 NiP、 NiP2 和 NiP3等的结构、成键以及相关的热力学稳定性,对于结构简易化合物（Ni2P和NiP3）的弹性行为进行了预测。这些数据有助于更好的理解磷化镍的催化活性。     

General rules for predicting where a catalytic reaction should occur on metal surfaces: a density functional theory study of C-H and C-O bond breaking/making on flat,stepped, and kinked metal surfaces

To predict where a catalytic reaction should occur is a fundamental issue scientifically. Technologically, it is also important because it can facilitate the catalyst's design. However, to date, the understanding of this issue is rather limited. In this work, two types of reactions, CH(4) <--> CH(3) + H and CO <--> C + O on two transition metal surfaces, were chosen as model systems aiming to address in general where a catalytic reaction should occur. The dissociations of CH(4) --> CH(3) + H and CO --> C + O and their reverse reactions on flat, stepped, and kinked Rh and Pd surfaces were studied in detail. We find the following: First, for the CH(4) <--> Ch(3) + H reaction, the dissociation barrier is reduced by approximately 0.3 eV on steps and kinks as compared to that on flat surfaces. On the other hand, there is essentially no difference in barrier for the association reaction of CH(3) + H on the flat surfaces and the defects. Second, for the CO <--> C + O reaction, the dissociation barrier decreases dramatically (more than 0.8 eV on Rh and Pd) on steps and kinks as compared to that on flat surfaces. In contrast to the CH(3) + H reaction, the C + O association reaction also preferentially occurs on steps and kinks. We also present a detailed analysis of the reaction barriers in which each barrier is decomposed quantitatively into a local electronic effect and a geometrical effect. Our DFT calculations show that surface defects such as steps and kinks can largely facilitate bond breaking, while whether the surface defects could promote bond formation depends on the individual reaction as well as the particular metal. The physical origin of these trends is identified and discussed. On the basis of our results, we arrive at some simple rules with respect to where a reaction should occur: (i) defects such as steps are always favored for dissociation reactions as compared to flat surfaces; and (ii) the reaction site of the association reactions is largely related to the magnitude of the bonding competition effect, which is determined by the reactant and metal valency. Reactions with high valency reactants are more likely to occur on defects (more structure-sensitive), as compared to reactions with low valency reactants. Moreover, the reactions on late transition metals are more likely to proceed on defects than those on the early transition metals.     

First-principles study of C adsorption, O adsorption, and CO dissociation on flat and stepped Ni surfaces

The adsorption of atomic oxygen and carbon was studied with plane wave density functional theory on four Ni surfaces, Ni(110), Ni(111), Ni(210), and Ni(531). Various adsorption sites on these surfaces are examined in order to identify the most favorable adsorption site for each atomic species. The dependence of surface bonding on adsorbate coverage is also investigated. Adsorption energies and structural information are obtained and compared with existing experimental results for Ni(110) and Ni(111). In addition, activation barriers to CO dissociation have been determined on Ni(111) and Ni(531) by locating the transition states for these processes. Our results indicate that the binding energies of C are comparatively stronger on stepped surfaces than on flat surfaces, and the energy barriers associated with CO dissociation strongly favor reactions occurring near surface steps.     

Density functional theory study of formaldehyde oligomers

Hydrogen‐bonded formaldehyde oligomers (dimer to pentamer) are studied using density functional theory (DFT), the B3LYP method, and the 6‐311+G* basis set. Many‐body interaction energies are obtained to study the contribution of many‐body terms to binding energy. The basis set superposition error (BSSE)‐corrected total energies are ?229.08170, ?343.61410, ?458.16660, and ?572.70901 hartrees for dimer, trimer, tetramer, and pentamer, respectively, with corresponding binding energies ?2.55, ?4.86, ?6.99, and ?9.49 kcal/mol. Two‐body energies have been found to contribute significantly to the total binding energy in dimer to pentamer, whereas higher‐order interaction energies are negligible. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional theory study of BnC clusters

B_nC clusters (n = 3–10) were studied at the density functional theory (DFT) (B3LYP)/6‐311G** level of theory. The calculations predicted that the most stable configurations of the B_nC clusters are the (n + 1)‐membered cyclic structures. For boron–carbon clusters, the configurations containing greater numbers of three‐membered boron rings are more favorable, except for the B₇C and B₉C clusters. Through molecular orbital analysis of these B_nC clusters, we have concluded that π‐electron delocalization plays a crucial role in the stability of n + 1‐membered cyclic structures. In this paper, the relative stability of each cluster is discussed based on their single atomic‐binding energies. The capability of clusters to obtain or lose an electron was also discussed, based on their vertical electron detachment energies (VDEs), adiabatic electron detachment energies (ADEs), vertical electron affinities (VEAs) and adiabatic electron affinities (AEAs). Copyright © 2011 John Wiley & Sons, Ltd.     

Density functional theory study of water adsorption at reduced and stoichiometric ceria (111) surfaces

We study the structure and energetics of water molecules adsorbed at ceria (111) surfaces for 0.5 and 1.0 ML coverages using density functional theory. The results of this study provide a theoretical framework for interpreting recent experimental results on the redox properties of water at ceria (111) surfaces. In particular, we have computed the structure and energetics of various absorption geometries at the stoichiometric ceria (111) surface. We find that single hydrogen bonds between the water and the oxide surface are favored in all cases. At stoichiometric surfaces, the water adsorption energy depends rather weakly on coverage. We predict that the observed coverage dependence of the water adsorption energy at stoichiometric surfaces is likely the result of dipole-dipole interactions between adsorbed water molecules. When oxygen vacancies are introduced in various surface layers, water molecules are attracted more strongly to the surface. We find that it is very slightly energetically favorable for adsorbed water to oxidized the reduced (111) surface with the evolution of H(2). In the event that water does not oxidize the surface, we predict that the effective attractive water-vacancy interaction will result in a significant enhancement of the vacancy concentration at the surface in agreement with experimental observations. Finally, we present our results in the context of recent experimental and theoretical studies of vacancy clustering at the (111) ceria surface.     

吲哚分子振动光谱的密度泛函理论研究

用多种密度泛函理论(DFT)方法(BLYP/6-31G^*^*,B3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)对吲哚分子的平衡几何构型进行了优化。在优化构型的基础上计算了吲哚分子的谐力场、振动基频和红外光谱强度。计算得到的振动频率与实验值比较平均偏差对四种计算方法(BLYP/6-31G^*^*,P3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)分别为16.3,40.5,45.1和26.4cm^-^1。BLYP/6-31G^*^*理论力场被用于吲哚分子的简正坐标分析计算中。根据振动率的势能分布(PEDs)对此分子的振动基频进行了理论归属。     

苯酚分子拉曼光谱的密度泛函理论研究

采用B3LYP杂化泛函,6-31++G(d,p)基组,对苯酚分子的结构进行了优化.通过频率计算,获得了苯酚分子的拉曼光谱,并利用势能函数分布(PED)对拉曼光谱进行了指认.绘制了苯酚分子的静电势分布图,讨论了苯酚分子发生化学反应的位置,同时计算了HOMO-LUMO的能级差.通过TD-DFT计算获得了苯酚分子的吸收光谱和激发态.     

Energetics and heterodiffusion of Cu on Ag(110) stepped surfaces

A molecular‐dynamics simulation study has been performed to investigate the Cu adatom diffusion on the (110) stepped surfaces of Ag, using interatomic potentials described by the embedded atom method. We have systematically calculated the energy barriers for different possible diffusion mechanisms, which occur on the terrace and near the step edge. Our findings show that the predominant atomistic diffusion process at step edge and on the terrace is the exchange mechanism with anES barrier about 220 meV lower than that via jumping (290 meV), indicating that the incorporation of Cu adatom into Ag(110) is ‘easier’ than making a jump on the surface. On the other hand, the calculation of the Ehrlich–Schwoebel (ES) barrier demonstrates that this quantity is equal to 0 meV for the exchange process near the step edge and about 60 meV for channel–channel migration. Thus, the mass transport across steps may be important due to the lack of the ES barriers for exchange mechanism, revealing the possible layer‐by‐layer growth mode for our heterogeneous system. Copyright © 2015 John Wiley & Sons, Ltd.     

Density functional theory study of the geometry, energetics, and reconstruction process of Si111 surfaces

We report the structures and energies from first principles density functional calculations of 12 different reconstructed (111) surfaces of silicon, including the 3x3 to 9x9 dimer-adatom-stacking fault (DAS) structures. These calculations used the Perdew-Burke-Ernzerhof generalized gradient approximation of density functional theory and Gaussian basis functions. We considered fully periodic slabs of various thicknesses. We find that the most stable surface is the DAS 7x7 structure, with a surface energy of 1.044 eV/1x1 cell (1310 dyn/cm). To analyze the origins of the stability of these systems and to predict energetics for more complex, less-ordered systems, we develop a model in which the surface energy is partitioned into contributions from seven different types of atom environments. This analysis is used to predict the surface energy of larger DAS structures (including their asymptotic behavior for very large unit cells) and to study the energetics of the sequential size change (SSC) model proposed by Shimada and Tochihara for the observed dynamical reconstruction of the Si(111) 1x1 structure. We obtain an energy barrier at the 2x2 cell size and confirm that the 7x7 regular stage of the SSC model (corresponding to the DAS 7x7 reconstruction) provides the highest energy reduction per unit cell with respect to the unreconstructed Si111 1x1 surface.     

儿茶素结构和振动光谱的密度泛函理论研究

本文利用密度泛函理论方法B3LYP在6-311 G(d,p)水平上研究了儿茶素及其异构体表儿茶素分子的几何构型,计算结果与实验所得结构参数一致.计算了儿茶素分子平衡构型下的力常数,使用Wilson的GF矩阵方法计算了振动基频以及相应的势能分布,据此结合理论计算的光谱强度,对儿茶素分子的振动基频进行了完善合理的理论归属.     

三聚氰胺结构和热力学性质的密度泛函理论研究

采用Materials Studio 软件中的DMol~3模块对三聚氰胺的结构和性质进行了理论研究.得到了分子的几何构型、振动频率、各原子上的电荷分布、热力学、以及Fukui指数和前线分子轨道.计算结果表明:三聚氰胺分子中的C原子易得电子,是亲核试剂进攻点,而胺基上的N原子因含孤对电子是亲电反应中心.     

Density functional theory study on the interaction of catechin and cytosine

The interacting patterns and mechanism of the catechin and cytosine have been investigated using the density functional theory B3LYP method with 6-31+G* basis set.Eleven stable structures of the catechin-cytosine complexes have been found respectively.The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions.Theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been utilized to investigate the hydrogen bonds involved in all the systems.The interactio...     

Density functional theory study of single-wall platinum nanotubes

Single-wall platinum nanotubes (SWPtN) were studied using spin-polarized density functional theory calculations. These nanotubes consist of 5-, 6-, and 8-Pt atoms coiling around the tubular axis forming 3.54–4.73 Å in diameter and 0.7–1.4 nm and infinite in length. Two types of wall structures, square and triangular, were investigated. The results show that triangular nanotubes are more stable. Our results suggest that it is also feasible to synthesize the 5- and 8-atom triangular nanotubes as the 6-atom Pt nanotubes were found experimentally. These SWPtN may provide a new dimension in the catalytic applications of platinum.     

Density functional theory study on electrochemical reduction of 2,4-dinitrophenol

Electrochemical reduction of 2,4-dinitrophenol was investigated by cyclic voltammetry (CV), square-wave voltammetry (SWV) and in situ UV-vis spectroelectrochemistry. The reduction peaks for 2,4-dinitrophenol predicted using density functional theory (DFT) method (B3LYP) with 6–31++g(d) and 6–31++g(d,p) basis sets are consistent with the experimental values. The reduction mechanism of 2,4-dinitrophenol is discussed.