Ab initio study on the adsorption of hydrated Na+ and Ag+ cations on a Ag(111) surface

The interactions of Na(+) and Ag(+) cations with an Ag(111) surface in the presence and absence of water molecules were investigated with cluster models and ab initio methods. The Ag surface was described with two-layered Ag(10) and Ag(18) cluster models, and MP2/RECP/6-31+G(d) was used as the computational method. The effect of the basis set superposition error (BSSE) was taken into account with counterpoise (CP) correction. The interactions between Na(+) and Ag(111) surface were found to be primarily electrostatic, and the interaction energies and equilibrium distances at the different adsorption sites were closely similar. The largest CP-corrected MP2 adsorption energy for Na(+) was -190.2 kJ/mol. Owing to the electrostatic nature of the Na(+)-Ag(111) interaction, Na(+) prefers to be completely surrounded by water molecules rather than directly adsorbed to the surface. Ag(+)-Ag(111) interactions were much stronger than Na(+)-Ag(111) interactions because they were dominated by orbital contributions. The largest CP-corrected MP2 adsorption energy for Ag(+) was -358.9 kJ/mol. Ag(+) prefers to adsorb on sites where it can bind to several surface atoms, and in the presence of water molecules, it remains adsorbed to the surface while the water molecules form hydrogen bonds with one another. The CP correction had an effect on the interaction energies but did not change the relative trends.     

MP2 study on adsorption of hydrated Na+ and Au+ cations on the Au(111) surface

The interactions of Na+ and Au+ cations with an Au(111) surface in the presence and absence of water molecules were investigated using Au18 and Au22 cluster models and the MP2 method with a triple-zeta valence basis set. The interactions between Na+ ions and the Au(111) surface were found to be primarily electrostatic, contrary to the much stronger Au+-Au(111) interactions that were dominated by orbital contributions. The largest CP-corrected MP2 adsorption energies were -156.9 kJ/mol for Na+ and -478.7 kJ/mol for Au+. When hydrated, Na+ prefers to be completely surrounded by water molecules rather than adsorbed to the surface, whereas Au+ remains adsorbed to the surface as water molecules bond with each other and with the Au surface. CP correction did not change the relative adsorption energy trends of Na+ or Au+ ions, but it had an effect on the interaction energy trends of the hydrated cations because of the weak water-surface and water-water interactions.     

H2O在Cu(100)表面吸附的从头算研究

用量子化学从头计算方法,以原子簇Cu₅为模拟表面,研究了水在Cu(100)面上不同吸附位的吸附情况,结果表明:水分子通过氧原子与表面成键,顶位是其最佳吸附位,吸附能约为70kJ/mol,平衡距离为0.213nm,氢原子远离表面.在氧原子不加极化函数时,水分子的二次轴垂直于表面时能量最低,但倾斜至50°所需能量仅在10kJ/mol以内.当考虑O原子d轨道的影响时,水分子倾斜时能量较低,得到了与实验相符的吸附构型.另外还研究了表面电荷对吸附体系的影响,结果表明:表面带正电荷时,水与表面间的相互作用增强,水上所转移电荷增多,Cu-O间平衡距离减小;表面带负电荷时,情况与之相反,且氢原子靠近表面时,势能曲线有最低点.     

DOPA醌在Cu(100)表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

Energy density analysis of cluster size dependence of surface-molecule interactions (II): formate adsorption onto a Cu(111) surface

Adsorption of formate (HCOO) onto a Cu(111) surface has been treated theoretically using 18 kinds of Cu(n) (6 < or = n < or = 56) clusters. The energy density analysis (EDA) proposed by Nakai has been adopted to examine surface-molecule interactions for different cluster sizes. EDA results for the largest model cluster Cu(56) have shown that the adsorption-induced energy density variation in Cu atoms decays with distance from the adsorption site. Analysis of this decay, which can be carried out using the EDA technique, is important because it enables verification of the reliability of the model cluster used. In the case of formate adsorption onto the Cu(111) surface, it is found that at least a four-layer model cluster is necessary to treat the surface-molecule interaction with chemical accuracy.     

Effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water coordination on the structure of glycine and zwitterionic glycine

Interactions between metal ions and amino acids are common both in solution and in the gas phase. Here, the effect of metal ions and water on the structure of glycine is examined. The effect of metal ions (Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) and water on structures of Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (m = 0, 2, 5) complexes have been determined theoretically by employing the hybrid B3LYP exchange-correlation functional and using extended basis sets. Selected calculations were carried out also by means of CBS-QB3 model chemistry. The interaction enthalpies, entropies, and Gibbs energies of eight complexes Gly.Mn+ (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) were determined at the B3LYP density functional level of theory. The computed Gibbs energies DeltaG degrees are negative and span a rather broad energy interval (from -90 to -1100 kJ mol(-1)), meaning that the ions studied form strong complexes. The largest interaction Gibbs energy (-1076 kJ mol(-1)) was computed for the NiGly2+ complex. Calculations of the molecular structure and relative stability of the Gly.Mn+(H2O)m and GlyZwitt.Mn+(H2O)m (Mn+ = Li+, Na+, K+, Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+; m = 0, 2, and 5) systems indicate that in the complexes with monovalent metal cations the most stable species are the NO coordinated metal cations in non-zwitterionic glycine. Divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ prefer coordination via the OO bifurcated bonds of the zwitterionic glycine. Stepwise addition of two and five water molecules leads to considerable changes in the relative stability of the hydrated species. Addition of two water molecules at the metal ion in both Gly.Mn+ and GlyZwitt.Mn+ complexes reduces the relative stability of metallic complexes of glycine. For Mn+ = Li+ or Na+, the addition of five water molecules does not change the relative order of stability. In the Gly.K+ complex, the solvation shell of water molecules around K+ ion has, because of the larger size of the potassium cation, a different structure with a reduced number of hydrogen-bonded contacts. This results in a net preference (by 10.3 kJ mol(-1)) of the GlyZwitt.K+H2O5 system. Addition of five water molecules to the glycine complexes containing divalent cations Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+ results in a net preference for non-zwitterionic glycine species. The computed relative Gibbs energies are quite high (-10 to -38 kJ mol(-1)), and the NO coordination is preferred in the Gly.Mn+(H2O)5 (Mn+ = Mg2+, Ca2+, Ni2+, Cu2+, and Zn2+) complexes over the OO coordination.     

Accurate quantum chemical energies for the interaction of hydrocarbons with oxide surfaces: CH(4)/MgO(001)

We examine the adsorption of CH(4) on the MgO(001) surface by a hybrid approach. It combines MP2 calculations with extrapolation to the complete basis set limit for the adsorption site and the CH(4)-CH(4) pair interactions in the adsorbate layer, with DFT+dispersion calculations under periodic boundary conditions for the whole system. To the total binding energy of 10.7 kJ mol(-1), the DFT+D(ispersion) correction contributes 0.7 kJ mol(-1) only, showing that the Mg(9)O(9) two-layer surface model is an excellent choice and that the interaction between the CH(4) molecules in the adsorbate layer is dominated by pair interactions. Contributions due to relaxation of the atom positions of 0.6 kJ mol(-1) (evaluated at DFT+dispersion) and of higher order correlation effects of 2.0 kJ mol(-1) (evaluated by CCSD(T)) yield a final estimate of 13.3 kJ mol(-1). To this total adsorption energy, the lateral interactions between the CH(4) molecules in the adsorbate layer contribute substantially, 4.1 kJ mol(-1)."Observed" desorption energies of 15.3 and 16.0 kJ mol(-1) have been derived from the observed Arrhenius desorption barriers (12.6 and 13.1 kJ mol(-1)) using thermal enthalpy contributions and a substantial zero-point energy (4.2 kJ mol(-1)) calculated from DFT+D vibrational frequencies. The comparison shows that our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate has reached chemical accuracy. It misses 2-3 kJ mol(-1) of binding only, which is most likely due to missing higher order correlation effects.PBE+D(ispersion) itself yields an adsorption energy that agrees within 1 kJ mol(-1) with our final hybrid MP2?:?PBE+D+ΔCCSD(T) estimate.     

Optimal binding site of a methane molecule on the silanol covered (010) surface of silicalite-1: ONIOM calculations

The binding energies and the corresponding structures of a methane molecule on the silanol covered (010) surface of silicalite-1 have been investigated using ab initio methods. Different levels of calculations, HF/6-31G(d), MP2/6-31G(d) and ONIOM (MP2/6-31G(d):HF/6-31G(d)) including the correction of an error due to an unbalance of the basis set, known as basis set super position error (BSSE), as well as the size of the cluster representing the silicalite-1 surface, were systematically examined to validate the model used. The ONIOM method with the BSSE correction was found to be a compromise between accuracy and computer time required. The optimal binding site on the silicalite-1 surface was observed at the configuration where the methane molecule points one H atom toward the O atom of the silanol group. The corresponding binding energy is -1.71 kJ/mol. This value is significantly higher than that of -5.65 kJ/mol when the methane molecule approaches the center of the straight channel. At this configuration, the C atom of methane was observed to locate exactly at the center of the channel. This leads to the conclusion that the methane molecule will relatively seldom be adsorbed on the silanol covered (010) surface of silicalite-1. Instead, the adsorption process will take place directly at the center of the straight channel.     

簇模型ZnO(100)面上吸附CO_2的密度泛函理论研究

采用电荷自洽方法, 以嵌入原子簇Zn4O4为模型, 使用量子化学的密度泛函理论, 研究了二氧化碳在六方ZnO非极化的(1010)面的可能吸附态。计算表明, CO2垂直底物表面吸附, 氧原子只能与Zn原子配位, 并且吸附能为很弱的1.8 kJ/mol;吸附质分子平行于底物表面时, 得到了5种平衡吸附构型, 其中采用CZn配位和η2O, O二齿配位时, 吸附很弱, 经BSSE校正后的吸附能在8.8~6.6 kJ/mol。 采用η2C, O方式分别与O和Zn配位时, 吸附能为31.1 kJ/mol; C原子与表面O配位时计算得到了唯一的一个化学吸附态, 吸附能为139.6 kJ/mol, 与实验结果一致。     

On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems

Geometries, harmonic vibrational frequencies and interaction energies of the water-hydrogen sulfide dimer, hydrogen fluoride dimer and glycine zwitterion-water dimer were determined by the counterpoise-corrected (CP-corrected) gradient optimization that explicitly corrects for the basis set superpusition error (BSSE) and CP-uncorrected (normal) gradient opfimization respectively at the B3LYP and MP2 levels of theory, employing the popular Pople‘s standard 6-31G(d), 6-31G(d,p) and 6-311 G(d,p) basis sets in order to assess the importance of CP-corrected gradient optimiTation in the study of hydrogen bonded systems. The normal optimization of these three H-bonded systems obtained using these popular basis sets all yielded erratic results, whereas use of CP-corrected gradient optimization led to consistent results with those from larger basis sets. So this CP receipt becomes useful and necessary to correctly describe large systems, where the use of small basis sets may be necessary.     

Theoretical Investigation on the Adsorption of Ag^＋ and Hydrated Ag^＋ Cations on Clean Si（111） Surface

In this paper, the adsorption of Ag^＋ and hydrated Ag^＋ cations on clean Si（111） surface were investigated by using cluster （Gaussian 03） and periodic （DMol^3） ab initio calculations. Si（111） surface was described with cluster models （Si14H17 and Si22H21） and a four-silicon layer slab with periodic boundary conditions. The effect of basis set superposition error （BSSE） was taken into account by applying the counterpoise correction. The calculated results indicated that the binding energies between hydrated Ag^＋ cations and clean Si（111） surface are large, suggesting a strong interaction between hydrated Ag^＋ cations and the semiconductor surface. With the increase of number, water molecules form hydrogen bond network with one another and only one water molecule binds directly to the Ag^＋ cation. The Ag^＋ cation in aqueous solution will safely attach to the clean Si（111） surface.     

A density functional theory study of molecular and dissociative adsorption of H2 on active sites in mordenite

Adsorption and chemisorption of H2 in mordenite is studied using ab initio density functional theory (DFT) calculations. The geometries of the adsorption complex, the adsorption energies, stretching frequencies, and the capacity to dissociate the adsorbed molecule are compared for different active sites. The active centers include a Br?nsted acid site, a three-coordinated surface Al site, and Lewis sites formed by extraframework cations: Na+, Cu+, Ag+, Zn2+, Cu2+, Ga3+, and Al3+. Adsorption properties of cations are compared for a location of the cation in the five-membered ring. This location differs from the location in the six-membered ring observed for hydrated cations. The five-membered ring, however, represents a stable location of the bare cation. In this position any cation exhibits higher reactivity compared with the location in the six-membered ring and is well accessible by molecules adsorbed in the main channel of the zeolite. Calculated adsorption energies range from 4 to 87 kJ/mol, depending on electronegativity and ionic radius of the cation and the stability of the cation-zeolite complex. The largest adsorption energy is observed for Cu+ and the lowest for Al3+ integrated into the interstitial site of the zeolite framework. A linear dependence is observed between the stretching frequency and the bond length of the adsorbed H2 molecule. The capacity of the metal-exchanged zeolite to dissociate the H2 molecule does not correlate with the adsorption energy. Dissociation is not possible on single Cu+ cation. The best performance is observed for the Ga3+, Zn2+, and Al3+ extraframework cations, in good agreement with experimental data.     

Adsorption of water molecules on selected charged sodium-chloride clusters

The adsorption of water molecules (H(2)O) on sodium chloride cluster cations and anions was studied at 298 K over a mass range of 100-1200 amu using a custom-built laser desorption ionization reactor and mass spectrometer. Under the conditions used, the cations Na(3)Cl(2)(+) and Na(4)Cl(3)(+) bind up to three water molecules, whereas the larger cations, Na(5)Cl(4)(+) to Na(19)Cl(18)(+), formed hydrates with one or two only. The overall trend is a decrease in hydration with increasing cluster size, with an abrupt drop occurring at the closed-shell Na(14)Cl(13)(+). As compared to the cluster cations, the cluster anions showed almost no adsorption. Among smaller clusters, a weak adsorption of one water molecule was observed for the cluster anions Na(6)Cl(7)(-) and Na(7)Cl(8)(-). In the higher mass region, a substantial adsorption of one water molecule was observed for Na(14)Cl(15)(-). Density functional theory (DFT) computations were carried out for the adsorption of one molecule of H(2)O on the cations Na(n)Cl(n-1)(+), for n = 2-8, and the anions Na(n)Cl(n+1)(-), for n = 1-7. For each ion, the structure of the hydrate, the hydration energy, and the standard-state enthalpy, entropy, and Gibbs energy of hydration at 298 K were computed. In addition, it was useful to compute the distortion energy, defined as the electronic energy lost due to weakening of the Na-Cl bonds upon adsorption of H(2)O. The results show that strong adsorption of a H(2)O molecule occurs for the linear cations only at an end Na ion and for the nonlinear cations only at a corner Na ion bonded to two Cl ions. An unexpected result of the theoretical investigation for the anions is that certain low-energy isomers of Na(6)Cl(7)(-) and Na(7)Cl(8)(-) bind H(2)O strongly enough to produce the observed weak adsorption. The possible implications of these results for the initial hydration of extended NaCl surfaces are discussed.     

DFT study of gas-phase adsorption of benzotriazole on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon

The adsorption of benzotriazole--an outstanding corrosion inhibitor for copper--on Cu(111), Cu(100), Cu(110), and low coordinated defects thereon has been studied and characterized using density functional theory (DFT) calculations. We find that benzotriazole can either chemisorb in an upright geometry or physisorb with the molecular plane being nearly parallel to the surface. While the magnitude of chemisorption energy increases as passing from densely packed Cu(111) to more open surfaces and low coordinated defects, the physisorption energy is instead rather similar on all three low Miller index surfaces. It is pointed out that due to a large dipole moment of benzotriazole the dipole-dipole interactions are rather important. For perpendicular chemisorption modes the lateral repulsion is very long ranged, extending up to the nearest-neighbor distance of about 60 bohrs, whereas for parallel adsorption modes the lateral interactions are far less pronounced and the molecules experience a weak attraction at distances ?25 bohrs. The chemisorption energies were therefore extrapolated to zero coverage by a recently developed scheme and the resulting values are -0.60, -0.73, and -0.92 eV for Cu(111), Cu(100), and Cu(110), respectively, whereas the zero-coverage physisorption energy is about -0.7 eV irrespective of the surface plane. While the more densely packed surfaces are not reactive enough to interact with the molecular π-system, the reactivity of Cu(110) appears to be at the onset of such interaction, resulting in a very stable parallel adsorption structure with an adsorption energy of -1.3 eV that is ascribed as an apparent chemisorption+physisorption mode.     

Theoretical Study on Intermolecular Interactions and Thermodynamic Properties of Nitroamine Dimers

Ab initio self-consistent field(SCF) and Mφller-Plesset correlation correction methods employing 6-31G^** basis set have been applied to the optimizations of nitroamine dimers.The binding energies have been corrected for the basis set superposition error (BSSE) and the zero-point energy.Theree optimized dimers have been obtained.The BSSE corrected binding energy of the most stable dimer is predicted to be -31.85kJ/mol at the MP4/6-31G^**//MP2/6-31G^** level.The energy barriers of the Walden conversion for -NH2 group are 19.7kJ/mol and 18.3kJ/mol for monomer and the most stable dimer,respectively.The molecular interaction makes the internal rotation around N1-N2 even more difficult.The thermodynamic properties of nitroamine and its dimers at different temperatures have been calculated on the basis of vibrational analyses.The change of the Gibbs free energy for the aggregation from monomer to the most stable dimer at standard pressure and 298.2 K is predicted to be 14.05kJ/mol.     

Rapid Evaluation of Individual Hydrogen Bonding Energies in Linear Water Chains

A model is proposed to rapidly evaluate the individual hydrogen bonding energies in linear water chains. We regarded the two O--H bonds of a water molecule as two dipoles. The magnitude of the O--H bond dipole mo- ment can be varied due to the other water molecules＇ presence. An analytic potential energy function, which explicitly contains the permanent dipole-dipole interactions, the polarization interactions, the van der Waals interactions and the covalent interactions, was therefore established. The individual hydrogen bonding energies in a series of linear water chains were evaluated via the analytic potential energy function and compared with those obtained from the CP-corrected MP2/aug-cc-pVTZ calculations. The results show that the analytic potential energy function not only can produce the individual hydrogen bonding energies as accurately as the CP-corrected MP2/aug-cc-pVTZ method, but is very efficient as well, demonstrating the model proposed is reasonable and useful. Based on the individual hy- drogen bonding energies obtained, the hydrogen bonding cooperativity in the linear water chains was explored and the natures of the hydrogen bonding in these water chains were discussed.     

High resolution electron energy loss measurements of Na/Cu(111) and H2O/Na/Cu(111): dependence of water reactivity as a function of Na coverage

Collective electronic excitations occurring in Na layers grown on Cu(111) and in H2O/Na/Cu(111) have been investigated at room temperature by high resolution electron energy loss spectroscopy. Loss spectra taken for a coverage between 0.55 and 0.70 ML of Na are characterized by a feature at 3.0 eV assigned to a Mie resonance. Further increasing the Na coverage leads to the appearance of the Na surface plasmon at 3.9 eV. Water molecules dissociate on Na layers as shown by the appearance of the OH-Na vibration. Upon water adsorption, relevant effects on both electronic excitations and vibrational modes were observed as a function of Na coverage.     

Pd(Cu)在MgO(100)表面吸附CO和O2的理论研究

采用固体镶嵌势能模型和DFT/B3LYP方法研究了在Pd/MgO和Cu/MgO表面吸附CO和O₂分子的电子性质. 计算结果表明, 在完美MgO(100)表面Pd原子对CO和O₂的吸附能分别为206.5和84.8 kJ/mol, 因此可知Pd原子更容易吸附CO分子; 而当Pd原子附着于有氧缺陷的MgO表面时, 它对两种分子的吸附都非常弱. 相反, 附着于MgO表面的Cu原子对O₂分子的吸附更为有利, 其吸附能在140～155 kJ/mol之间. 研究结果还表明, 对于双分子吸附体系, 即CO＋CO, CO＋O₂, O₂＋O₂体系, 双分子之间的结合力可减小完美MgO表面上Pd原子与被吸附分子的相互作用, 使吸附能减少了46～96 kJ/mol. 而对于在MgO表面上的Cu原子, 只有O₂＋O₂ 体系使吸附能减少了大约50～71 kJ/mol.