Nonstationarity and related measures for time‐dependent hartree–fock and multiconfigurational models

Based on an earlier article (Eberly and Singh, Phys. Rev. D 1973 , 7, 359) and related works on short‐time evolution, this article proposes a many‐electron formulation for the nonstationarity degree which can be assigned to quantum system at each time point. The key measure introduced, , is a nonstationarity index that can be thought of as an inverse nominal lifetime at each instance of time. The index is directly computed from the time derivative of one‐electron density matrix and is a size‐consistent quantity. In this article, the approach is developed for the time‐dependent Hartree–Fock (TDHF), single‐excitation (TDCIS), and time‐dependent full configuration interaction (TDFCI) models. As a rule, nonstationarity effects are more pronounced in correlated electron systems, and a joint analysis of and the multiconfigurational character of wave functions apparently provide a deeper insight into dynamical molecular processes. The performed calculations on small molecules in laser fields show a preference for the TDCIS model when comparing TDCIS and TDHF with the “exact” TDFCI model. © 2013 Wiley Periodicals, Inc.     

A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field

A general molecular mechanics (MM) model for treating aqueous Cu²⁺ and Zn²⁺ ions was developed based on valence bond (VB) theory and incorporated into the atomic multipole optimized energetics for biomolecular applications (AMOEBA) polarizable force field. Parameters were obtained by fitting MM energies to that computed by ab initio methods for gas‐phase tetra‐ and hexa‐aqua metal complexes. Molecular dynamics (MD) simulations using the proposed AMOEBA‐VB model were performed for each transition metal ion in aqueous solution, and solvent coordination was evaluated. Results show that the AMOEBA‐VB model generates the correct square‐planar geometry for gas‐phase tetra‐aqua Cu²⁺ complex and improves the accuracy of MM model energetics for a number of ligation geometries when compared to quantum mechanical (QM) computations. On the other hand, both AMOEBA and AMOEBA‐VB generate results for Zn²⁺–water complexes in good agreement with QM calculations. Analyses of the MD trajectories revealed a six‐coordination first solvation shell for both Cu²⁺ and Zn²⁺ ions in aqueous solution, with ligation geometries falling in the range reported by previous studies. © 2012 Wiley Periodicals, Inc.     

How the Generalized Anomeric Effect Influences the Conformational Preference

The generalized anomeric effect refers to the conformational preference of a gauche structure over an anti structure for molecules with a R‐X‐C‐Y moiety. Whereas there are conflicting reports regarding the origin of this ubiquitous effect, a general consensus is that both the steric (more specifically electrostatic) and hyperconjugative interactions contribute. Here we employed the block‐localized wavefunction (BLW) method, which is the simplest variant of ab initio valence bond (VB) theory and can define reference electron‐localized states self‐consistently, to evaluate the magnitude of the hyperconjugation effect in a number of acyclic molecules exhibiting the generalized anomeric effect. The BLW‐based energy decomposition analysis revealed that both the steric and hyperconjugation effects contribute to the conformational preferences of methoxymethyl fluoride and methoxymethyl chlorides. But for the other systems under investigation, including methanediol, methanediamine, aminomethanol and dimethoxymethane, the hyperconjugative interactions play a negative role in the conformational preferences and the steric effect is solely responsible for the generalized anomeric effect.     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

锰氧化物中氧空位的构建及其催化氧化苯系物作用机制研究进展

作为一种过渡金属氧化物,锰氧化物以其多晶型、储/释氧能力强、蕴含丰富氧物种、结构缺陷可控等优点被广泛应用于苯系物的热催化氧化。其中,具有众多特性的氧空位能有效促进苯系物的完全催化氧化,因而成为各界研究的焦点。我们综述了常见的氧空位构建方法及表征技术,并总结了在苯系物催化氧化过程中,锰氧化物中氧空位的几种重要作用机制对催化活性和抗水性能的积极影响。最后文章对氧空位构建新方法、形成机理、具体过程及其在锰氧化物热催化氧化苯系物领域中的应用进行了总结和展望。     

Cu Doping-Induced Transformation from [Ag62S12(SBut)32]2+ to [Ag62−xCuxS12(SBut)32]4+ Nanocluster

The change in the valence state of nanocluster can induce remarkable changes in the properties and structure. However, achieving the valence state changes in nanoclusters is still a challenge. In this work, we use Cu²⁺ as dopant to “oxidize” [Ag₆₂S₁₂(SBu^t)₃₂]²⁺ (4 free electrons) to obtain the new nanocluster: [Ag_62−xCu_xS₁₂(SBu^t)₃₂]⁴⁺ with 2 free electrons. As revealed by its structure, the [Ag_62−xCu_xS₁₂(SBu^t)₃₂]⁴⁺ (x=10∼21) has a similar structure to that of [Ag₆₂S₁₂(SBu^t)₃₂]²⁺ precursor and all the Cu atoms occupy the surface site of nanocluster. It′s worth noting that with the Cu atoms doping, the [Ag_62−xCu_xS₁₂(SBu^t)₃₂]⁴⁺ nanocluster is more stable than [Ag₆₂S₁₂(SBu^t)₃₂]²⁺ at higher temperature and in electrochemical cycle. This result has laid a foundation for the subsequent application and exploration. Overall, this work reveals crystals structure of a new Ag−Cu nanocluster and offers a new insight into the electron reduction/oxidation of nanocluster.     

Generation of a four-qubit cluster state for atoms in a thermal cavity

We propose two schemes for generating a four-atom cluster state in a thermal cavity. With the assistant of a strong classical field the photon-number-dependent parts in the effective Hamiltonian are canceled. Thus the schemes are insensitive to the thermal field. The schemes can also be used to generate the cluster state for the trapped ions in thermal motion.     

Interface formation of Al2O3 on n‐GaN(0001): Photoelectron spectroscopy studies

Al₂O₃ insulator layers were deposited step by step by the physical vapor deposition (PVD) method onto gallium nitride in the wurtzite form, n‐type and (0001)‐oriented. The substrate surface and the early stages of Al₂O₃/n‐GaN(0001) interface formation were characterized in situ under ultra‐high vacuum conditions by X‐ray and ultraviolet photoelectron spectroscopy (XPS, UPS). The electron affinity (EA) of the substrate cleaned by annealing was 3.6 eV. Binding energies of the Al 2p (76.0 eV) and the O 1s (532.9 eV) confirmed the creation of the Al₂O₃ compound in the deposited film for which the EA was 1.6 eV. The Al₂O₃ film was found to be amorphous with a bandgap of 6.9 eV determined from the O 1s loss feature. As a result, the calculated Al₂O₃/n‐GaN(0001) valence band offset (VBO) is ?1.3 eV and the corresponding conduction band offset (CBO) 2.2 eV.     

质子水合结构的振动态密度分析

使用基于多态经验价键模型的分子动力学模拟, 对水溶液中质子的水合结构及其在质子传递过程中的动力学过程进行了研究. 在价键模型的方法下, 质子的水合结构主要以H₉O₄⁺(Eigen)以及过渡态的H₅O₂⁺(Zundel)结构形态存在, 且在这两种结构中以Eigen的形态表现明显. 通过对质子传递过程中不同水合结构的态密度频谱分析, 发现一个在2000~3000 cm^-1范围内的明显连续的宽吸收谱带, 主要归因于Eigen结构的贡献, 这些特征峰的出现与水合氢离子第一溶剂化层内的强氢键作用密切相关. 对于Zundel的结构, 在1760 cm^-1处出现一个较为明显的肩峰, 归属为质子传递模式的特征振动. 通过对质子水合结构态密度频谱的分析, 可望增强对于稀酸溶液红外光谱中的连续宽吸收带以及质子传递的微观动力学过程的理解.