Møller-Plesset (MP2) perturbation theory for large molecules

Summary A novel formulation of MP2 theory is presented which starts from the Laplace transform MP2 ansatz, and subsequently moves from a molecular orbital (MO) representation to an atomic orbital (AO) representation. Consequently, the new formulation is denoted AO-MP2. As in traditional MP2 approaches electron repulsion integrals still need to be transformed. Strict bounds on the individual MP2 energy contribution of each intermediate four-index quantity allow to screen off numerically insignificant integrals with a single threshold parameter. Implicit in our formulation is a bound to two-particle density matrix elements. For small molecules the computational cost for AO-MP2 calculations is about a factor of 100 higher than for traditional MO-based approaches, but due to screening the computational effort in larger systems will only grow with the fourth power of the size of the system (or less) as is demonstrated both in theory and in application. MP2 calculations on (non-metallic) crystalline systems seem to be a feasible extension of the Laplace transform approach. In large molecules the AO-MP2 ansatz allows massively parallel MP2 calculations without input/output of four-index quantities provided that each processor has in-core memory for a limited number of two-index quantities. Energy gradient formulas for the AO-MP2 approach are derived.Dedicated to Prof. W. Kutzelnigg whose books on theoretical chemistry aroused my interest in this field     

Fine structures of zeolite-Linde-L (LTL): surface structures, growth unit and defects

High-resolution electron microscopy (HREM) has been used to image the surface structure of nano- and micrometer-sized synthetic crystals of zeolite-Linde-L (LTL). Columnar holes and rotational, nano-sized, wheel-like defects were observed within the crystals, where the hole has a minimum size equal to that of the rotational defect. Predictions of surface structure from atomistic computer simulation concur with the observations from HREM and provide insight into the crystal growth mechanism of perfect and defective LTL. Analysis of the energetics of the formation of rotational defect structures reveals that the driving force for defect creation is thermodynamic and furthermore, the rotational defects could be created in high concentrations. Formation of a columnar hole is found to be slightly energetically unfavourable and therefore we speculate that the incidence of both rotational and nano-sized vacancy defects is strongly dependent on kinetic factors and reaction conditions. The morphology of nano- and microcrystalline LTL is contradistinct and we use insights from simulation to propose an explanation of the disparity in crystal shape.     

Mechanical properties of twist grain boundaries in Cu

In a previous paper we studied the Young's and shear modulus of a high-angle twist grain boundary (5) in Cu, using the EAM, and related it to the uniaxial strain derivatives of single crystals. In this paper, we discuss elastic properties of ten additional twist grain boundaries, from 8.8–43.6°. The monolayer Young's modulus at each boundary was calculated and found to be 20–50% higher than the bulk value for all eleven boundaries for both csl and type1 structures. The monolayer shear modulus at each boundary was calculated and found to be 93–98% lower than the bulk value for six grain boundaries with csl structure and found to decrease with increasing twist angle. The critical shear stress was also calculated for eleven boundaries with csl structure and found to roughly decrease with increasing twist angle.     

Subtleties in data analysis related to the size of critical region

We comment on the analysis of the critical behavior of a layered driven diffusive system recently done by Achahbar and Marro. We discuss why we believe their method of taking the thermodynamic limit and determining the order-parameter exponent leads to unreliable estimates.     

Formation and morphology of latex monolayers. Computer simulation studies

The results of computer simulations of monolayers created from monodisperse latex particles are presented and discussed. Layers are characterized by the normalized coverage,NC (the actual coverage of the surface related to its maximum possible coverage with particles), and by the average number of neighbors,ANN, calculated as the number of particles being in contact with a given one and averaged over all the particles on the surface. Variable parameters used in simulations include: the rate of particles deposition, the probability of lateral movements, the probability of desorption of particles adsorbed on the surface, the probability of covalent immobilization of adsorbed particles, and the on-sphere slip parameter, OSS (characterizing the scattering of a falling particle on the particles being already attached to the surface). Morphology of monolayers is qualitatively characterized by relations betweenANN andNC. It is shown that for all monolayers formed without adhesion (and without repulsion) between the particles adsorbed on the surface the dependence ofANN vs.NC is described by a characteristic master curve (regardless of the values of probabilities of desorption and lateral movements of particles). For the monolayers created including adhesive forces between the adsorbed particles the plots ofANN vs.NC lie above the master curve, while similar plots obtained for the layers made of particles showing various types of repulsive interactions are always placed below it. Thus, the dependencies ofANN vs.NC, derived from computer simulations, can be used for the determination of the character of the interparticle interactions in the real systems.     

Interfacial segregation in Ag-Au,Au-Pd,and Cu-Ni alloys: I. (100) surfaces

Atomistic simulations of segregation to (100) free surface in Ag–Au, Au–Pd, and Cu–Ni alloy systems have been performed for a wide range of temperatures and compositions within the solid solution region of these alloy phase diagrams. In addition to the surface segregation profiles, surface free energies, enthalpies, and entropies were determined. These simulations were performed within the framework of the free energy simulation method, in which an approximate free energy functional is minimized with respect to atomic coordinates and atomic site occupation. The effects of the relaxation with respect to either the atomic positions or the atomic concentrations are discussed. For all alloy bulk compositions (0.05 C 0.95) and temperatures (400 T(K) 1,100) examined, Ag, Au, and Cu segregates to the surface in the Ag–Au, Au–Pd, and Cu–Ni alloy systems, respectively. The present results are compared with several theories for segregation. The resultant segregation profiles in Au–Pd and Ag–Au alloys are shown to be in good agreement with an empirical segregation theory, while in Cu–Ni alloys the disagreement in Ni-rich alloys is substantial. The width of the segregation profile is limited to approximately three to four atomic planes. The surface thermodynamic properties depend sensitively on the magnitude of the surface segregation, and some of them are shown to vary linearly with the magnitude of the surface segregation.     

Environment of the P b center at the Si(111)/oxide interface

We assess several models for the environment of the P _b center (Si dangling bond center) at the interface of Si(111) with its oxide. The comparison of hyperfine constants observed with those predicted using large cluster models favors a local structure in which there is an Si-Si bond within the oxide close to the Si dangling bond. Such Si-Si bonds are also suggested by a number of other experiments and are consistent with the reactive layer model proposed to rationalize a range of oxidation studies.     

手性氮磷配体与钌的配位过程的研究—原位变温 31P核磁及分子模拟计算

用原位变温 ³¹P NMR和分子模拟研究了手性氮磷配体与金属钌的配位过程。首先确定了配体及其与金属的配合物的化学位移信号分别在δ=-13.0ppm和δ=48.2ppm。配位过程在293～343K温度范围内,相继生成四配位和五配位中间体。四配位体在 ³¹P NMR上对应于30.8ppm和-15.0ppm的两个信号;五配位中间体对应于35.1ppm和-16.5ppm的两个信号;最后在343K,产物中只有六配位的配合物存在,其信号出现在48.2ppm。为了得到各种中间体的结构,用分子模拟方法进行了结构优化计算,并比较了它们的构象能。计算结果表明,四配位中间体有两种构象,能量相差9kcal·mol^-1,它们可能同时存在于平衡状态。而五配位中间体只有一种绝对优势构象,尚有一个磷原子未参与配位。六配位的钌金属配合物的结构优化结果显示,两个氯原子分别位于PNNP原子所构成平面的两侧。其构象能为162.0kcal·mol^-1,其中键角能的贡献是112.5kcal·mol^-1,而非键静电作用是-41.4kcal·mol^-1,这表明分子内的静电吸引力对于形成完全配位产物是十分有利的,但是收敛的配体分子却承受了较大的键角张力。     

Effect of enzyme concentration on the dynamic behavior of a membrane-bound enzyme system

The dynamic behavior of the reaction-diffusion system, composed of glucose oxidase (EC 1.1.3.4) immobilized at a uniform concentration in a membrane, used as a glucose electrode is represented by a diffusion equation with a nonlinear reaction-term in one-dimensional space. The mathematical model is analyzed by computer simulation, that is, numerical integration of the equation under various initial and boundary conditions, to examine the effect of enzyme concentration on the response characteristics (responsiveness and linearity in response) of the electrode. The analysis of the responses of the system to stepwise changes in the boundary value (glucose concentration in simple solution) infers that the enzyme concentration governs the patterns of the spatial distributions of the substrates (glucose and dissolved oxygen) in steady states and transient responses. It is also revealed that the response characteristics of the electrode are optimized with concentration of immobilized enzyme and that the system establishes the steady states at the same spatial distributions of the substrates, regardless of the boundary value. The diffusion of the substrates and the oxygen concentration also have significant effects on the response characteristics of the electrode.