PdCO(OH)-体系中OH-助催化性能的成键能研究

本文使用相对论赝势从头计算方法和成键能判据[1 ] 研究了模型化合物 Pd CO(OH) -的电子结构 ,讨论了 OH-的助催化作用。得出 OH-对 Pd CO的助催化作用既可以通过其与金属 Pd形成化学键 (通过金属 )来实现 ,也可以通过空间电荷静电作用 (通过空间 )来实现。由分子轨道成键能分析指出 CO分子的强成键占据分子轨道 3σ和 1π的削弱是活化 CO的关键。     

The accuracy of hyperfine integrals in relativistic NMR computations based on the zeroth-order regular approximation

The accuracy of the hyperfine integrals obtained in relativistic NMR computations based on the zeroth–order regular approximation (ZORA) is investigated. The matrix elements of the Fermi contact operator and its relativistic analogs for s orbitals obtained from numerical nonrelativistic, ZORA, and four–component Hartree–Fock–Slater calculations on atoms are compared. It is found that the ZORA yields very accurate hyperfine integrals for the valence shells of heavy atoms, but performs rather poorly for the innermost core shells. Because the important observables of the NMR experiment—chemical shifts and spin–spin coupling constants—can be understood as valence properties it is concluded that ZORA computations represent a reliable tool for the investigations of these properties. On the other hand, absolute shieldings calculated with the ZORA might be substantially in error. Because applications to molecules have so far exclusively been based on basis set expansions of the molecular orbitals, ZORA hyperfine integrals obtained from atomic Slater-type basis set computations for mercury are compared with the accurate numerical values. It is demonstrated that the core part of the basis set requires functions with Slater exponents only up to 10⁴ in the case where errors in the hyperfine integrals of a few percent are acceptable.     

Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy

The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme-ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen-atom scheme to GB calculations, a buffer region within the frozen-atom zone is generated based on a user-definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 A for the frozen-atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand-receptor binding conformations and energies in a solvated environment.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Investigation of phosphorus atomization using high-resolution continuum source electrothermal atomic absorption spectrometry

The atomization of phosphorus in electrothermal atomic absorption spectrometry has been investigated using a high-resolution continuum source atomic absorption spectrometer and atomization from a graphite platform as well as from a tantalum boat inserted in a graphite tube. A two-step atomization mechanism is proposed for phosphorus, where the first step is a thermal dissociation, resulting in a fast atomization signal early in the atomization stage, and the second step is a slow release of phosphorus atoms from the graphite tube surface following the adsorption of molecular phosphorus at active sites of the graphite surface. Depending on experimental conditions only one of the mechanisms or both might be active. In the absence of a modifier and with atomization from a graphite or tantalum platform the second mechanism appears to be dominant, whereas in the presence of sodium fluoride as a modifier both mechanisms are observed. Intercalation of phosphorus into the graphite platform in the condensed phase has also been observed; this phosphorus, however, appears to be permanently trapped in the structure of the graphite and does not contribute to the absorption signal.     

Reduction of silver cation in the cavity of diaza-18-crown-6: A theoretical study

The structure and stability of diaza-18-crown-6 (1) complex with silver cation was studied by the density functional method with the PBE functional. The reduction of the cation in the macrocycle cavity was simulated and possible stability of the resulting van der Waals complex of the crown ether 1 with silver atom was analyzed. It is shown that, after electron capture, two equilibrium conformers of Ag⁺·1 give two structures locally stable with respect to the dissociation into the silver atom and the crown ether in its nearest equilibrium conformation. One of the neutral structures, that of the C _s symmetry, corresponds to a global minimum on the potential energy surface of the Ag⁰—1 system. It ensures the thermodynamic stability of the reduced complex with respect to dissociation. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 395–399, March, 2007.     

Analytic and numerical evidence from quantum field theory for the hyperscaling relation dv = 2Δ−γ in the d=3 ising model

The hyperscaling relationdv = 2 - (d=3) for the Ising model has been shown to follow from a constructive approach proposed by one of the authors (R.S.) of a relativistic theory of self-interacting Bosons in d space-time dimensions. We present evidence that the two assumptions made in this approach are valid: On a finite Euclidean (hyper-) cubical lattice in d dimensions the renormalization map from the bare to the renormalized parameters should have nonvanishing Jacobian everywhere. We show this analytically and numerically on the boundary set of the parameters. The numerical analysis involves Monte Carlo calculations in the region where the bare coupling constantg ₀ is infinite, giving the Ising model. The linear sizen of the lattice (with periodic boundary conditions) was taken to be 5, 6, and 10. There we also checked the second assumption saying that the correlation length for the Ising model is a monotonic function of the temperature. We also comment on the possible numbers of zeros of the Callan-Symanzik function of this theory.     

The minimax technique in relativistic Hartree-Fock calculations

Using the set of trial spinors and the Dirac-Coulomb Hamiltonian (H _DC) we discuss the role of the minimax theorem in relativistic Hartree-Fock calculations. In principle, the minimax theorem guarantees the occurrence of an upper bound. We also consider a scaling of the functionsu _i and discuss the condition to derive the relativistic hypervirial theorem; the variational procedure represented by the condition serves as an example of the minimax technique. Single zeta calculations onH ₂ ⁺ ,H ₂ and He are analysed. The effect of enlarging the basis is investigated for the He atom. The “upper bound” obtained by usingcoherent basis spinors differs from the result of the (random) linear variation using the kinetically balanced basis set by an amount which is at most of orderc ⁻⁴. Use of thecoherent basis set is advocated. An erratum to this article is available at .     

A discrete negative AKNS equation: generalized Cauchy matrix approach

Generalized Cauchy matrix approach is used to investigate a discrete negative Ablowitz–Kaup–Newell–Segur (AKNS) equation. Several kinds of solutions more than multi-soliton solutions to this equation are derived by solving determining equation set. Furthermore, applying an appropriate continuum limit we obtain a semidiscrete negative AKNS equation and after a second continuum limit we derive the nonlinear negative AKNS equation. The reductions to discrete, semi-discrete and continuous sine-Gordon equations are also discussed.