生物大分子体系量子化学计算方法新进展

本文就近年来报道的4 种研究生物大分子体系的量子化学计算方法(计算显微镜方法、定域分子轨道方法、线性标度半经验量子化学方法和并行算法) 作了较为详细的介绍, 并展望了该领域的研究前景。     

Quantifying the symmetry content of the electronic structure of molecules: molecular orbitals and the wave function

A scheme to quantify the symmetry content of the electronic wave function and molecular orbitals for arbitrary molecules is developed within the formalism of Continuous Symmetry Measures (CSMs). After defining the symmetry operation expectation values (SOEVs) as the key quantity to gauge the symmetry content of molecular wavefunctions, we present the working equations to be implemented in order to carry out real calculations using standard quantum chemistry software. The potentialities of a symmetry analysis using this new method are shown by means of some illustrative examples such as the changes induced in the molecular orbitals of a diatomic molecule by an electronegativity perturbation, the breaking of orbital symmetry along the dissociation path of the H(2) molecule, the changes in the molecular orbitals upon a geometrical distortion of the benzene molecule, and the inversion symmetry content in the different spin states of the [Fe(CH(3))(4)](2-) complex.     

Interaction-induced negative differential resistance in asymmetric molecular junctions

Combining insights from quantum chemistry calculations with master equations, we discuss a mechanism for negative differential resistance (NDR) in molecular junctions, operated in the regime of weak tunnel coupling. The NDR originates from an interplay of orbital spatial asymmetry and strong electron-electron interaction, which causes the molecule to become trapped in a nonconducting state above a voltage threshold. We show how the desired asymmetry can be selectively introduced in individual orbitals in, e.g., oligo(phenyleneethynylene)-type molecules by functionalization with a suitable side group, which is in linear conjugation to one end of the molecule and cross-conjugated to the other end.     

Electron Flow in Reaction Mechanisms—Revealed from First Principles

The “curly arrow” of Robinson and Ingold is the primary tool for describing and rationalizing reaction mechanisms. Despite this approach’s ubiquity and stellar success, its physical basis has never been clarified and a direct connection to quantum chemistry has never been found. Here we report that the bond rearrangements expressed by curly arrows can be directly observed in ab initio computations, as transformations of intrinsic bond orbitals (IBOs) along the reaction coordinate. Our results clarify that curly arrows are rooted in physical reality—a notion which has been challenged before—and show how quantum chemistry can directly establish reaction mechanisms in intuitive terms and unprecedented detail.     

STM studies of single molecules: molecular orbital aspects

As a fundamental and frequently referred concept in modern chemistry, the molecular orbital plays a vital role in the science of single molecules, which has become an active field in recent years. For the study of single molecules, scanning tunneling microscopy (STM) has been proven to be a powerful scientific technique. Utilizing specific distribution of the molecular orbitals at spatial, energy, and spin scales, STM can explore many properties of single molecule systems, such as geometrical configuration, electronic structure, magnetic polarization, and so on. Various interactions between the substrate and adsorbed molecules are also understood in terms of the molecular orbitals. Molecular engineering methods, such as mode-selective chemistry based on the molecular orbitals, and resonance tunneling between the molecular orbitals of the molecular sample and STM tip, have stimulated new advances of single molecule science.     

Relativistic quantum chemistry and rigorous variational analysis

A brief review of relativistic quantum chemistry is given here. Relativistic effects and their importance in chemistry are discussed. An outline of different theoretical aspects is presented. Aspects of variation techniques relevant to relativistic calculations are discussed in detail. These involve the derivation of min-max theorems for Dirac, Dirac-Hartree-Fock and Dirac-Coulomb calculations. The consequence of relativistic Hamiltonians being unbounded are also discussed for other lines of investigation. The upper bounds derived are physically interpreted. Sample Dirac-Hartree-Fock results for the Be atom, calculated using both STO and GTO bases for the nonrelativistic orbitals and the upper components of the relativistic orbitals, are given. The inadequacy of the so-called kinetically balanced basis set is discussed and illustrated with these results. The importance of the variational or dynamical balance and hence the merit of the LCAS-MS scheme is pointed out. The possibility of calculating quantum electrodynamical pair energy from relativistic configuration interaction calculations on a two-electron atom is discussed and exemplified. The present status of relativistic molecular calculations is briefly reviewed. Conclusions on the aspects of variational analysis and molecular calculations are enclosed.     

Orbital mechanism of upright CO activation on Fe(100)

The knowledge of bond activation forms a cornerstone for modern chemistry, wherein symmetry rules of electronic activation lie in the heart of bond activation. However, the question as to how a chemical bond is activated remains elusive. By taking CO activated on Fe(100), herein, we have resolved the long-standing fundamental question; we have found that excitations in the adsorbate feature the bond activation. We essentially have discovered contrasting electronic processes in respective σ and π electron systems of the adsorbed CO molecule. The σ electron system is involved in reversible hidden excitations/deexcitations between two occupied σ orbitals, whereas the π electron system is subject to irreversible π to π* excitations dispersed along the d-band region, which is coupled to the rotational 2π electron couplings depending on the strength of molecule-metal interactions. The σ excitations pertain to the Pauli repulsion mediated quantum nature with energy and entropy marked by the two energy levels, whereas the π to π* excitations fall into a new category of electronic excitations contributing to energy and entropy exchanges in a wide and continuous d-band region. The findings that the internal states of the adsorbate are excited and that fundamental connections between the frontier orbitals and low-lying orbitals are established as the molecule comes to the surface may open up new channels to realize more efficient bond activation and renew our thinking on probing the quantum mechanical nature of bond activation at surfaces with further possible impact on manipulation of orbital activation in femtochemistry and attochemistry.     

Vibrational frequencies and structural determination of tetraazidogermane

The vibrational frequencies and corresponding normal mode assignments of tetraazidogermane are examined theoretically using the Gaussian98 set of quantum chemistry codes. All normal modes were successfully assigned to one of seven types of motion predicted by a group theoretical analysis (N-N-N asymmetric stretch, N-N-N symmetric stretch, Ge-N stretch, N-N-N bend, Ge-N-N bend, N-Ge-N bend, and N-Ge-N-N torsion) utilizing the S(4) symmetry of the molecule. The molecular orbitals of Ge(N(3))(4) are examined.     

Determination of extremely localized molecular orbitals in the framework of density functional theory

Extremely localized molecular orbitals are rigorously localized on only a preselected set of atoms and do not have any tails outside the localization region. The importance of these orbitals lies in their ability to be transferred from one molecule to another one. A new algorithm to determine extremely localized molecular orbitals in the framework of the density functional theory method is presented. This could also be a valuable tool in the quantum mechanics/molecular mechanics methodology where localized molecular orbitals are used to describe covalent bonds across the frontier region. The present approach is used to build up the electron density of thymopentin, a polypeptide constituted by five residues, starting from extremely localized molecular orbitals determined on a set of model molecules. The results obtained confirm good transferability properties for these orbitals.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

猪胰岛素的活力位置的电子结构分析

本文采用负因子计数方法对猪胰岛素分子作了完整分子的量子化学计算,其中对矩阵元的计算采用EHMO方法。我们将前线轨道的概念推广为靠近Fermi能级的能量区域中的分子轨道,将局域于少数氨基酸残基上的前线轨道简称为活性轨道。计算结果表明,猪胰岛素70％的活力敏感位置上局域有活性轨道。对全部结果的分析说明猪胰岛素的活性轨道和生物活力之间存在某些内在联系,但不是一一对应关系;猪胰岛素的三级构象的变化可以引起电子结构的变化;相同种类的氨基酸残基在分子的不同位置上可以有不同的活性轨道能级和轨道分布。     

Convergence behavior of the density-matrix renormalization group algorithm for optimized orbital orderings

The density-matrix renormalization group algorithm has emerged as a promising new method in ab initio quantum chemistry. However, many problems still need to be solved before this method can be applied routinely. At the start of such a calculation, the orbitals originating from a preceding quantum chemical calculation must be placed in a specific order on a one-dimensional lattice. This ordering affects the convergence of the density-matrix renormalization group iterations significantly. In this paper, we present two approaches to obtain optimized orderings of the orbitals. First, we use a genetic algorithm to optimize the ordering with respect to a low total electronic energy obtained at a predefined stage of the density-matrix renormalization group algorithm with a given number of total states kept. In addition to that, we derive orderings from the one- and two-electron integrals of our test system. This test molecule is the chromium dimer, which is known to possess a complicated electronic structure. For this molecule, we have carried out calculations for the various orbital orderings obtained. The convergence behavior of the density-matrix renormalization group iterations is discussed in detail.     

Orbitals and the Interpretation of Photoelectron Spectroscopy and (e,2e) Ionization Experiments

Electron momentum spectroscopy, scanning tunneling microscopy, and photoelectron spectroscopy provide unique information about electronic structure, but their interpretation has been controversial. This essay discusses a framework for interpretation. Although this interpretation is not new, we believe it is important to present this framework in light of recent publications. The key point is that these experiments provide information about how the electron distribution changes upon ionization, not how electrons behave in the pre‐ionized state. Therefore, these experiments do not lead to a “selection of the correct orbitals” in chemistry and do not overturn the well‐known conclusion that both delocalized molecular orbitals and localized molecular orbitals are useful for interpreting chemical structure and dynamics. The two types of orbitals can produce identical total molecular electron densities and therefore molecular properties. Different types of orbitals are useful for different purposes.     

First experimental characterization of a non-nuclear attractor in a dimeric magnesium(I) compound

High-resolution X-ray diffraction data, coupled with theoretical calculations, are used to demonstrate the presence of a non-nuclear local maximum in the electron density of a dimeric Mg(I) molecule. This is the first time such a non-nuclear attractor (NNA) has been observed in a stable molecular species. Multipole modeling of the Mg(I) centers requires use of expansion/contraction (κ) coefficients taken from density functional theory (DFT), since accurate scattering factors for Mg(I) are not available. The model developed accurately accounts for the electron density in the Mg-Mg region and is in excellent agreement with directly calculated DFT data. Within the quantum theory of atoms in molecules (QTAIM), this molecule is not bound by a Mg-Mg bond but rather by two Mg-"pseudo-atom" bonds. The NNA is associated with a large region of negative Laplacian in the Mg-Mg internuclear region and arises from the overlap of 3s orbitals in this long, nonpolar "bond". The pseudoatomic basin associated with the NNA contains 0.8 electrons, which are highly delocalized and hence weakly bound. Possible implications of this unusual electronic structure for the chemistry of such molecules, including their use as excellent reducing agents, are discussed.     

Vibrational frequencies and structural determinations of maleonitrile

The vibrational frequencies and corresponding normal mode assignments of maleonitrile are examined theoretically using the GAUSSIAN98 set of quantum chemistry codes. All normal modes were successfully assigned to one of eight types of motion predicted by a group theoretical analysis (C triple bond N stretch, C=C stretch, C-C stretch, C-H stretch, C-H bend, C-C triple bond N bend, C-C triple bond N bend, C-C=C-C torsion) utilizing the C(2v) symmetry of the molecule. The molecular orbitals of maleonitrile are also examined.     

Vibrational frequencies and structure determination of silylgermane

The normal mode frequencies and corresponding vibrational assignments of silylgermane are examined theoretically using the GAUSSIAN 98 set of quantum chemistry codes. All normal modes were successfully assigned to one of seven types of motion predicted by a group theoretical analysis (Si-H stretch, Ge-H stretch, Si-Ge stretch, H-Si-H bend, H-Ge-H bend, SiH(3) wag/GeH(3) wag and Si-Ge torsion) utilizing the C(3v) symmetry of the molecule. Predicted infrared and Raman intensities are presented. Molecular orbitals are presented and bonding is examined in terms of the molecular orbitals.     

分子轨道成分的计算

量子化学文献中经常涉及到“分子轨道成分”概念, 然而相应的计算方法却没有普遍得到重视, 甚至存在严重误区. 专门对分子轨道中基函数的成分、原子轨道的成分以及原子的成分这些基本概念和计算方法进行了详细讨论, 通过实例分析比较了不同方法间的差异, 同时指出了计算和分析时需要注意的问题, 给出了在方法选择上的建议.     

Role of quantum chemical calculations in molecular biophysics with a historical perspective

We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures, and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy.     

Vibrational frequencies and structural determinations of urazole

The vibrational frequencies and corresponding normal mode assignments of urazole are examined theoretically using the Gaussian98 set of quantum chemistry codes. All normal modes were successfully assigned to one of eight types of motion (N--H stretch, C=O stretch, C--N stretch, N--N stretch, N--H bend, C=O bend, N--C--N bend, ring torsion) utilizing the C2 symmetry of the molecule. The molecular orbitals of urazole are examined. The simultaneous double inversion of the amine groups in urazole is also examined.     

Studies on the structural rule of boranes

The authors discuss the structural rule of different kinds of polyhedral boranes and propose a general topological formula for calculating the number of bonding molecular orbitals. In the case of single polyhedral boranes, results obtained from the formula are the same as those from the famous Wade rule. Futhermore, the formula can also be used to calculate the number of bonding molecular orbitals of joined-type polyhedral boranes. We have also made some quantum chemistry calculations to verify the concept that the number of bonding molecular orbitals of boranes can be determined by considering only the corresponding boron polyhedral frameworks.