抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

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Revealing noncovalent interactions.

We introduce in this work a new approach to the identification of localized electronic groups in atomic and molecular systems. Our approach is based on local behavior of the Hartree–Fock parallel‐spin pair probability and is completely independent of unitary orbital transformations. We derive a simple ‘‘electron localization function’’ (ELF) which easily reveals atomic shell structure and core, binding, and lone electron pairs in simple molecular systems as well.

A Simple Measure of Electron Localization in Atomic and Molecular-Systems

I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865

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Conceptual density functional theory.

Atoms in molecules

The theory of molecular structure determined by the gradient vector field of the charge density ρ identifies the set of atomic interactions present in a molecule. The interactions so defined are characterized in terms of the properties of the Laplacian of the charge density ∇2ρ(r). A scalar field is concentrated in those regions of space where its Laplacian is negative and depleted in those where it is positive. An expression derived from the quantum mechanical stress tensor relates the sign of the Laplacian of ρ to the relative magnitudes of the local contributions of the potential and kinetic energy densities to their virial theorem averages. By obtaining a map of those regions where ∇2ρ(r) 0. The mechanics are characterized by the relatively large value of the kinetic energy, particularly the component parallel to the interaction line. In the closed‐shell interactions, the regions of dominant potential energy contributions are separately localized within the boundaries of each of the interacting atoms or molecules. In the shared interactions, a region of low potential energy is contiguous over the basins of both of the interacting atoms. The problem of further classifying a given interaction as belonging to a bound or unbound state of a system is also considered, first from the electrostatic point of view wherein the regions of charge concentration as determined by the Laplacian of ρ are related to the forces acting on the nuclei. This is followed by and linked to a discussion of the energetics of interactions in terms of the regions of dominant potential and kinetic energy contributions to the virial as again determined by the Laplacian of ρ. The properties of the Laplacian of the electronic charge thus yield a unified view of atomic interactions, one which incorporates the understandings afforded by both the Hellmann–Feynman and virial theorems.

The characterization of atomic interactions

A new derivation of the Born-Oppenheimer separation of electronic and nuclear motion is presented. The arguments used differ from those in earlier works in not being specially designed for molecules. Instead they aim at an intuitive understanding of the qualitative behavior of the low energy bound states of any, real or hypothetical, Coulomb interacting system of particles. The virial theorem is the starting point of the discussion. After a brief explanation of how it can be used to understand atomic structure it is applied to molecules. It is found that coordinates of collective and individual motion are natural coordinates for the approximate separation, rather than nuclear and electronic. It is also shown that it is the form of the interaction between the particles that is responsible for the separation; the smallness of m/sub el//M/sub Nu/ is irrelevant.

The physics of the born–oppenheimer approximation

The force acting on a spinning sphere moving in a rarefied gas is calculated. It is found to have three contributions with different directions. The transversal contribution is of opposite directio ...

Force on a spinning sphere moving in a rarefied gas

This paper reviews canonical and other quantization methods, gives a quantization rule that gives results that agree with those obtained by direct transformation of the Laplacian, and thus expresses the correct Hamiltonian operator in terms of proper conjugate momentum operators. It gives applications to a number of curvilinear coordinates, introduces the class of independent coordinates, presents generalized Jacobi coordinates, and discusses the molecular vibration‐rotation Hamiltonian.

Quantization and independent coordinates

A semiclassical RKR‐like inversion procedure for determining a repulsive diatomic molecule potential energy curve from structured bound–continuum transition intensity data is derived and tested. The method presumes a knowledge of the (attractive) initial state potential well and of the energy and vibrational assignment of the absorbing or emitting level. Its application to a structured emission continuum of NaK observed by Breford and Engelke [Chem. Phys. Lett. 53, 282 (1979)] yields a potential energy curve which is incompatible with other known properties of this system, a result which confirms the suggestion of Kato and Noda [J. Chem. Phys. 73, 4940 (1980)] that the original assignment of the initial state for this spectrum is in error.

Hanno Essén

Papers

The characterization of atomic interactions

The physics of the born–oppenheimer approximation

Force on a spinning sphere moving in a rarefied gas

Quantization and independent coordinates

An RKR‐like inversion procedure for bound–continuum transition intensities