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

We present a new local density functional, called M06-L, for main-group and transition element thermochemistry, thermochemical kinetics, and noncovalent interactions. The functional is designed to capture the main dependence of the exchange-correlation energy on local spin density, spin density gradient, and spin kinetic energy density, and it is parametrized to satisfy the uniform-electron-gas limit and to have good performance for both main-group chemistry and transition metal chemistry. The M06-L functional and 14 other functionals have been comparatively assessed against 22 energetic databases. Among the tested functionals, which include the popular B3LYP, BLYP, and BP86 functionals as well as our previous M05 functional, the M06-L functional gives the best overall performance for a combination of main-group thermochemistry, thermochemical kinetics, and organometallic, inorganometallic, biological, and noncovalent interactions. It also does very well for predicting geometries and vibrational frequencies. Because of the computational advantages of local functionals, the present functional should be very useful for many applications in chemistry, especially for simulations on moderate-sized and large systems and when long time scales must be addressed. © 2006 American Institute of Physics. DOI: 10.1063/1.2370993

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A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions.

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Density functional theory for transition metals and transition metal chemistry

Thiolate-protected gold surfaces and interfaces, relevant for self-assembled monolayers of organic molecules on gold, for passivated gold nanoclusters and for molecule-gold junctions, are archetypal systems in various fields of current nanoscience research, materials science, inorganic chemistry and surface science. Understanding this interface at the nanometre scale is essential for a wide range of potential applications for site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, functionalization of gold surfaces for sensing, molecular recognition and molecular electronics, and gold nanoparticle catalysis. During the past five years, considerable experimental and theoretical advances have furthered our understanding of the molecular structure of the gold-sulfur interface in these systems. This Review discusses the recent progress from the viewpoint of theory and computations, with connections to relevant experiments.

The gold–sulfur interface at the nanoscale

Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of molecular systems. When large molecules are studied, quantum chemical calculations are used to interpret the spectra. In many cases, experimentally driven questions are related to specific regions of a vibrational spectrum, so that an assignment is only required for a subset of vibrations. This holds true in particular for biomolecules, inorganic compounds which are stabilized by many bulky ligands, or other extended systems. In standard quantum chemical calculations of the vibrational spectrum, all normal modes and frequencies of the molecule under study are determined. However, the selective calculation of only relevant information can be made much more efficient by using mode-selective techniques as provided by the mode-tracking algorithm. A critical point for the performance of the mode-tracking scheme is the preparation of a guess vibration, which is then iteratively refined. The guess defines the scientific problem which is to be studied. Various examples are presented to highlight this aspect and the features of the mode-tracking algorithm in general.

Finding a Needle in a Haystack: Direct Determination of Vibrational Signatures in Complex Systems

We report transport measurements on tunable single-molecule junctions of the organic perchlorotrityl radical molecule, contacted with gold electrodes at low temperature. The current-voltage characteristics of a subset of junctions shows zero-bias anomalies due to the Kondo effect and in addition elevated magnetoresistance (MR). Junctions without Kondo resonance reveal a much stronger MR. Furthermore, we show that the amplitude of the MR can be tuned by mechanically stretching the junction. On the basis of these findings, we attribute the high MR to an interference effect involving spin-dependent scattering at the metal-molecule interface and assign the Kondo effect to the unpaired spin located in the center of the molecule in asymmetric junctions.

Interplay between Magnetoresistance and Kondo Resonance in Radical Single-Molecule Junctions.

Lithium Selectivity of Crown Ethers: The Effect of Heteroatoms and Cavity Size

Designing and understanding spin coupling within and between molecules is important for, e.g., nanoscale spintronics, magnetic materials, catalysis, and biochemistry. We review a recently developed approach to analyzing spin coupling in terms of local pathways, which allows to evaluate how much each part of a structure contributes to coupling, and present examples of how first-principles electronic structure theory can help to understand spin coupling in molecular systems which show the potential for photo- or redoxswitching, or where the ground state is stabilized with respect to spin flips by adding unpaired spins on a bridge connecting two spin centers. Finally, we make a connection between spin coupling and conductance through molecular bridges.

Designing and Understanding Building Blocks for Molecular Spintronics

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ijch.202200053

Carmen Herrmann

Papers

Finding a Needle in a Haystack: Direct Determination of Vibrational Signatures in Complex Systems

Interplay between Magnetoresistance and Kondo Resonance in Radical Single-Molecule Junctions.

Lithium Selectivity of Crown Ethers: The Effect of Heteroatoms and Cavity Size

Designing and Understanding Building Blocks for Molecular Spintronics

Common Trends of Chiral Induced Spin Selectivity and Optical Dichroism with Varying Helix Pitch: A First‐Principles Study