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

Electrons moving through chiral molecules are selected according to their spin orientation and the helicity of the molecule, an effect known as chiral-induced spin selectivity (CISS). The underlying physical mechanism is not yet completely understood. To help elucidate this mechanism, a non-equilibrium Green's function method, combined with a Landauer approach and density functional theory, is applied to carbon helices contacted by gold electrodes, resulting in spin polarization of transmitted electrons. Spin polarization is also observed in the non-equilibrium electronic structure of the junctions. While this spin polarization is small, its sign changes with the direction of the current and with the handedness of the molecule. While these calculations were performed with a pure exchange-correlation functional, previous studies suggest that computationally more expensive hybrid functionals may lead to considerably larger spin polarization in the electronic structure. Thus, non-equilibrium spin polarization could be a key component in understanding the CISS mechanism.

Chiral-Induced Spin Selectivity and Non-equilibrium Spin Accumulation in Molecules and Interfaces: A First-Principles Study.

We present an approach for calculating local electric dipole moments for fragments of molecular or supramolecular systems. This is important for understanding chemical gating and solvent effects in nanoelectronics, atomic force microscopy, and intensities in infrared spectroscopy. Owing to the nonzero partial charge of most fragments, "naively" defined local dipole moments are origin-dependent. Inspired by previous work based on Bader's atoms-in-molecules (AIM) partitioning, we derive a definition of fragment dipole moments which achieves origin-independence by relying on internal reference points. Instead of bond critical points (BCPs) as in existing approaches, we use as few reference points as possible, which are located between the fragment and the remainder(s) of the system and may be chosen based on chemical intuition. This allows our approach to be used with AIM implementations that circumvent the calculation of critical points for reasons of computational efficiency, for cases where no BCPs are found due to large interfragment distances, and with local partitioning schemes other than AIM which do not provide BCPs. It is applicable to both covalently and noncovalently bound systems. © 2016 Wiley Periodicals, Inc.

Local electric dipole moments: A generalized approach.

A reliable first-principles description of singlet diradical character is essential for predicting nonlinear optical and magnetic properties of molecules. As diradical and closed-shell electronic structures differ in their distribution of single, double, triple, and aromatic bonds, modeling electronic diradical character requires accurate bond-length patterns, in addition to accurate absolute bond lengths. We therefore introduce structural diradical character, which we suggest as an additional measure for comparing first-principles calculations with experimental data. We employ this measure to identify suitable exchange-correlation functionals for predicting the bond length patterns and electronic diradical character of a biscobaltocene with the potential for photoswitchable nonlinear optical activity. Out of four popular approximate exchange-correlation functionals with different exact-exchange admixtures (BP86, TPSS, B3LYP, TPSSh), the two hybrid functionals TPSSh and B3LYP perform best for diradical bond length patterns, with TPSSh being best for the organometallic validation systems and B3LYP for the organic ones (for which the D3 dispersion correction was included). Still, none of the functionals is suitable for correctly describing relative bond lengths across the range of molecules studied, so that none can be recommended for predictive studies of (potential) diradicals without reservation. © 2018 Wiley Periodicals, Inc.

Structural diradical character

The efficiency of photochromic switches can be modified by attaching organic or organometallic groups to the photochromic core. We studied ferrocene-substituted dithienylethene switches differing by the size of the cycloalkene ring bridging the two thiophene groups. The results were compared with their chlorine-substituted counterparts and an ethynyl-ferrocene substituted switch published earlier by Guirado and co-workers. From the measured UV/Vis spectra, both ferrocene-substituted compounds were found to be considerably less likely to switch than the corresponding chlorine-substituted ones. Kohn–Sham density functional theory calculations suggested that this is due to a multitude of energetically close-lying excited states in the former, which may offer multiple pathways for excitation and relaxation, out of which only one leads to ring opening or closing. By contrast, the chlorine-substituted switches have one energetically more isolated state that is responsible for the switching. The increase in the available excited states in the ferrocene-substituted switches was attributed to mixing between orbitals from the ferrocene units and the π system of the bridge.

Limits of Molecular Dithienylethene Switches Caused by Ferrocenyl Substitution

Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc.

Carmen Herrmann

Papers

Chiral-Induced Spin Selectivity and Non-equilibrium Spin Accumulation in Molecules and Interfaces: A First-Principles Study.

Local electric dipole moments: A generalized approach.

Structural diradical character

Limits of Molecular Dithienylethene Switches Caused by Ferrocenyl Substitution

GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments