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

/pdf/a-new-local-density-functional-for-main-group-1ipaurgil3.pdf

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

Toroidal carbon nanotubes (TCNTs), which have been evaluated for their potential applications in tera- hertz communication systems, provide a challenge of some magnitude from a purely scientific perspective. A design approach to TCNTs, as well as a clas- sification scheme, is presented based on the definition of the six hollow sec- tions that comprise the TCNT, slicing each of them to produce a (possibly creased) planar entity, and projecting that entity onto a graphene lattice. As a consequence of this folding approach, it is necessary to introduce five- and seven-membered rings as defect sites to allow the fusing together of the six segments into final symmetric TCNTs. This analysis permits the definition of a number of TCNT geometry families containing from 108 carbons up to much larger entities. Based on density functional theory (DFT) calculations, the energies of these structural candi- dates have been investigated and com- pared with (60)fullerene. The structures with the larger tube diameters are com- puted to be more stable than C60, whereas the smaller diameter ones are less stable, but may still be within syn- thetic reach. Computational studies reveal that, on account of the stiffness of the structures, the vibrational fre- quencies of characteristic low-frequen- cy modes decrease more slowly with in- creasing ring diameter than do the lowest optical excitation energies. It was found that this particular trend is true for the "breathing mode" vibra- tions when the diameter of the tubes is small, but not for more flexible toroi- dal nanotubes with larger diameters.

Optical and Vibrational Properties of Toroidal Carbon Nanotubes

Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of biomolecules. When small subsystems of large molecules such as active centers of enzymes are studied, quantum chemical calculations based on quantum mechanics/molecular mechanics (QM/MM) coupling schemes are a valuable means to interpret the spectra. The goal of this work is a methodological pilot study on how to selectively and thus efficiently extract certain vibrational information for extended molecular systems described by QM/MM methods. This is achieved by an extension of the mode tracking algorithm and a comparison with the partial Hessian diagonalization approach. After validating the methodology for the CO stretching vibration of 2-butanone and a delocalized CO stretch in acetylacetone, the stretching and bending modes of the CO ligand in CO myoglobin are tracked. Such systems represent an ideal application for mode tracking, because only a few strongly localized vibrations are sought for, while the large remainder of the molecule is of interest only as far as it affects these local vibrations. This influence is treated exactly by mode tracking.

QM/MM vibrational mode tracking.

Electronic communication through molecular bridges is important for different types of experiments, such as single-molecule conductance, electron transfer, superexchange spin coupling, and intramol...

https://pubs.acs.org/doi/pdf/10.1021/acs.jpca.9b05618

Electronic Communication as a Transferable Property of Molecular Bridges

We investigate the coherent electron transport properties of a selection of iron porphyrin complexes in their low-spin and high-spin states, binding the system to metallic electrodes with three different substitution patterns. We use a study of the local transmission through the complexes and their molecular orbitals to show the role of the various components of the molecular structure in mediating electron transport. While there are energies where the metal center and the axial ligands participate in transport, in the off-resonant energy range, these components simply form a scaffold, and the transport is dominated by transmission through the porphyrin macrocyle alone. This is still true when going from the low-spin to the high-spin state, except that now, an additional iron-centered MO contributes to transport in the formerly off-resonant region. It is found that while the choice of the exchange-correlation functional can strongly influence the quantitative results, our qualitative conclusions hold irrespective of the functional employed.

Local pathways in coherent electron transport through iron porphyrin complexes: A challenge for first-principles transport calculations

Common trends in communication through molecular bridges are ubiquitous in chemistry, such as the frequently observed exponential decay of conductance/electron transport and of exchange spin coupling with increasing bridge length, or the increased communication through a bridge upon closing a diarylethene photoswitch. For antiferromagnetically coupled diradicals in which two equivalent spin centers are connected by a closed-shell bridge, the molecular orbitals (MOs) whose energy splitting dominates the coupling strength are similar in shape to the MOs of the dithiolated bridges, which in turn can be used to rationalize conductance. Therefore, it appears reasonable to expect the observed common property trends to result from common orbital trends. We illustrate based on a set of model compounds that this assumption is not true, and that common property trends result from either different pairs of orbitals being involved, or from orbital energies not being the dominant contribution to property trends. For substituent effects, an effective modification of the π system can make a comparison difficult. © 2014 Wiley Periodicals, Inc.

Carmen Herrmann

Papers

Optical and Vibrational Properties of Toroidal Carbon Nanotubes

QM/MM vibrational mode tracking.

Electronic Communication as a Transferable Property of Molecular Bridges

Local pathways in coherent electron transport through iron porphyrin complexes: A challenge for first-principles transport calculations

Communication through molecular bridges: different bridge orbital trends result in common property trends.