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

Many, if not most, redox reactions are coupled to proton transfers. This includes most common sources of chemical potential energy, from the bioenergetic processes that power cells to the fossil fuel combustion that powers cars. These proton-coupled electron transfer or PCET processes may involve multiple electrons and multiple protons, as in the 4 e–, 4 H+ reduction of dioxygen (O2) to water (eq 1), or can involve one electron and one proton such as the formation of tyrosyl radicals from tyrosine residues (TyrOH) in enzymatic catalytic cycles (eq 2). In addition, many multi-electron, multi-proton processes proceed in one-electron and one-proton steps. Organic reactions that proceed in one-electron steps involve radical intermediates, which play critical roles in a wide range of chemical, biological, and industrial processes. This broad and diverse class of PCET reactions are central to a great many chemical and biochemical processes, from biological catalysis and energy transduction, to bulk industrial chemical processes, to new approaches to solar energy conversion. PCET is therefore of broad and increasing interest, as illustrated by this issue and a number of other recent reviews.

/pdf/thermochemistry-of-proton-coupled-electron-transfer-reagents-v04esq6den.pdf

Thermochemistry of Proton-Coupled Electron Transfer Reagents and its Implications

Electronic excitation energies are determined using the CAM-B3LYP Coulomb-attenuated functional [T. Yanai et al. Chem. Phys. Lett. 393, 51 (2004)], together with a standard generalized gradient approximation (GGA) and hybrid functional. The degree of spatial overlap between the occupied and virtual orbitals involved in an excitation is measured using a quantity Lambda, and the extent to which excitation energy errors correlate with Lambda is quantified. For a set of 59 excitations of local, Rydberg, and intramolecular charge-transfer character in 18 theoretically challenging main-group molecules, CAM-B3LYP provides by far the best overall performance; no correlation is observed between excitation energy errors and Lambda, reflecting the good quality, balanced description of all three categories of excitation. By contrast, a clear correlation is observed for the GGA and, to a lesser extent, the hybrid functional, allowing a simple diagnostic test to be proposed for judging the reliability of a general excitation from these functionals--when Lambda falls below a prescribed threshold, excitations are likely to be in very significant error. The study highlights the ambiguous nature of the term "charge transfer," providing insight into the observation that while many charge-transfer excitations are poorly described by GGA and hybrid functionals, others are accurately reproduced.

/pdf/excitation-energies-in-density-functional-theory-an-ep38p1jml8.pdf

Excitation energies in density functional theory : an evaluation and a diagnostic test.

Time-Dependent Density Functional Theory (TD-DFT) has become the most widely-used theoretical approach to simulate the optical properties of both organic and inorganic molecules. In this contribution, we review TD-DFT benchmarks that have been performed during the last decade. The aim is often to pinpoint the most accurate or adequate exchangecorrelation functional(s). We present both the different strategies used to assess the functionals and the main results obtained in terms of accuracy. In particular, we discuss both vertical and adiabatic benchmarks and comparisons with both experimental and theoretical reference transition energies. More specific benchmarks (oscillator strengths, excited-state geometries, dipole moments, vibronic shapes, etc.) are summarized as well. V C 2013 Wiley Periodicals, Inc.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24438

TD-DFT benchmarks: A review

Reaction Rates of Isotopic Molecules

Free energy changes of each elementary step involved in the formal hydride transfer (H(-)(T)) reactions (including the so-called "one-step" H(-)(T) and "multistep" H(-)(T) mechanisms) of the reduced nicotinamide adenine dinucleotide (NADH) models with various cations and quinones (17) were investigated either by direct thermodynamic measurements or by calculations from thermochemical cycles. Based on the energetic data thus derived, combined with kinetic observations (particularly kinetic isotope effects), the mechanistic characteristics of the NADH-mediated reductions were systematically analyzed. Practical guidelines that resulted from these analyses suggest that a mutistep mechanism (e(-)-H(*) or e(-)-H(+)-e(-)) would be followed if the energy gap of the initial electron transfer [DeltaG(e(-)(T))] between the NADH model compound and the reducing substrate is considerably smaller than the empirical critical limit of 1.0 V for an endothermic e(-)(T). In contrast, if DeltaG(e(-)(T)) is much greater than 1.0 V, a concerted one-step H(-)(T) may take place. The guideline also suggests that a "hybrid" mechanism is possible if the DeltaG(e(-)(T)) is in an intermdiate situation.

Energetics of Multistep versus One-step Hydride Transfer Reactions of Reduced Nicotinamide Adenine Dinucleotide (NADH) Models with Organic Cations and p-Quinones.

Various density functionals are applied to a number of weakly bound intermolecular pi-pi charge-transfer (CT) complexes. Most functionals, including the recently developed mPWPW91 and mPW1PW91, grossly underestimate experimental excitation energies; good agreement is obtained only with the half-and-half hybrid BH&HLYP functional. PW91PW91 provides the best agreement with intermolecular distances measured in crystal, while the BH&HLYP values are about 0.1 A too long. Various hybrid functionals with nonlocal exchange correction provide binding energies that compare favorably with the experimental heats of formation measured in solution.

Performance assessment of density-functional methods for study of charge-transfer complexes.

Charge-transfer (CT) spectra of the π−π complexes formed by several aromatic amines and nitrogen heterocycles [acting as donors (Ds)] with acceptor A [A = tetracyanoethylene (TCNE), chloranil (CA)]

DFT Calculations and Spectral Measurements of Charge-Transfer Complexes Formed by Aromatic Amines and Nitrogen Heterocycles with Tetracyanoethylene and Chloranil

Charge-transfer (CT) spectra of the π−π complexes formed by several aromatic amines and nitrogen heterocycles [acting as donors (Ds)] with acceptor A [A = tetracyanoethylene (TCNE), chloranil (CA)]...

DFT Calculations and Spectral Measurements of Charge-Transfer Complexes Formed by Aromatic Amines and Nitrogen Heterocycles with Tetracyanoethylene and with Chloranil

Heterolytic and homolytic N-H bond dissociation energies of 4-substituted Hantzsch 2,6-dimethyl-1,4-dihydropyridines and the effect of one-electron transfer on the N-H bond activation.

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