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

▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several are...

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Proton-Coupled Electron Transfer

Azobenzene undergoes trans → cisisomerization when irradiated with light tuned to an appropriate wavelength. The reverse cis →transisomerization can be driven by light or occurs thermally in the dark. Azobenzene's photochromatic properties make it an ideal component of numerous molecular devices and functional materials. Despite the abundance of application-driven research, azobenzene photochemistry and the isomerization mechanism remain topics of investigation. Additional substituents on the azobenzene ring system change the spectroscopic properties and isomerization mechanism. This critical review details the studies completed to date on the 3 main classes of azobenzene derivatives. Understanding the differences in photochemistry, which originate from substitution, is imperative in exploiting azobenzene in the desired applications.

Photoisomerization in different classes of azobenzene

: 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

The photoisomerization of azobenzene has been known for almost 75 years but only recently has this process been widely applied to biological systems. The central challenge of how to productively couple the isomerization process to a large functional change in a biomolecule has been met in a number of instances and it appears that effective photocontrol of a large variety of biomolecules may be possible. This critical review summarizes key properties of azobenzene that enable its use as a photoswitch in biological systems and describes strategies for using azobenzene photoswitches to drive functional changes in peptides, proteins, nucleic acids, lipids, and carbohydrates (192 references).

Azobenzene photoswitches for biomolecules.

In this paper the authors address the problem of internal consistency in trajectory surface hopping methods, i.e., the requirement that the fraction of trajectories running on each electronic state equals the probabilities computed by the electronic time-dependent Schrodinger equation, after averaging over all trajectories. They derive a formula for the hopping probability in Tully’s “fewest switches” spirit that would yield a rigorously consistent treatment. They show the relationship of Tully’s widely used surface hopping algorithm with the “exact” prescription that cannot be applied when running each trajectory independently. They also bring out the connection of the consistency problem with the coherent propagation of the electronic wave function and the artifacts caused by coherent Rabi-type oscillations of the state probabilities in weak coupling regimes. A real molecule (azobenzene) and two ad hoc models serve as examples to illustrate the above theoretical arguments. Following a proposal by Truhla...

Critical appraisal of the fewest switches algorithm for surface hopping

The great importance of ultrafast phenomena in photochemistry and photobiology has made dynamics simulations an essential methodology in these areas. In this work, we present the N ewton -X program package containing a new implementation of a direct dynamics approach to perform adiabatic (Born–Oppenheimer) and nonadiabatic simulations. The nonadiabatic dynamics is based on Tully's surface hopping approach. The program has been developed with the aim of (1) to create a flexible tool to be used in connection with a multitude of third-party electronic-structure program packages and (2) to provide the most common options for excited-state dynamics simulations. Benchmark calculations on the nonadiabatic dynamics are presented for the methaniminium, butatriene and pentadieniminium cations. The simulation of UV absorption spectra is presented for the methaniminium cation and pyrazine.

The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems

The Newton-X program is a general-purpose program package for excited-state molecular dynamics, including nonadiabatic methods. Its modular design allows Newton-X to be easily linked to any quantum-chemistry package that can provide excited-state energy gradients. At the current version, Newton-X can perform nonadiabatic dynamics using Columbus, Turbomole, Gaussian, and Gamess program packages with multireference configuration interaction, multiconfigurational self-consistent field, time-dependent density functional theory, and other methods. Nonadiabatic dynamics simulations with a hybrid combination of methods, such as Quantum-Mechanics/Molecular-Mechanics, are also possible. Moreover, Newton-X can be used for the simulation of absorption and emission spectra. The code is distributed free of charge for noncommercial and nonprofit uses at www.newtonx.org. WIREs Comput Mol Sci 2014, 4:26–33. doi: 10.1002/wcms.1158



The authors have declared no conflicts of interest in relation to this article.



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Newton-X: a surface-hopping program for nonadiabatic molecular dynamics

We describe a new method for the simulation of excited state dynamics, based on classical trajectories and surface hopping, with direct semiempirical calculation of the electronic wave functions and potential energy surfaces ~DTSH method!. Semiempirical self-consistent-field molecular orbitals ~SCF MO’s! are computed with geometry-dependent occupation numbers, in order to ensure correct homolytic dissociation, fragment orbital degeneracy, and partial optimization of the lowest virtuals. Electronic wave functions are of the MO active space configuration interaction ~CI! type, for which analytic energy gradients have been implemented. The time-dependent electronic wave function is propagated by means of a local diabatization algorithm which is inherently stable also in the case of surface crossings. The method is tested for the problem of excited ethylene nonadiabatic dynamics, and the results are compared with recent quantum mechanical calculations. © 2001 American Institute of Physics. @DOI: 10.1063/1.1376633#

Direct semiclassical simulation of photochemical processes with semiempirical wave functions

In this paper we set up a method called overlap decoherence correction (ODC) to take into account the quantum decoherence effect in a surface hopping framework. While keeping the standard surface hopping approach based on independent trajectories, our method allows to account for quantum decoherence by evaluating the overlap between frozen Gaussian wavepackets, the time evolution of which is obtained in an approximate way. The ODC scheme mainly depends on the parameter σ, which is the Gaussian width of the wavepackets. The performance of the ODC method is tested versus full quantum calculations on three model systems, and by comparison with full multiple spawning (FMS) results for the S(1)→S(0) decay in the azobenzene molecule.

Giovanni Granucci

Papers

Critical appraisal of the fewest switches algorithm for surface hopping

The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems

Newton-X: a surface-hopping program for nonadiabatic molecular dynamics

Direct semiclassical simulation of photochemical processes with semiempirical wave functions

Including quantum decoherence in surface hopping.