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

The fascinating story of olefin (or alkene) metathesis (eq
1) began almost five decades ago, when Anderson and
Merckling reported the first carbon-carbon double-bond
rearrangement reaction in the titanium-catalyzed polymerization of norbornene. Nine years later, Banks and Bailey reported “a new disproportionation reaction . . . in which olefins are converted to homologues of shorter and longer carbon chains...”. In 1967, Calderon and co-workers named this metal-catalyzed redistribution of carbon-carbon double bonds olefin metathesis, from the Greek word “μeτάθeση”, which means change of position. These contributions have since served as the foundation for an amazing research field, and olefin metathesis currently represents a powerful transformation in chemical synthesis, attracting a vast amount of interest both in industry and academia.

https://core.ac.uk/download/pdf/4884240.pdf

Ruthenium-based heterocyclic carbene-coordinated olefin metathesis catalysts.

: 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

Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local second-order Moller–Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. This performance is achieved through a utilization of the pseudospectral approximation and several levels of parallelization. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition-metal-containing systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling. The article describes the historical and new features of Jaguar, such as improved parallelization of many modules, innovations in ab initio pKa prediction, and new semiempirical corrections for nondynamic correlation errors in DFT. Jaguar applications in drug discovery, materials science, force field parameterization, and other areas of computational research are reviewed. Timing benchmarks and other results obtained from the most recent Jaguar code are provided. The article concludes with a discussion of challenges and directions for future development of the program. © 2013 Wiley Periodicals, Inc.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/qua.24481

Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences

Ligands, especially phosphines and carbenes, can play a key role in modifying and controlling homogeneous organometallic catalysts, and they often provide a convenient approach to fine-tuning the p...

/pdf/computational-ligand-descriptors-for-catalyst-design-esg5fxjprp.pdf

Computational Ligand Descriptors for Catalyst Design

Building ligand knowledge bases for organometallic chemistry: Computational description of phosphorus(III)-donor ligands and the metal–phosphorus bond

We have used dispersion-corrected DFT (DFT-D) together with solvation to examine possible mechanisms for reaction of PhX (X = Cl, Br, I) with Pd(PtBu3)2 and compare our results to recently published kinetic data (F. Barrios-Landeros, B. P. Carrow and J. F. Hartwig, J. Am. Chem. Soc., 2009, 131, 8141–8154).1 The calculated activation free energies agree near-quantitatively with experimentally observed rate constants.

Accurate modelling of Pd(0) + PhX oxidative addition kinetics

DFT calculations have been used to explore the full catalytic cycle of the Suzuki–Miyaura coupling between PhBr and PhB(OH)3− with four different palladium monophosphine catalysts derived from Pd(PMe3)2, Pd(P(CF3)3)2, Pd(PPh3)2 and Pd(PtBu3)2. All the steps of the reaction have been studied and the differences between the ligands have been analyzed; special attention has been devoted to the ligand dissociation and catalyst regeneration processes, as well as the typical cross-coupling steps of oxidative addition, transmetallation and reductive elimination. Multiple linear regressions of the computationally derived energy barriers have been carried out in order to quantify the ligand effects of the different phosphines on the key steps of the reaction. These ligand effects, relevant to the catalytic activity, are described in terms of the phosphine donor/acceptor and steric features. The regression models show that oxidative addition is mainly governed by electronic effects whereas the transmetallation and the reductive elimination processes are controlled by a mixture of both ligand effects. For transmetallation, electron-withdrawing ligands lower the energy barrier.

Natalie Fey

Papers

Computational Ligand Descriptors for Catalyst Design

Building ligand knowledge bases for organometallic chemistry: Computational description of phosphorus(III)-donor ligands and the metal–phosphorus bond

Accurate modelling of Pd(0) + PhX oxidative addition kinetics

A computational study of phosphine ligand effects in Suzuki-Miyaura coupling

Expansion of the Ligand Knowledge Base for Monodentate P-Donor Ligands (LKB-P)†