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 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

Bull. Chem. Soc. Jpn. への投稿のすすめ

We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.

Automated exploration of the low-energy chemical space with fast quantum chemical methods

Intersystem crossing (ISC), formally forbidden within nonrelativistic quantum theory, is the mechanism by which a molecule changes its spin state. It plays an important role in the excited state decay dynamics of many molecular systems and not just those containing heavy elements. In the simplest case, ISC is driven by direct spin–orbit coupling between two states of different multiplicities. This coupling is usually assumed to remain unchanged by vibrational motion. It is also often presumed that spin-allowed radiationless transitions, i.e. internal conversion, and the nonadiabatic coupling that drives them, can be considered separately from ISC and spin–orbit coupling owing to the vastly different time scales upon which these processes are assumed to occur. However, these assumptions are too restrictive. Indeed, the strong mixing brought about by the simultaneous presence of nonadiabatic and spin–orbit coupling means that often the spin, electronic, and vibrational dynamics cannot be described independe...

Spin-Vibronic Mechanism for Intersystem Crossing

Systematic reaction path exploration revealed the entire mechanism of Knowles's light-promoted catalytic intramolecular hydroamination. Bond formation/cleavage competes with single electron transfer (SET) between the catalyst and substrate. These processes are described by adiabatic processes through transition states in an electronic state and non-radiative transitions through the seam of crossings (SX) between different electronic states. This study determined the energetically favorable SET path by introducing a practical computational model representing SET as non-adiabatic transitions via SXs between substrate's potential energy surfaces for different charge states adjusted based on the catalyst's redox potential. Calculations showed that the reduction and proton shuttle process proceeded concertedly. Also, the relative importance of SET paths (giving the product and leading back to the reactant) varies depending on the catalyst's redox potential, affecting the yield.

/pdf/oxidation-and-reduction-pathways-in-the-knowles-2neplu9t.pdf

Oxidation and Reduction Pathways in the Knowles Hydroamination via a Photoredox-Catalyzed Radical Reaction.

Global Reaction Route Mapping Strategy: A Tool for Finding New Chemistry in Computers

The interactive chemical reaction platform, SCAN, is developed for analyzing the chemical reaction path network.

https://pubs.rsc.org/en/content/articlepdf/2023/dd/d3dd00026e

Searching chemical action and network (SCAN): an interactive chemical reaction path network platform

Switching the relaxation pathway by steric effects in conjugated dienes

The ligand screening process, in which an optimal ligand for a reaction of interest is identified from an enormous and diverse set of candidate molecules, is of particular importance in the development of transition metal catalysis. Conventionally, this process has been performed by experimental trial-and-error cycles, which require significant time and resources. Herein, we report a novel strategy called “virtual-ligand-assisted (VLA) screening” that enables practical in silico ligand screening based on the transition state theory. We developed a virtual ligand, PCl*3, which parameterizes both the electronic and steric effects of monodentate phosphorus(III) ligands in quantum chemical calculations, and used it to assess how these effects perturb the energy profile of a reaction. This parameter-based ligand screening approach allowed us to identify the optimal electronic and steric effects for a reaction of interest, thereby affording guiding principles for rational ligand design. The VLA screening strategy was demonstrated for the selectivity-determining step of the rhodium-catalyzed hydroformylation of a terminal olefin, and phosphorus(III) ligands with potentially high linear or branched selectivities were designed. These findings indicate that VLA screening is a promising approach for streamlining the ligand screening process.

Yu Harabuchi

Papers

Oxidation and Reduction Pathways in the Knowles Hydroamination via a Photoredox-Catalyzed Radical Reaction.

Global Reaction Route Mapping Strategy: A Tool for Finding New Chemistry in Computers

Searching chemical action and network (SCAN): an interactive chemical reaction path network platform

Switching the relaxation pathway by steric effects in conjugated dienes

Virtual-Ligand-Assisted Screening Strategy to Discover Enabling Ligands for Transition Metal Catalysis