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

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

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The HITRAN 2008 molecular spectroscopic database

https://th.fhi-berlin.mpg.de/site/uploads/Publications/CPC-180-2175-2009.pdf

Ab Initio Molecular Simulations with Numeric Atom-Centered Orbitals

The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties associated with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a molecule can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addition, 18F has been established as a useful positron emitting isotope for use with in vivo imaging technology that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compounds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug molecules and applications in po...

Applications of Fluorine in Medicinal Chemistry

The concept of isosterism between relatively simple chemical entities was originally contemplated by James Moir in 1909, a notion further refined by H. G. Grimm’s hydride displacement law and captured more effectively in the ideas advanced by Irving Langmuir based on experimental observations. Langmuir coined the term “isostere” and, 18 years in advance of its actual isolation and characterization, predicted that the physical properties of the then unknown ketene would resemble those of diazomethane. The emergence of bioisosteres as structurally distinct compounds recognized similarly by biological systems has its origins in a series of studies published byHans Erlenmeyer in the 1930s, who extended earlier work conducted by Karl Landsteiner. Erlenmeyer showed that antibodies were unable to discriminate between phenyl and thienyl rings or O, NH, and CH2 in the context of artificial antigens derived by reacting diazonium ions with proteins, a process that derivatized the ortho position of tyrosine, as summarized in Figure 1 The term “bioisostere” was introduced by Harris Friedman in 1950 who defined it as compounds eliciting a similar biological effect while recognizing that compounds may be isosteric but not necessarily bioisosteric. This notion anticipates that the application of bioisosterism will depend on context, relying much less on physicochemical properties as the underlying principle for biochemical mimicry. Bioisosteres are typically less than exact structural mimetics and are often more alike in biological rather than physical properties. Thus, an effective bioisostere for one biochemical application may not translate to another setting, necessitating the careful selection and tailoring of an isostere for a specific circumstance. Consequently, the design of bioisosteres frequently introduces structural changes that can be beneficial or deleterious depending on the context, with size, shape, electronic distribution, polarizability, dipole, polarity, lipophilicity, and pKa potentially playing key contributing roles in molecular recognition and mimicry. In the contemporary practice of medicinal chemistry, the development and application of bioisosteres have been adopted as a fundamental tactical approach useful to address a number of aspects associated with the design and development of drug candidates. The established utility of bioisosteres is broad in nature, extending to improving potency, enhancing selectivity, altering physical properties, reducing or redirecting metabolism, eliminating or modifying toxicophores, and acquiring novel intellectual property. In this Perspective, some contemporary themes exploring the role of isosteres in drug design are sampled, with an emphasis placed on tactical applications designed to solve the kinds of problems that impinge on compound optimization and the long-term success of drug candidates. Interesting concepts that may have been poorly effective in the context examined are captured, since the ideas may have merit in alternative circumstances. A comprehensive cataloging of bioisosteres is beyond the scope of what will be provided, although a synopsis of relevant isosteres of a particular functionality is summarized in a succinct fashion in several sections. Isosterism has also found productive application in the design and optimization of organocatalysts, and there are several examples in which functional mimicry established initially in a medicinal chemistry setting has been adopted by this community.

Synopsis of some recent tactical application of bioisosteres in drug design.

The family of correlation consistent polarized valence basis sets (cc-pVXZ) has been extended to include sextuple zeta sets (cc-pV6Z) for the atoms boron through neon. Potential energy functions have been calculated with these sets for the electronic ground states of N2 and HF using a number of correlated wave functions: MP2, MP3, MP4, CCSD, CCSD(T) and CAS+1+2. Spectroscopic constants have been calculated for each level of theory and have been compared with experiment. Combining these results with those of prior studies, complete basis set limits have been estimated for Ee, De and re. It is found that the cc-pV6Z basis sets yield dissociation energies that are within 0.6–0.8 kcal mol−1 (N2) and 0.1 kcal mol−1 (HF) of the estimated CBS limits. Adding core-core and core-valence contributions to the CCSD(T) CBS limits yields De's that are within 0.1 kcal mol−1 of the experimental values.

Gaussian basis sets for use in correlated molecular calculations. VI. Sextuple zeta correlation consistent basis sets for boron through neon

In recent literature, some authors claim to have successfully applied density functional theory (DFT) methods to the attractive interaction between rare-gas atoms. In this note, we make a critical survey of these works and come to the conclusion that, in contrast to the claims made, state-of-the-art DFT methods are incapable of accounting for dispersion effects in a quantitative way.

A critical note on density functional theory studies on rare-gas dimers

Standard and augmented correlation consistent sextuple zeta (cc-pV6Z and aug-cc-pV6Z) basis sets have been determined for the second-row atoms aluminum through argon. Using these sets, dissociation energies and spectroscopic constants for the ground states of HCl, PN, and P2 have been calculated using several theoretical methods, including Moller–Plesset perturbation theory, coupled cluster theory, and multireference configuration interaction theory (MRCI). The aug-cc-pV6Z and cc-pV6Z sets yield dissociation energies that are estimated to be within 0.1–0.2 kcal/mol of the complete basis set limit for HCl and within 1–1.5 kcal/mol for PN and P2. The MRCI and CCSD(T) methods are found to give the most consistently reliable results for the spectroscopic constants of all three species investigated. Use of the counterpoise correction improves the convergence behavior of the spectroscopic constants with increasing n for both the cc-pVnZ and aug-cc-pVnZ sets and should allow more accurate estimates of the complete basis set limit to be predicted. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 205–221, 2000

Gaussian basis sets for use in correlated molecular calculations. VIII. Standard and augmented sextuple zeta correlation consistent basis sets for aluminum through argon

We have performed a variety of high-level electronic structure calculations on two moderately sized organic molecules and found considerable sensitivity of the intramolecular potential energy surface to the method employed. The gas-phase structure of tyrosine-glycine varies qualitatively between B3LYP and MP2 optimizations, producing different close contacts between the tyrosine ring and the glycine moiety. The relative energies of the 2-(acetylamino)benzamide conformations found in its two polymorphs can vary by over 20 kJ mol -1 between MP2 and B3LYP calculations, using the same basis set. It is shown by a novel analysis that the intramolecular equivalent of basis set superposition error competes with the errors in the intramolecular dispersion in causing this sensitivity.

Tanja van Mourik

Papers

Gaussian basis sets for use in correlated molecular calculations. VI. Sextuple zeta correlation consistent basis sets for boron through neon

A critical note on density functional theory studies on rare-gas dimers

Gaussian basis sets for use in correlated molecular calculations. VIII. Standard and augmented sextuple zeta correlation consistent basis sets for aluminum through argon

Molecular conformations and relative stabilities can be as demanding of the electronic structure method as intermolecular calculations

Insufficient description of dispersion in B3LYP and large basis set superposition errors in MP2 calculations can hide peptide conformers