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

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.

Multiwfn: a multifunctional wavefunction analyzer.

We report re-optimization of a recently proposed long-range corrected (LC) hybrid density functional [J.-D. Chai and M. Head-Gordon, J. Chem. Phys., 2008, 128, 084106] to include empirical atom–atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent systems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density functionals, while for covalent systems and kinetics it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is significantly superior for non-bonded interactions, and very similar in performance for bonded interactions.

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Long-range corrected hybrid density functionals with damped atom–atom dispersion corrections

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecu- lar simulation program. It has been developed over the last three decades with a primary focus on molecules of bio- logical interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estima- tors, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numer- ous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

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CHARMM: the biomolecular simulation program.

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections Jeng-Da Chai ∗ and Martin Head-Gordon † Department of Chemistry, University of California and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA (Dated: June 14, 2008) We report re-optimization of a recently proposed long-range corrected (LC) hybrid density func- tionals [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)] to include empirical atom-atom dispersion corrections. The resulting functional, ωB97X-D yields satisfactory accuracy for thermochemistry, kinetics, and non-covalent interactions. Tests show that for non-covalent sys- tems, ωB97X-D shows slight improvement over other empirical dispersion-corrected density func- tionals, while for covalent systems and kinetics, it performs noticeably better. Relative to our previous functionals, such as ωB97X, the new functional is signiﬁcantly superior for non-bonded interactions, and very similar in performance for bonded interactions. I. INTRODUCTION Due to its favorable cost-to-performance ratio, Kohn- Sham density-functional theory (KS-DFT) [1, 2] has be- come the most popular electronic structure theory for large-scale ground-state systems [3–5]. Its extension for treating excited-state systems [6, 7], time-dependent den- sity functional theory (TDDFT), has also been developed to the stage where it is now very widely used. The essential ingredient of KS-DFT, the exchange- correlation energy functional E xc , remains unknown and needs to be approximated. Semi-local gradient-corrected density functionals, though successful in many applica- tions, lead to qualitative failures in some circumstances, where the accurate treatment of non-locality of exchange- correlation hole becomes crucial. These situations occur mostly in the asymptotic regions of molecular systems, such as spurious self-interaction eﬀects upon dissociation [8, 9] and dramatic failures for long-range charge-transfer excitations [10–12]. Widely used hybrid density function- als, like B3LYP [13, 14], do not qualitatively resolve these problems. These self-interaction errors can be qualitatively re- solved using the long-range corrected (LC) hybrid density functionals [15, 16, 18], which employ 100% Hartree-Fock (HF) exchange for long-range electron-electron interac- tions. This is accomplished by a partition of unity, using erf(ωr)/r for long-range (treated by HF exchange) and erfc(ωr)/r for short-range (treated by an exchange func- tional), with the parameter ω controlling the partition- ing. Over the past ﬁve years, the LC hybrid scheme has been attracting increasing attention [15] since its compu- tational cost is comparable with standard hybrid func- tionals [13]. However, LC functionals have tended to be inferior to the best hybrids for properties such as ther- mochemistry. ∗ Electronic † Author address: jdchai@berkeley.edu to whom correspondence should be addressed. Electronic address: mhg@cchem.berkeley.edu Recently we have improved the overall accuracy at- tainable with the LC functionals by using a systematic optimization procedure [18]. One important conclusion is that optimizing LC and hybrid functionals with identical numbers of parameters in their GGA exchange and cor- relation terms leads to noticeably better results for all properties using the LC form. The resulting LC func- tional is called ωB97. Further statistically signiﬁcant improvement results from re-optimizing the entire func- tional with one extra parameter corresponding to an ad- justable fraction of short-range exact exchange, deﬁning the ωB97X functional. Independent test sets covering thermochemistry and non-covalent interactions support these conclusions. However, problems associated with the lack of non-locality of the correlation hole, such as the lack of dispersion interactions (London forces), still remain, as the semi-local correlation functionals cannot capture long-range correlation eﬀects [19, 20]. There have been signiﬁcant eﬀorts to develop a frame- work that can account for long-range dispersion eﬀects within DFT. Zaremba and Kohn (ZK) [21] derived an exact expression for the second-order dispersion energy in terms of the exact density-density response functions of the two separate systems. To obtain a tractable non- local dispersion functional, Dobson and Dinite (DD) [22] made local density approximations to the ZK response functions. DD’s non-local correlation functional was ob- tained independently [23] by modifying the eﬀective den- sity deﬁned in the earlier work of Rapcewicz and Ashcroft Starting from the formally exact expression of KS- DFT, the adiabatic connection ﬂuctuation-dissipation theorem (ACFDT), for the ground-state exchange- correlation energy, Langreth and co-workers [25] devel- oped a so-called van der Waals density functional (vdW- DF) by making a series of reasonable approximations to yield a computationally tractable scheme. Recently, Becke and Johnson (BJ) developed a series of post-HF correlation models with a novel treatment for dispersion interactions based on the exchange-hole dipole moment [26]. The origin of dispersion claimed in the BJ models was recently questioned by Alonso, and A.

Long-Range Corrected Hybrid Density Functionals with Damped Atom-Atom Dispersion Corrections

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

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Holger Dachsel

Papers

Advances in methods and algorithms in a modern quantum chemistry program package