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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute−solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonho...

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

A new implementation of the conductor-like screening solvation model (COSMO) in the GAUSSIAN94 package is presented. It allows Hartree−Fock (HF), density functional (DF) and post-HF energy, and HF and DF gradient calculations:  the cavities are modeled on the molecular shape, using recently optimized parameters, and both electrostatic and nonelectrostatic contributions to energies and gradients are considered. The calculated solvation energies for 19 neutral molecules in water are found in very good agreement with experimental data; the solvent-induced geometry relaxation is studied for some closed and open shell molecules, at HF and DF levels. The computational times are very satisfying:  the self-consistent energy evaluation needs a time 15−30% longer than the corresponding procedure in vacuo, whereas the calculation of energy gradients is only 25% longer than in vacuo for medium size molecules.

Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model

We present a new integral equation formulation of the polarizable continuum model (PCM) which allows one to treat in a single approach dielectrics of different nature: standard isotropic liquids, intrinsically anisotropic medialike liquid crystals and solid matrices, or ionic solutions. The present work shows that integral equation methods may be used with success also for the latter cases, which are usually studied with three-dimensional methods, by far less competitive in terms of computational effort. We present the theoretical bases which underlie the method and some numerical tests which show both a complete equivalence with standard PCM versions for isotropic solvents, and a good efficiency for calculations with anisotropic dielectrics.

A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics

Gaussian 09W, revision A. 02

In continuum solvation models the definition of a cavity that embeds the solute molecule leads to problems related to the portion of solute’s electronic charge lying outside its boundaries (charge tails). The correction strategies developed so far can be shown to work insufficiently, since they only correct the global charge defect, but lead to considerable local errors. The present paper will be focused on the theoretical and technical aspects of this problem, and it will present in detail a new method which allows a very refined treatment of solute’s charge tails in the outer space; some numerical results of solutes in water will be shown and discussed. As further analyses, the introduction of Pauli repulsion term will be considered, and the implications all these effects have on molecular properties, such as (hyper)polarizabilities, numerically evaluated. The new approach has been implemented within the framework of the polarizable continuum model (PCM).

Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries

The integral equation formalism (IEF) is a recent method (the grounds have been elaborated at the beginning of 1997) addressed to solve the electrostatic solvation problem at the QM level with the aid of apparent surface charges (ASC). IEF uses a new formalism of this problem, based on integral operators never used before in the chemical community and it manages to treat on the same footing linear isotropic solvent models, as well as anisotropic liquid crystals and ionic solutions. In this overview we emphasize the good performances of IEF at the lowest level of its potentialities, i.e. for isotropic solvents, as a new approach to compute solvation free energies and properties (dipole hyperpolarizabilities) of molecular solutes, as well as energy gradients for geometry optimization procedures. Finally we present a new IEF implementation of the nonequilibrium problem for electronic spectra which appears to be decidedly competitive with the previous more standard ASC formulations.

Benedetta Mennucci

Papers

Quantum mechanical continuum solvation models.

A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics

Gaussian 09W, revision A. 02

Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries

The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level