Benedetta Mennucci

Bio: Benedetta Mennucci is an academic researcher from University of Pisa. The author has contributed to research in topics: Polarizable continuum model & Solvation. The author has an hindex of 75, co-authored 349 publications receiving 48307 citations. Previous affiliations of Benedetta Mennucci include University of Seville & Hungarian Academy of Sciences.

On the Metric of Charge Transfer Molecular Excitations: A Simple Chemical Descriptor.

Abstract: A new index is defined with the aim of further exploring the metric of excited electronic states in the framework of the time-dependent density functional theory. This descriptor, called Δr, is based on the charge centroids of the orbitals involved in the excitations and can be interpreted in term of the hole–electron distance. The tests carried out on a set of molecules characterized by a significant number of charge-transfer excitations well illustrate its ability in discriminating between short (Δr ≤ 1.5 A) and long-range (Δr ≥ 2.0 A) excitations. On the basis of the well-known pitfalls of TD-DFT, its values can be then associated to the functional performances in reproducing different type of transitions and allow for the definition of a “trust radius” for GGA and hybrid functionals. The study of other systems, including some well-known difficult cases for other metric descriptors, gives further evidence of the high discrimination power of the proposed index. The combined use with other density or orb...

Linear response theory for the polarizable continuum model

Abstract: This chapter presents the general aspects of the response theory for molecular solutes in the presence of time-dependent perturbing fields: (i) the non-equilibrium solvation, (ii) the variational formulation of the time-dependent non-linear QM problem, and (iii) the connection of the molecular response functions with their macroscopic counterparts. The linear and quadratic molecular response functions are described at the coupled-cluster level.

Excited-state calculations with TD-DFT: from benchmarks to simulations in complex environments

Abstract: In this perspective, we present an overview of recent progress on Time-Dependent Density Functional Theory (TD-DFT) with a specific focus on its accuracy and on models able to take into account environmental effects, including complex media. To this end, we first summarise recent benchmarks and define an average TD-DFT accuracy in reproducing excitation energies when a conventional approach is used. Next, coupling of TD-DFT with models able to account for different kinds of interactions between a central chromophore and nearby chemical objects (solvent, organic cage, metal as well as semi-conducting surface) is investigated. Examples of application to excitation properties are presented, allowing to briefly describe several recent computational strategies. In addition, an extension of TD-DFT to describe a phenomenon involving interacting chromophores, e.g. the electronic energy transfer (EET), is presented to illustrate that this methodology can be applied to processes beyond the vertical excitation. This perspective therefore aims to provide to non-specialists a flavour of recent trends in the field of simulations of excited states in “realistic” situations.

Molecular properties in solution described with a continuum solvation model

Abstract: The study of molecular systems in a condensed phase with quantum-mechanical tools introduces problems not present in analogous studies on isolated molecules. Some of these problems are presented in the introductory part to justify a strategy to elaborate a theoretical model starting from an accurate continuum description of the solvent. This is here achieved through the polarizable continuum model (PCM), which also permits explicit consideration of solvent molecules. The decision of relying on the description of a large number of properties to refine the model is then justified. The consideration of complex molecular properties of a various nature has led to the elaboration of numerous additional features not present in the basic version of PCM, some among which are here briefly presented: local field and nonequilibrium effects, specific solute–solute and solute–solvent interactions, description of condensed phase with more complex structure. The paper ends with the presentation of some results, selected among a larger set of available examples, and limited to a few properties, to show the potentialities of the approach.

Electronic excitation energies of molecules in solution: state specific and linear response methods for nonequilibrium continuum solvation models.

Abstract: We present a formal comparison between the two different approaches to the calculation of electronic excitation energies of molecules in solution within the continuum solvation model framework, taking also into account nonequilibrium effects. These two approaches, one based on the explicit evaluation of the excited state wave function of the solute and the other based on the linear response theory, are here proven to give formally different expressions for the excitation energies even when exact eigenstates are considered. Calculations performed for some illustrative examples show that this formal difference has sensible effects on absolute solvatochromic shifts (i.e., with respect to gas phase) while it has small effects on relative (i.e., nonpolar to polar solvent) solvatochromic shifts.

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

Abstract: 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。

Quantum mechanical continuum solvation models.

Abstract: 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

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.

Abstract: 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...

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

Abstract: 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.

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

Abstract: 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.