Polarizable continuum model problem

The most common approach to solvation studies using an implicit solvent is to add a self-consistent reaction field (SCRF) term to an ab initio (or semi-empirical) calculation. One of the problems with SCRF methods is the number of different possible approaches. Orozco and Luque28 and Colominas et al27 found that 6-31G ab initio calculations with the polarizable continuum model (PCM) method of Miertius, Scrocco, and Tomasi (referred to in these papers as the MST method)45 gave results in reasonable agreement with the MD-FEP results, but the AM1-AMSOL method differed by a number of kJ/mol, and sometimes gave qualitatively wrong results. 

C. S. Pomelli, J. Tomasi and V. Barone, An improved iterative solution to solve the electrostatic problem in the polarizable continuum model, Theor. Chem. Acc., 105 (2001) 446-451. 

A more sophisticated description of the solvent is achieved using an Apparent Surface Charge (ASC) [1,3] placed on the surface of a cavity containing the solute. This cavity, usually of molecular shape, is dug into a polarizable continuum medium and the proper electrostatic problem is solved on the cavity boundary, taking into account the mutual polarization of the solute and solvent. The Polarizable Continuum Model (PCM) [1,3,7] belongs to this class of ASC implicit solvent models. 

Different theoretical models and techniques have been used to approach the problem of the local environment including many-body QED [41,42], classical mechanics [43 15], polariton mediated interactions [46], and the polarizable continuum model [47,48] with... 

The most serious limitation remaining after modifying the reaction field method as mentioned above is the neglect of solute polarizability. The reaction field that acts back on the solute will affect its charge distribution as well as the cavity shape as the equipotential surface changes. To solve this problem while still using the polarizable continuum model (PCM) for the solvent, one has to calculate the surface charges on the solute by quantum chemical methods and represent their interaction with the solvent continuum as in classical electrostatics. The Hamiltonian of the system thus is written as the sum of the Hamilton operator for the isolated solute molecule and its interaction with the macroscopic... 

With the acronym PCM (polarizable continuum model) we indicate a set of methods addressed to the study of solvation problems at the Quantum Mechanical level with the use of continuum solvent distributions. 

Methods based on an ASC have a long history in quantum-mechanical (QM) calculations with continuum solvent [60, 61, 77], where they are generally known as polarizable continuum models (PCMs). However, PCMs have seen little use in the area of biomolecular electrostatics, for reasons that are unclear to us. In the QM context, such methods are inherently approximate, even with respect to the model problem defined by Poisson s equation, owing to the volume polarization that results from the tail of the QM electron density that penetrates beyond the cavity and into the continuum [13, 14, 89], The effects of volume polarization can be treated only approximately within the ASC formalism [14, 15, 89], For a classical solute, however, there is no such tail and certain methods in the PCM family do afford a numerically exact solution of Poisson s equation, up to discretization errors that are systematically eliminable. Moreover, ASC methods have been generalized to... 

Polarizable Continuum Model (PCM) This method was developed by Tomasi s group in 1981 and many applications have been proposed [2]. The most distinctive feature of this method is to be able to treat a molecular shaped cavity. Applications not only to Hartree-Fock methods, but to UHF, MCSCF, MBPT, CASSCF, MR-SDCI and DFT etc. have been reported. They also proposed a extension to nonequilibrium solvation problems. The basic concept of their method is that the reaction potential may be described in terms of an apparent charge distribution on the cavity boundary s surface. The charge distributions a and the potential from them can be evaluated as... 

An alternative to the use of finite differences or finite elements to discretize the differential operator is to use boundary element methods (BEM). " One of the most popular of these is the polarizable continuum model (PCM) developed originally by the Pisa group of Tomasi and co-workers. The main aspect of PCM is to reduce the electrostatic Poisson equation (1) into a boundary element problem with apparent charges (ASCs) on the solute cavity surface. 

A many-body perturbation theory (MBPT) approach has been combined with the polarizable continuum model (PCM) of the electrostatic solvation. The first approximation called by authors the perturbation theory at energy level (PTE) consists of the solution of the PCM problem at the Hartree-Fock level to find the solvent reaction potential and the wavefunction for the calculation of the MBPT correction to the energy. In the second approximation, called the perturbation theory at the density matrix level only (PTD), the calculation of the reaction potential and electrostatic free energy is based on the MBPT corrected wavefunction for the isolated molecule. At the next approximation (perturbation theory at the energy and density matrix level, PTED), both the energy and the wave function are solvent reaction field and MBPT corrected. The self-consistent reaction field model has been also applied within the complete active space self-consistent field (CAS SCF) theory and the eomplete aetive space second-order perturbation theory. ... 

The problem of the description of the excited states within the Polarizable Continuum Model leads to two non-equivalent approaches, the approach based on the linear response (LR) approach, and the state specific (SS) approach, as already said in the Introduction. Each approach has advantages and disadvantages. The LR approach is computationally more convenient, as it gives the whole spectrum of the excited states of interest in a single calculation, but is physically biased. In fact, in the LR approach the solute-solvent interaction contains a term related to the one-particle transition densities of the solute connecting the reference state adopted in the LR calculation, which usually corresponds to the electronic groimd state, to the excited electronic state. The SS approach is computationally more expensive, as it requires a separate calculation for each of the excited states of interest, but is physically im-biased. In fact, in the SS approach the solute-solvent interaction is determined by the effective one-particle electron density of the excited state. 

CSM = continuum solvation model COSMO = conductorlike screening model COSMO-RS = generalization of COSMO to real solvents QC = quantum chemical PCM = polarizable continuum model SAS = solvent accessible surface SES = solvent excluding surface NPPA = average number of segments per full atom vdW = van der Waals, VWN = Vosko-Wilk-Nusair functional (see Density Functional Theory Applications to Transition Metal Problems). 

In this contribution we will first outline the formalism of the ONIOM method. Although ONIOM has not yet been applied extensively to problems in the solvated phase, we will show how ONIOM has the potential to become a very valuable tool in both the explicit and implicit modeling of solvent effects. For the implicit modeling of solvent, we developed the ONIOM-PCM method, which combines ONIOM with the Polarizable Continuum Method (PCM). We will conclude with a case study on the vertical electronic transition to the it state in formamide, modeled with several explicit solvent molecules. 

For many chemical problems, it is crucial to consider solvent effects. This was demonstrated in our recent studies on the hydration free energy of U02 and the model reduction of uranyl by water [232,233]. The ParaGauss code [21,22] allows to carry out DKH DF calculations combined with a treatment of solvent effects via the self-consistent polarizable continuum method (PCM) COSMO [227]. If one aims at a realistic description of solvated species, it is not sufficient to represent an aqueous environment simply as a dielectric continuum because of the covalent nature of the bonding between an actinide and aqua ligands [232]. Ideally, one uses a combination model, in which one or more solvation shells (typically the first shell) are treated quantum-mechanically, while long-range electrostatic and other solvent effects are accounted for with a continuum model. Both contributions to the solvation free energy of U02 were... 

The effect of the solvent is usually modelled either by the use of the Onsager s self consistent reaction field (SCRF) [20] or by the polarizable continuum method (PCM) [21]. With regard to the relative stability of cytosine tautomers in aqueous solution, these methods provided results [14,15] which, in spite of some discrepancies, are in reasonable agreement with experimental data [3]. However, continuum-based methods do not explicitly take into consideration the local solvent-solute interaction which is instead important in the description of the proton transfer mechanism in hydrogen-bonded systems. A reasonable approach to the problem was recently proposed [22,23] in which the molecule of interest and few solvent molecules are treated as a supermolecule acting as solute, while the bulk of the solvent is represented as a polarizable dielectric. 

Our QM/MM model—the discrete (or direct) reaction field (DRF) model—treats the various terms in Eq. (3-1) separately and on the basis of their own intrinsic physical meaning [3,10,31,32,38,59,74], Historically, DRF was developed to study biochemical problems, in particular for unraveling the reaction mechanism of papain. For that we went stepwise from a model active site [75] to a model active site plus a point charge representation of an a-helix [76,77,78], then to a model with a polarizable helix [78,79], and finally to an all-atom treatment of the enzyme [41]. Furthermore, we extended these studies with an exercise—with the continuum version—to show that a solvent-exposed residue has no effect on the reaction mechanism [80], Up to then we considered the protein as a peculiar solvent the real solvents, requiring extensive MC or MD simulations, came later. 

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