Solvation effects explicit solvent

Onsager s SCRF is the simplest method for taking dielectric medium effects into account and more accurate approaches have been developed such as polarizable continuum modes, " continuum dielectric solvation models, - explicit-solvent dynamic-dielectric screening model, - and conductor-like screening model (COSMO). Extensive refinements of the SCRF method (spherical, elliptical, multicavity models) in conjunction with INDO/CIS were introduced by Zerner and co-workers ° as well. 

Also use constant dielectric Tor MM+aiul OPLS ciilciilatimis. Use the (lislance-flepeiident dielecinc for AMBER and BlO+to mimic the screening effects of solvation when no explicit solvent molecules are present. The scale factor for the dielectric permittivity, n. can vary from 1 to H(l. IlyperChem sets tt to 1. .5 for MM-r. Use 1.0 for AMBER and OPLS. and 1.0-2..5 for BlO-r. 

It is possible to go beyond the SASA/PB approximation and develop better approximations to current implicit solvent representations with sophisticated statistical mechanical models based on distribution functions or integral equations (see Section V.A). An alternative intermediate approach consists in including a small number of explicit solvent molecules near the solute while the influence of the remain bulk solvent molecules is taken into account implicitly (see Section V.B). On the other hand, in some cases it is necessary to use a treatment that is markedly simpler than SASA/PB to carry out extensive conformational searches. In such situations, it possible to use empirical models that describe the entire solvation free energy on the basis of the SASA (see Section V.C). An even simpler class of approximations consists in using infonnation-based potentials constructed to mimic and reproduce the statistical trends observed in macromolecular structures (see Section V.D). Although the microscopic basis of these approximations is not yet formally linked to a statistical mechanical formulation of implicit solvent, full SASA models and empirical information-based potentials may be very effective for particular problems. 

Two remaining problems relating to the treatment of solvation include the slowness of Poisson-Boltzmann calculations, when these are used to treat electrostatic effects, and the difficulty of keeping buried, explicit solvent in equilibrium with the external solvent when, e.g., there are changes in nearby solute groups in an alchemical simulation. Faster methods for solving the Poisson-Boltzmann equation by means of parallel finite element techniques are becoming available, however.22 24... 

In spectroscopy we may distinguish two types of process, adiabatic and vertical. Adiabatic excitation energies are by definition thermodynamic ones, and they are usually further defined to refer to at 0° K. In practice, at least for electronic spectroscopy, one is more likely to observe vertical processes, because of the Franck-Condon principle. The simplest principle for understandings solvation effects on vertical electronic transitions is the two-response-time model in which the solvent is assumed to have a fast response time associated with electronic polarization and a slow response time associated with translational, librational, and vibrational motions of the nuclei.92 One assumes that electronic excitation is slow compared with electronic response but fast compared with nuclear response. The latter assumption is quite reasonable, but the former is questionable since the time scale of electronic excitation is quite comparable to solvent electronic polarization (consider, e.g., the excitation of a 4.5 eV n — n carbonyl transition in a solvent whose frequency response is centered at 10 eV the corresponding time scales are 10 15 s and 2 x 10 15 s respectively). A theory that takes account of the similarity of these time scales would be very difficult, involving explicit electron correlation between the solute and the macroscopic solvent. One can, however, treat the limit where the solvent electronic response is fast compared to solute electronic transitions this is called the direct reaction field (DRF). 49,93 The accurate answer must lie somewhere between the SCRF and DRF limits 94 nevertheless one can obtain very useful results with a two-time-scale version of the more manageable SCRF limit, as illustrated by a very successful recent treatment... 

In addition to the continuum models, the explicit solvation has also been used to quantify the reactivity [48]. In this study, the effect of solvent on the... 

TvaroSka, KoS r and Hricovini in this book). One way to account for the effect of solvent on conforxnation might be to represent the molecule without environmental influences, and then explicitly include the solvent or other environmental molecules in the calculation. While avoiding built-in influences of environment is a satisfying concept, it is difficult to obtain by experiment parameters that lack those influences. Several methods have been used to study solvation effects, including continuum descriptions (24) and the explicit treatment of solvent molecules in Monte Carlo and molecular dynamics simulation. 

Having identified the strongest points of the explicit and implicit solvent models, it seems an obvious step to try to combine them in a way that takes advantage of the strengths of each. For instance, to the extent first-solvation-shell effects are qualitatively different from those deriving from the bulk, one might choose to include the first solvation shell explicitly and model the remainder of the system with a continuum (see, for instance, Chahnet, Rinaldi, and Ruiz-Lopez, 2001). 

Another thing to keep in mind is that most quantum chemistry calculations, by default, treat the molecules as gas-phase species in a vacuum. In contrast, most laboratory experiments are done in solvent. Today, fortunately, many of the widely used quantum chemistry programs have a way of approximating the effect of solvent on solute models. The solvent can be treated in two ways. Water is a common solvent, so we will use it as an example. One way is to use the so-called explicit waters in this approach, a few water molecules are sprinkled around the periphery of the solute to mimic the effect of a solvation shell or hydrogen bonding, and the whole ensemble is run in the calculation. The other way is to use implicit waters in which an average potential field that would be produced by water... 

Continuum solvation models are generally focused on purely electrostatic effects the solvent is a homogeneous continuous medium and its response is determined by its dielectric constant. Electrostatic effects usually constitute the dominating part of the solute - solvent interaction but in some cases explicit solute-solvent (or solute-solute)... 

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. 

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