Implicit solvent

In this model of electrostatic in teraction s, two atoms (i and j) have poin t charges tq and qj. The magnitude of the electrostatic energy (V[. , [ ) varies inversely with the distance between the atoms, Rjj. fh e effective dielectric constant is . For in vacuo simulations or simulation s with explicit water rn olecules, the den om in a tor equals uRjj, In some force fields, a distance-dependent dielectric, where the denominator is uRjj Rjj, represen is solvent implicitly. 

A key element of many simplified free energy methods is the use of an implicit description of the solvent. Implicit solvent models are based on the concept of a PMF, presented briefly in this section see [11] for a detailed review see Chap. 4 for applications of the PMF concept that are not related to implicit solvation. 

Solvent (implicit solvation model) Cosse-Bari 1994 Sulfated polysaccharides Ferro 1997... 

OpenMM Explicit solvent, implicit solvent (GB), PME, NVE, NVT, SHAKE All features Single GPU at present ATI/NVIDIA Free, open source ... 

In order to further explore the validity of the stepwise modified Marcus model, we developed recently [85] a simplified EVB model which represents the given conduction chain by an explicit EVB, while representing the rest of the environment (protein and solvent) implicitly. This is done by using the same type of solute surface as in Eq. (8.8), while omitting the explicit solute-solvent and solvent-solvent terms (the t/ss and Uss terms) and replacing them by implicit terms using ... 

A major reason why simulations of biological systems are so time-consuming is the large number of solvent molecules which must be included. Thus, it is important to try to develop accurate continuum models which can represent the solvent implicitly approaches are described in articles by Bashford Macroscopic Electrostatics Calculation of Solvated Interactions and Macromolecular Titration) and Sharp Continuum Solvation). 

Figure Bl.11.9. Integrated 250 MHz H NMR spectrum of dilute propan-1-ol in dinrethylsulfoxide solvent. Here, the shift order parallels the chemical order. Arr expansion of the H2-I nrultiplet is included, as is the implicit frequency scale, also referenced here to TMS = 0.

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

This method was introduced recently as an efficient technique to accurately model solvent and salt effects in an implicit fashion ([Gilson et al. 1993]). The forces are calculated as a sum of three terms ... 

The study of slow protein dynamics is a fascinating field with still many unknowns. We have presented a number of computational techniques that are currently being used to tackle those questions. Most promising for our case seems the development of methods that combine an implicit solvent description with techniques to induce conformational transitions. 

The GB equation is suitable for the description of solvent effects in molecular mechanics and dynamics [16], as well as in quantum mechanical calculations (17,18]. An excellent review of implicit solvation models, with more than 900 references, is given by Cramer and Truhlar [19]. 

As a starting point for identifying candidate solvents, all compounds having boiling points below that of any component in the mixture to be separated should be eliminated. This is necessary to yield the correct residue curve map for extractive distillation, but this process implicitly rules out other forms of homogeneous azeotropic distillation. In fact, compounds which boil as much as 50°C or more above the mixture have been recommended (68) in order to minimize the likelihood of azeotrope formation. On the other hand, the solvent should not bod so high that excessive temperatures are required in the solvent recovery column. 

Figure 2 Schematic representation of a biomolecular solute in a solvent environment that is taken into account implicitly.

II. BASIC FORMULATION OF IMPLICIT SOLVENT A. The Potential of Mean Force... 

As a first step, it is important to estabUsh implicit solvent models on fundamental principles. For the sake of concreteness, let us consider a solute u immersed in a bulk solution V. The configuration of the solute is represented by the vector X = xj, Xo,.... All other degrees of freedom of the bulk solution surrounding the solute, which may include solvent... 

In the following sections, we describe an implicit solvent model based on this free energy decomposition that is widely used in biophysics. It consists in representing the nonpolar free energy contributions on the basis of the solvent-accessible surface area... 

SASA), a concept introduced by Lee and Richards [9], and the electrostatic free energy contribution on the basis of the Poisson-Boltzmann (PB) equation of macroscopic electrostatics, an idea that goes back to Born [10], Debye and Htickel [11], Kirkwood [12], and Onsager [13]. The combination of these two approximations forms the SASA/PB implicit solvent model. In the next section we analyze the microscopic significance of the nonpolar and electrostatic free energy contributions and describe the SASA/PB implicit solvent model. 

B. Solvent Boundary Potentials and Implicit/Explicit Mixed Schemes... 

---