Hybrid solvation

Hybrid solvation Implicit solvation plus Explicit solvation microsolvation subjected to the continuum method. Here the solute molecule is associated with explicit solvent molecules, usually no more than a few and sometimes as few as one, and with its bound (usually hydrogen-bonded) solvent molecule(s) is subjected to a continuum calculation. Such hybrid calculations have been used in attempts to improve values of solvation free energies in connection with pKp. [42], and also [45] and references therein. Other examples of the use of hybrid solvation are the hydration of the environmentally important hydroxyl radical [52] and of the ubiquitous alkali metal and halide ions [53]. Hybrid solvation has been surveyed in a review oriented toward biomolecular applications [54]. 

I. A. Topol, G. J. Tawa, S. K. Burt and A. A. Rashin, On the structure and thermodynamics of solvated monoatomic ions using a hybrid solvation model, J. Chem. Phys. Ill (1999) 10998-11014. 

Abstract A comparative description of two different hybrid solvation models is presented, both of... 

This hybrid solvation model surrounds the solute with a small number of explicit solvent molecules, and then embeds this cluster into the implicit dielectric field. Local effects are addressed by the full quantum mechanical treatment of the interaction between the solute and the few explicit solvent molecules. Long-range effects are included through the interaction of the cluster with the dielectric field. A decision is still needed as to how many explicit solvent molecules should be included within the cluster, recognizing that each additional solvent molecule increases the size of the calculation and expands the configurational space that must be explored. 

No systematic study of the effect of different solvation models has been performed. A few reports have compared specific cases such as the study of cationic and anionic alanines, which shows a significant improvement in the chemical shift prediction using polarized continuum method (PCM) or better stiU a hybrid solvation approach (Section 1.4.3). However, the linear scaling correction discussed below can often account for the systematic solvent effect and so sometimes one can get away without any solvent computation at all. 

Pepin C, Goulet T, Houde D, Jay-Gerin J-P. (1994) Femtosecond kinetic measurements of excess electrons in methanol Substantiation for a hybrid solvation mechanism. J Phys Chem 98 7009-7013. 

The SM1-SM3 methods model solvation in water with various degrees of sophistication. The SM4 method models solvation in alkane solvents. The SM5 method is generalized to model any solvent. The SM5.42R method is designed to work with HF, DFT or hybrid HF/DFT calculations, as well as with AMI or PM3. SM5.42R is implemented using a SCRF algorithm as described below. A description of the differences between these methods can be found in the manual accompanying the AMSOL program and in the reviews listed at the end of this chapter. Available Hamiltonians and solvents are summarized in Table 24.1. 

The HE, GVB, local MP2, and DFT methods are available, as well as local, gradient-corrected, and hybrid density functionals. The GVB-RCI (restricted configuration interaction) method is available to give correlation and correct bond dissociation with a minimum amount of CPU time. There is also a GVB-DFT calculation available, which is a GVB-SCF calculation with a post-SCF DFT calculation. In addition, GVB-MP2 calculations are possible. Geometry optimizations can be performed with constraints. Both quasi-Newton and QST transition structure finding algorithms are available, as well as the SCRF solvation method. 

Figure 3 Mutation of a ligand Asp into Asn in solution and bound to a protein, (a) Thermodynamic cycle, (b) Dual topology description a hybrid ligand with two side chains. Blocks are used to define the hybrid energy function [Eq. (14)]. Only the ligand is shown the environment is either solvent or the solvated protein, (c) Single-topology description.

Stereochemical analysis can add detail to the mechanistic picture of the Sj l substitution reaction. The ionization mechanism results in foimation of a caibocation intermediate which is planar because of its hybridization. If the caibocation is sufficiently long-lived under the reaction conditions to diffirse away from the leaving group, it becomes symmetrically solvated and gives racemic product. If this condition is not met, the solvation is dissymmetric, and product with net retention or inversion of configuration may be obtained, even though an achiral caibocation is formed. The extent of inversion or retention depends upon the details of the system. Examples of this effect will be discussed in later sections of the chapter. 

It certainly does not seem that these interactions continue in solution, so that their magnitude is weaker than solvation forces. Theoretical explanation has suggested that the unused, filled, 6s-5dz2 hybrid (section 4.1) interacts with vacant 6px,py orbitals at right angles to the digonal bonds (Figure 4.49). 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Muino PL, Callis PR (1994) Hybrid simulations of solvation effects on electronic-spectra -indoles in water. J Chem Phys 100(6) 4093 1109... 

The incorporation of the generalized Bom model into free energy calculation methods using FEP/TI and A-dynamics was carried out by Banba and Brooks.81 They define the electrostatic solvation energy for the hybrid system as follows... 

The solvation models are used to predict the properties of small molecules and large biomolecules employing different levels of theory. In the prediction of solvent effect using electronic structure calculation, semiempirical, HF, post-HF, and DFT-based hybrid methods have been widely used [2-11], Since a wealth of literature is... 

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