Solvation free energy calculations

Within the framework of the same dielectric continuum model for the solvent, the Gibbs free energy of solvation of an ion of radius and charge may be estimated by calculating the electrostatic work done when hypothetically charging a sphere at constant radius from q = 0 q = This yields the Bom equation [13]... 

Eor instance, the contribution of water beyond 12 A from a singly charged ion is 13.7 kcal/mol to the solvation free energy or 27.3 kcal/mol to the solvation energy of that ion. The optimal treatment is to use Ewald sums, and the development of fast methods for biological systems is a valuable addition (see Chapter 4). However, proper account must be made for the finite size of the system in free energy calculations [48]. 

Procedures to compute acidities are essentially similar to those for the basicities discussed in the previous section. The acidities in the gas phase and in solution can be calculated as the free energy changes AG and AG" upon proton release of the isolated and solvated molecules, respectively. To discuss the relative strengths of acidity in the gas and aqueous solution phases, we only need the magnitude of —AG and — AG" for haloacetic acids relative to those for acetic acids. Thus the free energy calculations for acetic acid, haloacetic acids, and each conjugate base are carried out in the gas phase and in aqueous solution. 

The free energy of activation at the QCISD(T)/6-31 H-- -G(d,p) level amounts to 21.1 kcal/mol. According to the authors, the large electron density redistribution arising upon cyclization makes it necessary to use extended basis sets and high-order electron correlation methods to describe the gas-phase thermodynamics, which indicates clearly the gas-phase preference of the azido species. However, the equilibrium is shifted toward the tetrazole as the polarity of a solvent is increased. For instance, SCRF calculations (e = 78.4) yield a relative free energy of solvation with respect to the cw-azido isomer of —2.4 kcal/mol for the tmns-zziAo compound and of —6.8 kcal/mol for the tetrazole isomer. At a much lower level, the... 

MD simulations in expHcit solvents are stiU beyond the scope of the current computational power for screening of a large number of molecules. However, mining powerful quantum chemical parameters to predict log P via this approach remains a challenging task. QikProp [42] is based on a study [3] which used Monte Carlo simulations to calculate 11 parameters, including solute-solvent energies, solute dipole moment, number of solute-solvent interactions at different cutoff values, number of H-bond donors and acceptors (HBDN and HBAQ and some of their variations. These parameters made it possible to estimate a number of free energies of solvation of chemicals in hexadecane, octanol, water as well as octanol-water distribution coefficients. The equation calculated for the octanol-water coefficient is ... 

To calculate free energies of solvation for several organic molecules, Fortunelli and Tomasi applied the boundary element method for the reaction field in DFT/SCRF framework173. The authors demonstrated that the DFT/SCRF results obtained with the B88 exchange functional and with either the P86 or the LYP correlation functional are significantly closer to the experimental ones than the ones steming from the HF/SCRF calculations. The authors used the same cavity parameters for the HF/SCRF and DFT/SCRF calculations, which makes it possible to attribute the apparent superiority of the DFT/SCRF results to the density functional component of the model. The boundary element method appeared to be very efficient computationally. The DFT/SCRF calculations required only a few percent more CPU time than the corresponding gas-phase SCF calculations. 

Fig. 2.5. Possible applications of a coupling parameter, A, in free energy calculations, (a) and (b) correspond, respectively, to simple and coupled modifications of torsional degrees of freedom, involved in the study of conformational equilibria (c) represents an intramolecular, end-to-end reaction coordinate that may be used, for instance, to model the folding of a short peptide (d) symbolizes the alteration of selected nonbonded interactions to estimate relative free energies, in the spirit of site-directed mutagenesis experiments (e) is a simple distance separating chemical species that can be employed in potential of mean force (PMF) calculations and (f) corresponds to the annihilation of selected nonbonded interactions for the estimation of e.g., free energies of solvation. In the examples (a), (b), and (e), the coupling parameter, A, is not independent of the Cartesian coordinates, x. Appropriate metric tensor correction should be considered through a relevant transformation into generalized coordinates...

An alternative approach to calculating the free energy of solvation is to carry out simulations corresponding to the two vertical arrows in the thermodynamic cycle in Fig. 2.6. The transformation to nothing should not be taken literally -this means that the perturbed Hamiltonian contains not only terms responsible for solute-solvent interactions - viz. for the right vertical arrow - but also all the terms that involve intramolecular interactions in the solute. If they vanish, the solvent is reduced to a collection of noninteracting atoms. In this sense, it disappears or is annihilated from both the solution and the gas phase. For this reason, the corresponding computational scheme is called double annihilation. Calculations of... 

Resat, H. Mezei, M., Studies on free energy calculations, n. A theoretical approach to molecular solvation, J. Chem. Phys. 1994, 222, 6126-6140... 

Cornell, W. D. Cieplak, P. Bayly, C. I. Kollman, P. A., Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation, J. Am. Chem. Soc. 1993,115, 9620-9631. 

Villa, A. Mark, A. E., Calculation of the free energy of solvation for neutral analogs of amino acid side chains, J. Comput. Chem. 2002, 23, 548-553. 

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