Solvation model COSMO

Recently, Wichmann et al. [47] applied several COSMO-RS cr-moments as descriptors to model BBB permeability. The performance of the log BB model was reasonable given only four descriptors were applied n — 103, r2 = 0.71, RMSE = 0.4, LOO q2 — 0.68, RMSEtest = 0.42. The COSMO-RS cr-moments were obtained from quantum chemical calculations using the continuum solvation model COSMO and a subsequent statistical decomposition of the resulting polarization charge densities. 

The insight provided by studying 8-oxo-guanine, and the ability to substitute DNA with a nucleobase that could be selectively oxidized by a low-potential complex, prompted us to search for other minimally substituted, redox-active nucleobases [92]. We therefore developed a library of nucleobases that were investigated using density functional theory (DFT) [93, 94] calculations self-consistently coupled to the conductorlike solvation model (COSMO) [95, 96]. The case of oxidation of nucleobases, particularly guanine. 

As seen in Fig. 1.1, and as I will explain in detail in this book, the dielectric continuum solvation model COSMO and the subsequent COSMO-based thermodynamics COSMO-RS are two clearly separable and very different steps. However, I have found that many researchers in this field refer to both methods as COSMO, which is both inaccurate and confusing. To avoid this confusion, I find it necessary to emphasize the importance of using the correct notations—COSMO and COSMO-RS-for these methods in all discussions and written literature on these subjects. 

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). 

It is also noteworthy that urea interacts with the alkali halide surfaces in aqueous solution hence, the surrounding medium effect seems to be important. To examine the effect of the solvent, we performed calculations with the continuum solvation model (COSMO). The dielectrics ( = 78.4 for water) was used in these cases. The optimized gas-phase slabs for KCI 100, 110, and 111 with urea were computed with the COSMO model. The calculated interaction energies are shown in Table 8.2. Interaction energies were found to be lower in water compared to the gas-phase results. Importantly, the interaction energies for urea with all three surfaces were found to be comparable. Based on these calculated results, one could predict that the additional stabilization cannot be achieved for the unstable surfaces such as 111 ... 

QuantlogP, developed by Quantum Pharmaceuticals, uses another quantum-chemical model to calculate the solvation energy. As in COSMO-RS, the authors do not explicitly consider water molecules but use a continuum solvation model. However, while the COSMO-RS model simpUfies solvation to interaction of molecular surfaces, the new vector-field model of polar Uquids accounts for short-range (H-bond formation) and long-range dipole-dipole interactions of target and solute molecules [40]. The application of QuantlogP to calculate log P for over 900 molecules resulted in an RMSE of 0.7 and a correlation coefficient r of 0.94 [41]. 

A. Schiiurmann, G. COSMO a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkins Trans. 1993, 799-805. (c) Klamt, A. Jonas, V. Burger, T. Lohrenz, J. C. W. Refinement and parametrization of COSMO-RS. J. Phys. Chem. A 1998, 102, 5074—5085. (d) For a more comprehensive treatment of solvation models, see Cramer, C. J. Truhlar, D. G. Implicit solvation models equilibria, structure, spectra, and dynamics. Chem. Rev. 1999, 99, 2161— 2200. 

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],... 

Fig. 2.6 Comparison of the calculated structures for glycine in the gas-phase and in water (COSMO solvation model). Note that the central bond angle in the zwitterionic form 1 is distorted by the hydrogen bond length of 1.96A computed for this structure in the gas phase. When solvation effects are included in the calculation using COSMO, the electrostatic interaction is reduced in magnitude due to charge screening by water, and the bond angle distortion is no longer present.

The calculated reaction profile for H abstraction for the TauD Fe(IV)=0 model is shown in Fig. 2 (23). The calculations were carried out with the ORCA package (24), using the B3LYP density functional (25,26) and Karlsruhe basis sets for all atoms (27—29) in combination with the RIJONX (30) or RIJCOSX approximations (31) and appropriate auxiliary basis sets (32—34). The protein environment was modeled by the COSMO solvation model with a dielectric constant of... 

Quantum Chemistry with dielectric. .solvation models acetone. tike COSMO... 

Here, r denotes the position vector of the charges qt with respect to the center of the sphere, and r, the distance from the center. By applying the dielectric scaling function for dipoles (Eq. (2.3)), which—as we have seen in Fig. 2.1—is also a good approximation for most other multipole orders, it was immediately clear that the idea of using a scaled conductor instead of the EDBC leads to a considerable simplification of the mathematics of dielectric continuum solvation models, with very small loss of accuracy. It may also help the finding of closed analytic solutions where at present only multipole expansions are available, as in the case of the spherical cavity. Thus the Conductor-like Screening Model (COSMO) was bom. 

These immediate and simple findings motivated me to accept Gerrit Schuiirmann s request and to implement COSMO as a new kind of SCRF model in the semi-empirical quantum chemistry package MOPAC [39]. Shortly afterwards, I met Jimmy Stewart, the author of the MOPAC package, in a European Computational Chemistry Workshop in Oxford, where he was available as a supervisor for a entire workshop. I gave a short presentation of my COSMO ideas and he was interested to get COSMO as the first solvation model in MOPAC. Therefore, he introduced me to some extend to the MOPAC program code, and we identified the places where COSMO would have to link in. 

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