Atom-based parameters

This structure, based on the space group OjtPm in, involves about fifty atomic positional parameters, for which approximate values can be estimated from the Mg32(Al,Zn)49 parameters. Refinement of the structure would be laborious. 

In common with similar approaches that relate solvent accessible surface to cavity free energy90-93, the simple SMI model required careful parameterization, and assumed that atoms interacted with solvent in a manner independent of their immediate molecular environment and their hybridization76. In more recent implementations of the SMx approach, ak parameters are selected for particular atoms based on properties determined from the SCF wavefunction that is evaluated during calculation of the solute and solvent polarization energies27. On the other hand, the inclusion of more parameters in the solvation model requires access to substantial amounts of experimental data for the solvation free energies of molecules in the training set94 95. 

High resolution (between 1.4 and 2.0 A) Automated model building with ARP/wARP should work with most phase sets. RESOLVE, which uses a template-based rather than atom-based approach, should also perform well but may be computationally more consuming. Refinement can best be carried out with REEMAC or PHENIX using isotropic ADPs since the amount of data is no longer sufficient for an anisotropic description of atomic displacement parameters. The use of TLS (Winn et ah, 2003) is highly recommended. A use of NCS restraints should be critically evaluated and in most cases the refinement can proceed without them. Double conformations of side chains should be visible and modelled. Ordered solvent can be modelled automatically. 

While this has long been the most popular method to study crystal structures, it was not until the introduction of ADXRD on synchrotron sources in the 1990s that it became routine to determine atomic position parameters using this technique at high pressure. While such studies have been performed principally at synchrotron sources, laboratory-based studies have also been performed see for example [155-158]. 

The Formula (55) allows us to evaluate the hydrogen atoms distribution over O and 0 interstitial sites that are determined by temperature, the relation between a and P energy parameters and the total concentration of hydrogen atoms. Based on the relations (55), in the range 0 < c < 3 the dependences for hydrogen atoms distribution in O and interstitial sites are shown in the Figure 17. 

The dispersion and repulsion contributions have been modelled and computed with a variety of approaches [3,8], The most diffused PCM version adopts the procedure developed by Floris and Tomasi [10], based on atom-atom interaction parameters, proposed by Caillet and Claverie from crystallographic data [11] ... 

Toraya s WPPD approach is quite similar to the Rietveld method it requires knowledge of the chemical composition of the individual phases (mass absorption coefficients of phases of the sample), and their unit cell parameters from indexing. The benefit of this method is that it does not require the structural model required by the Rietveld method. Furthermore, if the quality of the crystallographic structure is poor and contains disordered pharmaceutical or poorly refined solvent molecules, quantification by the WPPD approach will be unbiased by an inadequate structural model, in contrast to the Rietveld method. If an appropriate internal standard of known quantity is introduced to the sample, the method can be applied to determine the amorphous phase composition as well as the crystalline components.9 The Rietveld method uses structural-based parameters such as atomic coordinates and atomic site occupancies are required for the calculation of the structure factor, in addition to the parameters refined by the WPPD method of Toraya. The additional complexity of the Rietveld method affords a greater amount of information to be extracted from the data set, due to the increased number of refinable parameters. Furthermore, the method is commonly referred to as a standardless method, since the structural model serves the role of a standard crystalline phase. It is generally best to minimize the effect of preferred orientation through sample preparation. In certain instances models of its influence on the powder pattern can be used to improve the refinement.12... 

Two further energy functions based on Poisson-Boltzmann electrostatics and atomic solvation parameter (ASP)-based parameterizations of the solvation free energy changes43 were evaluated by Weng et al.57 in the context of side-chain optimization after rigid-body docking. 

In BLH-NhaCo()2, the guest species in the galleries are highly disordered. MEM is quite effective for detailed structure analysis of such an intercalation compound. In MEM-based whole-pattern fitting (MPF), crystal structures are expressed not by structure parameters such as fractional coordinates and atomic displacement parameters but by electron densities in the unit cell. Therefore, MPF allows us to represent the disordered atomic configuration in a more appropriate way than conventional Rietveld analysis adopting a split-atom model. The... 

Force-field-based scoring functions use arbitrary empirical estimates of interaction energies obtained by molecular mechanics energy functions. This simple approximation, which takes into account only enthalpic contribution often correlates well with the experiment. Solvent effects are described by atom-based solvation parameters, which are computed for the surface of both ligand and receptor which is buried upon complexation. DOCK-chemical27 and CHARMm scoring functions represent this class. 

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