Force field treatments

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

The theoretical basis for a full valence force field treatment of extended lattices lies with the work of Kleinman and Spitzer published in 1962. ° These authors, who developed their force field to calculate the vibrational frequencies of quartz, felt that the most accurate way to represent the vibrational motion in a quartz crystal was to include the relative motion of oxygen and silicon atoms. The valence force field was the most effective method for treating this localized picture. 

Table 5 A comparison between quantum-mechanical and force-field treatment of dispersion and repulsive contributions to the free energy of solvation. The force field is given under method, and for each solvent the first line gives the root mean square deviation (rmsd, in kcal/ mol) and the second line gives the coefficient c that gives the best fit of y = cx with y being the force-field results and x being the quantum-mechanical results. All results are from ref 30...

In the conventional force-field treatment, these sublevels are split by the interaction (often referred to as Amat-Nielsen coupling [96])... 

While the earlier work on close S--0 contacts and halogen X---0 interactions provides specific parameters that can be used to improve force field treatment of certain interactions in small molecules, there are potentially many other interactions that could be amended with a special force field treatment. The approach presented earlier offers a straightforward way to improve specific aspects of a force field for the generation of accurate small-molecule conformations. The approach can be broken down into the following three steps ... 

The use of variable charge models clearly has great potential for future use as a compromise between simpler force-field treatments and full-blown quantum mechanics. A combination of the electronegativity equalization with point ion polarizability, where the polarizability is coupled to the charge-state, may prove even more accurate and... 

For polymer chains in a crystal lattice, however, acoustic vibrations of polymer chains are subject to interchain interactions, yielding the crystal vibrations of the acoustic and optical branches. Accordingly, for vibrational analyses of neutron-scattering spedra in the low-frequency region, it is required to treat the normal vibrations of the crystal, on the basis of the interchain force field as well as the intrachain force field. Treatments of crystal vibrations are also necessary for the theoretical study of specific heat, zero-point energy and temperature factor of x-ray diffraction. 

Force Field Treatment of Proton and Hydrogen Transfer in Molecular Systems... 

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