Molecular mechanical region

Fig. 1F36 The division of a molecule into quantum meehanical and molecular mechanical regions, with the molecuh mechanical contributions as indicated.

In the combined QM-MM methodology the system being studies is partitioned into a quantum mechanical region and a molecular mechanical region (Fig. 1). The quantum... 

The system may be partitioned as illustrated in Fig. I into three parts a quantum-motif, a classical or molecular mechanics region, and a boundary region. The quantum and classical regions contain the atoms that are explicitly treated in the calculation. The boundary region accounts for the surroundings that are neglected. As such either periodic boundaries or the stochastic boundary method can be used [23, 25]. 

Mutiscale simulations can also be performed by integrating quantum chemical and classical simulations in a same simulation box, e.g., quantum chemical and molecule mechanics (QMMM) or quantum chemical and molecular dynamics (QMMD) together. These methods are applied to model systems in the same simulation box by defining boundaries between quantum chemical and molecular mechanics region. Such representation can simply take care of the chemically important small region quantum... 

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

The algorithms of the mixed classical-quantum model used in HyperChem are different for semi-empirical and ab mi/io methods. The semi-empirical methods in HyperChem treat boundary atoms (atoms that are used to terminate a subset quantum mechanical region inside a single molecule) as specially parameterized pseudofluorine atoms. However, HyperChem will not carry on mixed model calculations, using ab initio quantum mechanical methods, if there are any boundary atoms in the molecular system. Thus, if you would like to compute a wavefunction for only a portion of a molecular system using ab initio methods, you must select single or multiple isolated molecules as your selected quantum mechanical region, without any boundary atoms. 

Figure 2 A glutamate side chain partitioned into quantum and classical regions. The terminal CH2C02 group IS treated quantum mechanically, and the backbone atoms are treated with the molecular mechanics force field.

A molecular mechanism for gene control Repressor and Cro proteins operate a procaryotic genetic switch region... 

Biochemists have different problems in mind they want to divide parts of a protein chain into regions of interest that ought to be treated quantum-mechanically and the remainder of the chain that can be treated according to the methods of molecular mechanics. 

Consider, for example, the protein shown in Figure 15.7. The bottom left-hand amino acid is valine, which is linked to proline. Suppose for the sake of argument that we wanted to treat this valine quantum-mechanically and the rest of the protein chain according to the methods of molecular mechanics. We would have to draw a QM/MM boundary somewhere between valine and the rest of the protein. The link atoms define the boundary between the QM and the MM regions. A great deal of care has to go into this choice of boundary. The boundary should not give two species whose chemical properties are quite different from those implied by the structural formulae on either side of this boundary. 

Though due to the fact that it is difficult to interprete amplitude dependence of the elastic modulus and to unreliable extrapolation to zero amplitude, the treatment of the data of dynamic measurements requires a special caution, nevertheless simplicity of dynamic measurements calls attention. Therefore it is important to find an adequate interpretation of the obtained results. Even if we think that we have managed to measure correctly the dependences G ( ) and G"( ), as we have spoken above, the treatment of a peculiar behavior of the G (to) dependence in the region of low frequencies (Fig. 5) as a yield stress is debatable. But since such an unusual behavior of dynamic functions is observed, a molecular mechanism corresponding to it must be established. 

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