Quantum atom

Having found a place (the sp -sp bon d t to establish the boundary between classical atom s and quantum atoms, the next cpiesiion is how to cap the quantum atoms. Let s first of all look at an illustrative example of the problem. ... 

CII3 methyl group and requested the extension to sp- , the selected quantum atoms would be the fragment NH CO Cq(H(CH3). This fragment has dangling bonds on both ends an d prior to perform in g a t uari turn mcchan ical calculation, you... 

How to decide on or form the boundary between the classical portion and the quantum portion. (Alternatively, you may ask which atoms will be quantum atoms and which will be classical atoms )... 

HyperChem assumes that it is easiest for you to just use subset selection to select that portion of the molecular system that is to be treated quantum mechanically. You can then extend the initial selection to form a convenient and universally acceptable boundary. Thus, you make a simple selection of atoms for the first pass at selecting the quantum mechanical portion. The selected atoms are quantum atoms and the unselected atoms are classical atoms. 

In this equation Exc is the exchange correlation functional [46], is the partial charge of an atom in the classical region, Z, is the nuclear charge of an atom in the quantum region, is the distance between an electron and quantum atom q, r, is the distance between an electron and a classical atom c is the distance between two quantum nuclei, and r is the coordinate of a second electron. Once the Kohn-Sham equations have been solved, the various energy terms of the DF-MM method are evaluated as... 

Finally, the parametrization of the van der Waals part of the QM-MM interaction must be considered. This applies to all QM-MM implementations irrespective of the quantum method being employed. From Eq. (9) it can be seen that each quantum atom needs to have two Lennard-Jones parameters associated with it in order to have a van der Walls interaction with classical atoms. Generally, there are two approaches to this problem. The first is to derive a set of parameters, e, and G, for each common atom type and then to use this standard set for any study that requires a QM-MM study. This is the most common aproach, and the derived Lennard-Jones parameters for the quantum atoms are simply the parameters found in the MM force field for the analogous atom types. For example, a study that employed a QM-MM method implemented in the program CHARMM [48] would use the appropriate Lennard-Jones parameters of the CHARMM force field [52] for the atoms in the quantum region. 

The second approach is to derive Lennard-Jones parameters for the quantum atoms that are specific to the problem in hand. This is a less common approach but has been shown to improve the quantitative accuracy of the QM-MM approach in specific cases [53,54]. The disadvantage of this approach, however, is that it is necessary to derive Lennard-Jones parameters for the quanmm region for every different study. Since the derivation of Lennard-Jones parameters is not a trivial exercise, this method of finding van der Walls parameters for the QM-MM interaction has not been widely used. 

The location of the quantum/classical boundary across a covalent bond also has implications for the energy terms evaluated in the Emm term. Classical energy terms that involve only quantum atoms are not evaluated. These are accounted for by the quantum Hamiltonian. Classical energy terms that include at least one classical atom are evaluated. Referring to Figure 2, the Ca—Cp bond term the N — Ca—Cp, C — Ca—Cp, Ha— Ca—Cp, Ca—Cp — Hpi, and Ca—Cp — Hp2 angle tenns and the proper dihedral terms involving a classical atom are all included. 

It was not until the advent of the quantum atom that chemists were able to understand their most abiding mystery why elements have the properties they do. Why is helium so inert and sodium so reactive Why do hydrogen atoms come in pairs in hydrogen gas, while carbon atoms join to four others in diamond ... 

These propensities are, as I indicated at the outset, largely codified in the Periodic Table. We shall shortly see that the quantum atom provides an explanation for the Periodic Table. But where did this table come from in the first place ... 

Following the wave-mechanical reformulation of the quantum atomic model it became evident that the observed angular momentum of an s-state was not the result of orbital rotation of charge. As a result, the Bohr model was finally rejected within twenty years of publication and replaced by a whole succession of more refined atomic models. Closer examination will show however, that even the most refined contemporary model is still beset by conceptual problems. It could therefore be argued that some other hidden assumption, rather than Bohr s quantization rule, is responsible for the failure of the entire family of quantum-mechanical atomic models. Not only should the Bohr model be re-examined for some fatal flaw, but also for the valid assumptions that led on to the successful features of the quantum approach. 

The force fields used in the QM/MM methods are typically adopted from fully classical force fields. While this is in general suitable for the solvent-solvent interactions it is not clear how to model, e.g., the van der Waals interaction between the solute and the solvent. The van der Waals interactions are typically treated as Lennard-Jones (LJ) potentials with parameters for the quantum atoms taken from the classical force field or optimized for the particular QM/MM method for some molecular complexes. However, it is not certain that optimizing the (dispersion and short-range repulsion) parameters on small complexes will improve the results in a QM/MM simulation of liquids [37],... 

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