Link atom semiempirical methods

A detailed comparison of LSCF, GHO, and link atom semiempirical methods has been done by Reuter et al. [30]. The advantages and disadvantages of the methods, as they were when the study was published, appear clearly. 

Another approach to treating the boundary between covalently bonded QM and MM systems is the connection atom method,119 120 in which rather than a link atom, a monovalent pseudoatom is used. This connection atom is parameterized to give the correct behavior of the partitioned covalent bond. The connection atoms interact with the other QM atoms as a (specifically parameterized) QM atom, and with the other MM atoms as a standard carbon atom. This avoids the problem of a supplementary atom in the system, as the connection atom and the classical frontier atom are unified. However, the need to reparameterize for each type of covalent bond at a given level of quantum chemical theory is a laborious task.121 The connection atom method has been implemented for semiempirical molecular orbital (AMI and PM3)119 and density functional theory120 levels of theory. Tests carried out by Antes and Thiel to validate the connection atom method at the semiempirical level suggested that the connection atom approach is more accurate than the standard link atom approach.119... 

In the QM/MM version introduced by Karplus et al. semiempirical methods of MNDO and AMI type in combination with MM treatment were suggested to determine the APE surface for further MD simulation of the system as a whole. As in the works above, the authors discuss in detail the inter-region QM-MM interaction problem and the saturation of the free valences by link atoms when the QM/MM separation cuts a bond. The method is implemented in a program package called CHARMM . Among... 

MD simulation using combined QM/MM potentials in application to a series of various biological systems were carried out by Merz et al. (see also ). The DFT/MM method (see the first realizations in is used to evaluate the APE by calculating the electronic structure in the QM region in the DFT approximation. In the works of Thiel et al a better account for the energy correction due to the introduction of the link atoms and other important improvements of the semiempirical QM/MM method are suggested. 

Using semiempirical (or other) QM methods calculate the electronic structure of the central fragment(s) with link atoms or atomic groups that saturate the open valences, as discussed above (Section II1.3.3.2), and optimize its geometry taking into account the interaction with other fragments after Eq. (21) ... 

The LA method was originally proposed by Singh and KoUman who implemented it with an ab initio QM/MM potential [16]. It was later developed and parametrized for a semiempirical QM/MM potential by Field et al [ 1]. A schematic diagram of the technique is shown in figure 2. In the method, an extra, dummy QM atom (the link atom) is introduced into the system for each covalent bond that occurs between the QM and MM atoms. These atoms are typically hydrogen atoms, with one electron, and they are placed along the QM/MM bonds at an appropriate bonding distance from the QM atom. The link atoms enter into the QM calculation as normal but they are typically made invisible to the MM atoms. 

While, even for semiempirical QM methods, the QM portion will be the most time-consuming part of the calculation, the most difficult part of the implementation of a hybrid potential is the parametrization of the QM/MM Hamiltonian which determines the precision of the interactions between the QM and MM regions. The parametrization has to be done for the nonbonded interactions between the atoms in the QM and MM regions and also for the covalent or link atom interactions. For the covalent interactions it is probably true to say that no... 

According to semiempirical calculations by the AMI method the 1,8-atoms of the naphthalene skeleton linked to silicon are the most electron-rich. An electrophilic attack should take this direction and is well demonstrated by the reaction of silete (84a) in air that suffers a fast deliquescence due to reaction with water vapor resulting in dimer 85 (Scheme 18). 

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