Boundary atom

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. 

Note The capping atoms are only supported in the semi-empirical quantum mechanics methods in HyperChem. If you want to use the mixed model in the ab mi/io method in HyperChem, you must select an entire molecule or molecules without any boundary atom between the selected and unselected regions and then carry out the calculation. 

In order to improve the accuracy and applicability of the pseudobond approach, very recently we have developed a new formulation to construct this seven-valence-electron boundary atom [29], The key difference is that the seven-valence-electron boundary atom has its own basis set instead of that of fluorine. Here a STO-2G... 

It is obvious that if electron densities in free atom-components of the solution at the distances of orbital radius r, are similar, the transition processes between boundary atoms of particles are minimal thus favoring the solution formation. 

Apparently, with the closeness of electron densities in free atoms-components, the transition processes between boundary atoms of particles will be minimum, thus favoring the formation of new structure. So, the evaluation of the degree of structural interactions in many cases comes to the comparative evaluation of electron density of valence electrons in free atoms (on averaged orbitals) participating in the process. 

The Tripos [73] force field was used to perform the molecular mechanics calculations, augmented with parameters developed by Doman et al. [74] for the ferrocenyl ligand. In the QM/MM hybrid AIMD simulations, the electronic structure calculation was performed on a reduced system in which each of the substituents that have been removed from the QM part was replaced by a hydrogen atom, in order to saturate the valence of the QM boundary atoms. 

C.A. Coulson, The electronic structure of the boundary atoms of a graphite layer, Fourth Conference on Carbon, Pergamon Press, University of Buffalo, Buffalo, NY, 1960, p. 215. 

The first reported approach along these lines was the localized self-consistent-field (LSCF) method of Ferenczy et al. (1992), originally described for the NDDO level of theory. In this case, the auxiliary region consists of a single frozen orbital on each QM boundary atom. 

These additional pseudo- and quasitorques produce the pseudo- and quasirotations of the hybridization tetrahedron of the boundary atom R. In the linear response approximation, it corresponds to the treatment of the corresponding pseudo- and quasitorques by the fV7/0 1 matrix which is simple (diagonal in the basis of the and SAi variables) in the case of symmetric hydride ... 

Gao JL, P Amara, C Alhambra, MJ Field (1998) A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations. J. Phys. Chem. A 102 (24) 4714-4721... 

Garcia-Viloca M, JL Gao (2004) Generalized hybrid orbital for the treatment of boundary atoms in combined quantum mechanical and molecular mechanical calculations using the semiempirical parameterized model 3 method. Theor. Chem. Acc. Ill (2-6) 280-286... 

Plenary 3. Yuichi Ikuhara (The University of Tokyo) Grain Boundary Atomic Structures in Oxide Ceramics 15 00-19 00 Excursion... 

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