Orbital generalized hybrid

General hybrid orbital functions and natural bond angles... 

To circumvent problems associated with the link atoms different approaches have been developed in which localized orbitals are added to model the bond between the QM and MM regions. Warshel and Levitt [17] were the first to suggest the use of localized orbitals in QM/MM studies. In the local self-consistent field (LSCF) method the QM/MM frontier bond is described with a strictly localized orbital, also called a frozen orbital [43]. These frozen orbitals are parameterized by use of small model molecules and are kept constant in the SCF calculation. The frozen orbitals, and the localized orbital methods in general, must be parameterized for each quantum mechanical model (i.e. energy-calculation method and basis set) to achieve reliable treatment of the boundary [34]. This restriction is partly circumvented in the generalized hybrid orbital (GHO) method [44], In this method, which is an extension of the LSCF method, the boundary MM atom is described by four hybrid orbitals. The three hybrid orbitals that would be attached to other MM atoms are fixed. The remaining hybrid orbital, which represents the bond to a QM atom, participates in the SCF calculation of the QM part. In contrast with LSCF approach the added flexibility of the optimized hybrid orbital means that no specific parameterization of this orbital is needed for each new system. 

For the majority of enzyme-catalysed reactions, covalently bonded parts of the system must be separated into QM and MM regions. There has been considerable research into methods for QM/MM partitioning of covalently bonded systems. Important methods include the local self-consistent field (LSCF) method,114115 and the generalized hybrid orbital (GHO) technique.116 Alternatively a QM atom (or QM pseudo-atom) can be added to allow a bond at the QM/MM frontier for example, the link atom method or the connection atom method. 

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... 

Pu JZ, JL Gao, DG Truhlar (2004a) Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by die generalized hybrid orbital (GHO) method. J. Phys. Chem. A 108 (25) 5454-5463... 

Pu JZ, JL Gao, DG Truhlar (2005) Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. ChemPhysChem 6 (9) 1853—1865... 

Gao J, Truhlar DG (2004) Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions with Molecular Mechanics. J. Phys. Chem. A 108 632-650... 

The local self-consistent field (LSCF) or fragment SCF method has been developed for treating large systems [105,134-139], in which the bonds at the QM/MM junction ( frontier bonds ) are described by strictly localized bond orbitals. These frozen localized bond orbitals are taken from calculations on small models, and remain unchanged in the QM/MM calculation. The LSCF method has been applied at the semiempirical level [134-137], and some developments for ab initio calculations have been made [139]. Gao et al. have developed a similar Generalized Hybrid Orbital method for semiempirical QM/MM calculations, in which the semiempirical parameters of atoms at the junction are modified to enhance the transferability of the localized bond orbitals [140]. Recent developments for ab initio QM/MM calculations include the method of Phillip and Friesner [141], who use Boys-localized orbitals in ab initio Hartree-Fock QM/MM calculations. These orbitals are again taken from calculations on small model systems, and kept frozen in QM/MM calculations. 

A modification of this approach, still at the semiempirical level, has been proposed by Gao et al. [29] under the appellation of generalized hybrid orbital (GHO). In this method, the hybrid orbital of atom Y, which occurs in the SLBO, is explicitly considered and is included in the SCF procedure, which involves now all the orbitals of atom X. The other hybrid orbitals of Y, which would define the bonds with the other neighbors of this atom, are considered to define a core potential of Y, which is reparameterized in the semiempirical scheme to describe the X—Y bond as correctly as possible. The parameterization of the Y atom and the X—Y bond requires the same care as above. 

The covalent bond (ii) is probably a hybrid bond, because generally hybrid orbitals form stronger bonds. As a first approximation we may describe the bond by the w ave-function... 

Kawashima Y, Nakano H, Jung J, Ten-no S (2011) A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals implementation for electronic excited states. Phys. Chem. Chem. Phys. 13 11,731-11,738... 

A similar concept is used in the generalized hybrid-orbital (GHO) method (69-71). In this approach, the QM subsystem is augmented by an additional atom at the QM/MM boundary. All the orbitals of this atom remain fi ozen except the one forming the boundary bond. 

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