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Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.

Christensen AS, Steinmann C, Fedorov DG, Jensen JH - PLoS ONE (2014)

Bottom Line: The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level.MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile.For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.

Show MeSH
denotes the frozen domain (green);  denotes the polarizable domain (blue);  denotes the active domain (red);  denotes fragment , for which the MP2 energy and gradients are evaluated (yellow).
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pone-0088800-g001: denotes the frozen domain (green); denotes the polarizable domain (blue); denotes the active domain (red); denotes fragment , for which the MP2 energy and gradients are evaluated (yellow).

Mentions: For a given molecular system, we define two domains (“frozen”) and (“active”). Domain is defined as all atoms having a frozen geometry and domain is defined as all atoms whose positions are optimized. Each domain is further divided into a number of molecular fragments. In the frozen domain and dimers methods (FDD) [20], the domain with frozen geometry is further divided as a polarizable domain with frozen geometry, and a domain with frozen geometry and fragment electron densities that are not updated after they have been calculated the first time. The EFMO energy [21] is then given by:(2)where and are the internal energies of domains and , respectively, is the interaction between domains and , is the interaction between domains and and is the classical total polarization energy of the whole system. In our EFMO-RHF:MP2 extension, we evaluate the internal energies of domain and at the RHF level. Furthermore, we specify a single fragment (“high level”) from the active domain to be treated at the MP2 level of theory (see Fig. 1 for a schematic overview). The total EFMO-RHF:MP2 energy is then given as(3)where is the MP2 correlation energy of fragment .


Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.

Christensen AS, Steinmann C, Fedorov DG, Jensen JH - PLoS ONE (2014)

denotes the frozen domain (green);  denotes the polarizable domain (blue);  denotes the active domain (red);  denotes fragment , for which the MP2 energy and gradients are evaluated (yellow).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928295&req=5

pone-0088800-g001: denotes the frozen domain (green); denotes the polarizable domain (blue); denotes the active domain (red); denotes fragment , for which the MP2 energy and gradients are evaluated (yellow).
Mentions: For a given molecular system, we define two domains (“frozen”) and (“active”). Domain is defined as all atoms having a frozen geometry and domain is defined as all atoms whose positions are optimized. Each domain is further divided into a number of molecular fragments. In the frozen domain and dimers methods (FDD) [20], the domain with frozen geometry is further divided as a polarizable domain with frozen geometry, and a domain with frozen geometry and fragment electron densities that are not updated after they have been calculated the first time. The EFMO energy [21] is then given by:(2)where and are the internal energies of domains and , respectively, is the interaction between domains and , is the interaction between domains and and is the classical total polarization energy of the whole system. In our EFMO-RHF:MP2 extension, we evaluate the internal energies of domain and at the RHF level. Furthermore, we specify a single fragment (“high level”) from the active domain to be treated at the MP2 level of theory (see Fig. 1 for a schematic overview). The total EFMO-RHF:MP2 energy is then given as(3)where is the MP2 correlation energy of fragment .

Bottom Line: The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level.MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile.For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta basis sets the increase in CPU time relative to RHF is roughly a factor of two.

Show MeSH