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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.

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Claisen rearrangement of chorismate to prephenate.The atoms describing the reaction coordinate are marked with numbers one through four [21].
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pone-0088800-g003: Claisen rearrangement of chorismate to prephenate.The atoms describing the reaction coordinate are marked with numbers one through four [21].

Mentions: We define the reaction coordinate similarly to Claeyssens et al.[28] as the difference in bond length between the breaking O2-C1 bond and the forming C4–C3 bond in chorismate, i.e. (see Fig. 3). The reaction coordinate of the transition state was found to be −0.17 Å using the 6-31G(d) basis set on the MP2 fragment and −0.43 Å for both the cc-pVTZ and cc-pVDZ basis set reaction paths. The convergence with respect to basis set is in good, quantitative agreement with the coordinates obtained by Claeyssens et al. [30] using a QM/MM approach, treating the reaction complex at the LCCSD(T0) level of theory (−0.4 Å). In comparison, the corresponding MP2:RHF ONIOM calculations by Steinmann et al. [21] resulted in transition state reaction coordinates of 0.13, −0.36, and 0.13 Å with the cc-pVDZ, cc-pVTZ and cc-pVQZ basis sets used in the MP2 calculation, respectively.


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

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

Claisen rearrangement of chorismate to prephenate.The atoms describing the reaction coordinate are marked with numbers one through four [21].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0088800-g003: Claisen rearrangement of chorismate to prephenate.The atoms describing the reaction coordinate are marked with numbers one through four [21].
Mentions: We define the reaction coordinate similarly to Claeyssens et al.[28] as the difference in bond length between the breaking O2-C1 bond and the forming C4–C3 bond in chorismate, i.e. (see Fig. 3). The reaction coordinate of the transition state was found to be −0.17 Å using the 6-31G(d) basis set on the MP2 fragment and −0.43 Å for both the cc-pVTZ and cc-pVDZ basis set reaction paths. The convergence with respect to basis set is in good, quantitative agreement with the coordinates obtained by Claeyssens et al. [30] using a QM/MM approach, treating the reaction complex at the LCCSD(T0) level of theory (−0.4 Å). In comparison, the corresponding MP2:RHF ONIOM calculations by Steinmann et al. [21] resulted in transition state reaction coordinates of 0.13, −0.36, and 0.13 Å with the cc-pVDZ, cc-pVTZ and cc-pVQZ basis sets used in the MP2 calculation, respectively.

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