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Integrating steepest-descent reaction pathways for large molecules
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10.1063/1.3593456
/content/aip/journal/jcp/134/20/10.1063/1.3593456
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/20/10.1063/1.3593456

Figures

Image of FIG. 1.
FIG. 1.

Reaction scheme of the β-lactam formation step in iso-penicillin synthesis by IPNS. For clarity, only the reactive core of the active site is shown. The atomic centers involved in the β-lactam ring closure are shown in light gray (red online).

Image of FIG. 2.
FIG. 2.

Optimized TS geometry. Atoms included in the ONIOM QM layer are shown in ball and stick form, while atoms included in the MM layer are shown in wire-frame form. (a) Full view of the 5368 atom system. (b) Close-up view of the active site. Atomic centers displayed with a red halo correspond to those shown in light gray (red online) in Fig. 1.

Image of FIG. 3.
FIG. 3.

Energy profile of the reaction path for the β-lactam formation reaction using EulerPC integration with a step size of 0.1 amu1/2 bohr using Hessian updating at all points (solid curve). Results of EulerPC integration with a step size of 0.2 amu1/2 bohr using analytic Hessian re-calculation every 10 points (□), analytic Hessian re-calculation every 20 points (◯), and all updated Hessians (△) are also shown.

Image of FIG. 4.
FIG. 4.

C–N bond distance as a function of the reaction coordinate for the β–lactam formation reaction using EulerPC integration with a step size of 0.1 amu1/2 bohr using Hessian updating at all points (solid curve). Results of EulerPC integration with a step size of 0.2 amu1/2 bohr using analytic Hessian re-calculation every 10 points (□), analytic Hessian re-calculation every 20 points (◯), and all updated Hessians (△) are also shown.

Image of FIG. 5.
FIG. 5.

Fe–S (a) and S–C (b) bond coordinates as functions of the reaction coordinate for the β–lactam formation reaction using EulerPC integration with a step size of 0.1 amu1/2 bohr using Hessian updating at all points (solid curve). Results of EulerPC integration with a step size of 0.2 amu1/2 bohr using analytic Hessian re-calculation every 10 points (□), analytic Hessian re-calculation every 20 points (◯), and all updated Hessians (△) are also shown.

Image of FIG. 6.
FIG. 6.

S–C–C angle as a function of the reaction coordinate for the β–lactam formation reaction using EulerPC integration with a step size of 0.1 amu1/2 bohr using Hessian updating at all points (solid curve). Results of EulerPC integration with a step size of 0.2 amu1/2 bohr using analytic Hessian re-calculation every 10 points (□), analytic Hessian re-calculation every 20 points (◯), and all updated Hessians (△) are also shown.

Image of FIG. 7.
FIG. 7.

C–C–C–O dihedral angle (all atoms shown in light gray (red online) in Fig. 1) as a function of the reaction coordinate for the β–lactam formation reaction using EulerPC integration with a step size of 0.1 amu1/2 bohr using Hessian updating at all points (solid curve). Results of EulerPC integration with a step size of 0.2 amu1/2 bohr using analytic Hessian re-calculation every 10 points (□), analytic Hessian re-calculation every 20 points (◯), and all updated Hessians (△) are also shown.

Tables

Generic image for table
Table I.

Performance of EulerPC IRC integration for the β–lactam formation reaction.

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/content/aip/journal/jcp/134/20/10.1063/1.3593456
2011-05-23
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Integrating steepest-descent reaction pathways for large molecules
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/20/10.1063/1.3593456
10.1063/1.3593456
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