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Accurate and efficient representation of intra ­ molecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models

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ABSTRACT

1172: The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput., 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.

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LAM placements for ROY. (a) Initial regular grid (20 LAMs), with  = ±20°. (b) Final LAM set (41 LAMs) derived by adaptive LAM placement algorithm. Crosses represent LAMs in the initial regular grid, circles LAMs added by adaptive placement algorithm; triangles show the positions of experimentally known conformations.
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fig5: LAM placements for ROY. (a) Initial regular grid (20 LAMs), with = ±20°. (b) Final LAM set (41 LAMs) derived by adaptive LAM placement algorithm. Crosses represent LAMs in the initial regular grid, circles LAMs added by adaptive placement algorithm; triangles show the positions of experimentally known conformations.

Mentions: Starting with an initial uniform grid generated with = ±20° and comprising 20 LAMs, at the B3LYP/6-31G(d,p) level of theory, the application of the LAM generation algorithm results in the final set of 41 LAMs shown in Fig. 5 ▸(b). The minimum spacing between these LAMs is 14°; a regular grid constructed over the original domain would require about 163 LAMs to achieve the same minimum spacing ( ≃ ±7°). However, many of these LAMs would be unnecessary: for example, we note that the adaptive algorithm does not introduce any new LAM points in the region . Fig. 5 ▸(b) also shows the positions of the six known experimental forms of ROY (Yu, 2010 ▸). This demonstrates that the algorithm does indeed focus computational effort on relevant areas of conformational space.


Accurate and efficient representation of intra ­ molecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models
LAM placements for ROY. (a) Initial regular grid (20 LAMs), with  = ±20°. (b) Final LAM set (41 LAMs) derived by adaptive LAM placement algorithm. Crosses represent LAMs in the initial regular grid, circles LAMs added by adaptive placement algorithm; triangles show the positions of experimentally known conformations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5134761&req=5

fig5: LAM placements for ROY. (a) Initial regular grid (20 LAMs), with = ±20°. (b) Final LAM set (41 LAMs) derived by adaptive LAM placement algorithm. Crosses represent LAMs in the initial regular grid, circles LAMs added by adaptive placement algorithm; triangles show the positions of experimentally known conformations.
Mentions: Starting with an initial uniform grid generated with = ±20° and comprising 20 LAMs, at the B3LYP/6-31G(d,p) level of theory, the application of the LAM generation algorithm results in the final set of 41 LAMs shown in Fig. 5 ▸(b). The minimum spacing between these LAMs is 14°; a regular grid constructed over the original domain would require about 163 LAMs to achieve the same minimum spacing ( ≃ ±7°). However, many of these LAMs would be unnecessary: for example, we note that the adaptive algorithm does not introduce any new LAM points in the region . Fig. 5 ▸(b) also shows the positions of the six known experimental forms of ROY (Yu, 2010 ▸). This demonstrates that the algorithm does indeed focus computational effort on relevant areas of conformational space.

View Article: PubMed Central - HTML - PubMed

ABSTRACT

1172: The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015 ▸). J. Chem. Theory Comput., 1957–1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement. The entire search space of the relevant molecule’s conformations is initially evaluated using a coarse, low accuracy grid. Additional LAM points are then placed at appropriate points determined via an automated process, aiming to minimize the computational effort expended in high-energy regions whilst maximizing the accuracy in low-energy regions. As the size, complexity and flexibility of molecules increase, the reduction in computational cost becomes marked. This improvement is illustrated with energy calculations for benzoic acid and the ROY molecule, and a CSP study of molecule (XXVI) from the sixth blind test [Reilly et al. (2016 ▸). Acta Cryst. B, 439–459], which is challenging due to its size and flexibility. Its known experimental form is successfully predicted as the global minimum. The computational cost of the study is tractable without the need to make unphysical simplifying assumptions.

No MeSH data available.


Related in: MedlinePlus