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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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Lattice energy landscape following CrystalOptimizer results for molecule (XXVI). The structures generated following the refinement of the 1413 structures generated by the global search stage within 30 kJ mol−1 of the lowest-energy structure are shown. The lowest 100 unique structures span a lattice energy range of 20.8 kJ mol−1 from the global minimum, whilst only 17 unique structures are identified with lattice energies within 10 kJ mol−1 of the global minimum. The square denotes the experimental form, the solid line is the 10 kJ mol−1 cut-off from the global minimum, and the heavy and light dashed lines are the 20 and 30 kJ mol−1 cut-offs from the global minimum, respectively.
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fig11: Lattice energy landscape following CrystalOptimizer results for molecule (XXVI). The structures generated following the refinement of the 1413 structures generated by the global search stage within 30 kJ mol−1 of the lowest-energy structure are shown. The lowest 100 unique structures span a lattice energy range of 20.8 kJ mol−1 from the global minimum, whilst only 17 unique structures are identified with lattice energies within 10 kJ mol−1 of the global minimum. The square denotes the experimental form, the solid line is the 10 kJ mol−1 cut-off from the global minimum, and the heavy and light dashed lines are the 20 and 30 kJ mol−1 cut-offs from the global minimum, respectively.

Mentions: The resulting energy landscape is presented in Fig. 11 ▸. The experimental form is found at the global minimum, with another 17 structures having lattice energy within 10 kJ mol−1 from the global minimum, and 92 within 20 kJ mol−1. We note that these numbers are significantly lower than the corresponding numbers of structures determined at the end of the global search (81 and 465, respectively); thus, refinement using a more accurate lattice energy model and taking account of a higher degree of conformational flexibility has resulted in substantial clarification of the polymorphic landscape. We also note that the geometry of the experimental structure is reproduced with good accuracy (RMSD20 = 0.330 Å), as illustrated in Fig. 12 ▸ and Table 3 ▸.


Accurate and efficient representation of intra ­ molecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models
Lattice energy landscape following CrystalOptimizer results for molecule (XXVI). The structures generated following the refinement of the 1413 structures generated by the global search stage within 30 kJ mol−1 of the lowest-energy structure are shown. The lowest 100 unique structures span a lattice energy range of 20.8 kJ mol−1 from the global minimum, whilst only 17 unique structures are identified with lattice energies within 10 kJ mol−1 of the global minimum. The square denotes the experimental form, the solid line is the 10 kJ mol−1 cut-off from the global minimum, and the heavy and light dashed lines are the 20 and 30 kJ mol−1 cut-offs from the global minimum, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5134761&req=5

fig11: Lattice energy landscape following CrystalOptimizer results for molecule (XXVI). The structures generated following the refinement of the 1413 structures generated by the global search stage within 30 kJ mol−1 of the lowest-energy structure are shown. The lowest 100 unique structures span a lattice energy range of 20.8 kJ mol−1 from the global minimum, whilst only 17 unique structures are identified with lattice energies within 10 kJ mol−1 of the global minimum. The square denotes the experimental form, the solid line is the 10 kJ mol−1 cut-off from the global minimum, and the heavy and light dashed lines are the 20 and 30 kJ mol−1 cut-offs from the global minimum, respectively.
Mentions: The resulting energy landscape is presented in Fig. 11 ▸. The experimental form is found at the global minimum, with another 17 structures having lattice energy within 10 kJ mol−1 from the global minimum, and 92 within 20 kJ mol−1. We note that these numbers are significantly lower than the corresponding numbers of structures determined at the end of the global search (81 and 465, respectively); thus, refinement using a more accurate lattice energy model and taking account of a higher degree of conformational flexibility has resulted in substantial clarification of the polymorphic landscape. We also note that the geometry of the experimental structure is reproduced with good accuracy (RMSD20 = 0.330 Å), as illustrated in Fig. 12 ▸ and Table 3 ▸.

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.