Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction

Lucaioli, Paolo; Nauha, Elisa; Gimondi, Ilaria; Price, Louise S.; Guo, Rui; Iuzzolino, Luca; Singh, Ishwar; Salvalaglio, Matteo; Price, Sarah L.; Blagden, Nicholas

doi:10.1039/c8ce00625c

Cited by 28 publications

(61 citation statements)

References 53 publications

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“…Isolated succinic acid molecules in the gas phase or in solution favour the folded conformation. 69 The two most common experimentally observed polymorphs of succinic acid, β and α are comprised of planar conformers whereas the folded conformer of (4) present in structures S1107, S18857 and S15665. (C) The α structure at 0 K (left) and its transformation at 300 K and 1 bar (right) using the GAFF force field.…”

Section: Succinic Acid: An Example Of Conformational Polymorphismmentioning

confidence: 99%

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

Francia

Price

Nyman

et al. 2020

Crystal Growth & Design

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Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures. File list (2) download file view on ChemRxiv manuscript_Francia_revised.pdf (16.99 MiB) download file view on ChemRxiv Supplementary_Information_Francia.pdf (7.35 MiB)

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Section: Succinic Acid: An Example Of Conformational Polymorphismmentioning

confidence: 99%

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

Francia

Price

Nyman

et al. 2020

Crystal Growth & Design

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“…3). 43 We were challenged to predict the structure. It was readily generated as a metastable polymorph by CSP.…”

Section: Csp_aimmentioning

confidence: 99%

Is zeroth order crystal structure prediction (CSP_0) coming to maturity? What should we aim for in an ideal crystal structure prediction code?

Price

2018

Faraday Discuss.

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Crystal structure prediction based on searching for the global minimum in the lattice energy (CSP_0) is growing in use for guiding the discovery of new materials, for example, new functional materials, new phases of interest to planetary scientists and new polymorphs relevant to pharmaceutical development. This Faraday Discussion can assess the progress of CSP_0 over the range of types of materials to which CSP is currently and could be applied, which depends on our ability to model the variety of interatomic forces in crystals. The basic hypothesis, that the outcome of crystallisation is determined by thermodynamics, needs examining by considering methods of modelling relative thermodynamic stability not only as a function of pressure and temperature, but also of size, solvent and the presence of heterogeneous templates or impurities (CSP_thd). Given that many important materials persist, and indeed may be formed, when they are not the most thermodynamically stable structure, we need to define what would be required of an ideal CSP code (CSP_aim).

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“…276 In the framework of crystal engineering, it has been crystallized with many other molecules in order to develop cocrystals and salts having desirable physicochemical properties. 251,[296][297][298][299] Succinic acid is employed as a precursor of polyesters, as a component of some resins, and to develop biodegradable polymers of interest in tissue engineering. 295,300 The characteristics and mechanical properties of many interesting polymers and materials based on, or related to, succinic acid have long been investigated.…”

Section: Succinic Acidmentioning

confidence: 99%

“…The computational results agree satisfactorily with the experimental results. [246][247][248][249][250][251] The experimental volume reported by Lucaioli et al 251 is underestimated by 3.9%. The effect of dispersion interactions in the structure of succinic acid is, as in the case of maleic acid, huge.…”

Section: Succinic Acidmentioning

confidence: 99%

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Organic acids under pressure: elastic properties, negative mechanical phenomena and pressure induced phase transitions in the lactic, maleic, succinic and citric acids

Colmenero

2020

Mater. Adv.

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Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction

Abstract: A new polymorph of succinic acid is an unusually challenging test for metastable polymorph prediction.

Cited by 28 publications

References 53 publications

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

Systematic Finite-Temperature Reduction of Crystal Energy Landscapes

Is zeroth order crystal structure prediction (CSP_0) coming to maturity? What should we aim for in an ideal crystal structure prediction code?

Organic acids under pressure: elastic properties, negative mechanical phenomena and pressure induced phase transitions in the lactic, maleic, succinic and citric acids

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