Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. II. Smoothed intramolecular potentials

2019 ◽  
Vol 75 (3) ◽  
pp. 423-433 ◽  
Author(s):  
Isaac J. Sugden ◽  
Claire S. Adjiman ◽  
Constantinos C. Pantelides
Keyword(s):  
Structure Prediction ◽  
Weighted Average ◽  
Lattice Energy ◽  
Comparative Investigation ◽  
Computational Effort ◽  
Flufenamic Acid ◽  
Computational Time ◽  
Crystal Structure Prediction ◽  
Efficient Representation ◽  
First Time

The application of crystal structure prediction (CSP) to industrially relevant molecules requires the handling of increasingly large and flexible compounds. A revised model for the effect of molecular flexibility on the lattice energy that removes the discontinuities and non-differentiabilities present in earlier models (Sugden et al., 2016), with a view to improving the performance of CSP is presented. The approach is based on the concept of computing a weighted average of local models, and has been implemented within the CrystalPredictor code. Through the comparative investigation of several compounds studied in earlier literature, it is shown that this new model results in large reductions in computational effort (of up to 65%) and in significant increases in reliability. The approach is further applied to investigate, for the first time, the computational polymorphic landscape of flufenamic acid for Z′ = 1 structures, resulting in the successful identification of all three experimentally resolved polymorphs within reasonable computational time.

scholarly journals Blind crystal structure prediction of a novel second polymorph of 1-hydroxy-7-azabenzotriazole

2006 ◽  
Vol 62 (4) ◽  
pp. 642-650 ◽  
Author(s):  
Harriott Nowell ◽  
Christopher S. Frampton ◽  
Julie Waite ◽  
Sarah L. Price
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Structure Refinement ◽  
Lattice Energy ◽  
Polymorphic Form ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Coupling Reagent ◽  
Energy Penalty ◽  
Alcohol Solvents

The commercially available peptide coupling reagent 1-hydroxy-7-azabenzotriazole has been shown to crystallize in two polymorphic forms. The two polymorphs differ in their hydrogen-bonding motif, with form I having an R_2^2(10) dimer motif and form II having a C(5) chain motif. The previously unreported form II was used as an informal blind test of computational crystal structure prediction for flexible molecules. The crystal structure of form II has been successfully predicted blind from lattice-energy minimization calculations following a series of searches using a large number of rigid conformers. The structure for form II was the third lowest in energy with form I found as the global minimum, with the energy calculated as the sum of the ab initio intramolecular energy penalty for conformational distortion and the intermolecular lattice energy which is calculated from a distributed multipole representation of the charge density. The predicted structure was sufficiently close to the experimental structure that it could be used as a starting model for crystal structure refinement. A subsequent limited polymorph screen failed to yield a third polymorphic form, but demonstrated that alcohol solvents are implicated in the formation of the form I dimer structure.

scholarly journals Accurate and efficient representation of intramolecular energy inab initiogeneration of crystal structures. I. Adaptive local approximate models

2016 ◽  
Vol 72 (6) ◽  
pp. 864-874 ◽  
Author(s):  
Isaac Sugden ◽  
Claire S. Adjiman ◽  
Constantinos C. Pantelides
Keyword(s):  
Structure Prediction ◽  
Computational Cost ◽  
Search Space ◽  
Approximate Model ◽  
High Energy ◽  
Computational Effort ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Acta Cryst ◽  
Simplifying Assumptions

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 theCrystalPredictor II[Habgoodet al.(2015).J. Chem. Theory Comput.11, 1957–1969] program is presented, where the most efficient use of computational effort is ensuredviathe 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 determinedviaan 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 [Reillyet al.(2016).Acta Cryst.B72, 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.

scholarly journals Insight from energy surfaces: structure prediction by lattice energy exploration

2014 ◽  
Vol 70 (a1) ◽  
pp. C28-C28
Author(s):  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Crystal Packing ◽  
Lattice Energy ◽  
Organic Crystals ◽  
Crystal Structure Prediction ◽  
Stability Order ◽  
The Stability ◽  
Solid Form ◽  
Energy Surfaces

A long-standing challenge for the application of computational chemistry in the field of crystallography is the prediction of crystal packing, given no more than the chemical bonding of the molecules being crystallised. Recent years have seen significant progress towards reliable crystal structure prediction methods, even for traditionally challenging systems involving flexible molecules and multi-component solids [1]. These methods are based on global searches of the lattice energy surface: a search is performed to locate all possible packing arrangements, and these structures are ranked by their calculated energy [2]. One aim of this lecture is to provide an overview of advances in methods for crystal structure prediction, focussing on molecular organic crystals, and highlighting strategies that are being explored to extend the reach of these methods to more complex systems. A second aim is to discuss the range applications of crystal structure prediction calculations, which have traditionally included solid form screening, particularly of pharmaceutically active molecules, and structure determination. As energy models become more reliable at correctly ranking the stability order of putative structures, and the timescale required for structure searching decreases, crystal structure prediction has the potential for the discovery of novel molecular materials with targeted properties. Prospects for computer-guided discovery of materials will be discussed.

The polymorphs of ROY: application of a systematic crystal structure prediction technique

2012 ◽  
Vol 68 (6) ◽  
pp. 677-685 ◽  
Author(s):  
Manolis Vasileiadis ◽  
Andrei V. Kazantsev ◽  
Panagiotis G. Karamertzanis ◽  
Claire S. Adjiman ◽  
Constantinos C. Pantelides
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Search Algorithm ◽  
Lattice Energy ◽  
Relative Energy ◽  
Quantum Mechanical ◽  
Crystal Structure Prediction ◽  
Worst Case ◽  
Prediction Technique ◽  
Prediction Techniques

We investigate the ability of current ab initio crystal structure prediction techniques to identify the polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, also known as ROY because of the red, orange and yellow colours of its polymorphs. We use a methodology combining the generation of a large number of structures based on a computationally inexpensive model using the CrystalPredictor global search algorithm, and the further minimization of the most promising of these structures using the CrystalOptimizer local minimization algorithm which employs an accurate, yet efficiently constructed, model based on isolated-molecule quantum-mechanical calculations. We demonstrate that this approach successfully predicts the seven experimentally resolved structures of ROY as lattice-energy minima, with five of these structures being within the 12 lowest energy structures predicted. Some of the other low-energy structures identified are likely candidates for the still unresolved polymorphs of this molecule. The relative stability of the predicted structures only partially matches that of the experimentally resolved polymorphs. The worst case is that of polymorph ON, whose relative energy with respect to Y is overestimated by 6.65 kJ mol−1. This highlights the need for further developments in the accuracy of the energy calculations.

Structural investigation ofN,N′-methylenebisacrylamideviaX-ray diffraction assisted by crystal structure prediction

2015 ◽  
Vol 48 (2) ◽  
pp. 550-557 ◽  
Author(s):  
Claudia Graiff ◽  
Daniele Pontiroli ◽  
Laura Bergamonti ◽  
Chiara Cavallari ◽  
Pier Paolo Lottici ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Prediction ◽  
Density Functional ◽  
Geometry Optimization ◽  
Lattice Energy ◽  
Strong Interactions ◽  
Crystal Structure Prediction ◽  
X Ray Diffraction ◽  
X Ray

The crystal structure ofN,N′-methylenebisacrylamide was determined through the geometry optimization of the molecular unit with density functional theory and conformational analysis, and then through the calculation of the packingviaa crystal structure prediction protocol, based on lattice energy minimization. All the calculated structures were ranked, comparing their powder pattern with the laboratory low-quality X-ray diffraction data. Rietveld refinement of the best three proposed structures allowed the most probable crystal arrangement of the molecules to be obtained. This approach was essential for disentangling the twinning problems affecting the single-crystal X-ray diffraction data, collected on samples obtainedviarecrystallization of powder, which definitely confirmed the predicted model. It was found thatN,N′-methylenebisacrylamide shows a monoclinic structure in the space groupC2/c, with lattice parametersa= 17.822 (12),b= 4.850 (3),c= 19.783 (14) Å, β = 102.370 (9)°,V= 1670 (2) Å3. Two strong interactions between the amide protons and the carbonyl groups of neighbouring molecules were found along thebaxis, determining the crystal growth in the form of wires in this direction. This work provides a further example of how computational methods may help to investigate low-quality molecular crystals with standard diffraction techniques.

scholarly journals Reducing Crystal Structure Overprediction of Ibuprofen with Large Scale Molecular Dynamics Simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Nicholas Francesco Francia ◽  
Louise Price ◽  
Matteo Salvalaglio
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Pharmaceutical Industry ◽  
Molecular Dynamics Simulations ◽  
Structure Prediction ◽  
Large Scale ◽  
Lattice Energy ◽  
Crystal Form ◽  
Crystal Structure Prediction ◽  
Dynamics Simulations

The control of the crystal form is a central issue in the pharmaceutical industry. The identification of putative polymorphs through Crystal Structure Prediction (CSP) methods is based on lattice energy...

scholarly journals Predicting Porous Molecular Crystals and Clathrates

2014 ◽  
Vol 70 (a1) ◽  
pp. C1625-C1625
Author(s):  
Jonas Nyman ◽  
Graeme Day
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Molecular Crystals ◽  
Volume Ratio ◽  
Lattice Energy ◽  
Computer Algorithms ◽  
Crystal Structure Prediction ◽  
Powerful Method ◽  
Simple Molecules

The last decade has seen dramatic improvements in the theories and computer algorithms underlying computational Crystal Structure Predictions [1]. It is now possible to reliably obtain the most likely crystal structures of at least simple molecules starting from nothing more than a drawing of the molecule. We can now go even further and look for rare and exotic kinds of crystals such as porous molecular crystals, clathrates and inclusion compounds among our predictions and calculate their physical properties [2], paving the way for the "science of hypothetical materials". In our poster, we present results on the prediction of fluorophenol xenon clathrates. We have performed crystal structure predictions by global lattice energy searches on o- and m-fluorophenol. The predicted structures have then been analyzed for porosity and their likelihood of being clathrates. From the several thousands of predicted structures, we select a few likely candidates according to an empirical rule based on the guest to host volume ratio [3]. Results from solid state xenon-129 NMR indicate that we have successfully determined the crystal structures of both o- and m-fluorophenol xenon clathrates and we suggest that Crystal Structure Prediction in combination with xenon-129 NMR is a powerful method for determining the structures of clathrates in general.

scholarly journals Solvent inclusion in the crystal structure of bis[(adamantan-1-yl)methanaminium chloride] 1,4-dioxane hemisolvate monohydrate explained using the computed crystal energy landscape

2016 ◽  
Vol 72 (9) ◽  
pp. 1348-1352 ◽  
Author(s):  
Sharmarke Mohamed
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Structure Prediction ◽  
Unit Cell Volume ◽  
Energy Landscape ◽  
Lattice Energy ◽  
Low Energy ◽  
Energy Minimum ◽  
Crystal Structure Prediction ◽  
Hydrogen Bonding Interactions

Repeated attempts to crystallize 1-adamantanemethylamine hydrochloride as an anhydrate failed but the salt was successfully crystallized as a solvate (2C11H20N+·2Cl−·0.5C4H8O2·H2O), with water and 1,4-dioxane playing a structural role in the crystal and engaging in hydrogen-bonding interactions with the cation and anion. Computational crystal-structure prediction was used to rationalize the solvent-inclusion behaviour of this salt by computing the solvent-accessible voids in the predicted low-energy structures for the anhydrate: the global lattice-energy minimum structure, which has the same packing of the ions as the solvate, has solvent-accessible voids that account for 3.71% of the total unit-cell volume and is 6 kJ mol−1more stable than the next most stable predicted structure.

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