1
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Yin X, Gounaris CE. Search methods for inorganic materials crystal structure prediction. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2021.100726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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2
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Beran GJO, Sugden IJ, Greenwell C, Bowskill DH, Pantelides CC, Adjiman CS. How many more polymorphs of ROY remain undiscovered. Chem Sci 2022; 13:1288-1297. [PMID: 35222912 PMCID: PMC8809489 DOI: 10.1039/d1sc06074k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (a.k.a. ROY) holds the current record for the largest number of fully characterized organic crystal polymorphs. Four of these polymorph structures have been reported since 2019, raising the question of how many more ROY polymorphs await future discovery. Employing crystal structure prediction and accurate energy rankings derived from conformational energy-corrected density functional theory, this study presents the first crystal energy landscape for ROY that agrees well with experiment. The lattice energies suggest that the seven most stable ROY polymorphs (and nine of the twelve lowest-energy forms) on the Z' = 1 landscape have already been discovered experimentally. Discovering any new polymorphs at ambient pressure will likely require specialized crystallization techniques capable of trapping metastable forms. At pressures above 10 GPa, however, a new crystal form is predicted to become enthalpically more stable than all known polymorphs, suggesting that further high-pressure experiments on ROY may be warranted. This work highlights the value of high-accuracy crystal structure prediction for solid-form screening and demonstrates how pragmatic conformational energy corrections can overcome the limitations of conventional density functionals for conformational polymorphs.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - Isaac J Sugden
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Chandler Greenwell
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - David H Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Constantinos C Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Claire S Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
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3
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Han Y, Luo H, Lu Q, Liu Z, Liu J, Zhang J, Wei Z, Li J. Quantum Mechanical-Based Stability Evaluation of Crystal Structures for HIV-Targeted Drug Cabotegravir. Molecules 2021; 26:molecules26237178. [PMID: 34885762 PMCID: PMC8659202 DOI: 10.3390/molecules26237178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/23/2022] Open
Abstract
The long-acting parenteral formulation of the HIV integrase inhibitor cabotegravir (GSK744) is currently being developed to prevent HIV infections, benefiting from infrequent dosing and high efficacy. The crystal structure can affect the bioavailability and efficacy of cabotegravir. However, the stability determination of crystal structures of GSK744 have remained a challenge. Here, we introduced an ab initio protocol to determine the stability of the crystal structures of pharmaceutical molecules, which were obtained from crystal structure prediction process starting from the molecular diagram. Using GSK744 as a case study, the ab initio predicted that Gibbs free energy provides reliable further refinement of the predicted crystal structures and presents its capability for becoming a crystal stability determination approach in the future. The proposed work can assist in the comprehensive screening of pharmaceutical design and can provide structural predictions and stability evaluation for pharmaceutical crystals.
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Affiliation(s)
- Yanqiang Han
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China; (Y.H.); (Z.L.)
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China; (H.L.); (Q.L.)
| | - Hongyuan Luo
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China; (H.L.); (Q.L.)
| | - Qianqian Lu
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China; (H.L.); (Q.L.)
| | - Zeying Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China; (Y.H.); (Z.L.)
| | - Jinyun Liu
- Key Laboratory of Functional Molecular Solids of the Ministry of Education, Anhui Provincial Engineering Laboratory for New-Energy Vehicle Battery Energy-Storage Materials, School of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, China
- Correspondence: (J.L.); (Z.W.); (J.L.)
| | - Jiarui Zhang
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Zhiyun Wei
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China; (Y.H.); (Z.L.)
- Correspondence: (J.L.); (Z.W.); (J.L.)
| | - Jinjin Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China; (Y.H.); (Z.L.)
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China; (H.L.); (Q.L.)
- Correspondence: (J.L.); (Z.W.); (J.L.)
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4
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Pawlak T, Sudgen I, Bujacz G, Iuga D, Brown SP, Potrzebowski MJ. Synergy of Solid-State NMR, Single-Crystal X-ray Diffraction, and Crystal Structure Prediction Methods: A Case Study of Teriflunomide (TFM). CRYSTAL GROWTH & DESIGN 2021; 21:3328-3343. [PMID: 34267599 PMCID: PMC8273857 DOI: 10.1021/acs.cgd.1c00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/27/2021] [Indexed: 06/13/2023]
Abstract
In this work, for the first time, we present the X-ray diffraction crystal structure and spectral properties of a new, room-temperature polymorph of teriflunomide (TFM), CSD code 1969989. As revealed by DSC, the low-temperature TFM polymorph recently reported by Gunnam et al. undergoes a reversible thermal transition at -40 °C. This reversible process is related to a change in Z' value, from 2 to 1, as observed by variable-temperature 1H-13C cross-polarization (CP) magic-angle spinning (MAS) solid-state NMR, while the crystallographic system is preserved (triclinic). Two-dimensional 13C-1H and 1H-1H double-quantum MAS NMR spectra are consistent with the new room-temperature structure, including comparison with GIPAW (gauge-including projector augmented waves) calculated NMR chemical shifts. A crystal structure prediction procedure found both experimental teriflunomide polymorphs in the energetic global minimum region. Differences between the polymorphs are seen for the torsional angle describing the orientation of the phenyl ring relative to the planarity of the TFM molecule. In the low-temperature structure, there are two torsion angles of 4.5 and 31.9° for the two Z' = 2 molecules, while in the room-temperature structure, there is disorder that is modeled with ∼50% occupancy between torsion angles of -7.8 and 28.6°. These observations are consistent with a broad energy minimum as revealed by DFT calculations. PISEMA solid-state NMR experiments show a reduction in the C-H dipolar coupling in comparison to the static limit for the aromatic CH moieties of 75% and 51% at 20 and 40 °C, respectively, that is indicative of ring flips at the higher temperature. Our study shows the power of combining experiments, namely DSC, X-ray diffraction, and MAS NMR, with DFT calculations and CSP to probe and understand the solid-state landscape, and in particular the role of dynamics, for pharmaceutical molecules.
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Affiliation(s)
- Tomasz Pawlak
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Isaac Sudgen
- Molecular
Systems Engineering Group, Centre for Process Systems Engineering,
Department of Chemical Engineering, Imperial
College London, London SW7 2AZ, U.K.
| | - Grzegorz Bujacz
- Institute
of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Dinu Iuga
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Steven P. Brown
- Department
of Physics, University of Warwick, Coventry CV4 7AL, U.K.
| | - Marek J. Potrzebowski
- Centre
of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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5
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Bowskill DH, Sugden IJ, Konstantinopoulos S, Adjiman CS, Pantelides CC. Crystal Structure Prediction Methods for Organic Molecules: State of the Art. Annu Rev Chem Biomol Eng 2021; 12:593-623. [PMID: 33770462 DOI: 10.1146/annurev-chembioeng-060718-030256] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.
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Affiliation(s)
- David H Bowskill
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Isaac J Sugden
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Stefanos Konstantinopoulos
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Claire S Adjiman
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Constantinos C Pantelides
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
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6
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Aina AA, Misquitta AJ, Price SL. A non-empirical intermolecular force-field for trinitrobenzene and its application in crystal structure prediction. J Chem Phys 2021; 154:094123. [PMID: 33685142 DOI: 10.1063/5.0043746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An anisotropic atom-atom distributed intermolecular force-field (DIFF) for rigid trinitrobenzene (TNB) is developed using distributed multipole moments, dipolar polarizabilities, and dispersion coefficients derived from the charge density of the isolated molecule. The short-range parameters of the force-field are fitted to first- and second-order symmetry-adapted perturbation theory dimer interaction energy calculations using the distributed density-overlap model to guide the parameterization of the short-range anisotropy. The second-order calculations are used for fitting the damping coefficients of the long-range dispersion and polarization and also for relaxing the isotropic short-range coefficients in the final model, DIFF-srL2(rel). We assess the accuracy of the unrelaxed model, DIFF-srL2(norel), and its equivalent without short-range anisotropy, DIFF-srL0(norel), as these models are easier to derive. The model potentials are contrasted with empirical models for the repulsion-dispersion fitted to organic crystal structures with multipoles of iterated stockholder atoms (ISAs), FIT(ISA,L4), and with Gaussian Distributed Analysis (GDMA) multipoles, FIT(GDMA,L4), commonly used in modeling organic crystals. The potentials are tested for their ability to model the solid state of TNB. The non-empirical models provide more reasonable relative lattice energies of the three polymorphs of TNB and propose more sensible hypothetical structures than the empirical force-field (FIT). The DIFF-srL2(rel) model successfully has the most stable structure as one of the many structures that match the coordination sphere of form III. The neglect of the conformational flexibility of the nitro-groups is a significant approximation. This methodology provides a step toward force-fields capable of representing all phases of a molecule in molecular dynamics simulations.
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Affiliation(s)
- Alex A Aina
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
| | - Alston J Misquitta
- School of Physics and Astronomy and The Thomas Young Centre for Theory and Simulation of Materials at Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Sarah L Price
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
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7
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Kamat K, Guo R, Reutzel-Edens SM, Price SL, Peters B. Diabat method for polymorph free energies: Extension to molecular crystals. J Chem Phys 2020; 153:244105. [PMID: 33380078 DOI: 10.1063/5.0024727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lattice-switch Monte Carlo and the related diabat methods have emerged as efficient and accurate ways to compute free energy differences between polymorphs. In this work, we introduce a one-to-one mapping from the reference positions and displacements in one molecular crystal to the positions and displacements in another. Two features of the mapping facilitate lattice-switch Monte Carlo and related diabat methods for computing polymorph free energy differences. First, the mapping is unitary so that its Jacobian does not complicate the free energy calculations. Second, the mapping is easily implemented for molecular crystals of arbitrary complexity. We demonstrate the mapping by computing free energy differences between polymorphs of benzene and carbamazepine. Free energy calculations for thermodynamic cycles, each involving three independently computed polymorph free energy differences, all return to the starting free energy with a high degree of precision. The calculations thus provide a force field independent validation of the method and allow us to estimate the precision of the individual free energy differences.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Rui Guo
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Susan M Reutzel-Edens
- Small Molecule Design and Development, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Sarah L Price
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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8
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Guo R, Uddin MN, Price LS, Price SL. Calculation of Diamagnetic Susceptibility Tensors of Organic Crystals: From Coronene to Pharmaceutical Polymorphs. J Phys Chem A 2020; 124:1409-1420. [PMID: 31951408 PMCID: PMC7145345 DOI: 10.1021/acs.jpca.9b07104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Understanding
why crystallization in strong magnetic fields can
lead to new polymorphs requires methods to calculate the diamagnetic
response of organic molecular crystals. We develop the calculation
of the macroscopic diamagnetic susceptibility tensor, χcryst, for organic molecular crystals using periodic density
functional methods. The crystal magnetic susceptibility tensor, χcryst, for all experimentally known polymorphs,
and its molecular counterpart, χmol,
are calculated for flexible pharmaceuticals such as carbamazepine,
flufenamic acid, and chalcones, and rigid molecules, such as benzene,
pyridine, acridine, anthracene, and coronene, whose molecular magnetic
properties have been traditionally studied. A tensor addition method
is developed to approximate the crystal diamagnetic susceptibility
tensor, χcryst, from the molecular one, χmol, giving good agreement with those calculated
directly using the more costly periodic density functional method
for χcryst. The response of pharmaceutical
molecules and crystals to magnetic fields, as embodied by χcryst, is largely determined by the packing in the crystal,
as well as the molecular conformation. The anisotropy of χcryst can vary considerably between polymorphs though
the isotropic terms are fairly constant. The implications for developing
a computational method for predicting whether crystallization in a
magnetic field could produce a novel or different polymorph are discussed.
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Affiliation(s)
- Rui Guo
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - M Nadia Uddin
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - Louise S Price
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
| | - Sarah L Price
- Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K
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9
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Kamat K, Peters B. Gibbs free-energy differences between polymorphs via a diabat approach. J Chem Phys 2018; 149:214106. [PMID: 30525715 DOI: 10.1063/1.5051448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Polymorph free-energy differences are critical to several applications. A recently proposed diabat interpolation framework estimated free-energy differences between polymorphs by quadratic interpolation of diabats. This work extends the Zwanzig-Bennett relation to the NPT ensemble so that the diabats directly give Gibbs free-energy differences. We also demonstrate how the approach can be used in cases where the diabats are not parabolic. We illustrate the diabat method for Gibbs free-energy difference of zirconium (BCC and HCP phases) and compare it with the conventional lattice switch Monte Carlo approach.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Baron Peters
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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10
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Price SL. Control and prediction of the organic solid state: a challenge to theory and experiment †. Proc Math Phys Eng Sci 2018; 474:20180351. [PMID: 30333710 PMCID: PMC6189584 DOI: 10.1098/rspa.2018.0351] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/15/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of theoretical chemists to quantitatively model the weak forces between organic molecules is being exploited to predict their crystal structures and estimate their physical properties. Evolving crystal structure prediction methods are increasingly being used to aid the design of organic functional materials and provide information about thermodynamically plausible polymorphs of speciality organic materials to aid, for example, pharmaceutical development. However, the increasingly sophisticated experimental studies for detecting the range of organic solid-state behaviours provide many challenges for improving quantitative theories that form the basis for the computer modelling. It is challenging to calculate the relative thermodynamic stability of different organic crystal structures, let alone understand the kinetic effects that determine which polymorphs can be observed and are practically important. However, collaborations between experiment and theory are reaching the stage of devising experiments to target the first crystallization of new polymorphs or create novel organic molecular materials.
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Affiliation(s)
- Sarah L. Price
- Department of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, UK
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11
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Bates JE, Sengupta N, Sensenig J, Ruzsinszky A. Adiabatic Connection without Coupling Constant Integration. J Chem Theory Comput 2018; 14:2979-2990. [DOI: 10.1021/acs.jctc.8b00067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jefferson E. Bates
- Department of Chemistry, Appalachian State University, Boone, North Carolina 28607, United States
| | - Niladri Sengupta
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Jonathon Sensenig
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
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12
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Iuzzolino L, McCabe P, Price SL, Brandenburg JG. Crystal structure prediction of flexible pharmaceutical-like molecules: density functional tight-binding as an intermediate optimisation method and for free energy estimation. Faraday Discuss 2018; 211:275-296. [PMID: 30035288 DOI: 10.1039/c8fd00010g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Successful methodologies for theoretical crystal structure prediction (CSP) on flexible pharmaceutical-like organic molecules explore the lattice energy surface to find a set of plausible crystal structures. The initial search stages of CSP studies use relatively simple lattice energy approximations as hundreds of thousands of minima have to be considered. These generated crystal structures often have poor molecular geometries, as well as inaccurate lattice energy rankings, and performing reasonably accurate but computationally affordable optimisations of the crystal structures generated in a search would be highly desirable. Here, we seek to explore whether semi-empirical quantum-mechanical methods can perform this task. We employed the dispersion-corrected tight-binding Hamiltonian (DFTB3-D3) to relax all the inter- and intra-molecular degrees of freedom of several thousands of generated crystal structures of five pharmaceutical-like molecules, saving a large amount of computational effort compared to earlier studies. The computational cost scales better with molecular size and flexibility than other CSP methods, suggesting that it could be extended to even larger and more flexible molecules. On average, this optimisation improved the average reproduction of the eight experimental crystal structures (RMSD15) and experimental conformers (RMSD1) by 4% and 23%, respectively. The intermolecular interactions were then further optimised using distributed multipoles, derived from the molecular wave-functions, to accurately describe the electrostatic components of the intermolecular energies. In all cases, the experimental crystal structures are close to the top of the lattice energy ranking. Phonon calculations on some of the lowest energy structures were also performed with DFTB3-D3 methods to calculate the vibrational component of the Helmholtz free energy, providing further insights into the solid-state behaviour of the target molecules. We conclude that DFTB3-D3 is a cost-effective method for optimising flexible molecules, bridging the gap between the approximate methods used in CSP searches for generating crystal structures and more accurate methods required in the final energy ranking.
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Affiliation(s)
- Luca Iuzzolino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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13
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Sugden I, Adjiman CS, Pantelides CC. Accurate and efficient representation of intramolecular energy in ab initio generation of crystal structures. I. Adaptive local approximate models. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:864-874. [PMID: 27910837 PMCID: PMC5134761 DOI: 10.1107/s2052520616015122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/26/2016] [Indexed: 05/14/2023]
Abstract
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. 11, 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. 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.
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Affiliation(s)
- Isaac Sugden
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Claire S. Adjiman
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
| | - Constantinos C. Pantelides
- Molecular Systems Engineering Group Centre for Process Systems Engineering Department of Chemical Engineering, Imperial College London, London SW7 2AZ, England
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14
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Price SL, Braun DE, Reutzel-Edens SM. Can computed crystal energy landscapes help understand pharmaceutical solids? Chem Commun (Camb) 2016; 52:7065-77. [PMID: 27067116 PMCID: PMC5486446 DOI: 10.1039/c6cc00721j] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape.
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Affiliation(s)
- Sarah L Price
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK.
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15
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Price SL, Reutzel-Edens SM. The potential of computed crystal energy landscapes to aid solid-form development. Drug Discov Today 2016; 21:912-23. [DOI: 10.1016/j.drudis.2016.01.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/04/2015] [Accepted: 01/26/2016] [Indexed: 11/29/2022]
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16
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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Sure R, Brandenburg JG, Grimme S. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources. ChemistryOpen 2016; 5:94-109. [PMID: 27308221 PMCID: PMC4906470 DOI: 10.1002/open.201500192] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/12/2022] Open
Abstract
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
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18
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Case D, Campbell JE, Bygrave PJ, Day GM. Convergence Properties of Crystal Structure Prediction by Quasi-Random Sampling. J Chem Theory Comput 2016; 12:910-24. [PMID: 26716361 PMCID: PMC4750085 DOI: 10.1021/acs.jctc.5b01112] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 12/05/2022]
Abstract
Generating sets of trial structures that sample the configurational space of crystal packing possibilities is an essential step in the process of ab initio crystal structure prediction (CSP). One effective methodology for performing such a search relies on low-discrepancy, quasi-random sampling, and our implementation of such a search for molecular crystals is described in this paper. Herein we restrict ourselves to rigid organic molecules and, by considering their geometric properties, build trial crystal packings as starting points for local lattice energy minimization. We also describe a method to match instances of the same structure, which we use to measure the convergence of our packing search toward completeness. The use of these tools is demonstrated for a set of molecules with diverse molecular characteristics and as representative of areas of application where CSP has been applied. An important finding is that the lowest energy crystal structures are typically located early and frequently during a quasi-random search of phase space. It is usually the complete sampling of higher energy structures that requires extended sampling. We show how the procedure can first be refined, through targetting the volume of the generated crystal structures, and then extended across a range of space groups to make a full CSP search and locate experimentally observed and lists of hypothetical polymorphs. As the described method has also been created to lie at the base of more involved approaches to CSP, which are being developed within the Global Lattice Energy Explorer (Glee) software, a few of these extensions are briefly discussed.
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Affiliation(s)
- David
H. Case
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Josh E. Campbell
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Peter J. Bygrave
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Graeme M. Day
- School
of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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19
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Grimme S, Brandenburg JG, Bannwarth C, Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J Chem Phys 2015; 143:054107. [PMID: 26254642 DOI: 10.1063/1.4927476] [Citation(s) in RCA: 531] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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20
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Habgood M, Sugden IJ, Kazantsev AV, Adjiman CS, Pantelides CC. Efficient Handling of Molecular Flexibility in Ab Initio Generation of Crystal Structures. J Chem Theory Comput 2015; 11:1957-69. [DOI: 10.1021/ct500621v] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Matthew Habgood
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Isaac J. Sugden
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrei V. Kazantsev
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire S. Adjiman
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Constantinos C. Pantelides
- Molecular Systems Engineering
Group, Centre for Process Systems Engineering, Department of Chemical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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21
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Vasileiadis M, Pantelides CC, Adjiman CS. Prediction of the crystal structures of axitinib, a polymorphic pharmaceutical molecule. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.08.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Brandenburg JG, Bender G, Ren J, Hansen A, Grimme S, Eckert H, Daniliuc CG, Kehr G, Erker G. Crystal Packing Induced Carbon–Carbon Double–Triple Bond Isomerization in a Zirconocene Complex. Organometallics 2014. [DOI: 10.1021/om500678p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische
und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Georg Bender
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Jinjun Ren
- Institut
für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Andreas Hansen
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische
und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische
und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Hellmut Eckert
- Institut
für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 28/30, 48149 Münster, Germany
| | - Constantin G. Daniliuc
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Gerald Kehr
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
| | - Gerhard Erker
- Organisch-Chemisches
Institut, Westfälische Wilhelms-Universität Münster, Corrensstraße
40, 48149 Münster, Germany
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23
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Brandenburg JG, Grimme S. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB). J Phys Chem Lett 2014; 5:1785-1789. [PMID: 26273854 DOI: 10.1021/jz500755u] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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