1
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Butler PV, Hafizi R, Day GM. Machine-Learned Potentials by Active Learning from Organic Crystal Structure Prediction Landscapes. J Phys Chem A 2024; 128:945-957. [PMID: 38277275 PMCID: PMC10860135 DOI: 10.1021/acs.jpca.3c07129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
A primary challenge in organic molecular crystal structure prediction (CSP) is accurately ranking the energies of potential structures. While high-level solid-state density functional theory (DFT) methods allow for mostly reliable discrimination of the low-energy structures, their high computational cost is problematic because of the need to evaluate tens to hundreds of thousands of trial crystal structures to fully explore typical crystal energy landscapes. Consequently, lower-cost but less accurate empirical force fields are often used, sometimes as the first stage of a hierarchical scheme involving multiple stages of increasingly accurate energy calculations. Machine-learned interatomic potentials (MLIPs), trained to reproduce the results of ab initio methods with computational costs close to those of force fields, can improve the efficiency of the CSP by reducing or eliminating the need for costly DFT calculations. Here, we investigate active learning methods for training MLIPs with CSP datasets. The combination of active learning with the well-developed sampling methods from CSP yields potentials in a highly automated workflow that are relevant over a wide range of the crystal packing space. To demonstrate these potentials, we illustrate efficiently reranking large, diverse crystal structure landscapes to near-DFT accuracy from force field-based CSP, improving the reliability of the final energy ranking. Furthermore, we demonstrate how these potentials can be extended to more accurately model structures far from lattice energy minima through additional on-the-fly training within Monte Carlo simulations.
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Affiliation(s)
| | - Roohollah Hafizi
- School of Chemistry, University
of Southampton, Southampton SO17 1BJ, U.K.
| | - Graeme M. Day
- School of Chemistry, University
of Southampton, Southampton SO17 1BJ, U.K.
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2
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Beran GJO. Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials. Chem Sci 2023; 14:13290-13312. [PMID: 38033897 PMCID: PMC10685338 DOI: 10.1039/d3sc03903j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
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3
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Price AJA, Otero-de-la-Roza A, Johnson ER. XDM-corrected hybrid DFT with numerical atomic orbitals predicts molecular crystal lattice energies with unprecedented accuracy. Chem Sci 2023; 14:1252-1262. [PMID: 36756332 PMCID: PMC9891363 DOI: 10.1039/d2sc05997e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Molecular crystals are important for many applications, including energetic materials, organic semiconductors, and the development and commercialization of pharmaceuticals. The exchange-hole dipole moment (XDM) dispersion model has shown good performance in the calculation of relative and absolute lattice energies of molecular crystals, although it has traditionally been applied in combination with plane-wave/pseudopotential approaches. This has limited XDM to use with semilocal functional approximations, which suffer from delocalization error and poor quality conformational energies, and to systems with a few hundreds of atoms at most due to unfavorable scaling. In this work, we combine XDM with numerical atomic orbitals, which enable the efficient use of XDM-corrected hybrid functionals for molecular crystals. We test the new XDM-corrected functionals for their ability to predict the lattice energies of molecular crystals for the X23 set and 13 ice phases, the latter being a particularly stringent test. A composite approach using a XDM-corrected, 25% hybrid functional based on B86bPBE achieves a mean absolute error of 0.48 kcal mol-1 per molecule for the X23 set and 0.19 kcal mol-1 for the total lattice energies of the ice phases, compared to recent diffusion Monte-Carlo data. These results make the new XDM-corrected hybrids not only far more computationally efficient than previous XDM implementations, but also the most accurate density-functional methods for molecular crystal lattice energies to date.
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Affiliation(s)
- Alastair J. A. Price
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo Oviedo 33006 Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University6274 Coburg RdHalifaxB3H 4R2Nova ScotiaCanada
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4
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Cook CJ, Li W, Lui BF, Gately TJ, Al-Kaysi RO, Mueller LJ, Bardeen CJ, Beran GJO. A theoretical framework for the design of molecular crystal engines. Chem Sci 2023; 14:937-949. [PMID: 36755715 PMCID: PMC9890974 DOI: 10.1039/d2sc05549j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Photomechanical molecular crystals have garnered attention for their ability to transform light into mechanical work, but difficulties in characterizing the structural changes and mechanical responses experimentally have hindered the development of practical organic crystal engines. This study proposes a new computational framework for predicting the solid-state crystal-to-crystal photochemical transformations entirely from first principles, and it establishes a photomechanical engine cycle that quantifies the anisotropic mechanical performance resulting from the transformation. The approach relies on crystal structure prediction, solid-state topochemical principles, and high-quality electronic structure methods. After validating the framework on the well-studied [4 + 4] cycloadditions in 9-methyl anthracene and 9-tert-butyl anthracene ester, the experimentally-unknown solid-state transformation of 9-carboxylic acid anthracene is predicted for the first time. The results illustrate how the mechanical work is done by relaxation of the crystal lattice to accommodate the photoproduct, rather than by the photochemistry itself. The large ∼107 J m-3 work densities computed for all three systems highlight the promise of photomechanical crystal engines. This study demonstrates the importance of crystal packing in determining molecular crystal engine performance and provides tools and insights to design improved materials in silico.
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Affiliation(s)
- Cameron J. Cook
- Department of Chemistry, University of California RiversideRiverside CA 92521USA
| | - Wangxiang Li
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - Brandon F. Lui
- Department of Chemistry, University of California RiversideRiverside CA 92521USA
| | - Thomas J. Gately
- Department of Chemistry, University of California RiversideRiverside CA 92521USA
| | - Rabih O. Al-Kaysi
- College of Science and Health Professions-3124, King Saud Bin Abdulaziz University for Health Sciences, and King Abdullah International Medical Research Center, Ministry of National Guard Health AffairsRiyadh 11426Kingdom of Saudi Arabia
| | - Leonard J. Mueller
- Department of Chemistry, University of California RiversideRiverside CA 92521USA
| | | | - Gregory J. O. Beran
- Department of Chemistry, University of California RiversideRiverside CA 92521USA
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5
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Ricci M, Silvestrelli PL, Dobson JF, Ambrosetti A. Exact Sum-Rule Approach to Polarizability and Asymptotic van der Waals Functionals─Derivation of Exact Single-Particle Benchmarks. J Phys Chem Lett 2022; 13:8298-8304. [PMID: 36037314 DOI: 10.1021/acs.jpclett.2c02197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using a sum-rule approach, we develop an exact theoretical framework for polarizability and asymptotic van der Waals correlation energy functionals of small isolated objects. The functionals require only monomer ground-state properties as input. Functional evaluation proceeds via solution of a single position-space differential equation, without the usual summations over excited states or frequency integrations. Explicit functional forms are reported for reference physical systems, including atomic hydrogen and single electrons subject to harmonic confinement, and immersed in a spherical-well potential. A direct comparison to the popular Vydrov-van Voorhis density functional shows that the best performance is obtained when density decay occurs at atomic scales. The adopted sum-rule approach implies general validity of our theory, enabling exact benchmarking of van der Waals density functionals and direct inspection of the subtle long-range correlation effects that constitute a major challenge for approximate (semi)local density functionals.
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Affiliation(s)
- Matteo Ricci
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy
| | - Pier Luigi Silvestrelli
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy
| | - John F Dobson
- Nanoscale Science and Technology Centre, Griffith University, Nathan, Queensland 4111, Australia
| | - Alberto Ambrosetti
- Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy
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6
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Tuca E, DiLabio G, Otero-de-la-Roza A. Minimal Basis Set Hartree-Fock Corrected with Atom-Centered Potentials for Molecular Crystal Modeling and Crystal Structure Prediction. J Chem Inf Model 2022; 62:4107-4121. [PMID: 35980964 DOI: 10.1021/acs.jcim.2c00656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Crystal structure prediction (CSP), determining the experimentally observable structure of a molecular crystal from the molecular diagram, is an important challenge with technologically relevant applications in materials manufacturing and drug design. For the purpose of screening the randomly generated candidate crystal structures, CSP protocols require energy ranking methods that are fast and can accurately capture the small energy differences between molecular crystals. In addition, a good ranking method should also produce accurate equilibrium geometries, both intramolecular and intermolecular. In this article, we explore the combination of minimal-basis-set Hartree-Fock (HF) with atom-centered potentials (ACPs) as a method for modeling the structure and energetics of molecular crystals. The ACPs are developed for the H, C, N, and O atoms and fitted to a set of reference data at the B86bPBE-XDM level in order to mitigate basis-set incompleteness and missing correlation. In particular, ACPs are developed in combination with two methods: HF-D3/MINIs and HF-3c. The application of ACPs greatly improves the performance of HF-D3/MINIs for lattice energies, crystal energy differences, energy-volume and energy-strain relations, and crystal geometries. In the case of HF-3c, the improvement in the crystal energy differences is much smaller than in HF-D3/MINIs, but lattice energies and particularly crystal geometries are considerably better when ACPs are used. The resulting methods may be useful for CSP but also for quick calculation of molecular crystal lattice energies and geometries.
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Affiliation(s)
- Emilian Tuca
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna V1 V 1 V7, British Columbia, Canada
| | - Gino DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna V1 V 1 V7, British Columbia, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
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7
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Reliable crystal structure predictions from first principles. Nat Commun 2022; 13:3095. [PMID: 35654882 PMCID: PMC9163189 DOI: 10.1038/s41467-022-30692-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
An inexpensive and reliable method for molecular crystal structure predictions (CSPs) has been developed. The new CSP protocol starts from a two-dimensional graph of crystal’s monomer(s) and utilizes no experimental information. Using results of quantum mechanical calculations for molecular dimers, an accurate two-body, rigid-monomer ab initio-based force field (aiFF) for the crystal is developed. Since CSPs with aiFFs are essentially as expensive as with empirical FFs, tens of thousands of plausible polymorphs generated by the crystal packing procedures can be optimized. Here we show the robustness of this protocol which found the experimental crystal within the 20 most stable predicted polymorphs for each of the 15 investigated molecules. The ranking was further refined by performing periodic density-functional theory (DFT) plus dispersion correction (pDFT+D) calculations for these 20 top-ranked polymorphs, resulting in the experimental crystal ranked as number one for all the systems studied (and the second polymorph, if known, ranked in the top few). Alternatively, the polymorphs generated can be used to improve aiFFs, which also leads to rank one predictions. The proposed CSP protocol should result in aiFFs replacing empirical FFs in CSP research. Developing theoretical frameworks to predict new polymorphs is highly desirable. Here the authors present an ab initio based force-field approach for crystal structure prediction offering a dramatic computational speed-up over fully ab initio schemes.
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8
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Weatherby JA, Rumson AF, Price AJA, Otero de la Roza A, Johnson ER. A density-functional benchmark of vibrational free-energy corrections for molecular crystal polymorphism. J Chem Phys 2022; 156:114108. [DOI: 10.1063/5.0083082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many crystal structure prediction protocols only concern themselves with the electronic energy of molecular crystals. However, vibrational contributions to the free energy ( Fvib) can be significant in determining accurate stability rankings for crystal candidates. While force-field studies have been conducted to gauge the magnitude of these free-energy corrections, highly accurate results from quantum mechanical methods, such as density-functional theory (DFT), are desirable. Here, we introduce the PV17 set of 17 polymorphic pairs of organic molecular crystals, for which plane wave DFT is used to calculate the vibrational free energies and free-energy differences (Δ Fvib) between each pair. Our DFT results confirm that the vibrational free-energy corrections are small, having a mean value of 1.0 kJ/mol and a maximum value of 2.3 kJ/mol for the PV17 set. Furthermore, we assess the accuracy of a series of lower-cost DFT, semi-empirical, and force-field models for computing Δ Fvib that have been proposed in the literature. It is found that calculating Fvib using the Γ-point frequencies does not provide Δ Fvib values of sufficiently high quality. In addition, Δ Fvib values calculated using various approximate methods have mean absolute errors relative to our converged DFT results of equivalent or larger magnitude than the vibrational free-energy corrections themselves. Thus, we conclude that, in a crystal structure prediction protocol, it is preferable to forego the inclusion of vibrational free-energy corrections than to estimate them with any of the approximate methods considered here.
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Affiliation(s)
- Joseph A. Weatherby
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Adrian F. Rumson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alastair J. A. Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alberto Otero de la Roza
- Departamento de Química Física y Analítica and MALTA Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
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9
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Beran GJO, Wright SE, Greenwell C, Cruz-Cabeza AJ. The interplay of intra- and intermolecular errors in modeling conformational polymorphs. J Chem Phys 2022; 156:104112. [DOI: 10.1063/5.0088027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Conformational polymorphs of organic molecular crystals represent a challenging test for quantum chemistry because they require careful balancing of the intra- and intermolecular interactions. This study examines 54 molecular conformations from 20 sets of conformational polymorphs, along with the relative lattice energies and 173 dimer interactions taken from six of the polymorph sets. These systems are studied with a variety of van der Waals-inclusive density functionals theory models; dispersion-corrected spin-component-scaled second-order Møller–Plesset perturbation theory (SCS-MP2D); and domain local pair natural orbital coupled cluster singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. We investigate how delocalization error in conventional density functionals impacts monomer conformational energies, systematic errors in the intermolecular interactions, and the nature of error cancellation that occurs in the overall crystal. The density functionals B86bPBE-XDM, PBE-D4, PBE-MBD, PBE0-D4, and PBE0-MBD are found to exhibit sizable one-body and two-body errors vs DLPNO-CCSD(T) benchmarks, and the level of success in predicting the relative polymorph energies relies heavily on error cancellation between different types of intermolecular interactions or between intra- and intermolecular interactions. The SCS-MP2D and, to a lesser extent, ωB97M-V models exhibit smaller errors and rely less on error cancellation. Implications for crystal structure prediction of flexible compounds are discussed. Finally, the one-body and two-body DLPNO-CCSD(T) energies taken from these conformational polymorphs establish the CP1b and CP2b benchmark datasets that could be useful for testing quantum chemistry models in challenging real-world systems with complex interplay between intra- and intermolecular interactions, a number of which are significantly impacted by delocalization error.
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Sarah E. Wright
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Chandler Greenwell
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Aurora J. Cruz-Cabeza
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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10
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Price L, Price SL. Packing Preferences of Chalcones: A Model Conjugated Pharmaceutical Scaffold. CRYSTAL GROWTH & DESIGN 2022; 22:1801-1816. [PMID: 35571354 PMCID: PMC9097456 DOI: 10.1021/acs.cgd.1c01381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/02/2022] [Indexed: 06/15/2023]
Abstract
We sought the crystal packing preferences of the chalcone scaffold by analyzing 232 single-component crystal structures of chalcones with a small (six or fewer non-hydrogen atoms) substituent on either or both rings, including the unsubstituted molecule. This covers 216 molecules, as some are polymorphic, and 277 independent molecular conformations, as 16% of the crystal structures have more than one symmetry independent molecule. Quantum mechanical conformational profiles of the unsubstituted molecule and the almost 5000 crystal structures within 20 kJ mol-1 of the global minimum generated in a crystal structure prediction (CSP) study have been used to complement this analysis. Although π conjugation would be expected to favor a planar molecule, there are a significant number of crystal structures containing nonplanar molecules with an approximately 50° angle between the aromatic rings. The relative orientations of the molecules in the inversion-related dimers and translation-related dimers in the experimental crystal structures show the same trends as in the CSP-generated structures for the unsubstituted molecule, allowing for the substituent making the side-to-side distances larger. There is no type of dimer geometry associated with particularly favorable lattice energies for the chalcone core. Less than a third of the experimental structures show a face-to-face contact associated with π···π stacking. Analysis of the experimental crystal structures with XPac and Mercury finds various pairs of isostructural crystals, but the largest isostructural set had only 15 structures, with all substituents (mainly halogens) in the para position. The most common one-dimensional motif, found in half of the experimental crystal structures, is a translation-related side-to-side packing, which can be adopted by all the observed conformations. This close-packed motif can be adopted by chalcones with a particularly wide variety of substituents as the substituents are at the periphery. Thus, although the crystal structures of the substituted chalcones show thermodynamically plausible packings of the chalcone scaffold, there is little evidence for any crystal engineering principle of preferred chalcone scaffold packing beyond close packing of the specific molecule.
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11
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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12
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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] [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. Crystal structure prediction suggests that the low-energy polymorphs of ROY have already been found, but a new high-pressure form is predicted.![]()
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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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13
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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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14
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Surov AO, Voronin AP, Drozd KV, Gruzdev MS, Perlovich GL, Prashanth J, Balasubramanian S. Polymorphic forms of antiandrogenic drug nilutamide: structural and thermodynamic aspects. Phys Chem Chem Phys 2021; 23:9695-9708. [PMID: 33908506 DOI: 10.1039/d1cp00793a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attempts to obtain new cocrystals of nonsteroidal antiandrogenic drug nilutamide produced alternative polymorphic forms of the compound (Form II and Form III) and their crystal structures were elucidated by single-crystal X-ray diffraction. Apart from the cocrystallization technique, lyophilization was found to be an effective strategy for achieving polymorph control of nilutamide, which was difficult to obtain by other methods. The physicochemical properties and relative stability of the commercial Form I and newly obtained Form II were comprehensively investigated by a variety of analytical methods (thermal analysis, solution calorimetry, solubility, and sublimation), whereas for Form III, only a handful of experimental parameters were obtained due to the elusive nature of the polymorph. Form I and Form II were found to be monotropically related, with Form I being confirmed as the thermodynamically most stable solid phase. In addition, the performance of different DFT-D and semi-empirical schemes for lattice energy calculation and polymorph energy ranking was compared and analysed. Lattice energy calculations using periodic DFT at B3LYP-D3/6-31(F+)G(d,p) and PBEh-3c/def2-mSVP levels of theory were found to provide the most accurate lattice energy values for Form I against experimental data, while PIXEL and PBEh-3c/def2-mSVP were the only methods that predicted the correct order of stability of Forms I and II.
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Affiliation(s)
- Artem O Surov
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., 153045 Ivanovo, Russia.
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15
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Cook C, McKinley JL, Beran GJO. Modeling the α- and β-resorcinol phase boundary via combination of density functional theory and density functional tight-binding. J Chem Phys 2021; 154:134109. [PMID: 33832233 PMCID: PMC8019358 DOI: 10.1063/5.0044385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 02/06/2023] Open
Abstract
The ability to predict not only what organic crystal structures might occur but also the thermodynamic conditions under which they are the most stable would be extremely useful for discovering and designing new organic materials. The present study takes a step in that direction by predicting the temperature- and pressure-dependent phase boundary between the α and β polymorphs of resorcinol using density functional theory (DFT) and the quasi-harmonic approximation. To circumvent the major computational bottleneck associated with computing a well-converged phonon density of states via the supercell approach, a recently developed approximation is employed, which combines a supercell phonon density of states from dispersion-corrected third-order density functional tight binding [DFTB3-D3(BJ)] with frequency corrections derived from a smaller B86bPBE-XDM functional DFT phonon calculation on the crystallographic unit cell. This mixed DFT/DFTB quasi-harmonic approach predicts the lattice constants and unit cell volumes to within 1%-2% at lower pressures. It predicts the thermodynamic phase boundary in almost perfect agreement with the experiment, although this excellent agreement does reflect fortuitous cancellation of errors between the enthalpy and entropy of transition.
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Affiliation(s)
- Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Jessica L. McKinley
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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16
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Buhse T, Cruz JM, Noble-Terán ME, Hochberg D, Ribó JM, Crusats J, Micheau JC. Spontaneous Deracemizations. Chem Rev 2021; 121:2147-2229. [DOI: 10.1021/acs.chemrev.0c00819] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Thomas Buhse
- Centro de Investigaciones Químicas−IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62209 Cuernavaca, Morelos Mexico
| | - José-Manuel Cruz
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Tuxtla Gutiérrez, Chiapas 29050, Mexico
| | - María E. Noble-Terán
- Centro de Investigaciones Químicas−IICBA, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, 62209 Cuernavaca, Morelos Mexico
| | - David Hochberg
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera Ajalvir, Km. 4, 28850 Torrejón de Ardoz, Madrid Spain
| | - Josep M. Ribó
- Institut de Ciències del Cosmos (IEEC-ICC) and Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalunya Spain
| | - Joaquim Crusats
- Institut de Ciències del Cosmos (IEEC-ICC) and Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalunya Spain
| | - Jean-Claude Micheau
- Laboratoire des IMRCP, UMR au CNRS No. 5623, Université Paul Sabatier, F-31062 Toulouse Cedex, France
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17
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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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18
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Cook C, Beran GJO. Reduced-cost supercell approach for computing accurate phonon density of states in organic crystals. J Chem Phys 2020; 153:224105. [PMID: 33317313 DOI: 10.1063/5.0032649] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Phonon contributions to organic crystal structures and thermochemical properties can be significant, but computing a well-converged phonon density of states with lattice dynamics and periodic density functional theory (DFT) is often computationally expensive due to the need for large supercells. Using semi-empirical methods like density functional tight binding (DFTB) instead of DFT can reduce the computational costs dramatically, albeit with noticeable reductions in accuracy. This work proposes approximating the phonon density of states via a relatively inexpensive DFTB supercell treatment of the phonon dispersion that is then corrected by shifting the individual phonon modes according to the difference between the DFT and DFTB phonon frequencies at the Γ-point. The acoustic modes are then computed at the DFT level from the elastic constants. In several small-molecule crystal test cases, this combined approach reproduces DFT thermochemistry with kJ/mol accuracy and 1-2 orders of magnitude less computational effort. Finally, this approach is applied to computing the free energy differences between the five crystal polymorphs of oxalyl dihydrazide.
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Affiliation(s)
- Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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19
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Xu F, Testoff TT, Wang L, Zhou X. Cause, Regulation and Utilization of Dye Aggregation in Dye-Sensitized Solar Cells. Molecules 2020; 25:E4478. [PMID: 33003462 PMCID: PMC7582523 DOI: 10.3390/molecules25194478] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/23/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022] Open
Abstract
As an important member of third generation solar cell, dye-sensitized solar cells (DSSCs) have the advantages of being low cost, having an easy fabrication process, utilizing rich raw materials and a high-power conversion efficiency (PCE), prompting nearly three decades as a research hotspot. Recently, increasing the photoelectric conversion efficiency of DSSCs has proven troublesome. Sensitizers, as the most important part, are no longer limited to molecular engineering, and the regulation of dye aggregation has become a widely held concern, especially in liquid DSSCs. This review first presents the operational mechanism of liquid and solid-state dye-sensitized solar cells, including the influencing factors of various parameters on device efficiency. Secondly, the mechanism of dye aggregation was explained by molecular exciton theory, and the influence of various factors on dye aggregation was summarized. We focused on a review of several methods for regulating dye aggregation in liquid and solid-state dye-sensitized solar cells, and the advantages and disadvantages of these methods were analyzed. In addition, the important application of quantum computational chemistry in the study of dye aggregation was introduced. Finally, an outlook was proposed that utilizing the advantages of dye aggregation by combining molecular engineering with dye aggregation regulation is a research direction to improve the performance of liquid DSSCs in the future. For solid-state dye-sensitized solar cells (ssDSSCs), the effects of solid electrolytes also need to be taken into account.
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Affiliation(s)
- Fang Xu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300345, China; (F.X.); (L.W.)
| | - Thomas T. Testoff
- Department of Chemistry and Biochemistry and the Materials Technology Center, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Lichang Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300345, China; (F.X.); (L.W.)
- Department of Chemistry and Biochemistry and the Materials Technology Center, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Xueqin Zhou
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300345, China; (F.X.); (L.W.)
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20
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Otero-de-la-Roza A, Johnson ER. Application of XDM to ionic solids: The importance of dispersion for bulk moduli and crystal geometries. J Chem Phys 2020; 153:054121. [PMID: 32770899 DOI: 10.1063/5.0015133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Dispersion corrections are essential in the description of intermolecular interactions; however, dispersion-corrected functionals must also be transferrable to hard solids. The exchange-hole dipole moment (XDM) model has demonstrated excellent performance for non-covalent interactions. In this article, we examine its ability to describe the relative stability, geometry, and compressibility of simple ionic solids. For the specific cases of the cesium halides, XDM-corrected functionals correctly predict the energy ranking of the B1 and B2 forms, and a dispersion contribution is required to obtain this result. Furthermore, for the lattice constants of the 20 alkali halides, the performance of XDM-corrected functionals is excellent, provided that the base functional's exchange enhancement factor properly captures non-bonded repulsion. The mean absolute errors in lattice constants obtained with B86bPBE-XDM and B86bPBE-25X-XDM are 0.060 Å and 0.039 Å, respectively, suggesting that delocalization error also plays a minor role in these systems. Finally, we considered the calculation of bulk moduli for alkali halides and alkaline-earth oxides. Previous claims in the literature that simple generalized gradient approximations, such as PBE, can reliably predict experimental bulk moduli have benefited from large error cancellations between neglecting both dispersion and vibrational effects. If vibrational effects are taken into account, dispersion-corrected functionals are quite accurate (4 GPa-5 GPa average error), again, if non-bonded repulsion is correctly represented. Careful comparisons of the calculated bulk moduli with experimental data are needed to avoid systematic biases and misleading conclusions.
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Affiliation(s)
- A Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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21
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Greenwell C, McKinley JL, Zhang P, Zeng Q, Sun G, Li B, Wen S, Beran GJO. Overcoming the difficulties of predicting conformational polymorph energetics in molecular crystals via correlated wavefunction methods. Chem Sci 2020; 11:2200-2214. [PMID: 32190277 PMCID: PMC7059316 DOI: 10.1039/c9sc05689k] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Molecular crystal structure prediction is increasingly being applied to study the solid form landscapes of larger, more flexible pharmaceutical molecules. Despite many successes in crystal structure prediction, van der Waals-inclusive density functional theory (DFT) methods exhibit serious failures predicting the polymorph stabilities for a number of systems exhibiting conformational polymorphism, where changes in intramolecular conformation lead to different intermolecular crystal packings. Here, the stabilities of the conformational polymorphs of o-acetamidobenzamide, ROY, and oxalyl dihydrazide are examined in detail. DFT functionals that have previously been very successful in crystal structure prediction perform poorly in all three systems, due primarily to the poor intramolecular conformational energies, but also due to the intermolecular description in oxalyl dihydrazide. In all three cases, a fragment-based dispersion-corrected second-order Møller-Plesset perturbation theory (MP2D) treatment of the crystals overcomes these difficulties and predicts conformational polymorph stabilities in good agreement with experiment. These results highlight the need for methods which go beyond current-generation DFT functionals to make crystal polymorph stability predictions truly reliable.
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Affiliation(s)
- Chandler Greenwell
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
| | - Peiyu Zhang
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Qun Zeng
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Guangxu Sun
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Bochen Li
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Shuhao Wen
- Xtalpi, Inc. , 245 Main St, 12th Floor , Cambridge , MA 02142 , USA
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , USA . ; Tel: +1-951-827-7869
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22
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Otero-de-la-Roza A, LeBlanc LM, Johnson ER. What is “many-body” dispersion and should I worry about it? Phys Chem Chem Phys 2020; 22:8266-8276. [DOI: 10.1039/d0cp01213k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
“Many-body” dispersion can refer to two distinct phenomena, here termed electronic and atomic many-body effects, both of which cause the dispersion energy to be non-additive.
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Affiliation(s)
- A. Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team
- Facultad de Química
- Universidad de Oviedo
- 33006 Oviedo
- Spain
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23
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Wang X, Zeng Q, Li J, Yang M. First-Principles-Based Force Field for 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105). ACS OMEGA 2019; 4:21054-21062. [PMID: 31867497 PMCID: PMC6921264 DOI: 10.1021/acsomega.9b02410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a highly promising energetic material (EM) with high safety. Understanding its microscopic response mechanisms within the external stimulus is meaningful for the design of EMs. In order to comprehend the complicated phenomena, it is necessary to employ molecular simulation methods to investigate the response mechanisms with the force field (FF) at an atomic level. In this work, we developed a tailored FF for LLM-105 based on first-principles calculations. The validity of the FF was evaluated by molecular dynamics simulations. The structural parameters of LLM-105 predicted by FF are in good agreement with the experimental values, such as lattice constant, bond length, bond angle, dihedral angle and center of mass, and so forth. Moreover, the FF possesses good performance to describe the structural response on pressure accurately. In general, our work not only builds a balanced FF in gas and condensed phases, but also provides a useful tool to study the properties about LLM-105 at a large scale, which is helpful to improve the understanding about the balance between energy and safety in EMs.
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Affiliation(s)
- Xian Wang
- Institute
of Chemical Materials, China Academy of
Engineering Physics (CAEP), Mianyang 621900, China
- Institute
of Atomic and Molecular Physics, Sichuan
University, Chengdu 610065, China
| | - Qun Zeng
- Institute
of Chemical Materials, China Academy of
Engineering Physics (CAEP), Mianyang 621900, China
| | - Jinshan Li
- Institute
of Chemical Materials, China Academy of
Engineering Physics (CAEP), Mianyang 621900, China
| | - Mingli Yang
- Institute
of Atomic and Molecular Physics, Sichuan
University, Chengdu 610065, China
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24
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Intermolecular Interactions in Molecular Organic Crystals upon Relaxation of Lattice Parameters. CRYSTALS 2019. [DOI: 10.3390/cryst9120665] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Crystal structure prediction is based on the assumption that the most thermodynamically stable structure will crystallize first. The existence of other structures such as polymorphs or from counterenantiomers requires an accurate calculation of the electronic energy. Using atom-centered Gaussian basis functions in periodic Density Functional Theory (DFT) calculations in Turbomole, the performance of two dispersion-corrected functionals, PBE-D3 and B97-D, is assessed for molecular organic crystals of the X23 benchmark set. B97-D shows a MAE (mean absolute error) of 4 kJ/mol, compared to 9 kJ/mol for PBE-D3. A strategy for the convergence of lattice energies towards the basis set limit is outlined. A simultaneous minimization of molecular structures and lattice parameters shows that both methods are able to reproduce experimental unit cell parameters to within 4–5%. Calculated lattice energies, however, deviate slightly more from the experiment, i.e., by 0.4 kJ/mol after unit cell optimization for PBE-D3 and 0.5 kJ/mol for B97-D. The accuracy of the calculated lattice energies compared to the experimental values demonstrates the ability of current DFT methods to assist in the quest for possible polymorphs and enantioselective crystallization processes.
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25
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Awoonor-Williams E, Isley WC, Dale SG, Johnson ER, Yu H, Becke AD, Roux B, Rowley CN. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. J Comput Chem 2019; 41:427-438. [PMID: 31512279 DOI: 10.1002/jcc.26064] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
Abstract
Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semiempirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the prereaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behavior of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were reasonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that molecular dynamics (MD) simulations using this functional were only stable if a fine integration grid was used. The low-cost semiempirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics is not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to methylvinyl ketone was calculated using quantum mechanical/molecular mechanical MD in an explicit polarizable aqueous solvent. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - William C Isley
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Stephen G Dale
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Axel D Becke
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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26
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McKinley JL, Beran GJO. Improving Predicted Nuclear Magnetic Resonance Chemical Shifts Using the Quasi-Harmonic Approximation. J Chem Theory Comput 2019; 15:5259-5274. [PMID: 31442040 DOI: 10.1021/acs.jctc.9b00481] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ab initio nuclear magnetic resonance chemical shift prediction plays an important role in the determination or validation of crystal structures. The ability to predict chemical shifts more accurately can translate to increased confidence in the resulting chemical shift or structural assignments. Standard electronic structure predictions for molecular crystal structures neglect thermal expansion, which can lead to an appreciable underestimation of the molar volumes. This study examines this volume error and its impact on 68 13C- and 28 15N-predicted chemical shifts taken from 20 molecular crystals. It assesses the ability to recover more realistic room-temperature crystal structures using the quasi-harmonic approximation and how refining the structures impacts the chemical shifts. Several pharmaceutical molecular crystals are also examined in more detail. On the whole, accounting for quasi-harmonic expansion changes the 13C and 15N chemical shifts by 0.5 and 1.0 ppm on average. This, in turn, reduces the root-mean-square errors relative to experiment by 0.3 ppm for 13C and 0.7 ppm for 15N. Although the statistical impacts are modest, changes in individual chemical shifts can reach multiple ppm. Accounting for thermal expansion in molecular crystal chemical shift prediction may not be needed routinely, but the systematic trend toward improved accuracy with the experiment could be useful in cases where discrimination between structural candidates is challenging, as in the pharmaceutical theophylline.
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Affiliation(s)
- Jessica L McKinley
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Gregory J O Beran
- Department of Chemistry , University of California , Riverside , California 92521 , United States
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27
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Otero-de-la-Roza A, LeBlanc LM, Johnson ER. Dispersion XDM with Hybrid Functionals: Delocalization Error and Halogen Bonding in Molecular Crystals. J Chem Theory Comput 2019; 15:4933-4944. [DOI: 10.1021/acs.jctc.9b00550] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Luc M. LeBlanc
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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28
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Ryder MR, Maul J, Civalleri B, Erba A. Quasi‐Harmonic Lattice Dynamics of a Prototypical Metal–Organic Framework. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew R. Ryder
- Neutron Scattering DivisionOak Ridge National LaboratoryOak Ridge TN 37831 USA
| | - Jefferson Maul
- Dipartimento di ChimicaUniversità di Torinovia Giuria 5 10125 Torino Italy
| | | | - Alessandro Erba
- Dipartimento di ChimicaUniversità di Torinovia Giuria 5 10125 Torino Italy
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29
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Beran GJO. Solid state photodimerization of 9-tert-butyl anthracene ester produces an exceptionally metastable polymorph according to first-principles calculations. CrystEngComm 2019. [DOI: 10.1039/c8ce01985a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular crystal engineering seeks to tune the material properties by controlling the crystal packing.
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30
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Dale SG, Becke AD, Johnson ER. Density-functional description of alkalides: introducing the alkalide state. Phys Chem Chem Phys 2018; 20:26710-26718. [PMID: 30324211 DOI: 10.1039/c8cp04014a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alkalides are crystalline salts in which the anion is a negatively charged alkali metal. A systematic investigation of the electronic structure of thirteen alkalides, with known crystal structures, is conducted using density-functional theory. For each alkalide, a high-lying valence state is identified that is localised on the alkali anions and is consistent with the low band gap and strong reducing power characteristic of these materials. This 'alkalide state' is compared to a similar state in the related class of electride materials, where the alkali anions are replaced by crystal voids occupied by localised, interstitial electrons. Finally, a thermodynamic cycle is constructed to examine the energy differences between the alkalides and electrides, revealing that the alkali-metal anion significantly stabilises the crystal.
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Affiliation(s)
- Stephen G Dale
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, P.O. Box 15000, B3H 4R2, Halifax, Nova Scotia, Canada.
| | - Axel D Becke
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, P.O. Box 15000, B3H 4R2, Halifax, Nova Scotia, Canada.
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, P.O. Box 15000, B3H 4R2, Halifax, Nova Scotia, Canada.
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31
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LeBlanc LM, Dale SG, Taylor CR, Becke AD, Day GM, Johnson ER. Pervasive Delocalisation Error Causes Spurious Proton Transfer in Organic Acid-Base Co-Crystals. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luc M. LeBlanc
- Department of Chemistry; Dalhousie University; P.O. Box 15000, 6274 Coburg Rd Halifax Nova Scotia B3H 4R2 Canada
| | - Stephen G. Dale
- Department of Chemistry; Dalhousie University; P.O. Box 15000, 6274 Coburg Rd Halifax Nova Scotia B3H 4R2 Canada
| | | | - Axel D. Becke
- Department of Chemistry; Dalhousie University; P.O. Box 15000, 6274 Coburg Rd Halifax Nova Scotia B3H 4R2 Canada
| | - Graeme M. Day
- School of Chemistry; University of Southampton, Highfield; Southampton SO17 1BJ UK
| | - Erin R. Johnson
- Department of Chemistry; Dalhousie University; P.O. Box 15000, 6274 Coburg Rd Halifax Nova Scotia B3H 4R2 Canada
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32
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LeBlanc LM, Dale SG, Taylor CR, Becke AD, Day GM, Johnson ER. Pervasive Delocalisation Error Causes Spurious Proton Transfer in Organic Acid-Base Co-Crystals. Angew Chem Int Ed Engl 2018; 57:14906-14910. [PMID: 30248221 DOI: 10.1002/anie.201809381] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 11/12/2022]
Abstract
Dispersion-corrected density-functional theory (DFT-D) methods have become the workhorse of many computational protocols for molecular crystal structure prediction due to their efficiency and convenience. However, certain limitations of DFT, such as delocalisation error, are often overlooked or are too expensive to remedy in solid-state applications. This error can lead to artificial stabilisation of charge transfer and, in this work, it is found to affect the correct identification of the protonation site in multicomponent acid-base crystals. As such, commonly used DFT-D methods cannot be applied with any reliability to the study of acid-base co-crystals or salts, while hybrid functionals remain too restrictive for routine use. This presents an impetus for the development of new functionals with reduced delocalisation error for solid-state applications; the structures studied herein constitute an excellent benchmark for this purpose.
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Affiliation(s)
- Luc M LeBlanc
- Department of Chemistry, Dalhousie University, P.O. Box 15000, 6274 Coburg Rd, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Stephen G Dale
- Department of Chemistry, Dalhousie University, P.O. Box 15000, 6274 Coburg Rd, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Christopher R Taylor
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Axel D Becke
- Department of Chemistry, Dalhousie University, P.O. Box 15000, 6274 Coburg Rd, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Graeme M Day
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, P.O. Box 15000, 6274 Coburg Rd, Halifax, Nova Scotia, B3H 4R2, Canada
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33
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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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34
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LeBlanc LM, Otero-de-la-Roza A, Johnson ER. Composite and Low-Cost Approaches for Molecular Crystal Structure Prediction. J Chem Theory Comput 2018; 14:2265-2276. [PMID: 29498837 DOI: 10.1021/acs.jctc.7b01179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crystal structure prediction (CSP) requires evaluating differences in lattice energy between candidate crystal structures accurately and efficiently. In this work, we explore and compare several low-cost alternatives to dispersion-corrected density-functional theory (DFT) in the plane-waves/pseudopotential approximation, the most accurate and general approach used for CSP at present. Three types of low-cost methods are considered: DFT with a small basis set of finite-support numerical orbitals (the SIESTA method), dispersion-corrected Gaussian small or minimal-basis-set Hartree-Fock and DFT with additional empirical corrections (HF-3c and PBEh-3c), and self-consistent-charge dispersion-corrected density-functional tight binding (SCC-DFTB3-D3). In addition, we study the performance of composite methods that comprise a geometry optimization using a low-cost approach followed by a single-point calculation using the accurate but comparatively expensive B86bPBE-XDM functional. All methods were tested for their abilities to produce absolute lattice energies, relative lattice energies, and crystal geometries. We show that assessing various methods by their ability to produce absolute lattice energies can be misleading and that relative lattice energies are a much better indicator of performance in CSP. The EE14 set of relative solubilities of homochiral and heterochiral chiral crystals is proposed for relative lattice-energy benchmarking. Our results show that PBE-D2 plus a DZP basis set of numerical orbitals coupled with a final B86bPBE-XDM single-point calculation gives excellent performance at a fraction of the cost of a full B86bPBE-XDM calculation, although the results are sensitive to the particular details of the computational protocol. The B86bPBE-XDM//PBE-D2/DZP method was subsequently tested in a practical CSP application from our recent work on the crystal structure of the enantiopure and racemate forms of 1-aza[6]helicene, a chiral organic semiconductor. Our results show that this multilevel method is able to correctly reproduce the energy ranking of both crystal forms.
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Affiliation(s)
- Luc M LeBlanc
- Department of Chemistry , Dalhousie University , 6274 Coburg Road , P.O. Box 15000, Halifax , Nova Scotia , Canada B3H 4R2
| | - Alberto Otero-de-la-Roza
- Department of Chemistry , University of British Columbia, Okanagan , 3247 University Way , Kelowna , British Columbia , Canada V1V 1V7
| | - Erin R Johnson
- Department of Chemistry , Dalhousie University , 6274 Coburg Road , P.O. Box 15000, Halifax , Nova Scotia , Canada B3H 4R2
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35
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Curtis F, Li X, Rose T, Vázquez-Mayagoitia Á, Bhattacharya S, Ghiringhelli LM, Marom N. GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction. J Chem Theory Comput 2018; 14:2246-2264. [PMID: 29481740 DOI: 10.1021/acs.jctc.7b01152] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.
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Affiliation(s)
- Farren Curtis
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Xiayue Li
- Google , Mountain View , California 94030 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Timothy Rose
- Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Álvaro Vázquez-Mayagoitia
- Argonne Leadership Computing Facility , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Saswata Bhattacharya
- Department of Physics , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Luca M Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 , Berlin , Germany
| | - Noa Marom
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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36
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Rice B, LeBlanc LM, Otero-de-la-Roza A, Fuchter MJ, Johnson ER, Nelson J, Jelfs KE. A computational exploration of the crystal energy and charge-carrier mobility landscapes of the chiral [6]helicene molecule. NANOSCALE 2018; 10:1865-1876. [PMID: 29313040 DOI: 10.1039/c7nr08890f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The potential of a given π-conjugated organic molecule in an organic semiconductor device is highly dependent on molecular packing, as it strongly influences the charge-carrier mobility of the material. Such solid-state packing is sensitive to subtle differences in their intermolecular interactions and is challenging to predict. Chirality of the organic molecule adds an additional element of complexity to intuitive packing prediction. Here we use crystal structure prediction to explore the lattice-energy landscape of a potential chiral organic semiconductor, [6]helicene. We reproduce the experimentally observed enantiopure crystal structure and explain the absence of an experimentally observed racemate structure. By exploring how the hole and electron-mobility varies across the energy-structure-function landscape for [6]helicene, we find that an energetically favourable and frequently occurring packing motif is particularly promising for electron-mobility, with a highest calculated mobility of 2.9 cm2 V-1 s-1 (assuming a reorganization energy of 0.46 eV). We also calculate relatively high hole-mobility in some structures, with a highest calculated mobility of 2.0 cm2 V-1 s-1 found for chains of helicenes packed in a herringbone fashion. Neither the energetically favourable nor high charge-carrier mobility packing motifs are intuitively obvious, and this demonstrates the utility of our approach to computationally explore the energy-structure-function landscape for organic semiconductors. Our work demonstrates a route for the use of computational simulations to aid in the design of new molecules for organic electronics, through the a priori prediction of their likely solid-state form and properties.
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Affiliation(s)
- Beth Rice
- Department of Physics, Imperial College London, South Kensington, London, SW7 2AZ, UK and Centre for Plastic Electronics, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Luc M LeBlanc
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alberto Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Matthew J Fuchter
- Centre for Plastic Electronics, Imperial College London, South Kensington, London, SW7 2AZ, UK. and Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jenny Nelson
- Department of Physics, Imperial College London, South Kensington, London, SW7 2AZ, UK and Centre for Plastic Electronics, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Kim E Jelfs
- Centre for Plastic Electronics, Imperial College London, South Kensington, London, SW7 2AZ, UK. and Department of Chemistry, Imperial College London, South Kensington, London, SW7 2AZ, UK
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37
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Mortazavi M, Brandenburg JG, Maurer RJ, Tkatchenko A. Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding. J Phys Chem Lett 2018; 9:399-405. [PMID: 29298075 DOI: 10.1021/acs.jpclett.7b03234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.
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Affiliation(s)
- Majid Mortazavi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Jan Gerit Brandenburg
- Department of Chemistry, University College London , 20 Gordon Street, WC1H 0AJ London, United Kingdom
- London Centre for Nanotechnology, University College London , 17-19 Gordon Street, WC1H 0AJ London, United Kingdom
- Thomas Young Centre, University College London , Gower Street, WC1E 6BT London, United Kingdom
| | - Reinhard J Maurer
- Department of Chemistry and Centre for Scientific Computing, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg , L-1511, Luxembourg
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38
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Losev E, Boldyreva E. The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β-alanine, γ-aminobutyric acid (GABA) and DL-α-aminobutyric acid (AABA). ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:177-185. [PMID: 29400333 DOI: 10.1107/s2053229617017909] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022]
Abstract
We report a novel 1:1 cocrystal of β-alanine with DL-tartaric acid, C3H7NO2·C4H6O6, (II), and three new molecular salts of DL-tartaric acid with β-alanine {3-azaniumylpropanoic acid-3-azaniumylpropanoate DL-tartaric acid-DL-tartrate, [H(C3H7NO2)2]+·[H(C4H5O6)2]-, (III)}, γ-aminobutyric acid [3-carboxypropanaminium DL-tartrate, C4H10NO2+·C4H5O6-, (IV)] and DL-α-aminobutyric acid {DL-2-azaniumylbutanoic acid-DL-2-azaniumylbutanoate DL-tartaric acid-DL-tartrate, [H(C4H9NO2)2]+·[H(C4H5O6)2]-, (V)}. The crystal structures of binary crystals of DL-tartaric acid with glycine, (I), β-alanine, (II) and (III), GABA, (IV), and DL-AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with DL-tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β-Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with DL-tartaric acid. The cocrystals of glycine and β-alanine with DL-tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β-alanine in (III), GABA in (IV) and DL-AABA in (V)], which are linked by strong O-H...O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A...A)+ in (III) and (V), and A+...A+ in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and DL-AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except DL-AABA) correlates with the melting point of its mixed crystal.
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Affiliation(s)
- Evgeniy Losev
- Group of Reactivity of Solids, Institute of Solid State Chemistry and Mechanochemistry SB RAS, Kutateladze 18 str., Novosibirsk 630128, Russian Federation
| | - Elena Boldyreva
- Group of Reactivity of Solids, Institute of Solid State Chemistry and Mechanochemistry SB RAS, Kutateladze 18 str., Novosibirsk 630128, Russian Federation
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39
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Atom-Centered Potentials with Dispersion-Corrected Minimal-Basis-Set Hartree–Fock: An Efficient and Accurate Computational Approach for Large Molecular Systems. J Chem Theory Comput 2018; 14:726-738. [DOI: 10.1021/acs.jctc.7b01158] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Viki Kumar Prasad
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Gino A. DiLabio
- Department
of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
- Faculty
of Management, University of British Columbia, 1137 Alumni Avenue, Kelowna, British Columbia, Canada V1V 1V7
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40
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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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41
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McKinley JL, Beran GJO. Identifying pragmatic quasi-harmonic electronic structure approaches for modeling molecular crystal thermal expansion. Faraday Discuss 2018; 211:181-207. [PMID: 30027972 DOI: 10.1039/c8fd00048d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Quasi-harmonic approaches provide an economical route to modeling the temperature dependence of molecular crystal structures and properties. Several studies have demonstrated good performance of these models, at least for rigid molecules, when using fragment-based approaches with correlated wavefunction techniques. Many others have found success employing dispersion-corrected density functional theory (DFT). Here, a hierarchy of models in which the energies, geometries, and phonons are computed either with correlated methods or DFT are examined to identify which combinations produce useful predictions for properties such as the molar volume, enthalpy, and entropy as a function of temperature. The results demonstrate that refining DFT geometries and phonons with single-point energies based on dispersion-corrected second-order Møller-Plesset perturbation theory can provide clear improvements in the molar volumes and enthalpies compared to those obtained from DFT alone. Predicted entropies, which are governed by vibrational contributions, benefit less clearly from the hybrid schemes. Using these hybrid techniques, the room-temperature thermochemistry of acetaminophen (paracetamol) is predicted to address the discrepancy between two experimental sublimation enthalpy measurements.
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Affiliation(s)
- Jessica L McKinley
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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42
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Hoja J, Tkatchenko A. First-principles stability ranking of molecular crystal polymorphs with the DFT+MBD approach. Faraday Discuss 2018; 211:253-274. [PMID: 30042995 DOI: 10.1039/c8fd00066b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to accurately calculate the relative stabilities of numerous polymorphs of a given molecular crystal is crucial for the success of any molecular crystal structure prediction (CSP) approach. We have recently presented a hierarchical CSP procedure based on van-der-Waals-inclusive density functional theory [Hoja et al., 2018, arXiv:1803.07503], which yields excellent stability rankings for molecular crystals involving rigid molecules, salts, co-crystals, and highly polymorphic drug-like molecules. This approach includes many-body dispersion effects, exact exchange, as well as vibrational free energies. Here, we discuss in detail the impact of these effects on the obtained stability rankings. In addition, we assess the impact of the approximations used in our hierarchical procedure. We show that our procedure is generally robust to 1-2 kJ mol-1 for the systems in the latest CSP blind test but vibrational free energies for crystals involving flexible molecules would benefit from directly including many-body dispersion interactions. In addition, we also discuss the effect of temperature on the structure of molecular crystals and a simple but effective method for estimating anharmonic effects.
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Affiliation(s)
- Johannes Hoja
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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43
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Mohebifar M, Johnson ER, Rowley CN. Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model. J Chem Theory Comput 2017; 13:6146-6157. [DOI: 10.1021/acs.jctc.7b00522] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohamad Mohebifar
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland
and Labrador, Canada
| | - Erin R. Johnson
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department
of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland
and Labrador, Canada
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44
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Whittleton SR, Otero-de-la-Roza A, Johnson ER. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction II: Nonplanar Molecules. J Chem Theory Comput 2017; 13:5332-5342. [PMID: 28933853 DOI: 10.1021/acs.jctc.7b00715] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment (XDM) dispersion model for crystal structure prediction. In this article, we study the relatively large, nonplanar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre. Four of the seven experimental structures are predicted as the energy minimum, and thermal effects are demonstrated to have a large impact on the ranking of at least another compound. As in the first part of this series, delocalization error affects the results for a single crystal (compound X), in this case by detrimentally overstabilizing the π-conjugated conformation of the monomer. Overall, B86bPBE-XDM correctly predicts 16 of the 21 compounds in the five blind tests, a result similar to the one obtained using the best CSP method available to date (dispersion-corrected PW91 by Neumann et al.). Perhaps more importantly, the systems for which B86bPBE-XDM fails to predict the experimental structure as the energy minimum are mostly the same as with Neumann's method, which suggests that similar difficulties (absence of vibrational free energy corrections, delocalization error,...) are not limited to B86bPBE-XDM but affect GGA-based DFT-methods in general. Our work confirms B86bPBE-XDM as an excellent option for crystal energy ranking in CSP and offers a guide to identify crystals (organic salts, conjugated flexible systems) where difficulties may appear.
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Affiliation(s)
- Sarah R Whittleton
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
| | - A Otero-de-la-Roza
- Department of Chemistry, University of British Columbia , Okanagan, 3247 University Way, Kelowna, British Columbia, Canada VIV 1V7
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
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45
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Yang Y, Rice B, Shi X, Brandt JR, Correa da Costa R, Hedley GJ, Smilgies DM, Frost JM, Samuel IDW, Otero-de-la-Roza A, Johnson ER, Jelfs KE, Nelson J, Campbell AJ, Fuchter MJ. Emergent Properties of an Organic Semiconductor Driven by its Molecular Chirality. ACS NANO 2017; 11:8329-8338. [PMID: 28696680 DOI: 10.1021/acsnano.7b03540] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chiral molecules exist as pairs of nonsuperimposable mirror images; a fundamental symmetry property vastly underexplored in organic electronic devices. Here, we show that organic field-effect transistors (OFETs) made from the helically chiral molecule 1-aza[6]helicene can display up to an 80-fold difference in hole mobility, together with differences in thin-film photophysics and morphology, solely depending on whether a single handedness or a 1:1 mixture of left- and right-handed molecules is employed under analogous fabrication conditions. As the molecular properties of either mirror image isomer are identical, these changes must be a result of the different bulk packing induced by chiral composition. Such underlying structures are investigated using crystal structure prediction, a computational methodology rarely applied to molecular materials, and linked to the difference in charge transport. These results illustrate that chirality may be used as a key tuning parameter in future device applications.
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Affiliation(s)
| | | | | | | | - Rosenildo Correa da Costa
- Faculty of Computing, Engineering and Science, University of South Wales , Cemetery Road, Glyntaff, Pontypridd CF37 4BD, United Kingdom
| | - Gordon J Hedley
- University of St. Andrews , North Haugh, Fife KY16 9SS, United Kingdom
| | - Detlef-M Smilgies
- Cornell High Energy Synchrotron Source (CHESS), Wilson Laboratory, Cornell University , Ithaca, New York 14853, United States
| | - Jarvist M Frost
- Department of Chemistry, University of Bath , Bath BA2 7AY, United Kingdom
- Department of Materials, Imperial College London , London SW7 2AZ, United Kingdom
| | - Ifor D W Samuel
- University of St. Andrews , North Haugh, Fife KY16 9SS, United Kingdom
| | - Alberto Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan , 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada
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46
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Otero-de-la-Roza A, DiLabio GA. Transferable Atom-Centered Potentials for the Correction of Basis Set Incompleteness Errors in Density-Functional Theory. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00300] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- Department
of Chemistry and ‡Faculty of Management, University of British Columbia, Okanagan, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Gino A. DiLabio
- Department
of Chemistry and ‡Faculty of Management, University of British Columbia, Okanagan, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
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47
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Shtukenberg AG, Zhu Q, Carter DJ, Vogt L, Hoja J, Schneider E, Song H, Pokroy B, Polishchuk I, Tkatchenko A, Oganov AR, Rohl AL, Tuckerman ME, Kahr B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs. Chem Sci 2017; 8:4926-4940. [PMID: 28959416 PMCID: PMC5607859 DOI: 10.1039/c7sc00168a] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/30/2017] [Indexed: 11/21/2022] Open
Abstract
Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.
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Affiliation(s)
- Alexander G Shtukenberg
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
| | - Qiang Zhu
- Department of Physics and Astronomy , High Pressure Science and Engineering Center , University of Nevada Las Vegas , Nevada 89154 , USA .
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Damien J Carter
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Leslie Vogt
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Elia Schneider
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Hongxing Song
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Boaz Pokroy
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology , Skolkovo Innovation Center , 3 Nobel St. , Moscow 143026 , Russia
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Mark E Tuckerman
- Department of Chemistry , New York University , New York City , NY 10003 , USA
- Courant Institute of Mathematical Sciences , New York University , New York City , NY 10003 , USA
- New York University-East China Normal University Center for Computational Chemistry at NYU Shanghai , 3663 Zhongshan Road North , Shanghai 200062 , China
| | - Bart Kahr
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
- Department of Advanced Science and Engineering (TWIns) , Waseda University , Wakamatsucho, 3-2 , Shinjuku , 162-0056 Tokyo , Japan
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48
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Červinka C, Beran GJO. Ab initio thermodynamic properties and their uncertainties for crystalline α-methanol. Phys Chem Chem Phys 2017; 19:29940-29953. [DOI: 10.1039/c7cp06605h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To investigate the performance of quasi-harmonic electronic structure methods for modeling molecular crystals at finite temperatures and pressures, thermodynamic properties are calculated for the low-temperature α polymorph of crystalline methanol and their computational uncertainties are analyzed.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry
- University of Chemistry and Technology Prague
- CZ-166 28 Prague 6
- Czech Republic
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