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Ludík J, Kostková V, Kocian Š, Touš P, Štejfa V, Červinka C. First-Principles Models of Polymorphism of Pharmaceuticals: Maximizing the Accuracy-to-Cost Ratio. J Chem Theory Comput 2024; 20:2858-2870. [PMID: 38531828 PMCID: PMC11008097 DOI: 10.1021/acs.jctc.4c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Accuracy and sophistication of in silico models of structure, internal dynamics, and cohesion of molecular materials at finite temperatures increase over time. Applicability limits of ab initio polymorph ranking that would be feasible at reasonable costs currently represent crystals of moderately sized molecules (less than 20 nonhydrogen atoms) and simple unit cells (containing rather only one symmetry-irreducible molecule). Extending the applicability range of the underlying first-principles methods to larger systems with a real-life significance, and enabling to perform such computations in a high-throughput regime represent additional challenges to be tackled in computational chemistry. This work presents a novel composite method that combines the computational efficiency of density-functional tight-binding (DFTB) methods with the accuracy of density-functional theory (DFT). Being rooted in the quasi-harmonic approximation, it uses a cheap method to perform all of the costly scans of how static and dynamic characteristics of the crystal vary with respect to its volume. Such data are subsequently corrected to agree with a higher-level model, which must be evaluated only at a single volume of the crystal. It thus enables predictions of structural, cohesive, and thermodynamic properties of complex molecular materials, such as pharmaceuticals or organic semiconductors, at a fraction of the original computational cost. As the composite model retains the solid physical background, it suffers from a minimum accuracy deterioration compared to the full treatment with the costly approach. The novel methodology is demonstrated to provide consistent results for the structural and thermodynamic properties of real-life molecular crystals and their polymorph ranking.
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Affiliation(s)
- Jan Ludík
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Veronika Kostková
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Štefan Kocian
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Petr Touš
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
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Pokorný V, Touš P, Štejfa V, Růžička K, Rohlíček J, Czernek J, Brus J, Červinka C. Anisotropy, segmental dynamics and polymorphism of crystalline biogenic carboxylic acids. Phys Chem Chem Phys 2022; 24:25904-25917. [PMID: 36260017 DOI: 10.1039/d2cp03698c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carboxylic acids of the Krebs cycle possess invaluable biochemical significance. Still, there are severe gaps in the availability of thermodynamic and crystallographic data, as well as ambiguities prevailing in the literature on the thermodynamic characterization and polymorph ranking. Providing an unambiguous description of the structure, thermodynamics and polymorphism of their neat crystalline phases requires a complex multidisciplinary approach. This work presents results of an extensive investigation of the structural anisotropy of the thermal expansion and local dynamics within these crystals, obtained from a beneficial cooperation of NMR crystallography and ab initio calculations of non-covalent interactions. The observed structural anisotropy and spin-lattice relaxation times are traced to large spatial variations in the strength of molecular interactions in the crystal lattice, especially in the orientation of the hydrogen bonds. A completely resolved crystal structure for oxaloacetic acid is reported for the first time. Thanks to multi-instrumental calorimetric effort, this work clarifies phase behavior, determines third-law entropies of the crystals, and states definitive polymorph ranking for succinic and fumaric acids. These thermodynamic observations are then interpreted in terms of first-principles quasi-harmonic calculations of cohesive properties. A sophisticated model capturing electronic, thermal, and configurational-entropic effects on the crystal structure approaches captures the subtle Gibbs energy differences governing polymorph ranking for succinic and fumaric acids, representing another success story of computational chemistry.
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Affiliation(s)
- Václav Pokorný
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Petr Touš
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Jan Rohlíček
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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Červinka C. Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory. J Comput Chem 2021; 43:448-456. [PMID: 34958138 DOI: 10.1002/jcc.26804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/06/2022]
Abstract
Five ionic liquids are selected for benchmarking the performance of quasi-harmonic density functional theory (DFT) calculations of structural, phonon, and thermodynamic properties of their crystals. Data predicted by individual computational setups are sorted, establishing a distinct hierarchy among the first-principles approaches. PBE-D3 and B3LYP-D3 functionals are coupled with various plane wave and Gaussian-type orbital (GTO) basis sets. Propagation of the basis set superposition error and of the imperfections of both functionals into finite-temperature properties is discussed in detail. PBE-D3 together with a triple-zeta GTO basis set often yields the most accurate predictions of predicted molar volume and heat capacity with errors at 1% and 8%, respectively, representing the state-of-the-art for quasi-harmonic DFT calculations for crystalline ionic liquids. Fortuitous error cancellation between the basis-set superposition (overbinding) and PBE imperfection (overexpanding) strongly affects the overall accuracy, unlike the case of B3LYP/GTO calculations, impeding systematic convergence of the methodology towards higher accuracy.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
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Crocker RD, Pace DP, Zhang B, Lyons DJM, Bhadbhade MM, Wong WWH, Mai BK, Nguyen TV. Unusual Alternating Crystallization-Induced Emission Enhancement Behavior in Nonconjugated ω-Phenylalkyl Tropylium Salts. J Am Chem Soc 2021; 143:20384-20394. [PMID: 34807589 DOI: 10.1021/jacs.1c10038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The alternating physical properties, especially melting points, of α,ω-disubstituted n-alkanes and their parent n-alkanes had been known since Baeyer's report in 1877. There is, however, no general and comprehensive explanation for such a phenomenon. Herein, we report the synthesis and examination of a series of novel ω-phenyl n-alkyl tropylium tetrafluoroborates, which also display alternation in their physicochemical characters. Despite being organic salts, the compounds with odd numbers of carbons in the alkyl bridge exist as room temperature ionic liquids. In stark contrast to this, the analogues with even numbers of carbons in the linker are crystalline solids. These solid nonconjugated molecules exhibit curious photoluminescent properties, which can be attributed to their ability to form through-space charge-transfer complexes to cause crystallization-induced emission enhancement. Most notably, the compound with the highest photoluminescent quantum yield in this series showed an unusual arrangement of carbocationic dimer in the solid state. A combination of XRD analysis and ab initio calculations revealed interesting insights into these systems.
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Affiliation(s)
- Reece D Crocker
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Domenic P Pace
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bolong Zhang
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia.,ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Demelza J M Lyons
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohan M Bhadbhade
- Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Wallace W H Wong
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia.,ARC Centre of Excellence in Exciton Science, School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Thanh Vinh Nguyen
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
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Abraham NS, Shirts MR. Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules. J Chem Theory Comput 2020; 16:6503-6512. [PMID: 32877183 DOI: 10.1021/acs.jctc.0c00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methods to efficiently determine the relative stability of polymorphs of organic crystals are highly desired in crystal structure predictions (CSPs). Current methodologies include calculating the free energy of static lattice phonons, quasi-harmonic approximations (QHA), and computing the full thermodynamic cycle using replica exchange molecular dynamics (REMD). We found that 13 out of the 29 systems minimized from experimental crystal structures restructured to a lower energy minimum when heated and annealed using REMD, a phenomenon that QHA alone cannot capture. Here, we present a series of methods that are intermediate in accuracy and expense between QHA and computing the full thermodynamic cycle, which can save 42-80% of the computational cost and introduces, on this benchmark, a relatively small (0.16 ± 0.04 kcal/mol) error relative to the full thermodynamic cycle. In particular, a method that Boltzmann weights harmonic free energies from along the trajectory of REMD replica exchange appears to be an appropriate intermediate between QHA and the full thermodynamic cycle using MD when screening crystal polymorph stability.
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Affiliation(s)
- Nathan S Abraham
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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