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Beran GJO, Greenwell C, Cook C, Řezáč J. Improved Description of Intra- and Intermolecular Interactions through Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory. Acc Chem Res 2023; 56:3525-3534. [PMID: 37963266 DOI: 10.1021/acs.accounts.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Chandler Greenwell
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
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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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Taniguchi T, Hosokawa M, Asahi T. Graph Comparison of Molecular Crystals in Band Gap Prediction Using Neural Networks. ACS OMEGA 2023; 8:39481-39489. [PMID: 37901497 PMCID: PMC10601046 DOI: 10.1021/acsomega.3c05224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023]
Abstract
In material informatics, the representation of the material structure is fundamentally essential to obtaining better prediction results, and graph representation has attracted much attention in recent years. Molecular crystals can be graphically represented in molecular and crystal representations, but a comparison of which representation is more effective has not been examined. In this study, we compared the prediction accuracy between molecular and crystal graphs for band gap prediction. The results showed that the prediction accuracies using crystal graphs were better than those obtained using molecular graphs. While this result is not surprising, error analysis quantitatively evaluated that the error of the crystal graph was 0.4 times that of the molecular graph with moderate correlation. The novelty of this study lies in the comparison of molecular crystal representations and in the quantitative evaluation of the contribution of crystal structures to the band gap.
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Affiliation(s)
- Takuya Taniguchi
- Center
for Data Science, Waseda University, 1-6-1 Nishiwaseda, Shinjuku-ku, Tokyo 169-8050, Japan
| | - Mayuko Hosokawa
- Department
of Advanced Science and Engineering, Graduate School of Advanced Science
and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Toru Asahi
- Department
of Advanced Science and Engineering, Graduate School of Advanced Science
and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
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Rana B, Beran GJO, Herbert JM. Correcting π-delocalisation errors in conformational energies using density-corrected DFT, with application to crystal polymorphs. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2138789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | | | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
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Beran GJO, Sugden IJ, Greenwell C, Bowskill DH, Pantelides CC, Adjiman CS. How many more polymorphs of ROY remain undiscovered. Chem Sci 2022; 13:1288-1297. [PMID: 35222912 PMCID: PMC8809489 DOI: 10.1039/d1sc06074k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (a.k.a. ROY) holds the current record for the largest number of fully characterized organic crystal polymorphs. Four of these polymorph structures have been reported since 2019, raising the question of how many more ROY polymorphs await future discovery. Employing crystal structure prediction and accurate energy rankings derived from conformational energy-corrected density functional theory, this study presents the first crystal energy landscape for ROY that agrees well with experiment. The lattice energies suggest that the seven most stable ROY polymorphs (and nine of the twelve lowest-energy forms) on the Z' = 1 landscape have already been discovered experimentally. Discovering any new polymorphs at ambient pressure will likely require specialized crystallization techniques capable of trapping metastable forms. At pressures above 10 GPa, however, a new crystal form is predicted to become enthalpically more stable than all known polymorphs, suggesting that further high-pressure experiments on ROY may be warranted. This work highlights the value of high-accuracy crystal structure prediction for solid-form screening and demonstrates how pragmatic conformational energy corrections can overcome the limitations of conventional density functionals for conformational polymorphs.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - Isaac J Sugden
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Chandler Greenwell
- Department of Chemistry, University of California Riverside Riverside CA 92521 USA
| | - David H Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Constantinos C Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
| | - Claire S Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London London SW7 2AZ UK
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Ito S. Luminescent polymorphic crystals: mechanoresponsive and multicolor-emissive properties. CrystEngComm 2022. [DOI: 10.1039/d1ce01614h] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polymorphic organic crystals that can switch their photophysical properties in response to mechanical stimuli are highlighted.
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Affiliation(s)
- Suguru Ito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Warren LR, McGowan E, Renton M, Morrison CA, Funnell NP. Direct evidence for distinct colour origins in ROY polymorphs. Chem Sci 2021; 12:12711-12718. [PMID: 34703557 PMCID: PMC8494124 DOI: 10.1039/d1sc04051k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
ROY is one of the most well-studied families of crystal structures owing to it being the most polymorphic organic material on record. The various red, orange, and yellow colours of its crystal structures are widely-believed to originate from molecular conformation, though the orange needle (ON) polymorph is thought to be an exception. We report high-pressure, single-crystal X-ray measurements which provide direct experimental evidence that the colour origin in ON is intermolecular, revealing that the molecule undergoes minimal deformation but still exhibits a pronounced, reversible, pale orange → dark red colour change between ambient pressure and 4.18 GPa. Our experimental data are rationalised with band structures, calculated using an accurate hybrid DFT approach, where we are able to account for the variation in colour for five polymorphs of ROY. We highlight the outlier behaviour of ON which shows marked π⋯π stacking interactions that are directly modified through application of pressure. Band structure calculations confirm these intermolecular interactions as the origin of the colour change.
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Affiliation(s)
- Lisette R Warren
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Evana McGowan
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Margaret Renton
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Carole A Morrison
- University of Edinburgh Joseph Black Building, David Brewster Road Edinburgh EH9 3FJ UK +44 (0)131 650 4725
| | - Nicholas P Funnell
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory Didcot OX11 0QX UK +44 (0)1235 445385
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Riaz S, Jaffar K, Perveen M, Riaz A, Nazir S, Iqbal J. Computational study of therapeutic potential of phosphorene as a nano-carrier for drug delivery of nebivolol for the prohibition of cardiovascular diseases: a DFT study. J Mol Model 2021; 27:306. [PMID: 34590181 DOI: 10.1007/s00894-021-04907-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Density functional theory (DFT) calculations were utilized to assess the drug delivery efficiency of phosphorene carrier for nebivolol drug to treat cardiovascular diseases. The optimized structures, excited state, and electronic properties of nebivolol, phosphorene, and nebivolol-phosphorene (nebivolol-PH) complex were considered to determine the drug delivery ability of phosphorene at the target site. The increased dipole moment (6.08 D) results in the higher solubility of the complex in polar solvents (water). Weak interactive forces between nebivolol and phosphorene were demonstrated by the non-covalent interaction (NCI) plot that facilitated the offloading of nebivolol at the targeted area. The analysis of frontier molecular orbitals (FMOs) revealed that during excitation, the charge was transferred from nebivolol as a higher occupied molecular orbital (HOMO) to phosphorene as a lower unoccupied molecular orbital (LUMO). Thus, the charge-transfer process was further studied by charge decomposition analysis (CDA). The calculated results at the excited state for the nebivolol-PH complex exhibited that the maximum wavelength (λmax) was red-shifted by 6 nm in the gas phase. The electron-hole theory and photoinduced electron transfer (PET) processes were carried out for the exploration of different excited states of the complex. Additionally, phosphorene with + 1 and - 1 charge states indicated the minor structural changes and provide the stable nebivolol-PH complex. This theoretical study also investigated that phosphorene can be exploited as an effective carrier for the delivery of a therapeutic agent as nebivolol to treat cardiovascular diseases. This work will also encourage the researchers to investigate the other 2D nanoparticles as a nano-drug delivery system (NDDS).
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Affiliation(s)
- Saima Riaz
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Kinza Jaffar
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Mehvish Perveen
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan
| | | | - Sidra Nazir
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad, 38000, Pakistan.
- Punjab Bio-Energy Institute, University of Agriculture, Faisalabad, 38000, Pakistan.
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