1
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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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2
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Christian MS, Nenoff TM, Rimsza JM. Effect of Linker Structure and Functionalization on Secondary Gas Formation in Metal-Organic Frameworks. J Phys Chem A 2023; 127:2881-2888. [PMID: 36947182 DOI: 10.1021/acs.jpca.2c07751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Rare-earth terephthalic acid (BDC)-based metal-organic frameworks (MOFs) are promising candidate materials for acid gas separation and adsorption from flue gas streams. However, previous simulations have shown that acid gases (H2O, NO2, and SO2) react with the hydroxyl on the BDC linkers to form protonated acid gases as a potential degradation mechanism. Herein, gas-phase computational approaches were used to identify the formation energies of these secondary protonated acid gases across multiple BDC linker molecules. Formation energies for secondary protonated acid gases were evaluated using both density functional theory (DFT) and correlated wave function methods for varying BDC-gas reaction mechanisms. Upon validation of DFT to reproduce wave function calculation results, rotated conformational linkers and chemically functionalized BDC linkers with -OH, -NH2, and -SH were investigated. The calculations show that the rotational conformation affects the molecule stability. Double-functionalized BDC linkers, where two functional groups are substituted onto BDC, showed varied reaction energies depending on whether the functional groups donate or withdraw electrons from the aromatic system. Based on these results, BDC linker design must balance adsorption performance with degradation via linker dehydrogenation for the design of stable MOFs for acid gas separations.
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Affiliation(s)
- Matthew S Christian
- Geochemistry Department, Sandia National Laboratories, P.O. Box 5800, Eubank Boulevard SE, Albuquerque, New Mexico 87185, United States
| | - Tina M Nenoff
- Advanced Science & Technology, Sandia National Laboratories, P.O. Box 5800, Eubank Boulevard SE, Albuquerque, New Mexico 87185, United States
| | - Jessica M Rimsza
- Geochemistry Department, Sandia National Laboratories, P.O. Box 5800, Eubank Boulevard SE, Albuquerque, New Mexico 87185, United States
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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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Thürlemann M, Böselt L, Riniker S. Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions. J Chem Theory Comput 2023; 19:562-579. [PMID: 36633918 PMCID: PMC9878731 DOI: 10.1021/acs.jctc.2c00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Indexed: 01/13/2023]
Abstract
Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals.
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Affiliation(s)
- Moritz Thürlemann
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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6
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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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7
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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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8
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Price AJA, Bryenton KR, Johnson ER. Requirements for an accurate dispersion-corrected density functional. J Chem Phys 2021; 154:230902. [PMID: 34241263 DOI: 10.1063/5.0050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.
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Affiliation(s)
- Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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9
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Mehta N, Fellowes T, White JM, Goerigk L. CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions? J Chem Theory Comput 2021; 17:2783-2806. [PMID: 33881869 DOI: 10.1021/acs.jctc.1c00006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Thomas Fellowes
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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10
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White MA, Kahwaji S, Freitas VLS, Siewert R, Weatherby JA, Ribeiro da Silva MDMC, Verevkin SP, Johnson ER, Zwanziger JW. The Relative Thermodynamic Stability of Diamond and Graphite. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202009897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mary Anne White
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute Dalhousie University Halifax Nova Scotia Canada
| | - Samer Kahwaji
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute Dalhousie University Halifax Nova Scotia Canada
| | - Vera L. S. Freitas
- Centro de Investigação em Química Universidade do Porto (CIQ-UP) Porto Portugal
| | - Riko Siewert
- Institute of Chemistry University of Rostock Rostock Germany
- Chemical Department Samara State Technical University Samara Russia
| | - Joseph A. Weatherby
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute Dalhousie University Halifax Nova Scotia Canada
| | | | - Sergey P. Verevkin
- Institute of Chemistry University of Rostock Rostock Germany
- Chemical Department Samara State Technical University Samara Russia
| | - Erin R. Johnson
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute Dalhousie University Halifax Nova Scotia Canada
| | - Josef W. Zwanziger
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute Dalhousie University Halifax Nova Scotia Canada
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11
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White MA, Kahwaji S, Freitas VLS, Siewert R, Weatherby JA, Ribeiro da Silva MDMC, Verevkin SP, Johnson ER, Zwanziger JW. The Relative Thermodynamic Stability of Diamond and Graphite. Angew Chem Int Ed Engl 2021; 60:1546-1549. [PMID: 32970365 DOI: 10.1002/anie.202009897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/22/2020] [Indexed: 11/09/2022]
Abstract
Recent density-functional theory (DFT) calculations raised the possibility that diamond could be degenerate with graphite at very low temperatures. Through high-accuracy calorimetric experiments closing gaps in available data, we reinvestigate the relative thermodynamic stability of diamond and graphite. For T<400 K, graphite is always more stable than diamond at ambient pressure. At low temperatures, the stability is enthalpically driven, and entropy terms add to the stability at higher temperatures. We also carried out DFT calculations: B86bPBE-25X-XDM//B86bPBE-XDM and PBE0-XDM//PBE-XDM results overlap with the experimental -TΔS results and bracket the experimental values of ΔH and ΔG, displaced by only about 2× the experimental uncertainty. Revised values of the standard thermodynamic functions for diamond are Δf Ho =-2150±150 J mol-1 , Δf So =3.44±0.03 J K-1 mol-1 and Δf Go =-3170±150 J mol-1 .
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Affiliation(s)
- Mary Anne White
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Samer Kahwaji
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Vera L S Freitas
- Centro de Investigação em Química, Universidade do Porto (CIQ-UP), Porto, Portugal
| | - Riko Siewert
- Institute of Chemistry, University of Rostock, Rostock, Germany.,Chemical Department, Samara State Technical University, Samara, Russia
| | - Joseph A Weatherby
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Sergey P Verevkin
- Institute of Chemistry, University of Rostock, Rostock, Germany.,Chemical Department, Samara State Technical University, Samara, Russia
| | - Erin R Johnson
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Josef W Zwanziger
- Department of Chemistry, Department of Physics & Atmospheric Science, and Clean Technology Research Institute, Dalhousie University, Halifax, Nova Scotia, Canada
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12
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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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13
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Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons. Int J Mol Sci 2020; 21:ijms21186571. [PMID: 32911856 PMCID: PMC7555031 DOI: 10.3390/ijms21186571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/02/2020] [Accepted: 09/04/2020] [Indexed: 01/15/2023] Open
Abstract
Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°).
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14
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Chakraborty D, Berland K, Thonhauser T. Next-Generation Nonlocal van der Waals Density Functional. J Chem Theory Comput 2020; 16:5893-5911. [PMID: 32786912 DOI: 10.1021/acs.jctc.0c00471] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fundamental ideas for a nonlocal density functional theory-capable of reliably capturing van der Waals interactions-were already conceived in the 1990s. In 2004, a seminal paper introduced the first practical nonlocal exchange-correlation functional called vdW-DF, which has become widely successful and laid the foundation for much further research. However, since then, the functional form of vdW-DF has remained unchanged. Several successful modifications paired the original functional with different (local) exchange functionals to improve performance, and the successor vdW-DF2 also updated one internal parameter. Bringing together different insights from almost 2 decades of development and testing, we present the next-generation nonlocal correlation functional called vdW-DF3, in which we change the functional form while staying true to the original design philosophy. Although many popular functionals show good performance around the binding separation of van der Waals complexes, they often result in significant errors at larger separations. With vdW-DF3, we address this problem by taking advantage of a recently uncovered and largely unconstrained degree of freedom within the vdW-DF framework that can be constrained through empirical input, making our functional semiempirical. For two different parameterizations, we benchmark vdW-DF3 against a large set of well-studied test cases and compare our results with the most popular functionals, finding good performance in general for a wide array of systems and a significant improvement in accuracy at larger separations. Finally, we discuss the achievable performance within the current vdW-DF framework, the flexibility in functional design offered by vdW-DF3, as well as possible future directions for nonlocal van der Waals density functional theory.
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Affiliation(s)
- D Chakraborty
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - K Berland
- Faculty of Science and Technology, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - T Thonhauser
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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15
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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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16
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Chen B, Xu X. XO-PBC: An Accurate and Efficient Method for Molecular Crystals. J Chem Theory Comput 2020; 16:4271-4285. [PMID: 32456429 DOI: 10.1021/acs.jctc.0c00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we propose the XO-PBC method, which combines the eXtended ONIOM method (XO) with the periodic boundary condition (PBC) for the description of molecular crystals. XO-PBC tries to embed a finite cluster cut out from the solid into the periodic environment, making it feasible to employ advanced molecular quantum chemistry methods, which are usually prohibitively expensive for direct PBC calculations. In particular, XO-PBC utilizes the results from force calculations to design the scheme to fragment the molecule when crystals are made of large molecules and to select cluster model systems automatically consisting of dimer up to tetramer interactions for embedding. By applying an appropriate theory to each model, a satisfactory accuracy for the system under study is ensured, while a high efficiency is achieved with massively parallel computing by distributing model systems onto different processors. A comparison of the XO-PBC calculations with the conventional direct PBC calculations at the B3LYP level demonstrates its accuracy at substantially low cost for the description of molecular crystals. The usefulness of the XO-PBC method is further exemplified, showing that XO-PBC is able to predict the lattice energies of various types of molecular crystals within chemical accuracy (<4 kJ/mol) when the doubly hybrid density functional XYG3 is used as the target high level and the periodic PBE as the basic low level. The XO-PBC method provides a general protocol that brings the great predictive power of advanced electronic structure methods from molecular systems to the extended solids.
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Affiliation(s)
- Bozhu Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Ministry of Education Key Laboratory of Computational Physical Sciences, Department of Chemistry, Fudan University, Shanghai, 200433, China
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17
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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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18
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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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19
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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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