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Wang Z, Han W, Shi R, Han X, Zheng Y, Xu J, Bu XH. Mechanoresponsive Flexible Crystals. JACS AU 2024; 4:279-300. [PMID: 38425899 PMCID: PMC10900217 DOI: 10.1021/jacsau.3c00481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024]
Abstract
Flexible crystals have gained significant attention owing to their remarkable pliability, plasticity, and adaptability, making them highly popular in various research and application fields. The main challenges in developing flexible crystals lie in the rational design, preparation, and performance optimization of such crystals. Therefore, a comprehensive understanding of the fundamental origins of crystal flexibility is crucial for establishing evaluation criteria and design principles. This Perspective offers a retrospective analysis of the development of flexible crystals over the past two decades. It summarizes the elastic standards and possible plastic bending mechanisms tailored to diverse flexible crystals and analyzes the assessment of their theoretical basis and applicability. Meanwhile, the compatibility between crystal elasticity and plasticity has been discussed, unveiling the immense prospects of elastic/plastic crystals for applications in biomedicine, flexible electronic devices, and flexible optics. Furthermore, this Perspective presents state-of-the-art experimental avenues and analysis methods for investigating molecular interactions in molecular crystals, which is vital for the future exploration of the mechanisms of crystal flexibility.
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Affiliation(s)
- Zhihua Wang
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
| | - Wenqing Han
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
| | - Rongchao Shi
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
| | - Xiao Han
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
| | - Yongshen Zheng
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
| | - Jialiang Xu
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300350, P. R. China
| | - Xian-He Bu
- School
of Materials Science and Engineering, Smart Sensing Interdisciplinary
Science Center, Frontiers Science Center for New Organic Matter, Nankai University, Tongyan Road 38, Tianjin 300350, P. R. China
- Collaborative
Innovation Center of Chemical Science and Engineering, Tianjin 300350, P. R. China
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2
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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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3
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MOHAMED IBRAHIM ABDISALAM, Morisset S, Baouche S, Dulieu F. Desorption of physisorbed molecular oxygen from coronene films and graphite surfaces. J Chem Phys 2022; 156:194307. [DOI: 10.1063/5.0087870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a study on the adsorption and desorption of molecular oxygen (O2) on highly oriented pyrolytic graphite (HOPG) and on coronene films deposited on it. To this end, DFT calculations were performed and experiments were made using the FORMOLISM device, which combines ultra-high vacuum, cryogenics, atomic or molecular beam and mass spectrometry techniques. We first studied the desorption kinetics of dioxygen (O2) on a coronene film and on graphite at 15K, using the TPD (Themally Programmed Desorption) technique. We observed that the desorption of O2 occurs at a lower temperature on coronene than on graphite. We deduce the binding energies which are 12.5 kJ/mol on graphite and 10.6 kJ/mol on coronene films (preexponentiel factor of 6.88x10^14 s^-1) . The graphite surfaces partially covered with coronene show both adsorption energies. These results are in good agreement with theoretical calculations, using as surfaces graphene and coronene adsorbed on graphene. It appears that O2 is better bound parallel to the surface and has a preference for the inner sites of the coronene
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Ehlert S, Huniar U, Ning J, Furness JW, Sun J, Kaplan AD, Perdew JP, Brandenburg JG. r2SCAN-D4: Dispersion corrected meta-generalized gradient approximation for general chemical applications. J Chem Phys 2021; 154:061101. [DOI: 10.1063/5.0041008] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Uwe Huniar
- Biovia, Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Jinliang Ning
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - James W. Furness
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - Jianwei Sun
- Department of Physics and Engineering Physics, Tulane University, New Orleans, Louisiana 70118, USA
| | - Aaron D. Kaplan
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - John P. Perdew
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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5
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Grimme S, Hansen A, Ehlert S, Mewes JM. r 2SCAN-3c: A "Swiss army knife" composite electronic-structure method. J Chem Phys 2021; 154:064103. [PMID: 33588555 DOI: 10.1063/5.0040021] [Citation(s) in RCA: 233] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The recently proposed r2SCAN meta-generalized-gradient approximation (mGGA) of Furness and co-workers is used to construct an efficient composite electronic-structure method termed r2SCAN-3c. To this end, the unaltered r2SCAN functional is combined with a tailor-made triple-ζ Gaussian atomic orbital basis set as well as with refitted D4 and geometrical counter-poise corrections for London-dispersion and basis set superposition error. The performance of the new method is evaluated for the GMTKN55 database covering large parts of chemical space with about 1500 data points, as well as additional benchmarks for non-covalent interactions, organometallic reactions, and lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r2SCAN-3c: It by far surpasses its predecessor B97-3c at only twice the cost and provides one of the best results of all semi-local density-functional theory (DFT)/QZ methods ever tested for the GMTKN55 database at one-tenth of the cost. Specifically, for reaction and conformational energies as well as non-covalent interactions, it outperforms prominent hybrid-DFT/QZ approaches at two to three orders of magnitude lower cost. Perhaps, the most relevant remaining issue of r2SCAN-3c is self-interaction error (SIE), owing to its mGGA nature. However, SIE is slightly reduced compared to other (m)GGAs, as is demonstrated in two examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous composite DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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6
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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: 21] [Impact Index Per Article: 5.3] [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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7
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Červinka C, Štejfa V. Sublimation Properties of α,ω-Diamines Revisited from First-Principles Calculations. Chemphyschem 2020; 21:1184-1194. [PMID: 32243713 DOI: 10.1002/cphc.202000108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/02/2020] [Indexed: 11/06/2022]
Abstract
Sublimation enthalpies of alkane-α,ω-diamines exhibit an odd-even pattern within their homologous series. First-principles calculations coupled with the quasi-harmonic approximation for crystals and with the conformation mixing model for the ideal gas are used to explain this phenomenon from the theoretical point of view. Crystals of the odd and even alkane-α,ω-diamines distinctly differ in their packing motifs. However, first-principles calculations indicate that it is a delicate interplay of the cohesive forces, phonons, molecular vibrations and conformational equilibrium which governs the odd-even pattern of the sublimation enthalpies within the homologous series. High molecular flexibility of the alkane-α,ω-diamines predetermines higher sensitivity of the computational model to the quality of the optimized geometries and relative conformational energies. Performance of high-throughput computational methods, such as the density functional tight binding (DFTB, GFN2-xTB) and the explicitly correlated dispersion-corrected Møller-Plesset perturbative method (MP2C-F12), are benchmarked against the consistent state-of-the-art calculations of conformational energies and interaction energies, respectively.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28, Prague 6, Czech Republic
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8
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Caldeweyher E, Mewes JM, Ehlert S, Grimme S. Extension and evaluation of the D4 London-dispersion model for periodic systems. Phys Chem Chem Phys 2020; 22:8499-8512. [PMID: 32292979 DOI: 10.1039/d0cp00502a] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present an extension of the DFT-D4 model [J. Chem. Phys., 2019, 150, 154122] for periodic systems. The main new ingredients are additional reference polarizabilities for highly-coordinated group 1-5 elements derived from pseudo-periodic electrostatically-embedded cluster calculations. To illustrate the performance of the updated method, several test cases are considered, for which we compare D4 to its predecessor D3(BJ), as well as to a comprehensive set of other dispersion-corrected methods. The largest improvements are observed for solid-state polarizabilities of 16 inorganic salts, where the D4 model achieves an unprecedented accuracy, surpassing its predecessor as well as other, computationally much more demanding approaches. For cell volumes and lattice energies of two sets of chemically diverse molecular crystals, the accuracy gain is less pronounced compared to the already excellently performing D3(BJ) method. For the challenging adsorption energies of small organic molecules on metallic as well as on ionic surfaces, DFT-D4 provides values in good agreement with experimental and/or high-level references. These results suggest the application of the proposed D4 model as a physically improved yet computationally efficient dispersion correction for standard DFT calculations as well as low-cost approaches like semi-empirical or even force-field models.
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Affiliation(s)
| | | | | | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Bonn, Germany.
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9
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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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10
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Marchese Robinson RL, Geatches D, Morris C, Mackenzie R, Maloney AGP, Roberts KJ, Moldovan A, Chow E, Pencheva K, Vatvani DRM. Evaluation of Force-Field Calculations of Lattice Energies on a Large Public Dataset, Assessment of Pharmaceutical Relevance, and Comparison to Density Functional Theory. J Chem Inf Model 2019; 59:4778-4792. [DOI: 10.1021/acs.jcim.9b00601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Richard L. Marchese Robinson
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dawn Geatches
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Chris Morris
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rebecca Mackenzie
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Andrew G. P. Maloney
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Kevin J. Roberts
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alexandru Moldovan
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ernest Chow
- Pfizer Worldwide R&D, Ramsgate Road, Sandwich CT13 9NJ, United Kingdom
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11
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Červinka C, Klajmon M, Štejfa V. Cohesive Properties of Ionic Liquids Calculated from First Principles. J Chem Theory Comput 2019; 15:5563-5578. [DOI: 10.1021/acs.jctc.9b00625] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Martin Klajmon
- 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
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12
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Fischer M, Kim WJ, Badawi M, Lebègue S. Benchmarking the performance of approximate van der Waals methods for the structural and energetic properties of SiO 2 and AlPO 4 frameworks. J Chem Phys 2019; 150:094102. [PMID: 30849891 DOI: 10.1063/1.5085394] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Density functional theory (DFT) calculations using sixteen different approaches, fourteen of which were designed to include dispersion interactions [DFT + D and van der Waals (vdW)-DF methods], were performed for a set of sixteen framework compounds with either SiO2 or AlPO4 composition. The compounds include four dense structures (α-quartz, α-cristobalite, and their AlPO4 analogues), eight all-silica zeolites, and four aluminophosphate zeotypes (AlPOs). We analyzed the performance in reproducing the equilibrium structure for all systems, and computed bulk moduli and relative stabilities were compared to experiments for those compounds where experimental data are available. We found that the results obtained with functionals that take into account dispersive interactions are closer to experiments than those obtained with a bare generalized gradient functional. However, the variation among individual methods is considerable, and functionals that perform well for one quantity may give rather large deviations for another. Taking together the whole body of results, it appears that the Perdew-Burke-Ernzerhof functional including a many-body dispersion correction and the rev-vdW-DF2 methods present the best performance for the description of SiO2 and AlPO4 materials.
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Affiliation(s)
- Michael Fischer
- Crystallography Group, Department of Geosciences, University of Bremen, Klagenfurter Straße 2-4, D-28359 Bremen, Germany
| | - Won June Kim
- Université de Lorraine and CNRS, LPCT, UMR 7019, 54506 Vandœuvre-lès-Nancy, France
| | - Michael Badawi
- Université de Lorraine and CNRS, LPCT, UMR 7019, 54506 Vandœuvre-lès-Nancy, France
| | - Sébastien Lebègue
- Université de Lorraine and CNRS, LPCT, UMR 7019, 54506 Vandœuvre-lès-Nancy, France
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13
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Al-Hamdani YS, Tkatchenko A. Understanding non-covalent interactions in larger molecular complexes from first principles. J Chem Phys 2019; 150:010901. [PMID: 30621423 PMCID: PMC6910608 DOI: 10.1063/1.5075487] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/05/2018] [Indexed: 01/02/2023] Open
Abstract
Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges.
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Affiliation(s)
- Yasmine S Al-Hamdani
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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14
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LeBlanc LM, Johnson ER. Crystal-energy landscapes of active pharmaceutical ingredients using composite approaches. CrystEngComm 2019. [DOI: 10.1039/c9ce00895k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Composite methods employing dispersion-corrected DFT consistently identify experimentally isolated polymorphs as the lowest-energy crystal structures of common APIs.
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Affiliation(s)
- Luc M. LeBlanc
- Department of Chemistry
- Dalhousie University
- Halifax
- Canada
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15
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Červinka C, Beran GJO. Towards reliable ab initio sublimation pressures for organic molecular crystals - are we there yet? Phys Chem Chem Phys 2019; 21:14799-14810. [PMID: 31225538 DOI: 10.1039/c9cp01572h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Knowledge of molecular crystal sublimation equilibrium data is vital in many industrial processes, but this data can be difficult to measure experimentally for low-volatility species. Theoretical prediction of sublimation pressures could provide a useful supplement to experiment, but the exponential temperature dependence of sublimation (or any saturated vapor) pressure curve makes this challenging. An uncertainty of only a few percent in the sublimation enthalpy or entropy can propagate to an error in the sublimation pressure exceeding several orders of magnitude for a given temperature interval. Despite this fundamental difficulty, this paper performs some of the first ab initio predictions of sublimation pressure curves. Four simple molecular crystals (ethane, methanol, benzene, and imidazole) have been selected for a case study showing the currently achievable accuracy of quantum chemistry calculations. Fragment-based ab initio techniques and the quasi-harmonic approximation are used for calculations of cohesive and phonon properties of the crystals, while the vapor phase is treated by the ideal gas model. Ab initio sublimation pressure curves for model compounds are compared against their experimental counterparts. The computational uncertainties are estimated, weak points of the computational methodology are identified, and further improvements are proposed.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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16
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Witte J, Neaton JB, Head-Gordon M. Push it to the limit: comparing periodic and local approaches to density functional theory for intermolecular interactions. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1542164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jonathon Witte
- Department of Chemistry, University of California, Berkeley, California, United States
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Jeffrey B. Neaton
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States
- Department of Physics, University of California, Berkeley, California, United States
- Kavli Energy Nanosciences Institute at Berkeley, Berkeley, California, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States
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17
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LeBlanc LM, Weatherby JA, Otero-de-la-Roza A, Johnson ER. Non-Covalent Interactions in Molecular Crystals: Exploring the Accuracy of the Exchange-Hole Dipole Moment Model with Local Orbitals. J Chem Theory Comput 2018; 14:5715-5724. [DOI: 10.1021/acs.jctc.8b00797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luc M. LeBlanc
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Joseph A. Weatherby
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Quı́mica Fı́sica y Analı́tica, Facultad de Quı́mica, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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18
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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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19
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Thomas SP, Spackman PR, Jayatilaka D, Spackman MA. Accurate Lattice Energies for Molecular Crystals from Experimental Crystal Structures. J Chem Theory Comput 2018; 14:1614-1623. [DOI: 10.1021/acs.jctc.7b01200] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sajesh P. Thomas
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Peter R. Spackman
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
| | - Mark A. Spackman
- School of Molecular Sciences, University of Western Australia, Perth 6009, Australia
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20
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Walsh TR, Knecht MR. Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials. Chem Rev 2017; 117:12641-12704. [DOI: 10.1021/acs.chemrev.7b00139] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Marc R. Knecht
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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21
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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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22
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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: 63] [Impact Index Per Article: 9.0] [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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23
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Červinka C, Fulem M. State-of-the-Art Calculations of Sublimation Enthalpies for Selected Molecular Crystals and Their Computational Uncertainty. J Chem Theory Comput 2017; 13:2840-2850. [PMID: 28437618 DOI: 10.1021/acs.jctc.7b00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A computational methodology for calculation of sublimation enthalpies of molecular crystals from first principles is developed and validated by comparison to critically evaluated literature experimental data. Temperature-dependent sublimation enthalpies for a set of selected 22 molecular crystals in their low-temperature phases are calculated. The computational methodology consists of several building blocks based on high-level electronic structure methods of quantum chemistry and statistical thermodynamics. Ab initio methods up to the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction with an estimated complete basis set description [CCSD(T)/CBS] are used to calculate the cohesive energies of crystalline phases within a fragment-based additive scheme. Density functional theory (DFT) calculations with periodic boundary conditions (PBC) coupled with the quasi-harmonic approximation are used to evaluate the thermal contributions to the enthalpy of the solid phase. The properties of the vapor phase are calculated within the ideal-gas model using the rigid-rotor harmonic-oscillator model with correction for internal rotation using a one-dimensional hindered rotor approximation and a proper treatment of the molecular rotational degrees of freedom in the vicinity of 0 K. All individual terms contributing to the sublimation enthalpy as a function of temperature are discussed and their uncertainties estimated by comparison to critically evaluated experimental data.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology , Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology , Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
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24
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Fischer M, Angel RJ. Accurate structures and energetics of neutral-framework zeotypes from dispersion-corrected DFT calculations. J Chem Phys 2017; 146:174111. [DOI: 10.1063/1.4981528] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Hermann J, DiStasio RA, Tkatchenko A. First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications. Chem Rev 2017; 117:4714-4758. [PMID: 28272886 DOI: 10.1021/acs.chemrev.6b00446] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.
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Affiliation(s)
- Jan Hermann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - 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, Luxembourg
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26
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Carter DJ, Raiteri P, Barnard KR, Gielink R, Mocerino M, Skelton BW, Vaughan JG, Ogden MI, Rohl AL. Difference Hirshfeld fingerprint plots: a tool for studying polymorphs. CrystEngComm 2017. [DOI: 10.1039/c6ce02535h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Yang F, Yan CX, Yang X, Zhou DG, Zhou PP. Fenamic acid crystal with two asymmetric units (Z′ = 2): why Z′ = 2 rather than Z′ = 1. CrystEngComm 2017. [DOI: 10.1039/c6ce02646j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Fischer M, Evers FO, Formalik F, Olejniczak A. Benchmarking DFT-GGA calculations for the structure optimisation of neutral-framework zeotypes. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2014-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Pyzer-Knapp EO, Thompson HPG, Day GM. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:477-87. [PMID: 27484370 PMCID: PMC4971546 DOI: 10.1107/s2052520616007708] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/09/2016] [Indexed: 06/01/2023]
Abstract
We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.
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Affiliation(s)
- Edward O. Pyzer-Knapp
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England
| | - Hugh P. G. Thompson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England
| | - Graeme M. Day
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, England
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30
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Brandenburg JG, Grimme S. Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:502-513. [PMID: 27484372 DOI: 10.1107/s2052520616007885] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/13/2016] [Indexed: 06/06/2023]
Abstract
We analyze the energy landscape of the sixth crystal structure prediction blind test targets with various first principles and semi-empirical quantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko-Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod-Teller-Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree-Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstrasse 4-6, 53115 Bonn, Germany
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31
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Cutini M, Civalleri B, Corno M, Orlando R, Brandenburg JG, Maschio L, Ugliengo P. Assessment of Different Quantum Mechanical Methods for the Prediction of Structure and Cohesive Energy of Molecular Crystals. J Chem Theory Comput 2016; 12:3340-52. [DOI: 10.1021/acs.jctc.6b00304] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Cutini
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Bartolomeo Civalleri
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Marta Corno
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Roberto Orlando
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Jan Gerit Brandenburg
- Mulliken
Center of Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
| | - Lorenzo Maschio
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
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32
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Červinka C, Fulem M, Růžička K. CCSD(T)/CBS fragment-based calculations of lattice energy of molecular crystals. J Chem Phys 2016; 144:064505. [PMID: 26874495 DOI: 10.1063/1.4941055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A comparative study of the lattice energy calculations for a data set of 25 molecular crystals is performed using an additive scheme based on the individual energies of up to four-body interactions calculated using the coupled clusters with iterative treatment of single and double excitations and perturbative triples correction (CCSD(T)) with an estimated complete basis set (CBS) description. The CCSD(T)/CBS values on lattice energies are used to estimate sublimation enthalpies which are compared with critically assessed and thermodynamically consistent experimental values. The average absolute percentage deviation of calculated sublimation enthalpies from experimental values amounts to 13% (corresponding to 4.8 kJ mol(-1) on absolute scale) with unbiased distribution of positive to negative deviations. As pair interaction energies present a dominant contribution to the lattice energy and CCSD(T)/CBS calculations still remain computationally costly, benchmark calculations of pair interaction energies defined by crystal parameters involving 17 levels of theory, including recently developed methods with local and explicit treatment of electronic correlation, such as LCC and LCC-F12, are also presented. Locally and explicitly correlated methods are found to be computationally effective and reliable methods enabling the application of fragment-based methods for larger systems.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- 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
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33
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Nyman J, Pundyke OS, Day GM. Accurate force fields and methods for modelling organic molecular crystals at finite temperatures. Phys Chem Chem Phys 2016; 18:15828-37. [PMID: 27230942 DOI: 10.1039/c6cp02261h] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present an assessment of the performance of several force fields for modelling intermolecular interactions in organic molecular crystals using the X23 benchmark set. The performance of the force fields is compared to several popular dispersion corrected density functional methods. In addition, we present our implementation of lattice vibrational free energy calculations in the quasi-harmonic approximation, using several methods to account for phonon dispersion. This allows us to also benchmark the force fields' reproduction of finite temperature crystal structures. The results demonstrate that anisotropic atom-atom multipole-based force fields can be as accurate as several popular DFT-D methods, but have errors 2-3 times larger than the current best DFT-D methods. The largest error in the examined force fields is a systematic underestimation of the (absolute) lattice energy.
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Affiliation(s)
- Jonas Nyman
- School of Chemistry, University of Southampton, Southampton, UK.
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34
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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35
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Sure R, Brandenburg JG, Grimme S. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources. ChemistryOpen 2016; 5:94-109. [PMID: 27308221 PMCID: PMC4906470 DOI: 10.1002/open.201500192] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/12/2022] Open
Abstract
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
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36
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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37
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Červinka C, Fulem M, Stoffel RP, Dronskowski R. Thermodynamic Properties of Molecular Crystals Calculated within the Quasi-Harmonic Approximation. J Phys Chem A 2016; 120:2022-34. [PMID: 26959684 DOI: 10.1021/acs.jpca.6b00401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A computational study of the possibilities of contemporary theoretical chemistry as regards calculated thermodynamic properties for molecular crystals from first-principles is presented. The study is performed for a testing set of 22 low-temperature crystalline phases whose properties such as densities of phonon states, isobaric heat capacities, and densities are computed as functions of temperature within the quasi-harmonic approximation. Electronic structure and lattice dynamics are treated by plane-wave based calculations with optPBE-vdW functional. Comparison of calculated results with reliable critically assessed experimental data is especially emphasized.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Ralf Peter Stoffel
- Institute of Inorganic Chemistry and Jülich-Aachen Research Alliance (JARA-HPC), RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Richard Dronskowski
- Institute of Inorganic Chemistry and Jülich-Aachen Research Alliance (JARA-HPC), RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
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38
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Eikeland E, Thomsen MK, Madsen SR, Overgaard J, Spackman MA, Iversen BB. Structural Collapse of the Hydroquinone-Formic Acid Clathrate: A Pressure-Medium-Dependent Phase Transition. Chemistry 2016; 22:4061-9. [PMID: 26879515 DOI: 10.1002/chem.201504908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Indexed: 11/06/2022]
Abstract
The energy landscape governing a new pressure-induced phase transition in the hydroquinone-formic acid clathrate is reported in which the host structure collapses, opening up the cavity channels within which the guest molecules migrate and order. The reversible isosymmetric phase transition causes significant changes in the morphology and the birefringence of the crystal. The subtle intermolecular interaction energies in the clathrate are quantified at varying pressures using novel model energies and energy frameworks. These calculations show that the high-pressure phase forms a more stable host network at the expense of less-stable host-guest interactions. The phase transition can be kinetically hindered using a nonhydrostatic pressure-transmitting medium, enabling the comparison of intermolecular energies in two polymorphic structures in the same pressure range. Overall this study illustrates a need for accurate intermolecular energies when analyzing self-assembly structures and supramolecular aggregates.
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Affiliation(s)
- Espen Eikeland
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, 8000, Aarhus C, Denmark
| | - Maja K Thomsen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, 8000, Aarhus C, Denmark
| | - Solveig R Madsen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, 8000, Aarhus C, Denmark
| | - Jacob Overgaard
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, 8000, Aarhus C, Denmark
| | - Mark A Spackman
- School of Chemistry and Biochemistry, M310, University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Australia
| | - Bo B Iversen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University, 8000, Aarhus C, Denmark.
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39
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Vaughan J, Carter DJ, Rohl AL, Ogden MI, Skelton BW, Simpson PV, Brown DH. Silver(I), gold(I) and palladium(II) complexes of a NHC-pincer ligand with an aminotriazine core: a comparison with pyridyl analogues. Dalton Trans 2016; 45:1484-95. [PMID: 26672744 DOI: 10.1039/c5dt04213e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Dinuclear silver, di- and tetra-nuclear gold, and mononuclear palladium complexes with chelating C,N,C diethylaminotriazinyl-bridged bis(NHC) pincer ligands were prepared and characterised. The silver and gold complexes exist in a twisted, helical conformation in both the solution- and the solid state. In contrast, an analogous dinuclear gold complex with pyridyl-bridged NHCs exists in a linear conformation. Computational studies have been performed to rationalise the formation of twisted/helical vs. linear forms.
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Affiliation(s)
- Jamila Vaughan
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - Damien J Carter
- Science & Maths Education Centre, Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Andrew L Rohl
- Curtin Institute for Computation, Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia
| | - Mark I Ogden
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - Brian W Skelton
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Peter V Simpson
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
| | - David H Brown
- Department of Chemistry, Curtin University, GPO Box U1987, Perth WA 6845, Australia.
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40
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Grimme S, Brandenburg JG, Bannwarth C, Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J Chem Phys 2015; 143:054107. [PMID: 26254642 DOI: 10.1063/1.4927476] [Citation(s) in RCA: 514] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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41
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Otero-de-la-Roza A, Johnson ER. Predicting Energetics of Supramolecular Systems Using the XDM Dispersion Model. J Chem Theory Comput 2015; 11:4033-40. [DOI: 10.1021/acs.jctc.5b00044] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2M9
| | - Erin R. Johnson
- Department
of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4R2
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Turner MJ, Grabowsky S, Jayatilaka D, Spackman MA. Accurate and Efficient Model Energies for Exploring Intermolecular Interactions in Molecular Crystals. J Phys Chem Lett 2014; 5:4249-55. [PMID: 26273970 DOI: 10.1021/jz502271c] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The energy of interaction between molecules is commonly expressed in terms of four key components: electrostatic, polarization, dispersion, and exchange-repulsion. Using monomer wave functions to obtain accurate estimates of electrostatic, polarization, and repulsion energies along with Grimme's dispersion corrections, a series of energy models are derived by fitting to dispersion-corrected DFT energies for a large number of molecular pairs extracted from organic and inorganic molecular crystals. The best performing model reproduces B3LYP-D2/6-31G(d,p) counterpoise-corrected energies with a mean absolute deviation (MAD) of just over 1 kJ mol(-1) but in considerably less computation time. It also performs surprisingly well against benchmark CCSD(T)/CBS energies, with a MAD of 2.5 kJ mol(-1) for a combined data set including Hobza's X40, S22, A24, and S66 dimers. Two of these energy models, the most accurate and the fastest, are expected to find widespread application in investigations of molecular crystals.
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43
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Carter DJ, Rohl AL. van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface. J Comput Chem 2014. [DOI: 10.1002/jcc.23745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Damien J. Carter
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
| | - Andrew L. Rohl
- Department of Chemistry and Nanochemistry Research Institute; Curtin University; GPO Box U1987, Perth, Western Australia 6845 Australia
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