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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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52
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Abstract
Triclabendazole is an effective medication to treat fascioliasis and paragonimiasis parasitic infections. We implemented a reliable quantum mechanical method which is density functional theory at the level of ωB97XD/6-31G* along with embedded fragments to elucidate stability and phase transition between two forms of triclabendazole. We calculated crystal structure parameters, volumes, Gibbs free energies, and vibrational spectra of two polymorphic forms of triclabendazole under different pressures and temperatures. We confirmed form I was more stable than form II at atmospheric pressure and room temperature. From high-pressure Gibbs free energy computations, we found a pressure-induced phase transformation between form I (triclinic unit cell) and form II (monoclinic unit cell). The phase transition between forms I and II was found at a pressure and temperature of 5.5 GPa and ≈350 K, respectively. In addition, we also studied the high-pressure polymorphic behavior of two forms of triclabendazole. At the pressure of 5.5 GPa and temperature from ≈350 K to 500 K, form II was more stable than form I. However, at temperatures lower than ≈350 K, form I was more stable than form II. We also studied the effects of pressures on volumes and Raman spectra. To the best of our knowledge, no such research has been conducted to determine the presence of phase transformation between two forms of triclabendazole. This is a case study that can be applied to various polymorphic crystals to study their structures, stabilities, spectra, and phase transformations. This research can assist scientists, chemists, and pharmacologists in selecting the desired polymorph and better drug design.
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53
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Abstract
Quantum embedding schemes are a promising way to extend multireference computations to large molecules with strong correlation effects localized on a small number of atoms. This work introduces a second-order active-space embedding theory [ASET(2)] which improves upon mean-field frozen embedding by treating fragment-environment interactions via an approximate canonical transformation. The canonical transformation employed in ASET(2) is formulated using the driven similarity renormalization group. The ASET(2) scheme is benchmarked on the N═N bond dissociation in pentyldiazene, the S0 to S1 excitation in 1-octene, and the interaction energy of the O2-benzene complex. The ASET(2) explicit treatment of fragment-environment interactions beyond the mean-field level generally improves the accuracy of embedded computations, and it becomes necessary to achieve an accurate description of excitation energies of 1-octene and the singlet-triplet gap of the O2-benzene complex.
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Affiliation(s)
- Nan He
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chenyang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Francesco A Evangelista
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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54
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Cheng C, Liang Q, Yan M, Liu Z, He Q, Wu T, Luo S, Pan Y, Zhao C, Liu Y. Advances in preparation, mechanism and applications of graphene quantum dots/semiconductor composite photocatalysts: A review. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127721. [PMID: 34865907 DOI: 10.1016/j.jhazmat.2021.127721] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Due to the low efficiency of single-component nano materials, there are more and more studies on high-efficiency composites. As zero dimensional (0D) non-metallic semiconductor material, the emergence of graphene quantum dots (GQDs) overcomes the shortcomings of traditional photocatalysts (rapid rate of electron-hole recombination and narrow range of optical response). Their uniqueness is that they can combine the advantages of quantum dots (rich functional groups at edge) and sp2 carbon materials (large specific surface area). The inherent inert carbon stabilizes chemical and physical properties, and brings new breakthroughs to the development of benchmark photocatalysts. The photocatalytic efficiency of GQDs composite with semiconductor materials (SCs) can be improved by the following three points: (1) accelerating charge transfer, (2) extending light absorption range, (3) increasing active sites. The methods of preparation (bottom-up and top-down), types of heterojunctions, mechanisms of photocatalysis, and applications of GQDs/SCs (wastewater treatment, energy storage, gas sensing, UV detection, antibiosis and biomedicine) are comprehensively discussed. And it is hoped that this review can provide some guidance for the future research on of GQDs/SCs on photocatalysis.
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Affiliation(s)
- Chunyu Cheng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Qinghua Liang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Ming Yan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Qingyun He
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Ting Wu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Songhao Luo
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yuan Pan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Chenhui Zhao
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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55
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Donà L, Brandenburg JG, Civalleri B. Metal-Organic Frameworks Properties from Hybrid Density Functional Approximations. J Chem Phys 2022; 156:094706. [DOI: 10.1063/5.0080359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lorenzo Donà
- Università degli Studi di Torino, Department of Chemistry, Italy
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56
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A complete description of thermodynamic stabilities of molecular crystals. Proc Natl Acad Sci U S A 2022; 119:2111769119. [PMID: 35131847 PMCID: PMC8832981 DOI: 10.1073/pnas.2111769119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2021] [Indexed: 12/27/2022] Open
Abstract
Predicting stable polymorphs of molecular crystals remains one of the grand challenges of computational science. Current methods invoke approximations to electronic structure and statistical mechanics and thus fail to consistently reproduce the delicate balance of physical effects determining thermodynamic stability. We compute the rigorous ab initio Gibbs free energies for competing polymorphs of paradigmatic compounds, using machine learning to mitigate costs. The accurate description of electronic structure and full treatment of quantum statistical mechanics allow us to predict the experimentally observed phase behavior. This constitutes a key step toward the first-principles design of functional materials for applications from photovoltaics to pharmaceuticals. Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free energy differences are sensitively affected by the description of electronic structure, the statistical mechanics of the nuclei and the cell, and thermal expansion. The importance of these effects has been individually established, but rigorous free energy calculations for general molecular compounds, which simultaneously account for all effects, have hitherto not been computationally viable. Here we present an efficient “end to end” framework that seamlessly combines state-of-the art electronic structure calculations, machine-learning potentials, and advanced free energy methods to calculate ab initio Gibbs free energies for general organic molecular materials. The facile generation of machine-learning potentials for a diverse set of polymorphic compounds—benzene, glycine, and succinic acid—and predictions of thermodynamic stabilities in qualitative and quantitative agreement with experiments highlight that predictive thermodynamic studies of industrially relevant molecular materials are no longer a daunting task.
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57
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Vaksler YA, Idrissi A, Shishkina SV. Is it possible to predict the stability of a crystal structure under the influence of pressure? Quantum chemical study of ibuprofen crystals. NEW J CHEM 2022. [DOI: 10.1039/d1nj05780d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantum chemical modeling was used to analyze the crystalline structure of ibuprofen under atmospheric pressure to determine the structural features, providing its stability under pressure.
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Affiliation(s)
- Yevhenii A. Vaksler
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine, 60 Nauky Ave., Kharkiv, 61001, Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61077, Ukraine
- Laboratoire de Spectroscopie Pour Les Interactions, La Réactivité et L’environnement (UMR CNRS A8516), Université de Lille, 59655, Villeneuve d’Ascq Cedex, France
| | - Abdenacer Idrissi
- Laboratoire de Spectroscopie Pour Les Interactions, La Réactivité et L’environnement (UMR CNRS A8516), Université de Lille, 59655, Villeneuve d’Ascq Cedex, France
| | - Svitlana V. Shishkina
- SSI “Institute for Single Crystals” National Academy of Science of Ukraine, 60 Nauky Ave., Kharkiv, 61001, Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61077, Ukraine
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58
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Shaffer CC, Oliver AG, Smith BD. Co-crystals of tetrahaloauric acid and 1,3,5-(methylacetamide)benzene-based tectons: consistent trapping of high energy molecular conformation. CrystEngComm 2022. [DOI: 10.1039/d2ce00463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Co-crystal engineering is a promising method to create new classes of advanced materials. Co-crystal structure prediction is more challenging when one or more of the lattice constituents (tectons) are flexible...
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59
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Dudek MK, Druzbicki K. Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules. CrystEngComm 2022. [DOI: 10.1039/d1ce01564h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...
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60
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Beran GJO, Sugden IJ, Greenwell C, Bowskill DH, Pantelides CC, Adjiman CS. How many more polymorphs of ROY remain undiscovered. Chem Sci 2022; 13:1288-1297. [PMID: 35222912 PMCID: PMC8809489 DOI: 10.1039/d1sc06074k] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (a.k.a. ROY) holds the current record for the largest number of fully characterized organic crystal polymorphs. Four of these polymorph structures have been reported since 2019, raising the question of how many more ROY polymorphs await future discovery. Employing crystal structure prediction and accurate energy rankings derived from conformational energy-corrected density functional theory, this study presents the first crystal energy landscape for ROY that agrees well with experiment. The lattice energies suggest that the seven most stable ROY polymorphs (and nine of the twelve lowest-energy forms) on the Z′ = 1 landscape have already been discovered experimentally. Discovering any new polymorphs at ambient pressure will likely require specialized crystallization techniques capable of trapping metastable forms. At pressures above 10 GPa, however, a new crystal form is predicted to become enthalpically more stable than all known polymorphs, suggesting that further high-pressure experiments on ROY may be warranted. This work highlights the value of high-accuracy crystal structure prediction for solid-form screening and demonstrates how pragmatic conformational energy corrections can overcome the limitations of conventional density functionals for conformational polymorphs. Crystal structure prediction suggests that the low-energy polymorphs of ROY have already been found, but a new high-pressure form is predicted.![]()
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Affiliation(s)
- Gregory J. O. Beran
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
| | - Isaac J. Sugden
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Chandler Greenwell
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
| | - David H. Bowskill
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Constantinos C. Pantelides
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Claire S. Adjiman
- Department of Chemical Engineering, Sargent Centre for Process Systems Engineering, Imperial College London, London, SW7 2AZ, UK
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61
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Dutta D, Sharma P, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Baruwa B, Bhattacharyya MK. Solvent-driven structural topologies in phenanthroline-based co-crystals of Zn( ii) involving fascinating infinite chair-like {[(bzH) 4Cl 2] 2−} n assemblies and unconventional layered infinite {bz-H 2O-Cl} n anion-water clusters: antiproliferative evaluation and theoretical studies. NEW J CHEM 2022. [DOI: 10.1039/d1nj05234a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Anticancer activities considering cell cytotoxicity, apoptosis and molecular docking have been explored in Zn(ii) co-crystals of phenanthroline involving infinite chair-like assemblies and unconventional layered infinite anion-water clusters.
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Affiliation(s)
- Debasish Dutta
- Department of Chemistry, Cotton University, Guwahati-781001, Assam, India
| | - Pranay Sharma
- Department of Chemistry, Cotton University, Guwahati-781001, Assam, India
| | - Rosa M. Gomila
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Miquel Barcelo-Oliver
- Departament de Química, Universitat de les Illes Balears, Crta de Valldemossa km 7.7, 07122 Palma de Mallorca (Baleares), Spain
| | - Akalesh K. Verma
- Department of Zoology, Cell & Biochemical Technology Laboratory, Cotton University, Guwahati-781001, India
| | - Bandita Baruwa
- Department of Zoology, Cell & Biochemical Technology Laboratory, Cotton University, Guwahati-781001, India
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62
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Červinka C. Tuning the quasi-harmonic treatment of crystalline ionic liquids within the density functional theory. J Comput Chem 2021; 43:448-456. [PMID: 34958138 DOI: 10.1002/jcc.26804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/06/2022]
Abstract
Five ionic liquids are selected for benchmarking the performance of quasi-harmonic density functional theory (DFT) calculations of structural, phonon, and thermodynamic properties of their crystals. Data predicted by individual computational setups are sorted, establishing a distinct hierarchy among the first-principles approaches. PBE-D3 and B3LYP-D3 functionals are coupled with various plane wave and Gaussian-type orbital (GTO) basis sets. Propagation of the basis set superposition error and of the imperfections of both functionals into finite-temperature properties is discussed in detail. PBE-D3 together with a triple-zeta GTO basis set often yields the most accurate predictions of predicted molar volume and heat capacity with errors at 1% and 8%, respectively, representing the state-of-the-art for quasi-harmonic DFT calculations for crystalline ionic liquids. Fortuitous error cancellation between the basis-set superposition (overbinding) and PBE imperfection (overexpanding) strongly affects the overall accuracy, unlike the case of B3LYP/GTO calculations, impeding systematic convergence of the methodology towards higher accuracy.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic
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63
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Yanes-Rodríguez R, Prosmiti R. Assessment of DFT approaches in noble gas clathrate-like clusters: stability and thermodynamics. Phys Chem Chem Phys 2021; 24:1475-1485. [PMID: 34935011 DOI: 10.1039/d1cp04935f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have assessed the performance and accuracy of different wavefunction-based electronic structure methods, such as DFMP2 and domain-based local pair-natural orbital (DLPNO-CCSD(T)), as well as a variety of density functional theory (DFT) approaches on He@(H2O)N cage systems. We have selected representative clathrate-like structures corresponding to the building blocks present in each of the sI, sII and sH natural gas clathrate hydrates, and we have carefully studied the interaction between a He atom with each of their individual cages. We reported well-converged DFMP2 and DLPNO-CCSD(T) reference data, together with interaction and cohesive energies of four different density functionals (two GGA, revPBE and PW86PBE, and two hybrids, B3LYP and PBE0), including diverse dispersion correction schemes (D3(0), D3(BJ), D4 and XDM) for both He-filled and empty clathrate-like cages. After the analysis of the results, we came to the conclusion that the PW86PBE functional, with both XDM and D4 corrections, and the PBE0-D4 functional present reasonably adequate approaches to describe the guest-host noncovalent interactions that take place in such He clathrate hydrates. Taking into account that the He@sII is the only helium clathrate that scientists have been able to synthesize recently, we have performed a thermodynamic study on the individual 512 and 51264 cages present in the sII crystal. We determined the change in enthalpy, ΔH, and in Gibbs free energy, ΔG, at various temperatures and pressures, and we found out that in the range of experimental conditions the reactions associated with the encapsulation of the He atom inside the cages are exothermic and spontaneous. Finally, we highlighted the importance of an accurate description of the interaction in He@water mixtures, as a crucial component in construction of reliable data-driven models.
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Affiliation(s)
- Raquel Yanes-Rodríguez
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain. .,Doctoral Programme in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, Spain
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain.
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64
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Liang Q, Yang J. Third-Order Many-Body Expansion of OSV-MP2 Wave Function for Low-Order Scaling Analytical Gradient Computation. J Chem Theory Comput 2021; 17:6841-6860. [PMID: 34704757 DOI: 10.1021/acs.jctc.1c00581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present a many-body expansion (MBE) formulation and implementation for efficient computation of analytical energy gradients from the orbital-specific-virtual second-order Møllet-Plesset perturbation theory (OSV-MP2) based on our earlier work (Zhou et al. J. Chem. Theory Comput. 2020, 16, 196-210). The third-order MBE(3) expansion of OSV-MP2 amplitudes and density matrices was developed to adopt the orbital-specific clustering and long-range termination schemes, which avoids term-by-term differentiations of the MBE energy bodies. We achieve better efficiency by exploiting the algorithmic sparsity that allows us to prune out insignificant fitting integrals and OSV relaxations. With these approximations, the present implementation is benchmarked on a range of molecules that show an economic scaling in the linear and quadratic regimes for computing MBE(3)-OSV-MP2 amplitude and gradient equations, respectively, and yields normal accuracy comparable to the original OSV-MP2 results. The MPI-3-based parallelism through shared memory one-sided communication is further developed for improving parallel scalability and memory accessibility by sorting the MBE(3) orbital clusters into independent tasks that are distributed on multiple processes across many nodes, supporting both global and local data locations in which selected MBE(3)-OSV-MP2 intermediates of different sizes are distinguished and accordingly placed. The accuracy and efficiency level of our MBE(3)-OSV-MP2 analytical gradient implementation is finally illustrated in two applications: we show that the subtle coordination structure differences of mechanically interlocked Cu-catenane complexes can be distinguished when tuning ligand lengths; and the porphycene molecular dynamics reveals the emergence of the vibrational signature arising from softened N-H stretching associated with hydrogen transfer, using an MP2 level of electron correlation and classical nuclei for the first time.
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Affiliation(s)
- Qiujiang Liang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
| | - Jun Yang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, P. R. China
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65
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Kumar A, DeGregorio N, Iyengar SS. Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions. J Chem Theory Comput 2021; 17:6671-6690. [PMID: 34623129 DOI: 10.1021/acs.jctc.1c00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicole DeGregorio
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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66
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Doran AE, Qiu DL, Hirata S. Monte Carlo MP2-F12 for Noncovalent Interactions: The C 60 Dimer. J Phys Chem A 2021; 125:7344-7351. [PMID: 34433271 DOI: 10.1021/acs.jpca.1c05021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A scalable stochastic algorithm is presented that can evaluate explicitly correlated (F12) second-order many-body perturbation (MP2) energies of weak, noncovalent, intermolecular interactions. It first transforms the formulas of the MP2 and F12 energy differences into a short sum of high-dimensional integrals of Green's functions in real space and imaginary time. These integrals are then evaluated by the Monte Carlo method augmented by parallel execution, redundant-walker convergence acceleration, direct-sampling autocorrelation elimination, and control-variate error reduction. By sharing electron-pair walkers across the supermolecule and its subsystems spanned by the joint basis set, the statistical uncertainty is reduced by one to 2 orders of magnitude in the MP2 binding energy corrected for the basis-set incompleteness and superposition errors. The method predicts the MP2-F12/aug-cc-pVDZ binding energy of 19.1 ± 4.0 kcal mol-1 for the C60 dimer at the center distance of 9.748 Å.
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Affiliation(s)
- Alexander E Doran
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - David L Qiu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - So Hirata
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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67
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Hetmańczyk Ł, Goremychkin EA, Waliszewski J, Vener MV, Lipkowski P, Tolstoy PM, Filarowski A. Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline. Molecules 2021; 26:molecules26165043. [PMID: 34443632 PMCID: PMC8401763 DOI: 10.3390/molecules26165043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm−1 spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D5-imino)methyl]phenol (SA-C6D5) has been studied by powder X-ray diffraction in the 20–320 K temperature range.
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Affiliation(s)
- Łukasz Hetmańczyk
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387 Cracow, Poland;
| | - Eugene A. Goremychkin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
| | - Janusz Waliszewski
- Faculty of Physics, University of Bialystok, 1L Ciolkowskiego str., 15-245 Bialystok, Poland;
| | - Mikhail V. Vener
- Quantum Chemistry Department, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia;
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii Prosp. 31, 119991 Moscow, Russia
| | - Paweł Lipkowski
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańnskiego 27, 50-370 Wrocław, Poland;
| | - Peter M. Tolstoy
- Institute of Chemistry, St. Petersburg State University, Universitetskij pr. 26, 198504 Saint Petersburg, Russia
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
| | - Aleksander Filarowski
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research 6 F. Joliot-Curie str., 141980 Dubna, Russia;
- Faculty of Chemistry, University of Wrocław 14 F. Joliot-Curie str., 50-383 Wrocław, Poland
- Correspondence: (P.M.T.); (A.F.); Tel.: +48-71-375-7229 (A.F.)
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Prentice JCA, Mostofi AA. Accurate and Efficient Computation of Optical Absorption Spectra of Molecular Crystals: The Case of the Polymorphs of ROY. J Chem Theory Comput 2021; 17:5214-5224. [PMID: 34291954 DOI: 10.1021/acs.jctc.1c00227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
When calculating the optical absorption spectra of molecular crystals from first principles, the influence of the crystalline environment on the excitations is of significant importance. For such systems, however, methods to describe the excitations accurately can be computationally prohibitive due to the relatively large system sizes involved. In this work, we demonstrate a method that allows optical absorption spectra to be computed both efficiently and at high accuracy. Our approach is based on the spectral warping method successfully applied to molecules in solvent. It involves calculating the absorption spectrum of a supercell of the full molecular crystal using semi-local time-dependent density functional theory (TDDFT), before warping the spectrum using a transformation derived from smaller-scale semi-local and hybrid TDDFT calculations on isolated dimers. We demonstrate the power of this method on three polymorphs of the well-known color polymorphic compound ROY and find that it outperforms both small-scale hybrid TDDFT dimer calculations and large-scale semi-local TDDFT supercell calculations, when compared to the experiment.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, U.K.,Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, U.K
| | - Arash A Mostofi
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, U.K
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70
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Schmitt-Monreal D, Jacob CR. Density-Based Many-Body Expansion as an Efficient and Accurate Quantum-Chemical Fragmentation Method: Application to Water Clusters. J Chem Theory Comput 2021; 17:4144-4156. [PMID: 34196558 DOI: 10.1021/acs.jctc.1c00340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fragmentation methods based on the many-body expansion offer an attractive approach for the quantum-chemical treatment of large molecular systems, such as molecular clusters and crystals. Conventionally, the many-body expansion is performed for the total energy, but such an energy-based many-body expansion often suffers from a slow convergence with respect to the expansion order. For systems that show strong polarization effects such as water clusters, this can render the energy-based many-body expansion infeasible. Here, we establish a density-based many-body expansion as a promising alternative approach. By performing the many-body expansion for the electron density instead of the total energy and inserting the resulting total electron density into the total energy functional of density functional theory, one can derive a density-based energy correction, which in principle accounts for all higher-order polarization effects. Here, we systematically assess the accuracy of such a density-based many-body expansion for test sets of water clusters. We show that already a density-based two-body expansion is able to reproduce interaction energies per fragment within chemical accuracy and is able to accurately predict the energetic ordering as well as the relative interaction energies of different isomers of water clusters.
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Affiliation(s)
- Daniel Schmitt-Monreal
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstr. 17, 38106 Braunschweig, Germany
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71
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Qiu QM, Li XY, Chen CA, Sun KN, Yang GY. Polar polymorphism: β-Ca2[B5O8(OH)]2[B(OH)3]·H2O—synthesis, structure and nonlinear optical property. J SOLID STATE CHEM 2021. [DOI: 10.1016/j.jssc.2021.122193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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72
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Zn(II) Heteroleptic Halide Complexes with 2-Halopyridines: Features of Halogen Bonding in Solid State. Molecules 2021; 26:molecules26113393. [PMID: 34205151 PMCID: PMC8199927 DOI: 10.3390/molecules26113393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Reactions between Zn(II) dihalides and 2-halogen-substituted pyridines 2-XPy result in a series of heteroleptic molecular complexes [(2-XPy)2ZnY2] (Y = Cl, X = Cl (1), Br (2), I (3); Y = Br, X = Cl (4), Br (5), I (6), Y = I, X = Cl (7), Br (8), and I (9)). Moreover, 1-7 are isostructural (triclinic), while 8 and 9 are monoclinic. In all cases, halogen bonding plays an important role in formation of crystal packing. Moreover, 1-9 demonstrate luminescence in asolid state; for the best emitting complexes, quantum yield (QY) exceeds 21%.
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73
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Fan J, Su Y, Zheng Z, Zhao J. Thermal properties of energetic materials from quasi-harmonic first-principles calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:275702. [PMID: 33906164 DOI: 10.1088/1361-648x/abfc11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
The structure and properties at a finite temperature are critical to understand the temperature effects on energetic materials (EMs). Combining dispersion-corrected density functional theory with quasi-harmonic approximation, the thermodynamic properties for several representative EMs, including nitromethane, PETN, HMX, and TATB, are calculated. The inclusion of zero-point energy and temperature effect could significantly improve the accuracy of lattice parameters at ambient condition; the deviations of calculated cell volumes and experimental values at room temperature are within 0.62%. The calculated lattice parameters and thermal expansion coefficients with increasing temperature show strong anisotropy. In particular, the expansion rate (2.61%) of inter-layer direction of TATB is higher than intra-layer direction and other EMs. Furthermore, the calculated heat capacities could reproduce the experimental trends and enrich the thermodynamic data set at finite temperatures. The predicted isothermal and adiabatic bulk moduli could reflect the softening behavior of EMs. These results would fundamentally provide a deep understanding and serve as a reference for the experimental measurement of the thermodynamic parameters of EMs.
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Affiliation(s)
- Junyu Fan
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
- Department of Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
- Institute of Computational and Applied Physics, Taiyuan Normal University, Jinzhong 030619, People's Republic of China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
| | - Zhaoyang Zheng
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, People's Republic of China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams (Dalian University of Technology), Ministry of Education, Dalian 116024, People's Republic of China
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74
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Banerjee A, Jasrasaria D, Niblett SP, Wales DJ. Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization. J Phys Chem A 2021; 125:3776-3784. [PMID: 33881850 PMCID: PMC8279651 DOI: 10.1021/acs.jpca.1c00903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/07/2021] [Indexed: 11/29/2022]
Abstract
Organic molecules can be stable in distinct crystalline forms, known as polymorphs, which have significant consequences for industrial applications. Here, we predict the polymorphs of crystalline benzene computationally for an accurate anisotropic model parametrized to reproduce electronic structure calculations. We adapt the basin-hopping global optimization procedure to the case of crystalline unit cells, simultaneously optimizing the molecular coordinates and unit cell parameters to locate multiple low-energy structures from a variety of crystal space groups. We rapidly locate all the well-established experimental polymorphs of benzene, each of which corresponds to a single local energy minimum of the model. Our results show that basin-hopping can be both an efficient and effective tool for polymorphic crystal structure prediction, requiring no a priori experimental knowledge of cell parameters or symmetry.
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Affiliation(s)
- Atreyee Banerjee
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Max
Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Dipti Jasrasaria
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
| | - Samuel P. Niblett
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
- Department
of Chemistry, University of California, Berkeley, California 94609, United States
- Materials
Science Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94609, United States
| | - David J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
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75
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Surov AO, Voronin AP, Drozd KV, Gruzdev MS, Perlovich GL, Prashanth J, Balasubramanian S. Polymorphic forms of antiandrogenic drug nilutamide: structural and thermodynamic aspects. Phys Chem Chem Phys 2021; 23:9695-9708. [PMID: 33908506 DOI: 10.1039/d1cp00793a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Attempts to obtain new cocrystals of nonsteroidal antiandrogenic drug nilutamide produced alternative polymorphic forms of the compound (Form II and Form III) and their crystal structures were elucidated by single-crystal X-ray diffraction. Apart from the cocrystallization technique, lyophilization was found to be an effective strategy for achieving polymorph control of nilutamide, which was difficult to obtain by other methods. The physicochemical properties and relative stability of the commercial Form I and newly obtained Form II were comprehensively investigated by a variety of analytical methods (thermal analysis, solution calorimetry, solubility, and sublimation), whereas for Form III, only a handful of experimental parameters were obtained due to the elusive nature of the polymorph. Form I and Form II were found to be monotropically related, with Form I being confirmed as the thermodynamically most stable solid phase. In addition, the performance of different DFT-D and semi-empirical schemes for lattice energy calculation and polymorph energy ranking was compared and analysed. Lattice energy calculations using periodic DFT at B3LYP-D3/6-31(F+)G(d,p) and PBEh-3c/def2-mSVP levels of theory were found to provide the most accurate lattice energy values for Form I against experimental data, while PIXEL and PBEh-3c/def2-mSVP were the only methods that predicted the correct order of stability of Forms I and II.
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Affiliation(s)
- Artem O Surov
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., 153045 Ivanovo, Russia.
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76
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Cook C, McKinley JL, Beran GJO. Modeling the α- and β-resorcinol phase boundary via combination of density functional theory and density functional tight-binding. J Chem Phys 2021; 154:134109. [PMID: 33832233 PMCID: PMC8019358 DOI: 10.1063/5.0044385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 02/06/2023] Open
Abstract
The ability to predict not only what organic crystal structures might occur but also the thermodynamic conditions under which they are the most stable would be extremely useful for discovering and designing new organic materials. The present study takes a step in that direction by predicting the temperature- and pressure-dependent phase boundary between the α and β polymorphs of resorcinol using density functional theory (DFT) and the quasi-harmonic approximation. To circumvent the major computational bottleneck associated with computing a well-converged phonon density of states via the supercell approach, a recently developed approximation is employed, which combines a supercell phonon density of states from dispersion-corrected third-order density functional tight binding [DFTB3-D3(BJ)] with frequency corrections derived from a smaller B86bPBE-XDM functional DFT phonon calculation on the crystallographic unit cell. This mixed DFT/DFTB quasi-harmonic approach predicts the lattice constants and unit cell volumes to within 1%-2% at lower pressures. It predicts the thermodynamic phase boundary in almost perfect agreement with the experiment, although this excellent agreement does reflect fortuitous cancellation of errors between the enthalpy and entropy of transition.
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Affiliation(s)
- Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Jessica L. McKinley
- Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, USA
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77
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Hao X, Liu J, Ali I, Luo H, Han Y, Hu W, Liu J, He X, Li J. Ab initio determination of crystal stability of di-p-tolyl disulfide. Sci Rep 2021; 11:7076. [PMID: 33782489 PMCID: PMC8007795 DOI: 10.1038/s41598-021-86519-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
Abstract
With the rapid growth of energy demand and the depletion of existing energy resources, the new materials with superior performances, low costs and environmental friendliness for energy production and storage are explored. Di-p-tolyl disulfide (p-Tol2S2) is a typical lubricating material, which has been applied in the field of energy storage. The conformational properties and phase transformations of p-Tol2S2 have been studied by pioneers, but their polymorphs and the polymorphism induced crystal structure changes require further analysis. In this study, we perform the crystal structural screening, prediction and optimization of p-Tol2S2 crystal with quantum mechanical calculations, i.e., density functional theory (DFT) and second-order Møller–Plesset perturbation (MP2) methods. A series of crystal structures with different molecular arrangements are generated based on the crystal structure screening. As compared to long-established lattice energy calculation, we take an advantage of using more accurate technique, which is Gibbs free energy calculation. It considers the effects of entropy and temperature to predict the crystal structures and energy landscape. By comparing the Gibbs free energies between predicted and experimental structures, we found that phase α is the most stable structure for p-Tol2S2 crystal at ambient temperature and standard atmospheric pressure. Furthermore, we provide an efficient method to discriminate different polymorphs that are otherwise difficult to be identified based on the Raman/IR spectra. The proposed work enable us to evaluate the quality of various crystal polymorphs rapidly.
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Affiliation(s)
- Xuan Hao
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, 200062, China.,Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Imran Ali
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongyuan Luo
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanqiang Han
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxin Hu
- School of Computer Science and Software Engineering, The Computer Center, East China Normal University, Shanghai, 200062, China
| | - Jinyun Liu
- Anhui Provincial Engineering Laboratory for New-Energy Vehicle Battery Energy-Storage Materials, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241002, Anhui, China.
| | - Xiao He
- School of Chemistry and Molecular Engineering, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, East China Normal University, Shanghai, 200062, China. .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
| | - Jinjin Li
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano-Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China.
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78
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Bowskill DH, Sugden IJ, Konstantinopoulos S, Adjiman CS, Pantelides CC. Crystal Structure Prediction Methods for Organic Molecules: State of the Art. Annu Rev Chem Biomol Eng 2021; 12:593-623. [PMID: 33770462 DOI: 10.1146/annurev-chembioeng-060718-030256] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.
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Affiliation(s)
- David H Bowskill
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Isaac J Sugden
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Stefanos Konstantinopoulos
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Claire S Adjiman
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
| | - Constantinos C Pantelides
- Molecular Systems Engineering Group, Centre for Process Systems Engineering, Department of Chemical Engineering, and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom;
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79
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Kodrycka M, Patkowski K. Efficient Density-Fitted Explicitly Correlated Dispersion and Exchange Dispersion Energies. J Chem Theory Comput 2021; 17:1435-1456. [PMID: 33606539 DOI: 10.1021/acs.jctc.0c01158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The leading-order dispersion and exchange-dispersion terms in symmetry-adapted perturbation theory (SAPT), Edisp(20) and Eexch-disp(20), suffer from slow convergence to the complete basis set limit. To alleviate this problem, explicitly correlated variants of these corrections, Edisp(20)-F12 and Eexch-disp(20)-F12, have been proposed recently. However, the original formalism (M., Kodrycka , J. Chem. Theory Comput. 2019, 15, 5965-5986), while highly successful in terms of improving convergence, was not competitive to conventional orbital-based SAPT in terms of computational efficiency due to the need to manipulate several kinds of two-electron integrals. In this work, we eliminate this need by decomposing all types of two-electron integrals using robust density fitting. We demonstrate that the error of the density fitting approximation is negligible when standard auxiliary bases such as aug-cc-pVXZ/MP2FIT are employed. The new implementation allowed us to study all complexes in the A24 database in basis sets up to aug-cc-pV5Z, and the Edisp(20)-F12 and Eexch-disp(20)-F12 values exhibit vastly improved basis set convergence over their conventional counterparts. The well-converged Edisp(20)-F12 and Eexch-disp(20)-F12 numbers can be substituted for conventional Edisp(20) and Eexch-disp(20) ones in a calculation of the total SAPT interaction energy at any level (SAPT0, SAPT2+3, ...). We show that the addition of F12 terms does not improve the accuracy of low-level SAPT treatments. However, when the theory errors are minimized in high-level SAPT approaches such as SAPT2+3(CCD)δMP2, the reduction of basis set incompleteness errors thanks to the F12 treatment substantially improves the accuracy of small-basis calculations.
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Affiliation(s)
- Monika Kodrycka
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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80
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Aina AA, Misquitta AJ, Price SL. A non-empirical intermolecular force-field for trinitrobenzene and its application in crystal structure prediction. J Chem Phys 2021; 154:094123. [PMID: 33685142 DOI: 10.1063/5.0043746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An anisotropic atom-atom distributed intermolecular force-field (DIFF) for rigid trinitrobenzene (TNB) is developed using distributed multipole moments, dipolar polarizabilities, and dispersion coefficients derived from the charge density of the isolated molecule. The short-range parameters of the force-field are fitted to first- and second-order symmetry-adapted perturbation theory dimer interaction energy calculations using the distributed density-overlap model to guide the parameterization of the short-range anisotropy. The second-order calculations are used for fitting the damping coefficients of the long-range dispersion and polarization and also for relaxing the isotropic short-range coefficients in the final model, DIFF-srL2(rel). We assess the accuracy of the unrelaxed model, DIFF-srL2(norel), and its equivalent without short-range anisotropy, DIFF-srL0(norel), as these models are easier to derive. The model potentials are contrasted with empirical models for the repulsion-dispersion fitted to organic crystal structures with multipoles of iterated stockholder atoms (ISAs), FIT(ISA,L4), and with Gaussian Distributed Analysis (GDMA) multipoles, FIT(GDMA,L4), commonly used in modeling organic crystals. The potentials are tested for their ability to model the solid state of TNB. The non-empirical models provide more reasonable relative lattice energies of the three polymorphs of TNB and propose more sensible hypothetical structures than the empirical force-field (FIT). The DIFF-srL2(rel) model successfully has the most stable structure as one of the many structures that match the coordination sphere of form III. The neglect of the conformational flexibility of the nitro-groups is a significant approximation. This methodology provides a step toward force-fields capable of representing all phases of a molecule in molecular dynamics simulations.
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Affiliation(s)
- Alex A Aina
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
| | - Alston J Misquitta
- School of Physics and Astronomy and The Thomas Young Centre for Theory and Simulation of Materials at Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Sarah L Price
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
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81
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Tang J, Han Y, Ali I, Luo H, Nowak A, Li J. Stability and phase transition investigation of olanzapine polymorphs. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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82
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Cabrera-Ramírez A, Arismendi-Arrieta DJ, Valdés Á, Prosmiti R. Exploring CO 2 @sI Clathrate Hydrates as CO 2 Storage Agents by Computational Density Functional Approaches. Chemphyschem 2021; 22:359-369. [PMID: 33368985 DOI: 10.1002/cphc.202001035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 12/21/2022]
Abstract
The formation of specific clathrate hydrates and their transformation at given thermodynamic conditions depends on the interactions between the guest molecule/s and the host water lattice. Understanding their structural stability is essential to control structure-property relations involved in different technological applications. Thus, the energetic aspects relative to CO2 @sI clathrate hydrate are investigated through the computation of the underlying interactions, dominated by hydrogen bonds and van der Waals forces, from first-principles electronic structure approaches. The stability of the CO2 @sI clathrate is evaluated by combining bottom-up and top-down approaches. Guest-free and CO2 guest-filled aperiodic cages, up to the gradually CO2 occupation of the entire sI periodic unit cells were considered. Saturation, cohesive and binding energies for the systems are determined by employing a variety of density functionals and their performance is assessed. The dispersion corrections on the non-covalent interactions are found to be important in the stabilization of the CO2 @sI energies, with the encapsulation of the CO2 into guest-free/empty cage/lattice being always an energetically favorable process for most of the functionals studied. The PW86PBE functional with XDM or D3(BJ) dispersion corrections predicts a lattice constant in accord to the experimental values available, and simultaneously provides a reliable description for the guest-host interactions in the periodic CO2 @sI crystal, as well as the energetics of its progressive single cage occupancy process. It has been found that the preferential orientation of the single CO2 in the large sI crystal cages has a stabilizing effect on the hydrate, concluding that the CO2 @sI structure is favored either by considering the individual building block cages or the complete sI unit cell crystal. Such benchmark and methodology cross-check studies benefit new data-driven model research by providing high-quality training information, with new insights that indicate the underlying factors governing their structure-driven stability, and triggering further investigations for controlling the stabilization of these promising long-term CO2 storage materials.
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Affiliation(s)
| | - Daniel J Arismendi-Arrieta
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018, Donostia-San Sebastián, Spain
| | - Álvaro Valdés
- Escuela de Física, Universidad Nacional de Colombia, Sede Medellín, A. A., 3840, Medellíın, Colombia
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006, Madrid, Spain
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83
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Peng Q, Ma H, Shuai Z. Theory of Long-Lived Room-Temperature Phosphorescence in Organic Aggregates. Acc Chem Res 2021; 54:940-949. [PMID: 33347277 DOI: 10.1021/acs.accounts.0c00556] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ConspectusRoom-temperature phosphorescence (RTP) with a long afterglow from purely organic molecular aggregates has recently attracted many investigations because traditionally only inorganic and transition-metal complexes can emit phosphorescence at room temperature. Purely organic molecules can exhibit phosphorescence only at cryogenic temperatures and under inert conditions in solution. However, recently, a number of organic compounds have been found to demonstrate bright RTP upon aggregation, sometimes with a remarkable morphology dependence. We intended to rationalize such aggregation-induced organic RTP through theoretical investigation and quantum chemistry calculations by invoking intermolecular interaction effects. And we have identified the molecular descriptors for the molecular design of RTP materials.In this Account, we started with the proposition of the mechanism of intermolecular electrostatic-interaction-induced RTP at the molecular level by using molecular dynamics simulations, hybrid quantum mechanics, and molecular mechanics (QM/MM) coupled with the thermal vibration correlation function (TVCF) formalism we developed earlier. The effective intermolecular electrostatic interactions could stem from a variety of interactions in different organic RTP crystals, such as hydrogen bonding, π-halogen bonding, anion-π+ interaction, and d-pπ bonds and so forth. We find that these interactions can change the molecular orbital compositions involved in the lowest-lying singlet and triplet excited states that are responsible for phosphorescence, either through facilitating intersystem crossing from the excited-state singlet to the triplet and/or suppressing the nonradiative decay process from the lowest triplet to the ground state. This underlying RTP mechanism is believed to be very helpful in systematically and comprehensively understanding the aggregation/crystal-induced persistent organic RTP, which has been applied to explain a number of experiments.We then propose the molecular descriptors to characterize the phosphorescence efficiency and lifetime, respectively, derived from fundamental photophysical processes and requirements to obey the El-Sayed rule and generate phosphorescence. For a prototypical RTP system consisting of a carbonyl group and π-conjugated segments, the excited states can be regarded as an admixture of n → π* (with portion α) and π → π* (with portion β). The intersystem crossing (ISC) rate of S1 → Tn is mostly governed by the modification of the product of α and β, and the nonradiative rate of T1 → S0 is determined by the β value of T1. Thus, we employ γ = α × β and β to describe the phosphorescence efficiency and lifetime, respectively, which have been successfully applied in the molecular design of efficient and long-lived RTP systems in experiments. The molecular descriptors outlined in this Account, which are easily obtained from simple quantum chemistry calculations, are expected to play important roles in the machine-learning-based molecular screening in the future.
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Affiliation(s)
- Qian Peng
- School of Chemical Sciences, University of Chinese Academy of Sciences, 100049 Beijing, P. R. China
- Key Laboraorty of Organic Solids, Institute of Chemistry of the Chinese Academy of Sciences, 100190 Beijing, P. R. China
| | - Huili Ma
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, P. R. China
| | - Zhigang Shuai
- MOE Key Laboratory of Organic OptoElectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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84
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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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85
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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: 240] [Impact Index Per Article: 80.0] [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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86
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Nguyen ALP, Mason TG, Freeman BD, Izgorodina EI. Prediction of lattice energy of benzene crystals: A robust theoretical approach. J Comput Chem 2021; 42:248-260. [PMID: 33231872 DOI: 10.1002/jcc.26452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/09/2023]
Abstract
We present an inexpensive and robust theoretical approach based on the fragment molecular orbital methodology and the spin-ratio scaled second-order Møller-Plesset perturbation theory to predict the lattice energy of benzene crystals within 2 kJ⋅mol-1 . Inspired by the Harrison method to estimate the Madelung constant, the proposed approach calculates the lattice energy as a sum of two- and three-body interaction energies between a reference molecule and the surrounding molecules arranged in a sphere. The lattice energy converges rapidly at a radius of 13 Å. Adding the corrections to account for a higher correlated level of theory and basis set superposition for the Hartree Fock (HF) level produced a lattice energy of -57.5 kJ⋅mol-1 for the benzene crystal structure at 138 K. This estimate is within 1.6 kJ⋅mol-1 off the best theoretical prediction of -55.9 kJ⋅mol-1 . We applied this approach to calculate lattice energies of the crystal structures of phase I and phase II-polymorphs of benzene-observed at a higher temperature of 295 K. The stability of these polymorphs was correctly predicted, with phase II being energetically preferred by 3.7 kJ⋅mol-1 over phase I. The proposed approach gives a tremendous potential to predict stability of other molecular crystal polymorphs.
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Affiliation(s)
- Anh L P Nguyen
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Thomas G Mason
- School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Benny D Freeman
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
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87
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Melissen STAG, Le Bahers T, Sautet P, Steinmann SN. What does graphitic carbon nitride really look like? Phys Chem Chem Phys 2021; 23:2853-2859. [PMID: 33470995 DOI: 10.1039/d0cp06063a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Graphitic carbon nitrides (g-CNs) have become popular light absorbers in photocatalytic water splitting cells. Early theoretical work on these structures focused on fully polymerized g-C3N4. Experimentally, it is known that the typically employed melamine polycondensation does not go toward completion, yielding structures with ∼15 at% hydrogen. Here, we study the conformational stability of "melon", with the [C6N9H3]n structural formula using DFT. Referencing to a 2D melon sheet, B3LYP-dDsC and PBE-MBD computations revealed the same qualitative trend in stability of the 3D structures, with several of them within 5 kJ mol-1 per tecton. Fina's orthorhombic melon is the most stable of the studied conformers, with Lotsch' monoclinic melon taking an intermediate value. Invoking a simple Wannier-Mott-type approach, Fina's and Lotsch' structures exhibited the lowest optical gaps (2.8 eV), within the error margin of the experimental value (2.7 eV). All conformers yielded gaps below that of the monolayer's (3.2 eV), suggesting Jelley-type ("J") aggregation effects.
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Affiliation(s)
- Sigismund T A G Melissen
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France
| | - Tangui Le Bahers
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, CNRS, 46 allée d'Italie, F-69007 Lyon Cedex, France.
| | - Philippe Sautet
- Department of Chemical and Biomolecular engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephan N Steinmann
- Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, CNRS, 46 allée d'Italie, F-69007 Lyon Cedex, France.
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88
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Cabrera-Ramírez A, Yanes-Rodríguez R, Prosmiti R. Computational density-functional approaches on finite-size and guest-lattice effects in CO 2@sII clathrate hydrate. J Chem Phys 2021; 154:044301. [PMID: 33514100 DOI: 10.1063/5.0039323] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We performed first-principles computations to investigate guest-host/host-host effects on the encapsulation of the CO2 molecule in sII clathrate hydrates from finite-size clusters up to periodic 3D crystal lattice systems. Structural and energetic properties were first computed for the individual and first-neighbors clathrate-like sII cages, where highly accurate ab initio quantum chemical methods are available nowadays, allowing in this way the assessment of the density functional (DFT) theoretical approaches employed. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. On this basis, structural relaxations of the CO2-filled and empty sII unit cells yield lattice and compressibility parameters comparable to experimental and previous theoretical values available for sII hydrates. According to these data, the CO2 enclathration in the sII clathrate cages is a stabilizing process, either by considering both guest-host and host-host interactions in the complete unit cell or only the guest-water energies for the individual clathrate-like sII cages. CO2@sII clathrates are predicted to be stable whatever the dispersion correction applied and in the case of single cage occupancy are found to be more stable than the CO2@sI structures. Our results reveal that DFT approaches could provide a good reasonable description of the underlying interactions, enabling the investigation of formation and transformation processes as a function of temperature and pressure.
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Affiliation(s)
| | | | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), CSIC, Serrano 123, 28006 Madrid, Spain
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89
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Unzueta PA, Greenwell CS, Beran GJO. Predicting Density Functional Theory-Quality Nuclear Magnetic Resonance Chemical Shifts via Δ-Machine Learning. J Chem Theory Comput 2021; 17:826-840. [DOI: 10.1021/acs.jctc.0c00979] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Pablo A. Unzueta
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Chandler S. Greenwell
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, United States
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90
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Mayo RA, Johnson ER. Improved quantitative crystal-structure comparison using powder diffractograms via anisotropic volume correction. CrystEngComm 2021. [DOI: 10.1039/d1ce01058a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A new anisotropic volume correction improves quantitative crystal structure comparison. Benchmarking against the 6th crystal structure prediction blind test data results in identification of two previously uncredited matching structures.
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Affiliation(s)
- R. Alex Mayo
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
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91
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Kamat K, Guo R, Reutzel-Edens SM, Price SL, Peters B. Diabat method for polymorph free energies: Extension to molecular crystals. J Chem Phys 2020; 153:244105. [PMID: 33380078 DOI: 10.1063/5.0024727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lattice-switch Monte Carlo and the related diabat methods have emerged as efficient and accurate ways to compute free energy differences between polymorphs. In this work, we introduce a one-to-one mapping from the reference positions and displacements in one molecular crystal to the positions and displacements in another. Two features of the mapping facilitate lattice-switch Monte Carlo and related diabat methods for computing polymorph free energy differences. First, the mapping is unitary so that its Jacobian does not complicate the free energy calculations. Second, the mapping is easily implemented for molecular crystals of arbitrary complexity. We demonstrate the mapping by computing free energy differences between polymorphs of benzene and carbamazepine. Free energy calculations for thermodynamic cycles, each involving three independently computed polymorph free energy differences, all return to the starting free energy with a high degree of precision. The calculations thus provide a force field independent validation of the method and allow us to estimate the precision of the individual free energy differences.
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Affiliation(s)
- Kartik Kamat
- Department of Chemical Engineering, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Rui Guo
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Susan M Reutzel-Edens
- Small Molecule Design and Development, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Sarah L Price
- Department of Chemistry, University College London, London WC1H 0AJ, United Kingdom
| | - Baron Peters
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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92
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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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93
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Turelli M, Alberga D, Lattanzi G, Ciofini I, Adamo C. Theoretical insights on acceptor-donor dyads for organic photovoltaics. Phys Chem Chem Phys 2020; 22:27413-27424. [PMID: 33231587 DOI: 10.1039/d0cp03038d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The field of organic photovoltaics has witnessed a steady growth in the last few decades and a recent renewal with the blossoming of single-material organic solar cells (SMOSCs). However, due to the intrinsic complexity of these devices (both in terms of their size and of the condensed phases involved), computational approaches to accurately predict their geometrical and electronic structure and to link their microscopic properties to the observed macroscopic behaviour are still lacking. In this work, we have focused on the rationalization of transport dynamics and we have set up a computational approach that makes a combined use of classical simulations and Density Functional Theory with the aim of disclosing the most relevant electronic and structural features of dyads used for SMOSC applications. As a prototype dyad, we have considered a molecule that consists in a dithiafulvalene-functionalized diketopyrrolopyrrole (DPP), acting as an electron donor, covalently linked to a fulleropyrrolidine (Ful), the electron acceptor. Our results, beside a quantitative agreement with experiments, show that the overall observed mobilities result from the competing packing mechanisms of the constituting units within the dyad both in the case of crystalline and amorphous phases. As a consequence, not all stable polymorphs have the same efficiency in transporting holes or electrons which often results in a highly directional carrier transport that is not, in general, a desirable feature for polycrystalline thin-films. The present work, linking microscopic packing to observed transport, thus opens the route for the in silico design of new dyads with enhanced and controlled structural and electronic features.
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Affiliation(s)
- Michele Turelli
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Paris, France.
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94
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Donà L, Brandenburg JG, Bush IJ, Civalleri B. Cost-effective composite methods for large-scale solid-state calculations. Faraday Discuss 2020; 224:292-308. [PMID: 32955053 DOI: 10.1039/d0fd00066c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Following the development in recent years of progressively more accurate approximations to the exchange-correlation functional, the use of density functional theory (DFT) methods to examine increasingly large and complex systems has grown, in particular for solids and other condensed matter systems. However the cost of these calculations is high, often requiring the use of specialist HPC facilities. As such, for the purpose of large-scale high-throughput screening of material properties, a hierarchy of simplified DFT methods has been proposed that allows rapid electronic structure calculation of large systems, and we have recently extended this scheme to the solid state (sol-3c). Here, we analyze the applicability and scaling of the new sol-3c DFT methods to molecules and crystals composed of light-elements, such as small proteins and model DNA-helices. Furthermore, the calculation of the electronic structure of large to very large porous systems, such as metal-organic frameworks and inorganic nanoparticles, is discussed. The new composite methods have been implemented in the CRYSTAL17 code, which efficiently implements hybrid functionals and enables routine application of the new methods to large-scale calculations of such materials with excellent performance, even with small-scale computing resources.
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Affiliation(s)
- L Donà
- Dipartimento di Chimica, Università di Torino, NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy.
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95
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Cabrera-Ramírez A, Arismendi-Arrieta DJ, Valdés Á, Prosmiti R. Structural Stability of the CO 2 @sI Hydrate: a Bottom-Up Quantum Chemistry Approach on the Guest-Cage and Inter-Cage Interactions. Chemphyschem 2020; 21:2618-2628. [PMID: 33001534 DOI: 10.1002/cphc.202000753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/30/2020] [Indexed: 12/27/2022]
Abstract
Through reliable first-principles computations, we have demonstrated the impact of CO2 molecules enclathration on the stability of sI clathrate hydrates. Given the delicate balance between the interaction energy components (van der Waals, hydrogen bonds) present on such systems, we follow a systematic bottom-up approach starting from the individual 512 and 512 62 sI cages, up to all existing combinations of two-adjacent sI crystal cages to evaluate how such clathrate-like models perform on the evaluation of the guest-host and first-neighbors inter-cage effects, respectively. Interaction and binding energies of the CO2 occupation of the sI cages were computed using DF-MP2 and different DFT/DFT-D electronic structure methodologies. The performance of selected DFT functionals, together with various semi-classical dispersion corrections schemes, were validated by comparison with reference ab initio DF-MP2 data, as well as experimental data from x-ray and neutron diffraction studies available. Our investigation confirms that the inclusion of the CO2 in the cage/s is an energetically favorable process, with the CO2 molecule preferring to occupy the large 512 62 sI cages compared to the 512 ones. Further, the present results conclude on the rigidity of the water cages arrangements, showing the importance of the inter-cage couplings in the cluster models under study. In particular, the guest-cage interaction is the key factor for the preferential orientation of the captured CO2 molecules in the sI cages, while the inter-cage interactions seems to cause minor distortions with the CO2 guest neighbors interactions do not extending beyond the large 512 62 sI cages. Such findings on these clathrate-like model systems are in accord with experimental observations, drawing a direct relevance to the structural stability of CO2 @sI clathrates.
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Affiliation(s)
| | - Daniel J Arismendi-Arrieta
- Donostia International Physics Center (DIPC), Paseo, Manuel de Lardizabal 4, 20018, Donostia-San Sebastián, Spain
| | - Álvaro Valdés
- Escuela de Física, Universidad Nacional de Colombia, Sede, A. A., 3840, Medellín, Colombia
| | - Rita Prosmiti
- Institute of Fundamental Physics (IFF-CSIC), Serrano 123, Madrid, Spain
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96
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Xiao R, Huang L, Han Y, Liu J, Li J. Ab initio phase transition prediction for ices XV/XIV/VIII at high pressures and low temperatures. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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97
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Pal R, Jelsch C, Malaspina LA, Edwards AJ, Murshed MM, Grabowsky S. syn and anti polymorphs of 2,6-dimethoxy benzoic acid and its molecular and ionic cocrystals: Structural analysis and energetic perspective. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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98
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Abstract
A broad range of approaches to many-body dispersion are discussed, including empirical approaches with multiple fitted parameters, augmented density functional-based approaches, symmetry adapted perturbation theory, and a supermolecule approach based on coupled cluster theory. Differing definitions of "body" are considered, specifically atom-based vs molecule-based approaches.
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Affiliation(s)
- Peng Xu
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Melisa Alkan
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
| | - Mark S Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50014, United States
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Liu C, Brandenburg JG, Valsson O, Kremer K, Bereau T. Free-energy landscape of polymer-crystal polymorphism. SOFT MATTER 2020; 16:9683-9692. [PMID: 33000842 DOI: 10.1039/d0sm01342k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-energy landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-grained metadynamics simulations allow us to efficiently sample the landscape at large. The free-energy difference between the two main polymorphs, α and β, is further investigated by quantum-chemical calculations. The results of the two methods are in line with experimental observations: they predict β as the more stable polymorph under standard conditions. Critically, the free-energy landscape suggests how the α polymorph may lead to experimentally observed kinetic traps. The combination of multiscale modeling, enhanced sampling, and quantum-chemical calculations offers an appealing strategy to uncover complex free-energy landscapes with polymorphic behavior.
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Affiliation(s)
- Chan Liu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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Courté M, Ye J, Jiang H, Ganguly R, Tang S, Kloc C, Fichou D. Tuning the π-π overlap and charge transport in single crystals of an organic semiconductor via solvation and polymorphism. Phys Chem Chem Phys 2020; 22:19855-19863. [PMID: 32851393 DOI: 10.1039/d0cp03109g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polymorphism is a central phenomenon in materials science that often results in important differences of the electronic properties of organic crystals due to slight variations in intermolecular distances and positions. Although a large number of π-conjugated organic compounds can grow as polymorphs, it is necessary to have at disposal a series of several polymorphs of the same molecule to establish clear and predictive structure-property relationships. We report here on the occurrence of two solvates and three polymorphs in single crystalline form of the organic p-type semiconductor 2,2',6,6'-tetraphenyldipyranylidene (DIPO). When grown from chlorobenzene or toluene, the DIPO crystals spontaneously capture solvent molecules to form two pseudopolymorphic 1 : 1 binary solvates. Independently, three solvent-free DIPO polymorphs are obtained either from the vapor phase or from acetonitrile and benzene. Surprisingly, single crystal field-effect transistors (SC-FETs) reveal that the DIPO 1 : 1 binary solvate grown from chlorobenzene possesses a higher hole mobility (1.1 cm2 V-1 s-1) than the three solvent-free polymorphs (0.02-0.64 cm2 V-1 s-1). A refined crystallographic analysis combined with a theoretical transport model clearly shows that the higher mobility of the solvate results from an improved π-π overlap. Our observations demonstrate that solvation allows to tune the π-π overlap and transport properties of organic semiconductors by selecting appropriate solvents.
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Affiliation(s)
- Marc Courté
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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