1
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Hoja J, List A, Boese AD. Multimer Embedding Approach for Molecular Crystals up to Harmonic Vibrational Properties. J Chem Theory Comput 2024; 20:357-367. [PMID: 38109226 PMCID: PMC10782452 DOI: 10.1021/acs.jctc.3c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Accurate calculations of molecular crystals are crucial for drug design and crystal engineering. However, periodic high-level density functional calculations using hybrid functionals are often prohibitively expensive for the relevant systems. These expensive periodic calculations can be circumvented by the usage of embedding methods in which, for instance, the periodic calculation is only performed at a lower-cost level and then monomer energies and dimer interactions are replaced by those of the higher-level method. Herein, we extend such a multimer embedding approach to enable energy corrections for trimer interactions and the calculation of harmonic vibrational properties up to the dimer level. We evaluate this approach for the X23 benchmark set of molecular crystals by approximating a periodic hybrid density functional (PBE0+MBD) by embedding multimers into less expensive calculations using a generalized-gradient approximation functional (PBE+MBD). We show that trimer interactions are crucial for accurately approximating lattice energies within 1 kJ/mol and might also be needed for further improvement of lattice constants and hence cell volumes. Finally, the vibrational properties are already very well captured at the monomer and dimer level, making it possible to approximate vibrational free energies at room temperature within 1 kJ/mol.
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Affiliation(s)
- Johannes Hoja
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
| | - Alexander List
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
| | - A. Daniel Boese
- Department of Chemistry, University
of Graz, Heinrichstraße 28/IV, Graz 8010, Austria
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2
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Liang YH, Ye HZ, Berkelbach TC. Can Spin-Component Scaled MP2 Achieve kJ/mol Accuracy for Cohesive Energies of Molecular Crystals? J Phys Chem Lett 2023; 14:10435-10441. [PMID: 37956873 DOI: 10.1021/acs.jpclett.3c02411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Attaining kJ/mol accuracy in cohesive energy for molecular crystals is a persistent challenge in computational materials science. In this study, we evaluate second-order Møller-Plesset perturbation theory (MP2) and its spin-component scaled models for calculating cohesive energies for 23 molecular crystals (X23 data set). Using periodic boundary conditions and Brillouin zone sampling, we converge results to the thermodynamic and complete basis set limits, achieving an accuracy of about 2 kJ/mol (0.5 kcal/mol), which is rarely achieved in previous MP2 calculations for molecular crystals. When compared to experimental data, our results have a mean absolute error of 12.9 kJ/mol, comparable to Density Functional Theory with the PBE functional and TS dispersion correction. By separately scaling the opposite-spin and same-spin correlation energy components, using predetermined parameters, we reduce the mean absolute error to 9.5 kJ/mol. Further fine-tuning of these scaling parameters specifically for the X23 data set brings the mean absolute error down to 7.5 kJ/mol.
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Affiliation(s)
- Yu Hsuan Liang
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Hong-Zhou Ye
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Timothy C Berkelbach
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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3
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Erba A, Desmarais JK, Casassa S, Civalleri B, Donà L, Bush IJ, Searle B, Maschio L, Edith-Daga L, Cossard A, Ribaldone C, Ascrizzi E, Marana NL, Flament JP, Kirtman B. CRYSTAL23: A Program for Computational Solid State Physics and Chemistry. J Chem Theory Comput 2023; 19:6891-6932. [PMID: 36502394 PMCID: PMC10601489 DOI: 10.1021/acs.jctc.2c00958] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Indexed: 12/14/2022]
Abstract
The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.
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Affiliation(s)
- Alessandro Erba
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jacques K. Desmarais
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Silvia Casassa
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Lorenzo Donà
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Ian J. Bush
- STFC
Rutherford Appleton Laboratory, Chilton Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - Barry Searle
- SFTC
Daresbury Laboratory, Daresbury, Cheshire WA4 4AD, United Kingdom
| | - Lorenzo Maschio
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Loredana Edith-Daga
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Alessandro Cossard
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Chiara Ribaldone
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Eleonora Ascrizzi
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Naiara L. Marana
- Dipartimento
di Chimica, Università di Torino, via Giuria 5, 10125 Torino, Italy
| | - Jean-Pierre Flament
- Université
de Lille, CNRS, UMR 8523 — PhLAM — Physique des Lasers, Atomes et Molécules, 59000 Lille, France
| | - Bernard Kirtman
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
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4
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Shimpi MT, Sajjad M, Öberg S, Larsson JA. Physical binding energies using the electron localization function in 4-hydroxyphenylboronic acid co-crystals with aza donors. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:505901. [PMID: 37659400 DOI: 10.1088/1361-648x/acf638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/01/2023] [Indexed: 09/04/2023]
Abstract
Binding energies are traditionally simulated using cluster models by computation of each synthon for each individual co-crystal former. However, our investigation of the binding strengths using the electron localization function (ELF) reveals that these can be determined directly from the crystal supercell computations. We propose a new modeling protocol for the computation of physical binding energies directly from bulk simulations using ELF analysis. In this work, we establish a correlation between ELF values and binding energies calculated for co-crystals of 4-hydroxyphenylboronic acid (4HPBA) with four different aza donors using density functional theory with varying descriptions of dispersion. Boronic acids are gaining significant interest in the field of crystal engineering, but theoretical studies on their use in materials are still very limited. Here, we present a systematic investigation of the non-covalent interactions in experimentally realized co-crystals. Prior diffraction studies on these complexes have shown the competitive nature between the boronic acid functional group and the para-substituted phenolic group forming heteromeric interactions with aza donors. We determine the stability of the co-crystals by simulating their lattice energies, and the different dispersion descriptions show similar trends in lattice energies and lattice parameters. Our study bolsters the experimental observation of the boronic acid group as a competitive co-crystal former in addition to the well-studied phenolic group. Further research on correlating ELF values for physical binding could potentially transform this approach to a viable alternative for the computation of binding energies.
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Affiliation(s)
- Mayura Talwelkar Shimpi
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, PO Box 591, 75124 Uppsala, Sweden
| | - Muhammad Sajjad
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China
| | - Sven Öberg
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - J Andreas Larsson
- Applied Physics, Division of Materials Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, SE-97187 Luleå, Sweden
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5
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O’Connor D, Bier I, Tom R, Hiszpanski AM, Steele BA, Marom N. Ab Initio Crystal Structure Prediction of the Energetic Materials LLM-105, RDX, and HMX. CRYSTAL GROWTH & DESIGN 2023; 23:6275-6289. [PMID: 38173900 PMCID: PMC10763925 DOI: 10.1021/acs.cgd.3c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 08/02/2023] [Indexed: 01/05/2024]
Abstract
Crystal structure prediction (CSP) is performed for the energetic materials (EMs) LLM-105 and α-RDX, as well as the α and β conformational polymorphs of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX), using the genetic algorithm (GA) code, GAtor, and its associated random structure generator, Genarris. Genarris and GAtor successfully generate the experimental structures of all targets. GAtor's symmetric crossover scheme, where the space group symmetries of parent structures are treated as genes inherited by offspring, is found to be particularly effective. However, conducting several GA runs with different settings is still important for achieving diverse samplings of the potential energy surface. For LLM-105 and α-RDX, the experimental structure is ranked as the most stable, with all of the dispersion-inclusive density functional theory (DFT) methods used here. For HMX, the α form was persistently ranked as more stable than the β form, in contrast to experimental observations, even when correcting for vibrational contributions and thermal expansion. This may be attributed to insufficient accuracy of dispersion-inclusive DFT methods or to kinetic effects not considered here. In general, the ranking of some putative structures is found to be sensitive to the choice of the DFT functional and the dispersion method. For LLM-105, GAtor generates a putative structure with a layered packing motif, which is desirable thanks to its correlation with low sensitivity. Our results demonstrate that CSP is a useful tool for studying the ubiquitous polymorphism of EMs and shows promise of becoming an integral part of the EM development pipeline.
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Affiliation(s)
- Dana O’Connor
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Imanuel Bier
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rithwik Tom
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Anna M. Hiszpanski
- Materials
Science Division, Lawrence Livermore National
Laboratory, Livermore, California 94550, United States
| | - Brad A. Steele
- Materials
Science Division, Lawrence Livermore National
Laboratory, Livermore, California 94550, United States
| | - Noa Marom
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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6
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Poier PP, Adjoua O, Lagardère L, Piquemal JP. Generalized Many-Body Dispersion Correction through Random-Phase Approximation for Chemically Accurate Density Functional Theory. J Phys Chem Lett 2023; 14:1609-1617. [PMID: 36749715 PMCID: PMC9940194 DOI: 10.1021/acs.jpclett.2c03722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
We extend our recently proposed Deep Learning-aided many-body dispersion (DNN-MBD) model to quadrupole polarizability (Q) terms using a generalized Random Phase Approximation (RPA) formalism, thus enabling the inclusion of van der Waals contributions beyond dipole. The resulting DNN-MBDQ model only relies on ab initio-derived quantities as the introduced quadrupole polarizabilities are recursively retrieved from dipole ones, in turn modeled via the Tkatchenko-Scheffler method. A transferable and efficient deep-neuronal network (DNN) provides atom-in-molecule volumes, while a single range-separation parameter is used to couple the model to Density Functional Theory (DFT). Since it can be computed at a negligible cost, the DNN-MBDQ approach can be coupled with DFT functionals, such as PBE, PBE0, and B86bPBE (dispersionless). The DNN-MBQ-corrected functionals reach chemical accuracy while exhibiting lower errors compared to their dipole-only counterparts.
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Affiliation(s)
| | - Olivier Adjoua
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
| | - Louis Lagardère
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
- Sorbonne
Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne
Université, LCT, UMR 7616 CNRS, 75252 Paris, France
- The
University of Texas at Austin, Department
of Biomedical Engineering, Austin, Texas 78712, United States
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7
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Tom R, Gao S, Yang Y, Zhao K, Bier I, Buchanan EA, Zaykov A, Havlas Z, Michl J, Marom N. Inverse Design of Tetracene Polymorphs with Enhanced Singlet Fission Performance by Property-Based Genetic Algorithm Optimization. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:1373-1386. [PMID: 36999121 PMCID: PMC10042130 DOI: 10.1021/acs.chemmater.2c03444] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/06/2023] [Indexed: 06/19/2023]
Abstract
The efficiency of solar cells may be improved by using singlet fission (SF), in which one singlet exciton splits into two triplet excitons. SF occurs in molecular crystals. A molecule may crystallize in more than one form, a phenomenon known as polymorphism. Crystal structure may affect SF performance. In the common form of tetracene, SF is experimentally known to be slightly endoergic. A second, metastable polymorph of tetracene has been found to exhibit better SF performance. Here, we conduct inverse design of the crystal packing of tetracene using a genetic algorithm (GA) with a fitness function tailored to simultaneously optimize the SF rate and the lattice energy. The property-based GA successfully generates more structures predicted to have higher SF rates and provides insight into packing motifs associated with improved SF performance. We find a putative polymorph predicted to have superior SF performance to the two forms of tetracene, whose structures have been determined experimentally. The putative structure has a lattice energy within 1.5 kJ/mol of the most stable common form of tetracene.
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Affiliation(s)
- Rithwik Tom
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Siyu Gao
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Yi Yang
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Kaiji Zhao
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Imanuel Bier
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania15213, United States
| | - Eric A. Buchanan
- Department
of Chemistry, University of Colorado, Boulder, Colorado80309, United States
| | - Alexandr Zaykov
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, 16610Prague 6, Czech
Republic
- Department
of Physical Chemistry, University of Chemistry
and Technology, 166 28Prague 6, Czech Republic
| | - Zdeněk Havlas
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, 16610Prague 6, Czech
Republic
| | - Josef Michl
- Department
of Chemistry, University of Colorado, Boulder, Colorado80309, United States
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, 16610Prague 6, Czech
Republic
| | - Noa Marom
- Department
of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
- Department
of Materials Science and Engineering, Carnegie
Mellon University, Pittsburgh, Pennsylvania15213, United States
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania15213, United States
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8
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Díaz Mirón JEZ, Stein M. A benchmark for non-covalent interactions in organometallic crystals. Phys Chem Chem Phys 2022; 24:29338-29349. [PMID: 36448535 DOI: 10.1039/d2cp04160j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Organometallic complexes are the basis for homogeneous catalysis, have applications in materials science and are also active pharmaceutical ingredients. The interaction between transition metal complexes in the solid state is determining their thermodynamics and bio-availability. Non-covalent interactions such as hydrogen bonding and van der Waals are stabilizing crystals of transition metal complexes. The variation of ligand field, central metal atoms and their oxidation and spin states are determinants of the magnitude of their inter-molecular interactions. A comparison of a set of 43 manually curated experimental heats of sublimation (the new XTMC43 set) and results from periodic DFT calculations shows that an agreement to within 9% can be achieved using GGA or mGGA functionals with atom-centred Gaussian-type basis functions. The need for careful assessments of consistency, calibration and reproducibility of experimental and computational data is discussed. Results regarding the new XTMC43 benchmark set are suggested to serve as a starting point for further method development, systematic screening and crystal engineering.
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Affiliation(s)
- José Eduardo Zamudio Díaz Mirón
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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9
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O'Connor D, Bier I, Hsieh YT, Marom N. Performance of Dispersion-Inclusive Density Functional Theory Methods for Energetic Materials. J Chem Theory Comput 2022; 18:4456-4471. [PMID: 35759249 DOI: 10.1021/acs.jctc.2c00350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crystals of energetic materials (EMs) are denser than typical molecular crystals and are characterized by distinct intermolecular interactions between nitrogen-containing moieties. To assess the performance of dispersion-inclusive density functional theory (DFT) methods, we have compiled a data set of experimental sublimation enthalpies of 31 energetic materials. We evaluate the performance of three methods: the semilocal Perdew-Burke-Ernzerhof (PBE) functional coupled with the pairwise Tkatchenko-Scheffler (TS) dispersion correction, PBE with the many-body dispersion (MBD) method, and the PBE-based hybrid functional (PBE0) with MBD. Zero-point energy contributions and thermal effects are described using the quasi-harmonic approximation (QHA), including explicit treatment of thermal expansion, which we find to be non-negligible for EMs. The lattice energies obtained with PBE0+MBD are the closest to experimental sublimation enthalpies with a mean absolute error of 9.89 kJ/mol. However, the state-of-the-art treatment of vibrational and thermal contributions makes the agreement with experiment worse. Pressure-volume curves are also examined for six representative materials. For pressure-volume curves, all three methods provide reasonable agreement with experimental data with mean absolute relative errors of 3% or less. Most of the intermolecular interactions typical of EMs, namely nitro-amine, nitro-nitro, and nitro-hydrogen interactions, are more sensitive to the choice of the dispersion method than to the choice of the exchange-correlation functional. The exception is π-π stacking interactions, which are also very sensitive to the choice of the functional. Overall, we find that PBE+TS, PBE+MBD, and PBE0+MBD do not perform as well for energetic materials as previously reported for other classes of molecular crystals. This highlights the importance of testing dispersion-inclusive DFT methods for diverse classes of materials and the need for further method development.
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Affiliation(s)
- Dana O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yun-Ting Hsieh
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.,Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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10
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Poier PP, Jaffrelot Inizan T, Adjoua O, Lagardère L, Piquemal JP. Accurate Deep Learning-Aided Density-Free Strategy for Many-Body Dispersion-Corrected Density Functional Theory. J Phys Chem Lett 2022; 13:4381-4388. [PMID: 35544748 DOI: 10.1021/acs.jpclett.2c00936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using a deep neuronal network (DNN) model trained on the large ANI-1 data set of small organic molecules, we propose a transferable density-free many-body dispersion (DNN-MBD) model. The DNN strategy bypasses the explicit Hirshfeld partitioning of the Kohn-Sham electron density required by MBD models to obtain the atom-in-molecules volumes used by the Tkatchenko-Scheffler polarizability rescaling. The resulting DNN-MBD model is trained with minimal basis iterative Stockholder atomic volumes and, coupled to density functional theory (DFT), exhibits comparable (if not greater) accuracy to other approaches based on different partitioning schemes. Implemented in the Tinker-HP package, the DNN-MBD model decreases the overall computational cost compared to MBD models where the explicit density partitioning is performed. Its coupling with the recently introduced Stochastic formulation of the MBD equations (J. Chem. Theory Comput. 2022, 18 (3), 1633-1645) enables large routine dispersion-corrected DFT calculations at preserved accuracy. Furthermore, the DNN electron density-free features extend the MBD model's applicability beyond electronic structure theory within methodologies such as force fields and neural networks.
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Affiliation(s)
| | | | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, Paris 75005, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, Paris 75005, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78713, United States
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11
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Poier PP, Lagardère L, Piquemal JP. O(N) Stochastic Evaluation of Many-Body van der Waals Energies in Large Complex Systems. J Chem Theory Comput 2022; 18:1633-1645. [PMID: 35133157 DOI: 10.1021/acs.jctc.1c01291] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a new strategy to solve the key equations of the many-body dispersion (MBD) model by Tkatchenko, DiStasio Jr., and Ambrosetti. Our approach overcomes the original O(N3) computational complexity that limits its applicability to large molecular systems within the context of O(N) density functional theory. First, to generate the required frequency-dependent screened polarizabilities, we introduce an efficient solution to the Dyson-like self-consistent screening equations. The scheme reduces the number of variables and, coupled to a direct inversion of the iterative subspace extrapolation, exhibits linear-scaling performances. Second, we apply a stochastic Lanczos trace estimator resolution to the equations evaluating the many-body interaction energy of coupled quantum harmonic oscillators. While scaling linearly, it also enables communication-free pleasingly parallel implementations. As the resulting O(N) stochastic massively parallel MBD approach is found to exhibit minimal memory requirements, it opens up the possibility of computing accurate many-body van der Waals interactions of millions-atoms' complex materials and solvated biosystems with computational times in the range of minutes.
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Affiliation(s)
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75052, France.,IP2CT, FR 2622 CNRS, Sorbonne Université, Paris 75005, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, Paris 75052, France.,Institut Universitaire de France, Paris 75231, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
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12
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Knol M, Arefi HH, Corken D, Gardner J, Tautz FS, Maurer RJ, Wagner C. The stabilization potential of a standing molecule. SCIENCE ADVANCES 2021; 7:eabj9751. [PMID: 34757779 PMCID: PMC8580301 DOI: 10.1126/sciadv.abj9751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The part-by-part assembly of functional nanoscale machinery is a central goal of nanotechnology. With the recent fabrication of an isolated standing molecule with a scanning probe microscope, the third dimension perpendicular to the surface will soon become accessible to molecule-based construction. Beyond the flatlands of the surface, a wealth of structures and functionalities is waiting for exploration, but issues of stability are becoming more critical. Here, we combine scanning probe experiments with ab initio potential energy calculations to investigate the thermal stability of a prototypical standing molecule. We reveal its generic stabilization mechanism, a fine balance between covalent and van der Waals interactions including the latter’s long-range screening by many-body effects, and find a remarkable agreement between measured and calculated stabilizing potentials. Beyond their relevance for the design and construction of three-dimensional molecular devices at surfaces, our results also indicate that standing molecules may serve as tunable mechanical gigahertz oscillators.
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Affiliation(s)
- Marvin Knol
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA)–Fundamentals of Future Information Technology, 52425 Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, Otto-Blumenthal-Straße, 52074 Aachen, Germany
| | - Hadi H. Arefi
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA)–Fundamentals of Future Information Technology, 52425 Jülich, Germany
| | - Daniel Corken
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - James Gardner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - F. Stefan Tautz
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA)–Fundamentals of Future Information Technology, 52425 Jülich, Germany
- Experimentalphysik IV A, RWTH Aachen University, Otto-Blumenthal-Straße, 52074 Aachen, Germany
| | - Reinhard J. Maurer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - Christian Wagner
- Peter Grünberg Institut (PGI-3), Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Aachen Research Alliance (JARA)–Fundamentals of Future Information Technology, 52425 Jülich, Germany
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13
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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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14
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Bier I, O'Connor D, Hsieh YT, Wen W, Hiszpanski AM, Han TYJ, Marom N. Crystal structure prediction of energetic materials and a twisted arene with Genarris and GAtor. CrystEngComm 2021. [DOI: 10.1039/d1ce00745a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A molecular crystal structure prediction workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is successfully applied to two energetic materials and a chiral arene.
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Affiliation(s)
- Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Dana O'Connor
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yun-Ting Hsieh
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Wen Wen
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anna M. Hiszpanski
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - T. Yong-Jin Han
- Materials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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15
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Holmes ST, Vojvodin CS, Schurko RW. Dispersion-Corrected DFT Methods for Applications in Nuclear Magnetic Resonance Crystallography. J Phys Chem A 2020; 124:10312-10323. [DOI: 10.1021/acs.jpca.0c06372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sean T. Holmes
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Cameron S. Vojvodin
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Robert W. Schurko
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
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16
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Yang S, Bier I, Wen W, Zhan J, Moayedpour S, Marom N. Ogre: A Python package for molecular crystal surface generation with applications to surface energy and crystal habit prediction. J Chem Phys 2020; 152:244122. [PMID: 32610993 DOI: 10.1063/5.0010615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We present Ogre, an open-source code for generating surface slab models from bulk molecular crystal structures. Ogre is written in Python and interfaces with the FHI-aims code to calculate surface energies at the level of density functional theory (DFT). The input of Ogre is the geometry of the bulk molecular crystal. The surface is cleaved from the bulk structure with the molecules on the surface kept intact. A slab model is constructed according to the user specifications for the number of molecular layers and the length of the vacuum region. Ogre automatically identifies all symmetrically unique surfaces for the user-specified Miller indices and detects all possible surface terminations. Ogre includes utilities to analyze the surface energy convergence and Wulff shape of the molecular crystal. We present the application of Ogre to three representative molecular crystals: the pharmaceutical aspirin, the organic semiconductor tetracene, and the energetic material HMX. The equilibrium crystal shapes predicted by Ogre are in agreement with experimentally grown crystals, demonstrating that DFT produces satisfactory predictions of the crystal habit for diverse classes of molecular crystals.
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Affiliation(s)
- Shuyang Yang
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Imanuel Bier
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Wen Wen
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jiawei Zhan
- School of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Saeed Moayedpour
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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17
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Mazurek AH, Szeleszczuk Ł, Pisklak DM. Periodic DFT Calculations-Review of Applications in the Pharmaceutical Sciences. Pharmaceutics 2020; 12:E415. [PMID: 32369915 PMCID: PMC7284980 DOI: 10.3390/pharmaceutics12050415] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
In the introduction to this review the complex chemistry of solid-state pharmaceutical compounds is summarized. It is also explained why the density functional theory (DFT) periodic calculations became recently so popular in studying the solid APIs (active pharmaceutical ingredients). Further, the most popular programs enabling DFT periodic calculations are presented and compared. Subsequently, on the large number of examples, the applications of such calculations in pharmaceutical sciences are discussed. The mentioned topics include, among others, validation of the experimentally obtained crystal structures and crystal structure prediction, insight into crystallization and solvation processes, development of new polymorph synthesis ways, and formulation techniques as well as application of the periodic DFT calculations in the drug analysis.
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Affiliation(s)
| | - Łukasz Szeleszczuk
- Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 str., 02-093 Warsaw, Poland; (A.H.M.); (D.M.P.)
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18
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Marchese Robinson RL, Geatches D, Morris C, Mackenzie R, Maloney AGP, Roberts KJ, Moldovan A, Chow E, Pencheva K, Vatvani DRM. Evaluation of Force-Field Calculations of Lattice Energies on a Large Public Dataset, Assessment of Pharmaceutical Relevance, and Comparison to Density Functional Theory. J Chem Inf Model 2019; 59:4778-4792. [DOI: 10.1021/acs.jcim.9b00601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Richard L. Marchese Robinson
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dawn Geatches
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Chris Morris
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Rebecca Mackenzie
- Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Andrew G. P. Maloney
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Kevin J. Roberts
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Alexandru Moldovan
- Centre for Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ernest Chow
- Pfizer Worldwide R&D, Ramsgate Road, Sandwich CT13 9NJ, United Kingdom
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19
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Doná L, Brandenburg JG, Civalleri B. Extending and assessing composite electronic structure methods to the solid state. J Chem Phys 2019; 151:121101. [PMID: 31575185 DOI: 10.1063/1.5123627] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A hierarchy of simplified Hartree-Fock (HF), density functional theory (DFT) methods, and their combinations has been recently proposed for the fast electronic structure computation of large systems. The covered methods are a minimal basis set Hartree-Fock (HF-3c), a small basis set global hybrid functional (PBEh-3c), and its screened exchange variant (HSE-3c), all augmented with semiclassical correction potentials. Here, we extend their applicability to inorganic covalent and ionic solids as well as layered materials. The new methods have been dubbed HFsol-3c, PBEsol0-3c, and HSEsol-3c, respectively, to indicate their parent functional as well as the correction potentials. They have been implemented in the CRYSTAL code to enable routine application for molecular as well as solid materials. We validate the new methods on diverse sets of solid state benchmarks that cover more than 90 solids ranging from covalent, ionic, semi-ionic, layered, and molecular crystals. While we focus on structural and energetic properties, we also test bandgaps, vibrational frequencies, elastic constants, and dielectric and piezoelectric tensors. HSEsol-3c appears to be most promising with mean absolute error for cohesive energies and unit cell volumes of molecular crystals of 1.5 kcal/mol and 2.8%, respectively. Lattice parameters of inorganic solids deviate by 3% from the references, and vibrational frequencies of α-quartz have standard deviations of 10 cm-1. Overall, this shows an accuracy competitive to converged basis set dispersion corrected DFT with a substantial increase in computational efficiency.
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Affiliation(s)
- L Doná
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
| | - J G Brandenburg
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 205A, 69120 Heidelberg, Germany
| | - B Civalleri
- Dipartimento di Chimica, Università di Torino and NIS (Nanostructured Interfaces and Surfaces) Centre, Via P. Giuria 5, 10125 Torino, Italy
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20
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Geatches D, Rosbottom I, Marchese Robinson RL, Byrne P, Hasnip P, Probert MIJ, Jochym D, Maloney A, Roberts KJ. Off-the-shelf DFT-DISPersion methods: Are they now “on-trend” for organic molecular crystals? J Chem Phys 2019; 151:044106. [PMID: 31370509 DOI: 10.1063/1.5108829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Dawn Geatches
- Science and Technologies Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Ian Rosbottom
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Richard L. Marchese Robinson
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter Byrne
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Phil Hasnip
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Matt I. J. Probert
- Department of Physics, University of York, Heslington YO10 5DD, United Kingdom
| | - Dominik Jochym
- Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 OQX, United Kingdom
| | - Andrew Maloney
- The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, United Kingdom
| | - Kevin J. Roberts
- Centre for the Digital Design of Drug Products, School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, United Kingdom
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21
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Xavier NF, Da Silva AM, Bauerfeldt GF. Supercell calculations of the geometry and lattice energy of α-glycine crystal. J Mol Model 2019; 25:244. [PMID: 31342179 DOI: 10.1007/s00894-019-4124-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/07/2019] [Indexed: 01/01/2023]
Abstract
Evidence about the presence of glycine in the interstellar medium (ISM) has been motivating studies aiming the understanding of the chemical behavior of this amino acid in such environment. Since glycine is expected to be predominantly found in the ISM in solid phase, this work focuses on the search for a theoretical methodology for obtaining a molecular cluster for α-glycine that provides a good description of the geometry of the unit cell and lattice energy. Calculations have been performed using the B3LYP-D3, PBE0-D3, and WB97X-D3 functionals, with def2-SVP, def2-TZVP, def2-TZVPP, and def2-QZVPP basis sets for two models: (a) the unit cell, containing 4 glycine units, and (b) the 2 × 1 × 2 expanded cell, with 16 glycine units. Corrections for the basis set superposition error have also been applied. No significant changes in geometries and lattice energy predictions from the different functionals and basis sets have been observed for each model. Nevertheless, results obtained for the larger molecular cluster are in better agreement with the experimental data. The best lattice energy prediction, obtained for the 2 × 1 × 2 supercell at the B3LYP-gCP-D3/def2-TZVPP level, is - 15.35 kcal mol-1, with a root mean square deviation of the predicted Cartesian coordinates of the inner molecules (with respect to the experimental α-glycine unit cell geometry) of 0.966 Å. This methodology is finally recommended for future studies of similar molecular cluster, and the predicted geometry is proposed for further studies aiming to describe glycine surface reactions in the ISM.
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Affiliation(s)
- Neubi F Xavier
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil
| | - Antônio M Da Silva
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil
| | - Glauco Favilla Bauerfeldt
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23890-000, Brazil.
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22
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Mortazavi M, Hoja J, Aerts L, Quéré L, van de Streek J, Neumann MA, Tkatchenko A. Computational polymorph screening reveals late-appearing and poorly-soluble form of rotigotine. Commun Chem 2019. [DOI: 10.1038/s42004-019-0171-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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23
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Abstract
There are a large number of materials with mild stiffness, which are not as soft as tissues and not as strong as metals. These semihard materials include energetic materials, molecular crystals, layered materials, and van der Waals crystals. The integrity and mechanical stability are mainly determined by the interactions between instantaneously induced dipoles, the so called London dispersion force or van der Waals force. It is challenging to accurately model the structural and mechanical properties of these semihard materials in the frame of density functional theory where the non-local correlation functionals are not well known. Here, we propose a van der Waals density functional named vdW-DFq to accurately model the density and geometry of semihard materials. Using β -cyclotetramethylene tetranitramine as a prototype, we adjust the enhancement factor of the exchange energy functional with generalized gradient approximations. We find this method to be simple and robust over a wide tuning range when calibrating the functional on-demand with experimental data. With a calibrated value q = 1.05 , the proposed vdW-DFq method shows good performance in predicting the geometries of 11 common energetic material molecular crystals and three typical layered van der Waals crystals. This success could be attributed to the similar electronic charge density gradients, suggesting a wide use in modeling semihard materials. This method could be useful in developing non-empirical density functional theories for semihard and soft materials.
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24
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Stöhr M, Van Voorhis T, Tkatchenko A. Theory and practice of modeling van der Waals interactions in electronic-structure calculations. Chem Soc Rev 2019; 48:4118-4154. [PMID: 31190037 DOI: 10.1039/c9cs00060g] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.
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Affiliation(s)
- Martin Stöhr
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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25
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Lao KU, Herbert JM. Atomic Orbital Implementation of Extended Symmetry-Adapted Perturbation Theory (XSAPT) and Benchmark Calculations for Large Supramolecular Complexes. J Chem Theory Comput 2018; 14:2955-2978. [DOI: 10.1021/acs.jctc.8b00058] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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26
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Curtis F, Li X, Rose T, Vázquez-Mayagoitia Á, Bhattacharya S, Ghiringhelli LM, Marom N. GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction. J Chem Theory Comput 2018; 14:2246-2264. [PMID: 29481740 DOI: 10.1021/acs.jctc.7b01152] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the implementation of GAtor, a massively parallel, first-principles genetic algorithm (GA) for molecular crystal structure prediction. GAtor is written in Python and currently interfaces with the FHI-aims code to perform local optimizations and energy evaluations using dispersion-inclusive density functional theory (DFT). GAtor offers a variety of fitness evaluation, selection, crossover, and mutation schemes. Breeding operators designed specifically for molecular crystals provide a balance between exploration and exploitation. Evolutionary niching is implemented in GAtor by using machine learning to cluster the dynamically updated population by structural similarity and then employing a cluster-based fitness function. Evolutionary niching promotes uniform sampling of the potential energy surface by evolving several subpopulations, which helps overcome initial pool biases and selection biases (genetic drift). The various settings offered by GAtor increase the likelihood of locating numerous low-energy minima, including those located in disconnected, hard to reach regions of the potential energy landscape. The best structures generated are re-relaxed and re-ranked using a hierarchy of increasingly accurate DFT functionals and dispersion methods. GAtor is applied to a chemically diverse set of four past blind test targets, characterized by different types of intermolecular interactions. The experimentally observed structures and other low-energy structures are found for all four targets. In particular, for Target II, 5-cyano-3-hydroxythiophene, the top ranked putative crystal structure is a Z' = 2 structure with P1̅ symmetry and a scaffold packing motif, which has not been reported previously.
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Affiliation(s)
- Farren Curtis
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Xiayue Li
- Google , Mountain View , California 94030 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Timothy Rose
- Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Álvaro Vázquez-Mayagoitia
- Argonne Leadership Computing Facility , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Saswata Bhattacharya
- Department of Physics , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Luca M Ghiringhelli
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 , Berlin , Germany
| | - Noa Marom
- Department of Physics , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Materials Science and Engineering , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States.,Department of Chemistry , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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27
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Buchholz HK, Stein M. Accurate lattice energies of organic molecular crystals from periodic turbomole calculations. J Comput Chem 2018; 39:1335-1343. [DOI: 10.1002/jcc.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Hannes Konrad Buchholz
- Physical and Chemical Foundations Group; Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1; Magdeburg 39106 Germany
- Molecular Simulations and Design Group; Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1; Magdeburg 39106 Germany
| | - Matthias Stein
- Molecular Simulations and Design Group; Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1; Magdeburg 39106 Germany
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28
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Mortazavi M, Brandenburg JG, Maurer RJ, Tkatchenko A. Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding. J Phys Chem Lett 2018; 9:399-405. [PMID: 29298075 DOI: 10.1021/acs.jpclett.7b03234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.
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Affiliation(s)
- Majid Mortazavi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Jan Gerit Brandenburg
- Department of Chemistry, University College London , 20 Gordon Street, WC1H 0AJ London, United Kingdom
- London Centre for Nanotechnology, University College London , 17-19 Gordon Street, WC1H 0AJ London, United Kingdom
- Thomas Young Centre, University College London , Gower Street, WC1E 6BT London, United Kingdom
| | - Reinhard J Maurer
- Department of Chemistry and Centre for Scientific Computing, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg , L-1511, Luxembourg
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29
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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30
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Hoja J, Tkatchenko A. First-principles stability ranking of molecular crystal polymorphs with the DFT+MBD approach. Faraday Discuss 2018; 211:253-274. [PMID: 30042995 DOI: 10.1039/c8fd00066b] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to accurately calculate the relative stabilities of numerous polymorphs of a given molecular crystal is crucial for the success of any molecular crystal structure prediction (CSP) approach. We have recently presented a hierarchical CSP procedure based on van-der-Waals-inclusive density functional theory [Hoja et al., 2018, arXiv:1803.07503], which yields excellent stability rankings for molecular crystals involving rigid molecules, salts, co-crystals, and highly polymorphic drug-like molecules. This approach includes many-body dispersion effects, exact exchange, as well as vibrational free energies. Here, we discuss in detail the impact of these effects on the obtained stability rankings. In addition, we assess the impact of the approximations used in our hierarchical procedure. We show that our procedure is generally robust to 1-2 kJ mol-1 for the systems in the latest CSP blind test but vibrational free energies for crystals involving flexible molecules would benefit from directly including many-body dispersion interactions. In addition, we also discuss the effect of temperature on the structure of molecular crystals and a simple but effective method for estimating anharmonic effects.
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Affiliation(s)
- Johannes Hoja
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
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31
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McDonagh JL, Silva AF, Vincent MA, Popelier PLA. Machine Learning of Dynamic Electron Correlation Energies from Topological Atoms. J Chem Theory Comput 2017; 14:216-224. [PMID: 29211469 DOI: 10.1021/acs.jctc.7b01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present an innovative method for predicting the dynamic electron correlation energy of an atom or a bond in a molecule utilizing topological atoms. Our approach uses the machine learning method Kriging (Gaussian Process Regression with a non-zero mean function) to predict these dynamic electron correlation energy contributions. The true energy values are calculated by partitioning the MP2 two-particle density-matrix via the Interacting Quantum Atoms (IQA) procedure. To our knowledge, this is the first time such energies have been predicted by a machine learning technique. We present here three important proof-of-concept cases: the water monomer, the water dimer, and the van der Waals complex H2···He. These cases represent the final step toward the design of a full IQA potential for molecular simulation. This final piece will enable us to consider situations in which dispersion is the dominant intermolecular interaction. The results from these examples suggest a new method by which dispersion potentials for molecular simulation can be generated.
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Affiliation(s)
- James L McDonagh
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain
| | - Arnaldo F Silva
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain
| | - Mark A Vincent
- School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
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32
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Shtukenberg AG, Zhu Q, Carter DJ, Vogt L, Hoja J, Schneider E, Song H, Pokroy B, Polishchuk I, Tkatchenko A, Oganov AR, Rohl AL, Tuckerman ME, Kahr B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs. Chem Sci 2017; 8:4926-4940. [PMID: 28959416 PMCID: PMC5607859 DOI: 10.1039/c7sc00168a] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/30/2017] [Indexed: 11/21/2022] Open
Abstract
Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.
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Affiliation(s)
- Alexander G Shtukenberg
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
| | - Qiang Zhu
- Department of Physics and Astronomy , High Pressure Science and Engineering Center , University of Nevada Las Vegas , Nevada 89154 , USA .
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Damien J Carter
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Leslie Vogt
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Elia Schneider
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Hongxing Song
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Boaz Pokroy
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology , Skolkovo Innovation Center , 3 Nobel St. , Moscow 143026 , Russia
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Mark E Tuckerman
- Department of Chemistry , New York University , New York City , NY 10003 , USA
- Courant Institute of Mathematical Sciences , New York University , New York City , NY 10003 , USA
- New York University-East China Normal University Center for Computational Chemistry at NYU Shanghai , 3663 Zhongshan Road North , Shanghai 200062 , China
| | - Bart Kahr
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
- Department of Advanced Science and Engineering (TWIns) , Waseda University , Wakamatsucho, 3-2 , Shinjuku , 162-0056 Tokyo , Japan
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33
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Hermann J, DiStasio RA, Tkatchenko A. First-Principles Models for van der Waals Interactions in Molecules and Materials: Concepts, Theory, and Applications. Chem Rev 2017; 117:4714-4758. [PMID: 28272886 DOI: 10.1021/acs.chemrev.6b00446] [Citation(s) in RCA: 269] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Noncovalent van der Waals (vdW) or dispersion forces are ubiquitous in nature and influence the structure, stability, dynamics, and function of molecules and materials throughout chemistry, biology, physics, and materials science. These forces are quantum mechanical in origin and arise from electrostatic interactions between fluctuations in the electronic charge density. Here, we explore the conceptual and mathematical ingredients required for an exact treatment of vdW interactions, and present a systematic and unified framework for classifying the current first-principles vdW methods based on the adiabatic-connection fluctuation-dissipation (ACFD) theorem (namely the Rutgers-Chalmers vdW-DF, Vydrov-Van Voorhis (VV), exchange-hole dipole moment (XDM), Tkatchenko-Scheffler (TS), many-body dispersion (MBD), and random-phase approximation (RPA) approaches). Particular attention is paid to the intriguing nature of many-body vdW interactions, whose fundamental relevance has recently been highlighted in several landmark experiments. The performance of these models in predicting binding energetics as well as structural, electronic, and thermodynamic properties is connected with the theoretical concepts and provides a numerical summary of the state-of-the-art in the field. We conclude with a roadmap of the conceptual, methodological, practical, and numerical challenges that remain in obtaining a universally applicable and truly predictive vdW method for realistic molecular systems and materials.
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Affiliation(s)
- Jan Hermann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6, 14195 Berlin, Germany.,Physics and Materials Science Research Unit, University of Luxembourg , L-1511 Luxembourg, Luxembourg
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34
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Katsyuba SA, Vener MV, Zvereva EE, Brandenburg JG. The role of London dispersion interactions in strong and moderate intermolecular hydrogen bonds in the crystal and in the gas phase. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Kratzer P, Tawfik SA, Cui XY, Stampfl C. Detection of adsorbed transition-metal porphyrins by spin-dependent conductance of graphene nanoribbon. RSC Adv 2017. [DOI: 10.1039/c7ra04594h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Electronic transport in a zig-zag-edge graphene nanoribbon (GNR) and its modification by adsorbed transition metal porphyrins is studied by means of density functional theory calculations.
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Affiliation(s)
- Peter Kratzer
- Faculty of Physics
- University of Duisburg-Essen
- 47057 Duisburg
- Germany
- School of Physics
| | | | - Xiang Yuan Cui
- Australian Centre for Microscopy and Microanalysis
- School of Aerospace, Mechanical and Mechatronic Engineering
- The University of Sydney
- Sydney
- Australia
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36
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Cole DJ, Hine NDM. Applications of large-scale density functional theory in biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:393001. [PMID: 27494095 DOI: 10.1088/0953-8984/28/39/393001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
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Affiliation(s)
- Daniel J Cole
- Theory of Condensed Matter group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK. School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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37
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Curtis F, Wang X, Marom N. Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2016; 72:562-570. [PMID: 27484377 DOI: 10.1107/s2052520616009227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within the GW approximation and the Bethe-Salpeter equation (BSE). We find that a structure with Pna21 symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π-π stacking and has markedly different electronic and optical properties than the experimentally observed P21/n structure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. The Pna21 bilayer structure is close in energy to the observed structure and may be feasible to grow.
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Affiliation(s)
- Farren Curtis
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiaopeng Wang
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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38
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Elking DM, Fusti-Molnar L, Nichols A. Crystal structure prediction of rigid molecules. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2016; 72:488-501. [DOI: 10.1107/s2052520616010118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/21/2016] [Indexed: 11/11/2022]
Abstract
A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties andab initiogas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r6dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.
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39
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Flores-Huerta AG, Tkatchenko A, Galván M. Nature of Hydrogen Bonds and S···S Interactions in the l-Cystine Crystal. J Phys Chem A 2016; 120:4223-30. [DOI: 10.1021/acs.jpca.6b03167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anaid G. Flores-Huerta
- Departamento
de Química, Área de Fisicoquímica
Teórica, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina CP 09340, México, D.F., Mexico
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Marcelo Galván
- Departamento
de Química, Área de Fisicoquímica
Teórica, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina CP 09340, México, D.F., Mexico
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40
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DiLabio GA, Otero-de-la-Roza A. Noncovalent Interactions in Density Functional Theory. REVIEWS IN COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1002/9781119148739.ch1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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41
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Stöhr M, Michelitsch GS, Tully JC, Reuter K, Maurer RJ. Communication: Charge-population based dispersion interactions for molecules and materials. J Chem Phys 2016; 144:151101. [DOI: 10.1063/1.4947214] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Martin Stöhr
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Georg S. Michelitsch
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - John C. Tully
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karsten Reuter
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Reinhard J. Maurer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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42
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Maurer RJ, Liu W, Poltavsky I, Stecher T, Oberhofer H, Reuter K, Tkatchenko A. Thermal and Electronic Fluctuations of Flexible Adsorbed Molecules: Azobenzene on Ag(111). PHYSICAL REVIEW LETTERS 2016; 116:146101. [PMID: 27104719 DOI: 10.1103/physrevlett.116.146101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Indexed: 05/09/2023]
Abstract
We investigate the thermal and electronic collective fluctuations that contribute to the finite-temperature adsorption properties of flexible adsorbates on surfaces on the example of the molecular switch azobenzene C_{12}H_{10}N_{2} on the Ag(111) surface. Using first-principles molecular dynamics simulations, we obtain the free energy of adsorption that accurately accounts for entropic contributions, whereas the inclusion of many-body dispersion interactions accounts for the electronic correlations that govern the adsorbate binding. We find the adsorbate properties to be strongly entropy driven, as can be judged by a kinetic molecular desorption prefactor of 10^{24} s^{-1} that largely exceeds previously reported estimates. We relate this effect to sizable fluctuations across structural and electronic observables. A comparison of our calculations to temperature-programed desorption measurements demonstrates that finite-temperature effects play a dominant role for flexible molecules in contact with polarizable surfaces, and that recently developed first-principles methods offer an optimal tool to reveal novel collective behavior in such complex systems.
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Affiliation(s)
- Reinhard J Maurer
- Department Chemie, Technische Universität München, D-85748 Garching, Germany
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Wei Liu
- Fritz-Haber Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- Nano Structural Materials Center, School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, Jiangsu, China
| | - Igor Poltavsky
- Fritz-Haber Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Thomas Stecher
- Department Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Harald Oberhofer
- Department Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Karsten Reuter
- Department Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Alexandre Tkatchenko
- Fritz-Haber Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
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43
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Ambrosetti A, Ferri N, DiStasio RA, Tkatchenko A. Wavelike charge density fluctuations and van der Waals interactions at the nanoscale. Science 2016; 351:1171-6. [PMID: 26965622 DOI: 10.1126/science.aae0509] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent experiments on noncovalent interactions at the nanoscale have challenged the basic assumptions of commonly used particle- or fragment-based models for describing van der Waals (vdW) or dispersion forces. We demonstrate that a qualitatively correct description of the vdW interactions between polarizable nanostructures over a wide range of finite distances can only be attained by accounting for the wavelike nature of charge density fluctuations. By considering a diverse set of materials and biological systems with markedly different dimensionalities, topologies, and polarizabilities, we find a visible enhancement in the nonlocality of the charge density response in the range of 10 to 20 nanometers. These collective wavelike fluctuations are responsible for the emergence of nontrivial modifications of the power laws that govern noncovalent interactions at the nanoscale.
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Affiliation(s)
- Alberto Ambrosetti
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany. Dipartimento di Fisica e Astronomia, Università degli Studi di Padova, 35131 Padova, Italy
| | - Nicola Ferri
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, D-14195 Berlin, Germany. Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg.
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44
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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45
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Červinka C, Fulem M, Stoffel RP, Dronskowski R. Thermodynamic Properties of Molecular Crystals Calculated within the Quasi-Harmonic Approximation. J Phys Chem A 2016; 120:2022-34. [PMID: 26959684 DOI: 10.1021/acs.jpca.6b00401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A computational study of the possibilities of contemporary theoretical chemistry as regards calculated thermodynamic properties for molecular crystals from first-principles is presented. The study is performed for a testing set of 22 low-temperature crystalline phases whose properties such as densities of phonon states, isobaric heat capacities, and densities are computed as functions of temperature within the quasi-harmonic approximation. Electronic structure and lattice dynamics are treated by plane-wave based calculations with optPBE-vdW functional. Comparison of calculated results with reliable critically assessed experimental data is especially emphasized.
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Affiliation(s)
- Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Ralf Peter Stoffel
- Institute of Inorganic Chemistry and Jülich-Aachen Research Alliance (JARA-HPC), RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Richard Dronskowski
- Institute of Inorganic Chemistry and Jülich-Aachen Research Alliance (JARA-HPC), RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
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46
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Řezáč J, Huang Y, Hobza P, Beran GJO. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods. J Chem Theory Comput 2016; 11:3065-79. [PMID: 26575743 DOI: 10.1021/acs.jctc.5b00281] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many-body noncovalent interactions are increasingly important in large and/or condensed-phase systems, but the current understanding of how well various models predict these interactions is limited. Here, benchmark complete-basis set coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations have been performed to generate a new test set for three-body intermolecular interactions. This "3B-69" benchmark set includes three-body interaction energies for 69 total trimer structures, consisting of three structures from each of 23 different molecular crystals. By including structures that exhibit a variety of intermolecular interactions and packing arrangements, this set provides a stringent test for the ability of electronic structure methods to describe the correct physics involved in the interactions. Both MP2.5 (the average of second- and third-order Møller-Plesset perturbation theory) and spin-component-scaled CCSD for noncovalent interactions (SCS-MI-CCSD) perform well. MP2 handles the polarization aspects reasonably well, but it omits three-body dispersion. In contrast, many widely used density functionals corrected with three-body D3 dispersion correction perform comparatively poorly. The primary difficulty stems from the treatment of exchange and polarization in the functionals rather than from the dispersion correction, though the three-body dispersion may also be moderately underestimated by the D3 correction.
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Affiliation(s)
- Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic
| | - Yuanhang Huang
- Department of Chemistry, University of California , Riverside, California 92521 United States
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic
| | - Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521 United States
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47
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Blood-Forsythe MA, Markovich T, DiStasio RA, Car R, Aspuru-Guzik A. Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions. Chem Sci 2016; 7:1712-1728. [PMID: 29899903 PMCID: PMC5964951 DOI: 10.1039/c5sc03234b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022] Open
Abstract
An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al., J. Chem. Phys., 2014, 140, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C60@C60H28 buckyball catcher host-guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.
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Affiliation(s)
| | - Thomas Markovich
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
| | - Robert A DiStasio
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , NY , USA
| | - Roberto Car
- Department of Chemistry , Princeton University , Princeton , NJ , USA
- Princeton Institute for the Science and Technology of Materials , Princeton University , Princeton , NJ , USA
- Department of Physics , Princeton University , Princeton , NJ , USA
- Program in Applied and Computational Mathematics , Princeton University , Princeton , NJ , USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA , USA .
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48
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Chen P, Marianski M, Baldauf C. H-Bond Isomerization in Crystalline Cellulose III I: Proton Hopping versus Hydroxyl Flip-Flop. ACS Macro Lett 2016; 5:50-54. [PMID: 35668603 DOI: 10.1021/acsmacrolett.5b00837] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Based on density-functional theory calculations, we discuss three forms of cellulose IIII that are characterized by different intersheet H-bonding patterns. Two alternative mechanisms can facilitate the interconversion between these H-bonding patterns: the rotation of hydroxy groups ("flip-flop") or a concerted proton transfer from one hydroxy group to the other ("proton hopping"). Both mechanisms have energy barriers of very similar height. Electronic structure theory methods allow us to study effects that involve the breaking/forming bonds, like the hopping of protons. In many of the force field formulations, in particular, the ones that are typically used to study cellulose, such effects are not considered. However, such insight at the atomistic and electronic scale can be the key to finding energy-efficient means for cellulose deconstruction.
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Affiliation(s)
- Pan Chen
- Aachener
Verfahrenstechnik, RWTH Aachen University, Turmstrasse 46, D-52062 Aachen, Germany
- AICES
Graduate School, RWTH Aachen University, Turmstrasse 46, D-52062 Aachen, Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, D-14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg
4-6, D-14195 Berlin, Germany
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49
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Skyner RE, McDonagh JL, Groom CR, van Mourik T, Mitchell JBO. A review of methods for the calculation of solution free energies and the modelling of systems in solution. Phys Chem Chem Phys 2016; 17:6174-91. [PMID: 25660403 DOI: 10.1039/c5cp00288e] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.
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Affiliation(s)
- R E Skyner
- School of Chemistry, University of St Andrews, Purdie Building, North Haugh, St Andrews, Fife KY16 9ST, UK.
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50
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Maurer RJ, Ruiz VG, Tkatchenko A. Many-body dispersion effects in the binding of adsorbates on metal surfaces. J Chem Phys 2015; 143:102808. [PMID: 26374001 DOI: 10.1063/1.4922688] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A correct description of electronic exchange and correlation effects for molecules in contact with extended (metal) surfaces is a challenging task for first-principles modeling. In this work, we demonstrate the importance of collective van der Waals dispersion effects beyond the pairwise approximation for organic-inorganic systems on the example of atoms, molecules, and nanostructures adsorbed on metals. We use the recently developed many-body dispersion (MBD) approach in the context of density-functional theory [Tkatchenko et al., Phys. Rev. Lett. 108, 236402 (2012) and Ambrosetti et al., J. Chem. Phys. 140, 18A508 (2014)] and assess its ability to correctly describe the binding of adsorbates on metal surfaces. We briefly review the MBD method and highlight its similarities to quantum-chemical approaches to electron correlation in a quasiparticle picture. In particular, we study the binding properties of xenon, 3,4,9,10-perylene-tetracarboxylic acid, and a graphene sheet adsorbed on the Ag(111) surface. Accounting for MBD effects, we are able to describe changes in the anisotropic polarizability tensor, improve the description of adsorbate vibrations, and correctly capture the adsorbate-surface interaction screening. Comparison to other methods and experiment reveals that inclusion of MBD effects improves adsorption energies and geometries, by reducing the overbinding typically found in pairwise additive dispersion-correction approaches.
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Affiliation(s)
- Reinhard J Maurer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Victor G Ruiz
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany
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