101
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Alfè D, Bartók AP, Csányi G, Gillan MJ. Analyzing the errors of DFT approximations for compressed water systems. J Chem Phys 2014; 141:014104. [DOI: 10.1063/1.4885440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- D. Alfè
- Department of Earth Sciences, UCL, London WC1E 6BT, United Kingdom
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
| | - A. P. Bartók
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - G. Csányi
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - M. J. Gillan
- London Centre for Nanotechnology, UCL, London WC1H 0AH, United Kingdom
- Thomas Young Centre, UCL, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, UCL, London WC1E 6BT, United Kingdom
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102
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Weymuth T, Couzijn EPA, Chen P, Reiher M. New Benchmark Set of Transition-Metal Coordination Reactions for the Assessment of Density Functionals. J Chem Theory Comput 2014; 10:3092-103. [DOI: 10.1021/ct500248h] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Weymuth
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| | - Erik P. A. Couzijn
- ETH Zürich, Laboratorium für Organische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| | - Peter Chen
- ETH Zürich, Laboratorium für Organische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische
Chemie, Vladimir-Prelog-Weg
2, CH-8093 Zürich, Switzerland
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103
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Benali A, Shulenburger L, Romero NA, Kim J, von Lilienfeld OA. Application of Diffusion Monte Carlo to Materials Dominated by van der Waals Interactions. J Chem Theory Comput 2014; 10:3417-22. [DOI: 10.1021/ct5003225] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anouar Benali
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Luke Shulenburger
- HEDP
Theory Department, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Nichols A. Romero
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jeongnim Kim
- Materials
Science and Technology Division and Computer Science and Mathematics
Division, Oak Ridge National Laboratory, Oak Ridge, Tenessee 37831, United States
| | - O. Anatole von Lilienfeld
- Argonne
Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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104
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DiStasio RA, Gobre VV, Tkatchenko A. Many-body van der Waals interactions in molecules and condensed matter. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:213202. [PMID: 24805055 DOI: 10.1088/0953-8984/26/21/213202] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This work reviews the increasing evidence that many-body van der Waals (vdW) or dispersion interactions play a crucial role in the structure, stability and function of a wide variety of systems in biology, chemistry and physics. Starting with the exact expression for the electron correlation energy provided by the adiabatic connection fluctuation-dissipation theorem, we derive both pairwise and many-body interatomic methods for computing the long-range dispersion energy by considering a model system of coupled quantum harmonic oscillators within the random-phase approximation. By coupling this approach to density functional theory, the resulting many-body dispersion (MBD) method provides an accurate and efficient scheme for computing the frequency-dependent polarizability and many-body vdW energy in molecules and materials with a finite electronic gap. A select collection of applications are presented that ascertain the fundamental importance of these non-bonded interactions across the spectrum of intermolecular (the S22 and S66 benchmark databases), intramolecular (conformational energies of alanine tetrapeptide) and supramolecular (binding energy of the 'buckyball catcher') complexes, as well as molecular crystals (cohesive energies in oligoacenes). These applications demonstrate that electrodynamic response screening and beyond-pairwise many-body vdW interactions--both captured at the MBD level of theory--play a quantitative, and sometimes even qualitative, role in describing the properties considered herein. This work is then concluded with an in-depth discussion of the challenges that remain in the future development of reliable (accurate and efficient) methods for treating many-body vdW interactions in complex materials and provides a roadmap for navigating many of the research avenues that are yet to be explored.
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Affiliation(s)
- Robert A DiStasio
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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105
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Anick DJ. Static Density Functional Study of Graphene–Hexagonal Bilayer Ice Interaction. J Phys Chem A 2014; 118:7498-506. [PMID: 24641236 DOI: 10.1021/jp500360n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David J. Anick
- Laboratory for Water and
Surface Studies Department of Chemistry, Tufts University, 62
Pearson Avenue, Medford, Massachusetts 02155, Unites States
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106
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McDaniel JG, Schmidt JR. First-Principles Many-Body Force Fields from the Gas Phase to Liquid: A “Universal” Approach. J Phys Chem B 2014; 118:8042-53. [DOI: 10.1021/jp501128w] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesse G. McDaniel
- Theoretical
Chemistry Institute
and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - J. R. Schmidt
- Theoretical
Chemistry Institute
and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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107
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108
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Reilly AM, Tkatchenko A. Understanding the role of vibrations, exact exchange, and many-body van der Waals interactions in the cohesive properties of molecular crystals. J Chem Phys 2014; 139:024705. [PMID: 23862957 DOI: 10.1063/1.4812819] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The development and application of computational methods for studying molecular crystals, particularly density-functional theory (DFT), is a large and ever-growing field, driven by their numerous applications. Here we expand on our recent study of the importance of many-body van der Waals interactions in molecular crystals [A. M. Reilly and A. Tkatchenko, J. Phys. Chem. Lett. 4, 1028 (2013)], with a larger database of 23 molecular crystals. Particular attention has been paid to the role of the vibrational contributions that are required to compare experiment sublimation enthalpies with calculated lattice energies, employing both phonon calculations and experimental heat-capacity data to provide harmonic and anharmonic estimates of the vibrational contributions. Exact exchange, which is rarely considered in DFT studies of molecular crystals, is shown to have a significant contribution to lattice energies, systematically improving agreement between theory and experiment. When the vibrational and exact-exchange contributions are coupled with a many-body approach to dispersion, DFT yields a mean absolute error (3.92 kJ/mol) within the coveted "chemical accuracy" target (4.2 kJ/mol). The role of many-body dispersion for structures has also been investigated for a subset of the database, showing good performance compared to X-ray and neutron diffraction crystal structures. The results show that the approach employed here can reach the demanding accuracy of crystal-structure prediction and organic material design with minimal empiricism.
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Affiliation(s)
- Anthony M Reilly
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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109
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Várnai C, Burkoff NS, Wild DL. Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach. J Chem Theory Comput 2013; 9:5718-5733. [PMID: 24683370 PMCID: PMC3966533 DOI: 10.1021/ct400628h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Indexed: 01/05/2023]
Abstract
Maximum Likelihood (ML) optimization schemes are widely used for parameter inference. They maximize the likelihood of some experimentally observed data, with respect to the model parameters iteratively, following the gradient of the logarithm of the likelihood. Here, we employ a ML inference scheme to infer a generalizable, physics-based coarse-grained protein model (which includes Go̅-like biasing terms to stabilize secondary structure elements in room-temperature simulations), using native conformations of a training set of proteins as the observed data. Contrastive divergence, a novel statistical machine learning technique, is used to efficiently approximate the direction of the gradient ascent, which enables the use of a large training set of proteins. Unlike previous work, the generalizability of the protein model allows the folding of peptides and a protein (protein G) which are not part of the training set. We compare the same force field with different van der Waals (vdW) potential forms: a hard cutoff model, and a Lennard-Jones (LJ) potential with vdW parameters inferred or adopted from the CHARMM or AMBER force fields. Simulations of peptides and protein G show that the LJ model with inferred parameters outperforms the hard cutoff potential, which is consistent with previous observations. Simulations using the LJ potential with inferred vdW parameters also outperforms the protein models with adopted vdW parameter values, demonstrating that model parameters generally cannot be used with force fields with different energy functions. The software is available at https://sites.google.com/site/crankite/.
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Affiliation(s)
- Csilla Várnai
- Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | | | - David L. Wild
- Systems Biology Centre, University of Warwick, Coventry, United Kingdom
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110
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A dispersion-corrected density functional theory case study on ethyl acetate conformers, dimer, and molecular crystal. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1399-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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111
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Gillan MJ, Alfè D, Bygrave PJ, Taylor CR, Manby FR. Energy benchmarks for water clusters and ice structures from an embedded many-body expansion. J Chem Phys 2013; 139:114101. [DOI: 10.1063/1.4820906] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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112
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Brandenburg JG, Alessio M, Civalleri B, Peintinger MF, Bredow T, Grimme S. Geometrical Correction for the Inter- and Intramolecular Basis Set Superposition Error in Periodic Density Functional Theory Calculations. J Phys Chem A 2013; 117:9282-92. [DOI: 10.1021/jp406658y] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
| | - Maristella Alessio
- Department
of Chemistry and Centre of Excellence NIS, University of Turin, Via P. Giuria 7, 10125 Torino, Italy
| | - Bartolomeo Civalleri
- Department
of Chemistry and Centre of Excellence NIS, University of Turin, Via P. Giuria 7, 10125 Torino, Italy
| | - Michael F. Peintinger
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
| | - Thomas Bredow
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
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113
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Tkatchenko A, Ambrosetti A, DiStasio RA. Interatomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem. J Chem Phys 2013; 138:074106. [PMID: 23444996 DOI: 10.1063/1.4789814] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory calculations. However, when applied to more than two atoms, these methods are still frequently perceived to be based on ad hoc assumptions, rather than a rigorous derivation from quantum mechanics. Starting from the adiabatic connection fluctuation-dissipation (ACFD) theorem, an exact expression for the electronic exchange-correlation energy, we demonstrate that the pairwise interatomic dispersion energy for an arbitrary collection of isotropic polarizable dipoles emerges from the second-order expansion of the ACFD formula upon invoking the random-phase approximation (RPA) or the full-potential approximation. Moreover, for a system of quantum harmonic oscillators coupled through a dipole-dipole potential, we prove the equivalence between the full interaction energy obtained from the Hamiltonian diagonalization and the ACFD-RPA correlation energy. This property makes the Hamiltonian diagonalization an efficient method for the calculation of the many-body dispersion energy. In addition, we show that the switching function used to damp the dispersion interaction at short distances arises from a short-range screened Coulomb potential, whose role is to account for the spatial spread of the individual atomic dipole moments. By using the ACFD formula, we gain a deeper understanding of the approximations made in the interatomic pairwise approaches, providing a powerful formalism for further development of accurate and efficient methods for the calculation of the dispersion energy.
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Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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114
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Vener MV, Shishkina AV, Rykounov AA, Tsirelson VG. Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis. J Phys Chem A 2013; 117:8459-67. [PMID: 23924151 DOI: 10.1021/jp405119x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.
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Affiliation(s)
- Mikhail V Vener
- Department of Quantum Chemistry, Mendeleev University of Chemical Technology, Miusskaya Square 9, 125047 Moscow, Russia.
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115
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Schatschneider B, Monaco S, Tkatchenko A, Liang JJ. Understanding the structure and electronic properties of molecular crystals under pressure: application of dispersion corrected DFT to oligoacenes. J Phys Chem A 2013; 117:8323-31. [PMID: 23901832 DOI: 10.1021/jp406573n] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Oligoacenes form a fundamental class of polycyclic aromatic hydrocarbons (PAH) which have been extensively explored for use as organic (semi) conductors in the bulk phase and thin films. For this reason it is important to understand their electronic properties in the condensed phase. In this investigation, we use density functional theory with Tkatchenko-Scheffler dispersion correction to explore several crystalline oligoacenes (naphthalene, anthracene, tetracene, and pentacene) under pressures up to 25 GPa in an effort to uncover unique electronic/optical properties. Excellent agreement with experiment is achieved for the pressure dependence of the crystal structure unit cell parameters, densities, and intermolecular close contacts. The pressure dependence of the band gaps is investigated as well as the pressure induced phase transition of tetracene using both generalized gradient approximated and hybrid functionals. It is concluded that none of the oligoacenes investigated become conducting under elevated pressures, assuming that the molecular identity of the system is maintained.
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Affiliation(s)
- Bohdan Schatschneider
- The Pennsylvania State University, Fayette-The Eberly Campus, Lemont Furnace, Pennsylvania 15456, United States.
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116
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Silvestrelli PL. Van der Waals interactions in density functional theory by combining the quantum harmonic oscillator-model with localized Wannier functions. J Chem Phys 2013; 139:054106. [DOI: 10.1063/1.4816964] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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117
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Addicoat MA, Nishimura Y, Sato T, Tsuneda T, Irle S. Stochastic Search of Molecular Cluster Interaction Energy Surfaces with Coupled Cluster Quality Prediction. The Phenylacetylene Dimer. J Chem Theory Comput 2013; 9:3848-54. [DOI: 10.1021/ct4003515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew A. Addicoat
- Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-4602,
Japan
| | - Yoshifumi Nishimura
- Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-4602,
Japan
| | - Takeshi Sato
- Photon Science Center, University of Tokyo, Tokyo 113-8656, Japan
| | - Takao Tsuneda
- Fuel Cell Nanomaterials Center, University of Yamanashi, Kofu 400-0021, Japan
| | - Stephan Irle
- Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku Nagoya 464-4602,
Japan
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118
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119
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Sancho-García JC, Aragó J, Ortí E, Olivier Y. Obtaining the lattice energy of the anthracene crystal by modern yet affordable first-principles methods. J Chem Phys 2013; 138:204304. [DOI: 10.1063/1.4806436] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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120
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Marom N, DiStasio RA, Atalla V, Levchenko S, Reilly AM, Chelikowsky JR, Leiserowitz L, Tkatchenko A. Many-Body Dispersion Interactions in Molecular Crystal Polymorphism. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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121
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Marom N, DiStasio RA, Atalla V, Levchenko S, Reilly AM, Chelikowsky JR, Leiserowitz L, Tkatchenko A. Many-Body Dispersion Interactions in Molecular Crystal Polymorphism. Angew Chem Int Ed Engl 2013; 52:6629-32. [DOI: 10.1002/anie.201301938] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Indexed: 11/07/2022]
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122
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Lilienfeld OAV. Force correcting atom centred potentials for generalised gradient approximated density functional theory: Approaching hybrid functional accuracy for geometries and harmonic frequencies in small chlorofluorocarbons. Mol Phys 2013. [DOI: 10.1080/00268976.2013.793834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- O. Anatole von Lilienfeld
- Argonne Leadership Computing Facility, Argonne National Laboratory , Argonne, IL, 60439, USA
- Department of Chemistry, University of Basel , Basel, Klingelbergstr, 80, 4056, Switzerland
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123
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Klimeš J, Michaelides A. Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory. J Chem Phys 2013; 137:120901. [PMID: 23020317 DOI: 10.1063/1.4754130] [Citation(s) in RCA: 599] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.
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Affiliation(s)
- Jirí Klimeš
- Thomas Young Centre, London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, United Kingdom
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124
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Risthaus T, Grimme S. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes. J Chem Theory Comput 2013; 9:1580-91. [DOI: 10.1021/ct301081n] [Citation(s) in RCA: 322] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tobias Risthaus
- Mulliken Center
for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie,
Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
- International NRW Graduate School
of Chemistry, Wilhelm-Klemm-Str. 10, D-48149 Münster, Germany
| | - Stefan Grimme
- Mulliken Center
for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie,
Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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125
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Otero-de-la-Roza A, Johnson ER. Many-body dispersion interactions from the exchange-hole dipole moment model. J Chem Phys 2013; 138:054103. [DOI: 10.1063/1.4789421] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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126
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Niskanen M, Kuisma M, Cramariuc O, Golovanov V, Hukka TI, Tkachenko N, Rantala TT. Porphyrin adsorbed on the (101̄0) surface of the wurtzite structure of ZnO – conformation induced effects on the electron transfer characteristics. Phys Chem Chem Phys 2013; 15:17408-18. [DOI: 10.1039/c3cp51685g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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127
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Dudenko DV, Yates JR, Harris KDM, Brown SP. An NMR crystallography DFT-D approach to analyse the role of intermolecular hydrogen bonding and π–π interactions in driving cocrystallisation of indomethacin and nicotinamide. CrystEngComm 2013. [DOI: 10.1039/c3ce41240g] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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128
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Otero-de-la-Roza A, Johnson ER. A benchmark for non-covalent interactions in solids. J Chem Phys 2012; 137:054103. [PMID: 22894328 DOI: 10.1063/1.4738961] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A benchmark for non-covalent interactions in solids (C21) based on the experimental sublimation enthalpies and geometries of 21 molecular crystals is presented. Thermal and zero-point effects are carefully accounted for and reference lattice energies and thermal pressures are provided, which allow dispersion-corrected density functionals to be assessed in a straightforward way. Other thermal corrections to the sublimation enthalpy (the 2RT term) are reexamined. We compare the recently implemented exchange-hole dipole moment (XDM) model with other approaches in the literature to find that XDM roughly doubles the accuracy of DFT-D2 and non-local functionals in computed lattice energies (4.8 kJ/mol mean absolute error) while, at the same time, predicting cell geometries within less than 2% of the experimental result on average. The XDM model of dispersion interactions is confirmed as a very promising approach in solid-state applications.
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Affiliation(s)
- A Otero-de-la-Roza
- Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA.
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129
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Sancho-García JC, Olivier Y. Reliable DFT-based estimates of cohesive energies of organic solids: The anthracene crystal. J Chem Phys 2012. [DOI: 10.1063/1.4766933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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130
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Hatz R, Korpinen M, Hänninen V, Halonen L. Characterization of the Dispersion Interactions and an ab Initio Study of van der Waals Potential Energy Parameters for Coinage Metal Clusters. J Phys Chem A 2012; 116:11685-93. [DOI: 10.1021/jp307448n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Hatz
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Markus Korpinen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Vesa Hänninen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
| | - Lauri Halonen
- Laboratory of Physical
Chemistry, Department
of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki,
Finland
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131
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Nanda KD, Beran GJO. Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations. J Chem Phys 2012; 137:174106. [DOI: 10.1063/1.4764063] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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132
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Graziano G, Klimeš J, Fernandez-Alonso F, Michaelides A. Improved description of soft layered materials with van der Waals density functional theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:424216. [PMID: 23032994 DOI: 10.1088/0953-8984/24/42/424216] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The accurate description of van der Waals forces within density functional theory is currently one of the most active areas of research in computational physics and chemistry. Here we report results on the structural and energetic properties of graphite and hexagonal boron nitride, two layered materials where interlayer binding is dominated by van der Waals forces. Results from several density functionals are reported, including the optimized Becke88 van der Waals (optB88-vdW) and the optimized PBE van der Waals (optPBE-vdW) (Klimeš et al 2010 J. Phys.: Condens. Matter 22 022201) functionals. Where comparison to experiment and higher-level theory is possible, the results obtained from the two new van der Waals density functionals are in good agreement. An analysis of the physical nature of the interlayer binding in both graphite and hexagonal boron nitride is also reported.
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Affiliation(s)
- Gabriella Graziano
- Thomas Young Centre, London Centre for Nanotechnology and Department of Chemistry, University College London, London WC1E 6BT, UK
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133
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Hanke F, Dyer MS, Björk J, Persson M. Structure and stability of weakly chemisorbed ethene adsorbed on low-index Cu surfaces: performance of density functionals with van der Waals interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:424217. [PMID: 23031831 DOI: 10.1088/0953-8984/24/42/424217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have investigated the performance of popular density functionals that include van der Waals interactions for the experimentally well-characterized problem of ethene (C(2)H(4)) adsorbed on the low-index surfaces of copper. This set of functionals does not only include three van der Waals density functionals-vdwDF-PBE, vdwDF-revPBE and optB86b-vdwDF-and two dispersion-corrected functionals-Grimme and TS-but also local and semi-local functionals such as LDA and PBE. The adsorption system of ethene on copper was chosen because it is a weakly chemisorbed system for which the vdW interactions are expected to give a significant contribution to the adsorption energy. Overall the density functionals that include vdW interactions increased substantially the adsorption energies compared to the PBE density functional but predicted the same adsorption sites and very similar C-C bonding distances except for two of the van der Waals functionals. The top adsorption site was predicted almost exclusively for all functionals on the (110), (100) and (111) surfaces, which is in agreement with experiment for the (110) surface but not for the (100) surface. On the (100) surface, all functionals except two van der Waals density functionals singled out the observed cross-hollow site from the calculated C-C bonding distances and adsorption heights. On the top sites on the (110) surface and the cross-hollow site on the Cu(100) surface, the ethene molecule was found to form a weak chemisorption bond. On the (111) surface, all functionals gave a C-C bonding distance and an adsorption height more typical for physisorption, in agreement with experiments.
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Affiliation(s)
- Felix Hanke
- Surface Science Research Centre, University of Liverpool, Liverpool L69 3BX, UK
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134
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Chwee TS, Sullivan MB. Adsorption studies of C6H6 on Cu (111), Ag (111), and Au (111) within dispersion corrected density functional theory. J Chem Phys 2012; 137:134703. [DOI: 10.1063/1.4755993] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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135
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DiStasio RA, von Lilienfeld OA, Tkatchenko A. Collective many-body van der Waals interactions in molecular systems. Proc Natl Acad Sci U S A 2012; 109:14791-5. [PMID: 22923693 PMCID: PMC3443155 DOI: 10.1073/pnas.1208121109] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Van der Waals (vdW) interactions are ubiquitous in molecules and condensed matter, and play a crucial role in determining the structure, stability, and function for a wide variety of systems. The accurate prediction of these interactions from first principles is a substantial challenge because they are inherently quantum mechanical phenomena that arise from correlations between many electrons within a given molecular system. We introduce an efficient method that accurately describes the nonadditive many-body vdW energy contributions arising from interactions that cannot be modeled by an effective pairwise approach, and demonstrate that such contributions can significantly exceed the energy of thermal fluctuations--a critical accuracy threshold highly coveted during molecular simulations--in the prediction of several relevant properties. Cases studied include the binding affinity of ellipticine, a DNA-intercalating anticancer agent, the relative energetics between the A- and B-conformations of DNA, and the thermodynamic stability among competing paracetamol molecular crystal polymorphs. Our findings suggest that inclusion of the many-body vdW energy is essential for achieving chemical accuracy and therefore must be accounted for in molecular simulations.
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Affiliation(s)
| | | | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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136
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Wen S, Beran GJO. Crystal Polymorphism in Oxalyl Dihydrazide: Is Empirical DFT-D Accurate Enough? J Chem Theory Comput 2012; 8:2698-705. [PMID: 26592115 DOI: 10.1021/ct300484h] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Crystalline oxalyl dihydrazide has five experimentally known polymorphs whose energetics are governed by subtle balances between intra- and intermolecular interactions, providing a severe challenge for theoretical crystal structure modeling. Previous work has shown that many common density functional methods that neglect van der Waals dispersion cannot correctly describe this system, but it has been argued that empirically dispersion-corrected DFT-D performs much better. Here, we examine these crystals with second-order Møller-Plesset perturbation theory (MP2) and related levels of theory using the fragment-based hybrid many-body interaction method. The energetics prove sensitive to the treatment of electron-electron correlation, the basis set, many-body induction, three-body dispersion, and zero-point contributions. Nevertheless, our best predictions for the polymorph energy ordering based on dispersion-corrected MP2C calculations agree with the available experimental data. In contrast, lower levels of theory, including the common B3LYP-D* and D-PW91 dispersion-corrected density functional approximations, fail to reproduce experimental observations and/or the high-level calculations.
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Affiliation(s)
- Shuhao Wen
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
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137
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KOLB BRIAN, THONHAUSER T. MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH? ACTA ACUST UNITED AC 2012. [DOI: 10.1142/s1793984412300063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical ground — can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within the density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent work utilizing these methods to study biologically relevant systems will be highlighted, and a vision for the future of density functional theory within molecular biology will be discussed.
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Affiliation(s)
- BRIAN KOLB
- Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
| | - T. THONHAUSER
- Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
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138
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Grimme S. Supramolecular binding thermodynamics by dispersion-corrected density functional theory. Chemistry 2012; 18:9955-64. [PMID: 22782805 DOI: 10.1002/chem.201200497] [Citation(s) in RCA: 1202] [Impact Index Per Article: 100.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Indexed: 11/07/2022]
Abstract
The equilibrium association free enthalpies ΔG(a) for typical supramolecular complexes in solution are calculated by ab initio quantum chemical methods. Ten neutral and three positively charged complexes with experimental ΔG(a) values in the range 0 to -21 kcal mol(-1) (on average -6 kcal mol(-1)) are investigated. The theoretical approach employs a (nondynamic) single-structure model, but computes the various energy terms accurately without any special empirical adjustments. Dispersion corrected density functional theory (DFT-D3) with extended basis sets (triple-ζ and quadruple-ζ quality) is used to determine structures and gas-phase interaction energies (ΔE), the COSMO-RS continuum solvation model (based on DFT data) provides solvation free enthalpies and the remaining ro-vibrational enthalpic/entropic contributions are obtained from harmonic frequency calculations. Low-lying vibrational modes are treated by a free-rotor approximation. The accurate account of London dispersion interactions is mandatory with contributions in the range -5 to -60 kcal mol(-1) (up to 200% of ΔE). Inclusion of three-body dispersion effects improves the results considerably. A semilocal (TPSS) and a hybrid density functional (PW6B95) have been tested. Although the ΔG(a) values result as a sum of individually large terms with opposite sign (ΔE vs. solvation and entropy change), the approach provides unprecedented accuracy for ΔG(a) values with errors of only 2 kcal mol(-1) on average. Relative affinities for different guests inside the same host are always obtained correctly. The procedure is suggested as a predictive tool in supramolecular chemistry and can be applied routinely to semirigid systems with 300-400 atoms. The various contributions to binding and enthalpy-entropy compensations are discussed.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
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139
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Tkatchenko A, DiStasio RA, Car R, Scheffler M. Accurate and efficient method for many-body van der Waals interactions. PHYSICAL REVIEW LETTERS 2012; 108:236402. [PMID: 23003978 DOI: 10.1103/physrevlett.108.236402] [Citation(s) in RCA: 733] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Indexed: 05/21/2023]
Abstract
An efficient method is developed for the microscopic description of the frequency-dependent polarizability of finite-gap molecules and solids. This is achieved by combining the Tkatchenko-Scheffler van der Waals (vdW) method [Phys. Rev. Lett. 102, 073005 (2009)] with the self-consistent screening equation of classical electrodynamics. This leads to a seamless description of polarization and depolarization for the polarizability tensor of molecules and solids. The screened long-range many-body vdW energy is obtained from the solution of the Schrödinger equation for a system of coupled oscillators. We show that the screening and the many-body vdW energy play a significant role even for rather small molecules, becoming crucial for an accurate treatment of conformational energies for biomolecules and binding of molecular crystals. The computational cost of the developed theory is negligible compared to the underlying electronic structure calculation.
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Affiliation(s)
- Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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140
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Al-Saidi WA, Voora VK, Jordan KD. An Assessment of the vdW-TS Method for Extended Systems. J Chem Theory Comput 2012; 8:1503-13. [DOI: 10.1021/ct200618b] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W. A. Al-Saidi
- Department of Chemistry and Center for Molecular and
Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- Department of Chemical
and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Vamsee K. Voora
- Department of Chemistry and Center for Molecular and
Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Kenneth D. Jordan
- Department of Chemistry and Center for Molecular and
Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
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141
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Schatschneider B, Liang JJ, Jezowski S, Tkatchenko A. Phase transition between cubic and monoclinic polymorphs of the tetracyanoethylene crystal: the role of temperature and kinetics. CrystEngComm 2012. [DOI: 10.1039/c2ce25321f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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142
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Wen S, Nanda K, Huang Y, Beran GJO. Practical quantum mechanics-based fragment methods for predicting molecular crystal properties. Phys Chem Chem Phys 2012; 14:7578-90. [DOI: 10.1039/c2cp23949c] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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143
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Henne S, Bredenkötter B, Dehghan Baghi AA, Schmid R, Volkmer D. Advanced buckyball joints: synthesis, complex formation and computational simulations of centrohexaindane-extended tribenzotriquinacene receptors for C60 fullerene. Dalton Trans 2012; 41:5995-6002. [DOI: 10.1039/c2dt12435a] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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144
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Getman RB, Bae YS, Wilmer CE, Snurr RQ. Review and Analysis of Molecular Simulations of Methane, Hydrogen, and Acetylene Storage in Metal–Organic Frameworks. Chem Rev 2011; 112:703-23. [DOI: 10.1021/cr200217c] [Citation(s) in RCA: 996] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Rachel B. Getman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Youn-Sang Bae
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher E. Wilmer
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Randall Q. Snurr
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
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145
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Johnson ER. Dependence of dispersion coefficients on atomic environment. J Chem Phys 2011; 135:234109. [DOI: 10.1063/1.3670015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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146
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Schatschneider B, Liang JJ. Simulated pressure response of crystalline indole. J Chem Phys 2011; 135:164508. [DOI: 10.1063/1.3655466] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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147
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Wen S, Beran GJO. Accurate Molecular Crystal Lattice Energies from a Fragment QM/MM Approach with On-the-Fly Ab Initio Force Field Parametrization. J Chem Theory Comput 2011; 7:3733-42. [DOI: 10.1021/ct200541h] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuhao Wen
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Gregory J. O. Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
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148
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Jiao D, Rempe SB. CO2solvation free energy using quasi-chemical theory. J Chem Phys 2011; 134:224506. [DOI: 10.1063/1.3598470] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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149
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150
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Grimme S. Density functional theory with London dispersion corrections. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.30] [Citation(s) in RCA: 1495] [Impact Index Per Article: 115.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stefan Grimme
- Theoretische Organische Chemie, Organisch‐Chemisches Institut der Universität Münster, Münster, Germany
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