1
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Prayogo GI, Shin H, Benali A, Maezono R, Hongo K. Importance of Van der Waals Interactions in Hydrogen Adsorption on a Silicon-carbide Nanotube Revisited with vdW-DFT and Quantum Monte Carlo. ACS OMEGA 2021; 6:24630-24636. [PMID: 34604645 PMCID: PMC8482461 DOI: 10.1021/acsomega.1c03318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Density functional theory (DFT) is a valuable tool for calculating adsorption energies toward designing materials for hydrogen storage. However, dispersion forces being absent from the local/semi-local theory, it remains unclear as to how the consideration of van der Waals (vdW) interactions affects such calculations. For the first time, we applied diffusion Monte Carlo (DMC) to evaluate the adsorption characteristics of a hydrogen molecule on a (5,5) armchair silicon-carbide nanotube (H2-SiCNT). Within the DFT framework, we benchmarked various exchange-correlation functionals, including those recently developed for treating dispersion or vdW interactions. We found that the vdW-corrected DFT methods agree well with DMC, whereas the local (semilocal) functional significantly over (under)-binds. Furthermore, we fully optimized the H2-SiCNT geometry within the DFT framework and investigated the correlation between the structure and charge density. The vdW contribution to the adsorption was found to be non-negligible at ∼1 kcal/mol per hydrogen molecule, which amounts to 9-29% of the ideal adsorption energy required for hydrogen storage applications.
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Affiliation(s)
- Genki I. Prayogo
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Hyeondeok Shin
- Computational
Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Anouar Benali
- Computational
Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Ryo Maezono
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Kenta Hongo
- Research
Center for Advanced Computing Infrastructure, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
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2
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Jezierska A, Błaziak K, Klahm S, Lüchow A, Panek JJ. Non-Covalent Forces in Naphthazarin-Cooperativity or Competition in the Light of Theoretical Approaches. Int J Mol Sci 2021; 22:ijms22158033. [PMID: 34360798 PMCID: PMC8348774 DOI: 10.3390/ijms22158033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/27/2022] Open
Abstract
Non-covalent interactions responsible for molecular features and self-assembly in Naphthazarin C polymorph were investigated on the basis of diverse theoretical approaches: Density Functional Theory (DFT), Diffusion Quantum Monte Carlo (DQMC), Symmetry-Adapted Perturbation Theory (SAPT) and Car-Parrinello Molecular Dynamics (CPMD). The proton reaction paths in the intramolecular hydrogen bridges were studied. Two potential energy minima were found indicating that the proton transfer phenomena occur in the electronic ground state. Diffusion Quantum Monte Carlo (DQMC) and other levels of theory including Coupled Cluster (CC) employment enabled an accurate inspection of Potential Energy Surface (PES) and revealed the energy barrier for the proton transfer. The structure and reactivity evolution associated with the proton transfer were investigated using Harmonic Oscillator Model of Aromaticity - HOMA index, Fukui functions and Atoms In Molecules (AIM) theory. The energy partitioning in the studied dimers was carried out based on Symmetry-Adapted Perturbation Theory (SAPT) indicating that dispersive forces are dominant in the structure stabilization. The CPMD simulations were performed at 60 K and 300 K in vacuo and in the crystalline phase. The temperature influence on the bridged protons dynamics was studied and showed that the proton transfer phenomena were not observed at 60 K, but the frequent events were noticed at 300 K in both studied phases. The spectroscopic signatures derived from the CPMD were computed using Fourier transformation of autocorrelation function of atomic velocity for the whole molecule and bridged protons. The computed gas-phase IR spectra showed two regions with OH absorption that covers frequencies from 2500 cm−1 to 2800 cm−1 at 60 K and from 2350 cm−1 to 3250 cm−1 at 300 K for both bridged protons. In comparison, the solid state computed IR spectra revealed the environmental influence on the vibrational features. For each of them absorption regions were found between 2700–3100 cm−1 and 2400–2850 cm−1 at 60 K and 2300–3300 cm−1 and 2300–3200 cm−1 at 300 K respectively. Therefore, the CPMD study results indicated that there is a cooperation of intramolecular hydrogen bonds in Naphthazarin molecule.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
- Correspondence: (A.J.); (K.B.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
- Correspondence: (A.J.); (K.B.)
| | - Sebastian Klahm
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Arne Lüchow
- Institute of Physical Chemistry, RWTH Aachen University, 52056 Aachen, Germany; (S.K.); (A.L.)
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
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3
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Fanta R, Dubecký M. Noncovalent Interactions by the Quantum Monte Carlo Method: Strong Influence of Isotropic Jastrow Cutoff Radii. J Chem Theory Comput 2021; 17:4242-4249. [PMID: 34169721 DOI: 10.1021/acs.jctc.1c00467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a paradigmatic example of a strong effect of Jastrow cutoff radii setup on the accuracy of noncovalent interaction energy differences within one-determinant Slater-Jastrow fixed-node diffusion Monte Carlo (1FNDMC) simulations using isotropic Jastrow terms and effective-core potentials. Analysis of total energies, absolute and relative errors, and local energy variance of energy differences vs the reference results suggests a simple procedure to marginalize the related biases. The presented data showcase improvements in dispersion-bounded systems within such a 1FNDMC method.
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Affiliation(s)
- Roman Fanta
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic.,ATRI, Faculty of Materials Science and Technology in Trnava, Slovak University of Technology in Bratislava, J. Bottu 25, 917 24 Trnava, Slovakia
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4
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Qin KS, Ichibha T, Hongo K, Maezono R. Inconsistencies in ab initio evaluations of non-additive contributions of DNA stacking energies. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2019.110554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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5
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Dubecký M, Jurečka P, Mitas L, Ditte M, Fanta R. Toward Accurate Hydrogen Bonds by Scalable Quantum Monte Carlo. J Chem Theory Comput 2019; 15:3552-3557. [DOI: 10.1021/acs.jctc.9b00096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matúš Dubecký
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
- ATRI, Slovak University of Technology, Paulínska 16, 917 24 Trnava, Slovakia
| | - Petr Jurečka
- Department of Physical Chemistry, Palackỳ University Olomouc, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Matej Ditte
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
| | - Roman Fanta
- Department of Physics, University of Ostrava, 30. dubna 22, 701 03 Ostrava, Czech Republic
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6
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Morgante P, Peverati R. ACCDB: A collection of chemistry databases for broad computational purposes. J Comput Chem 2018; 40:839-848. [DOI: 10.1002/jcc.25761] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 11/11/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Pierpaolo Morgante
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
| | - Roberto Peverati
- Chemistry Program; Florida Institute of Technology, 150 W. University Blvd.; Melbourne Florida, 32901
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7
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Hongo K, Maezono R. A Computational Scheme To Evaluate Hamaker Constants of Molecules with Practical Size and Anisotropy. J Chem Theory Comput 2017; 13:5217-5230. [PMID: 28981266 DOI: 10.1021/acs.jctc.6b01159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We propose a computational scheme to evaluate Hamaker constants, A, of molecules with practical sizes and anisotropies. Upon the increasing feasibility of diffusion Monte Carlo (DMC) methods to evaluate binding curves for such molecules to extract the constants, we discussed how to treat the averaging over anisotropy and how to correct the bias due to the nonadditivity. We have developed a computational procedure for dealing with the anisotropy and reducing statistical errors and biases in DMC evaluations, based on possible validations on predicted A. We applied the scheme to cyclohexasilane molecule, Si6H12, used in "printed electronics" fabrications, getting A ≈ 105 ± 2 zJ, being in plausible range supported even by other possible extrapolations. The scheme provided here would open a way to use handy ab initio evaluations to predict wettabilities as in the form of materials informatics over broader molecules.
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Affiliation(s)
- Kenta Hongo
- Research Center for Advanced Computing Infrastructure, JAIST , Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan.,Center for Materials Research by Information Integration, Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science , Tsukuba 305-0047, Japan.,PRESTO, Japan Science and Technology Agency (JST) , Kawaguchi, Saitama 332-0012, Japan
| | - Ryo Maezono
- School of Information Science, JAIST , Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
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8
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9
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Azadi S, Cohen RE. Chemical accuracy from quantum Monte Carlo for the benzene dimer. J Chem Phys 2016; 143:104301. [PMID: 26374029 DOI: 10.1063/1.4930137] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.
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Affiliation(s)
- Sam Azadi
- Department of Earth Science and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - R E Cohen
- London Centre for Nanotechnology, University College London, London WC1E 6BT, United Kingdom and Extreme Materials Initiative, Geophysical Laboratory, Carnegie Institution of Washington, Washington, D.C. 20015, USA
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10
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Affiliation(s)
- Matúš Dubecký
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
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11
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Ullah Z, Ata-ur-Rahman, Fazl-i-Sattar, Rauf A, Yaseen M, Hassan W, Tariq M, Ayub K, Tahir AA, Ullah H. Density functional theory and phytochemical study of 8-hydroxyisodiospyrin. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.04.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Silkowski M, Lesiuk M, Moszynski R. Calculation of the molecular integrals with the range-separated correlation factor. J Chem Phys 2015; 142:124102. [DOI: 10.1063/1.4915272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Michał Silkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michał Lesiuk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Robert Moszynski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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13
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Hongo K, Watson MA, Iitaka T, Aspuru-Guzik A, Maezono R. Diffusion Monte Carlo Study of Para-Diiodobenzene Polymorphism Revisited. J Chem Theory Comput 2015; 11:907-17. [DOI: 10.1021/ct500401p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Kenta Hongo
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Mark A. Watson
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Toshiaki Iitaka
- Computational
Astrophysics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Alán Aspuru-Guzik
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ryo Maezono
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
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14
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Kocman M, Jurečka P, Dubecký M, Otyepka M, Cho Y, Kim KS. Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals. Phys Chem Chem Phys 2015; 17:6423-32. [DOI: 10.1039/c4cp04354e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Various dispersion-corrected density functionals are compared with high level QM data for several model complexes for adsorptive hydrogen storage.
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Affiliation(s)
- Mikuláš Kocman
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Matúš Dubecký
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Yeonchoo Cho
- Center for Superfunctional Materials
- Department of Chemistry and Department of Physics
- Pohang University of Science and Technology
- Pohang 790-784
- Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
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15
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Husch T, Yilmazer ND, Balducci A, Korth M. Large-scale virtual high-throughput screening for the identification of new battery electrolyte solvents: computing infrastructure and collective properties. Phys Chem Chem Phys 2015; 17:3394-401. [DOI: 10.1039/c4cp04338c] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A volunteer computing approach is presented for the purpose of screening a large number of molecular structures with respect to their suitability as new battery electrolyte solvents.
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Affiliation(s)
- Tamara Husch
- Institute for Theoretical Chemistry
- Ulm University
- 89069 Ulm
- Germany
| | | | | | - Martin Korth
- Institute for Theoretical Chemistry
- Ulm University
- 89069 Ulm
- Germany
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16
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Dubecký M, Derian R, Jurečka P, Mitas L, Hobza P, Otyepka M. Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy. Phys Chem Chem Phys 2014; 16:20915-23. [DOI: 10.1039/c4cp02093f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Gillan MJ, Alfè D, Bartók AP, Csányi G. First-principles energetics of water clusters and ice: A many-body analysis. J Chem Phys 2013; 139:244504. [DOI: 10.1063/1.4852182] [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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18
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Multi-level quantum monte Carlo wave functions for complex reactions: The decomposition of α-hydroxy-dimethylnitrosamine. J Comput Chem 2013; 35:30-8. [DOI: 10.1002/jcc.23461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/07/2013] [Accepted: 09/16/2013] [Indexed: 12/31/2022]
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19
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Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L. Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J Chem Theory Comput 2013; 9:4287-92. [DOI: 10.1021/ct4006739] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matúš Dubecký
- Regional Centre of Advanced
Technologies and Materials, Department of
Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced
Technologies and Materials, Department of
Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - René Derian
- Institute
of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 845
11 Bratislava, Slovakia
| | - Pavel Hobza
- Regional Centre of Advanced
Technologies and Materials, Department of
Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nám. 2, 166 10 Prague 6, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced
Technologies and Materials, Department of
Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
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20
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Waller MP, Dresselhaus T, Yang J. JACOB: an enterprise framework for computational chemistry. J Comput Chem 2013; 34:1420-8. [PMID: 23553271 PMCID: PMC3664405 DOI: 10.1002/jcc.23272] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/15/2013] [Accepted: 02/18/2013] [Indexed: 12/03/2022]
Abstract
Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: http://www.wallerlab.org/jacob. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Mark P Waller
- Theoretical Chemistry, Organic Chemistry Institute, Westfälische Wilhelms Universität Münster, Correnstrasse 40, Münster 48149, Germany.
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21
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Hongo K, Cuong NT, Maezono R. The Importance of Electron Correlation on Stacking Interaction of Adenine-Thymine Base-Pair Step in B-DNA: A Quantum Monte Carlo Study. J Chem Theory Comput 2013; 9:1081-6. [DOI: 10.1021/ct301065f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kenta Hongo
- School of Information Science,
JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Nguyen Thanh Cuong
- Nanosystem Research Institute
(NRI), National Institute of Advanced Industrial Science and Technology
(AIST), Tsukuba 305-8568, Japan
| | - Ryo Maezono
- School of Information Science,
JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
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22
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Gillan MJ, Manby FR, Towler MD, Alfè D. Assessing the accuracy of quantum Monte Carlo and density functional theory for energetics of small water clusters. J Chem Phys 2012; 136:244105. [DOI: 10.1063/1.4730035] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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23
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Hättig C, Klopper W, Köhn A, Tew DP. Explicitly Correlated Electrons in Molecules. Chem Rev 2011; 112:4-74. [DOI: 10.1021/cr200168z] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Wim Klopper
- Abteilung für Theoretische Chemie, Institut für Physikalische Chemie, Karlsruher Institut für Technologie, KIT-Campus Süd, Postfach 6980, D-76049 Karlsruhe, Germany
| | - Andreas Köhn
- Institut für Physikalische Chemie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - David P. Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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24
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Affiliation(s)
- Brian M. Austin
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - Dmitry Yu. Zubarev
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
| | - William A. Lester
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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25
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Kumbhar S, Fischer FD, Waller MP. Assessment of Weak Intermolecular Interactions Across QM/MM Noncovalent Boundaries. J Chem Inf Model 2011; 52:93-8. [DOI: 10.1021/ci200406s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sadhana Kumbhar
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
| | - Frank D. Fischer
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
| | - Mark P. Waller
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
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26
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Affiliation(s)
- Martin Korth
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Stefan Grimme
- Theoretical Organic Chemistry, Organic Chemistry Institute, Corrensstrasse 40, 48149 Münster, Germany
| | - Mike D. Towler
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 J.J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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Lüchow A. Quantum Monte Carlo methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.40] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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Abstract
Abstract
The diffusion quantum Monte Carlo method (DMC) is capable of calculating accurately the electronic energy for molecules and molecular aggregates. An overview is given on recent developments for the optimization of the guide function that determines the accuracy of the method. Furthermore, the versatility of DMC is shown with applications to Rydberg states, transition metal compounds, and weakly interacting systems.
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Mutter S, Platts J. Modulation of Stacking Interactions by Transition-Metal Coordination: Ab Initio Benchmark Studies. Chemistry 2010; 16:5391-9. [DOI: 10.1002/chem.200902813] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Paton RS, Goodman JM. Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions. J Chem Inf Model 2009; 49:944-55. [PMID: 19309094 DOI: 10.1021/ci900009f] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.
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Affiliation(s)
- Robert S Paton
- Department of Chemistry, Unilever Centre for Molecular Science Informatics, Lensfield Road, Cambridge CB2 1EW, U.K
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Ma J, Alfè D, Michaelides A, Wang E. The water-benzene interaction: Insight from electronic structure theories. J Chem Phys 2009; 130:154303. [DOI: 10.1063/1.3111035] [Citation(s) in RCA: 67] [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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Toutounji M. Empirical relaxation function and spectral density for underdamped vibrations at low temperatures. J Chem Phys 2009; 130:094501. [DOI: 10.1063/1.3085066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pillsbury NR, Zwier TS. Conformational Isomerization of 5-Phenyl-1-pentene Probed by SEP-Population Transfer Spectroscopy. J Phys Chem A 2008; 113:126-34. [PMID: 19067571 DOI: 10.1021/jp806699e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nathan R. Pillsbury
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907
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Santra B, Michaelides A, Fuchs M, Tkatchenko A, Filippi C, Scheffler M. On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters. II. The water hexamer and van der Waals interactions. J Chem Phys 2008; 129:194111. [DOI: 10.1063/1.3012573] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pitoňák M, Riley KE, Neogrády P, Hobza P. Highly Accurate CCSD(T) and DFT-SAPT Stabilization Energies of H-Bonded and Stacked Structures of the Uracil Dimer. Chemphyschem 2008; 9:1636-44. [DOI: 10.1002/cphc.200800286] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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Affiliation(s)
- Jirí Sponer
- Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic
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Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P. Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples. ACTA ACUST UNITED AC 2008. [DOI: 10.1135/cccc20081261] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Our previous benchmark CCSD(T)/ complete basis set limit calculations were collected into a database named begdb - Benchmark Energy and Geometry DataBase. Web-based interface to this database was prepared and is available at www.begdb.com. Users can browse, search and plot the data online or download structures and energy tables.
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