1
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Herman KM, Xantheas SS. An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2-25. Phys Chem Chem Phys 2023; 25:7120-7143. [PMID: 36853239 DOI: 10.1039/d2cp03241d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2-11, 16-17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (De's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2-25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83-119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (De's) throughout the entire cluster range (n = 2-25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ∼4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6-3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.
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Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA. .,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, WA, 99352, USA.
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2
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Kolesár V, Dubecký M. Accuracy of Noncovalent Interactions Involving d-Elements by the 1-Determinant Fixed-Node Diffusion Monte Carlo Method with Effective Core Potentials. J Chem Theory Comput 2023; 19:1170-1176. [PMID: 36751996 DOI: 10.1021/acs.jctc.2c00872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
A critical assessment of effective core potential (ECP)-based single-determinant (SD) fixed-node diffusion quantum Monte Carlo (FNDMC) accuracy in prototypical noncovalent closed-shell systems involving d-elements is presented. Careful analysis of biases and elimination of possible bias sources leads to two findings of practical importance for SD FNDMC in these systems. First, in some systems (HCu:HCu, HCu:CuH), SD FNDMC reveals large biases of interaction energy differences (significantly exceeding the target 2% relative error) vs a reliable coupled-cluster CCSD(T)/CBS (complete basis set) reference. Second, the leading error of SD FNDMC with ECPs was attributed to a higher nuclear charge Z of d-group (pseudo) atoms, when compared to sp elements, in line with a previously reported finding that aggregate SD FNDMC bias tends to increase in systems with higher electronic densities. Therefore, SD FNDMC should only be used with caution in systems with a large Z.
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Affiliation(s)
- Vladimír Kolesár
- 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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3
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Gittus OR, Bresme F. Thermophysical properties of water using reactive force fields. J Chem Phys 2021; 155:114501. [PMID: 34551553 DOI: 10.1063/5.0057868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The widescale importance and rich phenomenology of water continue to motivate the development of computational models. ReaxFF force fields incorporate many characteristics desirable for modeling aqueous systems: molecular flexibility, polarization, and chemical reactivity (bond formation and breaking). However, their ability to model the general properties of water has not been evaluated in detail. We present comprehensive benchmarks of the thermophysical properties of water for two ReaxFF models, the water-2017 and CHON-2017_weak force fields. These include structural, electrostatic, vibrational, thermodynamic, coexistence, and transport properties at ambient conditions (300 K and 0.997 g cm-3) and along the standard pressure (1 bar) isobar. Overall, CHON-2017_weak predicts more accurate thermophysical properties than the water-2017 force field. Based on our results, we recommend potential avenues for improvement: the dipole moment to quadrupole moment ratio, the self-diffusion coefficient, especially for water-2017, and the gas phase vibrational frequencies with the aim to improve the vibrational properties of liquid water.
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Affiliation(s)
- Oliver R Gittus
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
| | - Fernando Bresme
- Department of Chemistry, Molecular Sciences Research Hub Imperial College, London W12 0BZ, United Kingdom
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4
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Yang DC, Kim DY, Kim KS. Quantum Monte Carlo Study of the Water Dimer Binding Energy and Halogen-π Interactions. J Phys Chem A 2019; 123:7785-7791. [PMID: 31418568 DOI: 10.1021/acs.jpca.9b04072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Halogen-π systems are involved with competition between halogen bonding and π-interaction. Using the diffusion quantum Monte Carlo (DMC) method, we compare the interaction of benzene with diatomic halogens (X2: Cl2/Br2) with the typical hydrogen bonding in the water dimer, taking into account explicit correlations of up to three bodies. The benzene-Cl2/Br2 binding energies (13.07 ± 0.42/16.62 ± 0.02 kJ/mol) attributed to both halogen bonding and dispersion are smaller than but comparable to the typical hydrogen bonding in the water dimer binding energy (20.88 ± 0.27 kJ/mol). All of the above values are in good agreement with those from the coupled-cluster with single, double, and noniterative triple excitations (CCSD(T)) results at the complete basis set limit (benzene-Cl2/Br2: 12.78/16.17 kJ/mol; water dimer: 21.0 kJ/mol).
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Affiliation(s)
- D ChangMo Yang
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
| | - Dong Yeon Kim
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
| | - Kwang S Kim
- Center for Superfunctional Materials, Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , Republic of Korea
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5
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Wang T, Zhou X, Wang F. Performance of the Diffusion Quantum Monte Carlo Method with a Single-Slater-Jastrow Trial Wavefunction Using Natural Orbitals and Density Functional Theory Orbitals on Atomization Energies of the Gaussian-2 Set. J Phys Chem A 2019; 123:3809-3817. [DOI: 10.1021/acs.jpca.9b01933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ting Wang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, P. R. China
| | - Xiaojun Zhou
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, P. R. China
| | - Fan Wang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu 610065, P. R. China
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6
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Ospadov E, Rothstein SM, Baer R. Quantum Monte Carlo assessment of density functionals for π-electron molecules: ethylene and bifuran. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1517905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Egor Ospadov
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | | | - Roi Baer
- Fritz Haber Center for Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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7
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Schmidt M, Roy PN. Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer. J Chem Phys 2018; 148:124116. [DOI: 10.1063/1.5017532] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matthew Schmidt
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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8
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Yang X, Rees RJ, Conway W, Puxty G, Yang Q, Winkler DA. Computational Modeling and Simulation of CO2 Capture by Aqueous Amines. Chem Rev 2017; 117:9524-9593. [PMID: 28517929 DOI: 10.1021/acs.chemrev.6b00662] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- College
of Chemistry, Key Lab of Green Chemistry and Technology in Ministry
of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Robert J. Rees
- Data61
- CSIRO, Door 34 Goods
Shed, Village Street, Docklands VIC 3008, Australia
| | | | | | - Qi Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
| | - David A. Winkler
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- Monash Institute of Pharmaceutical Sciences, 392 Royal Parade, Parkville 3052, Australia
- Latrobe Institute for Molecular Science, Bundoora 3046, Australia
- School
of
Chemical and Physical Science, Flinders University, Bedford Park 5042, Australia
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9
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Mouhat F, Sorella S, Vuilleumier R, Saitta AM, Casula M. Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics. J Chem Theory Comput 2017; 13:2400-2417. [DOI: 10.1021/acs.jctc.7b00017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Félix Mouhat
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Sandro Sorella
- International
School for Advanced Studies (SISSA), Via Bonomea 26, 34136 Trieste, Italy
- INFM Democritos
National Simulation Center, 34151 Trieste, Italy
| | - Rodolphe Vuilleumier
- PASTEUR,
Département de chimie, École normale supérieure,
UPMC Univ Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, École normale supérieure, CNRS, Processus d’activation
sélective par transfert d’énergie uni-électronique
ou radiatif (PASTEUR), 75005 Paris, France
| | - Antonino Marco Saitta
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
| | - Michele Casula
- IMPMC, Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS UMR 7590, IRD UMR 206, MNHN, 4 place Jussieu, 75252 Paris, France
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10
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Barborini M, Guidoni L. Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo. J Chem Phys 2016; 145:124107. [DOI: 10.1063/1.4963015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Matteo Barborini
- Dipartimento di Ingegneria, Scienze dell’Informazione e Matematica, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli studi dell’Aquila, Via Vetoio 2, 67100 Coppito, L’Aquila, Italy
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11
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Azadi S, Cohen RE. Low-pressure phase diagram of crystalline benzene from quantum Monte Carlo. J Chem Phys 2016. [DOI: 10.1063/1.4960434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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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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13
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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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14
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Localized Polycentric Orbital Basis Set for Quantum Monte Carlo Calculations Derived from the Decomposition of Kohn-Sham Optimized Orbitals. COMPUTATION 2016. [DOI: 10.3390/computation4010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Sorella S, Devaux N, Dagrada M, Mazzola G, Casula M. Geminal embedding scheme for optimal atomic basis set construction in correlated calculations. J Chem Phys 2015; 143:244112. [DOI: 10.1063/1.4938089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S. Sorella
- International School for Advanced Studies (SISSA), Via Beirut 2-4, 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste, Italy
| | - N. Devaux
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - M. Dagrada
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - G. Mazzola
- Theoretische Physik, ETH Zurich, 8093 Zurich, Switzerland
| | - M. Casula
- CNRS and Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05, France
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16
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Rees RJ, Spencer MJ. The science and life of Ian K. Snook. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2016.1091560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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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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18
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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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19
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Dagrada M, Casula M, Saitta AM, Sorella S, Mauri F. Quantum Monte Carlo Study of the Protonated Water Dimer. J Chem Theory Comput 2014; 10:1980-93. [DOI: 10.1021/ct401077x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Dagrada
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Michele Casula
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Antonino M. Saitta
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
| | - Sandro Sorella
- International School for Advanced Studies (SISSA) Via Beirut 2,4 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste, Italy
| | - Francesco Mauri
- Institut
de Minéralogie, de Physique des Matériaux, et de Cosmochimie
(IMPMC), Sorbonne Universités - UPMC Paris 06, UMR CNRS 7590, Muséum
National d’Histoire Naturelle, IRD UMR 206, 4 Place Jussieu, 75005 Paris, France
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20
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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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21
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Affiliation(s)
- Branko Ruscic
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States, and Computation Institute, University of Chicago, Chicago, Illinois 60637, United
States
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22
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Goto H, Kojo M, Sasaki A, Hirose K. Essentially exact ground-state calculations by superpositions of nonorthogonal Slater determinants. NANOSCALE RESEARCH LETTERS 2013; 8:200. [PMID: 23634829 PMCID: PMC3847990 DOI: 10.1186/1556-276x-8-200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/15/2013] [Indexed: 06/02/2023]
Abstract
An essentially exact ground-state calculation algorithm for few-electron systems based on superposition of nonorthogonal Slater determinants (SDs) is described, and its convergence properties to ground states are examined. A linear combination of SDs is adopted as many-electron wave functions, and all one-electron wave functions are updated by employing linearly independent multiple correction vectors on the basis of the variational principle. The improvement of the convergence performance to the ground state given by the multi-direction search is shown through comparisons with the conventional steepest descent method. The accuracy and applicability of the proposed scheme are also demonstrated by calculations of the potential energy curves of few-electron molecular systems, compared with the conventional quantum chemistry calculation techniques.
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Affiliation(s)
- Hidekazu Goto
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Kojo
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akira Sasaki
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kikuji Hirose
- Department of Precision Science and Technology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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Xu J, Deible MJ, Peterson KA, Jordan KD. Correlation Consistent Gaussian Basis Sets for H, B–Ne with Dirac–Fock AREP Pseudopotentials: Applications in Quantum Monte Carlo Calculations. J Chem Theory Comput 2013; 9:2170-8. [DOI: 10.1021/ct300983b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jiawei Xu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
| | - Michael J. Deible
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
| | - Kirk A. Peterson
- Department
of Chemistry, Washington State University, Pullman, Washington 99164,
United States
| | - Kenneth D. Jordan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15218, United States
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24
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Per MC, Walker KA, Russo SP. How Important is Orbital Choice in Single-Determinant Diffusion Quantum Monte Carlo Calculations? J Chem Theory Comput 2012; 8:2255-9. [DOI: 10.1021/ct200828s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Manolo C. Per
- Virtual
Nanoscience
Laboratory, CSIRO Materials Science and Engineering, Parkville, VIC 3052, Australia
- Applied Physics,
School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - Kelly A. Walker
- Applied Physics,
School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - Salvy P. Russo
- Applied Physics,
School of Applied Sciences, RMIT University, Melbourne 3001, Australia
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25
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Barborini M, Sorella S, Guidoni L. Structural Optimization by Quantum Monte Carlo: Investigating the Low-Lying Excited States of Ethylene. J Chem Theory Comput 2012; 8:1260-1269. [PMID: 24634617 PMCID: PMC3952241 DOI: 10.1021/ct200724q] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present full structural optimizations of the ground state and of the low lying triplet state of the ethylene molecule by means of Quantum Monte Carlo methods. Using the efficient structural optimization method based on renormalization techniques and on adjoint differentiation algorithms recently proposed [Sorella, S.; Capriotti, L. J. Chem. Phys.2010, 133, 234111], we present the variational convergence of both wave function parameters and atomic positions. All of the calculations were done using an accurate and compact wave function based on Pauling's resonating valence bond representation: the Jastrow Antisymmetrized Geminal Power (JAGP). All structural and wave function parameters are optimized, including coefficients and exponents of the Gaussian primitives of the AGP and the Jastrow atomic orbitals. Bond lengths and bond angles are calculated with a statistical error of about 0.1% and are in good agreement with the available experimental data. The Variational and Diffusion Monte Carlo calculations estimate vertical and adiabatic excitation energies in the ranges 4.623(10)-4.688(5) eV and 3.001(5)-3.091(5) eV, respectively. The adiabatic gap, which is in line with other correlated quantum chemistry methods, is slightly higher than the value estimated by recent photodissociation experiments. Our results demonstrate how Quantum Monte Carlo calculations have become a promising and computationally affordable tool for the structural optimization of correlated molecular systems.
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Affiliation(s)
- Matteo Barborini
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli studi dell’Aquila, Località Campo di Pile, 67100 L’Aquila, Italy
| | - Sandro Sorella
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) and Democritos National Simulation Center, Istituto Officina dei Materiali del CNR, via Bonomea 265, 34136 Trieste, Italy
| | - Leonardo Guidoni
- Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli studi dell’Aquila, Località Campo di Pile, 67100 L’Aquila, Italy
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26
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Clark BK, Morales MA, McMinis J, Kim J, Scuseria GE. Computing the energy of a water molecule using multideterminants: A simple, efficient algorithm. J Chem Phys 2011; 135:244105. [DOI: 10.1063/1.3665391] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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27
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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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28
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Steele RP, Tully JC. A tiered approach to Monte Carlo sampling with self-consistent field potentials. J Chem Phys 2011; 135:184107. [DOI: 10.1063/1.3660224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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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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30
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Krieg H, Grimme S. Thermochemical benchmarking of hydrocarbon bond separation reaction energies: Jacob's ladder is not reversed! Mol Phys 2010. [DOI: 10.1080/00268976.2010.519729] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Helge Krieg
- a Organisch-Chemisches Institut, Westfälische-Wilhelms-Universität Münster , D-48149 , Münster , Germany
| | - Stefan Grimme
- a Organisch-Chemisches Institut, Westfälische-Wilhelms-Universität Münster , D-48149 , Münster , Germany
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31
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Wu X, Hu X, Dai Y, Du C, Chu S, Hu L, Deng J, Feng Y. Quantum Monte Carlo calculated potential energy curve for the helium dimer. J Chem Phys 2010; 132:204304. [DOI: 10.1063/1.3432250] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Xu J, Jordan KD. Application of the Diffusion Monte Carlo Method to the Binding of Excess Electrons to Water Clusters. J Phys Chem A 2009; 114:1364-6. [DOI: 10.1021/jp9066108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- J. Xu
- Department of Chemistry and Center for Molecule and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - K. D. Jordan
- Department of Chemistry and Center for Molecule and Materials Simulations, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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33
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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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34
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Sterpone F, Spanu L, Ferraro L, Sorella S, Guidoni L. Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach. J Chem Theory Comput 2008; 4:1428-34. [DOI: 10.1021/ct800121e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabio Sterpone
- CASPUR, Via dei Tizii 6B, 00185, Roma, Italy, International School for Advanced Studied (SISSA/ISAS), Via Beirut 4, 34014 Trieste, Italy, Dipartimento di Fisica, La Sapienza - Universita di Roma, P.le A. Moro 2, 00185 Roma, Italy, and NAST Centre - Nanoscience & Nanotechnology & Instrumentation, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - Leonardo Spanu
- CASPUR, Via dei Tizii 6B, 00185, Roma, Italy, International School for Advanced Studied (SISSA/ISAS), Via Beirut 4, 34014 Trieste, Italy, Dipartimento di Fisica, La Sapienza - Universita di Roma, P.le A. Moro 2, 00185 Roma, Italy, and NAST Centre - Nanoscience & Nanotechnology & Instrumentation, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - Luca Ferraro
- CASPUR, Via dei Tizii 6B, 00185, Roma, Italy, International School for Advanced Studied (SISSA/ISAS), Via Beirut 4, 34014 Trieste, Italy, Dipartimento di Fisica, La Sapienza - Universita di Roma, P.le A. Moro 2, 00185 Roma, Italy, and NAST Centre - Nanoscience & Nanotechnology & Instrumentation, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - Sandro Sorella
- CASPUR, Via dei Tizii 6B, 00185, Roma, Italy, International School for Advanced Studied (SISSA/ISAS), Via Beirut 4, 34014 Trieste, Italy, Dipartimento di Fisica, La Sapienza - Universita di Roma, P.le A. Moro 2, 00185 Roma, Italy, and NAST Centre - Nanoscience & Nanotechnology & Instrumentation, Università degli Studi di Roma Tor Vergata, Roma, Italy
| | - Leonardo Guidoni
- CASPUR, Via dei Tizii 6B, 00185, Roma, Italy, International School for Advanced Studied (SISSA/ISAS), Via Beirut 4, 34014 Trieste, Italy, Dipartimento di Fisica, La Sapienza - Universita di Roma, P.le A. Moro 2, 00185 Roma, Italy, and NAST Centre - Nanoscience & Nanotechnology & Instrumentation, Università degli Studi di Roma Tor Vergata, Roma, Italy
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35
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Korth M, Lüchow A, Grimme S. Toward the exact solution of the electronic Schrödinger equation for noncovalent molecular interactions: worldwide distributed quantum monte carlo calculations. J Phys Chem A 2008; 112:2104-9. [PMID: 18201073 DOI: 10.1021/jp077592t] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum Monte Carlo (QMC) calculations on the stacked (st) and Watson/Crick (wc) bound adenine/thymine (A/T) and cytosine/guanine (C/G) DNA base pair complexes were made possible with the first large scale distributed computing project in ab initio quantum chemistry, Quantum Monte Carlo at Home (QMC@HOME). The results for the interaction energies (wc-A/T = 15.7 kcal/mol, wc-C/G = 30.2 kcal/mol, st-A/T = 13.1 kcal/mol, st-C/G = 19.6 kcal/mol) are in very good agreement with the best known coupled-cluster based estimates. The accuracy of these values is further supported by calculations on the S22 benchmark set of noncovalently bound systems, for which we obtain a small mean absolute deviation of 0.68 kcal/mol. Our results support previous claims that the stacking energies are of comparable magnitude to the interactions of the commonly discussed hydrogen-bonded motif. Furthermore, we show that QMC can serve as an advantageous alternative to conventional wave function methods for large noncovalently bound systems. We also investigated in detail all technical parameters of the QMC simulations and recommend a careful optimization procedure of the Jastrow correlation factors in order to obtain numerically stable and reliable results.
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Affiliation(s)
- Martin Korth
- Organisch-Chemisches Institut, Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
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36
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Gurtubay IG, Needs RJ. Dissociation energy of the water dimer from quantum Monte Carlo calculations. J Chem Phys 2007; 127:124306. [PMID: 17902902 DOI: 10.1063/1.2770711] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a study of the electronic dissociation energy of the water dimer using quantum Monte Carlo techniques. We have performed variational quantum Monte Carlo and diffusion quantum Monte Carlo (DMC) calculations of the electronic ground state of the water monomer and dimer using all-electron and pseudopotential approaches. We have used Slater-Jastrow trial wave functions with B3LYP type single-particle orbitals, into which we have incorporated backflow correlations. When backflow correlations are introduced, the total energy of the water monomer decreases by about 4-5 mhartree, yielding a DMC energy of -76.428 30(5) hartree, which is only 10 mhartree above the experimental value. In our pseudopotential DMC calculations, we have compared the total energies of the water monomer and dimer obtained using the locality approximation with those from the variational scheme recently proposed by Casula [Phys. Rev. B 74, 161102(R) (2006)]. The time step errors in the Casula scheme are larger, and the extrapolation of the energy to zero time step always lies above the result obtained with the locality approximation. However, the errors cancel when energy differences are taken, yielding electronic dissociation energies within error bars of each other. The dissociation energies obtained in our various all-electron and pseudopotential calculations range between 5.03(7) and 5.47(9) kcalmol and are in good agreement with experiment. Our calculations give monomer dipole moments which range between 1.897(2) and 1.909(4) D and dimer dipole moments which range between 2.628(6) and 2.672(5) D.
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Affiliation(s)
- I G Gurtubay
- Theory of Condensed Matter Group, Cavendish Laboratory, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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37
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Tan C, Song H, Niemi J, You L. A synthetic biology challenge: making cells compute. MOLECULAR BIOSYSTEMS 2007; 3:343-53. [PMID: 17460793 DOI: 10.1039/b618473c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Advances in biology and engineering have enabled the reprogramming of cells with well-defined functions, leading to the emergence of synthetic biology. Early successes in this nascent field suggest its potential to impact diverse areas. Here, we examine the feasibility of engineering circuits for cell-based computation. We illustrate the basic concepts by describing the mapping of several computational problems to engineered gene circuits. Revolving around these examples and past studies, we discuss technologies and computational methods available to design, test, and optimize gene circuits. We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation.
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Affiliation(s)
- Cheemeng Tan
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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38
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Livshits E, Baer R. A well-tempered density functional theory of electrons in molecules. Phys Chem Chem Phys 2007; 9:2932-41. [PMID: 17551616 DOI: 10.1039/b617919c] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This Invited Article reports extensions of a recently developed approach to density functional theory with correct long-range behavior (R. Baer and D. Neuhauser, Phys. Rev. Lett., 2005, 94, 043002). The central quantities are a splitting functional gamma[n] and a complementary exchange-correlation functional E[n]. We give a practical method for determining the value of gamma in molecules, assuming an approximation for E is given. The resulting theory shows good ability to reproduce the ionization potentials for various molecules. However it is not of sufficient accuracy for forming a satisfactory framework for studying molecular properties. A somewhat different approach is then adopted, which depends on a density-independent gamma and an additional parameter w eliminating part of the local exchange functional. The values of these two parameters are obtained by best-fitting to experimental atomization energies and bond lengths of the molecules in the G2(1) database. The optimized values are gamma = 0.5 a and w = 0.1. We then examine the performance of this slightly semi-empirical functional for a variety of molecular properties, comparing to related works and experiment. We show that this approach can be used for describing in a satisfactory manner a broad range of molecular properties, be they static or dynamic. Most satisfactory is the ability to describe valence, Rydberg and inter-molecular charge-transfer excitations.
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Affiliation(s)
- Ester Livshits
- Department of Physical Chemistry and the Fritz Haber Center for Molecular Dynamics, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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39
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Grimme S, Antony J, Schwabe T, Mück-Lichtenfeld C. Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules. Org Biomol Chem 2007; 5:741-58. [PMID: 17315059 DOI: 10.1039/b615319b] [Citation(s) in RCA: 519] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Kohn-Sham density functional theory (KS-DFT) is nowadays the most widely used quantum chemical method for electronic structure calculations in chemistry and physics. Its further application in e.g. supramolecular chemistry or biochemistry has mainly been hampered by the inability of almost all current density functionals to describe the ubiquitous attractive long-range van der Waals (dispersion) interactions. We review here methods to overcome this defect, and describe in detail a very successful correction that is based on damped -C(6).R(-6) potentials (DFT-D). As examples we consider the non-covalent inter- and intra-molecular interactions in unsaturated organic molecules (so-called pi-pi stacking in benzenes and dyes), in biologically relevant systems (nucleic acid bases/pairs, proteins, and 'folding' models), between fluorinated molecules, between curved aromatics (corannulene and carbon nanotubes) and small molecules, and for the encapsulation of methane in water clusters. In selected cases we partition the interaction energies into the most relevant contributions from exchange-repulsion, electrostatics, and dispersion in order to provide qualitative insight into the binding character.
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Affiliation(s)
- Stefan Grimme
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany.
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