RI‐MP3 calculations of biomolecules based on the fragment molecular orbital method

Ishikawa, Takeshi; Sakakura, Kota; Mochizuki, Yuji

doi:10.1002/jcc.25368

Cited by 6 publications

(4 citation statements)

References 59 publications

(97 reference statements)

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“…The conventional MP3/def2-TZVPP turned out to be something of a bottleneck for the largest systems. This could obviously be mitigated with an RI-MP3 algorithm (e.g., such as reported in refs and ), but none was available to us. This prompted the question at what price the middle tier could be eliminated.…”

Section: Resultsmentioning

confidence: 99%

Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT?

Semidalas

Martin

2020

J. Chem. Theory Comput.

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The large and chemically diverse GMTKN55 benchmark was used as a training set for parametrizing composite wave function thermochemistry protocols akin to G4(MP2)XK theory Karton, A.; Raghavachari, K. J. Chem. Theory Comput. 2019, 15, 4478−4484). On account of their availability for elements H through Rn, Karlsruhe def2 basis sets were employed. Even after reparametrization, the GMTKN55 WTMAD2 (weighted mean absolute deviation, type 2) for G4(MP2)-XK is actually inferior to that of the best rung-4 DFT functional, ωB97M-V. By increasing the basis set for the MP2 part to def2-QZVPPD, we were able to substantially improve performance at modest cost (if an RI-MP2 approximation is made), with WTMAD2 for this G4(MP2)-XK-D method now comparable to the better rung-5 functionals (albeit at greater cost). A three-tier approach with a scaled MP3/def2-TZVPP intermediate step, however, leads to a G4(MP3)-D method that is markedly superior to even the best double hybrids ωB97M(2) and revDSD-PBEP86-D4. Evaluating the CCSD(T) component with a triple-ζ, rather than split-valence, basis set yields only a modest further improvement that is incommensurate with the drastic increase in computational cost. G4(MP3)-D and G4(MP2)-XK-D have about 40% better WTMAD2, at similar or lower computational cost, than their counterparts G4 and G4(MP2), respectively: detailed comparison reveals that the difference lies in larger molecules due to basis set incompleteness error. An E2/ {T,Q} extrapolation and a CCSD(T)/def2-TZVP step provided the G4-T method of high accuracy and with just three fitted parameters. Using KS orbitals in MP2 leads to the G4(MP3|KS)-D method, which entirely eliminates the CCSD(T) step and has no steps costlier than scaled MP3; this shows a path forward to further improvements in double-hybrid density functional methods. None of our final selections require an empirical HLC correction; this cuts the number of empirical parameters in half and avoids discontinuities on potential energy surfaces. G4-T-DLPNO, a variant in which post-MP2 corrections are evaluated at the DLPNO-CCSD(T) level, achieves nearly the accuracy of G4-T but is applicable to much larger systems.

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Section: Resultsmentioning

confidence: 99%

Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT?

Semidalas

Martin

2020

J. Chem. Theory Comput.

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“…Particularly when using range-separated hybrid GGA orbitals, we achieved a significant improvement in WTMAD2. Especially in conjunction with RI-MP3 or with further acceleration techniques like fragment molecular orbital-based FMO-RI-MP3 79 or the chain-of-spheres approximation for SCS-MP3 as implemented by Izsák and Neese, 80 this approach could potentially be very useful. Head-Gordon and co-workers have very recently shown 81 that the use of DFT orbitals for regular MP3 level calculation results significantly improved performance for thermochemistry, barrier heights, noncovalent interactions, and dipole moments compared to the conventional HF-based MP3.…”

Section: Discussionmentioning

confidence: 99%

Exploring Avenues beyond Revised DSD Functionals: II. Random-Phase Approximation and Scaled MP3 Corrections

2021

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For revDSD double hybrids, the Görling–Levy second-order perturbation theory component is an Achilles’ heel when applied to systems with significant near-degeneracy (“static”) correlation. We have explored its replacement by the direct random phase approximation (dRPA), inspired by the SCS-dRPA75 functional of Kállay and co-workers. The addition to the final energy of both a D4 empirical dispersion correction and of a semilocal correlation component lead to significant improvements, with DSD-PBEdRPA 75 -D4 approaching the performance of revDSD-PBEP86-D4 and the Berkeley ωB97M(2). This form appears to be fairly insensitive to the choice of the semilocal functional but does exhibit stronger basis set sensitivity than the PT2-based double hybrids (due to much larger prefactors for the nonlocal correlation). As an alternative, we explored adding an MP3-like correction term (in a medium-sized basis set) to a range-separated ωDSD-PBEP86-D4 double hybrid and found it to have significantly lower WTMAD2 (weighted mean absolute deviation) for the large and chemically diverse GMTKN55 benchmark suite; the added computational cost can be mitigated through density fitting techniques.

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“…27 and 34 )) was implemented with an integral-direct parallelism in ABINIT-MP; 22 MP3 has been recently available also in another FMO program PAICS. 35 Furthermore, ABINIT-MP supports several higher-order treatments 24 up to the coupled cluster singles and double with perturbative triples (CCSD(T)). 27,34 In our demonstrative applications, 36,37 the scaling modification 38 was utilized to estimate the interaction energies at the CCSD(T) level, where the incremental correlation energies of MP3 and fourth-order MP with singles, doubles, and quadruples (MP4(SDQ)) 23 were halved and added to the MP2 energy, termed MP2.5 (ref.…”

Section: Methodsmentioning

confidence: 99%

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

et al. 2021

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RI‐MP3 calculations of biomolecules based on the fragment molecular orbital method

Cited by 6 publications

References 59 publications

Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT?

Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT?

Exploring Avenues beyond Revised DSD Functionals: II. Random-Phase Approximation and Scaled MP3 Corrections

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

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