Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory

Lynch, Benjamin J.; Zhao, Yan; Truhlar, Donald G.

doi:10.1021/jp021590l

Cited by 718 publications

(677 citation statements)

References 38 publications

(73 reference statements)

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“…While PARI-K yields impressive accuracy in its own right, the accuracy of occ-RI-K is clearly superior. The errors per electron in the absolute energies of all molecules in the test set are quite 73,74 0.00 0.00 Butanediol65 75 0.00 0.00 BzDC215 76 0.00 0.00 CT20 77 0.00 0.00 DIE60 78 0.00 0.00 DS14 79 0.00 0.01 EA13 80 0.01 0.01 EIE22 81 0.00 0.00 FmH2O10 82,83 0.01 0.16 ACONF 84,85 0.00 0.01 BHPERI 85,86 0.00 0.00 CYCONF 85,87 0.00 0.00 G21EA 85,88 0.00 0.00 G21IP 85,88 0.00 0.00 NBPRC 85 0.00 0.02 WATER27 85,89 0.00 0.03 NHTBH38 85,90 0.01 0.02 HTBH38 85,91 0.00 0.01 BH76RC 85 0.00 0.00 DBH24 86 0.00 0.01 H2O6Bind8 83,92 0.00 0.05 HB15 93 0.00 0.01 HSG 94,95 0.00 0.00 HW30 96 0.00 0.01 HW6Cl 82,83 0.00 0.04 HW6F 82,83 0.00 0.04 IP13 80 0.00 0.00 NBC10 95 0.01 0.01 NC15 97 0.00 0.00 Pentane14 98 0.00 0.01 RG10 99 0.00 0.00 S22 …”

Section: A Accuracymentioning

confidence: 99%

Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm

Manzer

Horn

Mardirossian

et al. 2015

The Journal of Chemical Physics

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Construction of the exact exchange matrix, K, is typically the rate-determining step in hybrid density functional theory, and therefore, new approaches with increased efficiency are highly desirable. We present a framework with potential for greatly improved efficiency by computing a compressed exchange matrix that yields the exact exchange energy, gradient, and direct inversion of the iterative subspace (DIIS) error vector. The compressed exchange matrix is constructed with one index in the compact molecular orbital basis and the other index in the full atomic orbital basis. To illustrate the advantages, we present a practical algorithm that uses this framework in conjunction with the resolution of the identity (RI) approximation. We demonstrate that convergence using this method, referred to hereafter as occupied orbital RI-K (occ-RI-K), in combination with the DIIS algorithm is well-behaved, that the accuracy of computed energetics is excellent (identical to conventional RI-K), and that significant speedups can be obtained over existing integral-direct and RI-K methods. For a 4400 basis function C 68 H 22 hydrogen-terminated graphene fragment, our algorithm yields a 14× speedup over the conventional algorithm and a speedup of 3.3× over RI-K. C 2015 AIP Publishing LLC. [http://dx

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Section: A Accuracymentioning

confidence: 99%

Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm

Manzer

Horn

Mardirossian

et al. 2015

The Journal of Chemical Physics

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“…The HL calculations were carry out by means of the M06-2X functional 71 with the 6-31+G(d,p) basis set 72 following Truhlar and co-workers suggestions. 71,73 The 6-311+G(2df,2p) basis set 74,75 was also checked for the F system (mechanism I), since this is the one specifically recommended for this element. Test on the use of both basis sets rendered almost quantitatively equivalent results (see Figure S2 of Supporting Information) and consequently the 6-31+G(d,p) basis set was used for all calculations.…”

Section: Computational Modelmentioning

confidence: 99%

First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones

2015

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Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing an effective therapy against the disease. In this paper, the mechanism of inhibition of cruzain by two different irreversible peptidyl halomethyl ketones (PHK) inhibitors has been studied by means of hybrid quantum mechanics/molecular mechanics−molecular dynamics (MD) simulations to obtain a complete representation of the possible free energy reaction paths. These have been traced on free energy surfaces in terms of the potential of mean force computed at AM1d/MM and DFT/MM levels of theory. An analysis of the possible reaction mechanisms of the inhibition process has been performed showing that the nucleophilic attack of an active site cysteine, Cys25, on a carbon atom of the inhibitor and the cleavage of the halogen−carbon bond take place in a single step. PClK appears to be much more favorable than PFK from a kinetic point of view. This result would be in agreement with experimental studies in other papain-like enzymes. A deeper analysis of the results suggests that the origin of the differences between PClK and PFK can be the different stabilizing interactions established between the inhibitors and the residues of the active site of the protein. Any attempt to explore the viability of the inhibition process through a stepwise mechanism involving the formation of a thiohemiketal intermediate and a three-membered sulfonium intermediate has been unsuccessful. Nevertheless, a mechanism through a protonated thiohemiketal, with participation of His159 as a proton donor, appears to be feasible despite showing higher free energy barriers. Our results suggest that PClK can be used as a starting point to develop a proper inhibitor of cruzain.

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“…IV. For the calculations on those databases, we used the MG3S basis set 47 for main-group elements and the def2-TZVP basis set 48 for calculations that involve transition metals.…”

Section: B Software Basis Sets Relativistic Effectsmentioning

confidence: 99%

Performance of the M11-L density functional for bandgaps and lattice constants of unary and binary semiconductors

Peverati¹,

Truhlar²

2012

The Journal of Chemical Physics

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The recently developed SOGGA11 and M11-L density functionals have been tested for the prediction of bandgaps and lattice constants by comparing to databases containing 31 bandgaps and 34 lattice constants. To make a comparative assessment we also test several other density functionals against the same databases; in particular, we test the local spin density approximation, PBE, PBEsol, SOGGA, TPSS, revTPSS, and M06-L local density functionals and the HSE screened-exchange hybrid nonlocal density functional; and for a subset of 13 lattice constants we also compare the mean errors to those of the AM05 and WC local density functionals and the HISS and HSEsol nonlocal density functionals. The tests show that, of the ten functionals tested against all 65 data, the SOGGA, PBEsol, and HSE functionals are the most accurate for lattice constants, whereas the HSE, M11-L, and M06-L density functionals are the most accurate for bandgaps. However, the SOGGA11 density functional is the most accurate generalized gradient approximation for bandgaps.

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Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory

Cited by 718 publications

References 38 publications

Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm

Fast, accurate evaluation of exact exchange: The occ-RI-K algorithm

First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones

Performance of the M11-L density functional for bandgaps and lattice constants of unary and binary semiconductors

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