The performance of a family of density functional methods

Johnson, Benny G.; Gill, Peter M. W.; Pople, John A.

doi:10.1063/1.464906

Cited by 1,862 publications

(984 citation statements)

References 43 publications

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“…In eq 13, W xc X arises from the derivative of the grid weights of E xc X [ρ X ]. 44 The reader is referred to ref 44 for more details about the derivative of grid weights. The internal fragment Fock matrix element is…”

Section: Analytic Gradient For Fmo−dftmentioning

confidence: 99%

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Brorsen

Zahariev

Nakata

et al. 2014

J. Chem. Theory Comput.

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The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO-DFT gradient, which lacks response terms, the FMO-DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO-DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn-Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO-DFT is a nonvariational method and the FMO-DFT gradient is unique compared to standard DFT gradients in that the FMO-DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories. Disciplines Chemistry CommentsReprinted ( ABSTRACT: The equations for the response terms for the fragment molecular orbital (FMO) method interfaced with the density functional theory (DFT) gradient are derived and implemented. Compared to the previous FMO−DFT gradient, which lacks response terms, the FMO−DFT analytic gradient has improved accuracy for a variety of functionals, when compared to numerical gradients. The FMO−DFT gradient agrees with the fully ab initio DFT gradient in which no fragmentation is performed, while reducing the nonlinear scaling associated with standard DFT. Solving for the response terms requires the solution of the coupled perturbed Kohn− Sham (CPKS) equations, where the CPKS equations are solved through a decoupled Z-vector procedure called the self-consistent Z-vector method. FMO−DFT is a nonvariational method and the FMO−DFT gradient is unique compared to standard DFT gradients in that the FMO−DFT gradient requires terms from both DFT and time-dependent density functional theory (TDDFT) theories.

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Section: Analytic Gradient For Fmo−dftmentioning

confidence: 99%

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Brorsen

Zahariev

Nakata

et al. 2014

J. Chem. Theory Comput.

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“…17,20 Vibrational frequencies are calculated by numerical differentiation (single differencing) of analytical gradients for optimized geometries and are based on the harmonic approximation. The capability to calculate ECP analytic second derivatives does not yet exist in GAMESS, although previous studies suggest that the differences between analytic and numerical differentiation 3,4 are well within the experimental uncertainties of vibrational frequencies of most TM complexes. Frequencies derived by ECP-based computations are compared with experimental values in three different ways: (1) raw (i.e., calculated using the harmonic approximation), (2) scaled, and (3) by means of a linear, least-squares correction.…”

Section: Methodsmentioning

confidence: 99%

“…[1][2][3][4][5][6][7] The majority of this work has focused on organic compounds, with much less attention given to transition metal (TM) complexes. [8][9][10][11] Frenking and co-workers 8 studied a small group of oxo and nitrido complexes, as well as OsO 4-x F 2x (x ) 0-4) using Hartree-Fock methods.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Estimation of Vibrational Frequencies Involving Transition Metal Compounds

Cundari

Raby

1997

J. Phys. Chem. A

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The reliability of effective core potentials (ECPs) for estimating vibrational frequencies of transition metal (TM) complexes is assessed in relation to all-electron methods for main group compounds. Complexes with a multiple bond between a transition metal and chalcogen (O, S, or Se), chalcogenides, are investigated using the Stevens ECP/valence basis set scheme. Statistical treatment of the data indicates that ECPs, in addition to reliably modeling electronic structure, can be successful in estimating vibrational frequencies for TM complexes. As expected, theoretical prediction of vibrational data is not as accurate as the prediction of metric data for chalcogenides. However, agreement with experiment is still very good at the Hartree-Fock level of theory and is in even better accord upon the use of simple corrections to model well-known computational deficiencies (e.g., the neglect of anharmonic effects). Analysis of the data show interesting differences in predictive ability for first row transition metals versus second-and third-row analogues and oxo complexes versus their congeners with heavier chalcogens.

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“…Regions with high densities of hydrogen bond sites (Danziger & Dean, 1989a, 1989b and with favorable electrostatic properties (Goodford, 1985) have been used to optimize chemical complementarity as well as to search selected surfaces for possible binding sites. Quantum chemical and statistical mechanical studies using the algorithmic tools of molecular dynamics simulations ( Brooks et al, 1988), semi-empirical methods (Rullmann & van Duijen, 1990), and density functional methods (Bethe, 1993;Johnson et al, 1993) have also been applied within the framework of theoretical chemistry to understand better the essential characteristics of molecular associations (Janin & Chothia, 1990).…”

mentioning

confidence: 99%

A role for surface hydrophobicity in protein‐protein recognition

1994

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The role of hydrophobicity as a determinant of protein-protein interactions is examined. Surfaces of apo-protein targets comprising 9 classes of enzymes, 7 antibody fragments, hirudin, growth hormone, and retinol-binding protein, and their associated ligands with available X-ray structures for their complexed forms, are scanned to determine clusters of surface-accessible amino acids. Clusters of surface residues are ranked on the basis of the hydrophobicity of their constituent amino acids. The results indicate that the location of the co-crystallized ligand is commonly found to correspond with one of the strongest hydrophobic clusters on the surface of the target molecule. In 25 of 38 cases, the correspondence is exact, with the position of the most hydrophobic cluster coinciding with more than one-third of the surface buried by the bound ligand. The remaining 13 cases demonstrate this correspondence within the top 6 hydrophobic clusters. These results suggest that surface hydrophobicity can be used to identify regions of a protein's surface most likely to interact with a binding ligand. This fast and simple procedure may be useful for identifying small sets of well-defined loci for possible ligand attachment.

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The performance of a family of density functional methods

Cited by 1,862 publications

References 43 publications

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Analytic Gradient for Density Functional Theory Based on the Fragment Molecular Orbital Method

Theoretical Estimation of Vibrational Frequencies Involving Transition Metal Compounds

A role for surface hydrophobicity in protein‐protein recognition

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