Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics.

ABSTRACT: We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling-Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn-Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction barrier heights, and nonbond interactions of main group molecules. In addition, the accuracy remains nearly constant with system size.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC2664054 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Doubly hybrid density functional for accurate descriptions of nonbond interactions, thermochemistry, and thermochemical kinetics.

Zhang Ying Y Xu Xin X Goddard William A WA

Proceedings of the National Academy of Sciences of the United States of America 20090310 13

We develop and validate a density functional, XYG3, based on the adiabatic connection formalism and the Görling-Levy coupling-constant perturbation expansion to the second order (PT2). XYG3 is a doubly hybrid functional, containing 3 mixing parameters. It has a nonlocal orbital-dependent component in the exchange term (exact exchange) plus information about the unoccupied Kohn-Sham orbitals in the correlation part (PT2 double excitation). XYG3 is remarkably accurate for thermochemistry, reaction ...[more]

PMID: 19276116

Similar Datasets

A Benchmark of Density Functional Approximations For Thermochemistry and Kinetics of Hydride Reductions of Cyclohexanones.

Project description:The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions.

| S-EPMC6594353 | biostudies-literature

Doubly hybrid density functionals that correctly describe both density and energy for atoms.

Project description:Recently, it was argued [Medvedev MG, et al. (2017) Science 355:49-52] that the development of density functional approximations (DFAs) is "straying from the path toward the exact functional." The exact functional should yield both exact energy and density for a system of interest; nevertheless, they found that many heavily fitted functionals for molecular energies actually lead to poor electron densities of atoms. They also observed a trend that, for the nonempirical and few-parameter functionals, densities can be improved as one climbs up the first four rungs of the Jacob's ladder of DFAs. The XYG3 type of doubly hybrid functionals (xDHs) represents a less-empirical and fewer-parameter functional on the top fifth rung, in which both the Hartree-Fock-like exchange and the second-order perturbative (MP2-like) correlation are hybridized with the low rung functionals. Here, we show that xDHs can well describe both density and energy for the same atomic set of Medvedev et al., showing that the latter trend can well be extended to the top fifth rung.

| S-EPMC5878006 | biostudies-literature

Pairing double hybrid functionals with a tailored basis set for an accurate thermochemistry of hydrocarbons.

Project description:A collection of five challenging datasets, including noncovalent interactions, reaction barriers and electronic rearrangements of medium-sized hydrocarbons, has been selected to verify the robustness of double-hybrid functionals used in conjunction with the small DH-SVPD basis set, especially developed for noncovalent interactions. The analysis is completed by other, more standard functionals, for a total of 17 models, including also empirical corrections for dispersion. The obtained results show that the chemical accuracy threshold, that is an error lower than 1.0 kcal mol-1, can be obtained by pairing the nonempirical PBE-QIDH functional with the DH-SVPD basis set, as well as by other semi-empirical functionals, such as DSD-PBEP86, using larger basis sets and empirical corrections. More in general, a significant improvement can be obtained using the DH-SVPD basis set with DHs, without resorting to any empirical corrections. This choice leads to a fast computational protocol that, avoiding any empirical potential, remains on a fully quantum ground.

| S-EPMC9037073 | biostudies-literature

A fast doubly hybrid density functional method close to chemical accuracy using a local opposite spin ansatz.

Project description:We develop and validate the XYGJ-OS functional, based on the adiabatic connection formalism and Görling-Levy perturbation theory to second order and using the opposite-spin (OS) ansatz combined with locality of electron correlation. XYGJ-OS with local implementation scales as N(3) with an overall accuracy of 1.28 kcal/mol for thermochemistry, bond dissociation energies, reaction barrier heights, and nonbonded interactions, comparable to that of 1.06 kcal/mol for the accurate coupled-cluster based G3 method (scales as N(7)) and much better than many popular density functional theory methods: B3LYP (4.98), PBE0 (4.36), and PBE (12.10).

| S-EPMC3250148 | biostudies-literature

Accurate van der Waals coefficients from density functional theory.

Project description:The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C(6), C(8), C(10) for atom pairs with a mean absolute relative error of only 3%.

| S-EPMC3252946 | biostudies-literature

Simple and Accurate Exchange Energy for Density Functional Theory.

Project description:A non-empirical exchange functional based on an interpolation between two limits of electron density, slowly varying limit and asymptotic limit, is proposed. In the slowly varying limit, we follow the study by Kleinman from 1984 which considered the response of a free-electron gas to an external periodic potential, but further assume that the perturbing potential also induces Bragg diffraction of the Fermi electrons. The interpolation function is motivated by the exact exchange functional of a hydrogen atom. Combined with our recently proposed correlation functional, tests on 56 small molecules show that, for the first-row molecules, the exchange-correlation combo predicts the total energies four times more accurately than the presently available Quantum Monte Carlo results. For the second-row molecules, errors of the core electrons exchange energies can be corrected, leading to the most accurate first- and second-row molecular total energy predictions reported to date despite minimal computational efforts. The calculated bond energies, zero point energies, and dipole moments are also presented, which do not outperform other methods.

| S-EPMC7436057 | biostudies-literature

Rapid and accurate assessment of GPCR-ligand interactions Using the fragment molecular orbital-based density-functional tight-binding method.

Project description:The reliable and precise evaluation of receptor-ligand interactions and pair-interaction energy is an essential element of rational drug design. While quantum mechanical (QM) methods have been a promising means by which to achieve this, traditional QM is not applicable for large biological systems due to its high computational cost. Here, the fragment molecular orbital (FMO) method has been used to accelerate QM calculations, and by combining FMO with the density-functional tight-binding (DFTB) method we are able to decrease computational cost 1000 times, achieving results in seconds, instead of hours. We have applied FMO-DFTB to three different GPCR-ligand systems. Our results correlate well with site directed mutagenesis data and findings presented in the published literature, demonstrating that FMO-DFTB is a rapid and accurate means of GPCR-ligand interactions. © 2017 Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

| S-EPMC5600120 | biostudies-literature

Accurate Spectral Properties within Double-Hybrid Density Functional Theory: A Spin-Scaled Range-Separated Second-Order Algebraic-Diagrammatic Construction-Based Approach.

Project description:Our second-order algebraic-diagrammatic construction [ADC(2)]-based double-hybrid (DH) ansatz (J. Chem. Theory Comput. 2019, 15, 4440. DOI: 10.1021/acs.jctc.9b00391) is combined with range-separation techniques. In the present scheme, both the exchange and the correlation contributions are range-separated, while spin-scaling approaches are also applied. The new methods are thoroughly tested for the most popular benchmark sets including 250 singlet and 156 triplet excitations, as well as 80 oscillator strengths. It is demonstrated that the range separation for the correlation contributions is highly recommended for both the genuine and the ADC(2)-based DH approaches. Our results show that the latter scheme slightly but consistently outperforms the former one for single excitation dominated transitions. Furthermore, states with larger fractions of double excitations are assessed as well, and challenging charge-transfer excitations are also discussed, where the recently proposed spin-scaled long-range corrected DHs fail. The suggested iterative fourth-power scaling RS-PBE-P86/SOS-ADC(2) method, using only three adjustable parameters, provides the most robust and accurate excitation energies within the DH theory. In addition, the relative error of the oscillator strengths is reduced by 65% compared to the best genuine DH functionals.

| S-EPMC8830052 | biostudies-literature

Coupling across a DNA helical turn yields a hybrid DNA/organic catenane doubly tailed with functional termini.

Project description:We describe the synthesis of a hybrid DNA/organic macrocycle that is prepared by formation of an amide linkage across one full turn of DNA. Formation of a catenane proved that the linkage crossed a turn rather than running along the phosphodiester backbone contour. The product, a doubly tailed catenane, contains 5'- and 3'-termini that can be functionalized further or used to incorporate the catenane structure into other DNA assemblies.

| S-EPMC2712227 | biostudies-literature

Thermochemistry and Kinetics of the Thermal Degradation of 2-Methoxyethanol as Possible Biofuel Additives.

Project description:Oxygenated organic compounds derived from biomass (biofuel) are a promising alternative renewable energy resource. Alcohols are widely used as biofuels, but studies on bifunctional alcohols are still limited. This work investigates the unimolecular thermal degradation of 2-methoxyethanol (2ME) using DFT/BMK and ab initio (CBS-QB3 and G3) methods. Enthalpies of the formation of 2ME and its decomposition species have been calculated. Conventional transition state theory has been used to estimate the rate constant of the pyrolysis of 2ME over a temperature range of 298-2000 K. Production of methoxyethene via 1,3-H atom transfer represents the most kinetically favored path in the course of 2ME pyrolysis at room temperature and requires less energy than the weakest Cα - Cβ simple bond fission. Thermodynamically, the most preferred channel is methane and glycoladhyde formation. A ninefold frequency factor gives a superiority of the Cα - Cβ bond breaking over the Cγ - Oβ bond fission despite comparable activation energies of these two processes.

| S-EPMC6418115 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data