Insights from the density functional performance of water and water–solid interactions: SCAN in relation to other meta-GGAs

2020 ◽  
Vol 153 (21) ◽  
pp. 214116
Author(s):  
Subrata Jana ◽  
Abhilash Patra ◽  
Szymon Śmiga ◽  
Lucian A. Constantin ◽  
Prasanjit Samal
Keyword(s):  
Density Functional ◽  
Functional Performance

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

scholarly journals Benchmarking London dispersion corrected density functional theory for noncovalent ion-pi interactions

2021 ◽  
Author(s):  
Sebastian Spicher ◽  
Eike Caldeweyher ◽  
Andreas Hansen ◽  
Stefan Grimme
Keyword(s):  
Electrostatic Interactions ◽  
Density Functional ◽  
Functional Performance ◽  
Dispersion Model ◽  
Coupled Cluster ◽  
Interaction Energies ◽  
Binding Motifs ◽  
Hybrid Functionals ◽  
London Dispersion ◽  
Pi Interactions

<p>The strongly attractive noncovalent interactions of charged atoms or molecules with p-systems are important binding motifs in many chemical and biological systems. These so-called ion-pi interactions play a major role in enzymes, molecular recognition, and for the structure of proteins. In this work, a molecular test set termed IONPI19 is compiled for inter- and intramolecular ion-pi interactions, which is well balanced between anionic and cationic systems. The IONPI19 set includes interaction energies of significantly larger molecules (up to 133 atoms) than in other ion-pi test sets and covers a broad range of binding motifs. Accurate (local) coupled cluster values are provided as reference. Overall, 18 density functional approximations, including seven (meta-)GGAs, seven hybrid functionals, and four double hybrid functionals combined with three different London dispersion corrections, are benchmarked for interaction energies. DFT results are further compared to wave function based methods such as MP2 and dispersion corrected Hartree-Fock. Also the performance</p><p>of semiempirical QM methods such as the GFNn-xTB and PMx family of methods is tested. It is shown that dispersion-uncorrected DFT underestimates ion-pi interactions significantly, even though electrostatic interactions dominate the overall binding. Accordingly, the new charge dependent D4 dispersion model is found to be consistently better than the standard D3 correction. Furthermore, the functional performance trend along Jacob’s ladder is generally obeyed and the reduction of the self-interaction error leads to an improvement of (double) hybrid functionals over (meta-)GGAs, even though the effect of the SIE is smaller than expected. Overall, the double hybrids PWPB95-D4/QZ and revDSD-PBEP86-D4/QZ turned out to be the most reliable among all assessed methods in predicting ion-pi interactions, which opens up new perspectives for systems where coupled cluster calculations are no longer computationally feasible.</p>

scholarly journals Benchmarking London dispersion corrected density functional theory for noncovalent ion-pi interactions

2021 ◽  
Author(s):  
Sebastian Spicher ◽  
Eike Caldeweyher ◽  
Andreas Hansen ◽  
Stefan Grimme
Keyword(s):  
Electrostatic Interactions ◽  
Density Functional ◽  
Functional Performance ◽  
Dispersion Model ◽  
Coupled Cluster ◽  
Interaction Energies ◽  
Binding Motifs ◽  
Hybrid Functionals ◽  
London Dispersion ◽  
Pi Interactions

<p>The strongly attractive noncovalent interactions of charged atoms or molecules with p-systems are important binding motifs in many chemical and biological systems. These so-called ion-pi interactions play a major role in enzymes, molecular recognition, and for the structure of proteins. In this work, a molecular test set termed IONPI19 is compiled for inter- and intramolecular ion-pi interactions, which is well balanced between anionic and cationic systems. The IONPI19 set includes interaction energies of significantly larger molecules (up to 133 atoms) than in other ion-pi test sets and covers a broad range of binding motifs. Accurate (local) coupled cluster values are provided as reference. Overall, 18 density functional approximations, including seven (meta-)GGAs, seven hybrid functionals, and four double hybrid functionals combined with three different London dispersion corrections, are benchmarked for interaction energies. DFT results are further compared to wave function based methods such as MP2 and dispersion corrected Hartree-Fock. Also the performance</p><p>of semiempirical QM methods such as the GFNn-xTB and PMx family of methods is tested. It is shown that dispersion-uncorrected DFT underestimates ion-pi interactions significantly, even though electrostatic interactions dominate the overall binding. Accordingly, the new charge dependent D4 dispersion model is found to be consistently better than the standard D3 correction. Furthermore, the functional performance trend along Jacob’s ladder is generally obeyed and the reduction of the self-interaction error leads to an improvement of (double) hybrid functionals over (meta-)GGAs, even though the effect of the SIE is smaller than expected. Overall, the double hybrids PWPB95-D4/QZ and revDSD-PBEP86-D4/QZ turned out to be the most reliable among all assessed methods in predicting ion-pi interactions, which opens up new perspectives for systems where coupled cluster calculations are no longer computationally feasible.</p>

scholarly journals Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

2019 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
William Isley ◽  
Stephen Dale ◽  
Erin Johnson ◽  
Haibo Yu ◽  
...  
Keyword(s):  
Density Functional ◽  
Functional Performance ◽  
Low Cost ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
Covalent Modification ◽  
Dft Methods ◽  
Aqueous Solvent ◽  
Exact Exchange ◽  
Semi Empirical

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semi-empirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the pre-reaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally-optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behaviour of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were easonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that MD simulations using this functional were only stable if a fine integration grid was used. The low-cost semi-empirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics are not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to MVK was calculated using QM/MM MD in an explicit polarizable aqueous solvent.<br>

Doping effects on the geometric and electronic structure of tin clusters

2019 ◽  
Vol 21 (44) ◽  
pp. 24478-24488 ◽  
Author(s):  
Martin Gleditzsch ◽  
Marc Jäger ◽  
Lukáš F. Pašteka ◽  
Armin Shayeghi ◽  
Rolf Schäfer
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Beam Deflection ◽  
Functional Theory ◽  
Doping Effects ◽  
Depth Analysis ◽  
Trajectory Simulations

In depth analysis of doping effects on the geometric and electronic structure of tin clusters via electric beam deflection, numerical trajectory simulations and density functional theory.

What correlation effects are covered by density functional theory?

2000 ◽  
Vol 98 (20) ◽  
pp. 1639-1658 ◽  
Author(s):  
Yuan He, Jurgen Grafenstein, Elfi Kraka,
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Correlation Effects ◽  
Functional Theory

Accurate density functional thermochemistry for larger molecules

1997 ◽  
Vol 91 (3) ◽  
pp. 555-559 ◽  
Author(s):  
KRISHNAN RAGHAVACHARI ◽  
BORIS STEFANOV ◽  
LARRY CURTISS
Keyword(s):  
Density Functional
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