The CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions?

2021 ◽  
Author(s):  
Nisha Mehta ◽  
Thomas Fellowes ◽  
JONATHAN WHITE ◽  
Lars Goerigk
Keyword(s):  
Density Functional ◽  
Noncovalent Interactions ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
The Past ◽  
Quantum Chemical Methods ◽  
London Dispersion ◽  
High Level ◽  
Selection Of

<div> <div> <div> <p>We present the CHAL336 benchmark set—the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re- emphasize the need for using proper London-dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction, but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 98 variations of dispersion- corrected and -uncorrected DFT methods, and carry out a detailed analysis of 72 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using any lower-rung DFT methods nor the popular B3LYP and MP2 approaches, which have been used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations. </p> </div> </div> </div>

scholarly journals The CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions?

2021 ◽  
Author(s):  
Nisha Mehta ◽  
Thomas Fellowes ◽  
JONATHAN WHITE ◽  
Lars Goerigk
Keyword(s):  
Density Functional ◽  
Noncovalent Interactions ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
The Past ◽  
Quantum Chemical Methods ◽  
London Dispersion ◽  
High Level ◽  
Selection Of

<div> <div> <div> <p>We present the CHAL336 benchmark set—the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re- emphasize the need for using proper London-dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction, but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 98 variations of dispersion- corrected and -uncorrected DFT methods, and carry out a detailed analysis of 72 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using any lower-rung DFT methods nor the popular B3LYP and MP2 approaches, which have been used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations. </p> </div> </div> </div>

The CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions?

2021 ◽  
Author(s):  
Nisha Mehta ◽  
Thomas Fellowes ◽  
JONATHAN WHITE ◽  
Lars Goerigk
Keyword(s):  
Density Functional ◽  
Noncovalent Interactions ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
The Past ◽  
Quantum Chemical Methods ◽  
London Dispersion ◽  
High Level ◽  
Selection Of

<div> <div> <p> </p><div> <div> <div> <p>We present the CHAL336 benchmark set—the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction, but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and -uncorrected DFT methods, and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations. </p> </div> </div> </div> </div> </div>

scholarly journals How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters?

2020 ◽  
Vol 22 (7) ◽  
pp. 3855-3866 ◽  
Author(s):  
Junbo Chen ◽  
Bun Chan ◽  
Yihan Shao ◽  
Junming Ho
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
Solvent Interactions ◽  
Quantum Chemical Methods ◽  
Composite Methods ◽  
Wide Range

In this paper, the performance of ab initio composite methods, and a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water.

SPECTROSCOPIC AND QUANTUM-CHEMICAL INVESTIGATION OF TESTOSTERONE PROPIONATE, A COMMONLY MISUSED ANABOLIC STEROID

2021 ◽  
Author(s):  
Nikola Ristivojević ◽  
◽  
Dušan Dimić ◽  
Marko Đošić ◽  
Stefan Mišić ◽  
...  
Keyword(s):  
Quantum Chemical ◽  
Density Functional ◽  
Testosterone Propionate ◽  
Anabolic Steroids ◽  
Chemical Methods ◽  
Dft Methods ◽  
Functional Theory ◽  
Quantum Chemical Methods ◽  
Td Dft ◽  
Ir And Raman

Anabolic steroids are a group of commonly counterfeit substances used by individuals who want to gain weight and muscles. Testosterone propionate (TP), an ester analog of testosterone, belongs to this group and its spectroscopic analysis is important especially when it is improperly labeled and misused. In this contribution quantum chemical methods, at the B3LYP/6- 311++G(d,p) level of theory, were applied for the prediction of the vibrational (IR and Raman) and UV-VIS spectra of TP. The applicability of the chosen level of theory was proven based on the comparison between experimental and theoretical bond lengths and angles. The most prominent bands in the IR and Raman spectra were assigned and correlated with the calculated ones. The electronic spectra were also analyzed and the assignments were made based on the Time-Dependent Density Functional Theory (TD-DFT) calculations. The orbitals included in the most intense transitions were visualized and possible solvent effects were discussed. The presented results proved the applicability of the DFT methods for the prediction of spectra that could lead to the counterfeit substances determination.

scholarly journals Sulfate radical oxidation of aromatic contaminants: a detailed assessment of density functional theory and high-level quantum chemical methods

2017 ◽  
Vol 19 (3) ◽  
pp. 395-404 ◽  
Author(s):  
Sangavi Pari ◽  
Inger A. Wang ◽  
Haizhou Liu ◽  
Bryan M. Wong
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
Sulfate Radical ◽  
Chemical Methods ◽  
Functional Theory ◽  
Radical Oxidation ◽  
Quantum Chemical Methods ◽  
Detailed Assessment ◽  
High Level

DFT and high-level quantum methods are utilized to explore sulfate radical-driven oxidation.

scholarly journals The INV24 test set: how well do quantum-chemical methods describe inversion and racemization barriers?

2016 ◽  
Vol 94 (12) ◽  
pp. 1133-1143 ◽  
Author(s):  
Lars Goerigk ◽  
Rahul Sharma
Keyword(s):  
Quantum Chemical ◽  
Computational Study ◽  
Basis Sets ◽  
Generalized Gradient ◽  
Chemical Methods ◽  
Generalized Gradient Approximation ◽  
Quantum Chemical Methods ◽  
London Dispersion ◽  
High Level ◽  
Jacob's Ladder

For years, there has been ongoing interest in experimentally and theoretically understanding inversion and racemization processes. However, to the best of our knowledge, there has been no computational study that systematically investigated how well low-level quantum-chemical methods predict inversion barriers. Herein, we provide an answer to this question and we present the INV24 benchmark set of 24 high-level, ab initio inversion barriers. INV24 covers inversion in triatomics, in pyramidal molecules, in one cyclic system, and in various helical and bowl-shaped compounds. Our results indicate that previously applied DFT approximations combined with small basis sets are not reliable enough and that at least a triple-ζ basis is needed for meaningful results. Moreover, we show that intramolecular London dispersion influences the barriers by 2 kcal/mol or more and that dispersion corrections should always be applied to DFT results. With our analysis of 34 DFT approximations, we can reproduce the well-known Jacob’s Ladder scheme with (meta-)generalized-gradient-approximation methods underestimating barriers and global-hybrid DFT functionals performing better. Range-separated hybrids or Minnesota-type hybrids are not particularly superior to more conventional methods, such as B3LYP-D3. The by far best results are achieved with dispersion-corrected double hybrids, which give results below the chemical accuracy target of 1 kcal/mol. They also outperform wave-function second-order perturbation theory approaches and we recommend using them whenever possible. Given that our systematic study of INV24 is the first of its kind, our findings have the potential to change common practice in this field and they will guide future investigations of inversion processes.

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

2013 ◽  
Vol 91 (7) ◽  
pp. 559-572 ◽  
Author(s):  
Jennifer L. Kellie ◽  
Stacey D. Wetmore
Keyword(s):  
Active Sites ◽  
Noncovalent Interactions ◽  
Single Point ◽  
Enzymatic Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dna Glycosylases ◽  
Dft Methods ◽  
Primary Focus ◽  
High Level

When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

Quantum chemistry in the 21st century (Special topic article)

2000 ◽  
Vol 72 (8) ◽  
pp. 1405-1423 ◽  
Author(s):  
Christopher J. Barden ◽  
Henry F. Schaefer
Keyword(s):  
Quantum Chemistry ◽  
Density Functional ◽  
Special Topic ◽  
Future Research ◽  
New Era ◽  
Incremental Development ◽  
Quantum Chemical Methods ◽  
Theoretical Predictions ◽  
Ready Availability ◽  
High Level

Quantum chemistry is the field in which solutions to the Schrödinger equation are used to predict the properties of molecules and solve chemical problems. This paper considers possible future research directions in light of the discipline's past successes. After decades of incremental development—accompanied by a healthy dose of skepticism from the experimental community—the ready availability of fast computers has ushered in a "golden age" of quantum chemistry. In this new era of acceptance, theoretical predictions often precede experiment in small molecule chemistry, and quantum chemical methods play an ever greater role in biochemical and other larger systems. Quantum chemists increasingly divide their efforts along three fronts: high-level (spectroscopic) accuracy for small molecules, characterized by such techniques as Brueckner methods, r12 formalisms, and multireference calculations; parameterization- or extrapolation-based intermediate-level schemes (such as Gaussian-N theory) for medium molecules; and lower-level (chemical) accuracy for large molecules, characterized by density functional theory and linear scaling techniques. These tools, and quantum chemistry as a whole, are examined here from a historical perspective and with a view toward their future applications.

Halogen bonded supramolecular capsules: a challenging test case for quantum chemical methods

2016 ◽  
Vol 52 (64) ◽  
pp. 9893-9896 ◽  
Author(s):  
Rebecca Sure ◽  
Stefan Grimme
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical ◽  
Density Functional ◽  
State Of The Art ◽  
Test Case ◽  
Binding Affinities ◽  
Chemical Methods ◽  
Functional Theory ◽  
Quantum Chemical Methods

By state-of-the-art dispersion corrected density functional theory, the complexation properties of a recently synthesized halogen-bonded capsule with about 400 atoms are investigated and predictions for improved binding affinities are made.

Sign in / Sign up

Export Citation Format

Share Document