scholarly journals Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space

Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sampling of an extended chemical space, while the D442×10 set features dissociation curves for selected complexes. In total, they provide 5,178 new CCSD(T)/CBS data points of the highest quality. The new data have been combined with previous NCIA data sets in a comprehensive test of dispersion-corrected DFT methods, identifying the ones that achieve high accuracy in all types of non-covalent interactions in a broad chemical space. Additional tests of dispersion-corrected MP2 and semiempirical QM methods are also reported.

2020 ◽  
Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas (www.nciatlas.org) aims to provide a new generation of benchmark data sets for non-covalent interactions. The HB300SPX data set presented here extends the coverage of hydrogen bonds to phosphorus, sulfur and halogens up to iodine. It is again complemented by a set of dissociation curves, HB300SPX×10. The new data make it possible to analyze the transferability of the parametrization of e.g. dispersion corrections for DFT from simple organic molecules to a broader chemical space. The HB300SPX×10 has also been used for the extension of the parametrization of hydrogen-bonding corrections in the semiempirical PM6-D3H4X and DFTB3-D3H5 methods to additional elements.<br>


2020 ◽  
Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas (www.nciatlas.org) aims to provide a new generation of benchmark data sets for non-covalent interactions. The HB300SPX data set presented here extends the coverage of hydrogen bonds to phosphorus, sulfur and halogens up to iodine. It is again complemented by a set of dissociation curves, HB300SPX×10. The new data make it possible to analyze the transferability of the parametrization of e.g. dispersion corrections for DFT from simple organic molecules to a broader chemical space. The HB300SPX×10 has also been used for the extension of the parametrization of hydrogen-bonding corrections in the semiempirical PM6-D3H4X and DFTB3-D3H5 methods to additional elements.<br>


2019 ◽  
Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas project (www.nciatlas.org) aims to cover a wide range of non-covalent interactions with a new generation of benchmark data sets. This paper presents the first two data sets focused on hydrogen bonding: HB375, featuring neutral systems, and IHB100 for ionic H-bonds. Both data sets are complemented by ten-point dissociation curves (HB375x10, IHB100x10). The interaction energies are extrapolated to the CCSD(T)/CBS limit from calculations in large basis sets. The paper also summarizes the design principles that will be used to construct the subsequent data sets in the series. The testing of DFT-D methods on the HB375 set has revealed interesting, previously unnoticed issues. The application of the new data to the testing and parameterization of semiempirical QM methods is also discussed.


2020 ◽  
Author(s):  
Kristian Kříž ◽  
Martin Nováček ◽  
Jan Řezáč

The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations.


2020 ◽  
Author(s):  
Kristian Kříž ◽  
Martin Nováček ◽  
Jan Řezáč

The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations.


2019 ◽  
Author(s):  
Jan Řezáč

The Non-Covalent Interactions Atlas project (www.nciatlas.org) aims to cover a wide range of non-covalent interactions with a new generation of benchmark data sets. This paper presents the first two data sets focused on hydrogen bonding: HB375, featuring neutral systems, and IHB100 for ionic H-bonds. Both data sets are complemented by ten-point dissociation curves (HB375x10, IHB100x10). The interaction energies are extrapolated to the CCSD(T)/CBS limit from calculations in large basis sets. The paper also summarizes the design principles that will be used to construct the subsequent data sets in the series. The testing of DFT-D methods on the HB375 set has revealed interesting, previously unnoticed issues. The application of the new data to the testing and parameterization of semiempirical QM methods is also discussed.


2021 ◽  
Vol 17 (3) ◽  
pp. 1548-1561
Author(s):  
Kristian Kříž ◽  
Martin Nováček ◽  
Jan Řezáč

2018 ◽  
Vol 11 (2) ◽  
pp. 53-67
Author(s):  
Ajay Kumar ◽  
Shishir Kumar

Several initial center selection algorithms are proposed in the literature for numerical data, but the values of the categorical data are unordered so, these methods are not applicable to a categorical data set. This article investigates the initial center selection process for the categorical data and after that present a new support based initial center selection algorithm. The proposed algorithm measures the weight of unique data points of an attribute with the help of support and then integrates these weights along the rows, to get the support of every row. Further, a data object having the largest support is chosen as an initial center followed by finding other centers that are at the greatest distance from the initially selected center. The quality of the proposed algorithm is compared with the random initial center selection method, Cao's method, Wu method and the method introduced by Khan and Ahmad. Experimental analysis on real data sets shows the effectiveness of the proposed algorithm.


2021 ◽  
Author(s):  
Kate Nicastri ◽  
Soren Zappia ◽  
Jared Pratt ◽  
Julia Duncan ◽  
Ilia Guzei ◽  
...  

Methods for rapid preparation of densely functionalized and stereochemically complex N-heterocyclic scaffolds are in demand for exploring potential new bioactive chemical space. This work describes experimental and computational studies to better understand the features of aziridinium ylides as intermediates for the synthesis of highly substituted dehydromorpholines. The development of this chemistry has enabled the extension of aziridinium ylide chemistry to the concomitant formation of both a C–N and a C–O bond in a manner that preserves the stereochemical information embedded in the substrate. The chemistry is tolerant of a wide range of functionalities that can be employed for DNA-encoded library (DEL) synthesis to prepare diverse libraries of heterocycles with potential bioactivity. In addition, we have uncovered several key insights that describe the importance of steric effects, rotational barriers around the C–N bond of the aziridinium ylide, and non-covalent interactions (NCIs) on the ultimate reaction outcome. These critical insights will assist in the further development of this chemistry to generate novel and complex N-heterocycles that will further expand complex amine chemical space.


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