Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies

2012 ◽  
Vol 45 (4) ◽  
pp. 663-672 ◽  
Author(s):  
Pavel Hobza
Keyword(s):  
Noncovalent Interactions ◽  
Interaction Energies

scholarly journals Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

2017 ◽  
Vol 114 (10) ◽  
pp. 2474-2478 ◽  
Author(s):  
Anup Kumar ◽  
Eyal Capua ◽  
Manoj K. Kesharwani ◽  
Jan M. L. Martin ◽  
Einat Sitbon ◽  
...  
Keyword(s):  
Spin Polarization ◽  
Noncovalent Interactions ◽  
Electronic Charge ◽  
Biological Processes ◽  
Interaction Energies ◽  
Hall Voltage ◽  
Charge Redistribution ◽  
Chiral Molecules ◽  
Quantum Chemistry Calculations ◽  
Symmetry Constraints

Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device. An electric field that is applied along the molecules causes charge redistribution, and for chiral molecules, a Hall voltage is measured that indicates the spin polarization. Based on this observation, we conjecture that the spin polarization enforces symmetry constraints on the biorecognition process between two chiral molecules, and we describe how these constraints can lead to selectivity in the interaction between enantiomers based on their handedness. Model quantum chemistry calculations that rigorously enforce these constraints show that the interaction energy for methyl groups on homochiral molecules differs significantly from that found for heterochiral molecules at van der Waals contact and shorter (i.e., ∼0.5 kcal/mol at 0.26 nm).

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 Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1533
Author(s):  
Jayashree Nagesh
Keyword(s):  
Small Molecules ◽  
Polypeptide Chain ◽  
Noncovalent Interactions ◽  
Side Chain ◽  
Interaction Energies ◽  
Structural Element ◽  
Comprehensive Picture ◽  
Conformation Stability

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.

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 Quantifying intermolecular interactions for isoindole derivatives: substituent effect vs. crystal packing

2018 ◽  
Vol 233 (9-10) ◽  
pp. 675-687 ◽  
Author(s):  
Lilianna Chęcińska ◽  
Andrzej Jóźwiak ◽  
Magdalena Ciechańska ◽  
Carsten Paulmann ◽  
Julian J. Holstein ◽  
...  
Keyword(s):  
Intermolecular Interactions ◽  
Substituent Effect ◽  
Crystal Packing ◽  
Weak Interactions ◽  
Noncovalent Interactions ◽  
Pairwise Interaction ◽  
Interaction Energies ◽  
Framework Analysis ◽  
Quantitative Manner ◽  
Crystal Packings

Abstract The aim of the study was to examine noncovalent interactions in considerably different crystal packings of three isoindole compounds. Their structures were compared to three other closely-related derivatives described earlier in the literature. Here we discuss the crystal structures in the context of the hydrogen-bonded motifs and other weak interactions. The hierarchy of investigated intermolecular interactions was examined in a quantitative manner through pairwise interaction energies and energy framework analysis.

Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽  
2021 ◽  
Author(s):  
Viktor N. Serezhkin ◽  
Anton V. Savchenkov
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Noncovalent Interactions ◽  
Organic Molecular Crystal ◽  
Universal Approach ◽  
Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

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