Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies

2019 ◽  
Vol 33 (8) ◽  
pp. 745-757 ◽  
Author(s):  
Saw Simeon ◽  
Nathjanan Jongkon ◽  
Warot Chotpatiwetchkul ◽  
M. Paul Gleeson
Keyword(s):  
Pairwise Interaction ◽  
Quantum Mechanical ◽  
Interaction Energies

scholarly journals Interactions between large molecules pose a puzzle for reference quantum mechanical methods

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yasmine S. Al-Hamdani ◽  
Péter R. Nagy ◽  
Andrea Zen ◽  
Dennis Barton ◽  
Mihály Kállay ◽  
...  
Keyword(s):  
Experimental Information ◽  
Quantum Mechanical ◽  
Interaction Energies ◽  
Small Organic Molecules ◽  
Large Molecules ◽  
Reference Information ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Semi Empirical ◽  
Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations

1999 ◽  
Vol 110 (3) ◽  
pp. 1329-1337 ◽  
Author(s):  
Robert H. Wood ◽  
Eric M. Yezdimer ◽  
Shinichi Sakane ◽  
Jose A. Barriocanal ◽  
Douglas J. Doren
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies ◽  
Free Energies ◽  
Mechanical Interaction

Three polymorphs of 3-(3-phenyl-1H-1,2,4-triazol-5-yl)-2H-1-benzopyran-2-one formed from different solvents

2019 ◽  
Vol 75 (6) ◽  
pp. 822-832 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Irina S. Konovalova ◽  
Pavlo V. Trostianko ◽  
Anna O. Geleverya ◽  
Sergiy M. Kovalenko ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Pairwise Interaction ◽  
Structural Motif ◽  
Monoclinic Space Group ◽  
Interaction Energies ◽  
Orthorhombic Space Group ◽  
Structure Packing ◽  
Triclinic Space Group ◽  
Space Group ◽  
Polymorphic Modifications

The polymorphic study of 3-(3-phenyl-1H-1,2,4-triazol-5-yl)-2H-1-benzopyran-2-one, C17H11N3O2, was performed due to its potential biological activity and revealed three polymorphic modifications in the triclinic space group P\overline{1}, the monoclinic space group P21 and the orthorhombic space group Pbca. These polymorphs have a one-column layered type of crystal organization. The strongest interactions between the molecules of the studied structures is stacking between π-systems, while N—H...N and C—H...O hydrogen bonds link stacked columns forming layers as a secondary basic structural motif. C—H...π hydrogen bonds were observed between neighbouring layers and their role is the least significant in the formation of the crystal structure. Packing differences between the polymorphic modifications are minor and can be identified only using an analysis based on a comparison of the pairwise interaction energies.

scholarly journals Quantum mechanical synthon interaction energies

2017 ◽  
Vol 73 (a2) ◽  
pp. C682-C682
Author(s):  
Dylan Jayatilaka ◽  
Samuel Thompson ◽  
Sajesh Thomas ◽  
Peter Spackman ◽  
Mark Spackman
Keyword(s):  
Quantum Mechanical ◽  
Interaction Energies

scholarly journals Van der Waals interactions between polymers with sequence-specific polarizabilities: Stiff polymers and Gaussian coils

2016 ◽  
Vol 31 (02n03) ◽  
pp. 1641035 ◽  
Author(s):  
Bing-Sui Lu ◽  
Ali Naji ◽  
Rudolf Podgornik
Keyword(s):  
Interaction Energy ◽  
Van Der Waals ◽  
Pairwise Interaction ◽  
Van Der Waals Interaction ◽  
Van Der Waals Interactions ◽  
Attractive Interaction ◽  
Gyration Radius ◽  
Interaction Energies ◽  
Anisotropic Interaction ◽  
Decay Behavior

We consider the van der Waals interaction between a pair of polymers with quenched heterogeneous sequences of local polarizabilities along their backbones, and study the effective pairwise interaction energy for both stiff polymers and flexible Gaussian coils. In particular, we focus on the cases where the pair of polarizability sequences are (i) distinct and (ii) identical. We find that the pairwise interaction energies of distinct and identical Gaussian coils are both isotropic and exhibit the same decay behavior for separations larger than their gyration radius, in contradistinction to the orientationally anisotropic interaction energies of distinct and identical stiff polymers. For both Gaussian coils and stiff polymers, the attractive interaction between identical polymers is enhanced if the polarizability sequence is more heterogeneous.

Polymorphism of 3-(5-phenyl-1,3,4-oxadiazol-2-yl)- and 3-[5-(pyridin-4-yl)-1,3,4-oxadiazol-2-yl]-2H-chromen-2-ones

2019 ◽  
Vol 75 (11) ◽  
pp. 1541-1553
Author(s):  
Svitlana V. Shishkina ◽  
Irina S. Konovalova ◽  
Pavlo V. Trostianko ◽  
Anna O. Geleverya ◽  
Sergiy M. Kovalenko ◽  
...  
Keyword(s):  
Anticancer Activity ◽  
Intermolecular Interactions ◽  
Pairwise Interaction ◽  
Interaction Energies ◽  
The Third ◽  
Weak Intermolecular Interactions ◽  
Polymorphic Modifications ◽  
The Difference ◽  
Polymorphic Structure ◽  
Head Type

This study of 3-(5-phenyl-1,3,4-oxadiazol-2-yl)-2H-chromen-2-one, C17H10N2O3, 1, and 3-[5-(pyridin-4-yl)-1,3,4-oxadiazol-2-yl]-2H-chromen-2-one, C16H9N3O3, 2, was performed on the assumption of the potential anticancer activity of the compounds. Three polymorphic structures for 1 and two polymorphic structures for 2 have been studied thoroughly. The strongest intermolecular interaction is stacking of the `head-to-head' type in all the studied crystals. The polymorphic structures of 1 differ with respect to the intermolecular interactions between stacked columns. Two of the polymorphs have a columnar or double columnar type of crystal organization, while the third polymorphic structure can be classified as columnar-layered. The difference between the two structures of 2 is less pronounced. Both crystals can be considered as having very similar arrangements of neighbouring columns. The formation of polymorphic modifications is caused by a subtle balance of very weak intermolecular interactions and packing differences can be identified only using an analysis based on a study of the pairwise interaction energies.

scholarly journals Energy Disorder in Liquid Fe-Si Alloy

2011 ◽  
Vol 1 ◽  
pp. 37-40
Author(s):  
D. Adhikari ◽  
I. S. Jha ◽  
B. P. Singh
Keyword(s):  
Pairwise Interaction ◽  
Heat Of Mixing ◽  
Interaction Energies ◽  
Molten State ◽  
Energy Disorder ◽  
Energy Of Mixing ◽  
Free Energy Of Mixing ◽  
Alloy Clusters ◽  
Associated Solution Model ◽  
Associated Solution

The observed asymmetry in the properties of mixing of Fe-Si alloy in molten state is successfully explained on the basis of regular associated solution model. We have determined the free energy of mixing, heat of mixing and entropy of mixing of Fe-Si alloys in molten state at 1873 K. The analysis suggests that heterocoordination leading to the formation of complex Fe 2Si is likely to exist in the liquid and is of a strongly interacting nature. The theoretical analysis reveals that the pairwise interaction energies between the species depend considerably on temperature.Keywords: Liquid alloy; Clusters; Thermodynamic propertiesThe Himalayan Physics Vol.1, No.1, May, 2010Page: 37-40Uploaded Date: 28 July, 2011

scholarly journals Estimating Interprotein Pairwise Interaction Energies in Cell Lysates from a Single Native Mass Spectrum

2018 ◽  
Vol 90 (17) ◽  
pp. 10090-10094 ◽  
Author(s):  
Jelena Cveticanin ◽  
Ravit Netzer ◽  
Galina Arkind ◽  
Sarel J. Fleishman ◽  
Amnon Horovitz ◽  
...  
Keyword(s):  
Mass Spectrum ◽  
Pairwise Interaction ◽  
Interaction Energies ◽  
Cell Lysates

Polymorphic modifications of a 1H-pyrrolo[3,2,1-ij]quinoline-5-carboxamide possessing strong diuretic properties

2018 ◽  
Vol 74 (12) ◽  
pp. 1759-1767 ◽  
Author(s):  
Svitlana V. Shishkina ◽  
Igor A. Levandovskiy ◽  
Igor V. Ukrainets ◽  
Lyudmila V. Sidorenko ◽  
Lina A. Grinevich ◽  
...  
Keyword(s):  
Crystal Packing ◽  
Pairwise Interaction ◽  
Structural Motif ◽  
Interaction Energies ◽  
Asymmetric Unit ◽  
Space Group ◽  
Monoclinic Form ◽  
Polymorphic Modifications ◽  
A Chain ◽  
Triclinic Form

6-Hydroxy-N-(4-methoxyphenyl)-4-oxo-2,4-dihydro-1H-pyrrolo[3,2,1-ij]quinoline-5-carboxamide, C19H16N2O4, possesses strong diuretic properties and can be used as a new hypertension remedy. Two polymorphic modifications of this compound have been found, namely the triclinic polymorph (space group P\overline{1}), with one molecule in the asymmetric unit, and the monoclinic polymorph (space group P21/n), with two molecules in asymmetric unit. An analysis of the pairwise interaction energies between the molecules in the crystal phase revealed differences in the crystal packing. The triclinic form has only one level of organization, namely a chain/column, while the monoclinic form has two levels of organization, with a chain/column as the primary basic structural motif and a layer as the secondary basic structural motif.

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