The electronic density obtained from a QTAIM analysis used as molecular descriptor. A study performed in a new series of DHFR inhibitors

Tosso, Rodrigo D.; Vettorazzi, Marcela Cristina; Andújar, Sebastián Antonio; Gutiérrez, Lucas; Garro, Juan C.; Angelina, Emilio; Rodríguez, Ricaurte; Suvire, Fernando D.; Nogueras, Manuel; Cobo, Justo; Enriz, Ricardo D.

doi:10.1016/j.molstruc.2016.12.060

Cited by 19 publications

(21 citation statements)

References 46 publications

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“…The quantum theory of atoms in molecules (QTAIM) has been extensively applied to analyze the nature of interactions in various molecular systems and to classify bonding interactions in terms of a quantum mechanical parameter as electron density. , The quantity of electron density at the BCP provides the information about the nature and strength of bonding between the two monomers in any inclusion complex . The sign of Laplacian is determined by energy that dominates in the bonding zone.…”

Section: Resultsmentioning

confidence: 99%

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Venkataramanan

Suvitha

2017

J. Phys. Chem. B

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The encapsulation of nucleobases inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions existing in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules when they are aligned in parallel configuration. The computed association energy using the two- and three-body correction method computed at B3LYP-D3 level is close to the experimental estimate. The use of dispersion corrected DFs is essential to identify the correct binding energies. The solvation energy plays a vital role in the estimation of association energy. QTAIM analysis shows that the Laplacian of the charge density (∇ρ) is negative and the presence of covalent interaction between the guest and host molecule. The NCI-RDG isosurface shows the presence of noncovalent intermolecular interactions such as van der Waals and hydrogen bonding. The existence of "splattering" of charges in guanine@CB7 molecule is responsible for its higher stability. From the AIM, NCI-RDG, and EDA results, we conclude that noncovalent and electrostatic interaction with partial covalent character exists in the intermolecular bonding between the host and the guest nucleobases. The ramification of such intermolecular bonds is reflected in the H NMR andNMR spectra.

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Section: Resultsmentioning

confidence: 99%

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Venkataramanan

Suvitha

2017

J. Phys. Chem. B

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“…However, a new terminology was recently proposed: line critical point, (LCP), which is adopted herein. In this work, different topological properties evaluated at the LCPs were used to characterize the interactions: the electron charge density, ρ (r c ), which measures the accumulation of charge between the bonded nuclei and reflects the bond strength; the Laplacian of the electron density ∇ 2 ρ ( r c ), that reveals the local charge concentration (∇ 2 ρ ( r c ) < 0) or depletion (∇ 2 ρ ( r c ) > 0); the ellipticity ϵ at the LCP, that shows structural and topological instability,; and the index | V ( r c )|/ G ( r c ), that quantifies the strength of an HB within three regions,: an HB interaction is defined as a weak when | V ( r c )|/ G ( r c ) < 1, as closed‐shared with some covalent character when the ratio falls between 1 and 2, and as strong HBs and covalent bonds when | V ( r c )|/ G ( r c ) > 2 . A minimum potential energy structure was extracted from the production simulations without considering all water molecules, which is shown in Figure a.…”

Section: Resultsmentioning

confidence: 99%

Molecular Insights into Protein‐Polyphenols Aggregation: A Dynamic and Topological Description

et al. 2017

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Protein-polyphenols interactions are of greatest interest in several fields like food technology and leather industry. Also, it is thought that these interactions are responsible for the undesired phenomenon of colloidal turbidity. However, there is sparse information about the molecular implications leading to this phenomenon. In this study, Molecular Dynamic (MD) simulations in conjunction with the analysis of the topology of the electron density are used to study protein/polyphenol interactions in a model system which consists of a ternary mixture of water, the flavonoids Catechin and Procianidin B3 and proline pentapeptides. After 50 ns of simulation, root mean square deviation, root mean square fluctuation and number of hydrogen bonds were calculated. Information about the intermolecular interactions that drive the assembly of colloidal complexes has been obtained by the analysis of the electron charge density. Results show the formation of a stable adduct, with a very complex network of conventional and nonconventional hydrogen bonds. This study has also shown the significance of C-H···O and C-H···p interactions in the phenomenon of colloidal turbidity.

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“…22 Moreover, the value of the charge density at the BCP (r b ) has been used to quantify hydrogen bonds (H-bond) as well as other non-covalent interactions. 23 There are several reports in the literature which illustrate that r b displays a linear relationship with the H-bond strength. 24 Fig.…”

Section: Njc Papermentioning

confidence: 99%

Study of polyphenols fromCaesalpinia paraguariensisas α-glucosidase inhibitors: kinetics and structure–activity relationship

et al. 2022

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The electronic density obtained from a QTAIM analysis used as molecular descriptor. A study performed in a new series of DHFR inhibitors

Cited by 19 publications

References 46 publications

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Theoretical Investigation of the Binding of Nucleobases to Cucurbiturils by Dispersion Corrected DFT Approaches

Molecular Insights into Protein‐Polyphenols Aggregation: A Dynamic and Topological Description

Study of polyphenols fromCaesalpinia paraguariensisas α-glucosidase inhibitors: kinetics and structure–activity relationship

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