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

Abstract

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.

A computational study on the complexation of bisbenzimidazolyl derivatives with cucurbituril and cyclohexylcucurbituril

“…The computed cavity diameter between the oxygen portals and the cavity depth of CB6 is 6.92 Å and 6.09 Å respectively with D6h symmetry. The observed values are in close agreement with the previously reported theoretical values [34]. The computed oxygen portals diameter in CCB6 is 6.77 Å and its cavity diameter is 5.96 Å, which are shorter than the values computed for the CB6 molecule [35].…”

“…A positive ∇ 2 ρ is observed in closed-shell systems/noncovalent interaction and is indicative of the depletion of electronic charge between the nuclei, and a negative value indicates a covalent bond [49,50]. More basic information on the AIM can be found in previous publications [34,35,38,39]. Furthermore a positive value of H(ρ), also indicates the existence of noncovalent interaction at the BCP.…”

Density functional theory study on the dihydrogen bond cooperativity in the growth behavior of dimethyl sulfoxide clusters

“…The quantum theory of atoms in molecules (QTAIM) has been extensively applied to classify and understand bonding interactions in terms of quantum mechanical parameter such as electron density (), the Laplacian of the charge density (∇ 2 ρ), total energy density (H(r)) (H(r)= local gradient kinetic energy density G(r) + local potential energy density Venkataramanan Page 17 V(r)) [49,50]. In an effort to shed some light on the nature of interaction in the DMSO clusters, we applied the QTAIM methodology.…”

Surface modification induced enhanced CO2 sorption in cucurbit[6]uril, an organic porous material

“…48,49 Later, we have attempted to improve the adsorption properties by modifying the material using physical and chemical means, ultimately realising modified materials with superior CO 2 absorption performance.…”