Nabanita Saikia

First principles calculation on the structure and electronic properties of BNNTs functionalized with isoniazid drug molecule

One-dimensional nanostructures such as nanowires and nanotubes are stimulating tremendous research interest due to their structural, electronic and magnetic properties. We perform first principles calculation using density functional theory on the structural, and electronics properties of BNNTs adsorbed with isoniazid (INH) drug via noncovalent functionalization using the GGA/PBE functional and DZP basis set implemented in SIESTA program. The band structure, density of states and projected density of states (PDOS) plots suggest that isoniazid prefers to get adsorbed at the hollow site in case of (5,5) BNNT, whereas in (10,0) BNNT it favours the bridge site. The adsorption energy of INH onto (5,5) BNNT is smaller than in (10,0) BNNT which proposes that (10,0) BNNT with a larger radius compared to (5,5) BNNT is more favourable for INH adsorption as the corresponding distortion energy will also be quite lower. Functionalization of (5,5) and (10,0) BNNTs with isoniazid displays the presence of new impurity states (dispersionless bands) within the HOMO–LUMO energy gap of pristine BNNT leading to an increase in reactivity of the INH/BNNT system and lowering of the energy gap of the BNNTs. The PDOS plots show the major contribution towards the dispersionless impurity states is from INH molecule itself rather than from BNNT near the Fermi energy region. To summarize, noncovalent functionalization of BNNTs with isoniazid drug modulates the electronic properties of the pristine BNNT by lowering its energy gap with respect to the Fermi level, as well as demonstrating the preferential site selectivity for adsorption of isoniazid onto the nanotube sidewalls of varying chirality.

Density functional study on the adsorption of the drug isoniazid onto pristine and B-doped single wall carbon nanotubes.

AbstractThe current study explores a new strategy to incorporate single wall carbon nanotubes (SWNTs)/doped SWNTs as carrier modules in target-specific administration of antitubercular chemotherapeutics through covalent and noncovalent functionalization onto the nanotube sidewall. Density functional studies illustrate that noncovalent functionalization of isoniazid (INH) is preferred over covalent attachment, exhibiting low adsorption energy values, HOMO–LUMO gap and comparison of quantum molecular descriptors performed in (5,5) and (9,0) SWNT systems. Substitution doping of boron facilitates the adsorption of INH onto the otherwise inert nanotube. Frontier orbital analysis reveals reorientation of electronic charge in the nanotubes after functionalization, the effect being more pronounced in the case of doped nanotubes. The charge transfer is significant in covalent functionalization of INH via the B-dopant atom, whereas in noncovalent functionalization a small amount of charge transfer is noted. Solvation studies demonstrate the dissolution of INH in B-doped (5,5) and (9,0) SWNTs to be higher compared to pristine nanotube-INH complexes. Functionalization of nanotubes via covalent and noncovalent means can foster pioneering prospects especially for experimental studies in this area of research. FigureDensity functional study on the adsorption of the antitubercular drug isoniazid (INH) onto pristine and B-doped single wall carbon nanotubes (SWNTs) through covalent and noncovalent functionalization

Ab initio study on the noncovalent adsorption of camptothecin anticancer drug onto graphene, defect modified graphene and graphene oxide

The application of graphene and related nanomaterials like boron nitride (BN) nanosheets, BN-graphene hybrid nanomaterials, and graphene oxide (GO) for adsorption of anticancer chemotherapeutic camptothecin (CPT) along with the effect on electronic properties prior to functionalization and after functionalization has been reported using density functional theory (DFT) calculations. The inclusion of dispersion correction to DFT is instrumental in accounting for van der Waals π–π stacking between CPT and the nanomaterial. The adsorption of CPT exhibits significant strain within the nanosheets and noncovalent adsorption of CPT is thermodynamically favoured onto the nanosheets. In case of GO, surface incorporation of functional groups result in significant crumpling along the basal plane and the interaction is basically mediated by H-bonding rather than π–π stacking. Docking studies predict the plausible binding of CPT, CPT functionalized graphene and GO with topoisomerase I (top 1) signifying that CPT interacts through π stacking with AT and GC base pairs of DNA and in presence of nano support, DNA bases preferentially gets bound to the basal plane of graphene and GO rather than the edges. At a theoretical level of understanding, our studies point out the noncovalent interaction of CPT with graphene based nanomaterials and GO for loading and delivery of anticancer chemotherapeutic along with active binding to Top1 protein.

Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein

The potential biomedical application of carbon nanotubes (CNTs) pertinent to drug delivery is highly manifested considering the remarkable electronic and structural properties exhibited by CNT. To simulate the interaction of nanomaterials with biomolecular systems, we have performed density functional calculations on the interaction of pyrazinamide (PZA) drug with functionalized single-wall CNT (fSWCNT) as a function of nanotube chirality and length using two different approaches of covalent functionalization, followed by docking simulation of fSWCNT with pncA protein. The functionalization of pristine SWCNT facilitates in enhancing the reactivity of the nanotubes and formation of such type of nanotube-drug conjugate is thermodynamically feasible. Docking studies predict the plausible binding mechanism and suggests that PZA loaded fSWCNT facilitates in the target specific binding of PZA within the protein following a lock and key mechanism. Interestingly, no major structural deformation in the protein was observed after binding with CNT and the interaction between ligand and receptor is mainly hydrophobic in nature. We anticipate that these findings may provide new routes towards the drug delivery mechanism by CNTs with long term practical implications in tuberculosis chemotherapy.

Density functional study on noncovalent functionalization of pyrazinamide chemotherapeutic with graphene and its prototypes

We perform density functional studies to comprehend the structure and energetics of the interaction of the drug pyrazinamide (PZA) with graphene-based nanomaterials using a noncovalent functionalization approach, followed by molecular docking on the PZA–nanosheet system with the pncA protein. The structural deformation within the nanosheet induced by adsorbed PZA, adsorption energies and global reactivity descriptors are compared for the studied systems at all probable adsorption sites. Significant crumpling of the nanosheets is observed upon adsorption of PZA, with the effect being more pronounced for defect modified, BN and Stone–Wales (SW) defect nanosheets. The inclusion of dispersion corrected DFT (DFT-D) calculations takes into account the weak noncovalent van der Waals π–π stacking and the variation of adsorption energy, energy gap and dipole moment are compared with the results of DFT–GGA. Docking studies help in predicting the plausible binding mechanism between nanosheet–PZA systems and pncA protein and suggests that PZA loaded onto the nanomaterials facilitates the target binding of the drug within the protein. Interestingly, presence of nanosheets does not induce any major structural deformation in the protein, with the interaction between ligand and receptor being mainly hydrophobic in nature, and the doped nanosheets are found to be better docked compared to perfect sheets.

Lycopene coupled ‘trifoliate’ polyaniline nanofibers as multi-functional biomaterial

Bio-conjugation seems to be an unparalleled avenue to tailor the shape-size-bioactivity accord of nanomaterials. In this backdrop, conjugation of tomato peel lycopene through the green chemistry tool of sonication, under statistically optimized parameters led to the morphological alteration of polyaniline (PAni) nanofiber from linear to biomimetic ‘runner’ morphology with trifoliate branching as observed under TEM. X-ray diffractogram was suggestive of alterations in the d-spacing and strain in the polymer backbone post lycopene binding. Post bio-conjugation, the semiconducting-behavior of the PAni nanofibers was retained although lycopene coupling resulted in a decrease in the formers conductivity. DMol3 was employed for the quantum molecular calculations of lycopene interacting with PAni (via non-covalent functionalization involving π–π stacking) and its solvation study. The contribution to HOMO came from the lycopene unit whereas the LUMO had contribution from the aromatic ring of PAni in the conjugated system. The bioactivity of the PAni nanofibers post bio-conjugation was attested by free radical scavenging and anti-lipid peroxidation of liver tissue homogenate. Epiflorescence microscopic imaging demonstrated the cytocompatibility with L929 normal cell line while the nuclear fragmentation and membrane blebbing of apoptotic HeLa cells vouched for the anticancer action of the conjugated system. Furthermore, the reported system exhibited a stimulatory effect on Cucumis sativus seed germination. Thus the study marshals in support of modulated morphology and desirable bio-action of nanoscaled biomaterials via bio-conjugation for advanced applications.

Interaction of pyrazinamide drug functionalized carbon and boron nitride nanotubes with pncA protein: a molecular dynamics and density functional approach

First principles calculations are performed to study the noncovalent functionalization of single-wall carbon nanotubes (SWCNTs) and boron nitride nanotubes (BNNTs) with pyrazinamide (PZA), an antitubercular chemotherapeutic, providing a detailed insight into the nanotube structure and electronic properties prior to and after functionalization. The simulations highlight the modification in electronic structure of both SWCNTs and BNNTs with the enhancement of electronic states within the valence and conduction band regions of the PZA–SWCNT system, significant lowering of the energy gap and the presence of new dispersionless bands in the PZA–BNNT system. Depending on the chirality of the nanotubes, PZA exhibits a preferential selectivity for adsorption, which is further affirmed from the band structure, density of the states, total projected density of the states and frontier orbital analysis with a charge transfer between PZA and a nanotube. A molecular docking simulation suggests that SWCNTs facilitate the targeted release of PZA within the protein through a lock and key mechanism. The intermolecular interaction between PZA–SWCNT and pncA was compared using a molecular dynamics simulation, and by observing any structural change induced within the system due to the interactions. Thus, functionalization of SWCNTs and BNNTs with PZA mediated by π–π stacking is an effective method to engineer nanotubes’ electronic properties and band gaps for applications pertinent to tuberculosis chemotherapy.

Adsorption of 3,4-dihydroxybenzoic acid onto hematite surface in aqueous medium: Importance of position of phenolic –OH groups and understanding of the same using catechol as an auxiliary model

A comparative adsorption kinetics, isotherms, dissolution and surface complexation of 3,4-dihydroxybenzoic acid (3,4-DHBA) and 1,2-dihydroxybenzene (catechol) at the hematite/electrolyte interface were investigated. The kinetics at pH 10 and 298.15K suggested that the adsorption behaviour of 3,4-DHBA and catechol onto hematite surface is similar and attain same equilibration time of 60 min. The adsorption kinetics data of 3,4-DHBA and catechol fit the pseudo-second-order kinetic equation of nonlinear form best. The adsorption density of 3,4-DHBA at pH≥9 increases and thereby mimics the behaviour of catechol. The solubility of hematite depends on both pH of the suspension and concentration of adsorbate. The inner-sphere complex is formed by 3,4-DHBA and catechol onto hematite surface but the mode orientation is likely to be different in the pH range 5-8 and 9-10. The advance microscopic scanning in conjunction with the vibration spectroscopy would provide better pictorial presentation of the mode of orientation of 3,4-DHBA and catechol onto hematite surface at different pH.

Adsorption of isoniazid and pyrazinamide drug molecules onto nitrogen-doped single-wall carbon nanotubes: an ab initio study

Abstract The noncovalent functionalizations of isoniazid (INH) and pyrazinamide (PZA) antitubercular drugs adsorbed onto perfect and N-doped (6,6) and (10,0) single-wall carbon nanotubes (SWCNTs) have been studied using density functional theory (DFT). The binding energies (B.Es), electronic properties, and nature of interaction for the two nanotube model systems have been compared for both periodic and cluster models. The variations in energy values with distance at the DFT/LDA and DFT/GGA levels of calculation can help in correlating the weak noncovalent functionalization governed by the Lennard-Jones type of interactions. The two molecules exhibit a similar pattern of adsorption onto the nanotube sidewall for periodic and cluster models; however, the B.E. values are comparatively higher for the periodic model counterparts. The negative B.E. values suggest the thermodynamic favorability toward the adsorption and presence of N dopant atom facilitates in better drug binding with the tube sidewall. The frontier orbital analysis and global reactivity descriptors before and after functionalization of INH and PZA onto the SWCNTs corresponding to cluster models are compared and the results analyzed. At a theoretical level of understanding through this study we focus that N ad atom doping onto SWCNTs facilitate in enhancing the reactivity of pristine nanotubes toward drug binding thereby modulating its electronic properties and influencing the adsorption.

Dynamics of self-assembled cytosine nucleobases on graphene

Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.