Density functional theory evaluation of pristine and BN-doped biphenylene nanosheets to detect HCN

Theoretical studies of phosphorene as a drug delivery nanocarrier for fluorouracil

The interactions between phosphorene nanosheets (PNSs) and 5-fluorouracil (FLU) were explored using the density functional theory (DFT) method and molecular dynamics (MD) simulations. DFT calculations were performed utilizing M06-2X functional and the 6-31G(d,p) basis set in both gas and solvent phases. Results showed that the FLU molecule is adsorbed horizontally on the PNS surface with an adsorption energy (Eads) of -18.64 kcal mol-1. The energy gap (Eg) between the highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) of PNS remains constant after the adsorption process. The adsorption behavior of PNS is not affected by carbon and nitrogen doping. The dynamical behavior of PNS-FLU was studied at T = 298, 310, and 326 K reminiscent of room temperature, body temperature, and temperature of the tumor after exposure to 808 nm laser radiation, respectively. The D value decreases significantly after the equilibration of all systems so that the equilibrated value of D is about 1.1 × 10-6, 4.0 × 10-8, and 5.0 × 10-9 cm2 s-1 at T = 298, 310, and 326 K, respectively. About 60 FLU molecules can be adsorbed on both sides of each PNS, indicating its high loading capacity. PMF calculations demonstrated that the release of FLU from PNS is not spontaneous, which is favorable from a sustained drug delivery point of view.

Theoretical evaluation of poly(amidoamine) dendrimers with different peripheral groups as a purinethol drug delivery system in aqueous medium

In this work, density functional theory calculations were used to study the association of PUR with amine- and acetyl-terminated PAMAM dendrimers considering implicit solvent effect at neutral and low pH conditions. Frontier molecular orbitals' analysis indicates that the electronic properties of dendrimers are extremely sensitive to the presence of PUR molecule at both neutral and low pH conditions. Encapsulation of PUR molecule into the both amine- and acetyl-terminated PAMAM dendrimers leads to a Gibbs free energy of (ΔG) - 20.25 kcal.mol^-1 at physiological pH. The corresponding ΔG values reduce to the - 1.45 and - 0.91 kcal.mol^-1 at low pH, indicating that the drug molecule is released easily at low pH. The calculated recovery times for amine- (3.87 ×10² and 3.87 ×10², at neutral and low pH, respectively) and acetyl-terminated (5.34 ×10¹⁰ and 1.81 ×10^-1, at neutral and low pH, respectively) dendrimers suggest that acetylation can improve the release pattern of drug molecule.

Exploration of phosphorene as doxorubicin nanocarrier: An atomistic view from DFT calculations and MD simulations

Potential capability of phosphorene nanosheet (PNS) as doxorubicin (DOX) nanocarrier was investigated using density functional theory (DFT) method and molecular dynamics (MD) simulations. Both DFT calculations and MD simulations revealed that the DOX molecule is adsorbed horizontally onto the PNS surface with the nearest interaction distance of 2.5 Å. The binding energy of DOX is predicted to be about - 49.5 kcal.mol^-1, based on the DFT calculations. After DOX adsorption, the E_g value of PNS remains almost constant in both gas and solvent phases. The dynamical behavior of PNS-DOX was studied at T = 298, 310, and 326 K that reminiscent of room temperature, body temperature, and temperature of tumor after exposure to 808 nm laser radiation, respectively. The diffusion coefficient values of DOX molecule are proportional to temperature. We found that PNS can hold a high amount of DOX on both sides of its surface (66% in weight). MD simulations showed that the dynamical behavior of simulated systems are not affected by pH variances.

On the mechanical properties and fracture patterns of the nonbenzenoid carbon allotrope (biphenylene network): a reactive molecular dynamics study

Recently, a new two-dimensional carbon allotrope named biphenylene network (BPN) was experimentally realized. The BPN structure consists of four-, six-, and eight-membered rings of sp²-hybridized carbon atoms. In this work, we carried out fully-atomistic reactive (ReaxFF) molecular dynamics simulations to study the mechanical properties and fracture patterns of non-defective and defective (nanocracks) BPN. Results show that, under uniaxial tensile loading, BPN is converted into four distinct morphologies before fracture starts. This conversion process is dependent on the stretching direction. Some of the formed structures contain mainly eight-membered rings, which have different shapes in each morphology. In one of them, a graphitization process occurs before the complete fracture. Importantly, in the presence of nanocracks, no new morphologies are formed. BPN exhibits a distinct fracture process when contrasted to graphene. After the critical strain threshold, the graphene transitions from an elastic to a brittle regime, while BPN can exhibit different inelastic stages. These stages are associated with the appearance of new morphologies. However, BPN shares some of the exceptional graphene properties. BPN Young's modulus and melting point are comparable to graphene, about 1019.4 GPa and 4024 K, respectively.

Emerging properties of carbon based 2D material beyond graphene

Graphene turns out to be the pioneering material for setting up boulevard to a new zoo of recently proposed carbon based novel two dimensional (2D) analogues. It is evident that their electronic, optical and other related properties are utterly different from that of graphene because of the distinct intriguing morphology. For instance, the revolutionary emergence of Dirac cones in graphene is particularly hard to find in most of the other 2D materials. As a consequence the crystal symmetries indeed act as a major role for predicting electronic band structure. Since tight binding calculations have become an indispensable tool in electronic band structure calculation, we indicate the implication of such method in graphene's allotropes beyond hexagonal symmetry. It is to be noted that some of these graphene allotropes successfully overcome the inherent drawback of the zero band gap nature of graphene. As a result, these 2D nanomaterials exhibit great potential in a broad spectrum of applications, viz nanoelectronics, nanooptics, gas sensors, gas storages, catalysis, and other specific applications. The miniaturization of high performance graphene allotrope based gas sensors to microscopic or even nanosized range has also been critically discussed. In addition, various optical properties like the dielectric functions, optical conductivity, electron energy loss spectra reveal that these systems can be used in opto-electronic devices. Nonetheless, the honeycomb lattice of graphene is not superconducting. However, it is proposed that the tetragonal form of graphene can be intruded to form new hybrid 2D materials to achieve novel superconducting device at attainable conditions. These dynamic experimental prospects demand further functionalization of these systems to enhance the efficiency and the field of multifunctionality. This topical review aims to highlight the latest advances in carbon based 2D materials beyond graphene from the basic theoretical as well as future application perspectives.

Exploration of interaction behavior between spiro[indene-2,2'-[1,3,5]oxathiazine]-1,3-diones and DNA with the help of DFT, molecular docking, and MD simulations

A detailed computational study covering density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulations of some spirocyclic compounds interacting with a B-DNA has been performed. DFT calculations were performed using the B3LYP functional with 6-311++G(d,p) basis set and were used to identify the electrophilic and nucleophilic centers in electrostatic forces. NMR results were in agreement with previous experimental data and approved the reliability of the used method and basis set. The in silico screening results showed that spirocyclic compounds fulfill the Lipinski's rule of five and can be developed as potential oral bioavailable drug candidates. Based on molecular docking results, the binding affinities follow the 4c < 4d < 4a = 4b < 4e < 4g < 4f order and ranged from -8.6 to -9.7 kcal/mol indicating a reasonably favorable interaction between DNA and investigated compounds. The adducts were stabilized by hydrophobic and hydrogen bonding interactions. The MD simulations performed for 100 ns and the results are reported in terms of variables such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), center of mass (COM) separation distance between DNA and ligands, intermolecular hydrogen bonds, and radial distribution functions (RDF). The MD simulations demonstrated that compounds 4a and 4d bind into the minor groove of 1BNA and may act as potential biological probes for B-DNA.Communicated by Ramaswamy H. Sarma.