Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces

BeO nanotube as a promising material for anticancer drugs delivery system

In this research, the application of BeO nanotube (BeONT) as a nanocarrier for Fluorouracil (5-FU) anticancer drug has been studied by density functional theory (DFT) approach. The method ωB97XD with 6-31 G** basis set were employed. A precise surface study, shows that there are two directions for 5-FU adsorption that did not deliver any of the imaginary frequency vibrational spectra, identifying that all relaxation structures are at the lowest energy level. Based on our calculations, the energy of adsorption for 5FU@BeONT structures are range -120 to -168 kJ/mol, in the gas phase and -395 to 4-00 kJ/mol in the aqueous phase. The highest and the lowest values of adsorption energy are both in strong physical adsorption. Due to receiving an electronic charge from 5-FU, BeONT exhibited a p-type semiconducting feature for all positions. In addition, based on natural bond orbital (NBO) analysis, the direction of charge transfer was from fluorine's σ orbitals of the drug to n* orbitals (O and Be atoms) of BeONT with a considerable amount of transferred energy. BeONT can be employed as a potential strong carrier for 5-FU drugs for practical purposes based on our findings.

Density functional theory computation of the intermolecular interactions of Al2@C24 and Al2@Mg12O12 semiconducting quantum dots conjugated with the glycine tripeptide

The nature of intermolecular forces within semiconductor quantum dot systems can determine various physicochemical properties, as well as their functions, in nanomedical applications. The purpose of this study has been to investigate the nature of the intermolecular forces operating between Al2@C24 and Al2@Mg12O12 semiconducting quantum dots and the glycine tripeptide (GlyGlyGly), and also consider whether permanent electric dipole-dipole interactions play a significant role vis-à-vis these molecular systems. The energy computations, including the Keesom and the total electronic interactions and the energy decomposition, together with the quantum topology analyses were performed. Our results demonstrate that no significant correlation is found between the magnitude and orientation of the electrical dipole moments, and the interaction energy of the Al2@C24 and Al2@Mg12O12 with GlyGlyGly tripeptide. The Pearson correlation coefficient test revealed a very weak correlation between the quantum and the Keesom interaction energies. Apart from the quantum topology analyses, the energy decomposition consideration confirmed that the dominant share of the interaction energies was associated with the electrostatic interactions, yet both the steric and the quantum effects also made appreciable contributions. We conclude that, beside the electrical dipole-dipole interactions, other prominent intermolecular forces, such as the polarization attraction, the hydrogen bond, and the van der Waals interactions can also influence the interaction energy of the system. The findings of this study can be utilized in several areas in the field of nanobiomedicine, including the rational design of cell-penetrating and intracellular drug delivery systems using semiconducting quantum dots functionalized with a peptide.

Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding

The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence-morphology-stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemical properties for applications as biomaterials. Moreover, by comparative examinations of the single-stranded segments of three oncogene promoter G-quadruplexes, we assess their druggability potential for future therapeutic strategies. Finally, on the basis of a thorough analysis at the quantum mechanical level of theory on a series of guanine assemblies, we demonstrate how a valence tautomerism, triggered by a coordination of cations, initiates the process of G-quadruplex folding, and we propose a sequential folding mechanism, otherwise dictated by the cancellation of the dipole moments on guanines.

N/OB dative bond supplemented by N-HN/HC Hydrogen Bonds make BN-cages an attractive candidate for DNA-nucleobase adsorption – An MP2 prediction

The response of B12N12-nanocage towards DNA-nucleobases (adenine, guanine, cytosine, and thymine) is investigated using MP2 and DFT (M06-2X) levels of theory with 6-311+G** basis set. Multiple BN-cage-nucleobase structures for each...

Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface

Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.

Two-Dimensional As/BlueP van der Waals Hetero-Structure as a Promising Photocatalyst for Water Splitting: A DFT Study

Constructing van der Waals (vdW) hetero-structure by stacking different two-dimensional (2D) materials has become an effective method for designing new-type and high-quality electronic and optoelectronic nano-devices. In this work, we designed a 2D As/BlueP vdW hetero-structure by stacking monolayer arsenene (As) and monolayer blue phosphorous (BlueP) vertically, which were recently implemented in experiments, and investigated its structural, electronic, and photocatalytic water splitting properties by using the standard first principles calculation method with HSE06 hybrid exchange-correlation functional. Numerical results show that the As/BlueP vdW hetero-structure is structural robust, even at room temperature. It presents semi-conducting behavior, and the conduction band minimum (CBM) and the valence band maximum (VBM) are dominated by BlueP and As, respectively. The typical type-II band alignment predicts the potential application of the hetero-structure in highly efficient optoelectronics and solar energy conversion. Moreover, the CBM and the VBM straddle the redox potentials of water in acid environment, predicting the possibility of the As/BlueP hetero-structure as a 2D photocatalyst for water splitting. When an in-plane strain is applied, the band edges and, further, the optoelectronic properties of the hetero-structure can be effectively tuned. Especially, when tensile strain is equal to 4.5%, the optical absorption spectrum is effectively broadened in a visible light region, which will largely improve its photocatalytic efficiency, although the pH value of the solution range reduction. This work provides theoretical evidence that the As/BlueP hetero-structure has potential application as a 2D photocatalyst in water splitting.

Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure

Recent advances in nanotechnology have facilitated fabrication of various solid state nanopores as a versatile alternative to biological nanopores; however, effective transport of a single-stranded DNA (ssDNA) molecule through solid state nanopores for sequencing has remained a challenge. In particular, the nonspecific interactions between the ssDNA and the engineered nanopore surface are known to impose difficulties on both transport and interrogation. Here, we show that a two-dimensional (2D) nanopore patterned on an in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) can be utilized to transport the ssDNA electrophoretically. Energetically, a ssDNA molecule prefers to stay on the hBN domain than the graphene one since the former has a stronger van der Waals attraction with the ssDNA, as demonstrated in both classic molecular dynamics (MD) simulations and density functional theory (DFT) based calculations, which leads to the confinement of the ssDNA in the 2D nanopore. Therefore, this nanopore enables the manipulation of the conformation of a highly flexible ssDNA molecule on a flat 2D heterostructure surface, making it possible for sensing ssDNA bases using the high resolution atomic force microscopy (AFM) or scanning tunneling microscopy (STM) in the third dimension (perpendicular to the 2D surface).

Printed gas sensors

This review presents the recent development of printed gas sensors based on functional inks.

Controlled current confinement in interfaced 2D nanosensor for electrical identification of DNA

The controlled synthesis of hybrid two-dimensional (2D) materials and the development of atomically precise nanopore fabrication techniques have opened up entirely new possibilities for sensing applications via nanoelectronics. Here, we investigate the electronic transport properties of an in-plane hybrid graphene/h-BN device, containing a graphene nanopore, to assess its feasibility to act as a molecular sensor. The results from our calculations based on density functional theory and the non-equilibrium Green's function formalism reveal the capability to confine the electric current pathways to the two carbon wires lining either edge of the nanopore, thereby creating conditions in which the conductance is highly sensitive to any changes in the electrical potential inside the nanopore. We apply this setup to assess whether it is possible to electrically determine the base sequence in a DNA molecule. Indeed, the modulation of the device conductance reveals a characteristic fingerprint of each nucleotide, which manifests itself in a pronounced difference in the sensitivity of the four different nucleotides, thereby allowing electrical discrimination. These findings lead us to propose this device architecture as a promising nanobiosensor. While fabrication in the lab may represent a profound experimental challenge, it should nevertheless in principle be feasible with existing contemporary techniques of hybrid 2D material synthesis, in conjunction with approaches for highly controlled nanopore creation.

Tunable, Multifunctional Ceramic Composites via Intercalation of Fused Graphene Boron Nitride Nanosheets

Ternary two-dimensional (2D) materials such as fused graphene-boron nitride (GBN) nanosheets exhibit attractive physical and tunable properties far beyond their parent structures. Although these features impart several multifunctional properties in various matrices, a fundamental understanding on the nature of the interfacial interactions of these ternary 2D materials with host matrices and the role of their individual components has been elusive. Herein, we focus on intercalated GBN/ceramic composites as a model system and perform a series of density functional theory calculations to fill this knowledge gap. Propelled by more polarity and negative Gibbs free energy, our results demonstrate that GBN is more water-soluble than graphene and hexagonal boron nitride (h-BN), making it a preferred choice for slurry preparation and resultant intercalations. Further, a chief attribute of the intercalated GBN/ceramic is the formation of covalent C-O and B-O bonds between the two structures, changing the hybridization of GBN from sp² to sp³. This change, combined with the electron release in the vicinity of the interfacial regions, leads to several nonintuitive mechanical and electrical alterations of the composite such as exhibiting higher young's modulus, strength, and ductility as well as sharp decline in the band gap. As a limiting case, though both tobermorite ceramic and h-BN are wide band gap materials, their intercalated composite becomes a p-type semiconductor, contrary to intuition. These multifunctional features, along with our fundamental electronic descriptions of the origin of property change, provide key guidelines for synthesizing next generation of multifunctional bilayer ceramics with remarkable properties on demand.