Theoretical elucidation of the amino acid interaction with graphene and functionalized graphene nanosheets: insights from DFT calculation and MD simulation

Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene

There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.

A critical review on graphene and graphene-based derivatives from natural sources emphasizing on CO2 adsorption potential

Accelerated release of carbon dioxide (CO2) into the atmosphere has become a critical environmental issue, and therefore, efficient methods for capturing CO2 are in high demand. Graphene and graphene-based derivatives have demonstrated promising potential as adsorbents due to their unique properties. This review aims to provide an overview of the latest research on graphene and its derivatives fabricated from natural sources which have been utilized and may be explored for CO2 adsorption. The necessity of this review lies in the need to explore alternative, sustainable sources of graphene that can contribute to the development of viable environmentally benign CO2 capture technologies. The review will aim to highlight graphene as an excellent CO2 adsorbent and the possible avenues, advantages, and limitations of the processes involved in fabricating graphene and its derivatives sourced from both industrial resources and organic waste-based naturally occurring carbon precursors for CO2 adsorption. This review will also highlight the CO2 adsorption mechanisms focusing on density functional theory (DFT) and molecular dynamics (MD)-based studies over the last decade.

Probing interaction of atherogenic lysophosphatidylcholine with functionalized graphene nanosheets: theoretical modelling and experimental validation

CONTEXT

The potential of graphene derivatives for theranostic applications depends on their compatibility with cellular and biomolecular components. Lysophosphatidylcholine (LPC), a lipid component present in oxidized low-density lipoproteins, microvesicles and free circulation in blood, plays a critical role in the pathophysiology of various diseases. Using density functional theory-based methods, we systematically investigated the interaction of atherogenic LPC molecule with different derivatives of graphene, including pristine graphene, graphene with defect, N-doped graphene, amine-functionalized graphene, various graphene oxides and hydroxylated graphene oxides. We observed that the adsorption of LPC on graphene derivatives is highly selective based on the orientation of the functional groups of LPC interacting with the surface of the derivatives. Hydroxylated graphene oxide exhibited the strongest interaction with LPC with adsorption energy of - 2.1 eV due to the interaction between the hydroxyl group on graphene and the phosphate group of LPC. The presence of aqueous medium further enhanced this interaction indicating favourable adsorption of LPC and graphene oxide in biological systems. Such strong interaction leads to substantial change in the electronic structure of the LPC molecule, which results in the activation of this molecule. In contrast, amine-modified graphene showed the least interaction. These theoretical results are in line with our experimental fluorescence spectroscopic data of LPC/1-anilino-8-napthalene sulfonic acid complex. Our present comprehensive investigation employing both theoretical and experimental methods provides a deeper understanding of graphene-lipid interaction, which holds paramount importance in the design and fabrication of graphene-based nanomaterials for biomedical applications.

METHODS

In this study, we employed the density functional theory-based methods to investigate the electronic and structural properties of graphene derivatives and LPC molecule using the Quantum Espresso package. The exchange-correlation functional was described within generalized gradient approximation (GGA) as parameterized by Perdew, Burke and Ernzerhof (PBE). The valence electrons were represented using plane wave basis sets. `The Grimme's dispersion method was used to include the van der Waals dispersion correction.

A Density Functional Theory (DFT) Perspective on Optical Absorption of Modified Graphene Interacting with the Main Amino Acids of Spider Silk

We investigated the possible adsorption of each of the main building blocks of spider silk: alanine, glycine, leucine, and proline. This knowledge could help develop new biocompatible materials and favors the creation of new biosensors. We used ab initio density functional theory methods to study the variations in the optical absorption, reflectivity, and band structure of a modified graphene surface interacting with these four molecules. Four modification cases were considered: graphene with vacancies at 5.55% and fluorine, nitrogen, or oxygen doping, also at 5.55%. We found that, among the cases considered, graphene with vacancies is the best candidate to develop optical biosensors to detect C=O amide and differentiate glycine and leucine from alanine and proline in the visible spectrum region. Finally, from the projected density of states, the main changes occur at deep energies. Thus, all modified graphene's electronic energy band structure undergoes only tiny changes when interacting with amino acids.

Molecular level insight into the different interaction intensity between microplastics and aromatic hydrocarbon in pure water and seawater

The interaction of MPs and aromatic hydrocarbons in seawater and pure water was examined using experimental measurements, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations in light of the potential health risks posed by microplastic (MPs)-associated aromatic hydrocarbon pollutants. Isothermal studies and MD simulations suggested that MPs have a stronger affinity for aromatic hydrocarbons in seawater. To uncover the mechanism, MPs' surface characteristics and their intermolecular interactions with aromatic hydrocarbons were examined. According to the research, MPs in seawater have less compact structure, bigger pores, and a higher specific surface area, all of which contribute to more sorption sites. Analysis of the intermolecular interaction indicated that MPs have a greater ability for molecular interactions in seawater and the interaction energy between MPs and aromatic hydrocarbons in seawater is higher. Additionally, seawater cations may act as bridges, which also accelerate sorption in seawater. In summary, this study provides a molecular-level understanding of MPs-aromatic hydrocarbons interaction and demonstrates that the interaction is stronger in seawater.

Theoretical model study of adsorbed antimalarial-graphene dimers: doping effects, photophysical parameters, intermolecular interactions, edge adsorption, and SERS

Future diagnostics and therapy applications are in part riding on the discovery and implementation of new optical techniques and strategies (which often derive from dyads) for example, prediction of features in surface-enhanced Raman spectroscopy requires the study of chromophore-chromophore interactions involve intermolecular forces, drug delivery, and photo mechanisms which are of great interest. New matches between chromophore systems (i.e. FRET), and π-delocalized surfaces are important to study. We explore low-molecular weight drug molecules and their interaction with the reporter material/surface of graphene. Bonding, charge transfer and orbital interactions for 2-amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazole (megazol or AMIT) on graphene were carried out. The graphene model substrate was monotonically/monatomically substituted (doped) with one neutral heteroatom (N/O/S/B) in place of one carbon center; chemical adsorption of AMIT is due to charge transfer from doped graphene to AMIT (DFT). Our AMIT-nanocluster studies show that the nanoclusters will act as a sensor component for the detection of drugs due to SERS. Our findings identified that the greater the energy of the charge transfer, the stronger the calculated chemical adsorption. Additionally, charge transfer is highest for the N-doped systems and least for pristine graphene, resulting in a stronger adsorption energy for N-doped graphene. Mulliken charge analysis of structures confirms enhancement found in QD-AMIT systems.Communicated by Ramaswamy H. Sarma.

Theoretical Study on the Aggregation and Adsorption Behaviors of Anticancer Drug Molecules on Graphene/Graphene Oxide Surface

Graphene and its derivatives are frequently used in cancer therapy, and there has been widespread interest in improving the therapeutic efficiency of targeted drugs. In this paper, the geometrical structure and electronic effects of anastrozole(Anas), camptothecin(CPT), gefitinib (Gefi), and resveratrol (Res) on graphene and graphene oxide(GO) were investigated by density functional theory (DFT) calculations and molecular dynamics (MD) simulation. Meanwhile, we explored and compared the adsorption process between graphene/GO and four drug molecules, as well as the adsorption sites between carriers and payloads. In addition, we calculated the interaction forces between four drug molecules and graphene. We believe that this work will contribute to deepening the understanding of the loading behaviors of anticancer drugs onto nanomaterials and their interaction.

A computational study of metal-organic frameworks (MOFs) as potential nanostructures to combat SARS-CoV-2

The COVID-19 causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has a critical surface protein called spike protein (S protein), which is the target of many vaccines and drugs developments. Among non-structural proteins of SARS-CoV-2, main protease (M^pro) has drawn much attention to itself for designing antiviral drugs since it is very crucial for the virus replication in host cells. In the first part of the present study, the application of metal-organic frameworks (MOFs), one of the developing nanomaterials in the deformation and consequently inhibition of S protein binding to the receptor, angiotensin-converting enzyme 2 (ACE 2), is investigated. In this line, various S protein inhibitors were designed virtually, including ZIF, UIO, and IRMOF that their interactions with S protein and were investigated using molecular dynamics (MD) simulation. The results revealed that ZIF is the best candidate among the investigated MOFs with the least amount of energy interference with S protein. In the second part, the interaction of three-dimensional (3D) MOFs (such as ZIF, IRMOF, and HKUST) with SARS-CoV-2 M^pro was investigated. HKUST had the most potent interaction with M^pro and showed more promise in deforming this protein's secondary structure among all materials tested. Furthermore, we investigated the interaction of HKUST-OH with M^pro to determine the effect of functionalization. The findings of this study could be used in future studies to introduce bioconjugates of MOFs and biological molecules (e.g., antibody or nanobody) or to use MOFs as carriers for antiviral drug delivery.

Selective adsorption and dissociation of NO, NO2, and N2O molecules on Si-doped haeckelite boron nitride nanotube: an investigation for sensitive molecular sensors and catalysts

The current study describes the investigation of the adsorption NO, N₂O, and NO₂ on haeckelite boron nitride nanotube doped with Si (Si-doped haeck-BNNT) by means of density functional theory calculation (DFT). The obtained results confirmed the energetic stability of the optimized geometries and revealed that the adsorption of the gas molecules with the nanotube sidewall is a spontaneous process. The calculated work function of Si-doped haeck-BNNT in the presence of gas molecules is greater than that of a bare Si-doped haeck-BNNT sheet. The energy gap of the Si-doped haeck-BNNT is sensitive to the adsorption of the gas molecules, which implies possible future applications in gas sensors. For most of the adsorption configurations studied, the adsorption energies for the Si_B-doped haeck-BNNT are higher than those for Si_N-doped haeck-BNNTones. The N₂O gas molecule is totally dissociated into N₂ and O species through the adsorption process, while the other gas molecules retain their molecular forms. Thus, the Si_N-doped haeck-BNNT is a likely catalyst for dissociation of the N₂O gas molecule. Our findings divulge promising potential of the doped haeck-BNNT as a highly sensitive molecular sensor for NO and NO₂ detection and a catalyst for N₂O dissociation.

Electroanalysis of Biomolecules: Rational Selection of Sensor Construction

Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.