An investigation on the molecular structure, interaction with metal clusters, anti-Covid-19 ability of 2-deoxy-D-glucose: DFT calculations, MD and docking simulations

Examining the adsorption and sensing characteristics of cytosine (CTE) on Y9N9 (Y = Al, B, Ga) nanorings using solvent effects, DFT, AIM and SERS analyses

Nucleobases are nitrogenous biological compounds that are more significant in a range of biological and in medical applications. They are constituents of nucleotides in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Therefore, we assessed the sensing applicability by studying the cytosine (CTE)-Y9N9 (Y = Al, B, Ga) nanoring interaction using density functional theory. It was evident that CTE interacted strongly with each ring. Due to charge transfer between the nanoring and CTE, a dipole moment (DM) is generated. All complexes have band gaps less than that of CTE. Complexes' band gap energies are lower in aqueous phase and vacuum than they are in pristine rings. All complexes exhibit higher adsorption energies in solvent medium in comparison with that in vacuum. Changes in the frontier molecular orbitals (FMOs) energies of nanorings after interaction have a major impact on their electrical conductivity and work function. In addition to being an electrical sensor, the Y9N9 nanorings for CTE can also be utilized as a work function-based sensor. But Y9N9's CTE recovery time indicates that it can be used to extract or store CTE depending on the environment. The current work can be expanded to examine the impact of Ag/Au/Cu doping using Y9N9 in order to examine the characteristics of drug delivery carriers and the consequence of doping. The interaction between the analyte and substrate was further studied using reduced density gradient (RDG) analysis, comparing the nature and strength of the interaction in both vacuum and aqueous medium. The observations revealed a stronger interaction in the presence of an aqueous medium, which aligns with the higher adsorption energy values.

A new natural Cyperol A together with five known compounds from Cyperus rotundus L.: isolation, structure elucidation, DFT analysis, insecticidal and enzyme-inhibition activities and in silico study

One new natural benzaldehyde derivative (1), together with five known compounds, was isolated from the methanolic extract of the whole plant of Cyperus rotundus L., which is a globally distributed noxious weed. The structure of compound (1) (named Cyperol A) was determined using various NMR methods, including 1H, 13C, COSY, HMBC, HSQC and NOESY, and mass spectrometric techniques, including EIMS. The newly isolated compound (1) was subjected to optimization using computer-assisted calculation via DFT methods for natural bond orbital (NBO) and frontier molecular orbital (FMO) analyses and compared with carbofuran, which is used to control the pest brown planthopper. The in vitro insecticidal efficacy of compounds 1-6 was evaluated against Nilaparvata lugens. Compound 1 demonstrated exceptional lethal and notable enzyme inhibitory effects. Furthermore, compound 1 was investigated in silico for its anti-pesticidal activities targeting the BPH (Nilaparvata lugens (Stål)) key enzymes, such as glutathione S-transferase (GST) and acetylcholinesterase (AChE). Compound 1 showed good docking scores of -9.75 kcal mol-1 against GST, forming hydrogen bonds with its active site, and -10.56 kcal mol-1 with AChE owing to its high potential for hydrogen bonding.

Structural and electronic properties of AgNPs adsorbed by glucose molecules determined using DFT theory

In order to build and design stable molecular structures of α-D-glucose molecules after adding to a cluster of silver atoms, an optimization process was precisely carried out for α-D glucose/Ag3 molecule at low energy. The correlation between glucose molecule and silver atoms is evaluated by investigating configurational and electronic features of the named molecules by adopting the Density functional theory DFT using the hybrid B3LYP functional and 6-311+G∗ as a basis set for C, O, and H atoms, while LANL2DZ set for silver (Ag) atoms. Frequencies of vibrational modes are essential analyses that have been instrumental in understanding the IR spectra of studied molecules. These analyses enable the detection of the active groups along the spectrum chart including C-O-C, C=O, C-O, O-H, C-C and C-H peaks confirming the previous experimental findings. Another important finding is the energy gap (E g ) obtained by the difference between the higher occupied molecular orbital (HOMO) and lower unoccupied molecular orbital (LUMO). Remarkably, E g was found to increase from 3.440 to 4.358 eV in a configuration consisting of two glucose molecules with one Ag atom (2α-D glucose/Ag-C12H24O12Ag) to another with one glucose molecule with three Ag atoms (α-D glucose/Ag3-C6H12O6Ag3) configuration. Additionally, the potential of the molecular electrostatic isosurface (MEP) in 3D diagram for two configurations is clarified by the colour-coded bar with the distributions of charge density distributions to examine the nucleophilicity and electrophilicity behaviour.

Interactions of coinage metal nanoclusters with low-molecular-weight biocompounds

Nowadays, coinage metal nanoclusters (NCs) are largely presented in diagnostics, bioimaging, and biocatalysis due to their high biocompatibility, chemical stability, and sensitivity to surrounding biomolecules. Silver and gold NCs are usually characterized by intense luminescence and photostability, which is in great demand in the detection of organic compounds, ions, pH, temperature, etc. The experimental synthesis of metal NCs often occurs on biopolymer templates, mostly DNA and proteins. However, this review mainly focuses on the interactions with small biomolecules (SBMs) of a molecular weight less than 1000 Da: amino acids, nucleobases, thiolates, oligopeptides, etc. Such molecules can serve as the templates for an eco-friendly facile one-pot synthesis of biocompatible luminescent NCs. The latter aspect makes NCs suitable for diagnostics and intracellular bioimaging. Another important aspect is the interaction of clusters with biomarkers, which is largely exploited by nanosensors: biomarker detection often occurs through either fluorescence emission "turn-on" or "turn-off" mechanisms. Moreover, as theoretical studies show, electronic absorption spectra and Raman spectra of the metal-organic complexes allow efficient detection of various analytes. In this regard, both theoretical and experimental studies of SBM complexes with metal NCs are in great demand. Therefore, this review aims to summarize up-to-date studies on the interaction of small biomolecules with coinage metal NCs from both theoretical and experimental viewpoints.

Central Countries' and Brazil's Contributions to Nanotechnology

Abstract:

Nanotechnology is a cornerstone of the scientific advances witnessed over the past few years. Nanotechnology applications are extensively broad, and an overview of the main trends worldwide can give an insight into the most researched areas and gaps to be covered. This document presents an overview of the trend topics of the three leading countries studying in this area, as well as Brazil for comparison. The data mining was made from the Scopus database and analyzed using the VOSviewer and Voyant Tools software. More than 44.000 indexed articles published from 2010 to 2020 revealed that the countries responsible for the highest number of published articles are The United States, China, and India, while Brazil is in the fifteenth position. Thematic global networks revealed that the standing-out research topics are health science, energy, wastewater treatment, and electronics. In a temporal observation, the primary topics of research are: India (2020), which was devoted to facing SARS-COV 2; Brazil (2019), which is developing promising strategies to combat cancer; China (2018), whit research on nanomedicine and triboelectric nanogenerators; the United States (2017) and the Global tendencies (2018) are also related to the development of triboelectric nanogenerators. The collected data are available on GitHub. This study demonstrates the innovative use of data-mining technologies to gain a comprehensive understanding of nanotechnology's contributions and trends and highlights the diverse priorities of nations in this cutting-edge field.

Synthesis and Spectroscopic Characterization of Schiff Base Metal Complexes, Biological Activity, and Molecular Docking Studies

New cobalt(II), copper(II), and zinc(II) Schiff metal complexes were synthesized by the condensation reaction of 4-nitrobenzene-1,2-diamine with 3-4-(diethylamino)-2-hydroxybenzaldehyde. Fourier transform infrared, nuclear magnetic resonance, ultraviolet-visible, electron paramagnetic resonance, and high-resolution electrospray ionization mass spectrometry and powder X-ray diffraction were used to characterize the synthesized H2L and its metal complexes. Conductance measurements, magnetic moment estimation, and metal estimation have all been determined and discussed. The electrochemical properties of the synthesized compounds have been determined and discussed using cyclic voltammetry. The molecular structures of H2L and its metal complexes have been optimized using the B3LYP functional and the 6-31G (d,p) basis set, and their parameters have been discussed. The quantum chemical properties of these synthesized compounds have been predicted through charge distribution and molecular orbital analysis. The biological properties of the synthesized compounds' antioxidant, antifungal, and antibacterial activity have been studied and discussed. Furthermore, H2L and its complexes have been docked with HER2-associated target proteins in breast cancer.

Understanding the Interaction Mechanism between the Epinephrine Neurotransmitter and Small Gold Nanoclusters (Aun; n = 6, 8, and 10): A Computational Insight

In this study, the interaction between the neurotransmitter epinephrine and small gold nanoclusters (AunNCs) with n = 6, 8, and 10 is described by density functional theory calculations. The interaction of Au6, Au8, and Au10 nanoclusters with epinephrine is governed by Au-X (X = N and O) anchoring bonding and Au···H-X conventional hydrogen bonding. The interaction mechanism of epinephrine with gold nanoclusters is investigated in terms of electronic energy and geometrical properties. The adsorption energy values for the most favorable configurations of Au6NC@epinephrine, Au8NC@epinephrine, and Au10NC@epinephrine were calculated to be -17.45, -17.86, and -16.07 kcal/mol, respectively, in the gas phase. The results indicate a significant interaction of epinephrine with AunNCs and point to the application of the biomolecular complex AunNC@epinephrine in the fields of biosensing, drug delivery, bioimaging, and other applications. In addition, some important electronic properties, namely, the energy gap between HOMO and LUMO, the Fermi level, and the work function, were computed. The effect of aqueous media on adsorption energy and electronic parameters for the most favorable configurations was also studied to explore the influence of physical biological conditions.

In silico investigation on interaction of small Ag6 nano-particle cluster with tyramine neurotransmitter

The interaction of tyramine neurotransmitter with silver nano-particle (Ag6) cluster is explored in terms of the molecular structure, electronic properties and NBO analysis of tyramine-AgNPs bio-molecular conjugate. The adsorption mechanism of tyramine onto the Ag6 cluster has been investigated through computing of the electronic and geometrical properties in addition to the adsorption energies in various possible configurations. The magnitude of adsorption energy corresponding to the most favorable tyramine-Ag6 bio-molecular conjugate has been computed to be - 14.36 kcal/mol in the gas phase, which infers a good adsorption of tyramine with AgNPs cluster suggesting the practical applications of tyramine-AgNPs bio-molecular conjugates in bio-sensing, drug delivery, bio-imaging and other applications. Different electronic properties such as the energy gap of HOMO-LUMO, Fermi level and work function have been investigated in detail. Moreover, the effect of aqueous media on adsorption energy and electronic properties of the most favorable tyramine-AgNPs bio-molecular conjugate is investigated in order to understand the impact of the real biological situation.

TD-DFT, DFT, docking, MD simulations, and concentration-dependent SERS investigations of a bioactive trifluoromethyl derivative having human acetylcholinesterase and butyrylcholinesterase in silver colloids

CONTEXT

Various concentrations of (E)-4-methoxy-N'-(2-(trifluoromethyl)benzylidene) benzohydrazide (EMT) adsorbed on colloidal silver nanoparticles were studied using SERS and results were compared to the normal Raman spectrum. DFT calculations were used to validate experimental findings. Theoretically, the structures of the EMT and EMT-Ag6 systems were optimized. The UV-Vis spectral analysis's red shift and lower intensity behavior show that EMT has chemisorbed onto Ag nanoparticles. Charge transfer (CT) from Ag to EMT is highlighted by FMO analysis. The CT interaction in EMT and EMT-Ag6 was further verified by MEP and Mulliken charge analyses. The EMT was adsorbed on Ag nanoparticles with tilted orientation and orientation changes with colloidal concentration, according to SERS spectrum analysis. Docking EMT with 4PQE and 5DYW binding affinities are found to be -9.7 and -8.1 kcal/mol. MD simulations give the competence of 5DYW-EMT and 4PQE-EMT in their intended binding interactions and their ability to establish enduring associations with the protein of interest.

METHODS

DFT was used to optimize the molecular structures of EMT and EMT-Ag6 using B3LYP/6-311++G* (LANL2DZ basis set for Ag). A molecular dynamics simulation study was conducted on the 4PQE-EMT and 5DYW-EMT systems using the Desmond software for 100 ns.

2-Deoxy-D-Glucose: A Novel Pharmacological Agent for Killing Hypoxic Tumor Cells, Oxygen Dependence-Lowering in Covid-19, and Other Pharmacological Activities

The nonmetabolizable glucose analog 2-deoxy-D-glucose (2-DG) has shown promising pharmacological activities, including inhibition of cancerous cell growth and N-glycosylation. It has been used as a glycolysis inhibitor and as a potential energy restriction mimetic agent, inhibiting pathogen-associated molecular patterns. Radioisotope derivatives of 2-DG have applications as tracers. Recently, 2-DG has been used as an anti-COVID-19 drug to lower the need for supplemental oxygen. In the present review, various pharmaceutical properties of 2-DG are discussed.

Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.