Covalent hybridization of CNT by thymine and uracil: A computational study

Adsorption of a thione derivative on carbon, AlN, and BN nanotubes: a detailed DFT and MD investigation

The performance of nanotubes (NT) of carbon (CC), aluminium-nitrogen (AlN), and boron-nitrogen (BN) as a sensor and nanocarrier for mercaptopurine (MCP) was investigated by means of a theoretical approach. The calculated negative values of adsorption energy showed the interaction and adsorption of MCP. Highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) distributions were only found on the NT counter portion of the drug-nanotube not on MCP for AlN-NT and BN-NT while HOMO is over MCP and LUMO is over NT for CC-NT. The polarizability of MCP-NTs is greater than that of MCP. Raman wavenumbers of MCP are enhanced in NTs, and hence, NTs can act as a sensor for the detection of MCP. Solvent dependency on adsorption behaviour is also presented in the manuscript, where we found that the AlN nanotube showed exceptionally high free energy of adsorption over other nanotubes in all solvent mediums. Solvation-free energies were also reported. Noncovalent interaction scattered plot also showed significant intermolecular interaction between AlN nanotubes and the mercaptopurine when compared to other nanotubes under study. To find the antiviral activity of MCP and MCP-NTs against antiviral activities, docking and molecular dynamics simulations were performed with 1HMP PDB. Recovery times show that MCP desorption occurs quickly. The MD simulations and docking results show that BN and CC-NTs with MCP show good activity as drug carriers.

Different metal-decorated aluminum phosphide nanotubes as hydrazine sensors for biomedical applications

B3LYP, B97D, and M06-2X density functionals are utilized for probing the effect of decorating X (X = Co, Ti, Sc, or Ca) metals on the sensing performance of an aluminum phosphide nanotube (AlPNT) in detecting the hydrazine (HZ) gas. We predict that the interaction of pristine AlPNT with HZ is physisorption, and our calculated sensing response (SR) of AlPNT is approximately 2.7. The adsorption energy of HZ changes from - 4.6 to - 21.0, - 21.9, - 22.4, and - 23.8 kcal/mol by decorating the Co, Ti, Sc, and Ca metals into the AlPNT surface, respectively. Also, Co, Ti, Sc, and Ca rise the SR to 22.5, 36.8, 50.4, and 89.0, respectively, indicating that by increasing the atomic radius of metals, the sensitivity is more increased. So, we concluded that Ca much more increases the sensitivity of AlPNT toward HZ. Our calculations demonstrate that the electrostatic interaction has the main contribution in the formation of HZ/X decorated AlPNT (X@AlPNT) complexes. The expected recovery time is 22.0 s for the HZ desorption from the Ca@AlPNT at 298 K. Finally, we found that all of the X@AlPNTs have superior sensing performance toward HZ compared to the X@carbon nanotubes.

Density functional theory investigation of ozone gas uptake by a BeO nanoflake

Due to importance of the gas uptake topic in environment and energy issues, this work was performed for investigating ozone (Oz) gas uptake by means of a beryllium oxide (BeO) nanoflake. To this aim, density functional theory (DFT) calculations and the quantum theory of atoms in molecules (QTAIM) analysis were performed. The monolayer BeO nanoflake was decorated by a HEME-like N4Fe region to prepare an interacting region towards the Oz uptake. Accordingly, three models were optimized based on configurations of Oz molecule relaxation at the BeO surface, in which two types of O ... Fe and O ... N interactions were observed. In this case, Oz3@BeO model was involved with two mentioned types of interactions and three occurred interaction between Oz and BeO making it as the strongest bimolecular formation model of Oz@BeO. Moreover, electronic molecular orbital features indicated that the models formations could be also related to sensor functions by variations of electric conductivity because of Oz gas uptake. As a consequence, the investigated BeO nanoflake of this work was proposed for employing in Oz gas uptake for different purposes.

Double chelation of Iron through dimer formation of favipiravir: Density functional theory analysis

This work was performed to examine an idea about full chelation of Iron (Fe) by well-known favipiravir (Fav) as a possible mechanism of action for medication of COVID-19 patients. To this aim, formations of Fe- mediated dimers of Fav were investigated by performing density functional theory (DFT) computations of electronic and structural features for singular and dimer models. The results indicated that the models of dimers were suitable for formation, in which two cis (D1) and trans (D2) models were obtained regarding the configurations of two Fav counterparts towards each other. Energy results indicated that formation of D1 was slightly more favorable than formation of D2. Molecular orbital features affirmed hypothesized interacting sites of Fav for Fe-mediated dimers formations, in which atomic charges and other molecular orbital related representations affirmed such achievements. Moreover, detection of such dimer formation was also possible by monitoring variations of molecular orbitals features. As a consequence, formations of Fe-mediated dimers of Fav could be achievable for possible removal of excess of Fe as a proposed mechanism of action for Fav in medication of COVID-19 patients.

Exploring curcumin interactions with BN nanostructures: A DFT approach

Density functional theory (DFT) calculations were performed to investigate the curcumin adsorption at the surfaces of two boron nitride (BN) nanostructures including nanosheet (BNNS) and nanotube (BNNT). The singular models were optimized to reach the stabilized structures and to evaluate electronic features. Next, performing optimization processes on interacting systems yielded formations of bimolecular complexes through occurrence of physical interactions. For curcumin, keto and enol tautomeric forms were investigated for participating in interactions with the BN nanostructures, in which the enol form was seen for participating in stronger interactions with both of BNNS and BNNT surfaces in comparison with the keto form. Based on such interactions, electronic molecular orbital features detected the effects of molecular communications to show benefit of employing BN nanostructures for drug delivery purposes. Moreover, BNNS was seen to work better than BNNT for such purpose of adsorption and detection of curcumin substance.

Isolation and identification of Streptomyces tunisiensis from Garmsar salt cave soil with antibacterial and gene expression activity against Pseudomonas aeruginosa

It is known that more than 70% of the current antibiotics have been produced by Streptomyces; therefore, the main goal of the present study was to isolate halophiles Streptomyces to investigate their antimicrobial properties on the expression of the pathogenic genes of clinically resistant Pseudomonas aeruginosa. To this aim, isolation of Streptomyces from soil was performed by serial dilution method, and cultivation on ISP2 and SCA medium. The secondary metabolite was extracted by ethyl acetate method. The presence of exo A, alg D and oprl genes were determined by PCR in 50 clinical isolates of Pseudomonas aeruginosa. The inhibitory effect of active metabolites on gene expression were investigated by employing the real-time PCR technique. The purification of secondary metabolites were performed by employing the HPLC technique. Moreover, the FTIR technique was employed to determine the functional groups to help performing identifications by employing the LC-MS technique. Finally, selected Streptomyces was identified by 16S ribosomal RNA gene. Accordingly, the possible forms of Streptomyces were isolated and identified, in which Streptomyces number 25 had the highest growth inhibition zone against the clinical strains of Pseudomonas aeruginosa. The obtained results of molecular analysis showed 95.4% similarity to Streptomyces tunisiensis. The effect of selected Streptomyces secondary metabolites reduced expressions of both of exo A and algD genes in 1024μg/mL concentration. In this regard, the potent fraction could be known as an isobutyl Nonactin analogue. The concluding remarks of this work showed the antimicrobial activity of halophilus Streptomyces species against the resistant strains of Pseudomonas aeruginosa with the ability of producing antibiotics proposing for running further investigations to determine the active compound structures.

Investigating a promising iron-doped graphene sensor for SO2 gas: DFT calculations and QTAIM analysis

Examination of a promising iron-doped graphene (FG) sensor for the sulfur oxide (SO2) toxic gas was done in this work at the molecular and atomic scales of density functional theory (DFT). The models were stabilized by performing optimization calculations and their electronic features were evaluated. Two models were obtained by relaxing each of the O or S atoms towards the Fe-doped region of surface. Energy values indicated higher strength for formation of the O@FG model in comparison with the S@FG model. The evaluated quantities and qualities of electronic molecular orbitals indicated the effects of occurrence of adsorption processes on the electronic conductivity property of FG as a required feature of a sensor material. As a consequence, the idea of proposing the investigated FG as a promising sensor of the hazardous SO2 gas was affirmed in this work based on the obtained structural and electronic features.

Interaction of a conical carbon scaffold with the thio-substituted model of fluorouracil towards approaching the drug delivery purposes

A representative FeN4-doped conical carbon (C) scaffold was investigated for participating in interactions with the thio-substituted fluorouracil (SFU) anticancer drug by performing density functional theory (DFT) calculations. In this regard, all possible relaxation configurations of SFU at the doped tip of C scaffold were examined, in which three models were obtained including one horizontal relaxation configuration (FC1) and two vertical relaxation configurations (FC2 and FC3). The results indicate the highest stability and strength for FC1 model. Examining formations and strengths of interactions showed two medium strength interactions in each of FC1, FC2, and FC3 models. Moreover, the evaluated electronic molecular orbitals features indicated availability of sensor function for the proposed C scaffold towards the interacting SFU substance. As a consequence, the models were determined to work in dual functions of sensor and carrier towards drug delivery purpose of SFU anticancer drug.

Catalytic nanoparticles and magnetic nanocatalysts in organic reactions: A mini review

Nanocatalysts, as a part of nanotechnology, have been seen very useful for various fileds of applications capturing a large contribution of the world market. Indeed, several unsolved issues of catalysts have been reconsidered by employing the new nanocatalysts including single core metal atoms and ions with surrounding holes. Moreover, it was expected that the future of catalytic reactions, especially those organic ones, will deal with the nanocatalyst applications. To this aim, the features of catalytic nanoparticles and magnetic nanocatalysts regarding evaluation of their advantages and applications in organic reactions were investigated in this work. Developments of catalytic nanoparticles and magnetic nanocatalysts were discussed in this work regarding the novel applications of such materials at the nanoscale for approaching advantageous features. Increased availability, activity, and stability are very important for applications of the catalysts in various organic reactions. Therefore, it is a must to discuss features of such nanocatalytic systems to provide more information about their advantages and even disadvantages of their applications.

Structural analysis of dexrazoxane: Exploring tautomeric conformations

Structural analysis of dexrazoxane, as a cardioprotective agent, was done in this work by exploring formations of tautomeric conformations and investigating the corresponding effects. Density functional theory (DFT) calculations were performed to optimize the structures to evaluate their molecular and atomic descriptors. In addition to the original structure of dexrazoxane, eight tautomers were obtained with lower stability than the original compound. Movements of two hydrogen atoms in between nitrogen and oxygen atoms of heterocyclic ring put such significant effects. Moreover, electronic molecular orbital features showed effects of such tautomerism processes on distribution patterns and surfaces, in which evaluating the quadrupole coupling constants helped to show the role of atomic sites for resulting the features. As a consequence, the results indicated that the tautomeric formations could significantly change the features of dexrazoxane reminding the importance of carful medication of this drug for patients.

Investigating fullerene-oxide nanostructure as an adsorbent of ammonia: Complexation efficiency by density functional theory

A model of OC20 fullerene-oxide (FO) was investigated in this work for adsorbing the ammonia (NH3) substance by the hypothesis of formations of bimolecular complexes of the two substances. To affirm such hypothesis, the models of singular NH3 and FO were optimized to reach the minimized energy structures and all possibilities of their interactions configurations were examined. As a consequence, three NH3@FO bimolecular complex models were obtained for reaching the point of complex formations. Details of interactions indicated both direct and indirect contributions of the oxidized region of FO to interactions with both H and N atomic sites of NH3. In this regard, CPLX3 with two types of H. . . O and N. . . C interactions was seen to be at the highest strength of adsorption and complex formation in comparison with CPLX1 and CPLX2 models including only one interaction of each of H. . . O and N. . . C type, respectively. Moreover, the obtained electronic molecular orbital features revealed the sensor function of FO material versus the NH3 substance. As a consequence, the hypothesis of NH3@FO complexes formation was affirmed with two proposed functions of removal and detection for the investigated FO material. All results of this work were obtained by details through performing density functional theory (DFT) calculations.

Investigating drug delivery of 5-fluorouracil by assistance of an iron-modified graphene scaffold: Computational studies

This computational work was performed to investigate drug delivery of 5-fluorouracil (FU) anti-cancer by assistance of an iron(Fe)-modified graphene (G) scaffold. The models were optimized to reach the minimized energy structures in both of singular and bimolecular models. Two models of FU@G complex were obtained including O2@G and O4@G by relaxation of FU through O2 and O4 atoms towards the Fe-atom region of G surface. The obtained results of energies indicated a higher stability and strength for the O2@G model in comparison with the O4@G model. The quantitative and qualitative features of electronic molecular orbitals indicated the investigated G surface could work as a carrier of FU by reducing the unwanted side effects and also playing the sensor role. As a final remark of this work, the investigated G model could be proposed for employing in the targeted drug delivery of FU in both of carrier and sensor agents.

Interactions of coumarin derivatives with monoamine oxidase biomarkers: In silico approach

A list of coumarin derivatives (A-P) were investigated in this work for recognizing their reactivity features and their functions towards the monoamine oxidase (MAO) enzyme biomarkers. In this regard, the models showed that he additional of molecular groups to the original scaffold of coumarin could significantly change the reactivity features leading to various tendency for contributing to reactions with other substances. In this case, were varied based on the obtained values of chemical hardness and softness parameters. Subsequently, formations of interacting ligand-target complexes indicated the coumarin derivatives could work as selective substances for interacting with each of MAOA (D) and MAOB (L) enzyme biomarkers, in which a common substance (E) was also observed for formation of interacting complexes with both of MAOA and MAOB targets. As a consequence, the models of coumarin were seen suitable for interacting with the MAO enzyme biomarkers with the purposes of detection and medication. All required information of this work were obtained in the in silico medium.

HOMO-LUMO photosensitization analyses of coronene-cytosine complexes

Photosensitization analyses of models of (–HC = CH–)n assisted coronene-cytosine complexes assigned by Cor-n-Cyt; n varying by 0, 1, 2, and 3, were investigated in this work by performing density functional theory (DFT) calculations. The investigated models were optimized and chemical descriptors were evaluated. To achieve the goal of this work, energy levels of the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) were evaluated to reach the absorption energy requirement for innovating photosensitizer (PS) compounds. The models indicated that the complex formations could help the structures to participate in interactions easier than the singular models, in which HOMO-LUMO descriptors indicated lower required absorption energy for them to increase their safety for human health level. The required absorption energies of complexes with n = 0, 1, and 2, were in ultraviolet (UV) region whereas that of complex with n = 3 was moved to visible region. In this regard, the idea of new PS compounds innovation was examined here to introduce Cor-n-Cyt complexes for possible applications in photodynamic therapy (PDT).

Structural analysis of an iron-assisted carbon monolayer for delivery of 2-thiouracil

An idea of employing an iron-assisted carbon (FeC) monolayer for delivery of 2-thiouracil (2TU) was examined in this work by analyzing structural features for singular and bimolecular models. Density functional theory (DFT) calculations were performed for optimizing the structures and evaluating molecular and atomic descriptors for analyzing the models systems. Two bimolecular models were obtained assigning by S-FeC and O-FeC models, in which each of S and O atom of 2TU was relaxed towards the Fe region of FeC surface in the mentioned models, respectively. The results indicated that both models were achievable with slightly more favorability for formation of S-FeC model. The obtained molecular orbital properties revealed the dominant role of FeC monolayer for managing future interactions of attached 2TU, which is indeed a major role for employing nanomaterials for targeted drug delivery purposes. In addition to energies and molecular orbital features, atomic quadrupole coupling constants indicated the benefit of employing FeC monolayer for drug delivery of 2TU.

Electronic and structural features of uranium-doped graphene: DFT study

Electronic and structural features of uranium-doped models of graphene (UG) were investigated in this work by employing the density functional theory (DFT) approach. Three sizes of models were investigated based on the numbers of surrounding layers around the central U-doped region including UG1, UG2, and UG3. In this regard, stabilized structures were obtained and their electronic molecular orbital features were evaluated, accordingly. The results indicated that the stabilized structures could be obtained, in which their electronic features are indeed size-dependent. The conductivity feature was expected at a higher level for the UG3 model whereas that of the UG1 model was at a lower level. Energy levels of the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) were indeed the evidence of such achievement for electronic conductivity features. As a consequence, the model size of UG could determine its electronic feature providing it for specified applications.

Exploring chemistry features of favipiravir in octanol/water solutions

Favipiravir (Fav) has become a well-known drug for medication of patients by appearance of COVID-19. Heterocyclic structure and connected peptide group could make changes for Fav yielding different features from those required features. Therefore, it is indeed a challenging task to prepare a Fav compound with specific features of desired function. In this work, existence of eight Fav structures by tautomeric formations and peptide group rotations were obtained using density functional theory (DFT) optimization calculations. Gas phase, octanol solution, and water solution were employed to show impact of solution on features of Fav besides obtaining partition coefficients (LogP) for Fav compounds. Significant impacts of solutions were seen on features of Fav with the obtained LogP order: Fav-7 >  Fav-8 >  Fav-4 >  Fav-3 >  Fav-2 >  Fav-5 >  Fav-1 >  Fav-6. As a consequence, internal changes yielded significant impacts on features of Fav affirming its carful medication of COVID-19 patients.

DFT Studies of Single Lithium Adsorption on Coronene

Density functional theory (DFT) calculations were performed to study the adsorption of neutral and cationic forms of single lithium (Li) on representative original and each of oxygen/sulfur-terminated coronene monolayer surfaces. First, the monolayers of coronene structures were prepared. Next, Li/Li+ adsorptions were investigated on the surfaces of the already optimised coronene models. The results indicate that the singular coronene models can be considered as appropriate surfaces for Li/Li+ adsorption, with stronger Li+ adsorption. Localisations of LI/Li+ species were carefully examined at the central carbon zone of the monolayer surface; however, only one model showed discrepancy by getting localised at the monolayer edge. Energy levels and distribution patters for the molecular orbitals indicate the effects of atomic terminations and Li/Li+ adsorptions, in which the singular and Li+-adsorbed models reveal identical results. Atomic-scale nuclear quadrupole resonance (NQR) properties were also evaluated, with the results indicating that the atomic properties can determine the major electronic properties for applying the coronene structure for specific applications.