RuC nanosheet as a promising biosensing material for detecting the aromatic amino acids: a DFT study

Density functional theory (DFT) calculations were performed to examine the potential of the RuC nanosheet as a biosensor towards the aromatic amino acids (AAA; tryptophan (TRP), histidine (HIS), tyrosine (TYR), and phenylalanine (PHE)). The AAA molecules were placed vertically and horizontally with respect to the RuC surface and then subjected to geometrical relaxation. According to the geometry relaxation results, it was found that all AAA molecules preferred to be adsorbed on the RuC surface in a horizontal configuration rather than a vertical one, except the HIS molecule, which desired to be vertically adsorbed on the RuC nanosheet. From the energy manifestations, the adsorption process within the TRP⋯RuC complexes had the greatest desired negative adsorption energy (E ads), followed by HIS⋯, TYR⋯, and then PHE⋯RuC complexes (E ads = -40.22, -36.54, -23.95, and -16.62 kcal mol-1, respectively). As indicated by the FMO data, changes in the E HOMO, E LUMO, and E gap values of the RuC nanosheet following the adsorption process demonstrated the capacity of the RuC nanosheet to adsorb the AAA molecules. The outcomes of Bader charge transfer revealed that the RuC nanosheet had the ability to donate electrons to the AAA molecules during the adsorption process, supported by the positive Q t values. Consistent with the E ads conclusions, the TRP⋯RuC complexes had the largest Q t values, indicating the potential affinity of the RuC nanosheet to adsorb the TRP molecule. Following the adsorption of AAA molecules on the RuC nanosheet, new peaks and bands were discovered based on the DOS and the band structure plots, respectively, revealing the validity of the adsorption process. Additionally, the current adsorption findings on the RuC nanosheet were compared to those on the graphene (GN) nanosheet. The outcomes of the comparison demonstrated the outperformance of the RuC nanosheet over the GN nanosheet in adsorbing the AAA molecules. These outcomes provide a solid foundation for further research on the RuC nanosheets to detect small biomolecules.

First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

Novel chair graphene nanotubes as adsorbing medium for alanine and asparagine amino acids - A DFT outlook

Amino acids are required to make protein. The deficiency of amino acids leads to a lack of sleep and mood. Among various amino acids, we conducted the adsorption studies of alanine and asparagine amino acids on a novel one-dimensional material, chair graphene nanotube. The stability of the chair graphene nanotube is ensured with the negative formation energy, which is -6.490 eV/atom. The energy band gap of bare chair graphene nanotube is 1.022 eV, which possesses a semiconductor nature. The stable chair graphene nanotube is used as adsorbing material for alanine and asparagine amino acids. Besides, alanine and asparagine are physisorbed on chair graphene nanotubes that are confirmed by the range of adsorption energy from -0.107 eV to -0.718 eV. Upon adsorption of amino acids, the charge transfer outcome shows that chair graphene nanotubes behave as donors of electrons to alanine and asparagine. Further, the changes in the band gap of the chair graphene nanotube are noticed from the results of band structure and PDOS spectrum. The changes in the electron density also reveal the changes in the electronic properties of the chair graphene nanotube owing to alanine and asparagine sorption. The proposed report portrays the adsorption attributes of alanine and asparagine amino acids on 1D chair graphene nanotubes.

Theoretical study of protein adsorption on graphene/h-BN heterostructures

The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.

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.

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.

Interaction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation

Nowadays, a nanostructure-based drug delivery system is one of the most noticeable topics to be studied, and in this regard, boron nitride nanoclusters are promising drug carriers for targeted drug delivery systems. In this article, the interaction mechanism of Anagrelide (AG) drug with B12N12 and Al- and Ga-doped B12N12 nanocages have been investigated using DFT with B3LYP/6-31 G (d, p) method in both gas and water media. All our studied complexes are thermodynamically stable, and doped nanocage complexes have higher negative adsorption energy (EAd.) and negative solvation energy than AG/B12N12 complexes which correspond to the stability of these systems in both media. The negative highest EAd value is 64.98 kcal/mol (63.17 kcal/mol) and 65.69 kcal/mol (65.11 kcal/mol) in gas (water) media for complex F (AG/AlB11N12) and complex I (AG/GaB11N12) respectively, which refers to the highest stability of these systems. The enhanced values of dipole moment (from 12.40 (12.65) Debye to 17.21 (17.69) Debye in complex F (complex I)) also confirm their stability. The QTAIM and RDG analysis endorse the strong adsorption nature of the AG drug onto the AlB11N12, and GaB11N12 nanocages, which is consistent with the adsorption energy as chemisorption occurs for these complexes. According to the electronic properties, doped nanocages show high sensitivity that infers their promising nature for drug delivery purposes. Thus, complex F and complex I are promising drug delivery systems, and doped nanocages (AlB11N12 and GaB11N12) are better carriers than pristine nanocages for the AG drug delivery system.Communicated by Ramaswamy H. Sarma.

The computational quantum mechanical investigation of the functionalized boron nitride nanocage as the smart carriers for favipiravir drug delivery: a DFT and QTAIM analysis

Favipiravir (FPV) is an antiviral drug used for the cure of Influenza virus, Ebola virus, Lassa virus etc. because it has excellent preventing ability of entry/exit of the virus into/from the human cells. Boron nitride nanocages have already drawn enormous attention as the delivery vehicle of various drug molecules for their nontoxicity and other lucrative properties. In this research, we have scrutinized the adsorption mechanism of FPV molecule on the exterior surface of pristine, Zn functionalized, and Ni functionalized B12N12 (BN, Zn f-BN, and Ni f-BN) nanocages by applying the DFT/QTAIM method and B3LYP/6-31G(d,p) approach. The adsorption energy (E_Ad) data reveal that the functionalized BN adsorbents can adsorb FPV drug very efficiently compared with the pristine adsorbent (Highest E_Ad is -56.40 kcal/mol for FPV adsorbed Ni f-BN complex). The reduction of the HOMO-LUMO gap up to 67.79% indicates that this drug can be detected by the produced electrical signal very promisingly in the case of f-BN nanocages. The topological parameters also validate the ability of the f-BN nanocages to adsorb the FPV molecule. The effect of the biological environment of our investigated structures has been studied by using water as a solvent, and spontaneous adsorption with high solubility is observed in our calculations. This analysis also reveals that f-BN nanocages can be a potential nanocarrier for the delivery of FPV drug molecule.Communicated by Ramaswamy H. Sarma.

A molecular modeling on the potential application of beryllium oxide nanotube for delivery of hydroxyurea anticancer drug

Within this work, we scrutinized the use of BeO nanotube (BeONT) as a nanocarrier for the anticancer drug hydroxyurea (HU) through density functional theory (DFT) calculations. We utilized the functional ꞷB97XD and the basis set 6-31G**. Based on a detailed surface analysis, HU was adsorbed on the surface of the nanotube through 4 different orientations. Also, no vibrational spectra exhibited imaginary frequencies, showing the minimum energy of the relaxed structures. The maximum adsorption energy and the minimum adsorption energy are in strong physical adsorption. The BeONT exhibited p-type semiconducting characteristics in all orientations since it received electronic charge from HU. The results demonstrate the possibility of using the BeONT as a promising carrier for HU drugs.

Adsorption of thiotepa anticancer drugs on the C3N nanotube as promising nanocarriers for drug delivery

This paper focused on the efficiency of carbon nitride nanotubes functionalized with alanine amino acid (f-C₃NNTs) in thiotepa (TPA) anti-cancerous drug delivery via density functional theory (DFT). Pristine C₃NNTs were incorporated for comparison. TPA was found to spontaneously undergo exothermic adsorption onto the nanostructures. The f-C₃NNT/TPA complexes showed the highest interaction strength. The adsorption distance of TPA was found to be smaller, with a greater adsorption capacity and solubility on the f-C₃NNT surface than on the pristine C₃NNT surface. As they were polar, all the complexes were concluded to be insoluble within an aqueous phase. The quantum molecular descriptors revealed the f-C₃NNT nanocarriers to be more reactive than the C₃NNT carrier. The drug was found to spontaneously and exothermically interact with f-C₃NNT. As a result, f-C₃NNT would be promising for TPA adsorption in drug delivery applications.

On the effects of induced polarizability at the water-graphene interface via classical charge-on-spring models

Molecular models of the water-graphene interaction are essential to describe graphene in condensed phases. Different challenges are associated with the generation of these models, in particular π-π and dispersion interactions; thus quantum and classical models have been developed and due to the numerical efficiency of the latter, they have been extensively employed. In this work, we have systematically studied, via molecular dynamics, two polarizable graphene models, denominated CCCP and CCCPD, employing the charge-on-spring model of the GROMOS forcefield, both being compatible with the polarizable water models COS/G2 and COS/D2, respectively. These models were compared with non-polarizable graphene and SPC water models. We focused the study on the water-graphene interface in two distinct systems and under the influence of an electric field: one composed of graphene immersed in water and the other composed of graphene with a water droplet above it. In the former, the orientation of water close to the graphene layer is affected by polarizable graphene in comparison to non-polarizable graphene. This effect is emphasised when an electric field is applied. In the latter, carbon polarizability reduced water contact angles, but graphene retained its hydrophobicity and the computed angles are within the experimental data. Given the significant extra computational cost, the use of polarizable models instead of the traditional fixed-charged approach for the graphene-water interaction may be justified when polarizability effects are relevant, for example, when applying relatively strong fields or in very anisotropic systems, such as the vacuum-bulk interface, as these models are more responsive to such conditions.

DFT and TD-DFT study of adsorption behavior of Zejula drug on surface of the B12N12 nanocluster

The adsorption of the Zejula drug on the surface of B12N12 nanocluster has studied using DFT and TD-DFT. The quantum calculations have performed at the M062X/6–311 + + G(d,p) level of theory in the solvent water. The adsorption of the Zejula from N13 atom on the B12N12 leads to the higher electrical conductivity due to the low Eg rather. The change of DM also displays a charge transfer between Zejula and nanocluster. The UV absorption and IR spectra were calculated. The adsorption of Zejula drug over B12N12 nanocluster in the complexes Zejula/B12N12 can be considered as a bathochromic shift. According to QTAIM analysis, -G(r)/V(r) values for B-O and B-N bonds confirming the electrostatic and partial covalent character. The values of LOL and ELF confirm that the interactions are dominated by electrostatic interaction contributions. The calculated data reveal the B12N12 nanocluster can be appropriate as a biomedical system for the delivery of Zejula drug.

Computational Study of CO2 Reduction Catalyzed by Iron(I) Complex at Different Spin States: Cooperativity of Hydrogen Bonding and Auxiliary Group Effect

To explore alternative approaches to the CO₂ reduction to formate and provide an insight into the spin state effect on the CO₂ reduction, we theoretically designed a kind of low-valence iron(I) model complex, whose doublet, quartet, and sextet states are denoted as ² Fe(I), ⁴ Fe(I), and ⁶ Fe(I), respectively. This complex is featured with an iron(I) center, which bonds to a 1,2-ethanediamine (en) and a 2-hydroxy-biphenyl group. Reaction mechanisms for the CO₂ reduction to formate catalyzed by this iron(I) model complex were explored using density functional theory (DFT) computations. Studies showed that the univalent iron(I) compound can efficiently fix and activate a CO₂ molecule, whereas its oxidized forms with trivalent iron(III) or bivalent iron(II) cannot activate CO₂. For the iron(I) compound, it was found that the lowest spin state ² Fe(I) is the most favorable for the CO₂ reduction as the reactions barriers involving ² Fe(I), ⁴ Fe(I), and ⁶ Fe(I) are 25.6, 37.2, and 35.9 kcal/mol, respectively. Yet, a photosensitizer-free visible-light-mediated high-low spin shift from ⁴ Fe(I) and ⁶ Fe(I) to ² Fe(I) is likely through the reverse intersystem crossing (RIC) because the ⁴ Fe(I) and ⁶ Fe(I) compounds have strong absorption in the visible-light range. Notably, the synergistic interaction between the hydrogen bonding from the auxiliary hydroxyl group in the 2-hydroxy-biphenyl moiety to CO₂ and an intermediate five-membered ring promotes the proton transfer, leading to the formation of the -COOH moiety from CO₂ and the Fe-O bond. With the addition of H₂, one H₂ molecule is split by the Fe-O bond and thus serves as H atom sources for both the CO₂ reduction and the recovery of the auxiliary hydroxyl group. The present theoretical study provides a novel solution for the challenging CO₂ reduction, which calls for further experimental verifications.

Theoretical investigation into the solvent effect on the thermal decomposition of RDX in tetrahydrofuran, acetone, toluene, and benzene

In order to clarify the solvent effect on the thermal decomposition of explosive, the N-NO₂ trigger-bond strengths and ring strains of RDX (cyclotrimethylenetrinitramine) in its H-bonded complexes with solvent molecules (i.e., tetrahydrofuran, acetone, toluene, and benzene), and the activation energies of the intermolecular hydrogen exchanges between the solvent molecules and C₃H₈O₂N₄ or CH₄O₂N₂, as the model molecule of RDX, were investigated by the BHandHLYP, B3LYP, MP2(full), and M06-2X methods with the 6-311 +  + G(2df,2p) basis set, accompanied by a comparison with the calculations by the integral equation formalism polarized continuum model. The solvent effects ignore the ring strain while strengthening the N-NO₂ bond, leading to a possible decreased sensitivity, as is opposite to the experimental results. However, the activation energies are in the order of C₃H₈O₂N₄/CH₄O₂N₂∙∙∙acetone < C₃H₈O₂N₄/CH₄O₂N₂∙∙∙THF < C₃H₈O₂N₄/CH₄O₂N₂∙∙∙toluene < C₃H₈O₂N₄/CH₄O₂N₂∙∙∙benzene < C₃H₈O₂N₄/CH₄O₂N₂, suggesting that the order of the critical explosion temperatures might be RDX∙∙∙acetone < RDX∙∙∙THF < RDX∙∙∙toluene < RDX∙∙∙benzene < RDX, as is roughly consistent with the experimental results. Therefore, the intermolecular hydrogen exchange with the HONO elimination is a possible mechanism of the solvent effect on the initial thermal decomposition of RDX. The solvent effect on the sensitivity is analyzed by the surface electrostatic potentials.

Theoretical assessments on the interaction between amino acids and the g-Mg3N2 monolayer: dispersion corrected DFT and DFT-MD simulations

The interaction of a few amino acids (AAs) with the graphene-like magnesium nitride (g-Mg₃N₂) monolayer has been investigated with density functional theory (DFT) simulations. The Mg site was found to cause significant attraction with the polar active sites of AAs. Such AAs, are capable of producing electrostatics bonding with -48.012 (kcal mol^-1) of interaction energy for tyrosine. The good consistency of the DFT interaction energy with the second-order Møller-Plesset method was found. Furthermore, the DFT-MD simulation of the tyrosine/g-Mg₃N₂ system demonstrated that this host-guest system is stable at ambient conditions. The electronic structures and quantum molecular descriptors were calculated, and the results revealed that the g-Mg₃N₂ monolayer is sensitive to the interaction with AAs. Our first-principles outcomes suggest comprehensive visions into the functionalization of g-Mg₃N₂, and anticipate its applicability as an unprecedented nanovector for AAs. In addition, g-Mg₃N₂ nanosheets can be utilized as biosensors for biomolecules detection. These are very hopeful for promising biological and pharmaceutical applications of g-Mg₃N₂.

Adsorption behavior of mercaptopurine and 6-thioguanine drugs on the B12N12, AlB11N12 and GaB11N12 nanoclusters, a comparative DFT study

Lately, drug delivery systems established on nanostructures have become the most proficient to be studied. There are different studies suggested that the BN nanoclusters can be used as drug carriers and transport drugs in the target cell. Therefore, the interactions and adsorption behavior of Mercaptopurine (MC) and 6-thioguanine (TG) as anti-cancer drugs on the B₁₂N₁₂ (BN), AlB₁₁N₁₂ (AlBN) and GaB₁₁N₁₂ (GaBN) nanoclusters were studied by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to find a new drug delivery system. Our results showed strong adsorption obtained in BN-MC/TG and AlBN-MC/TG complexes can be decomposed by the BN and AlBN indicating that these nanostructures are not suitable in drug efficiency of MC and TG drugs. Unlike the BN and AlBN nanoclusters, GaBN significantly makes the MC and TG drugs adsorption energetically favorable. The high solvation energy of GaBN when interacting with MC and TG drugs led it to applicability as nanocarriers for these drugs in the drug delivery systems. Furthermore, GaBN has a short recovery time for MC, and TG drugs desorption compared to BN and AlBN nanoclusters. It is predicted that the MC, and TG drugs over GaBN can be used as a drug delivery system.Communicated by Ramaswamy H. Sarma.

Possible effects of fluxionality of a cavitand on its catalytic activity through confinement

The discovery of fullerenes was a huge milestone in the scientific community, and with it came the urge to discover and analyze various small and large atomic and molecular clusters having a cavity. These cavitands of varied shapes and sizes have wide applications in the encapsulation of rare gas atoms to induce bond formation between them, storage of hydrogen and hydrocarbons to be used as alternative sources of fuel, catalyzation of otherwise slow reactions without using a catalyst, activation of small gas molecules, etc. Various cavitands like fullerenes, [ExBox]4+, cucurbit[n]urils, borospherenes, octa acid, etc. have been used for this purpose. Some clusters including cavitands exhibit fluxional behaviour. Systems in a confined environment often manifest interesting variations in their properties and behaviour, compared to their unconfined counterparts, facilitating the aforementioned applications. In this perspective article, we explore the possibility of making use of this extra degree of freedom, viz., the fluxionality, in changing the catalytic activity of the cavitand.

Recuperative Amino Acids Separation through Cellulose Derivative Membranes with Microporous Polypropylene Fiber Matrix

The separation, concentration and transport of the amino acids through membranes have been continuously developed due to the multitude of interest amino acids of interest and the sources from which they must be recovered. At the same time, the types of membranes used in the sepa-ration of the amino acids are the most diverse: liquids, ion exchangers, inorganic, polymeric or composites. This paper addresses the recuperative separation of three amino acids (alanine, phe-nylalanine, and methionine) using membranes from cellulosic derivatives in polypropylene ma-trix. The microfiltration membranes (polypropylene hollow fibers) were impregnated with solu-tions of some cellulosic derivatives: cellulose acetate, 2-hydroxyethyl-cellulose, methyl 2-hydroxyethyl-celluloseand sodium carboxymethyl-cellulose. The obtained membranes were characterized in terms of the separation performance of the amino acids considered (retention, flux, and selectivity) and from a morphological and structural point of view: scanning electron microscopy (SEM), high resolution SEM (HR-SEM), Fourier transform infrared spectroscopy (FT-IR), energy dispersive spectroscopy (EDS) and thermal gravimetric analyzer (TGA). The re-sults obtained show that phenylalanine has the highest fluxes through all four types of mem-branes, followed by methionine and alanine. Of the four kinds of membrane, the most suitable for recuperative separation of the considered amino acids are those based on cellulose acetate and methyl 2-hydroxyethyl-cellulose.

Advancing Rational Control of Peptide-Surface Complexes

Understanding peptide-surface interactions is crucial for programming self-assembly of peptides at surfaces and in realizing their applications, such as biosensors and biomimetic materials. In this study, we developed insights into the dependence of a residue's interaction with a surface on its neighboring residue in a tripeptide using molecular dynamics simulations. This knowledge is integral for designing rational mutations to control peptide-surface complexes. Using graphene as our model surface, we estimated the free energy of adsorption (ΔA_ads) and extracted predominant conformations of 26 tripeptides with the motif LNR-CR-Gly, where LNR and CR are variable left-neighboring and central residues, respectively. We considered a combination of strongly adsorbing (Phe, Trp, and Arg) and weakly adsorbing (Ala, Val, Leu, Ser, and Thr) amino acids on graphene identified in a prior study to form the tripeptides. Our results indicate that ΔA_ads of a tripeptide cannot be estimated as the sum of ΔA_ads of each residue indicating that the residues in a tripeptide do not behave as independent entities. We observed that the contributions from the strongly adsorbing amino acids were dominant, which suggests that such residues could be used for strengthening peptide-graphene interactions irrespective of their neighboring residues. In contrast, the adsorption of weakly adsorbing central residues is dependent on their neighboring residues. Our structural analysis revealed that the dihedral angles of LNR are more correlated with that of CR in the adsorbed state than in bulk state. Together with ΔA_ads trends, this implies that different backbone structures of a given CR can be accessed for a similar ΔA_ads by varying the LNR. Therefore, incorporation of context effects in designing mutations can lead to desired peptide structure at surfaces. Our results also emphasize that these cooperative effects in ΔA_ads and structure are not easily predicted a priori. The collective results have applications in guiding rational mutagenesis techniques to control orientation of peptides at surfaces and in developing peptide structure prediction algorithms in adsorbed state from its sequence.

Density functional theory study to functionalization of BC2N nanotubes with cysteine amino acid

The density functional theory (DFT) was used to study the interaction of cysteine amino acid with (8, 0) zigzag single-walled BC₂N nanotubes (BC₂NNTs) both in gas and solvent phases. The interaction between cysteine amino acid and BC₂NNTs is found to be energetically favorable in both phases. Based on the calculations of solvation energy, it can be seen that the dissolution of BC₂NNT/amino acid complex in water is spontaneous. During the functionalization process, the quantum molecular descriptor and the energy of adsorption changed significantly. Findings suggest that the cysteine amino acid can be considerably adsorbed chemically onto the surface of BC₂NNTs. Based on the E_g values obtained, the cysteine molecule caused a reduction in the E_g value, which also increased the reactivity and conductivity of functionalized BC₂NNTs. According to the findings of chemical hardness, the kinetic stability of the functionalized nanotubes was better than pure nanotubes. As a result of this approach, E_g values are indicative of high propensity reaction and electron transfer. Our findings have shown that BC₂NNTs can function as an appropriate drug delivery system for cysteine amino acid within biological systems for the adsorption of the drug and controlled drug release.

Metalloradical complex Co-C˙Ph3 catalyzes the CO2 reduction in gas phase: a theoretical study

Metal-stabilized radicals have been increasingly exploited in modern organic synthesis. Here, we theoretically designed a metalloradical complex Co-C˙Ph3 with the triplet characters through the transition metal cobalt (Co0) coordinating a triphenylmethyl radical. The potential catalytic role of this novel metalloradical in the CO2 reduction with H2/CH4 in the gas phase was explored via density functional theory (DFT) calculations. For the CO2 reduction reaction with H2, there are two possible pathways: one (path A) is the activation of CO2 by Co-C˙Ph3, followed by the hydrogenation of CO2. The other (path B) starts from the splitting of the H-H bond by Co-C˙Ph3, leading to the transition-metal hydride complex CoH-H, which can reduce CO2. DFT computations show that path B is more favorable than path A as their rate-determining free energy barriers are 18.3 and 27.2 kcal mol-1, respectively. However, for the reduction of CO2 by CH4 two different products, CH3COOH and HCOOCH3, can be generated following different reaction routes. Both routes begin with one CH4 molecule approaching the metalloradical Co-C˙Ph3 to form the intermediate CoH-CH3. This intermediate can evolve following two different pathways, depending on whether the H bonded to Co is transferred to the O (pathway PO) or the C (pathway PC) of CO2. Comparing their rate-determining steps, we identified that the PO route is more favorable for the reduction of CO2 by CH4 to CH3COOH with the reaction barrier 24.5 kcal mol-1. Thus, the present Co0-based metalloradical system represents a viable catalytic protocol that can contribute to the effective utilization of small molecules (H2 and CH4) to reduce CO2, and provides an alternative strategy for the exploration of CO2 conversion.

Theoretical study of the adsorption of analgesic environmental pollutants on pristine and nitrogen-doped graphene nanosheets

Interactions of the analgesic medications dextropropoxyphene (DPP, opioid), paracetamol (PCL, nonnarcotic), tramadol (TDL, nonnarcotic), ibuprofen (IBN, nonsteroidal anti-inflammatory drug (NSAID)), and naproxen (NPX, NSAID) with pristine graphene (GN) and nitrogen-doped GN (NGN; containing only graphitic N atoms) nanosheets were explored using density functional theory (DFT) in the gas and aqueous phases. Calculations in the aqueous phase were performed using the integral equation formalism polarized continuum model (IEFPCM). Calculated geometry-optimized structures, partial atomic charges (determined using Natural Bond Orbital analysis), highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, work functions (determined using time-dependent DFT), and molecular electrostatic potential plots showed that the adsorption process is physical in nature (viz. physisorption), primarily due to noncovalent π-π and van der Waals interactions. In addition, calculated adsorption energies (ΔEad) were exergonic, indicating that formation of the analgesic/GN and analgesic/NGN complexes is thermodynamically favorable in the gas (ΔEad values for analgesic/GN and analgesic/NGN were in the range of -66.56 kJ mol-1 to -106.78 kJ mol-1) and aqueous phases (ΔEad values for analgesic/GN and analgesic/NGN complexes were in the range of -58.75 kJ mol-1 to -100.46 kJ mol-1). Generally, for GN and NGN, adsorption was more endergonic in the aqueous phase by as much as +10.41 kJ mol-1. Calculated solvation energies (ΔEsolvation) were exergonic for all analgesic/GN complexes (ΔEsolvation values were in the range of -56.50 kJ mol-1 to -66.17 kJ mol-1) and analgesic/NGN complexes (ΔEsolvation values were in the range of -77.26 kJ mol-1 to -87.96 kJ mol-1), with analgesic/NGN complexes exhibiting greater stability in aqueous solutions (∼20 kJ mol-1 more stable). In summary, the results of this theoretical study demonstrate that the adsorption and solvation of analgesics on GN and NGN nanosheets is thermodynamically favorable. In addition, generally, analgesic/NGN complexes exhibit higher adsorption affinities and solvation energies in the gas and aqueous phases. Therefore, GN and NGN nanosheets are potential adsorbents for extracting analgesic contaminants from aqueous environments such as aquatic ecosystems.

The validation of molecular interaction among dimer chitosan with urea and creatinine using density functional theory: In application for hemodyalisis membrane

The formation of chitosan dimer and its interaction with urea and creatinine have been investigated at the density functional theory (DFT) level (B3LYP-D3/6-31++G**) to study the transport phenomena in hemodialysis membrane. The interaction energy of chitosan-creatinine and chitosan-urea complexes are in range -4 kcal/mol < interaction energy <-20 kcal/mol which were classified in medium hydrogen bond interaction. The chemical reactivity parameter proved that creatinine was more electrophilic and easier to bind chitosan than urea. The energy gap of HOMO-LUMO of chitosan-creatinine complex was lower than chitosan-urea complex that indicating chitosan-creatinine complex was more reactive and easier to transport electron than chitosan-urea complex. Moreover, the natural bond orbital (NBO) analysis showed a high contribution of hydrogen bond between chitosan-creatinine and chitosan-urea. The chitosan-creatinine interaction has a stronger hydrogen bond than chitosan-urea through the interaction O18-H34....N56 with stabilizing energy = -13 kcal/mol. The quantum theory atom in molecule (QTAIM) also supported NBO data. All data presented that creatinine can make hydrogen bond interaction stronger with chitosan than urea, that indicated creatinine easier to transport in the chitosan membrane than urea during hemodialysis process.

Adsorption of acetylsalicylic acid on the aluminum nitride nanotube in both gas and solvent medium: a DFT study

The adsorption of acetylsalicylic acid (ASA) on the outer surfaces of a (1 , 1) aluminum nitride single-wall nanotube (AlNNT) was studied by quantum chemical study calculation. The adsorption energy of ASA on the AlNNT surface was calculated about - 15.62 kcal/mol. The more negative adsorption energy is ascribed to the electrostatic interaction of ASA with AlNNT. By absorbing the aspirin drug on the surface of AlNNT, the nanotube electrical conductivity has increased dramatically by about 21.75%, which can be used as a drug detection signal. Based on the polarizable continuum model (PCM) calculation, the AlNNT-ASA complex in water medium is more stable compared with that in the gas medium. Finally, our findings also revealed that the AlNNT would selectively identify the ASA molecule in the presence of environmental pollutants.