Ab Initio Evaluation of Complexation Energies for Cyclodextrin-Drug Inclusion Complexes

Manipulating Intrapore Energy Barriers in Graphene Oxide Nanochannels for Targeted Removal of Short-Chain PFAS

Removal of per- and polyfluoroalkyl substances (PFAS) from water has become a research topic of interest in recent times. However, it is very challenging to remove short-chain ( Collapse

Key Words

• asymmetrical nanochannels
• energy barriers
• graphene oxide membrane
• host−guest complexation
• nanofiltration
• short-chain PFAS
• β-cyclodextrin

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Affiliation(s)

Eubert Mahofa Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia
Sally El Meragawi Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia
Muhammed A Vilayatteri Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia
Swarit Dwivedi Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
Manas Ranjan Panda Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia
Petar Jovanović Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia
Adri C T van Duin Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
Benny Freeman Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
Akshat Tanksale Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
Mainak Majumder Nanoscale Science and Engineering Laboratory (NSEL), Department of Mechanical and Aerospace Engineering, Monash University, 20 Research Way, Clayton, VIC 3800, Australia ARC Research Hub for Advanced Manufacturing of 2D Materials, Monash University, 20 Research Way, Clayton, VIC 3800, Australia

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A new generation of effective core potentials: Selected lanthanides and heavy elements

We construct correlation-consistent effective core potentials (ccECPs) for a selected set of heavy atoms and f elements that are currently of significant interest in materials and chemical applications, including Y, Zr, Nb, Rh, Ta, Re, Pt, Gd, and Tb. As is customary, ccECPs consist of spin-orbit (SO) averaged relativistic effective potential (AREP) and effective SO terms. For the AREP part, our constructions are carried out within a relativistic coupled-cluster framework while also taking into account objective function one-particle characteristics for improved convergence in optimizations. The transferability is adjusted using binding curves of hydride and oxide molecules. We address the difficulties encountered with f elements, such as the presence of large cores and multiple near-degeneracies of excited levels. For these elements, we construct ccECPs with core-valence partitioning that includes 4f subshell in the valence space. The developed ccECPs achieve an excellent balance between accuracy, size of the valence space, and transferability and are also suitable to be used in plane wave codes with reasonable energy cutoffs.

How are N-methylcarbamates encapsulated by β-cyclodextrin: insight into the binding mechanism

Guest molecules containing chromophore groups encapsulated by β-cyclodextrin (β-CD) generate circular dichroism (CD) signals, which enables a preliminary prediction of their binding modes. However, the accurate determination of the representative binding conformation (RC) remains a challenging task due to the complex conformational space of these host-guest systems. Here, we combine a molecular dynamics/quantum mechanics/continuum solvent model (MD/QM/CSM) with induced circular dichroism (ICD) data (N. L. Pacioni, A. B. Pierini and A. V. Veglia, Spectrochim. Acta A Mol. Biomol. Spectrosc., 2013, 103, 319-324.) to explore the binding mechanism of β-CD with four N-methylcarbamate molecules: promecarb (PC), bendiocarb (BC), carbaryl (CY) and carbofuran (CF). In aqueous solution, their stability decreases as: PC > BC > CY > CF. Comparing the ECD spectra computed from TD-DFT with the ICD data can help eliminate many common binding configurations and identify the RC. The host-guest binding affinities (BAs) estimated using a ONIOM2(B971:PM6)/SMD model reproduce the measured binding trend, reveal the competition between the non-covalent interaction and solvent effect and explain the large difference in their binding modes. We also examine the fluctuations in the computed BA using similar structures.

A Theoretical Analysis of Interaction Energies and Intermolecular Interactions between Amphotericin B and Potential Bioconjugates Used in the Modification of Nanocarriers for Drug Delivery

Amphotericin B (AmB) is an antibiotic with a wide spectrum of action and low multidrug resistance, although it exhibits self-aggregation, low specificity, and solubility in aqueous media. An alternative for its oral administration is its encapsulation in polymers modified with bioconjugates. The aim of the present computational research is to determine the affinity between AmB and six bioconjugates to define which one could be more suitable. The CAM-B3LYP-D3/6-31+G(d,p) method was used for all computational calculations. The dimerization enthalpy of the most stable and abundant systems at pH = 7 allows obtaining this affinity order: AmB_1,2-distearoyl-sn-glycerol-3-phosphorylethanolamine (DSPE) > AmB_γ-cyclodextrin > AmB_DSPEc > AmB_retinol > AmB_cholesterol > AmB_dodecanol, where DSPEc is a DSPE analog. Quantum theory of atoms in molecules, the non-covalent interactions index, and natural bond orbital analysis revealed the highest abundance of noncovalent interactions for AmB-DSPE (51), about twice the number of interactions of the other dimers. Depending on the interactions’ strength and abundance of the AmB-DSPE dimer, these are classified as strong: O-H---O (2), N-H---O (3) and weak: C-H---O (25), H---H (18), C-H---C (3). Although the C-H---O hydrogen bond is weak, the number of interactions involved in all dimers cannot be underestimated. Thus, non-covalent interactions drive the stabilization of copolymers, and from our analysis, the most promising candidates for encapsulating are DSPE and γ-cyclodextrin.

Current Status of Quantum Chemical Studies of Cyclodextrin Host-Guest Complexes

This article aims to review the application of various quantum chemical methods (semi-empirical, density functional theory (DFT), second order Møller-Plesset perturbation theory (MP2)) in the studies of cyclodextrin host-guest complexes. The details of applied approaches such as functionals, basis sets, dispersion corrections or solvent treatment methods are analyzed, pointing to the best possible options for such theoretical studies. Apart from reviewing the ways that the computations are usually performed, the reasons for such studies are presented and discussed. The successful applications of theoretical calculations are not limited to the determination of stable conformations but also include the prediction of thermodynamic properties as well as UV-Vis, IR, and NMR spectra. It has been shown that quantum chemical calculations, when applied to the studies of CD complexes, can provide results unobtainable by any other methods, both experimental and computational.

A Dispersion Corrected DFT Investigation of the Inclusion Complexation of Dexamethasone with β-Cyclodextrin and Molecular Docking Study of Its Potential Activity against COVID-19

The encapsulation mode of dexamethasone (Dex) into the cavity of β-cyclodextrin (β-CD), as well as its potential as an inhibitor of the COVID-19 main protease, were investigated using density functional theory with the recent dispersion corrections D4 and molecular docking calculations. Independent gradient model and natural bond orbital approaches allowed for the characterization of the host–guest interactions in the studied systems. Structural and energetic computation results revealed that hydrogen bonds and van der Waals interactions played significant roles in the stabilization of the formed Dex@β-CD complex. The complexation energy significantly decreased from −179.50 kJ/mol in the gas phase to −74.14 kJ/mol in the aqueous phase. A molecular docking study was performed to investigate the inhibitory activity of dexamethasone against the COVID-19 target protein (PDB ID: 6LU7). The dexamethasone showed potential therapeutic activity as a SARS CoV-2 main protease inhibitor due to its strong binding to the active sites of the protein target, with predicted free energy of binding values of −29.97 and −32.19 kJ/mol as calculated from AutoDock4 and AutoDock Vina, respectively. This study was intended to explore the potential use of the Dex@β-CD complex in drug delivery to enhance dexamethasone dissolution, thus improving its bioavailability and reducing its side effects.

Importance of Van der Waals Interactions in Hydrogen Adsorption on a Silicon-carbide Nanotube Revisited with vdW-DFT and Quantum Monte Carlo

Density functional theory (DFT) is a valuable tool for calculating adsorption energies toward designing materials for hydrogen storage. However, dispersion forces being absent from the local/semi-local theory, it remains unclear as to how the consideration of van der Waals (vdW) interactions affects such calculations. For the first time, we applied diffusion Monte Carlo (DMC) to evaluate the adsorption characteristics of a hydrogen molecule on a (5,5) armchair silicon-carbide nanotube (H₂-SiCNT). Within the DFT framework, we benchmarked various exchange-correlation functionals, including those recently developed for treating dispersion or vdW interactions. We found that the vdW-corrected DFT methods agree well with DMC, whereas the local (semilocal) functional significantly over (under)-binds. Furthermore, we fully optimized the H₂-SiCNT geometry within the DFT framework and investigated the correlation between the structure and charge density. The vdW contribution to the adsorption was found to be non-negligible at ∼1 kcal/mol per hydrogen molecule, which amounts to 9-29% of the ideal adsorption energy required for hydrogen storage applications.

Caffeine-Cyclodextrin Complexes as Solids: Synthesis, Biological and Physicochemical Characterization

Mechanochemical and in-solution synthesis of caffeine complexes with α-, β-, and γ-cyclodextrins was optimized. It was found that short-duration, low-energy cogrinding, and evaporation (instead of freeze-drying) are effective methods for the formation and isolation of these complexes. The products obtained, their pure components, and their mixtures were examined by powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), FT-IR and Raman spectroscopy. Moreover, molecular modeling provided an improved understanding of the association process between the guest and host molecules in these complexes. The complexes were found to exhibit high toxicity in zebrafish (Danio rerio) embryos, in contrast to pure caffeine and cyclodextrins at the same molar concentrations. HPLC measurements of the caffeine levels in zebrafish embryos showed that the observed cytotoxicity is not caused by an increased caffeine concentration in the body of the organism, as the concentrations are similar regardless of the administered caffeine form. Therefore, the observed high toxicity could be the result of the synergistic effect of caffeine and cyclodextrins.