Electronic origins of the stereochemistry in ß-lactam formed through the Staudinger reaction catalyzed by a nucleophile.

This paper evaluates the electronic effects of molecular substituents on the stereoselectivity of the umpolung Staudinger catalytic reaction. This is especially important because experimental studies on constructing the ß-lactam ring, a core structure of most antibiotics, through catalyzed Staudinger reactions have been massively progressing over the last century. Yet, there is a necessity for an in-depth understanding of the reaction mechanisms to help chemists, working on the well-established discoveries, improve these to optimize the stereoselectivity and yield of synthetic methods. Access to practical and effective advancements in forming optically pure ß-lactam is paramount in the field of medical chemistry. This paper specifically investigates how changing the N-protecting group in the imine fragment can switch the stereoselectivity of the PPY-catalyzed Staudinger reaction. To do so, we employed the density functional theory (DFT) for geometry optimization and electronic analysis at the B3LYP/6-31G(d) level of theory to examine and compare the role of N-tosyl (N-Ts) and N-triflyl (N-Tf) imine on the mechanism pathways, i.e., imine-first or ketene-first, and stereochemistry of the reaction, i.e., cis or trans ß-lactam. Our results show that the reaction mechanism pathway cannot be simply switched from ketene-first to imine-first by changing the substituent on the imine nitrogen atom, which is contrary to the reported experimental results, and both imines go through the ketene-first mechanism with different stereochemistries, which is cis selective for imine-Ts and trans selective for imine-Tf. Based on electronic analyses, the reversal in diastereoselectivity in the N-triflyl imine system could be attributed to the charge transfers and electron-density distribution over the transition states. Therefore, the cis/trans selectivity of the PPY-catalyzed Staudinger reaction could be effectively controlled by the electronic characteristics of the molecular substituents in the reactants. A N-protecting group in imine with a more electron-withdrawing nature seems to accelerate the stereo-determining step, ring closure, and increase the stabilization charge transfers in the transition state, leading to a preference for trans ß-lactam formation. It seems that using a N-substituent with a higher electron-withdrawing nature can initially activate the imine by the nucleophilic catalyst in competition with ketene, i.e., imine-first versus ketene-first. These results can provide an insight into select proper substituents for the fragments to synthesis ß-lactam with a desired stereochemistry. Also, a comprehensive comparison was performed between calculations with and without dispersion.

Effect of quaternary ammonium surfactants on biomembranes using molecular dynamics simulation.

Research conducted both prior to and after the emergence of the COVID-19 pandemic reveals a notable rise in human exposure to cleaning products, hand sanitizers, and personal care items. Moreover, there has been a corresponding increase in the environmental release of these chemicals. Cleaning and disinfecting products often contain quaternary ammonium compounds (QACs) with alkyl chains as long as 8-12 carbon atoms. The attachment of quaternary ammonium surfactants to the membrane resulted in the deformation of the bilayer and membrane disruption. Before interactions with cell membranes, these surfactant molecules may form different aggregates depending on their architecture. Interaction of surfactant monomers or clusters with the cell membrane changes the physiochemical properties of the biomembranes. To investigate this interaction and its influence on membrane properties, we conducted molecular dynamics simulations of cationic quaternary ammonium surfactants interacting with dipalmitoylphosphatidylcholine (DPPC) membranes. Our simulations revealed significant interactions between the surfactants and the phospholipids, leading to substantial alterations in the structure of the bilayer. The results are compared with the simulated anionic (SDS) and nonionic surfactants/bilayer systems. Various aspects were considered, including the aggregation process, migration behavior, and eventual equilibrium of these molecules at the interface between the membrane and water. This analysis used various techniques such as density profiles, distribution functions, cluster analysis, order parameters, hydrogen bonding (H-bonding), and mean-square displacements. The results indicate that while surfactants with shorter alkyl tails (N-(2-hydroxyethyl)-N,N-dimethyloctan-1-aminium chloride (HEDMOAC)) make strong hydrogen bonds with the phosphate group and ester oxygen of the phosphatidylcholine bilayer and enter toward the bilayer in the monomer form, surfactants of longer alkyl tails aggregated on the membrane head-water interface and interact minimally with the head groups of the DPPC bilayer. For DDEDMEAC, a quaternary ammonium surfactant with a hydrophobic alkyl chain consisting of two decanoate groups, alteration of the structural and dynamical properties of the bilayer is expected to be governed by two different factors. First, the structural order of DPPC increases as surfactant aggregates interact with the membrane head group. Second, the decrease in the order of the bilayer occurs due to the insertion of surfactant monomers within the hydrophobic region of the bilayer. Strong interactions between constituents of tetraoctylammonium bromide (TOABr) and lipid head groups lead to a reduction in interlipid interactions and order, which further results in increased porosity of cellular membranes. Understanding the extent of these interactions plays a pivotal role in the toxicological assessment of these surfactants.

The effect of various partial atomic charges on the bulk and liquid/vacuum interface properties of iodobenzene derivatives at their melting points.

In this work, various atomic charge schemes including natural bond orbital (NBO), electrostatic potential based (CHELPG), and σ-hole model charges were applied in the OPLS-AA force field to investigate their effects on the thermophysical and structural properties of iodobenzene and its derivatives. Molecular dynamics simulations presented in this work show that the studied structural and thermophysical properties are in good agreement with experiments when the CHELPG charge was coupled with the OPLS-AA force field. Also, the arrangement of iodobenzene derivatives in the liquid phase was investigated via combined radial/angular distribution functions (CDFs) analyses and halogen-bonding theory. The most probable orientation of iodobenzene derivatives at the liquid/vacuum interface was assigned by atom density profile and bivariate orientational distribution maps. For all studied iodobenzene derivatives, benzene rings are oriented such that the iodine atoms tend toward the vacuum phase.

Significant Improvement in CO2 Absorption by Deep Eutectic Solvents as Immobilized Sorbents: Computational Analysis.

To find an alternative way for improving the efficacy of deep eutectic solvents (DESs) to dissolve carbon dioxide, a computational study of DES systems comprising choline chloride and different hydrogen-bond donors (ethylene glycol and glycerol) immobilized on hydrophobic (graphite) and hydrophilic (titanium dioxide) solid surfaces was performed. This research provides quantitative molecular understanding of the role of the DES thickness and also the type of solid support in CO2 sorption and diffusion using molecular dynamics simulations. In general, the proposed model based on supported DESs immobilized on different supports was developed to correlate the solubility of CO2 in DESs based on choline chloride. The simulated systems illustrate that CO2 molecules mainly accumulate at the gas/DES interface in short times, whereas diffusion of CO2 to the bulk DESs is slower as the thickness of the immobilized DES increases. In addition, the CO2 absorption capacity of both DESs coated on the TiO2 surface is larger than that on the graphite surface. Structural and dynamic characteristics were determined using density profiles, distribution functions, orientational analysis, and mean-square displacements. We further demonstrate the effective interaction parameters associated with CO2 capture by DESs via density functional theory.

Encapsulation and Release of Doxorubicin from TiO2 Nanotubes: Experiment, Density Functional Theory Calculations, and Molecular Dynamics Simulation.

Titanium dioxide (TiO2) nanotubes are attractive materials for drug-delivery systems because of their biocompatibility, chemical stability, and simple preparation. In this study, we loaded TiO2 nanotubes with anticancer drug doxorubicin (DOX) experimentally and in all-atom molecular dynamics (MD) simulations. The release of doxorubicin from the nanotubes was studied by high-performance liquid chromatography (HPLC) and confocal Raman spectroscopy, and drug-release profiles were evaluated under various conditions. The polyethylene glycol (PEG) coating and capping of the nanotubes led to a marked increase in the water contact angles from about 16 to 33° in keeping with reduced wettability. The capping retarded the release rate without decreasing the overall release amount. The MD simulations further show that the DOX molecule diffusion coefficients (Di) are in the order of 10-10 m2/s. The DOX molecules show a plethora of short- and long-range H-bonding interactions with TiO2 nanotube walls and water. Calculated radial distribution functions (RDFs) and combined radial/angular distribution functions (CDFs) allowed gauging the strength of these hydrogen bonds. The strength does not fully correlate with the pKa values of DOX atoms which we assign to the confinement of DOX and water in the tubes. The lifetimes of hydrogen bonds between the DOX atoms and water molecules are shorter than that of the DOX...TiO2 interactions, and DOX...DOX aggregation does not play an important role. These results suggest TiO2 nanotubes as promising candidates for controllable drug-delivery systems for DOX or similar antiproliferative molecules.

Synthesis of some new distyrylbenzene derivatives using immobilized Pd on an NHC-functionalized MIL-101(Cr) catalyst: photophysical property evaluation, DFT and TD-DFT calculations.

In this study the catalytic application of a heterogeneous Pd-catalyst system based on metal organic framework [Pd-NHC-MIL-101(Cr)] was investigated in the synthesis of distyrylbenzene derivatives using the Heck reaction. The Pd-NHC-MIL-101(Cr) catalyst showed high efficiency in the synthesis of these π-conjugated materials and products were obtained in high yields with low Pd-contamination based on ICP analysis. The photophysical behaviors for some of the synthesized distyrylbenzene derivatives were evaluated. The DFT and TD-DFT methods were employed to determine the optimized molecular geometry, band gap energy, and the electronic absorption and emission wavelengths of the new synthesized donor-π-acceptor (D-π-A) molecules in the gas phase and in various solvents using the chemical model B3LYP/6-31+G(d,p) level of theory.

The interactions of folate with the enzyme furin: a computational study.

Entrance of coronavirus into cells happens through the spike proteins on the virus surface, for which the spike protein should be cleaved into S1 and S2 domains. This cleavage is mediated by furin, a member of the proprotein convertases family, which can specifically cleave Arg-X-X-Arg↓ sites of the substrates. Here, folate (folic acid), a water-soluble B vitamin, is introduced for the inhibition of furin activity. Therefore, molecular insight into the prevention of furin activity in the presence of folic acid derivatives is presented. To this aim, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were performed to clarify the inhibitory mechanism of these compounds. In this regard, molecular docking studies were conducted to probe the furin binding sites of folic acid derivatives. The MD simulation results indicated that these drugs can efficiently bind to the furin active site. While the folic acid molecule tended to be positioned slightly towards the Glu271, Tyr313, Ala532, Gln488, and Asp530 amino acids of furin at short and long ranges, the folinic acid molecule interacted with Glu271, Ser311, Arg490, Gln488, and Lys499 amino acids. Consequently, binding free energy calculations illustrated that folic acid (-27.90 kcal mol-1) has better binding in comparison with folinic acid (-12.84 kcal mol-1).

Aqueous solutions of binary ionic liquids: insight into structure, dynamics, and interface properties by molecular dynamics simulations and DFT methods.

The behavior of aqueous solutions of mixtures of ionic liquids (ILs) is of special interest because of their amphiphilic character, from both a fundamental and application viewpoint. In this work, we conducted molecular dynamics (MD) simulations and density functional theory (DFT) calculations to understand the effect of water on the intermolecular interactions in three IL binary mixtures [C4mim]/[Cl]/[BF4], [C4mim]/[Cl]/[PF6] and [C4mim]/[BF4]/[PF6] containing the well-characterized cation, 1-n-butyl-3-methylimidazolium [C4mim]+ and the anions chloride [Cl]-, tetrafluoroborate [BF4]-, and hexafluorophosphate [PF6]-. The perturbation of the structures in the binary IL mixture by water molecules was analyzed in the bulk and at the liquid/vacuum interface using distribution functions, hydrogen-bond statistics, and density profiles. Interactions between anions and cations change drastically when the IL mixtures are dissolved in water. In particular, anion-water interactions are stronger than anion-cation interactions. H-Bonds are the dominant interactions. They are prevalently electrostatic and strong for the two [Cl]-containing systems in both the water-free and the water-containing systems. The very hydrophobic [C4mim]/[BF4]/[PF6] system gains stability from dispersive interactions and consequently segregates water markedly when admixed. The most probable orientations of IL cations in the bulk and at the vicinity of the interface were examined using bivariate distribution calculations and show [PF6]- segregating to the surface in keeping with its highly hydrophobic nature. DFT calculated structures, energies, dipole moments, global hardness and solvation energies using model ion pairs [C4mim][X] or complexes [C4mim]2[X][Y], with [X/Y]- = [Cl]-, [BF4]-, or [PF6]- are completely consistent with the findings for the bulk.

New insight into electrosynthesis of ordered TiO2 nanotubes in EG-based electrolyte solutions: combined experimental and computational assessment.

To obtain a better understanding of TiO2 nanotube (TiO2-NT) synthesis in different ethylene glycol (EG)-based electrolyte solutions by electrochemical anodization, the primary steps of TiO2-NT formation were studied by experimental techniques. In this regard, three different EG-based electrolyte solutions were used for anodic oxidation of titanium foil. The first electrolyte solution contains conventional ammonium fluoride (NH4F) dissolved in EG/water (98 : 2 v/v). In the second one, Ti foil anodization is performed in an electrolyte solution containing the 1-butyl-3-methyl-imidazolium tetrafluoroborate (Bmim-BF4) ionic liquid. Finally, the fluorine-containing species was replaced by the 1-butyl-3-methyl-imidazolium chloride (Bmim-Cl) ionic liquid. The results indicate that the TiO2-NTs did not form by anodization in the EG/H2O/Bmim-Cl electrolyte solution at 60 V. Interestingly, this electrolyte solution is less viscous than the fluorine-containing electrolyte solutions. In addition, we report a detailed study on the structural arrangement of electrolyte solution components near the solid surfaces using molecular dynamics (MD) simulation methods to reveal the factors governing the difference of the ionic species distribution. The MD results elucidate the role of the ionic constituents in the length of the nanotube arrays at a certain anodization condition. Furthermore, as reported herein for the first time, the lifetimes of ion-ion contacts and the interactions of ionic species with TiO2 walls have a substantial effect on the resulting nanotubes. These characteristics are analyzed by using radial distribution functions, density profiles, distance analysis, time correlation functions, and mean-square-displacements, complemented by DFT calculations.

The interactions of an Aß protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances.

Recent studies have shown that the aggregation of the amyloid-beta peptide (Aß) in the brain cell membrane is responsible for the emergence of Alzheimer's disease (AD); the exploration of effective factors involved in the extension of the aggregation process and alternatively the examination of an effective inhibitor via theoretical and experimental tools are among the main research topics in the field of AD treatment. Therefore, in this study, we used all-atom molecular dynamics (MD) simulations to clarify the impact of cell membrane cholesterol on the interaction of Aß with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) as a membrane model. Moreover, the effect of the P7C3-S243 molecule on the abovementioned process was investigated. The simulation results disclosed the neuroprotective property of the P7C3-S243 molecule. The MD simulation results indicate that the interaction of cholesterol molecules with the Aß oligomer is negligible and cannot enhance membrane rupture. However, strong hydrogen bonding between the POPC molecules and the oligomers led to membrane perturbation. According to our modellings, the P7C3-S243 molecular layer can protect the cell membrane by inhibiting the direct interaction between the bilayer and Aß. In addition, free-energy calculations were conducted to determine the possible penetration of Aß fibrils into the cholesterol-enriched membrane.

Interactions of neutral gold nanoparticles with DPPC and POPC lipid bilayers: simulation and experiment.

Molecular dynamics simulations of neutral gold nanoparticles (AuNPs) interacting with dipalmitoylphosphatidylcholine (DPPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes were studied using a model system. Spontaneous membrane insertion of AuNPs did not occur on the time scale of atomistic simulations. To overcome the limitations of time scale, we used a harmonic restraining potential to force the AuNPs into the membranes. Free energy calculations indicate that a NP has to cross a free energy barrier of about 134 kJ mol-1 prior to forming a stable contact with the membrane. This energy barrier between lipids and NPs comes from the repulsion between headgroups of lipids and AuNPs. The experimental investigations indicate that, contrary to hydrophobic AuNPs, neutral AuNPs cannot form ion channels across lipid membranes. The adsorption of NPs induces the formation of a highly ordered region in phospholipid bilayers. Our simulation results propose that the cell penetration of small uncoated AuNPs does not involve energy-independent membrane translocation but rather involves the energy-dependent formation of nanoscale membrane holes or energy-dependent endocytosis.

Confinement of aqueous mixtures of ionic liquids between amorphous TiO2 slit nanopores: electrostatic field induction.

Electrostatic potential in the vicinity of the surface is induced when aqueous mixtures of hydrophobic and hydrophilic ionic liquids (ILs) are confined between a slit nanopore of amorphous but not crystalline TiO2 semiconductors. According to our molecular dynamics (MD) simulations, the extent of ion-pairing lifetime under such nanoscale confinement is substantially lower than its value in the bulk. It becomes still lower when aqueous mixtures of ionic liquid electrolytes are used. Ion-ion correlation is broken completely in the confined dilute aqueous electrolyte systems. The anions and cations of the ILs migrate and accumulate at the opposite amorphous TiO2 electrodes that are separated by 10 nm to arrange a nanosize pore. In contrast, we have shown that the electrostatic interactions between the IL ions are dominant when the electrolyte is confined between anatase (101) TiO2. A similar trend is observed for the inorganic electrolyte system. These findings shed light on the design of new cells for electrochemical applications.

How Does the P7C3-Series of Neuroprotective Small Molecules Prevent Membrane Disruption?

Molecular dynamics (MD) simulations are conducted to suggest a mechanism of action for the aminopropyl dibromocarbazole derivative (P7C3) small molecule, which protects neurons from apoptotic cell death. At first, the influence of embedded Aß42 stacks on the structure of membrane is studied. Then, the effect of P7C3 molecules on the Aß42 fibril enriched membrane and Aß42 fibril depleted membrane (when Aß42 fibrils are originally dissolved in the aqueous phase) are evaluated. Also, the formation of an amyloid ion channel in the Aß42 enriched membrane is examined by calculating deuterium order parameter, density profile, and surface thickness. For Aß42 in the fully inserted state, ion channel-like structures are formed. The presence of P7C3 molecules in this case just postpones membrane destruction but could not prevent pore formation. In contrast, when both Aß42 and P7C3 molecules are embedded in the aqueous solution, the P7C3 molecules are self-assembled at membrane/ionic aqueous solution interface and prevent the precipitation and deposition of Aß42 fibrils into the membrane.

Novel curcumin-based pyrano[2,3-d]pyrimidine anti-oxidant inhibitors for α-amylase and α-glucosidase: Implications for their pleiotropic effects against diabetes complications.

Curcumin (bis-α,ß-unsaturated ß-diketone), the chief constituent of turmeric plant (Curcuma longa), plays significant role in prevention of various diseases including diabetes. The research objective in the current study was to synthesize novel anti-diabetic curcumin derivatives with inhibitory properties against α-amylase (α-Amy) and α-glucosidase (α-Gls), as these two carbohydrate-hydrolysing enzymes are known to be important molecular targets for attenuation of postprandial hyperglycemia. The curcumin-based pyrano[2,3-d]pyrimidine derivatives were synthesized in the presence of curcumin, barbituric acids and aldehydes, using a multi-component reaction (MCR). Also, their inhibitory properties against α-Amy and α-Gls were evaluated spectroscopically. The curcumin-derived compounds with two invariant substructures (curcumin-based subunit and barbituric acid moiety) and one variable aryl (Ar) group demonstrated inhibitory action against α-Amy and α-Gls. Moreover, the synthetic compounds revealed prominent antioxidant activities, when examined by a 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) decolorization assay system. Overall, these antioxidant inhibitors are potentially important anti-diabetic drugs, not only to restore euglysemic condition, but also to limit activity of the major reactive oxygen species (ROS) producing pathways in diabetic patients.

Studies of structural, dynamical, and interfacial properties of 1-alkyl-3-methylimidazolium iodide ionic liquids by molecular dynamics simulation.

Bulk and surface properties of the ionic liquids 1-alkyl-3-methyl-imidazolium iodides ([C(n)mim]I) were simulated by classical molecular dynamics using all atom non-polarizable force field (n = 4, butyl; 6, hexyl; 8, octyl). The structure of ionic liquids were initially optimized by density functional theory and atomic charges obtained by CHELPG method. Reduction of partial atomic charges (by 20% for simulation of density and surface tension, and by 10% for viscosity) found to improve the accuracy, while a non-polarizable force field was applied. Additionally, the simulation ensembles approach the equilibrium faster when the charge reduction is applied. By these refined force field parameters, simulated surface tensions in the range of 323-393 k are quite in agreement with the experiments. Simulation of temperature dependent surface tension of [C(4)mim]I well beyond room temperature (up to 700 K) permits prediction of the critical temperature in agreement with that predicted from experimental surface tension data. Simulated densities in the range of 298-450 K for the three ionic liquids are within 0.8% of the experimental data. Structural properties for [C(4)mim]I were found to be in agreement with the results of Car-Parrinello molecular dynamics simulation we performed, which indicates a rather well-structured cation-anion interaction and occurs essentially through the imidazolium ring cation. Diffusion coefficient changes with alkyl chain length in the order of [C(8)mim]I > [C(6)mim]I > [C(4)mim]I for the cation and the anion. Formation of a dense domain in subsurface region is quite evident, and progressively becomes denser as the alkyl chain length increases. Bivariate orientational analysis was used to determine the average orientation of molecule in ionic liquids surface, subsurface, and bulk regions. Dynamic bisector-wise and side-wise movement of the imodazolium ring cation in the surface region can be deduced from the bivariate maps. Atom-atom density profile and bivariate analysis indicate that the imidazolium cation takes a spoon like configuration in the surface region and the tilt of alkyl group is a function length of alkyl chain exposing as linear as possible to the vapor phase.

The extent of molecular orientation at liquid/vapor interface of pyridine and its alkyl derivatives by molecular dynamics simulation.

In this paper, molecular dynamics simulation was performed to investigate the liquid∕vapor interfacial structure of neat polar liquids. Large-scale ensembles of liquid pyridine and its alkyl derivatives, 4-methylpyridine and 4-ethylpyridine, were simulated by classical molecular dynamics at 298 K. For the liquid system of low polarity, the surface density profile of the atoms meet exactly at the middle of interfacial region, and atoms of hydrophobic nature can be hardly discriminated from hydrophilic ones in either vapor or liquid sides. For a liquid system of high polarity, the density profile of atoms with different nature is highly discriminated all over the interfacial region, and as the polarity increases, a dense region of atomic density is clearly developed in the subsurface region. The recognized bivariate method was also used to study the molecular orientational distribution quantitatively. Orientational analysis of the three liquid systems indicates that the pyridine ring plane in the outmost surface tends to be vertical. Its tendency in the innermost interfacial region is parallel. The orientational states available to 4-ethylpyridine and pyridine are discriminated by predicting the possibility of a bisector-wise tumbling for the ring plane in pyridine and a side-wise tumbling in 4-ethylpyridine. The orientational distribution maps explain the trend of experimental surface tension and surface entropy. As the dipole moment of these liquids increases with the alkyl chain length, the surface structural profile changes from a regular definite one to a surface of complex atomic structure involving a dense phase near the interface. The development of dense region in alkyl derivatives is the result of segregation of molecules due to the alkyl group, which is captured and discriminated by molecular dynamics simulation even when the length of a short alkyl chain is increased by one carbon atom.