A Classical Molecular Dynamics Simulation Study of Interfacial and Bulk Solution Aggregation Properties of Dirhamnolipids.

The rhamnolipids are a unique class of biosurfactants produced by the bacteria Pseudomonas aeruginosa. These molecules display a high level of surface activity as well as biodegradability. In this study nonionic dirhamnolipid was investigated by utilizing molecular dynamics simulation at the air-water interface as well as in bulk water. Detailed structural analysis is presented for both the interfacial simulations and the simulations in solution. A systematic comparison was made between our previous work on the monorhamnolipid at the air-water interface and in bulk water. The presence of a second rhamnose group in dirhamnolipid did not show any significant change in the aggregation at the air-water interface. An increase in the molecular weight resulted in the larger surface area per monomer for dirhamnolipid compared to monorhamnolipid at the air-water interface. However, aggregation of dirhamnolipid in bulk water was affected by the presence of a second rhamnose group. Dirhamnolipid aggregates into micellar structure around ∼N22 which was lower than the monorhamnolipid aggregation number ∼N40. The hydrophobic component of the dirhamnolipid was enhanced to balance the higher hydrophilic component. An increase in alkyl chain length has shown that the enhanced hydrophobic component supports the formation of micellar aggregates up to ∼N30 and above, which was not observed in dirhamnolipid with a shorter alkyl chain length.

Unraveling the Differential Aggregation of Anionic and Nonionic Monorhamnolipids at Air-Water and Oil-Water Interfaces: A Classical Molecular Dynamics Simulation Study.

The molecular structure of a surfactant molecule is known to have a great effect on the interfacial properties. We employ molecular dynamics simulations for a detailed atomistic study of monolayers of the nonionic and anionic form of the most common congener of monorhamnolipids, α-rhamnopyranosyl-ß-hydroxydecanoyl-ß-hydroxydecanoate (( R, R)-Rha-C10-C10), at the air-water and oil-water interfaces. An atomistic-level understanding of monolayer aggregation is necessary to explain a recent experimental observation indicating that nonionic and anionic Rha-C10-C10 show surprisingly different surface area per molecule at the critical micelle concentration. Surface-pressure analysis, interface formation energy calculations, and mass density profiles of the monolayers at the air-water interface show similar properties between nonionic and anionic Rha-C10-C10 aggregation. It is found that there is a significant difference in the headgroup conformations of Rha-C10-C10 in the nonionic and anionic monolayers. Hydrogen bonding interactions between the Rha-C10-C10 molecules in the monolayers is also significantly different between nonionic and anionic forms. Representative snapshots of the simulated system at different surface concentrations show the segregation of molecular aggregates from the interface into the bulk water in the anionic Rha-C10-C10 monolayer at higher concentrations, whereas in the nonionic Rha-C10-C10 monolayer, the molecules are still located at the interface. The present work provides insight into the different aggregation properties of nonionic and anionic Rha-C10-C10 at the air-water interface. Further analyses were carried out to understand the aggregation behavior of nonionic and anionic Rha-C10-C10 at the oil-water interface. It is observed that the presence of oil molecules does not significantly influence the aggregation properties of Rha-C10-C10 as compared to those of the air-water interface.

Molecular Dynamics Simulation of the Oil Sequestration Properties of a Nonionic Rhamnolipid.

A detailed molecular dynamics simulation study is presented on the behavior of aggregates composed of the nonionic monorhamnolipid α-rhamnopyranosyl-ß-hydroxydecanoyl-ß-hydroxydecanoate (Rha-C10-C10) and decane in bulk water. A graph theoretical approach was utilized to characterize the size and composition of the many aggregates generated in our simulations. Overall, we observe that the formation of oil in Rha-C10-C10 aggregates is a favorable process. Detailed analysis on the surfactant/oil aggregate shows that larger aggregates are stable. The shape and size of the aggregates are widely distributed, with the majority of the aggregates preferring ellipsoidal or cylindrical structures. Irrespective of the decane concentration in the system, we did not observe free decane in any of the simulations. Further insights into the binding energy of decane were carried out using free-energy perturbation calculations. The results showed that the trapped decane molecules provide stability to the Rha-C10-C10 aggregates of size N = 50 which are shown to be unstable in our previous study and allow for the growth of larger aggregates than pure Rha-C10-C10 in water. The density profile plots show that decane molecules encapsulated inside the aggregate preferred to remain closer to the center of mass. This study points to the feasibility of using this biosurfactant as an environmental remediation agent.

Evolution of Aggregate Structure in Solutions of Anionic Monorhamnolipids: Experimental and Computational Results.

The evolution of solution aggregates of the anionic form of the native monorhamnolipid (mRL) mixture produced by Pseudomonas aeruginosa ATCC 9027 is explored at pH 8.0 using both experimental and computational approaches. Experiments utilizing surface tension measurements, dynamic light scattering, and both steady-state and time-resolved fluorescence spectroscopy reveal solution aggregation properties. All-atom molecular dynamics simulations on self-assemblies of the most abundant monorhamnolipid molecule, l-rhamnosyl-ß-hydroxydecanoyl-ß-hydroxydecanoate (Rha-C10-C10), in its anionic state explore the formation of aggregates and the role of hydrogen bonding, substantiating the experimental results. At pH 8.0, at concentrations above the critical aggregation concentration of 201 µM but below ∼7.5 mM, small premicelles exist in solution; above ∼7.5 mM, micelles with hydrodynamic radii of ∼2.5 nm dominate, although two discrete populations of larger lamellar aggregates (hydrodynamic radii of ∼10 and 90 nm) are also present in solution in much smaller number densities. The critical aggregation number for the micelles is determined to be ∼26 monomers/micelle using fluorescence quenching measurements, with micelles gradually increasing in size with monorhamnolipid concentration. Molecular dynamics simulations on systems with between 10 and 100 molecules of Rha-C10-C10 indicate the presence of stable premicelles of seven monomers with the most prevalent micelle being ∼25 monomers and relatively spherical. A range of slightly larger micelles of comparable stability can also exist that become increasing elliptical with increasing monomer number. Intermolecular hydrogen bonding is shown to play a significant role in stabilization of these aggregates. In total, the computational results are in excellent agreement with the experimental results.

Structural Properties of Nonionic Monorhamnolipid Aggregates in Water Studied by Classical Molecular Dynamics Simulations.

Molecular dynamics simulations were carried out to investigate the structure and stabilizing factors of aggregates of the nonionic form of the most common congener of monorhamnolipids, α-rhamnopyranosyl-ß-hydroxydecanoyl-ß-hydroxydecanoate (Rha-C10-C10), in water. Aggregates of size ranging from 5 to 810 monomers were observed in the simulation forming spherical and ellipsoidal structures, a torus-like structure, and a unilamellar vesicle. The effects of the hydrophobic chain conformation and alignment in the aggregate, role of monomer···monomer and monomer···water H-bonds, and conformations of monomers in the aggregate were studied in detail. The unilamellar vesicle is highly stable due to the presence of isolated water molecules inside the core adding to the binding energy. Dissociation of a monomer from a larger micellar aggregate is relatively easy compared to that from smaller aggregates as seen from potential of mean force calculations. This analysis also shows that monomers are held more strongly in aggregates of Rha-C10-C10 than the widely used surfactant sodium dodecyl sulfate. Comparisons between the aggregation behavior of nonionic and anionic forms of Rha-C10-C10 are presented.

Endohedral and exohedral complexes of substituted benzenes with carbon nanotubes and graphene.

Non-covalent complexes of cyclohexane and a series of substituted benzenes with short carbon nanotube (CNT) models are investigated primarily at the B97-D3∕TZV(2d,2p) level of theory. Understanding non-covalent interactions of arenes with CNTs is vital for the development of next-generation organic electronic materials and for harnessing CNTs as nano-reactors and vehicles for drug delivery. The interaction of benzene and cyclohexane with the interior and exterior of CNTs depends on the nanotube diameter, particularly for endohedral complexes. Both benzene and cyclohexane interact more strongly with the interior of CNTs than the outside, with benzene exhibiting stronger interactions than cyclohexane for CNTs larger than (8,8). Studies of two benzenes inside of CNTs predict the formation of one-dimensional sandwich and parallel-displaced stacks of benzenes within certain sized CNTs, which could have interesting optoelectronic properties. Concerning the impact of substituents on the interaction of benzene with CNTs, we find that electrostatic interactions do not control substituent effects. That is, the electron-donating or -withdrawing character of the substituents is not correlated with the predicted interaction energies. Moreover, substituent effects are the same for both endohedral and exohedral complexes, despite the different electronic character of the interior and exterior CNT walls. Ultimately, substituent effects in π-stacking interactions with CNTs and graphene are explained by differences in dispersion interactions between the substituents and CNT walls or graphene surface.

Modulation of aldose reductase inhibition by halogen bond tuning.

In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions. The role of the single halogen bond in AR-ligand binding was elucidated by advanced binding free energy calculations involving the semiempirical quantum chemical Hamiltonian. The results were complemented with ultrahigh-resolution X-ray crystallography and IC50 measurements. All of the AR inhibitors studied were shown by X-ray crystallography to bind in an identical manner. Further, it was demonstrated that it was possible to decrease the IC50 value by about 1 order of magnitude by tuning the strength of the halogen bond by a monoatomic substitution. The calculations revealed that the protein-ligand interaction energy increased upon the substitution of iodine for bromine or upon the addition of electron-withdrawing fluorine atoms to the ring. However, the effect on the binding affinity was found to be more complex due to the change of the solvation/desolvation properties within the ligand series. The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.

Time-resolved surface-enhanced coherent sensing of nanoscale molecular complexes.

Nanoscale real-time molecular sensing requires large signal enhancement, small background, short detection time and high spectral resolution. We demonstrate a new vibrational spectroscopic technique which satisfies all of these conditions. This time-resolved surface-enhanced coherent anti-Stokes Raman scattering (tr-SECARS) spectroscopy is used to detect hydrogen-bonded molecular complexes of pyridine with water in the near field of gold nanoparticles with large signal enhancement and a fraction of a second collection time. Optimal spectral width and time delays of ultrashort laser pulses suppress the surface-enhanced non-resonant background. Time-resolved signals increase the spectral resolution which is limited by the width of the probe pulse and allow measuring nanoscale vibrational dephasing dynamics. This technique combined with quantum chemistry simulations may be used for the investigation of complex mixtures at the nanoscale and surface environment of artificial nanostructures and biological systems.

On the nature of the stabilization of benzene···dihalogen and benzene···dinitrogen complexes: CCSD(T)/CBS and DFT-SAPT calculations.

The structure and stabilization energies of benzene (and methylated benzenes)···X(2) (X=F, Cl, Br, N) complexes were investigated by performing CCSD(T)/complete basis set limit and density functional theory/symmetry-adapted perturbation theory (DFT-SAPT) calculations. The global minimum of the benzene···dihalogen complexes corresponds to the T-shaped structure, whereas that of benzene···dinitrogen corresponds to the sandwich one. The different binding motifs of these complexes arise from the different quadrupole moments of dihalogens and dinitrogen. The different sign of the quadrupole moments of these diatomics is explained based on the electrostatic potential (ESP). Whereas all dihalogens, including difluorine, possess a positive σ hole, such a positive area of the ESP is completely missing in the case of dinitrogen. Moreover, benzene···X(2) (X=Br, Cl) complexes are stronger than benzene···X(2) (X=F, N) complexes. When analyzing DFT-SAPT electrostatic, dispersion, induction, and δ(Hartree-Fock) energies, we recapitulate that the former complexes are stabilized mainly by dispersion energy, followed by electrostatic energy, whereas the latter complexes are stabilized mostly by the dispersion interaction. The charge-transfer energy of benzene···dibromine complexes, and surprisingly, also of methylated benzenes···dibromine complexes is only moderate, and thus, not responsible for their stabilization. Benzene···dichlorine and benzene···dibromine complexes can thus be characterized merely as complexes with a halogen bond rather than as charge-transfer complexes.