Reversible Hydrogen Bond Network Dynamics: Molecular Dynamics Simulations of Calix[4]arene-Catenanes

Heterogeneous Rate Constant for Amorphous Silica Nanoparticle Adsorption on Phospholipid Monolayers

The interaction of amorphous silica nanoparticles with phospholipid monolayers and bilayers has received a great deal of interest in recent years and is of importance for assessing potential cellular toxicity of such species, whether natural or synthesized for the purpose of nanomedical drug delivery and other applications. This present communication studies the rate of silica nanoparticle adsorption on to phospholipid monolayers in order to extract a heterogeneous rate constant from the data. This rate constant relates to the initial rate of growth of an adsorbed layer of nanoparticles as SiO2 on a unit area of the monolayer surface from unit concentration in dispersion. Experiments were carried out using the system of dioleoyl phosphatidylcholine (DOPC) monolayers deposited on Pt/Hg electrodes in a flow cell. Additional studies were carried out on the interaction of soluble silica with these layers. Results show that the rate constant is effectively constant with respect to silica nanoparticle size. This is interpreted as indicating that the interaction of hydrated SiO2 molecular species with phospholipid polar groups is the molecular initiating event (MIE) defined as the initial interaction of the silica particle surface with the phospholipid layer surface promoting the adsorption of silica nanoparticles on DOPC. The conclusion is consistent with the observed significant interaction of soluble SiO2 with the DOPC layer and the established properties of the silica-water interface.

Force probe simulations using an adaptive resolution scheme

Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute are described in a coarse-grained manner. We use the adaptive resolution scheme (AdResS) that has very successfully been applied to various examples of equilibrium simulations. We perform FPMD simulations using AdResS on a well studied system, a dimer formed from mechanically interlocked calixarene capsules. The results of the multiscale simulations are compared to all-atom simulations of the identical system and we observe that the size of the region in which atomistic resolution is required depends on the pulling velocity, i.e. the particular non-equilibrium situation. For large pulling velocities a larger all atom region is required. Our results show that multiscale simulations can be applied also in the strong non-equilibrium situations that the system experiences in FPMD simulations.

Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules

We present force probe molecular dynamics simulations of dimers of interlocked calixarene nanocapsules and study the impact of structural details and solvent properties on the mechanical unfolding pathways. The system consists of two calixarene "cups" that form a catenane structure via interlocked aliphatic loops of tunable length. The dimer shows reversible rebinding, and the kinetics of the system can be understood in terms of a two-state model for shorter loops (≤14 CH₂ units) and a three-state model for longer loops (≥15 CH₂ units). The various conformational states of the dimer are stabilized by networks of hydrogen bonds, the mechanical susceptibility of which can be altered by changing the polarity and proticity of the solvent. The variation of the loop length and the solvent properties in combination with changes in the pulling protocol allows to tune the reversibility of the conformational transitions.

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10^-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

Force probe simulations using a hybrid scheme with virtual sites

Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method and the force matching procedure, and find that both methodologies give similar results. The results of the FPMD simulations are compared to all-atom simulations of the same system and we find that differences between these simulations and the ones using the hybrid scheme are in a similar range as the differences obtained when using different atomistic force fields. Thus, a hybrid scheme yields qualitatively correct results in the strong non-equilibrium situation the system is experiencing in FPMD simulations.

Through-the-annulus threading of the larger calix[8]arene macrocycle

A complete study of the through-the-annulus threading of the larger calix[8]arene macrocycle with di-n-alkylammonium cations has been performed in the presence of the "superweak" TFPB counterion. Thus, it was found that such threading occurs only upon partial preorganization of the calix[8]arene macroring by intramolecular bridging. In particular, 1,5-bridged calix[8]arenes with a meta- or para-xylylene bridge (2 and 3) gave pseudo[2]rotaxanes in which one dialkylammonium axle (4a-4e(+)) was threaded into one of the two subcavities of the calix[8]-wheel. Conformational studies by using chemical shift surface maps and DFT calculations evidenced a 3/4-cone geometry for these subcavities. Higher pseudorotaxane K(ass) values were obtained for calix[8]-wheels 2 and 3, with respect to calix[6]-host 1a, due to the cooperative effect of their two subcavities. Dynamic NMR studies on calix[8]-pseudorotaxanes evidenced a direct correlation between K(ass) (and ΔG(ass)) values and energy barriers for calix inversion due to the effectiveness of thread templation. In accordance with DFT calculations, an endo-alkyl preference, over the endo-benzyl one, was observed by threading calix[8]-wheel 3 with the directional n-butylbenzylammonium axle 4d(+).

Catenation of calixarene annulus

Through-the-annulus-catenated calixarenes have been obtained, for the first time, by exploiting the "superweak anion" approach that allows the threading of the calix cavity with functionalized dialkylammonium axles. In addition, the first example of a stereoprogrammed synthesis of a catenane orientational isomer (an oriented calix[2]catenane) has been obtained, after macrocyclization, by using a directional alkylbenzylammonium axle.