Counterintuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites.

The consecutive binding of two potassium ions to a bis(18-crown-6) analogue of Tröger's base (BCETB) in water was studied by isothermal titration calorimetry using four different salts, KCl, KI, KSCN, and K2SO4. A counterintuitive result was observed: the enthalpy change associated with the binding of the second ion is more negative than that of the first (ΔHbind,2° < ΔHbind,1°). This remarkable finding is supported by continuum electrostatic theory as well as by atomic scale replica exchange molecular dynamics simulations, where the latter robustly reproduces experimental trends for all simulated salts, KCl, KI, and KSCN, using multiple force fields. While an enthalpic K+-K+ attraction in water poses a small, but fundamentally important, contribution to the overall interaction, the probability of the collapsed conformation (COL) of BCETB, where both crown ether moieties (CEs) of BCETB are bent in toward the cavity, was found to increase successively upon binding of the first and second potassium ions. The promotion of the COL conformation reveals favorable intrinsic interactions between the potassium coordinated CEs, which further contribute to the observation that ΔHbind,2° < ΔHbind,1°. While the observed trend is independent of the counterion, the origin of the significantly larger magnitude of the difference ΔHbind,2° - ΔHbind,1° observed experimentally for KSCN was studied in light of the weaker hydration of the thiocyanate anion, resulting in an enrichment of thiocyanate ions close to BCETB compared to the other studied counterions.

Tuning the selective permeability of polydisperse polymer networks.

We study the permeability and selectivity ('permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. In our work, permeability P is determined on the linear-response level using the solution-diffusion model, P = KDin, i.e., by calculating the equilibrium penetrant partition ratio K and penetrant diffusivity Din inside the membrane. We vary two key parameters, namely the network-network interaction, which controls the degree of swelling and collapse of the network, and the network-penetrant interaction, which tunes the selective penetrant uptake and microscopic energy landscape for diffusive transport. We find that the partitioning K covers four orders of magnitude and is a non-monotonic function of the parameters, well interpreted by a second-order virial expansion of the free energy of transferring one penetrant from a reservoir into the membrane. Moreover, we find that the penetrant diffusivity Din in the polydisperse networks, in contrast to highly ordered membrane structures, exhibits relatively simple exponential decays. We propose a semi-empirical scaling law for the penetrant diffusion that describes the simulation data for a wide range of densities and interaction parameters. The resulting permeability P turns out to follow the qualitative behavior (including maximization and minimization) of partitioning. However, partitioning and diffusion are typically anti-correlated, yielding large quantitative cancellations, controlled and fine-tuned by the network density and interactions, as rationalized by our scaling laws. We finally demonstrate that even small changes of network-penetrant interactions, e.g., by half a kBT, modify the permselectivity by almost one order of magnitude.

Cross-linker effect on solute adsorption in swollen thermoresponsive polymer networks.

The selective solute partitioning within a polymeric network is of key importance to applications in which controlled release or uptake of solutes in a responsive hydrogel is required. In this work we investigate the impact of cross-links on solute adsorption in a swollen polymer network by means of all-atom, explicit-water molecular dynamics simulations. We focus on a representative network subunit consisting of poly(N-isopropylacrylamide) (PNIPAM) and N,N'-methylenebisacrylamide (BIS/MBA) cross-linker types. Our studied system consists of one BIS-linker with four atactic PNIPAM chains attached in a tetrahedral geometry. The adsorption of several representative solutes of different polarity in the low concentration limit at the linker region is examined. We subdivide the solute adsorption regions and distinguish between contributions stemming from polymer chains and cross-link parts. In comparison to a single polymer chain, we observe that the adsorption of the solutes to the cross-link region can significantly differ, with details depending on the specific compounds' size and polarity. In particular, for solutes that have already a relatively large affinity to PNIPAM chains the dense cross-link region (where many-body attractions are at play) amplifies the local adsorption by an order of magnitude. We also find that the cross-link region can serve as a seed for the aggregation of mutually attractive solutes at higher solute concentrations. Utilizing the microscopic adsorption coefficients in a mean-field model of an idealized macroscopic polymer network, we extrapolate these results to the global solute partitioning in a swollen hydrogel and predict that these adsorption features may lead to non-monotonic partition ratios as a function of the cross-link density.

Tuning the collapse transition of weakly charged polymers by ion-specific screening and adsorption.

The experimentally observed swelling and collapse response of weakly charged polymers to the addition of specific salts displays quite convoluted behavior that is not easy to categorize. Here we use a minimalistic implicit-solvent/explicit-salt simulation model with a focus on ion-specific interactions between ions and a single weakly charged polyelectrolyte to qualitatively explain the observed effects. In particular, we demonstrate ion-specific screening and bridging effects cause collapse at low salt concentrations whereas the same strong ion-specific direct interactions drive re-entrant swelling at high concentrations. Consistently with experiments, a distinct salt concentration at which the salting-out power of anions inverts from the reverse to direct Hofmeister series is observed. At this so called isospheric point, the ion-specific effects vanish. Furthermore, with additional simplifying assumptions, an ion-specific mean-field model is developed for the collapse transition which quantitatively agrees with the simulations. Our work demonstrates the sensitivity of the structural behavior of charged polymers to the addition of specific salt beyond simple screening and shall be useful for further guidance of experiments.

Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets.

Using explicit-water molecular dynamics simulations of a generic pocket-ligand model, we investigate how chemical and shape anisotropy of small ligands influences the affinities, kinetic rates, and pathways for their association with hydrophobic binding sites. In particular, we investigate aromatic compounds, all of similar molecular size, but distinct by various hydrophilic or hydrophobic residues. We demonstrate that the most hydrophobic sections are in general desolvated primarily upon binding to the cavity, suggesting that specific hydration of the different chemical units can steer the orientation pathways via a "hydrophobic torque." Moreover, we find that ligands with bimodal orientation fluctuations have significantly increased kinetic barriers for binding compared to the kinetic barriers previously observed for spherical ligands due to translational fluctuations. We exemplify that these kinetic barriers, which are ligand specific, impact both binding and unbinding times for which we observe considerable differences between our studied ligands.

Selective solute adsorption and partitioning around single PNIPAM chains.

Thermoresponsive polymer architectures have become integral building blocks of 'smart' functional materials in modern applications. For a large range of developments, e.g. for drug delivery or nanocatalytic carrier systems, the selective adsorption and partitioning of molecules (ligands or reactants) inside the polymeric matrix are key processes that have to be controlled and tuned for the desired material function. In order to gain insights into the nanoscale structure and binding details in such systems, we here employ molecular dynamics simulations of the popular poly(N-isopropylacrylamide) (PNIPAM) polymer in explicit water in the presence of various representative solute types with a focus on aromatic model reactants. We study a single polymer chain and explore the influence of its elongation, stereochemistry, and temperature on the solute binding affinities. While we find that the excess adsorption generally increases with the size of the solute, the temperature-dependent affinity to the chain is highly solute specific and has a considerable dependence on the polymer elongation (i.e. polymer swelling state). We elucidate the molecular mechanisms of the selective binding in detail and eventually present how the results can be extrapolated to macroscopic partitioning of the solutes in swollen polymer architectures, such as hydrogels.

Tuning the critical solution temperature of polymers by copolymerization.

We study statistical copolymerization effects on the upper critical solution temperature (CST) of generic homopolymers by means of coarse-grained Langevin dynamics computer simulations and mean-field theory. Our systematic investigation reveals that the CST can change monotonically or non-monotonically with copolymerization, as observed in experimental studies, depending on the degree of non-additivity of the monomer (A-B) cross-interactions. The simulation findings are confirmed and qualitatively explained by a combination of a two-component Flory-de Gennes model for polymer collapse and a simple thermodynamic expansion approach. Our findings provide some rationale behind the effects of copolymerization and may be helpful for tuning CST behavior of polymers in soft material design.

A novel high-resolution chipCE assay for rapid detection of EGFR gene mutations and amplifications in lung cancer therapy by a combination of fragment analysis, denaturing CE and MLPA.

There is a growing interest in evaluating molecular markers as predictors of response to new generation of targeted cancer therapies. One of such areas is biological therapy targeting epidermal growth factor receptor gene (EGFR) in lung cancer. The testing of tumor tissue is focused on specific EGFR mutations and EGFR gene amplification, since tumors exhibiting positivity of either of the two marker types are highly sensitive towards the treatment. Although traditional methods of DNA sequencing and fluorescence in situ hybridization are still in use for the detection of EGFR mutations and gene amplification, respectively, there is a need for new dedicated techniques with the primary emphasis on simplicity, sensitivity, speed and cost effectiveness. The main purpose of this work was to integrate diverse assays for both EGFR tests onto a single platform to eliminate the need for different instruments and separate processing. We demonstrate a chip capillary electrophoresis (chipCE) application for EGFR mutation detection by a combination of fragment analysis and denaturing CE along with multiplex ligation-dependent probe amplification (MLPA) for evaluation of EGFR amplification. All separations are carried out in denaturing sieving polymer on a modified Bioanalyzer 2100 chipCE instrument running at temperatures of up to 65°C. The main strength of the resulting high-resolution chipCE application is in its simplicity, speed of analysis and minimal amount of sample required for complete testing of EGFR status. Such an approach could potentially fit medium throughput laboratories providing molecular pathology services for clinical oncologists with fast turnaround times and limited consumption of tissue material.

Occurrence and behavior of system peaks in RP HPLC with solely aqueous mobile phases.

System peaks are important but often also disturbing phenomena occurring in separation systems. Behavior of system peaks was studied in reversed phase high performance liquid chromatography (RP HPLC) systems consisting of an RP Amide C16 column and aqueous solutions of organic acids with alkaline metal hydroxides as mobile phases. Binary mobile phases, composed of benzoic acid and lithium hydroxide (LiOH) or cesium hydroxide (CsOH), yielded two system peaks. The first peak was stationary and the second one moved with dilution of the mobile phase or with changes of the alkaline metal hydroxide concentration. The latter changes affected dissociation of the benzoic acid present in the mobile phase and thereby its retention. The presumption that the first system peak is not influenced by the type of alkaline metal cation and that it is related to the non-adsorbed component of the mobile phase was confirmed by a cyclic procedure. Three-component mobile phases composed of benzoic acid, tropic acid, and a hydroxide gave rise to three system peaks as expected. The first peak was again stationary and the two others shifted depending on the concentration variation of both acids. Resonance causing a zigzag peak, well described in capillary zone electrophoresis (CZE), was observed if 1-pentanol was injected into a chromatographic system with one-component mobile phase.

Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution.

A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are postrefined by benchmarking to experimental data of the radius of gyration. For better handling and a fully continuous transferability in T-space, the pair potentials are conveniently truncated and mapped to an analytic formula with three structural parameters expressed as explicit continuous functions of T. It is then demonstrated that this model without further adjustments successfully reproduces other experimentally known key thermodynamic properties of semidilute PEG solutions such as the full equation of state (i.e., T-dependent osmotic pressure) for various chain lengths as well as their cloud point (or collapse) temperature.

Determination of nitrite and nitrate in cerebrospinal fluid by microchip electrophoresis with microsolid phase extraction pre-treatment.

A new method for the determination of nitrite and nitrate, indicators of various neurological diseases (meningitis, multiple sclerosis, Parkinson's disease) in cerebrospinal fluid (CSF) on an electrophoresis chip was developed. An on-line combination of isotachophoresis (ITP) with capillary electrophoresis (CE) on a poly(methylmethacrylate) chip assembled with coupled separation channels (CC) and contact conductivity detectors was employed. ITP separations performed at low pH (3.6) in the first separation channel enabled a highly selective transfer of the analytes to the second CE stage working under micellar conditions implemented by zwitterionic surfactant, 3-(N,N-dimethyldodecylammonio)-propanesulfonate. The proposed method achieved low limits of detection varied from 0.2 to 0.4µgL(-1) when the sample volume injected onto the chip (9.9µl) was almost the same as the volume of both separation channels. Preferable working conditions on the CC chip (suppressed hydrodynamic and electroosmotic flow) contributed for reproducible migration velocities (intra-day reproducibility up to 2.1% RSD) and determinations of trace concentrations of nitrite and nitrate (intra-day precision up to 3.0% RSD). Huge amount of chloride present in CSF (approx. 4.5gL(-1)) was removed from analyzed CSF samples by microsolid phase extraction performed on silver-form resin prior to the ITP-CE analysis. Developed method provided fast (approx. 20min total analysis time) and reliable determinations of trace nitrite and nitrate and could be fully integrated into the analysis of CSF samples.