MOF-Hosted Enzymes for Continuous Flow Catalysis in Aqueous and Organic Solvents.

Fully exploiting the potential of enzymes in cell-free biocatalysis requires stabilization of the catalytically active proteins and their integration into efficient reactor systems. Although in recent years initial steps towards the immobilization of such biomolecules in metal-organic frameworks (MOFs) have been taken, these demonstrations have been limited to batch experiments and to aqueous conditions. Here we demonstrate a MOF-based continuous flow enzyme reactor system, with high productivity and stability, which is also suitable for organic solvents. Under aqueous conditions, the stability of the enzyme was increased 30-fold, and the space-time yield exceeded that obtained with other enzyme immobilization strategies by an order of magnitude. Importantly, the infiltration of the proteins into the MOF did not require additional functionalization, thus allowing for time- and cost-efficient fabrication of the biocatalysts using label-free enzymes.

Probing the tricationic ionic liquid/vacuum interface: insights from molecular dynamics simulations.

The surface properties of three symmetric linear tricationic ionic liquids (LTILs) with the common anion, bis(trifluoromethylsulfonyl)imide ([NTf2]-), were studied using atomistic molecular dynamics simulation and identification of the truly interfacial molecules (ITIM) analysis. A refined version of the CL&P force field with the partial charges based on quantum calculations for isolated ion quartets was used to calculate the number densities, orientation of the cations, charge densities and surface tensions. The densities obtained from the simulation of the interface are on average 3% smaller than the densities of bulk NPT simulations, which is due to applying long-range corrections in the simulations of bulk liquids. New observations were reported for this new class of ILs through density profiles and orientational analysis. The ITIM analysis shows that the surface of the LTILs is more populated with anions rather than cations and it becomes smoother with a decrease in the alkyl chain length of the cations. The microscopic structural analysis of the orientational ordering at the interface shows that although for LTIL-1 and LTIL-2, the surface is more populated with anions and therefore has a negative charge, for LTIL-3 the surface is more populated with linkage alkyl chains and therefore has a small positive charge. This difference in the interfacial structures arises from the difference in the alkyl chain lengths. The results show that the LTILs with shorter alkyl chains (i.e. n = 3 and 6) form an inverse-arc shape structure while LTILs with longer alkyl chains (i.e. n = 10) form a sinuous like structure at the interface. The surface tension values of these ILs were calculated at 298 K using the mechanical definition. The simulations resulted in acceptable values for surface tension compared to the experimental trends.

Evaluating the Effects of Geometry and Charge Flux in Force Field Modeling.

We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the R-(CH2) n-R structure (R = Cl, F, OH, SH, COOH, CONH2, and NH2 and n = 4-6). Atomic charges were obtained by fitting to results from density functional theory calculations using the HLY procedure, and their geometry dependence is decomposed into contributions from changes in bond lengths, bond angles, and torsional angles. The torsional degrees of freedom are the main contribution to the conformational dependence of atomic charges and molecular dipole moments, but indirect effects due to changes in bond distances and angles account for ∼15% of the variations. While the magnitude of charge flux and geometry effects have been found to be independent of the number of internal degrees of freedom, the nature of the R- group has a moderate influence. The indirect effects are comparable for all of the R-groups and are approximately one-half the magnitude of the corresponding effects in peptide models. However, the magnitudes are different, yet the relative importance of geometry and charge flux effects are completely similar to those of the peptide models, which suggests that modeling the charge flux effects for changes in bond lengths, bond angles, and torsional angles should be considered for developing improved force fields.

Molecular dynamics simulation of geminal dicationic ionic liquids [Cn(mim)2][NTf2]2 - structural and dynamical properties.

In this work, the structural and dynamical properties of two imidazolium-based geminal dicationic ionic liquids (GDILs), i.e. [Cn(mim)2][NTf2]2 with n = 3 and 5, have been studied to obtain a fundamental understanding of the molecular basis of the macroscopic and microscopic properties of the bulk liquid phase. To achieve this purpose, molecular dynamics (MD) simulation, density functional theory (DFT) and atoms in molecule (AIM) methods were used. Interaction energies, charge transfers and hydrogen bonds between the cation and anions of each studied GDIL were investigated by DFT calculations and also AIM. The mean square displacement (MSD), self-diffusion coefficient, and transference number of the cation and anions, and also the density, viscosity and electrical conductivity of the studied GDILs, were computed at 333.15 K and at 1 atm. The simulated values were in good agreement with the experimental data. The effect of linkage alkyl chain length on the thermodynamic, transport and structural properties of these GDILs has been investigated. The structural features of these GDILs were characterized by calculating the partial site-site radial distribution functions (RDFs) and spatial distribution functions (SDFs). The heterogeneity order parameter (HOP) has been used to describe the spatial structures of these GDILs and the distribution of the angles formed between two cation heads and the middle carbon atom of the linkage alkyl chain was analyzed in these ILs. To investigate the temporal heterogeneity of the studied GDILs, the deviation of the self-part of the van Hove correlation function, Gs(r[combining right harpoon above],t), from the Gaussian distribution of particle displacement and also the second-order non-Gaussian parameter, α2(t), were used. Since, the transport and interfacial properties and ionic characteristics of these GDILs were studied experimentally in our previous studies as a function of linkage chain length and temperature, in this work, we try to give a better perspective of the structure and dynamics of these systems at a molecular level.

All-atom modeling of methacrylate-based multi-modal chromatography resins for Langmuir constant prediction of peptides.

In downstream processing, the intricate nature of the interactions between biomolecules and adsorbent materials presents a significant challenge in the prediction of their binding and elution behaviors. This complexity is further heightened in multi-modal chromatography (MMC), which employs two distinct binding mechanisms. To gain a deeper understanding of the involved interactions, simulating the adsorption of biomolecules on resin surfaces is a focal point of ongoing research. However, previous studies often simplified the adsorbent surface, modeling it as a flat or slightly curved plane without including a realistic backbone structure. Here, we introduce and validate two novel workflows aimed at predicting peptide binding behaviors in MMC, specifically targeting methacrylate-based resins. Our first achievement was the development of an all-atom model of a commercial MMC resin surface, incorporating its polymethacrylic backbone. Furthermore, we established and tested a workflow for rapid calculations of binding free energies (ΔG) with 10 linear peptides as target molecules. These ΔG calculations were effectively used to predict Langmuir constants, achieving a high coefficient of determination (R²) of 0.96. In subsequent benchmarking tests, our model outperformed established, simpler resin surface models in terms of predictive capabilities.

Challenges and limits of mechanical stability in 3D direct laser writing.

Direct laser writing is an effective technique for fabrication of complex 3D polymer networks using ultrashort laser pulses. Practically, it remains a challenge to design and fabricate high performance materials with different functions that possess a combination of high strength, substantial ductility, and tailored functionality, in particular for small feature sizes. To date, it is difficult to obtain a time-resolved microscopic picture of the printing process in operando. To close this gap, we herewith present a molecular dynamics simulation approach to model direct laser writing and investigate the effect of writing condition and aspect ratio on the mechanical properties of the printed polymer network. We show that writing conditions provide a possibility to tune the mechanical properties and an optimum writing condition can be applied to fabricate structures with improved mechanical properties. We reveal that beyond the writing parameters, aspect ratio plays an important role to tune the stiffness of the printed structures.

Tough, Transparent, 3D-Printable, and Self-Healing Poly(ethylene glycol)-Gel (PEGgel).

Polymer gels, such as hydrogels, have been widely used in biomedical applications, flexible electronics, and soft machines. Polymer network design and its contribution to the performance of gels has been extensively studied. In this study, the critical influence of the solvent nature on the mechanical properties and performance of soft polymer gels is demonstrated. A polymer gel platform based on poly(ethylene glycol) (PEG) as solvent is reported (PEGgel). Compared to the corresponding hydrogel or ethylene glycol gel, the PEGgel with physically cross-linked poly(hydroxyethyl methacrylate-co-acrylic acid) demonstrates high stretchability and toughness, rapid self-healing, and long-term stability. Depending on the molecular weight and fraction of PEG, the tensile strength of the PEGgels varies from 0.22 to 41.3 MPa, fracture strain from 12% to 4336%, modulus from 0.08 to 352 MPa, and toughness from 2.89 to 56.23 MJ m-3 . Finally, rapid self-healing of the PEGgel is demonstrated and a self-healing pneumatic actuator is fabricated by 3D-printing. The enhanced mechanical properties of the PEGgel system may be extended to other polymer networks (both chemically and physically cross-linked). Such a simple 3D-printable, self-healing, and tough soft material holds promise for broad applications in wearable electronics, soft actuators and robotics.

Enantiomeric Separation of Semiconducting Single-Walled Carbon Nanotubes by Acid Cleavable Chiral Polyfluorene.

Helical wrapping by conjugated polymer has been demonstrated as a powerful tool for the sorting of single-walled carbon nanotubes (SWCNTs) according to their electronic type, chiral index, and even handedness. However, a method of one-step extraction of left-handed (M) and right-handed (P) semiconducting SWCNTs (s-SWCNTs) with subsequent cleavage of the polymer has not yet been published. In this work, we designed and synthesized one pair of acid cleavable polyfluorenes with defined chirality for handedness separation of s-SWCNTs from as-produced nanotubes. Each monomer contains a chiral center on the fluorene backbone in the 9-position, and the amino and carbonyl groups in the 2- and 7-positions maintain the head-to-tail regioselective polymerization resulting in polyimines with strictly all-(R) or all-(S) configuration. The obtained chiral polymers exhibit a strong recognition ability toward left- or right-handed s-SWCNTs from commercially available CoMoCAT SWCNTs with a sorting process requiring only bath sonication and centrifugation. Interestingly, the remaining polymer on each single nanotube, which helps to prevent aggregation, does not interfere with the circular dichroism signals from the nanotube at all. Therefore, we observed all four interband transition peaks (E11, E22, E33, E44) in the circular dichroism (CD) spectra of the still wrapped optically enriched left-handed and right-handed (6,5) SWCNTs in toluene. Binding energies obtained from molecular dynamics simulations were consistent with our experimental results and showed a significant preference for one specific handedness from each chiral polymer. Moreover, the imine bonds along the polymer chains enable the release of the nanotubes upon acid treatment. After s-SWNT separation, the polymer can be decomposed into monomers and be cleanly removed under mild acidic conditions, yielding dispersant-free handedness sorted s-SWNTs. The monomers can be almost quantitatively recovered to resynthesize the chiral polymer. This approach enables high selective isolation of polymer-free s-SWNT enantiomers for their further applications in carbon nanotube (CNT) devices.

Sampling of the conformational landscape of small proteins with Monte Carlo methods.

Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the ß-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.

Tricationic Ionic Liquids: Structural and Dynamical Properties via Molecular Dynamics Simulations.

Three imidazolium-based linear tricationic ionic liquids (LTILs) have been simulated to study their structural and dynamical properties and obtain a fundamental understanding of the molecular basis of the microscopic and macroscopic properties of their bulk liquid phase. The effects of temperature and alkyl chain length on the physiochemical, transport, and structural properties of these LTILs have been investigated. A nonpolarizable all-atom force field, which is a refined version of the Canongia Lopes and Paudua force field, was adopted for the simulations. Densities, mean square displacements, self-diffusivities, viscosities, electrical conductivities, and transference numbers have been presented for various ions from MD simulations. The detailed microscopic structures have been discussed in terms of radial distribution functions and spatial distribution functions. The results show that, similar to that in monocationic and dicationic ILs (MILs and DILs, respectively), the anions are mainly organized around the imidazolium rings. The diffusion coefficients of the studied LTILs are smaller than those of both MILs and DILs, with comparable viscosities. Unlike those of MILs and DILs, the diffusion coefficients of the cations and anions of the studied LTILs increase with an increase in the length of the alkyl chain between the rings for LTIL-1 and LTIL-2 but then decrease for LTIL-3, which is in a good agreement with the trend of viscosity data. The calculated transference numbers show that, similar to that in MILs and DILs, cations have a major role in carrying electric current in LTILs, but this role increases from MILs to LTILs.

Probing the Importance of Charge Flux in Force Field Modeling.

We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.