PEGDA hydrogel structure from semi-dilute concentrations: insights from experiments and molecular simulations.

The efficacy of hydrogel materials used in biomedical applications is dependent on polymer network topology and the structure of water-laden pore space. Hydrogel microstructure can be tuned by adjusting synthesis parameters such as macromer molar mass and concentration. Moreover, hydrogels beyond dilute conditions are needed to produce mechanically robust and dense networks for tissue engineering and/or drug delivery systems. Thus, this study utilizes a combined experimental and molecular simulation approach to characterize structural features for 4.8 and 10 kDa poly (ethylene glycol) diacrylate (PEGDA) hydrogels formed from a range of semi-dilute solution concentrations. The connection between chain-chain interactions in polymer solutions, hydrogel structure, and equilibrium swelling behavior is presented. Bulk rheology analysis revealed an entanglement concentration for PEGDA pre-gel solutions around 28 wt% for both macromers studied. A similar transition in swelling behavior was revealed around the same concentration where hydrogel capacity to retain water was drastically reduced. To understand this transition, the hydrogel structure was characterized using the swollen polymer network hypothesis and compared to pore size distributions from molecular dynamics simulations. We find in both approaches a structural transition concentration at the hydrogel swelling inflection point that is comparable to the entanglement concentration. Calculated mesh sizes from theory are compared with computationally determined average maximum pore diameters; mesh sizes from theory yielded greater feature sizes across all concentrations considered. Molecular simulations are further used to assess pore dynamics, which are shown to vary in distribution shape and number of modes compared to the time-averaged hydrogel pore features. Altogether, this work provides insights into hydrogel network features and their dynamic behavior at physiological conditions (37 °C) as a basis for hydrogel design beyond dilute conditions for biomedical applications.

Molecular Dynamics-Guided Design of a Functional Protein-ATRP Conjugate That Eliminates Protein-Protein Interactions.

Even the most advanced protein-polymer conjugate therapeutics do not eliminate antibody-protein and receptor-protein recognition. Next-generation bioconjugate drugs will need to replace stochastic selection with rational design to select desirable levels of protein-protein interaction while retaining function. The "Holy Grail" for rational design would be to generate functional enzymes that are fully catalytic with small molecule substrates while eliminating interaction between the protein surface and larger molecules. Using chymotrypsin, an important enzyme that is used to treat pancreatic insufficiency, we have designed a series of molecular chimeras with varied grafting densities and shapes. Guided by molecular dynamic simulations and next-generation molecular chimera characterization with asymmetric flow field-flow fractionation chromatography, we grew linear, branched, and comb-shaped architectures from the surface of the protein by atom-transfer radical polymerization. Comb-shaped polymers, grafted from the surface of chymotrypsin, completely prevented enzyme inhibition with protein inhibitors without sacrificing the ability of the enzyme to catalyze the hydrolysis of a peptide substrate. Asymmetric flow field-flow fractionation coupled with multiangle laser light scattering including dynamic light scattering showed that nanoarmor designed with comb-shaped polymers was particularly compact and spherical. The polymer structure significantly increased protein stability and reduced protein-protein interactions. Atomistic molecular dynamic simulations predicted that a dense nanoarmor with long-armed comb-shaped polymer would act as an almost perfect molecular sieve to filter large ligands from substrates. Surprisingly, a conjugate that was composed of 99% polymer was needed before the elimination of protein-protein interactions.

Atomistic insight towards the impact of polymer architecture and grafting density on structure-dynamics of PEGylated bovine serum albumin and their applications.

Macromolecules such as proteins conjugated to polyethylene glycol (PEG) have been employed in therapeutic drug applications, and recent research has emphasized the potential of varying polymer architectures and conjugation strategies to achieve improved efficacy. In this study, we performed atomistic molecular dynamics simulations of bovine serum albumin (BSA) conjugated to 5 kDa PEG polymers in an array of schemes, including varied numbers of attached chains, grafting density, and nonlinear architectures. Nonlinear architectures included U-shaped PEG, Y-shaped PEG, and poly(oligoethylene glycol methacrylate) (POEGMA). Buried surface area calculations and polymer volume map analyses revealed that volume exclusion behaviors of the high grafting density conjugate promoted additional protein-polymer interactions when compared to simply increasing numbers of conjugated chains uniformly across the protein surface. Investigation of nonlinear polymer architectures showed that stable polymer-lysine loop-like conformations seen in previous conjugate designs were more variable in prevalence, especially in POEGMA, which contained short oligomer PEG chains. The findings of this comprehensive study of alternate PEGylation schemes of BSA provide critical insight into molecular patterns of interaction within bioconjugates and highlight their importance in the future of controlled modification of conjugate system parameters.

Structure-function-dynamics of α-chymotrypsin based conjugates as a function of polymer charge.

The field of protein-polymer conjugates has suffered from a lack of predictive tools and design guidelines to synthesize highly active and stable conjugates. In order to develop this type of information, structure-function-dynamics relationships must be understood. These relationships depend strongly on protein-polymer interactions and how these influence protein dynamics and conformations. Probing nanoscale interactions is experimentally difficult, but computational tools, such as molecular dynamics simulations, can easily obtain atomic resolution. Atomistic molecular dynamics simulations were used to study α-chymotrypsin (CT) densely conjugated with either zwitterionic, positively charged, or negatively charged polymers. Charged polymers interacted with the protein surface to varying degrees and in different regions of the polymer, depending on their flexibilities. Specific interactions of the negatively charged polymer with CT caused structural deformations in CT's substrate binding pocket and active site while no deformations were observed for zwitterionic and positively charged polymers. Attachment of polymers displaced water molecules from CT's surface into the polymer phase and polymer hydration correlated with the Hofmeister series.

Modeling Amorphous Microporous Polymers for CO2 Capture and Separations.

This review concentrates on the advances of atomistic molecular simulations to design and evaluate amorphous microporous polymeric materials for CO2 capture and separations. A description of atomistic molecular simulations is provided, including simulation techniques, structural generation approaches, relaxation and equilibration methodologies, and considerations needed for validation of simulated samples. The review provides general guidelines and a comprehensive update of the recent literature (since 2007) to promote the acceleration of the discovery and screening of amorphous microporous polymers for CO2 capture and separation processes.

PEGylation within a confined hydrophobic cavity of a protein.

The conjugation of polyethylene glycol (PEG) to proteins, known as PEGylation, has increasingly been employed to expand the efficacy of therapeutic drugs. Recently, research has emphasized the effect of the conjugation site on protein-polymer interactions. In this study, we performed atomistic molecular dynamics (MD) simulations of lysine 116 PEGylated bovine serum albumin (BSA) to illustrate how conjugation near a hydrophobic pocket affects the conjugate's dynamics and observed altered low mode vibrations in the protein. MD simulations were performed for a total of 1.5 µs for each PEG chain molecular mass from 2 to 20 kDa. Analysis of preferential PEG-BSA interactions showed that polymer behavior was also affected as proximity to the attractive protein surface patches promoted interactions in small (2 kDa) PEG chains, while the confined environment of the conjugation site reduced the expected BSA surface coverage when the polymer molecular mass increased to 10 kDa. This thorough analysis of PEG-BSA interactions and polymer dynamics increases the molecular understanding of site-specific PEGylation and enhances the use of protein-polymer conjugates as therapeutics.

Polymer ultrapermeability from the inefficient packing of 2D chains.

The promise of ultrapermeable polymers, such as poly(trimethylsilylpropyne) (PTMSP), for reducing the size and increasing the efficiency of membranes for gas separations remains unfulfilled due to their poor selectivity. We report an ultrapermeable polymer of intrinsic microporosity (PIM-TMN-Trip) that is substantially more selective than PTMSP. From molecular simulations and experimental measurement we find that the inefficient packing of the two-dimensional (2D) chains of PIM-TMN-Trip generates a high concentration of both small (<0.7 nm) and large (0.7-1.0 nm) micropores, the former enhancing selectivity and the latter permeability. Gas permeability data for PIM-TMN-Trip surpass the 2008 Robeson upper bounds for O2/N2, H2/N2, CO2/N2, H2/CH4 and CO2/CH4, with the potential for biogas purification and carbon capture demonstrated for relevant gas mixtures. Comparisons between PIM-TMN-Trip and structurally similar polymers with three-dimensional (3D) contorted chains confirm that its additional intrinsic microporosity is generated from the awkward packing of its 2D polymer chains in a 3D amorphous solid. This strategy of shape-directed packing of chains of microporous polymers may be applied to other rigid polymers for gas separations.

Ionic-Functionalized Polymers of Intrinsic Microporosity for Gas Separation Applications.

Ionic-functionalized microporous materials are attractive for energy-efficient gas adsorption and separation processes and have shown promising results in gas mixtures at pressure ranges and compositions that are relevant for industrial applications. In this work, we studied the influence of different counterions (Li+, Na+, K+, Rb+, and Mg2+) on the porosity, carbon dioxide (CO2) gas adsorption, and selectivity in ionic-functionalized PIM-1 (IonomIMs), a polymer belonging to the class of linear and amorphous microporous polymers known as polymers of intrinsic microporosity (PIMs). It was found that an increase in the concentration of ionic groups led to a decrease in the free volume, resulting in a less porous polymer framework, and Mg2+-functionalized IonomIMs exhibited a relatively larger porosity compared to other IonomIMs. The CO2 adsorption capacity was affected by the different counterions for IonomIM-1, and a higher loading capacity for pure CO2 was observed for Mg2+. Furthermore, the IonomIMs showed an enhanced CO2 selectivity in CO2/CH4 and CO2/N2 gas mixtures at conditions used in pressure swing adsorption and vacuum swing adsorption applications. It was also observed that the concentration of ionic groups plays a vital role in changing the CO2 gas adsorption and selectivity.

Intramolecular Interactions of Conjugated Polymers Mimic Molecular Chaperones to Stabilize Protein-Polymer Conjugates.

The power and elegance of protein-polymer conjugates has solved many vexing problems for society. Rational design of these complex covalent hybrids depends on a deep understanding of how polymer physicochemical properties impact the conjugate structure-function-dynamic relationships. We have generated a large family of chymotrypsin-polymer conjugates which differ in polymer length and charge, using grafting-from atom-transfer radical polymerization, to elucidate how the polymers influenced enzyme structure and function at pHs that would unfold and inactivate the enzyme. We also used molecular dynamics simulations to deepen our understanding of protein-polymer intramolecular interactions. Remarkably, the data revealed that, contrary to current thoughts on how polymers stabilize proteins, appropriately designed polymers actually stabilize partially unfolded intermediates and assist in refolding to an active conformation. Long, hydrophilic polymers minimized interfacial interactions in partially unfolded conjugates leading to increased stabilization. The design of covalently attached intramolecular biomimetic chaperones that drive protein refolding could have far reaching consequences.

NLDFT Pore Size Distribution in Amorphous Microporous Materials.

The pore size distribution (PSD) is one of the most important properties when characterizing and designing materials for gas storage and separation applications. Experimentally, one of the current standards for determining microscopic PSD is using indirect molecular adsorption methods such as nonlocal density functional theory (NLDFT) and N2 isotherms at 77 K. Because determining the PSD from NLDFT is an indirect method, the validation can be a nontrivial task for amorphous microporous materials. This is especially crucial since this method is known to produce artifacts. In this work, the accuracy of NLDFT PSD was compared against the exact geometric PSD for 11 different simulated amorphous microporous materials. The geometric surface area and micropore volumes of these materials were between 5 and 1698 m2/g and 0.039 and 0.55 cm3/g, respectively. N2 isotherms at 77 K were constructed using Gibbs ensemble Monte Carlo (GEMC) simulations. Our results show that the discrepancies between NLDFT and geometric PSD are significant. NLDFT PSD produced several artificial gaps and peaks that were further confirmed by the coordinates of inserted particles of a specific size. We found that dominant peaks from NLDFT typically reported in the literature do not necessarily represent the truly dominant pore size within the system. The confirmation provides concrete evidence for artifacts that arise from the NLDFT method. Furthermore, a sensitivity analysis was performed to show the high dependency of PSD as a function of the regularization parameter, λ. A higher value of λ produced a broader and smoother PSD that closely resembles geometric PSD. As an alternative, a new criterion for choosing λ, called here the smooth-shift method (SSNLDFT), is proposed that tuned the NLDFT PSD to better match the true geometric PSD. Using the geometric pore size distribution as our reference, the smooth-shift method reduced the root-mean-square deviation by ∼70% when the geometric surface area of the material is greater than 100 m2/g.

Flow and aggregation of rod-like proteins in slit and cylindrical pores coated with polymer brushes: an insight from dissipative particle dynamics.

We use a meso-scale dissipative particle dynamics method to simulate the flow and aggregation of rod-like protein solutions through pores grafted with a solvent-sensitive polymer brush. The coated pores can control protein permeability and aggregation by a stretch-to-collapse conformational transition of the brush polymers in response to changes in the solvent quality. The protein solutions mimic aqueous glycoprotein solutions and proteins are represented as rod-like objects formed by coarse-grain beads. The model further employs two types of beads to represent the existence of cystein-like terminal groups in real glycoproteins and mimic the aggregation of real glycoproteins in aqueous solutions. We vary the solvent quality with respect to the brush chains and study the flow and aggregation of rod-like proteins in the slit and cylindrical pores as the brush polymers undergo the stretch-to-collapse transition. The results show that stretched brush chains close the pore, hamper proteins' flow and promote proteins' aggregation. The collapsed brush chains open the pores for proteins' flow and suppress their aggregation. Therefore, we observe more than a ten-fold reduction in the permeation rate of proteins in both pore geometries. Finally, due to pore confinement, larger proteins' aggregates are formed in the slit pore than in the cylindrical pore, while more pronounced orientation of proteins in the flow direction is seen in the cylindrical pore than in the slit pore.

Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.

RNA viruses encoding high- or low-fidelity RNA-dependent RNA polymerases (RdRp) are attenuated. The ability to predict residues of the RdRp required for faithful incorporation of nucleotides represents an essential step in any pipeline intended to exploit perturbed fidelity as the basis for rational design of vaccine candidates. We used x-ray crystallography, molecular dynamics simulations, NMR spectroscopy, and pre-steady-state kinetics to compare a mutator (H273R) RdRp from poliovirus to the wild-type (WT) enzyme. We show that the nucleotide-binding site toggles between the nucleotide binding-occluded and nucleotide binding-competent states. The conformational dynamics between these states were enhanced by binding to primed template RNA. For the WT, the occluded conformation was favored; for H273R, the competent conformation was favored. The resonance for Met-187 in our NMR spectra reported on the ability of the enzyme to check the correctness of the bound nucleotide. Kinetic experiments were consistent with the conformational dynamics contributing to the established pre-incorporation conformational change and fidelity checkpoint. For H273R, residues comprising the active site spent more time in the catalytically competent conformation and were more positively correlated than the WT. We propose that by linking the equilibrium between the binding-occluded and binding-competent conformations of the nucleotide-binding pocket and other active-site dynamics to the correctness of the bound nucleotide, faithful nucleotide incorporation is achieved. These studies underscore the need to apply multiple biophysical and biochemical approaches to the elucidation of the physical basis for polymerase fidelity.

Ionomers of intrinsic microporosity: in silico development of ionic-functionalized gas-separation membranes.

This work presents the predictive molecular simulations of a functionalized polymer of intrinsic microporosity (PIM) with an ionic backbone (carboxylate) and extra-framework counterions (Na(+)) for CO2 gas storage and separation applications. The CO2-philic carboxylate-functionalized polymers are predicted to contain similar degrees of free volume to PIM-1, with Brunauer-Emmett-Teller (BET) surface areas from 510 to 890 m(2)/g, depending on concentration of ionic groups from 100% to 17%. As a result of ionic groups enhancing the CO2 enthalpy of adsorption (to 42-50 kJ/mol), the uptake of the proposed polymers at 293 K exceeded 1.7 mmol/g at 10 kPa and 3.3 mmol/g at 100 kPa for the polymers containing 100% and 50% ionic functional groups, respectively. In addition, CO2/CH4 and CO2/N2 mixed-gas separation performance was evaluated under several industrially relevant conditions, where the IonomIMs are shown to increase both the working capacity and selection performance in certain pressure swing applications (e.g., natural gas separations). These simulations reveal that intrinsically microporous ionomers show great potential as the future of energy-efficient gas-separation polymeric materials.

Morphology and molecular bridging in comb- and star-shaped diblock copolymers.

Block copolymers spontaneously self-assemble into nanostructured morphologies with industrially attractive properties; however, the relationships between polymer architecture and self-assembled morphology are difficult to tailor for copolymers with increased conformational restrictions. Using Dissipative Particle Dynamics, the self-assembled morphology of comb- and star-shaped diblock copolymers was simulated as a function of the number of arms, arm length, weight fraction, and A-B incompatibility. As the number of arms on the star, or grafting points for the comb, was increased from three to four to six, the ability to self-assemble into ordered morphologies was restricted. The molecular bridging between adjacent ordered domains was observed for both comb- and star-shaped copolymers, which was found to be enhanced with increasing number of arms. This study illustrates that comb- and star-shaped copolymers are viable alternatives for applications that would benefit from highly bridged nanostructural domains.

Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies.

Spin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circular dichroism spectroscopy, Michaelis-Menten kinetic parameters and EPR spectroscopy data validate the success of this approach to computationally select reporter sites for future magnetic resonance investigations of hydration and hydration changes induced by polymer conjugation, tethering, immobilization, or amino acid substitution in BSLA. Analysis of molecular dynamic simulations of the impact of substitutions on the secondary structure agree well with experimental findings. We propose that this computationally guided approach for choosing spin-labeled EPR reporter sites, which evaluates relative surface accessibility coupled with hydrogen bonding occupancy of amino acids to the catalytic pocket via atomistic simulations, should be readily transferable to other macromolecular systems of interest including selecting sites for paramagnetic relaxation enhancement NMR studies, other spin-labeling EPR studies or any method requiring a tagging method where it is desirable to not alter enzyme stability or activity.

Simulated swelling during low-temperature N2 adsorption in polymers of intrinsic microporosity.

Polymers of intrinsic microporosity (PIMs) are a promising alternative in gas separation applications; however, their industrial applicability is greatly reduced by their susceptibility toward sorption-induced plasticization. In this study, the effects of swelling during nitrogen adsorption isotherms at 77 K for five PIMs (PIM-1, PIM-1c, PIM-SBF, PIM-SBF-Me, and sPIM-1) were examined through predictive molecular simulations. The structural changes and adsorptive implications of swelling each PIM from 0 to 15% were analyzed by generating swollen "snapshots" of the PIM during the swelling process by means of an effective swelling procedure. The size of the free volume elements increased with the simulated swelling percentage, while the closely packed polymer chains remained associated. By comparing the simulated swollen and available experimental isotherms, this investigation shows that the amount of swelling observed during low-temperature nitrogen adsorption is strongly correlated with the interaction strength of the polymer matrix. Therefore, this study provides further support that PIMs should be designed with functionalities to increase the associative interactions of adjacent polymer chains while simultaneously prohibiting efficient packing to construct a gas separation membrane with limited low-temperature N2 swelling and high free volumes.

Two-Dimensional Energy Histograms as Features for Machine Learning to Predict Adsorption in Diverse Nanoporous Materials.

A major obstacle for machine learning (ML) in chemical science is the lack of physically informed feature representations that provide both accurate prediction and easy interpretability of the ML model. In this work, we describe adsorption systems using novel two-dimensional energy histogram (2D-EH) features, which are obtained from the probe-adsorbent energies and energy gradients at grid points located throughout the adsorbent. The 2D-EH features encode both energetic and structural information of the material and lead to highly accurate ML models (coefficient of determination R2 ∼ 0.94-0.99) for predicting single-component adsorption capacity in metal-organic frameworks (MOFs). We consider the adsorption of spherical molecules (Kr and Xe), linear alkanes with a wide range of aspect ratios (ethane, propane, n-butane, and n-hexane), and a branched alkane (2,2-dimethylbutane) over a wide range of temperatures and pressures. The interpretable 2D-EH features enable the ML model to learn the basic physics of adsorption in pores from the training data. We show that these MOF-data-trained ML models are transferrable to different families of amorphous nanoporous materials. We also identify several adsorption systems where capillary condensation occurs, and ML predictions are more challenging. Nevertheless, our 2D-EH features still outperform structural features including those derived from persistent homology. The novel 2D-EH features may help accelerate the discovery and design of advanced nanoporous materials using ML for gas storage and separation in the future.

Temperature Effects in Flexible Adsorption Processes for Amorphous Microporous Polymers.

A collection of atomistic molecular simulations is reported that illustrate the impact of adsorption temperature on species uptake and adsorbate-induced structural rearrangement for amorphous polymers of intrinsic microporosity. Temperature-sensitive structural rearrangement is evaluated by contrasting two methods: standard grand canonical Monte Carlo simulations using a rigid framework approximation and a combined Monte Carlo/molecular dynamics approach that fully incorporates framework flexibility. We report single-component gas phase adsorption isotherms for CH4, C2H4, C2H6, C3H6, C3H8, and CO2 across a temperature range of 250-400 K for models of an archetypal polymer of intrinsic microporosity, PIM-1. A quadratic model is presented that captures two main mechanisms of temperature-dependent adsorption-induced deformation of PIM-1 up to a relative swelling of 1.15: thermal expansion and an increased propensity to swell as a function of species uptake. Two case studies are reported that highlight the critical role of operating temperature in industrial storage and separation applications. The first study focuses on methane storage and delivery applications using a pressure-temperature swing adsorption application (PTSA). We demonstrate that larger working capacities are accompanied by increased volumetric strain between adsorption-desorption steps. The second case study considers PIM-1 as an adsorbent to separate an exemplar ternary syngas mixture at operating temperatures ranging 300-550 K. A temperature threshold of ∼400 K is identified, beyond which adsorption-induced PIM-1 swelling is negligible and the solubility selectivity-loading curve transitions to exhibiting a nearly linear relationship.

Incorporating Flexibility Effects into Metal-Organic Framework Adsorption Simulations Using Different Models.

High-throughput calculations based on molecular simulations to predict the adsorption of molecules inside metal-organic frameworks (MOFs) have become a useful complement to experimental efforts to identify promising adsorbents for chemical separations and storage. For computational convenience, all existing efforts of this kind have relied on simulations in which the MOF is approximated as rigid. In this paper, we use extensive adsorption-relaxation simulations that fully include MOF flexibility effects to explore the validity of the rigid framework approximation. We also examine the accuracy of several approximate methods to incorporate framework flexibility that are more computationally efficient than adsorption-relaxation calculations. We first benchmark various models of MOF flexibility for four MOFs with well-established CO2 experimental consensus isotherms. We then consider a range of adsorption properties, including Henry's constants, nondilute loadings, and adsorption selectivity, for seven adsorbates in 15 MOFs randomly selected from the CoRE MOF database. Our results indicate that in many MOFs adsorption-relaxation simulations are necessary to make quantitative predictions of adsorption, particularly for adsorption at dilute concentrations, although more standard calculations based on rigid structures can provide useful information. Finally, we investigate whether a correlation exists between the elastic properties of empty MOFs and the importance of including framework flexibility in making accurate predictions of molecular adsorption. Our results did not identify a simple correlation of this type.