Thermodynamic Driving Forces for the Self-Assembly of Diblock Polypeptoids.

Peptoid polymers with sequence-defined side chains are observed to self-assemble into a variety of structures spanning nanometer and micron scales. We explored a diblock copolypeptoid, poly(-decylglycine)--poly(-2-(2-(2-methoxyethoxy)ethoxy)-ethylglycine) (abbreviated as Ndc-Nte), which forms crystalline nanofibers and nanosheets as evidenced by recent cryo-transmission electron microscopy, atomic force microscopy, X-ray diffraction, and calorimetry. Using all-atom molecular dynamics simulations, we examined the thermodynamic forces driving such self-assembly and how nanoscale morphology is tailored through modification of the N-terminus or via the addition of small molecules (urea).

Importance of the Positively Charged σ-Hole in Crystal Engineering of Halogenated Polypeptoids.

Crystalline nanosheets formed by amphiphilic block copolypeptoids with halogenated phenyl side chains were imaged at the atomic-scale using cryogenic transmission electron microscopy (cryo-TEM). In general, the polypeptoid molecules adopt V-shaped configurations in the crystalline state, and adjacent molecules can pack with one another in either parallel or antiparallel arrangements, depending on the chemical composition. The halogen bond, which can have characteristic energies ranging from 1 to 5 kcal/mol, is commensurate with the parallel configuration.

Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations.

The stimuli-responsive character of elastin-like polypeptides (ELP) has led to their use in a wide range of applications. The temperature-triggered aggregation, or LCST behavior, of ELPs is a complex and multistep phenomenon, which proposed to include the structural transitions, loss of hydrophobic hydration, expulsion of water molecules and physical association of chains. Thus, the origin and detailed mechanism of LCST in ELPs is difficult to elucidate.

Cooperative Intramolecular Hydrogen Bonding Strongly Enforces -Peptoid Folding.

Sequence-defined peptoids, or -substituted glycines, are an attractive class of bioispired polymer due to their biostability and efficient synthesis. However, the design of folded peptoids with precise three-dimensional structures has been hindered by limited means to deterministically control backbone conformation. Peptoid folds are generally destabilized by the / backbone-amide isomerization, and few side-chains are capable of enforcing a specific amide conformation.

Intrinsically disordered proteins access a range of hysteretic phase separation behaviors.

The phase separation behavior of intrinsically disordered proteins (IDPs) is thought of as analogous to that of polymers that undergo equilibrium lower or upper critical solution temperature (LCST and UCST, respectively) phase transition. This view, however, ignores possible nonequilibrium properties of protein assemblies. Here, by studying IDP polymers (IDPPs) composed of repeat motifs that encode LCST or UCST phase behavior, we discovered that IDPs can access a wide spectrum of nonequilibrium, hysteretic phase behaviors.

Atomic-level engineering and imaging of polypeptoid crystal lattices.

Rational design of supramolecular nanomaterials fundamentally depends upon an atomic-level understanding of their structure and how it responds to chemical modifications. Here we studied a series of crystalline diblock copolypeptoids by a combination of sequence-controlled synthesis, cryogenic transmission electron microscopy, and molecular dynamics simulation. This family of amphiphilic polypeptoids formed free-floating 2-dimensional monolayer nanosheets, in which individual polymer chains and their relative orientations could be directly observed.

Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides.

Elastin-like polypeptides (ELP) exhibit an inverse temperature transition or lower critical solution temperature (LCST) transition phase behavior in aqueous solutions. In this paper, the thermal responsive properties of the canonical ELP, poly(VPGVG), and its reverse sequence poly(VGPVG) were investigated by turbidity measurements of the cloud point behavior, circular dichroism (CD) measurements, and all-atom molecular dynamics (MD) simulations to gain a molecular understanding of mechanism that controls hysteretic phase behavior. It was shown experimentally that both poly(VPGVG) and poly(VGPVG) undergo a transition from soluble to insoluble in aqueous solution upon heating above the transition temperature ( T).

Functional Modification of Silica through Enhanced Adsorption of Elastin-Like Polypeptide Block Copolymers.

A powerful tool for controlling interfacial properties and molecular architecture relies on the tailored adsorption of stimuli-responsive block copolymers onto surfaces. Here, we use computational and experimental approaches to investigate the adsorption behavior of thermally responsive polypeptide block copolymers (elastin-like polypeptides, ELPs) onto silica surfaces, and to explore the effects of surface affinity and micellization on the adsorption kinetics and the resultant polypeptide layers. We demonstrate that genetic incorporation of a silica-binding peptide (silaffin R5) results in enhanced adsorption of these block copolymers onto silica surfaces as measured by quartz crystal microbalance and ellipsometry.

Salt Responsive Morphologies of ssDNA-Based Triblock Polyelectrolytes in Semi-Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length.

A comprehensive study is reported on the effect of salt concentration, polyelectrolyte block length, and polymer concentration on the morphology and structural properties of nanoaggregates self-assembled from BAB single-strand DNA (ssDNA) triblock polynucleotides in which A represents polyelectrolyte blocks and B represents hydrophobic neutral blocks. A morphological phase diagram above the gelation point is developed as a function of solvent ionic strength and polyelectrolyte block length utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations. As the solvent ionic strength increases, the self-assembled DNA network structures shrinks considerably, leading to a morphological transition from a micellar network to worm-like or hamburger-shape aggregates.

Emulsion-Based RIR-MAPLE Deposition of Conjugated Polymers: Primary Solvent Effect and Its Implications on Organic Solar Cell Performance.

Emulsion-based, resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) has been demonstrated as an alternative technique to deposit conjugated polymer films for photovoltaic applications; yet, a fundamental understanding of how the emulsion target characteristics translate into film properties and solar cell performance is unclear. Such understanding is crucial to enable the rational improvement of organic solar cell (OSC) efficiency and to realize the expected advantages of emulsion-based RIR-MAPLE for OSC fabrication. In this paper, the effect of the primary solvent used in the emulsion target is studied, both experimentally and theoretically, and it is found to determine the conjugated polymer cluster size in the emulsion as well as surface roughness and internal morphology of resulting polymer films.

LCST Behavior is Manifested in a Single Molecule: Elastin-Like polypeptide (VPGVG)n.

The physical origin of the lower critical solution temperature (LCST) behavior of a variety of fluids, including elastin-like polypeptides (ELPs), has been studied for the past few decades. As is the case for polymer solutions, LCST behavior of ELPs is invariably reported for large systems of molecules and is considered evidence for collective behavior. In contrast, we find evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences (Val-Pro-Gly-Val-Gly)n for four different length peptides over a wide range of temperatures.

Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics.

The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction.

Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles.

Self-assembly processes of polyelectrolyte block copolymers are ubiquitous in industrial and biological processes; understanding their physical properties can also provide insights into the design of polyelectrolyte materials with novel and tailored properties. Here, we report systematic analysis on how the ionic strength of the solvent and the length of the polyelectrolyte block affect the self-assembly and morphology of the polyelectrolyte block copolymer materials by constructing a salt-dependent morphological phase diagram using an implicit solvent ionic strength (ISIS) method for dissipative particle dynamics (DPD) simulations. This diagram permits the determination of the conditions for the morphological transition into a specific shape, namely vesicles or lamellar aggregates, wormlike/cylindrical micelles, and spherical micelles.

Molecular description of the LCST behavior of an elastin-like polypeptide.

Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as β-strands.