DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups.

Vibrational sum frequency generation (SFG) spectroscopy has been extensively used for obtaining structural information of molecular functional groups at two-dimensional (2D) interfaces buried in the gas or liquid medium. Although the SFG experiment can be done elegantly, interpreting the measured intensity in terms of molecular orientation with respect to the lab coordinate is quite complicated. One of the main reasons is the difficulty of determining the hyperpolarizability tensors of even simple molecules that govern their SFG responses. The single-bond polarizability derivative model has been proposed to estimate the relative magnitude of SFG-active hyperpolarizability by assuming that the perturbation associated to each vibration is negligible. In this study, density functional theory was used to calculate the polarizability and dipole derivative tensors of the CH3 stretch mode of CH3I, CH3CH2I, CH3OH, and CH3CH2OH. Then, the hyperpolarizability tensors of symmetric and asymmetric vibration modes were calculated considering the Boltzmann distribution of representative conformers, which allowed us to theoretically calculate their SFG intensities at all polarization combinations as a function of the tilt angle of the CH3 group with respect to the surface normal direction. Then, the ratios of the calculated SFG intensities for the CH3 symmetric and asymmetric stretch peaks used in experimental studies for the CH3 tilt angle determination were compared. This comparison clearly showed that the effect of vibrational coupling among neighboring functional groups is significant and cannot be assumed to be negligible. This study presents new parameters that can be used in determining the average tilt angle of the CH3 group at the 2D interface with SFG measurements as well as limitations of the method.

Computer-Assisted Design and Characterization of RNA Nanostructures.

Molecular dynamics (MD) simulations can aid in the design and characterization of RNA nanomaterials, providing details about structural and dynamical properties as a function of sequence and environment. Here, we describe how to perform explicit and implicit solvent all-atom MD simulations for RNA nanoring systems.

Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8.

Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.

Solvent Effects in Ligand Stripping Behavior of Colloidal Nanoparticles.

Inorganic colloidal nanoparticle (NP) properties can be tuned by stripping stabilizing ligands using a poor solvent. However, the mechanism behind ligand stripping is poorly understood, in part because in situ measurements of ligand stripping are challenging at the nanoscale. Here, we investigate ethanol solvent-mediated oleylamine ligand stripping from magnetite (Fe3O4) NPs in different compositions of ethanol/hexane mixtures using atomistic molecular dynamics (MD) simulations and thermogravimetric analysis (TGA). Our study elucidates a complex interplay of ethanol interactions with system components and indicates the existence of a threshold concentration of ∼34 vol % ethanol, above which ligand stripping saturates. Moreover, hydrogen bonding between ethanol and stripped ligands inhibits subsequent readsorption of the ligands on the NP surface. A proposed modification of the Langmuir isotherm explains the role of the enthalpy of mixing of the ligands and solvents on the ligand stripping mechanism. A good agreement between the MD predictions and TGA measurements of ligand stripping from Fe3O4 NPs validates the simulation observations. Our findings demonstrate that the ligand coverage of NPs can be controlled by using a poor solvent below the threshold concentration and highlight the importance of ligand-solvent interactions that modulate the properties of colloidal NPs. The study also provides an approach for a detailed in silico study of ligand stripping and exchange from colloidal NPs that are crucial for applications of NPs spanning self-assembly, optoelectronics, nanomedicine, and catalysis.

Correlation of Emulsion Chemistry, Film Morphology, and Device Performance in Polyfluorene LEDs Deposited by RIR-MAPLE.

Thin films of polyfluorene (PFO) were deposited using emulsion-based resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE). Here, it is shown that properly selected surfactant chemistry in the emulsion can increase crystalline ß phase (ß-PFO) content and consequently improve the color purity of light emission. To determine the impact of surfactant on the device performance of resulting films, blue light-emitting diodes (LEDs) with PFO as an active region were fabricated and compared. Molecular dynamics (MD) simulations were used to explain the physical and chemical changes in the emulsion properties as a function of the surfactant. The results indicate that the experimental film morphology and device performance are highly correlated to the emulsion droplet micelle structure and interaction energy among PFO, primary solvent, and water obtained from MD simulations. While the champion device performance was lower than other reported devices (luminous flux ∼0.0206 lm, brightness ∼725.58 cd/m2, luminous efficacy ∼0.0548 lm/W, and luminous efficiency ∼0.174 cd/A), deep blue emission with good color purity (CIE chromaticity diagram coordinate of (0.177,0.141)) was achieved for low operating voltages around 3 V. Furthermore, a much higher ß-phase content of 21% was achieved in annealed films (without the pinholes typically found in ß-PFO deposited by other techniques) by using sodium dodecyl sulfate (SDS) as the surfactant.

Effect of solvent on the emulsion and morphology of polyfluorene films: all-atom molecular dynamics approach.

The morphology of conjugated polymer thin films deposited by the resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) process is related to the emulsion characteristics. However, a fundamental understanding of how and why the emulsion characteristics control the film properties and device performance is yet unclear. We performed all-atom molecular dynamics simulations of emulsions containing a mixture of polyfluorene (PFO) polymer, various primary solvents, secondary solvent, and water. The emulsion properties were then examined as a function of variable primary solvent and correlated with the morphology of deposited PFO thin films. The examination of the explicit interactions between all components of the emulsion indicated that using a primary solvent with a lower solubility-in-water and a higher non-bonded interaction energy ratio, between the solvent, polymer, and water in the emulsion recipe, produced the best result with smoother and denser films. Additionally, our simulation results are consistent with the AFM experimental results, indicating that interactions driven by trichlorobenzene (TCB) primary solvent within the emulsion are responsible for high-quality, smooth, and continuous thin film surfaces. Overall, this study can support the choice of a suitable primary solvent and provides the computational framework for predictions of new recipes for polymeric emulsion systems.

Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8.

Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation. Highlights: Cryo-EM structures of substrate and product bound poplar cellulose synthase provide insights into substrate selectivitySite directed mutagenesis signifies a critical function of the gating loop for catalysisMolecular dynamics simulations support persistent gating loop - substrate interactionsGating loop helps in positioning the substrate molecule to facilitate cellulose elongationConserved cellulose synthesis substrate binding mechanism across the kingdoms.

Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures.

The fascination with the optical properties of naturally occurring systems has been driven in part by nature's ability to produce a diverse palette of vibrant colors from a relatively small number of common structural motifs. Within this context, some cephalopod species have evolved skin cells called iridophores and leucophores whose constituent ultrastructures reflect light in different ways but are composed of the same high refractive index material─a protein called reflectin. Although such natural optical systems have attracted much research interest, measuring the refractive indices of biomaterial-based structures across multiple different environments and establishing theoretical frameworks for accurately describing the obtained refractive index values has proven challenging. Herein, we employ a synergistic combination of experimental and computational methodologies to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro. When considered together, our findings may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques.

Gold nanoparticle design for RNA compaction.

RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.

Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes.

Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. We report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.

All-Atom Simulation Method for Zeeman Alignment and Dipolar Assembly of Magnetic Nanoparticles.

Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics simulation method to enable detailed studies of the dynamics, self-assembly, structure, and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe3O4) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The algorithm has been parallelized to take advantage of multiple processors of a modern computer and can be used as a plugin for the popular simulation software LAMMPS to study the behavior of small MNPs and gain insights into the physics and chemistry of different magnetic assembly processes with atomistic details.

Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles.

Peptide-polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure-assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.

Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms.

Understanding protein structure and function relationships in cellulose synthase (CesA), including divergent isomers, is an important goal. Here, we report results from mutant complementation assays that tested the ability of sequence variants of AtCesA7, a secondary wall CesA of Arabidopsis thaliana, to rescue the collapsed vessels, short stems, and low cellulose content of the irx3-1 AtCesA7 null mutant. We tested a catalytic null mutation and seven missense or small domain changes in and near the AtCesA7 FTVTSK motif, which lies near the catalytic domain and may, analogously to bacterial CesA, exist within a substrate "gating loop." A low-to-high gradient of rescue occurred, and even inactive AtCesA7 had a small positive effect on stem cellulose content but not stem elongation. Overall, secondary wall cellulose content and stem length were moderately correlated, but the results were consistent with threshold amounts of cellulose supporting particular developmental processes. Vibrational sum frequency generation microscopy allowed tissue-specific analysis of cellulose content in stem xylem and interfascicular fibers, revealing subtle differences between selected genotypes that correlated with the extent of rescue of the collapsing xylem phenotype. Similar tests on PpCesA5 from the moss Physcomitrium (formerly Physcomitrella) patens helped us to synergize the AtCesA7 results with prior results on AtCesA1 and PpCesA5. The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work.

Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities.

Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.

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. Here, to gain insights into structure and dynamics of coacervates, we performed all-atom molecular dynamics simulations of 27 90-mer ELPs in explicit water at 350 K. Two sequences, poly(VGPVG)18 and poly(VPGVG)18, were examined due to their experimentally observed differences in thermal hysteresis albeit identical overall composition but different arrangement of amino acids. The simulation results indicate that surface hydrophobicity of poly(VGPVG) aggregate is less than that of the poly(VPGVG) aggregate, and there are marked changes in torsion angles and the propensities of secondary structural motifs during the aggregation process. Moreover, there are significant differences between structure of a single polypeptide in water and structure within the aggregate. Overall, the aggregation process is driven by the formation of peptide-peptide interactions whereas the average hydration of peptides remains almost the same between dissolved and aggregated states. Even though the aggregation is driven by the hydrophobic interactions, ELP coacervate has no hydrophobic core and contains many water molecules. Overall, our findings provide an insight into the sequence-dependent structure of coacervates and molecular behavior of individual peptides during aggregation.

Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model.

The molecular dynamics (MD) simulation technique is among the most broadly used computational methods to investigate atomistic phenomena in a variety of chemical and biological systems. One of the most common (and most uncertain) parametrization steps in MD simulations of soft materials is the assignment of partial charges to atoms. Here, we apply uncertainty quantification and sensitivity analysis calculations to assess the uncertainty associated with partial charge assignment in the context of MD simulations of an organic solvent. Our results indicate that the effect of partial charge variance on bulk properties, such as solubility parameters, diffusivity, dipole moment, and density, measured from MD simulations is significant; however, measured properties are observed to be less sensitive to partial charges of less accessible (or buried) atoms. Diffusivity, for example, exhibits a global sensitivity of up to 22 × 10-5 cm2/s per electron charge on some acetonitrile atoms. We then demonstrate that machine learning techniques, such as Gaussian process regression (GPR), can be effective and rapid tools for uncertainty quantification of MD simulations. We show that the formulation and application of an efficient GPR surrogate model for the prediction of responses effectively reduces the computational time of additional sample points from hours to milliseconds. This study provides a much-needed context for the effect that partial charge uncertainty has on MD-derived material properties to illustrate the benefit of considering partial charges as distributions rather than point-values. To aid in this treatment, this work then demonstrates methods for rapid characterization of resulting sensitivity in MD simulations.

Weakly Ionically Bound Thermosensitive Hyperbranched Polymers.

We synthesized novel amphiphilic hyperbranched polymers (HBPs) with variable contents of weakly ionically tethered thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) macrocations in contrast to traditional covalent linking. Their assembling behavior was studied below and above the lower critical solution temperature (LCST). The HBPs underwent a morphological transition under changing temperature and ionic strength due to the LCST transition of PNIPAM and the reduction in the ionization degree of terminal ionic groups, respectively. We suggest that, in contrast to traditional branched polymers, ionically linked PNIPAM macrocations can reversibly disassociate from the sulfonate groups and form mobile coronas, endowing the dynamic micellar morphologies. In addition, assembly at the air-water interface confined PNIPAM macrocations and resulted in the formation of heterogeneous Langmuir-Blodgett (LB) monolayers with diverse surface morphologies for different peripheral compositions with circular domains formed in the condensed state. The HBPs with 25% PNIPAM showed larger and more stable circular domains that were partially preserved at high compression than those of HBPs with 50% PNIPAM. Moreover, the LB monolayers showed variable surface mechanical and surface charge distribution, which can be attributed to net dipole redistribution caused by the behavior of mobile PNIPAM macrocations and core sulfonate groups.

Assessment of AMBER Force Fields for Simulations of ssDNA.

Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.

Structure, self-assembly, and properties of a truncated reflectin variant.

Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.

Co-assembling Polysaccharide Nanocrystals and Nanofibers for Robust Chiral Iridescent Films.

Assembling robust chiral biopolymer structures without compromising vivid optical iridescence is a grand challenge for biocomposite materials. Herein, we report a hierarchical nanocellulose nanostructure with a helicoidal organization co-assembled from chiral rigid cellulose nanocrystals (CNCs) and longer nanofibers isolated from the hydrolyzed wood pulp. This resulting highly iridescent chiral nanocellulose material is much tougher than traditional chiral CNC films. We found that the mixed nanocellulose are composed of needle-like nanocrystals and very long (up to 800 nm) flexible cellulose nanofibers (CNFs). Large-scale molecular simulation indicates that enhanced dynamic hydrogen bonding with labile networking facilitates mechanical reinforcement, owing to increased nanocrystal length, the co-assembly of nanofibrils in mixed bundles, and interchain entanglements. This study provides a novel strategy to transform the wood pulp residues into high-value-added photonic-bound polysaccharide materials. These hierarchical biomaterials can overcome the conflicting trends in designing balanced mechanical and optical performance of chiral biofilms and their conversion to robust chiral photonic materials with enhanced performance.