Foldamer Architectures of Triazine-Based Sequence-Defined Polymers Investigated with Molecular Dynamics Simulations and Enhanced Sampling Methods.

Triazine-based sequence-defined polymers have recently been developed that are biomimetic and robust. In molecular dynamics (MD) simulations, the triazine polymers were shown to form linear nanorod foldamers through hydrogen bonding and π-π interactions. The nanorod foldamers have motifs resembling those of DNA, α-helices, and ß-sheets and have potential to be useful building blocks for new macromolecules and materials. To understand the formation of nanorod foldamers, we investigate how linker structures in the middle of the triazine polymers lead to folding using MD simulations. We found that a variety of linkers can participate in folding but that specific linker structures are more favorable than others, depending on the polymer length. Folding of hexamers into well-defined nanorod foldamers was most favorable with pentanediamine and ortho-xylenediamine linkers in the center of the polymers. Foldamers with ortho-xylenediamine linkers in the center were investigated for longer polymers, i.e., octamers and decamers, using two different enhanced sampling methods, since regular MD simulations had failed to show any folding for these longer polymers. In particular, the recently developed concurrent adaptive sampling (CAS) algorithm and replica exchange molecular dynamics (REMD) were used. We found that the two enhanced sampling methods did lead to the observation of foldamers and that REMD revealed new foldamer architectures where cis-trans isomerizations had occurred. Foldamer formation, diversity, and the strengths and limitations of simulation techniques are discussed. These findings provide new insights into the diversity of foldamer architectures for a new type of biomimetic synthetic polymer.

Microfluidic Sensors with Impregnated Fluorophores for Simultaneous Imaging of Spatial Structure and Chemical Oxygen Gradients.

Interior surfaces of polystyrene microfluidic structures were impregnated with the oxygen sensing dye Pt(II) tetra(pentafluorophenyl)porphyrin (PtTFPP) using a solvent-induced fluorophore impregnation (SIFI) method. Using this technique, microfluidic oxygen sensors are obtained that enable simultaneous imaging of both chemical oxygen gradients and the physical structure of the microfluidic interior. A gentle method of fluorophore impregnation using acetonitrile solutions of PtTFPP at 50 °C was developed leading to a 10-µm-deep region containing fluorophore. This region is localized at the surface to sense oxygen in the interior fluid during use. Regions of the device that do not contact the interior fluid pathways lack fluorophores and are dark in fluorescent imaging. The technique was demonstrated on straight microchannel and pore network devices, the latter having pillars of 300 µm diameter spaced center to center at 340 µm providing pore throats of 40 µm. Sensing within channels or pores and imaging across the pore network devices were performed using a Lambert LIFA-P frequency domain fluorescence lifetime imaging system on a Leica microscope platform. Calibrations of different devices prepared by the SIFI method were indistinguishable. Gradient imaging showed fluorescent regions corresponding to the fluid pore network, dark pillars, and fluorescent lifetime varying across the gradient, thus providing both physical and chemical imaging. More generally, the SIFI technique can impregnate the interior surfaces of other polystyrene containers, such as cuvettes or cell and tissue culture containers, to enable sensing of interior conditions.

Manipulation of mass transport rates using bead-in-a-tube method.

In ultralow Pu analyses, the gold standard is thermal ionization mass spectrometry (TIMS), which requires pure sources to achieve its performance. This purity is achieved through step-wise purifications. In this work single, anion-exchange beads were trapped in the tubing to allow for dynamic solution cycling over the surface of the beads to improve the rates of metal complex uptake. Rates of Pu sorption on single ∼900 µm SIR-1200 and ∼620 µm Reillex-HPQ beads were determined for single beads trapped in a tube with syringe pump driven dynamic solution cycling over the bead, improving sorption and desorption rates. A static control was used as a comparison. Using 238Pu to enable facile activity-based measurements, rates were determined by measuring the residual Pu after contact with beads using liquid scintillation analysis (LSA) for fixed periods of time. Syringe pump driven dynamic solution cycling results in ∼5 and ∼15-fold improvements in the sorption rates for SIR-1200 and Reillex-HPQ. Impacts on desorption were also examined.

Investigating the role of non-covalent interactions in conformation and assembly of triazine-based sequence-defined polymers.

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and π-π interactions, and conserve their cis/trans conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated with the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimers of triazine trimers. We found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.

A review of flow analysis methods for determination of radionuclides in nuclear wastes and nuclear reactor coolants.

The safety and security of nuclear power plant operations depend on the application of the most appropriate techniques and methods of chemical analysis, where modern flow analysis methods prevail. Nevertheless, the current status of the development of these methods is more limited than it might be expected based on their genuine advantages. The main aim of this paper is to review the automated flow analysis procedures developed with various detection methods for the nuclear energy industry. The flow analysis methods for the determination of radionuclides, that have been reported to date, are primarily focused on their environmental applications. The benefits of the application of flow methods in both monitoring of the nuclear wastes and process analysis of the primary circuit coolants of light water nuclear reactors will also be discussed. The application of either continuous flow methods (CFA) or injection methods (FIA, SIA) of the flow analysis with the ß-radiometric detection shortens the analysis time and improves the precision of determination due to mechanization of certain time-consuming operations of the sample processing. Compared to the radiometric detection, the mass spectrometry (MS) detection enables one to perform multicomponent analyses as well as the determination of transuranic isotopes with much better limits of detection.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm.

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

Solid matrix transformation and tracer addition using molten ammonium bifluoride salt as a sample preparation method for laser ablation inductively coupled plasma mass spectrometry.

Solid sampling and analysis methods, such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), are challenged by matrix effects and calibration difficulties. Matrix-matched standards for external calibration are seldom available and it is difficult to distribute spikes evenly into a solid matrix as internal standards. While isotopic ratios of the same element can be measured to high precision, matrix-dependent effects in the sampling and analysis process frustrate accurate quantification and elemental ratio determinations. Here we introduce a potentially general solid matrix transformation approach entailing chemical reactions in molten ammonium bifluoride (ABF) salt that enables the introduction of spikes as tracers or internal standards. Proof of principle experiments show that the decomposition of uranium ore in sealed PFA fluoropolymer vials at 230 °C yields, after cooling, new solids suitable for direct solid sampling by LA. When spikes are included in the molten salt reaction, subsequent LA-ICP-MS sampling at several spots indicate that the spikes are evenly distributed, and that U-235 tracer dramatically improves reproducibility in U-238 analysis. Precisions improved from 17% relative standard deviation for U-238 signals to 0.1% for the ratio of sample U-238 to spiked U-235, a factor of over two orders of magnitude. These results introduce the concept of solid matrix transformation (SMT) using ABF, and provide proof of principle for a new method of incorporating internal standards into a solid for LA-ICP-MS. This new approach, SMT-LA-ICP-MS, provides opportunities to improve calibration and quantification in solids based analysis. Looking forward, tracer addition to transformed solids opens up LA-based methods to analytical methodologies such as standard addition, isotope dilution, preparation of matrix-matched solid standards, external calibration, and monitoring instrument drift against external calibration standards.

Mass Spectrometric Determination of Uranium and Thorium in High Radiopurity Polymers Using Ultra Low Background Electroformed Copper Crucibles for Dry Ashing.

A rapid new method for determining the U and Th mass concentrations in high radiopurity plastics is described, consisting of (1) dry ashing the plastic sample and tracers in low mass crucibles made of ultra low background electroformed copper (ULB EF-Cu) foil cut and folded into boats, (2) dissolving both the ash and the boat in acid, (3) performing a column separation to remove copper, and (4) determining the elements of interest by isotope dilution mass spectrometry. This method was demonstrated on both unfluorinated and fluorinated plastics, demonstrating high tracer recoveries and detection limits to pg/g (i.e., parts per trillion) levels or below, corresponding to µBq/kg of material. Samples of biomedical polyester (Max-Prene 955) and a fluoropolymer (polyvinylidene fluoride, PVDF) were analyzed in powder raw material forms as well as solids in the form of pellets or injection molded parts. The polyester powder contained 6 pg/g and 2 pg/g for 232Th and 238U, respectively. These levels correspond to 25 and 25 µBq/kg radioactivity, respectively. Determinations on samples of PVDF powder were typically below 1 pg/g for 232Th and 2 pg/g for 238U, corresponding to 4 and 25 µBq/kg radioactivity, respectively. The use of low mass ULB EF-Cu boats for dry ashing successfully overcame the problem of crucible-generated contaminants in the analysis; absolute detection limits, calculated as 3 × standard deviation of the process blanks, were typically 20-100 fg within a sample set. Complete dissolution of the ash and low mass boat provided high tracer recoveries and provides a convincing method to recover both the tracer and sample isotopes when full equilibration of tracer isotopes with sample isotopes is not possible prior to beginning chemical sample processing on solids.

Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions.

Alexa fluor-labeled fluorescent cellulose nanocrystals for bioimaging solid cellulose in spatially structured microenvironments.

Methods to covalently conjugate Alexa Fluor dyes to cellulose nanocrystals, at limiting amounts that retain the overall structure of the nanocrystals as model cellulose materials, were developed using two approaches. In the first, aldehyde groups are created on the cellulose surfaces by reaction with limiting amounts of sodium periodate, a reaction well-known for oxidizing vicinal diols to create dialdehyde structures. Reductive amination reactions were then applied to bind Alexa Fluor dyes with terminal amino-groups on the linker section. In the absence of the reductive step, dye washes out of the nanocrystal suspension, whereas with the reductive step, a colored product is obtained with the characteristic spectral bands of the conjugated dye. In the second approach, Alexa Fluor dyes were modified to contain chloro-substituted triazine ring at the end of the linker section. These modified dyes then were reacted with cellulose nanocrystals in acetonitrile at elevated temperature, again isolating material with the characteristic spectral bands of the Alexa Fluor dye. Reactions with Alexa Fluor 546 are given as detailed examples, labeling on the order of 1% of the total glucopyranose rings of the cellulose nanocrystals at dye loadings of ca. 5 µg/mg cellulose. Fluorescent cellulose nanocrystals were deposited in pore network microfluidic structures (PDMS) and proof-of-principle bioimaging experiments showed that the spatial localization of the solid cellulose deposits could be determined, and their disappearance under the action of Celluclast enzymes or microbes could be observed over time. In addition, single molecule fluorescence microscopy was demonstrated as a method to follow the disappearance of solid cellulose deposits over time, following the decrease in the number of single blinking dye molecules with time instead of fluorescent intensity.

Silicon-on-glass pore network micromodels with oxygen-sensing fluorophore films for chemical imaging and defined spatial structure.

Pore network microfluidic models were fabricated by a silicon-on-glass technique that provides the precision advantage of dry etched silicon while creating a structure that is transparent across all microfluidic channels and pores, and can be imaged from either side. A silicon layer is bonded to an underlying borosilicate glass substrate and thinned to the desired height of the microfluidic channels and pores. The silicon is then patterned and through-etched by deep reactive ion etching (DRIE), with the underlying glass serving as an etch stop. After bonding on a transparent glass cover plate, one obtains a micromodel in oxygen impermeable materials with water-wet surfaces where the microfluidic channels are transparent and structural elements such as the pillars creating the pore network are opaque. The advantageous features of this approach in a chemical imaging application are demonstrated by incorporating a Pt porphyrin fluorophore in a PDMS film serving as the oxygen-sensing layer and a bonding surface, or in a polystyrene film coated with a PDMS layer for bonding. The sensing of a dissolved oxygen gradient was demonstrated using fluorescence lifetime imaging, and it is shown that different matrix polymers lead to optimal use in different ranges of oxygen concentration. Imaging with the opaque pillars in between the observation direction and the continuous fluorophore film yields images that retain defined spatial structure in the sensor image.

Automated radioanalytical system incorporating microwave-assisted sample preparation, chemical separation, and online radiometric detection for the monitoring of total 99Tc in nuclear waste processing streams.

An automated fluidic instrument is described that rapidly determines the total (99)Tc content of aged nuclear waste samples, where the matrix is chemically and radiologically complex and the existing speciation of the (99)Tc is variable. The monitor links microwave-assisted sample preparation with an automated anion exchange column separation and detection using a flow-through solid scintillator detector. The sample preparation steps acidify the sample, decompose organics, and convert all Tc species to the pertechnetate anion. The column-based anion exchange procedure separates the pertechnetate from the complex sample matrix, so that radiometric detection can provide accurate measurement of (99)Tc. We developed a preprogrammed spike addition procedure to automatically determine matrix-matched calibration. The overall measurement efficiency that is determined simultaneously provides a self-diagnostic parameter for the radiochemical separation and overall instrument function. Continuous, automated operation was demonstrated over the course of 54 h, which resulted in the analysis of 215 samples plus 54 hly spike-addition samples, with consistent overall measurement efficiency for the operation of the monitor. A sample can be processed and measured automatically in just 12.5 min with a detection limit of 23.5 Bq/mL of (99)Tc in low activity waste (0.495 mL sample volume), with better than 10% RSD precision at concentrations above the quantification limit. This rapid automated analysis method was developed to support nuclear waste processing operations planned for the Hanford nuclear site.

Correlation of oil-water and air-water contact angles of diverse silanized surfaces and relationship to fluid interfacial tensions.

The use of air-water, θ(wa), or air-liquid contact angles is customary in surface science, while oil-water contact angles, θ(ow), are of paramount importance in subsurface multiphase flow phenomena including petroleum recovery, nonaqueous phase liquid fate and transport, and geological carbon sequestration. In this paper we determine both the air-water and oil-water contact angles of silica surfaces modified with a diverse selection of silanes, using hexadecane as the oil. The silanes included alkylsilanes, alkylarylsilanes, and silanes with alkyl or aryl groups that are functionalized with heteroatoms such as N, O, and S. These silanes yielded surfaces with wettabilities from water wet to oil wet, including specific silanized surfaces functionalized with heteroatoms that yield intermediate wet surfaces. The oil-water contact angles for clean and silanized surfaces, excluding one partially fluorinated surface, correlate linearly with air-water contact angles with a slope of 1.41 (R = 0.981, n = 13). These data were used to examine a previously untested theoretical treatment relating air-water and oil-water contact angles in terms of fluid interfacial energies. Plotting the cosines of these contact angles against one another, we obtain the relationship cos θ(wa) = 0.667 cos θ(ow) + 0.384 (R = 0.981, n = 13), intercepting cos θ(ow) = -1 at -0.284, which is in excellent agreement with the linear assumption of the theory. The theoretical slope, based on the fluid interfacial tensions σ(wa), σ(ow), and σ(oa), is 0.67. We also demonstrate how silanes can be used to alter the wettability of the interior of a pore network micromodel device constructed in silicon/silica with a glass cover plate. Such micromodels are used to study multiphase flow phenomena. The contact angle of the resulting interior was determined in situ. An intermediate wet micromodel gave a contact angle in excellent agreement with that obtained on an open planar silica surface using the same silane.

Facile xenon capture and release at room temperature using a metal-organic framework: a comparison with activated charcoal.

Two well-known metal-organic frameworks (MOF-5, NiDOBDC) were synthesized and studied for facile xenon capture and separation. Our results indicate that NiDOBDC adsorbs significantly more xenon than MOF-5, and is more selective for xenon over krypton than activated carbon.

Extraction chromatographic methods in the sample preparation sequence for thermal ionization mass spectrometric analysis of plutonium isotopes.

A sample preparation sequence for actinide isotopic analysis by thermal ionization mass spectrometry (TIMS) is described that includes column-based extraction chromatography as the first separation step, followed by anion-exchange column separations. The sequence is designed to include a wet ashing step after the extraction chromatography to prevent any leached extractant or oxalic acid eluent reagents from interfering with subsequent separations, source preparation, or TIMS ionization. TEVA resin and DGA resin materials, containing extractants that consist only of C, N, O, and H atoms, were investigated for isolation of plutonium. Radiotracer level studies confirmed expected high yields from column-based separation procedures. Femtogram-level studies were carried out with TIMS detection, using multiple monoisotopic spikes applied sequentially throughout the separation sequence. Pu recoveries were 87% and 86% for TEVA and DGA resin separations, respectively. The Pu recoveries from 400 µL anion-exchange column separation sequences were 89% and 93% for trial sequences incorporating TEVA and DGA resin. Thus, a prior extraction chromatography step in the sequence did not interfere with the subsequent anion-exchange separation when a simple wet ash step was carried out in between these column separations. The average measurement efficiency for Pu, encompassing the chemical separation recoveries and the TIMS ionization efficiency, was 2.73% ± 0.77% (2σ) for the DGA resin trials and 2.67% ± 0.54% for the TEVA resin trials, compared to 3.41% and 2.37% (average 2.89%) for two control trials. These compare with an average measurement efficiency of 2.78% ± 1.70%, n = 33 from process benchmark analyses using Pu spikes processed through a sequence of oxalate precipitation, wet ash, iron hydroxide precipitation, and anion-exchange column separations. We conclude that extraction chromatography can be a viable separation procedure as part of a multistep sequence for TIMS sample preparation.

Liquid CO2 displacement of water in a dual-permeability pore network micromodel.

Permeability contrasts exist in multilayer geological formations under consideration for carbon sequestration. To improve our understanding of heterogeneous pore-scale displacements, liquid CO(2) (LCO(2))-water displacement was evaluated in a pore network micromodel with two distinct permeability zones. Due to the low viscosity ratio (logM = -1.1), unstable displacement occurred at all injection rates over 2 orders of magnitude. LCO(2) displaced water only in the high permeability zone at low injection rates with the mechanism shifting from capillary fingering to viscous fingering with increasing flow rate. At high injection rates, LCO(2) displaced water in the low permeability zone with capillary fingering as the dominant mechanism. LCO(2) saturation (S(LCO2)) as a function of injection rate was quantified using fluorescent microscopy. In all experiments, more than 50% of LCO(2) resided in the active flowpaths, and this fraction increased as displacement transitioned from capillary to viscous fingering. A continuum-scale two-phase flow model with independently determined fluid and hydraulic parameters was used to predict S(LCO2) in the dual-permeability field. Agreement with the micromodel experiments was obtained for low injection rates. However, the numerical model does not account for the unstable viscous fingering processes observed experimentally at higher rates and hence overestimated S(LCO2).

Quantum dot immunoassays in renewable surface column and 96-well plate formats for the fluorescence detection of botulinum neurotoxin using high-affinity antibodies.

A fluorescence sandwich immunoassay using high-affinity antibodies and quantum dot (QD) reporters has been developed for detection of botulinum neurotoxin serotype A (BoNT/A) using a nontoxic recombinant fragment of the holotoxin (BoNT/A-H(C)-fragment) as a structurally valid simulant for the full toxin molecule. The antibodies used, AR4 and RAZ1, bind to nonoverlapping epitopes present on both the full toxin and on the recombinant fragment. In one format, the immunoassay is carried out in a 96-well plate with detection in a standard plate reader using AR4 as the capture antibody and QD-coupled RAZ1 as the reporter. Detection to 31 pM with a total incubation time of 3 h was demonstrated. In a second format, the AR4 capture antibody was coupled to Sepharose beads, and the reactions were carried out in microcentrifuge tubes with an incubation time of 1 h. The beads were subsequently captured and concentrated in a rotating rod "renewable surface" flow cell equipped with a fiber optic system for fluorescence measurements. In PBS buffer, the BoNT/A-H(C)-fragment was detected to concentrations as low as 5 pM using the fluidic measurement approach.