Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes.

Differential scanning fluorimetry (DSF) is a technique that reports protein thermal stability via the selective recognition of unfolded states by fluorogenic dyes. However, DSF applications remain limited by protein incompatibilities with existing DSF dyes. Here we overcome this obstacle with the development of a protein-adaptive DSF platform (paDSF) that combines a dye library 'Aurora' with a streamlined procedure to identify protein-dye pairs on demand. paDSF was successfully applied to 94% (66 of 70) of proteins, tripling the previous compatibility and delivering assays for 66 functionally and biochemically diverse proteins, including 10 from severe acute respiratory syndrome coronavirus 2. We find that paDSF can be used to monitor biological processes that were previously inaccessible, demonstrated for the interdomain allostery of O-GlcNAc transferase. The chemical diversity and varied selectivities of Aurora dyes suggest that paDSF functionality may be readily extended. paDSF is a generalizable tool to interrogate protein stability, dynamics and ligand binding.

Conformationally responsive dyes enable protein-adaptive differential scanning fluorimetry.

Flexible in vitro methods alter the course of biological discoveries. Differential Scanning Fluorimetry (DSF) is a particularly versatile technique which reports protein thermal unfolding via fluorogenic dye. However, applications of DSF are limited by widespread protein incompatibilities with the available DSF dyes. Here, we enable DSF applications for 66 of 70 tested proteins (94%) including 10 from the SARS-CoV2 virus using a chemically diverse dye library, Aurora, to identify compatible dye-protein pairs in high throughput. We find that this protein-adaptive DSF platform (paDSF) not only triples the previous protein compatibility, but also fundamentally extends the processes observable by DSF, including interdomain allostery in O-GlcNAc Transferase (OGT). paDSF enables routine measurement of protein stability, dynamics, and ligand binding.

Synthetic dyes: A mass spectrometry approach and applications.

Synthetic dyes are found in a wide variety of applications today, including but not limited to textiles, foods, and medicine. The analysis of these molecules is pertinent to several fields such as forensics, environmental monitoring, and quality control, all of which require the sensitivity and selectivity of analysis provided by mass spectrometry (MS). Recently, there has been an increase in the implementation of MS evaluation of synthetic dyes by various methods, with the majority of research thus far falling under electrospray ionization and moving toward direct ionization methods. This review covers an overview of the chemistry of synthetic dyes needed for the understanding of MS sample preparation and spectral results, current fields of application, ionization methods, and fragmentation trends and works that have been reported in recent years.

Quantification of docusate antimicrobial finishing after simulated landfill degradation via tandem mass spectrometry and QuEChERS extraction.

An analytical method for the detection and quantification of silver docusate antimicrobial finishing in soil was developed through a combination of the QuEChERS extraction method and tandem mass spectrometry (MS/MS) quantification with isotopically labeled internal standard. First, the calibration system was established in the matrix where QuEChERS extraction removed docusate from soil. The addition of an isotopically labeled internal standard reduces ionization suppression due to instrumental fluctuation and run-to-run deviation. After establishing the calibration system, this quantification method was validated according to a guideline from the U.S. Food and Drug Administration. A series of variables for quantification were validated including coefficient of determination (R2 = 0.989 ± 0.002), percent error (% error = 3 ± 4%), coefficient of variation (% CV = 6 ± 1%), limit of detection (LOD = 8 ± 2 ng mL-1), lower limit of quantification (LLOQ = 27 ± 5 ng mL-1), recovery and matrix effect (matrix effect = 0.944 ± 0.026). Those parameters were obtained from the inter- and intra-day measurements for both calibration and the quality control standards. Later, samples extracted from a simulated landfill degradation of cotton fabrics applied with sliver docusate antimicrobial finishing were measured. It was observed that the concentration measured (51 ± 5 ng mL-1 or 252 ± 25 ng g-1) fell into the ranges defined by the method development with good precision (% CV = 4 ± 1%). Results from this study could further the understanding of textile landfill degradation and facilitate further study regarding docusate contamination in soil.

The characterization of disperse dyes in polyester fibers using DART mass spectrometry.

Textile fibers alone are highly prevalent in our environment, and not only are there a wide variety of fibers, but generally, consumer textiles are colored. Given the variety of crime locations where dyes are encountered and the potential circumstances, a rapid, preparation free analysis of samples is highly beneficial. This study has characterized a collection of commercially available textiles dyes by verifying the chemical structure, collecting reference spectra, and developing a method to analyze dyed fibers via Direct Analysis in Real-Time (DART) mass spectrometry. A methodology for direct analysis of pieces of fabric and single thread samples of polyester fibers dyed with disperse dyes was developed. The presence of 31 target dyes on fibers whose structures were previously established via high-resolution mass spectrometry was confirmed. Dyed fabrics containing mixtures of dyes in varying concentrations were also evaluated to determine whether each dye in the composition could be detected. The DART-MS methodology was sensitive and positively characterized disperse dyes in polyester fibers, allowing for blind identification of mixtures with the assistance of a high-resolution mass spectrometry database.

Molecular characterization and ecotoxicological evaluation of the natural dye madder and its chlorinated products.

There has been increased interest in the use of natural dyes for textile coloration as alternatives to synthetic dyes, due to the general belief that natural dyes are more environmentally friendly. However, natural dyes have poor affinity for textiles, which can lead to high dye levels in the resultant wastewater. While chlorine treatment has proven to be effective for dye wastewater disinfection and decolorization, this process can also lead to the formation of more toxic degradation products for certain synthetic dyes. On the other hand, little information is available regarding the ecotoxicity of natural dyes and their chlorination products. To advance knowledge in this area, madder was selected due to its historical importance and wide application in the textile industry. Specifically, we sought to characterize the chlorine-induced degradation products of an aqueous madder solution and to assess their ecotoxicity. The main component of the present madder sample was Alizarin (89.8%). Chlorination led to complete decolorization, and 2-hydroxynaphthalene-1,4-dione and phthalic anhydride were identified as key degradation products. Chlorination of madder decreased toxicity to Daphnia similis (microcrustacean) 10-fold and removed the toxicity to Raphidocellis subcapitata (algae), when compared to the parent dye.

Are all charge-transfer parameters created equally? A study of functional dependence and excited-state charge-transfer quantification across two dye families.

Small molecule organic dyes have many potential uses in medicine, textiles, forensics, and light-harvesting technology. Being able to computationally predict the spectroscopic properties of these dyes could greatly expedite screening efforts, saving time and materials. Time-dependent density functional theory (TD-DFT) has been shown to be a good tool for this in many instances, but characterizing electronic excitations with charge-transfer (CT) character has historically been challenging and can be highly sensitive to the chosen exchange-correlation functional. Here we present a combined experimental and computational study of the excited-state electronic structure of twenty organic dyes obtained from the Max Weaver Dye Library at NCSU. Results of UV-vis spectra calculations on these dyes with six different exchange-correlation functionals, BP86, B3LYP, PBE0, M06, BH and HLYP, and CAM-B3LYP, were compared against their measured UV-vis spectra. It was found that hybrid functionals with modest amounts (20-30%) of included Hartree-Fock exchange are the most effective at matching the experimentally determined λmax. The interplay between the observed error, the functional chosen, and the degree of CT was analyzed by quantifying the CT character of λmax using four orbital and density-based metrics, Λ, Δr, SC and DCT, as well as the change in the dipole moment, Δµ. The results showed that the relationship between CT character and the functional dependence of error is not straightforward, with the observed behavior being dependent both on how CT was quantified and the functional groups present in the molecules themselves. It is concluded that this may be a result of the examined excitations having intermediate CT character. Ultimately it was found that the nature of the molecular "family" influenced how a given functional behaved as a function of CT character, with only two of the examined CT quantification methods, Δr and DCT, showing consistent behavior between the different molecular families. This suggests that further work needs to be done to ensure that currently used CT quantification methods show the same general trends across large sets of multiple dye families.

Study on the Gas-Phase Reactivity of Charged Pyridynes.

The reactivities of three isomeric, charged ortho-pyridynes, the 1,2-, 2,3-, and 3,4-didehydropyridinium cations, were examined in the gas phase using Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry. The structures of selected product ions were probed using collision-activated dissociation (CAD) experiments in a linear quadrupole ion trap (LQIT) mass spectrometer. Mechanisms based on quantum chemical calculations are proposed for the formation of all major products. The products of the reactions of the charged ortho-pyridynes in the gas phase were found to closely resemble those formed upon reactions of neutral ortho-arynes in solution, but the mechanisms of these reactions exhibit striking differences. Additionally, no radical reactions were observed for any of the charged ortho-pyridynes examined, in contrast to previous proposals that ortho-benzyne can occasionally react via radical mechanisms. Finally, the relative reactivities of those charged gaseous ortho-pyridynes that yielded similar product distributions were found to be affected mainly by the (calculated) vertical electron affinities of the dehydrocarbon sites, which suggests that the reactivity of these species is controlled by polar effects.

Characterization of synthetic dyes for environmental and forensic assessments: A chromatography and mass spectrometry approach.

Dyes have become common substances since they are employed in mostly all objects surrounding our daily activities such as clothing and upholstery. Based on the usage and disposal of these objects, the transfer of the dyes to other media such as soil and water increases their prevalence in our environment. However, this prevalence could help to solve crimes and pollution problems if detection techniques are proper. For that reason, the detection and characterization of dyes in complex matrices is important to determine the possible events leading to their deposition (natural degradation, attempts of removal, possible match with evidence, among others). Currently, there are several chromatographic and mass spectrometric approaches used for the identification of these organic molecules and their derivatives with high specificity and accuracy. This review presents current chromatographic and mass spectrometric methods that are used for the detection and characterization of disperse, acid, basic, and reactive dyes, and their derivatives.

Quantification of anthracene after dermal absorption test via APCI-tandem mass spectrometry.

An analytical method for the detection and quantification of anthracene from interstitial fluid samples was developed by using Atmospheric Pressure Chemical Ionization-Tandem Mass Spectrometry (APCI-MS/MS). The anthracene samples were obtained using intradermal microdialysis to assess dermal absorption of this polycyclic aromatic hydrocarbon (PAH). The experimental considerations were evaluated based on the chemical properties of this PAH and the detection limits of the instrumentation. The addition of an isotopically labeled internal standard allows the reduction of ionization suppression due to instrumental fluctuation and run-to-run deviation. The dermal extraction samples were prepared considering the proceeding conditions for measurement enhancement. Several variables for method validation including coefficient of determination (R2 = 0.993 ± 0.003), percent error (% error = 0 ± 2%), coefficient of variation (% CV = 5 ± 1%), lowest limit of detection (LOD = 39 ± 3 ng mL-1), and lowest limit of quantification (LLOQ = 129 ± 10 ng mL-1) were obtained from the inter- and intra-day measurements for the calibration and the quality control samples. Posterior to this, actual dermal interstitial fluid samples were measured, and it was observed they fitted into the ranges defined from the method development with good accuracy and precision. It was observed that the introduction of an internal standard while performing APCI-MS/MS allows an accurate and precise measurement of the concentration of anthracene to be obtained from dermal extraction samples. This method could be further used for complex mixtures to enhance our understanding of hazardous exposure of PAH on firefighter gear.

Physical Characterization of Inclusion Complexes of Triphenyl Phosphate and Cyclodextrins in Solution.

The goal of this work is to provide physical insights into the formation and stability of inclusion complexes (ICs) in aqueous solution between cyclodextrins (CDs) and a common flame retardant, triphenyl phosphate (TPP). Quantum chemistry calculations reveal the possible energetically favorable geometries of TPP in their 1:1 IC form with α-, ß-, and γ-CDs as well as their associated complexation, conformational, and interaction energies. High-resolution mass spectrometry (MS) and tandem MS were used with electrospray ionization to study the soluble ICs formed between TPP and CDs. Successful formation of TPP ICs with both ß- and γ-CD in solution was detected in the ratio of 1:1 using high-resolution MS in the positive ion mode. Collision-induced dissociation confirmed the formation of TPP ICs with ß- and γ-CDs by generating two product ions, TPP and ß- or γ-CD, in both cases. Although quantum chemistry calculations suggest that IC formation with α-CD is energetically possible, an IC with α-CD is not observed in aqueous solution using MS, which aligns with what we also previously observed in the solid state. Since TPP forms stable ICs with ß- and γ-CDs both in the solid state and in solution suggests that complexation could be a safer alternative than applying TPP directly to a substrate. In addition, complexation with CDs in solution also opens up new processing methods to create flame-retardant fabrics and foams with TPP.

Effects of hydrogen bonding on the gas-phase reactivity of didehydroisoquinolinium cation isomers.

Two previously unreported isomeric biradicals with a 1,4-radical topology, the 1,5-didehydroisoquinolinium cation and the 4,8-didehydroisoquinolinium cation, and an additional, previously reported isomer, the 4,5-didehydroisoquinolinium cation, were studied to examine the importance of the exact location of the radical sites on their reactivities in the gas phase. The experimental results suggest that hydrogen bonding in the transition state enhances the reactivity of the 1,5-didehydroisoquinolinium cation towards tetrahydrofuran but not towards allyl iodide, dimethyl disulfide or tert-butyl isocyanide. The observation of no such enhancement of reactivity towards tetrahydrofuran for the 4,8-didehydroisoquinolinium and 4,5-didehydroisoquinolinium cations supports this hypothesis as these two biradicals are not able to engage in hydrogen bonding in their transition states for hydrogen atom abstraction from tetrahydrofuran. Quantum chemical transition state calculations indicate that abstraction of a hydrogen atom from tetrahydrofuran by the 1,5-didehydroisoquinolinium cation occurs at the C-1 radical site and that the transition state is stabilized by hydrogen bonding.

Direct analysis of textile dyes from trace fibers by automated microfluidics extraction system coupled with Q-TOF mass spectrometer for forensic applications.

Textile fiber is a common form of transferable trace evidence at the crime scene. Different techniques such as microscopy or spectroscopy are currently being used for trace fiber analysis. Dye characterization in trace fiber adds an important molecular specificity during the analysis. In this study, we performed a direct trace fiber analysis method via dye characterization by a novel automated microfluidics device (MFD) dye extraction system coupled with a quadrupole-time-of-flight (Q-TOF) mass spectrometer (MS). The MFD system used an in-house made automated procedure which requires only 10µL of organic solvent for the extraction. The total extraction and identification time by the system is under 12min. A variety of sulfonated azo and anthraquinone dyes were analyzed from ∼1mm length nylon fiber samples. This methodology successfully characterized multiple dyes (≥3 dyes) from a single fiber thread. Additionally, it was possible to do dye characterization from single fibers with a diameter of ∼10µm. The MFD-MS system was used for elemental composition and isotopic distribution analysis where MFD-MS/MS was used for structural characterization of dyes on fibers.

Rapid Quadrupole-Time-of-Flight Mass Spectrometry Method Quantifies Oxygen-Rich Lignin Compound in Complex Mixtures.

Complex mixture analysis is a costly and time-consuming task facing researchers with foci as varied as food science and fuel analysis. When faced with the task of quantifying oxygen-rich bio-oil molecules in a complex diesel mixture, we asked whether complex mixtures could be qualitatively and quantitatively analyzed on a single mass spectrometer with mid-range resolving power without the use of lengthy separations. To answer this question, we developed and evaluated a quantitation method that eliminated chromatography steps and expanded the use of quadrupole-time-of-flight mass spectrometry from primarily qualitative to quantitative as well. To account for mixture complexity, the method employed an ionization dopant, targeted tandem mass spectrometry, and an internal standard. This combination of three techniques achieved reliable quantitation of oxygen-rich eugenol in diesel from 300 to 2500 ng/mL with sufficient linearity (R2 = 0.97 ± 0.01) and excellent accuracy (percent error = 0% ± 5). To understand the limitations of the method, it was compared to quantitation attained on a triple quadrupole mass spectrometer, the gold standard for quantitation. The triple quadrupole quantified eugenol from 50 to 2500 ng/mL with stronger linearity (R2 = 0.996 ± 0.003) than the quadrupole-time-of-flight and comparable accuracy (percent error = 4% ± 5). This demonstrates that a quadrupole-time-of-flight can be used for not only qualitative analysis but also targeted quantitation of oxygen-rich lignin molecules in complex mixtures without extensive sample preparation. The rapid and cost-effective method presented here offers new possibilities for bio-oil research, including: (1) allowing for bio-oil studies that demand repetitive analysis as process parameters are changed and (2) making this research accessible to more laboratories. Graphical Abstract ᅟ.

Weaver's historic accessible collection of synthetic dyes: a cheminformatics analysis.

We present the Max Weaver Dye Library, a collection of ∼98 000 vials of custom-made and largely sparingly water-soluble dyes. Two years ago, the Eastman Chemical Company donated the library to North Carolina State University. This unique collection of chemicals, housed in the College of Textiles, also includes tens of thousands of fabric samples dyed using some of the library's compounds. Although the collection lies at the core of hundreds of patented inventions, the overwhelming majority of this chemical treasure trove has never been published or shared outside of a small group of scientists. Thus, the goal of this donation was to make this chemical collection, and associated data, available to interested parties in the research community. To date, we have digitized a subset of 2700 dyes which allowed us to start the constitutional and structural analysis of the collection using cheminformatics approaches. Herein, we open the discussion regarding the research opportunities offered by this unique library.

Reactivity Controlling Factors for an Aromatic Carbon-Centered σ,σ,σ-Triradical: The 4,5,8-Tridehydroisoquinolinium Ion.

The chemical properties of the 4,5,8-tridehydroisoquinolinium ion (doublet ground state) and related mono- and biradicals were examined in the gas phase in a dual-cell Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer. The triradical abstracted three hydrogen atoms in a consecutive manner from tetrahydrofuran (THF) and cyclohexane molecules; this demonstrates the presence of three reactive radical sites in this molecule. The high (calculated) electron affinity (EA=6.06 eV) at the radical sites makes the triradical more reactive than two related monoradicals, the 5- and 8-dehydroisoquinolinium ions (EA=4.87 and 5.06 eV, respectively), the reactivity of which is controlled predominantly by polar effects. Calculated triradical stabilization energies predict that the most reactive radical site in the triradical is not position C4, as expected based on the high EA of this radical site, but instead position C5. The latter radical site actually destabilizes the 4,8-biradical moiety, which is singlet coupled. Indeed, experimental reactivity studies show that the radical site at C5 reacts first. This explains why the triradical is not more reactive than the 4-dehydroisoquinolinium ion because the C5 site is the intrinsically least reactive of the three radical sites due to its low EA. Although both EA and spin-spin coupling play major roles in controlling the overall reactivity of the triradical, spin-spin coupling determines the relative reactivity of the three radical sites.

On-line mass spectrometric methods for the determination of the primary products of fast pyrolysis of carbohydrates and for their gas-phase manipulation.

Mass spectrometric methodology was developed for the determination and manipulation of the primary products of fast pyrolysis of carbohydrates. To determine the true primary pyrolysis products, a very fast heating pyroprobe was coupled to a linear quadrupole ion trap mass spectrometer through a custom-built adaptor. A home-built flow tube that simulates pyrolysis reactor conditions was used to examine the secondary reactions of the primary products. Depending on the experiment, the pyrolysis products were either evaporated and quenched or allowed to react for a period of time. The quenched products were ionized in an atmospheric pressure chemical ionization (APCI) source infused with one of two ionization reagents, chloroform or ammonium hydroxide, to aid in ionization. During APCI in negative ion mode, chloroform produces chloride anions that are known to readily add to carbohydrates with little bias and little to no fragmentation. On the other hand, in positive ion mode APCI, ammonium hydroxide forms ammonium adducts with carbohydrates with little to no fragmentation. The latter method ionizes compounds that are not readily ionized upon negative ion mode APCI, such as furan derivatives. Six model compounds were studied to verify the ability of the ionization methods to ionize known pyrolysis products: glycolaldehyde, hydroxyacetone, furfural, 5-hydroxymethylfurfural, levoglucosan, and cellobiosan. The method was then used to examine fast pyrolysis of cellobiose. The primary fast pyrolysis products were determined to consist of only a handful of compounds that quickly polymerize to form anhydro-oligosaccharides when allowed to react at high temperatures for an extended period of time.

Analysis of xyloglucans by ambient chloride attachment ionization tandem mass spectrometry.

Xyloglucan oligomers obtained upon enzyme digestion from Hymenaea courbaril, Arabidopsis Columbia-0 and mur3 were ionized and analyzed by using chloride anion attachment electrospray ionization (ESI) and tandem mass spectrometry. MW determination and structural elucidation of several xyloglucan oligomers was performed directly from the mixture solutions without sample pretreatment or derivatization. Sodium cation attachment was used to determine the number of xyloglucans present in the mixtures and their MWs. However, tandem mass spectrometry results showed that structure elucidation based on the sodium adducts is ambiguous. Chloride anion also forms stable adducts with these xyloglucans upon ESI. These adducts can be readily identified due to the chlorine isotope pattern. The mass spectral profile of xyloglucans obtained for the mixtures matches the HPAEC results, thus validating this methodology for the determination of the xyloglucan composition and the MW of each xyloglucan. Upon collisional activation in MS(2) experiments, the chloride anion adducts readily lose HCl, which helps verify the molecular weight of each xyloglucan. Isolating the resulting anion (deprotonated oligomer) and subjecting it to further collision-activated dissociation experiments (MS(n); n=3-4) yields useful structural information that allows the differentiation between isomeric anions and hence determination of the sequence of the xyloglucan oligomers. The deprotonated oligomers fragment by a stepwise loss of sugar units from the reducing end.

Experimental and computational studies on the formation of three para-benzyne analogues in the gas phase.

Experimental and computational studies on the formation of three gaseous, positively-charged para-benzyne analogues in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer are reported. The structures of the cations were examined by isolating them and allowing them to react with various neutral reagents whose reactions with aromatic carbon-centered σ-type mono- and biradicals are well understood. Cleavage of two iodine-carbon bonds in N-deuterated 1,4-diiodoisoquinolinium cation by collision-activated dissociation (CAD) produced a long-lived cation that showed nonradical reactivity, which was unexpected for a para-benzyne. However, the reactivity closely resembles that of an isomeric enediyne, N-deuterated 2-ethynylbenzonitrilium cation. A theoretical study on possible rearrangement reactions occurring during CAD revealed that the cation formed upon the first iodine atom loss undergoes ring-opening before the second iodine atom loss to form an enediyne instead of a para-benzyne. Similar results were obtained for the 5,8-didehydroisoquinolinium cation and the 2,5-didehydropyridinium cation. The findings for the 5,8-didehydroisoquinolinium cation are in contradiction with an earlier report on this cation. The cation described in the literature was regenerated by using the literature method and demonstrated to be the isomeric 5,7-didehydro-isoquinolinium cation and not the expected 5,8-isomer.

Does the 2,6-didehydropyridinium cation exist?

Reactive intermediates are key species involved in many chemical and biochemical processes. For example, carbon-centered aromatic σ,σ-biradicals formed in biological systems from naturally occurring enediyne antitumor antibiotics are responsible for the irreversible cleavage of double-stranded DNA caused by these prodrugs. However, because of their high reactivity, it is very difficult or impossible to isolate and investigate these biradicals. The aromatic σ,σ-biradical, 2,6-didehydropyridine, has been speculated for many years to be formed in certain organic reactions; however, no definitive proof of its generation has been obtained. We report here the successful generation of protonated 2,6-didehydropyridine and the examination of its chemical properties in the gas phase by using a Fourier transform ion cyclotron resonance mass spectrometer. The results suggest that a mixture of singlet (ground) state and triplet (excited) state 2,6-didehydropyridinium cations was generated. The two different states show qualitatively different reactivity, with the triplet state showing greater Brønsted acidity than that of the singlet state. The triplet state also shows much greater radical reactivity than that of the singlet state, as expected because of the coupling of the nonbonding electrons in the singlet state.