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1. Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11

   https://doi.org/10.1039/d0ra04956e  

   Porter, J.; Dit Fouque, K. Jeanne; Miksovska, J.; Fernandez-Lima, F. (September 2020, RSC Advances)

   null (Ed.)

   In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH ( e.g. , pH 3.1–6.1) and concentration ( e.g. , 1–50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged ( e.g. , [M] + , [M − 2H + NH 4 ] + , [M − H + Na] + and [M − H + K] + ) and doubly charged ( e.g. , [M + H] 2+ , [M − H + NH 4 ] 2+ , [M + Na] 2+ and [M + K] 2+ ) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity ( e.g. , number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges ( e.g. , NH 4 + , Na + and K + vs. H + ). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge ( i.e. , a CE 50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H] 3+ , [2M − H + NH 4 ] 3+ , [2M + Na] 3+ and [2M + K] 3+ , respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species. 

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2. Self-Diffusion of Star and Linear Polyelectrolytes in Salt-Free and Salt Solutions

   https://doi.org/10.1021/acs.macromol.4c01374  

   Aliakseyeu, Aliaksei; Truong, Erica; Hu, Yan-Yan; Sayko, Ryan; Dobrynin, Andrey V; Sukhishvili, Svetlana A (December 2024, Macromolecules)

   This work explored solution properties of linear and star poly(methacrylic acids) with four, six, and eight arms (LPMAA, 4PMAA, PMAA, and 8PMAA, respectively) of matched molecular weights in a wide range of pH, salt, and polymer concentrations. Experimental measurements of self-diffusion were performed by fluorescence correlation spectroscopy (FCS), and the results were interpreted using the scaling theory of polyelectrolyte solutions. While all PMAAs were pH sensitive and showed an increase in hydrodynamic radius (Rh) with pH in the dilute regime, the Rh of star polymers (measured at basic pH values) was significantly smaller for the star polyacids due to their more compact structure. Fully ionized star PMAAs were also found to be less sensitive to changes in salt concentration and type of the counterion compared to linear PMAA. While Rh of fully ionized linear PMAA decreased in the series Li+ > Na+ > K+ > Cs+ in agreement with the Hofmeister series, Rh of star PMAAs was virtually independent of type of the counterion for eight-arm PMAA. However, molecular architecture strongly affected interactions of counterions with PMAAs. In particular, 7Li NMR revealed that the spin−lattice relaxation time T1 of Li+ ions in low-salt solutions of eight-arm PMAA was ∼2-fold smaller than that in the solution of linear PMAA, suggesting slower Li+-ion dynamics within star polymers. An increase in concentration of monovalent chloride salts, cs, above that of the PMAA monomer unit concentration (cm) resulted in shrinking of both linear and star molecules, with the hydrodynamic size Rh scaling as Rh ∝ cs −0.11±0.01. Self-diffusion of linear and star polyelectrolytes was then studied in a wide range of polyelectrolyte concentrations (10−3 mol/L < cm < 0.5 mol/L) in low-salt (<10−4 mol/L of added salt) and high-salt (1 mol/L) solutions. In both the low-salt and high-salt regimes, diffusion coefficient D was lower for PMAAs with a larger number of arms at a fixed cm. In addition, in both cases, D plateaued at low polymer concentrations and decreased at higher polymer concentrations. However, while in the high-salt conditions, the concentration dependence of D reflected transitions between the dilute to semidilute solution regimes as expected for neutral chains in good and theta solvents, analysis of the diffusion data in the low-salt conditions using the scaling theory revealed a different origin of the concentration dependence of D. Specifically, in the low-salt solutions, both linear and star PMAAs exhibited unentangled (Rouse-like) dynamics in the entire range of polyelectrolyte concentrations. 

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3. Distinguishing Isomeric Cyclobutane Thymidine Dimers by Ion Mobility and Tandem Mass Spectrometry

   https://doi.org/10.1021/jasms.4c00133  

   Yang, Hsin-Chieh; Scruggs, Savannah S; Chai, Mengqi; Mathai, George; Taylor, John-Stephen; Gross, Michael L (August 2024, Journal of the American Society for Mass Spectrometry)

   Irradiation of the major conformation of duplex DNA found in cells (B form) produces cyclobutane pyrimidine dimers (CPDs) from adjacent pyrimidines in a head-to-head orientation (syn) with the C5 substituents in a cis stereochemistry. These CPDs have crucial implications in skin cancer. Irradiation of G-quadruplexes and other non-B DNA conformations in vitro produces, however, CPDs between non-adjacent pyrimidines in nearby loops with syn and head-to-tail orientations (anti) with both cis and trans stereochemistry to yield a mixture of six possible isomers of the T=T dimer. This outcome is further complicated by formation of mixtures of non-adjacent CPDs of dC=dT, dT=dC, and dC=dC, and successful analysis depends on development of specific and sensitive methods. Towards meeting this need, we investigated whether ion mobility mass spectrometry (IMMS) and MS/MS can distinguish the cis,syn and trans-anti T=T CPDs. Ion mobility can afford base-line separation and give relative mobilities that are in accord with predicted cross sections. Complementing this ability to distinguish isomers is MS/MS collisional activation where fragmentation also distinguishes the two isomers and confirms conclusions drawn from ion mobility analysis. The observations offer early support that ion mobility and MS/MS can enable the distinction of DNA photoproduct isomers. 

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4. Effect of relative humidity on the composition of secondary organic aerosol from the oxidation of toluene

   https://doi.org/10.5194/acp-18-1643-2018  

   Hinks, Mallory L.; Montoya-Aguilera, Julia; Ellison, Lucas; Lin, Peng; Laskin, Alexander; Laskin, Julia; Shiraiwa, Manabu; Dabdub, Donald; Nizkorodov, Sergey A. (January 2018, Atmospheric Chemistry and Physics)

   The effect of relative humidity (RH) on the chemical composition of secondary organic aerosol (SOA) formed from low-NO_x toluene oxidation in the absence of seed particles was investigated. SOA samples were prepared in an aerosol smog chamber at &lt;&thinsp;2 % RH and 75 % RH, collected on Teflon filters, and analyzed with nanospray desorption electrospray ionization high-resolution mass spectrometry (nano-DESI&ndash;HRMS). Measurements revealed a significant reduction in the fraction of oligomers present in the SOA generated at 75 % RH compared to SOA generated under dry conditions. In a separate set of experiments, the particle mass concentrations were measured with a scanning mobility particle sizer (SMPS) at RHs ranging from &lt;&thinsp;2 to 90 %. It was found that the particle mass loading decreased by nearly an order of magnitude when RH increased from &lt;&thinsp;2 to 75&ndash;90 % for low-NO_x toluene SOA. The volatility distributions of the SOA compounds, estimated from the distribution of molecular formulas using the molecular corridor approach, confirmed that low-NO_x toluene SOA became more volatile on average under high-RH conditions. In contrast, the effect of RH on SOA mass loading was found to be much smaller for high-NO_x toluene SOA. The observed increase in the oligomer fraction and particle mass loading under dry conditions were attributed to the enhancement of condensation reactions, which produce water and oligomers from smaller compounds in low-NO_x toluene SOA. The reduction in the fraction of oligomeric compounds under humid conditions is predicted to partly counteract the previously observed enhancement in the toluene SOA yield driven by the aerosol liquid water chemistry in deliquesced inorganic seed particles. 

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5. Analysis of Fentanyl and Fentanyl Analogs Using Atmospheric Pressure Chemical Ionization Gas Chromatography–Mass Spectrometry (APCI-GC-MS)

   https://doi.org/10.1021/jasms.4c00455  

   Reyes_Monroy, Karen A; McCrary, Richard; Parry, Isabelle; Webber, Catherine; Golden, Teresa D; Verbeck, Guido F (March 2025, Journal of the American Society for Mass Spectrometry)

   Illicit fentanyl and fentanyl analogs are a growing concern in the United States as opioid related deaths rise. Given that fentanyl analogs are readily obtained by modifying the structure of fentanyl, illicit fentanyl analogs appearing on the black market often contain similar structures, making analogue differentiation and identification difficult. Thus, obtaining both precursor and product ion data during analysis is becoming increasingly valuable in fentanyl analog characterization. In this paper, we provide GC column retention time, precursor, and product ion mass spectrum data for 74 fentanyl analogs that were analyzed using atmospheric pressure chemical ionization-gas chromatography−mass spectrometry (APCI-GC-MS) utilizing a triple quadrupole mass analyzer. During analysis, precursor ions underwent collision induced dissociation (CID) by increasing the collision energy (10, 20, 30, 40, and 50 V) throughout a single run. Data reveal that APCI readily produces product ions of the piperidine and N-alkyl chain but rarely provides data on the acyl group. Furthermore, fentanyl analogs with greater substitution at the N-alkyl chain demonstrate a greater preference for dissociation at the N-αC and αC-βC bond, while greater substitution at the amide group leads to fragmentation at the N−C4 bond. 

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