Unimolecular isomerizations of C6H6•+ radical cations: a computational study.

CONCEPT: Eighteen concerted isomerization reactions of various C6H6•+ radical cation (RC) species are studied and found to proceed via well-defined transition states, whose relative positions along the reaction pathway generally agree with Hammond's postulate. From the barrier heights, the rate coefficients of these reactions are estimated by using transition state theory, and the activation energies are computed. Through combination among themselves, these 18 isomerizations yielded 15 multi-step conversion routes of various C6H6•+ species to the lowest energy benzene radical cation isomer 1, which routes are compared. METHODS: Use is made of DFT with the B3LYP and M06-2X functionals, along with the CBS-QB3 approach to arrive at better energies. From the barrier heights for each of the concerted reactions, canonical transition state theory was applied to evaluate rate coefficients k over the temperature range 200-500 K. The Arrhenius activation energies were computed using the plot of ln k vs. 1/T.

Temperature-Induced Restructuring of Mycolic Acid Bilayers Modeling the Mycobacterium tuberculosis Outer Membrane: A Molecular Dynamics Study.

The emergence of new drug-resistant strains of the tuberculosis pathogen Mycobacterium tuberculosis (Mtb) is a new challenge for modern medicine. Its resistance capacity is closely related to the properties of the outer membrane of the Mtb cell wall, which is a bilayer membrane formed by mycolic acids (MAs) and their derivatives. To date, the molecular mechanisms of the response of the Mtb outer membrane to external factors and, in particular, elevated temperatures have not been sufficiently studied. In this work, we consider the temperature-induced changes in the structure, ordering, and molecular mobility of bilayer MA membranes of various chemical and conformational compositions. Using all-atom long-term molecular dynamics simulations of various MA membranes, we report the kinetic parameters of temperature-dependent changes in the MA self-diffusion coefficients and conformational compositions, including the apparent activation energies of these processes, as well as the characteristic times of ordering changes and the features of phase transitions occurring over a wide range of elevated temperatures. Understanding these effects could be useful for the prevention of drug resistance and the development of membrane-targeting pharmaceuticals, as well as in the design of membrane-based materials.

Composition-Property Relations for GAx FAy MA1- x - y PbI3 Perovskites.

Halide perovskites are materials for diverse optoelectronic applications owing to a combination of factors, including their compositional flexibility. A major source of this diversity of compositions comes from the use of mixed organic cations in the A-site of such compounds to form solid solutions. Many organic cations are possible for this purpose. Although significant progress is made over years of intensive research, the determination of systematic relationships between the compositions and properties of halide perovskites is not exploited accordingly. Using the MAPbI3 prototype, a wide range of compositions substituted by formamidinium (FA+ ) and guanidinium (GA+ ) cations are studied. From a detailed collection of experimental data and results reported in the literature, heat maps correlating the composition of GAx FAy MA1- x - y PbI3 solid solutions with phase transition temperatures, dielectric permittivity, and activation energies are constructed. Considering the characteristics of organic cations, namely their sizes, dipole moments, and the number of N─H bonds, it is possible to interpret the heat maps as consequences of these characteristics. This work brings a systematization of how obtaining specific properties of halide perovskites might be possible by customizing the characteristics of the A-site organic cations.

Non-Isothermal Crystallization Kinetics and Activation Energy for Crystal Growth of Polyamide 66/Short Glass Fiber/Carbon Black Composites.

This study presents the effect of the addition of 0.4 wt.% carbon black (CB) to polyamide 66 (PA66) containing 30 wt.% short glass fibers (GFs) on the behavior of composite thermal crystallization. Composites were studied by differential scanning calorimetry analysis (DSC) at different cooling rates using wide-angle X-ray scattering (WAXS) and scanning electron microscopy (SEM). This thermal crystallization study highlights the nucleation effect of GFs that promote PA66 crystallization by significantly increasing crystallization kinetics and rates. The activation energies (Eas) calculated by model-free (FWO; KAS) and model-fitting (Kissinger method and C-R method) approaches showed that the combination of both GF and CB decreases the activation energy with respect to neat PA66, meaning that the presence of both additives facilitates crystallization. The Coats-Redfern and Criado methods showed that the crystallization of neat PA66 and related composites follows the second-order reaction, i.e., the decelerated reaction, evidencing compatibility between GFs and the matrix.

Catalysis of the Nitroso-Diels-Alder cycloaddition reaction between CH3N=O and cis-1,3-butadiene by pnictogen bonding, a theoretical study.

Density functional theory calculations at the M06-2X/aug-cc-pVTZ level of theory have been used to examine the Nitroso-Diels-Alder (N-D-A) cycloaddition reaction between the CH3N=O and cis-1,3-butadiene in the presence of PO2X (X=F, Cl, OH) as a catalyst. The effect of the above PO2X compounds on the activation energy of the N-D-A reaction, has been studied here. In the first stage, the energies of two different bonding interactions, via P⋯N versus P⋯O binding, between the PO2X and CH3N=O molecules were calculated. The results showed that the largest values of the interaction energy between the above molecules belong to the PO2F, when connects to the nitrogen atom of the CH3N=O. Also, calculations showed that all the above PO2X compounds, decrease the activation energies of N-D-A reaction studied here via both P⋯N and P⋯O interactions. However, the largest effect on activation energies of the reaction belongs to the PO2F catalyst when acts via P⋯N bonding. The activation strain model (ASM) was used to analyze the influence of the PO2X catalyst on the studied reaction. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis were performed to understand the nature of forming interactions at the TS structures. The results of this study showed that the PO2X (X=F, Cl, OH) compounds may be suggested as efficient catalysts for N-D-A reactions.

Chlorination of amides: Kinetics and mechanisms of formation of N-chloramides and their reactions with phenolic compounds.

Amides are common constituents in natural organic matter and synthetic chemicals. In this study, we investigated kinetics and mechanisms of the reactions of chlorine with seven amides, including acetamide, N-methylformamide, N-methylacetamide, benzamide, N-methylbenzamide, N-propylbenzamide, and N-(benzoylglycyl)glycine amide. Apparent second-order rate constants for the reactions of the amides with chlorine at pH 8 are in the range of 5.8 × 10-3 - 1.8 M-1s-1 and activation energies in the range of 62-88 kJ/mol. The second-order rate constants for the reactions of chlorine with different amides decrease with increasing electron donor character of the substituents on the amide-N and N-carbonyl-C in the amide structures. Hypochlorite (‒OCl) dominates the reactions of chlorine with amides yielding N-chloramides with species-specific second-order rate constants in the range of 7.3 × 10-3 - 2.3 M-1s-1. Kinetic model simulations suggest that N-chlorinated primary amides further react with HOCl with second-order rate constants in the order of 10 M-1s-1. The chlorination products of amides, N-chloramides are reactive towards phenolic compounds, forming chlorinated phenols via electrophilic aromatic substitution (phenol and resorcinol) and quinone via electron transfer (hydroquinone). Meanwhile, N-chloramides were recycled to the parent amides. At neutral pH, apparent second-order rate constants for the reactions between phenols and N-chloramides are in the order of 10-4-0.1 M-1s-1, comparable to those with chloramine. The findings of this study improve the understanding of the fate of amides and chlorine during chlorination processes.

Omnibearing Interpretation of External Ions Passivated Ion Migration in Mixed Halide Perovskites.

Fundamental understanding of ion migration inside perovskites is of vital importance for commercial advancements of photovoltaics. However, the mechanism for external ions incorporation and its effect on ion migration remains elusive. Herein, taking K+ and Cs+ co-incorporated mixed halide perovskites as a model, the impact of external ions on ion migration behavior has been interpreted via multiple dimensional characterization aspects. The space-effect on phase segregation inhibition has been revealed by the photoluminescence evolution and in situ dynamic cathodoluminescence behaviors. The plane-effect on current suppression along grain boundary has been evidenced via visualized surface current mapping, local current hysteresis, and time-resolved current decay. And the point-effect on activation energy incremental for individual ions has been also probed by cryogenic electronic quantification. All these results sufficiently demonstrate the passivated ion migration results in the eventually improved phase stability of perovskite, of which the origin lies in various ion migration energy barriers.

Kinetics of CBD, Δ9-THC Degradation and Cannabinol Formation in Cannabis Resin at Various Temperature and pH Conditions.

Introduction: Cannabidiol (CBD), cannabinol (CBN), and Δ9-tetrahydrocannabinol (Δ9-THC) are major cannabinoids in cannabis resin and products. The kinetic of the chemical reaction of resin cannabis is important for product development and storage. A few reports are available in the literature on the rate of CBD and Δ9-THC degradation, and CBN formation in dried resin and solutions of various pH. Materials and Methods: Thermal degradation of CBD, Δ9-THC, and formation of CBN was studied at 50°C, 60°C, 70°C, and 80°C for dried cannabis resin. The effect of pH and temperature on cannabinoids transformation in cannabis solution was also examined at pH 2, 4, 6, 8, 10, and 12 and at 40°C, 50°C, 60°C, and 70°C. High-performance chromatography coupled with diode-array detection (HPLC-DAD) was used for the analysis of CBD, CBN, and Δ9-THC transformation. The values of activation energies (Ea), shelf-life (t90% - t110%), and rate constant (k) were calculated for the CBD, Δ9-THC, and CBN. The effect of temperature and pH on the dried cannabis resin was adequately modeled with the Arrhenius equation. Results: The results indicated that the chemical kinetics in the thermal degradation of CBD, Δ9-THC, and formation of CBN were the zero-order, pseudo-zero-order, and first-order reactions, respectively, in cannabis resin. The first-order and pseudo-first-order degradation kinetics were evidenced for CBD and Δ9-THC, respectively, in cannabis solutions, whereas the zero-order formation kinetic was detected for the CBN. The transformation rate of the CBD, CBN, and Δ9-THC increased with increasing temperature, especially as temperature increased to 70°C at pH 2.0. The optimum pH for CBD stability was between pH 4 and 6, whereas the optimum pH for Δ9-THC stability was between pH 4 and 12. Conclusion: The major cannabinoids (CBD, CBN, and Δ9-THC) reacted more quickly at high temperature and in an acidic solution. Especially, the minimum transformation of CBD, CBN, and Δ9-THC was achieved by using on a low temperature, slightly to moderately acidic pH values, and short-time processing. These results may help to improve the storage condition of CBD, CBN, and Δ9-THC products and in the manufacturing process.

Heterotrophic bacterioplankton responses in coral- and algae-dominated Red Sea reefs show they might benefit from future regime shift.

In coral reefs, dissolved organic matter (DOM) cycling is a critical process for sustaining ecosystem functioning. However, global and local stressors have caused persistent shifts from coral- to algae-dominated benthic communities. The influence of such phase shifts on DOM nature and its utilization by heterotrophic bacterioplankton remains poorly studied. Every second month for one year, we retrieved seawater samples enriched in DOM produced by coral- and algae-dominated benthic communities in a central Red Sea reef during a full annual cycle. Seawater incubations were conducted in the laboratory under in situ temperature and light conditions by inoculating enriched DOM samples with bacterial assemblages collected in the surrounding waters. Dissolved organic carbon (DOC) concentrations were higher in the warmer months (May-September) in both communities, resulting in higher specific growth rates and bacterial growth efficiencies (BGE). However, these high summer values were significantly enhanced in algal-DOM relative to coral-DOM, suggesting the potential for bacterioplankton biomass increase in reefs with algae replacing healthy coral cover under warmer conditions. The potential exacerbation of heterotrophic bacterial activity in the ongoing widespread regime shift from coral- to algae-dominated communities may have detrimental consequences for the overall health of tropical coral reefs.

Mass Spectrometric Analysis of Antibody-Epitope Peptide Complex Dissociation: Theoretical Concept and Practical Procedure of Binding Strength Characterization.

Electrospray mass spectrometry is applied to determine apparent binding energies and quasi equilibrium dissociation constants of immune complex dissociation reactions in the gas phase. Myoglobin, a natural protein-ligand complex, has been used to develop the procedure which starts from determining mean charge states and normalized and averaged ion intensities. The apparent dissociation constant KD m0g#= 3.60 × 10-12 for the gas phase heme dissociation process was calculated from the mass spectrometry data and by subsequent extrapolation to room temperature to mimic collision conditions for neutral and resting myoglobin. Similarly, for RNAse S dissociation at room temperature a KD m0g#= 4.03 × 10-12 was determined. The protocol was tested with two immune complexes consisting of epitope peptides and monoclonal antibodies. For the epitope peptide dissociation reaction of the FLAG peptide from the antiFLAG antibody complex an apparent gas phase dissociation constant KD m0g#= 4.04 × 10-12 was calculated. Likewise, an apparent KD m0g#= 4.58 × 10-12 was calculated for the troponin I epitope peptide-antiTroponin I antibody immune complex dissociation. Electrospray mass spectrometry is a rapid method, which requires small sample amounts for either identification of protein-bound ligands or for determination of the apparent gas phase protein-ligand complex binding strengths.

A Guide to Tracking Single Membrane Proteins and Their Interactions in Supported Lipid Bilayers.

The purpose of this chapter is to serve as a guide for those who wish to carry out experiments tracking single proteins in planar supported biomimetic membranes. This chapter describes, in detail, the construction of a simple single molecule microscope, which includes: (1) a parts list, (2) temperature control, (3) an alignment procedure, (4) a calibration procedure, and (5) a procedure for measuring the mechanical stability of the instrument. It also gives procedures for making planar supported bilayers on hydrophilically treated borosilicate and quartz. These include (1) POPC bilayers, (2) POPC/PEG-PE cushioned bilayers, (3) POPC/PEG-PE cushioned bilayers on BSA passivated substrates, and (4) a cushioned biomimetic membrane of the endoplasmic reticulum (ER). A procedure for the detergent mediated incorporation of the transmembrane protein 5HT3A (a serotonin receptor) is also described and can be used as a starting point for other large non-self-inserting transmembrane proteins. A procedure for the detergent-free incorporation of cytochrome P450 reductase (CPR) and cytochrome P450 enzymes (P450) into an ER biomimetic is also described. The final experimental section of this chapter details different procedures for data analysis including (1) quantitative analysis of mean squared displacements from individually tracked proteins, (2) gamma distribution analysis of diffusion coefficients from a small ensemble of individually tracked proteins, (3) average mean squared displacement analysis, (4) Gaussian analysis of step-size distributions, (5) Arrhenius analysis of temperature dependent data, (6) the determination of equilibrium constants from a step-size distribution, and (7) a perspective associated with the interpretation of single particle tracking data.

Energetics and Kinetics of S-State Transitions Monitored by Delayed Chlorophyll Fluorescence.

Understanding energetic and kinetic parameters of intermediates formed in the course of the reaction cycle (S-state cycle) of photosynthetic water oxidation is of high interest and could support the rationale designs of artificial systems for solar fuels. We use time-resolved measurements of the delayed chlorophyll fluorescence to estimate rate constants, activation energies, free energy differences, and to discriminate between the enthalpic and the entropic contributions to the decrease of the Gibbs free energy of the individual transitions. Using a joint-fit simulation approach, kinetic parameters are determined for the reaction intermediates in the S-state transitions in buffers with different pH in H2O and in D2O.

Thermal Degradation and Flame Retardant Mechanism of the Rigid Polyurethane Foam Including Functionalized Graphene Oxide.

A flame retardant rigid polyurethane foam (RPUF) system containing functionalized graphene oxide (fGO), expandable graphite (EG), and dimethyl methyl phosphonate (DMMP) was prepared and investigated. The results show that the limiting oxygen index (LOI) of the flame-retardant-polyurethane-fGO (FRPU/fGO) composites reached 28.1% and UL-94 V-0 rating by adding only 0.25 g fGO. The thermal degradation of FRPU samples was studied using thermogravimetric analysis (TG) and the Fourier transform infrared (FT-IR) analysis. The activation energies (Ea) for the main stage of thermal degradation were obtained using the Kissinger equation. It was found that the fGO can considerably increase the thermal stability and decrease the flammability of RPUF. Additionally, the Ea of FRPU/fGO reached 191 kJ·mol-1, which was 61 kJ·mol-1 higher than that of the pure RPUF (130 kJ·mol-1). Moreover, scanning electron microscopy (SEM) results showed that fGO strengthened the compactness and the strength of the "vermicular" intumescent char layer improved the insulation capability of the char layer to gas and heat.

Two models based on local microscopic relaxations to explain long-term basic creep of concrete.

In this study, we propose an exhaustion model and an adapted work-hardening model to explain the long-term basic creep of concrete. In both models, the macroscopic creep strain originates from local microscopic relaxations. The two models differ in how the activation energies of those relaxations are distributed and evolve during the creep process. With those models, at least up to a few dozen MPa, the applied stress must not modify the rate at which those relaxations occur, but only enables the manifestation of each local microscopic relaxation into an infinitesimal increment of basic creep strain. The two models capture equally well several phenomenological features of the basic creep of concrete. They also make it possible to explain why the indentation technique enables the quantitative characterization of the long-term kinetics of logarithmic creep of cement-based materials orders of magnitude faster than by macroscopic testing. The models hint at a physical origin for the relaxations that is related to disjoining pressures.

Fast Surface Acoustic Wave-Based Sensors to Investigate the Kinetics of Gas Uptake in Ultra-Microporous Frameworks.

Observation of the kinetics and measurement of the activation energies for gas diffusion in porous materials requires very fast and sensitive sensors. In this work, thin films of metal-organic frameworks (MOFs) with different pore sizes are grown on a surface acoustic wave (SAW) substrate, resulting in very sensitive and specific sensor systems for the detection of various gases at very short time scales. Using specially designed SAW delay lines for the detection, up to 200-nm-wide cubic MOF crystals were grown directly from a solution on the sensitive sensor chip area. One example, MFU-4, exhibits a smallest pore aperture of 2.5 Å and shows a highly sensitive and specific response to CO2, H2, He, NH3, and H2O. It is shown that such a MOF@SAW sensor responds within milliseconds to gas loading and its sensitivity reaches levels as low as 1 ppmv, currently only limited by the gas mixing system. This unique combination of sensitivity and fast response characteristics allows even for real-time investigations of the sorption kinetics during gas uptake and release. As is typical for SAW sensors, the production of the chips is very straightforward and inexpensive and-combined with the unique properties of the MOFs with their tunable pore sizes and adjustable internal surface properties-holds promise for different sensor applications.

Isothermal titration calorimetry determination of individual rate constants of trypsin catalytic activity.

Determination of individual rate constants for enzyme-catalyzed reactions is central to the understanding of their mechanism of action and is commonly obtained by stopped-flow kinetic experiments. However, most natural substrates either do not fluoresce/absorb or lack a significant change in their spectra while reacting and, therefore, are frequently chemically modified to render adequate molecules for their spectroscopic detection. Here, isothermal titration calorimetry (ITC) was used to obtain Michaelis-Menten plots for the trypsin-catalyzed hydrolysis of several substrates at different temperatures (278-318K): four spectrophotometrically blind lysine and arginine N-free esters, one N-substituted arginine ester, and one amide. A global fitting of these data provided the individual rate constants and activation energies for the acylation and deacylation reactions, and the ratio of the formation and dissociation rates of the enzyme-substrate complex, leading also to the corresponding free energies of activation. The results indicate that for lysine and arginine N-free esters deacylation is the rate-limiting step, but for the N-substituted ester and the amide acylation is the slowest step. It is shown that ITC is able to produce quality kinetic data and is particularly well suited for those enzymatic reactions that cannot be measured by absorption or fluorescence spectroscopy.

A hydrogen bond network in the active site of Anabaena ferredoxin-NADP(+) reductase modulates its catalytic efficiency.

Ferredoxin-nicotinamide-adenine dinucleotide phosphate (NADP(+)) reductase (FNR) catalyses the production of reduced nicotinamide-adenine dinucleotide phosphate (NADPH) in photosynthetic organisms, where its flavin adenine dinucleotide (FAD) cofactor takes two electrons from two reduced ferredoxin (Fd) molecules in two sequential steps, and transfers them to NADP(+) in a single hydride transfer (HT) step. Despite the good knowledge of this catalytic machinery, additional roles can still be envisaged for already reported key residues, and new features are added to residues not previously identified as having a particular role in the mechanism. Here, we analyse for the first time the role of Ser59 in Anabaena FNR, a residue suggested by recent theoretical simulations as putatively involved in competent binding of the coenzyme in the active site by cooperating with Ser80. We show that Ser59 indirectly modulates the geometry of the active site, the interaction with substrates and the electronic properties of the isoalloxazine ring, and in consequence the electron transfer (ET) and HT processes. Additionally, we revise the role of Tyr79 and Ser80, previously investigated in homologous enzymes from plants. Our results probe that the active site of FNR is tuned by a H-bond network that involves the side-chains of these residues and that results to critical optimal substrate binding, exchange of electrons and, particularly, competent disposition of the C4n (hydride acceptor/donor) of the nicotinamide moiety of the coenzyme during the reversible HT event.

Pushing the Limit of Infrared Multiphoton Dissociation to Megadalton-Size DNA Ions.

We report the use of infrared multiphoton dissociation (IRMPD) for the determination of relative activation energies for unimolecular dissociation of megadalton DNA ions. Single ions with masses in the megadalton range were stored in an electrostatic ion trap for a few tens of milliseconds and the image current generated by the roundtrips of ions in the trap was recorded. While being trapped, single ions were irradiated by a CO2 laser and fragmented, owing to multiphoton IR activation. The analysis of the single-ion image current during the heating period allows us to measure changes in the charge of the trapped ion. We estimated the activation energy associated with the dissociation of megadalton-size DNA ions in the frame of an Arrhenius-like model by analyzing a large set of individual ions in order to construct a frequency histogram of the dissociation rates for a collection of ions.

SU-E-T-89: Characterization of Dental Restoration Material for Cs-137 Radiation Dosimetry.

PURPOSE: The purpose of this work is to characterize the radiation-induced thermoluminescence properties of a dental restoration material and to see if the material might be feasible for use in retrospective radiation dosimetry. METHODS: Retrospective, or accidental, dosimetry is the study of using nearby materials to measure radiation received by individuals. In this project we obtained samples of Ivoclar Vivadent e.max CAD material, a glass-ceramic used for making dental restorations such as full or partial crowns. The samples were machined into square chips .32 cm × .32 cm × .089 cm and annealed in the same furnace used by the dentist. The samples were exposed to a Cs-137 source using a PMMA source holder and then read in a Harshaw 3500 TLD reader. The samples were read without nitrogen gas flux using heating rates of 5 degrees C/s or 10 degrees C/s up to a maximum temperature of 400 degrees Celsius. The glow curves were analyzed using Systat PeakFIT peak-fitting software and Microsoft Excel spreadsheets. The authors gratefully thank Dr. Aaron Imdieke and the staff of River City Dental, St. Cloud, MN for the dental restoration materials and the use of their dental furnace. RESULTS: A sample subjected to a radiation exposure of .04 C/kg exhibits a glow curve with a prominent peak at approximately 140 degrees Celsius, which is well-modeled by the first order glow curve deconvolution formula developed by Kitis, Gomez-Ros, and Tuyn. The activation energy corresponding to this peak is approximately 1 eV. The thermoluminescent signal fades with time after exposure. CONCLUSIONS: Ivoclar Vivadent e.max CAD dental restoration material has the potential to be used as a material for retrospective Cs-137 radiation dosimetry. Future work could look at its thermoluminescent dosimetry properties in more detail and also at other dental restoration materials. The authors would like to thank Dr. Aaron Imdieke and the staff of River City Dental, St. Cloud, MN, for the donation of scrap dental restoration materials and the use of their dental furnace.