Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy

Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy. (Graph Presented).

Computer control of chemical process plants with special reference to distillation

A sieve plate distillation column has been constructed and interfaced to a minicomputer with the necessary instrumentation for dynamic, estimation and control studies with special bearing on low-cost and noise-free instrumentation. A dynamic simulation of the column with a binary liquid system has been compiled using deterministic models that include fluid dynamics via Brambilla's equation for tray liquid holdup calculations. The simulation predictions have been tested experimentally under steady-state and transient conditions. The simulator's predictions of the tray temperatures have shown reasonably close agreement with the measured values under steady-state conditions and in the face of a step change in the feed rate. A method of extending linear filtering theory to highly nonlinear systems with very nonlinear measurement functional relationships has been proposed and tested by simulation on binary distillation. The simulation results have proved that the proposed methodology can overcome the typical instability problems associated with the Kalman filters. Three extended Kalman filters have been formulated and tested by simulation. The filters have been used to refine a much simplified model sequentially and to estimate parameters such as the unmeasured feed composition using information from the column simulation. It is first assumed that corrupted tray composition measurements are made available to the filter and then corrupted tray temperature measurements are accessed instead. The simulation results have demonstrated the powerful capability of the Kalman filters to overcome the typical hardware problems associated with the operation of on-line analyzers in relation to distillation dynamics and control by, in effect, replacirig them. A method of implementing estimator-aided feedforward (EAFF) control schemes has been proposed and tested by simulation on binary distillation. The results have shown that the EAFF scheme provides much better control and energy conservation than the conventional feedback temperature control in the face of a sustained step change in the feed rate or multiple changes in the feed rate, composition and temperature. Further extensions of this work are recommended as regards simulation, estimation and EAFF control.

Dynamic simulation of chemical plant

A CSSL- type modular FORTRAN package, called ACES, has been developed to assist in the simulation of the dynamic behaviour of chemical plant. ACES can be harnessed, for instance, to simulate the transients in startups or after a throughput change. ACES has benefited from two existing simulators. The structure was adapted from ICL SLAM and most plant models originate in DYFLO. The latter employs sequential modularisation which is not always applicable to chemical engineering problems. A novel device of twice- round execution enables ACES to achieve general simultaneous modularisation. During the FIRST ROUND, STATE-VARIABLES are retrieved from the integrator and local calculations performed. During the SECOND ROUND, fresh derivatives are estimated and stored for simultaneous integration. ACES further includes a version of DIFSUB, a variable-step integrator capable of handling stiff differential systems. ACES is highly formalised . It does not use pseudo steady- state approximations and excludes inconsistent and arbitrary features of DYFLO. Built- in debug traps make ACES robust. ACES shows generality, flexibility, versatility and portability, and is very convenient to use. It undertakes substantial housekeeping behind the scenes and thus minimises the detailed involvement of the user. ACES provides a working set of defaults for simulation to proceed as far as possible. Built- in interfaces allow for reactions and user supplied algorithms to be incorporated . New plant models can be easily appended. Boundary- value problems and optimisation may be tackled using the RERUN feature. ACES is file oriented; a STATE can be saved in a readable form and reactivated later. Thus piecewise simulation is possible. ACES has been illustrated and verified to a large extent using some literature-based examples. Actual plant tests are desirable however to complete the verification of the library. Interaction and graphics are recommended for future work.

Simultaneous chemical reaction and distillation of formaldehyde

The thesis is concerned with the development and testing of a mathematical model of a distillation process in which the components react chemically. The formaldehyde-methanol-water system was selected and only the reversible reactions between formaldehyde and water giving methylene glycol and between formaldehyde and methanol producing hemiformal were assumed to occur under the distillation conditions. Accordingly the system has been treated as a five component system. The vapour-liquid equilibrium calculations were performed by solving iteratively the thermodynamic relationships expressing the phase equilibria with the stoichiometric equations expressing the chemical equilibria. Using optimisation techniques, the Wilson single parameters and Henry's constants were calculated for binary systems containing formaldehyde which was assumed to be a supercritical component whilst Wilson binary parameters were calculated for the remaining binary systems. Thus the phase equilibria for the formaldehyde system could be calculated using these parameters and good accuracy was obtained when calculated values were compared with experimental values. The distillation process was modelled using the mass and energy balance equations together with the phase equilibria calculations. The plate efficiencies were obtained from a modified A.I.Ch.E. Bubble Tray method. The resulting equations were solved by an iterative plate to plate calculation based on the Newton Raphson method. Experiments were carried out in a 76mm I.D., eight sieve plate distillation column and the results were compared with the mathematical model calculations. Overall, good agreement was obtained but some discrepancies were observed in the concentration profiles and these may have been caused by the effect of limited physical property data and a limited understanding of the reactions mechanism. The model equations were solved in the form of modular computer programs. Although they were written to describe the steady state distillation with simultaneous chemical reaction of the formaldehyde system, the approach used may be of wider application.

Significant quantum effects in hydrogen activation

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature reveal completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H2 up to ∼190 K and for D2 up to ∼140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.

Designing intrinsically photostable low band gap polymers:a smart tool combining EPR spectroscopy and DFT calculations

A rapid and efficient method to identify the weak points of the complex chemical structure of low band gap (LBG) polymers, designed for efficient solar cells, when submitted to light exposure is reported. This tool combines Electron Paramagnetic Resonance (EPR) using the 'spin trapping method' coupled with density functional theory modelling (DFT). First, the nature of the short life-time radicals formed during the early-stages of photo-degradation processes are determined by a spin-trapping technique. Two kinds of short life-time radical (R and R′O) are formed after 'short-duration' illumination in an inert atmosphere and in ambient air, respectively. Second, simulation allows the identification of the chemical structures of these radicals revealing the most probable photochemical process, namely homolytical scission between the Si atom of the conjugated skeleton and its pendent side-chains. Finally, DFT calculations confirm the homolytical cleavage observed by EPR, as well as the presence of a group that is highly susceptible to photooxidative attack. Therefore, the synergetic coupling of a spin trapping method with DFT calculations is shown to be a rapid and efficient method for providing unprecedented information on photochemical mechanisms. This approach will allow the design of LBG polymers without the need to trial the material within actual solar cell devices, an often long and costly screening procedure.