Protein gas-phase

The simulation correctly reproduces the closeness of the gas phase and protein absorption A. Geometry optimizations in the different environments indicate that the protein, gas phase and solution spectral features are related to the nature of the chromophore structure. Notice that, remarkably, as shown in Fig. 12.7, the equilibrium structures in the protein (Fig. 12.7a) and in the gas phase (Fig. 12.7c) display close absorption maxima in spite of the different geometrical structures. In contrast, the solution equilibrium structure (Fig. 12.7b) differs dramatically. Thus, even the geometrical analysis is consistent with the spectroscopy. 

The CASSCF/AMBER method allows for geometry optimization on the excited state. Thus, we can also predict the emission maxima. The results, schematically illustrated in Scheme 12.5, indicate that the protein/gas-phase similarity also holds for the emission suggesting that the protein matrix mimics the gas phase even for the relaxed excited state chromophore. 

In the present case, each endpoint involves—in addition to the fully interacting solute—an intact side chain fragment without any interactions with its environment. This fragment is equivalent to a molecule in the gas phase (acetamide or acetate) and contributes an additional term to the overall free energy that is easily calculated from ideal gas statistical mechanics [18]. This contribution is similar but not identical at the two endpoints. However, the corresponding contributions are the same for the transfonnation in solution and in complex with the protein therefore, they cancel exactly when the upper and lower legs of the thermodynamic cycle are subtracted (Fig. 3a). 

Proteins do not exist as isolated entities in the gas phase. They are always solvated by water molecules or embedded in membranes. Trying to obtain a... 

In addition to chemical reactions, the isokinetic relationship can be applied to various physical processes accompanied by enthalpy change. Correlations of this kind were found between enthalpies and entropies of solution (20, 83-92), vaporization (86, 91), sublimation (93, 94), desorption (95), and diffusion (96, 97) and between the two parameters characterizing the temperature dependence of thermochromic transitions (98). A kind of isokinetic relationship was claimed even for enthalpy and entropy of pure substances when relative values referred to those at 298° K are used (99). Enthalpies and entropies of intermolecular interaction were correlated for solutions, pure liquids, and crystals (6). Quite generally, for any temperature-dependent physical quantity, the activation parameters can be computed in a formal way, and correlations between them have been observed for dielectric absorption (100) and resistance of semiconductors (101-105) or fluidity (40, 106). On the other hand, the isokinetic relationship seems to hold in reactions of widely different kinds, starting from elementary processes in the gas phase (107) and including recombination reactions in the solid phase (108), polymerization reactions (109), and inorganic complex formation (110-112), up to such biochemical reactions as denaturation of proteins (113) and even such biological processes as hemolysis of erythrocytes (114). 

Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YXX, Murphy RB, Zhou RH, Halgren TA (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry first generation model and gas phase tests. J Comput Chem 23(16) 1515—1531... 

A characteristic feature of ESMS is the detection of multiply charged analytes. Macromolecules, such as proteins have multiple sites where protonation or deprotonation (the two most common charge inducing mechanisms in electrospray—other routes to charge induction include, ionization through adduct formation, through gas-phase reactions, and through electrochemical oxidation or reduction) occur. These are desorbed effectively in ESMS and... 

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