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Thermodynamics is a universal science. The language of thermodynamics is energy and its derivatives such as entropy and power. The physical theory of thermodynamics reigns across a full spectrum of non-living objects as well as living beings. In the traditions of the past, the dichotomy between matter and life resulted in the natural sciences studying matter while the social sciences focused on living beings. As the state of human knowledge continues to evolve, anticipating the sciences of matter (natural science) and of life (social science) becoming unified under a single overarching theory is not unnatural. This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 1)'.

This article describes the utilization of laminar microflows for time-resolved emission measurements with steady-state excitation and detection. Passing a laminar flow through a short illuminated section of a microchannel provided a means for pulsed-like photoexcitation of the moieties carried by the fluid. Imaging the microchannel flows carrying thus photoexcited chelates of lanthanide ions allowed us to extract their excited-state lifetimes from the spatial distribution of the changes in the emission intensity. The lifetime values obtained using this space-domain approach agreed well with the lifetimes from time-domain measurements. This validated space-domain microfluidic approach reveals a means for miniaturization of time-resolved emission spectroscopy.

Green fluorescent protein (GFP) fluoresces efficiently under blue excitation despite major electrostatic rearrangements resulting from photoionization of the chromophore and neutralization of Glu-222. A competing phototransformation process, which ionizes the chromophore and decarboxylates Glu-222, mimics the electrostatic and structural changes in the fluorescence photocycle. Structural and spectroscopic analysis of the cryogenically stabilized photoproduct at 100 K and a structurally annealed intermediate of the phototransformed protein at 170 K reveals distinct structural relaxations involving protein, chromophore, solvent, and photogenerated CO2. Strong structural changes of the 100 K photoproduct after decarboxylation appear exclusively within 15 angstroms of the chromophore and include the electrostatically driven perturbations of Gln-69, Cys-70, and water molecules in an H-bonding network connecting the chromophore. X-ray crystallography to 1.85 angstroms resolution and static and picosecond time-resolved IR spectroscopy identify structural mechanisms common to phototransformation and to the fluorescence photocycle. In particular, the appearance of a 1697 cm(-1) (+) difference band in both photocycle and phototransformation intermediates is a spectroscopic signature for the structural perturbation of Gln-69. This is taken as evidence for an electrostatically driven dynamic response that is common to both photoreaction pathways. The interactions between the chromophore and the perturbed residues and solvent are decreased or removed in the T203H single and T203H/Q69L double mutants, resulting in a strong reduction of the fluorescence quantum yield. This suggests that the electrostatic response to the transient formation of a buried charge in the wild type is important for the bright fluorescence.

We use nuclear resonance vibrational spectroscopy (NRVS) to identify the Fe-NO stretching frequency in the NO adduct of myoglobin (MbNO) and in the related six-coordinate porphyrin Fe(TPP)(1-MeIm)(NO). Frequency shifts observed in MbNO Raman spectra upon isotopic substitution of Fe or the nitrosyl nitrogen confirm and extend the NRVS results. In contrast with previous assignments, the Fe-NO frequency of these six-coordinate complexes lies 70-100 cm-1 lower than in the analogous five-coordinate nitrosyl complexes, indicating a significant weakening of the Fe-NO bond in the presence of a trans imidazole ligand. This result supports proposed mechanisms for NO activation of heme proteins and underscores the value of NRVS as a direct probe of metal reactivity in complex biomolecules.

The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H(p), to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: DeltaG(D) approximately 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin ( approximately 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H(D) approximately 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).

We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound heme complexes to study proximal and distal influences on ligand rebinding kinetics. We report kinetics of CO rebinding to microperoxidase (MP) and 2-methylimidazole ligated Fe protoporphyrin IX in the 10 ns to 10 ms time window. We also report CO rebinding kinetics of MP in the 150 fs to 140 ps time window. For dilute, micelle-encapsulated (monodisperse) samples of MP, we do not observe the large amplitude geminate decay at approximately 100 ps previously reported in time-resolved IR measurements on highly concentrated samples [Lim, M., Jackson, T. A., and Anfinrud, P. A. (1997) J. Biol. Inorg. Chem. 2, 531-536]. However, for high concentration aggregated samples, we do observe the large amplitude picosecond CO geminate rebinding and find that it is correlated with the absence of the iron-histidine vibrational mode in the time-resolved Raman spectrum. On the basis of these results, the energetic significance of a putative distal pocket CO docking site proposed by Lim et al. may need to be reconsidered. Finally, when high concentration samples of native myoglobin (Mb) were studied as a control, an analogous increase in the geminate rebinding kinetics was not observed. This verifies that studies of Mb under dilute conditions are applicable to the more concentrated regime found in the cellular milieu.