Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.     

Identification and properties of the 1La and 1Lb states of pyranine

The spectroscopic locations of the 1La and 1Lb electronic states of pyranine (1-hydroxy-3,6,8-pyrenetrisulfonic acid, commonly referred to as HPTS), as well as several related compounds, are found using magnetic circular dichroism spectroscopy as well as absorption and fluorescence spectroscopies. These electronic states have been discussed in connection with the photoacid properties of HPTS. Polarization selective fluorescence spectroscopy is used to identify the transition dipole directions of the electronic states of the compounds studied. The issue of the origin for the changes in vibronic structure of HPTS in different solvents is addressed. It is demonstrated that a Brownian oscillator model, in which the strength of the coupling of the electronic states to the solvent changes with solvent, is sufficient to reproduce the trends in the shapes of the vibronic structure.     

Proton transport and the water environment in nafion fuel cell membranes and AOT reverse micelles

The properties of confined water and diffusive proton-transfer kinetics in the nanoscopic water channels of Nafion fuel cell membranes at various hydration levels are compared to water in a series of well-characterized AOT reverse micelles with known water nanopool sizes using the photoacid pyranine as a molecular probe. The side chains of Nafion are terminated by sulfonate groups with sodium counterions that are arrayed along the water channels. AOT has sulfonate head groups with sodium counterions that form the interface with the reverse micelle's water nanopool. The extent of excited-state deprotonation is observed by steady-state fluorescence measurements. Proton-transfer kinetics and orientational relaxation are measured by time-dependent fluorescence using time-correlated single photon counting. The time dependence of deprotonation is related to diffusive proton transport away from the photoacid. The fluorescence reflecting the long time scale proton transport has an approximately t-0.8 power law decay in contrast to bulk water, which has a t-3/2 power law. For a given hydration level of Nafion, the excited-state proton transfer and the orientational relaxation are similar to those observed for a related size AOT water nanopool. The effective size of the Nafion water channels at various hydration levels are estimated by the known size of the AOT reverse micelles that display the corresponding proton-transfer kinetics and orientational relaxation.     

Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations

Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.     

Formation and dissociation of intra-intermolecular hydrogen-bonded solute-solvent complexes: chemical exchange two-dimensional infrared vibrational echo spectroscopy

2-Methoxyphenol (2MP) solutes form weak complexes with toluene solvent molecules. The complexes are unusual in that the 2MP hydroxyl has an intramolecular hydrogen bond and simultaneously forms an intermolecular hydrogen bond with toluene and other aromatic solvents. In the equilibrated solute-solvent solution, there exists approximately the same concentration of 2MP-toluene complex and free 2MP. The very fast formation and dissociation (chemical exchange) of this type of three-centered hydrogen bond complex were observed in real time under thermal equilibrium conditions with two-dimensional (2D) infrared vibrational echo spectroscopy. Chemical exchange is manifested in the 2D spectrum by the growth of off-diagonal peaks. Both the formation and dissociation can be characterized in terms of the dissociation time constant, which was determined to be 3 ps for the 2MP-toluene complex. The intra-intermolecular hydrogen bond formation is influenced by subtle details of the molecular structure. Although 2MP forms a complex with toluene, it is demonstrated that 2-ethoxyphenol (2EP) does not form complexes to any significant extent. Density functional calculations at the B3LYP/6-31+G(d,p) level suggest that steric effects caused by the extra methyl group in 2EP are responsible for the difference.     

What nonlinear-IR experiments can tell you about water that the IR spectrum cannot

Frequently, the IR spectrum of water is used to characterize the structure and strength of the associated hydrogen bond network. Here, we use nonlinear-IR spectroscopy to investigate the dynamics of four aqueous systems that have very similar absorption spectra. We address the question: to what extent can the dynamics of water vary in systems with very similar absorption spectra? The results illustrate that the vibrational lifetimes and orientational relaxation time scales vary dramatically between the four samples and do not correlate with the amount of water relative to surfactant or solute in solution. Nonlinear-IR spectroscopies are therefore important for providing detailed information necessary to understand hydrogen bonded systems.     

Dynamics of a discotic liquid crystal in the isotropic phase

Optically heterodyne-detected optical Kerr effect (OHD-OKE) experiments are conducted to study the orientational dynamics of a discotic liquid crystal 2,3,6,7,10,11-hexakis(pentyloxy)triphenylene (HPT) in the isotropic phase near the columnar-isotropic (C-I) phase transition. The OHD-OKE signal of HPT is characterized by an intermediate power law t(-0.76+/-0.02) at short times (a few picoseconds), a von Schweidler power law t(-0.26+/-0.01) at intermediate times (hundreds of picoseconds), and an exponential decay at long times (tens of nanoseconds). The exponential decay has Arrhenius temperature dependence. The functional form of the total time dependent decay is identical to the one observed previously for a large number of molecular supercooled liquids. The mode coupling theory schematic model based on the Sjogren [Phys. Rev. A 33, 1254 (1986)] model is able to reproduce the HPT data over a wide range of times from <1 ps to tens of nanoseconds. The studies indicate that the HPT C-I phase transition is a strong first order transition, and the dynamics in the isotropic phase display a complex time dependent profile that is common to other molecular liquids that lack mesoscopic structure.     

Dynamics in supercooled ionic organic liquids and mode coupling theory analysis

Optically heterodyne-detected optical Kerr effect experiments are applied to study the orientational dynamics of the supercooled ionic organic liquids N-propyl-3-methylpyridinium bis(trifluoromethylsulfonyl)imide (PMPIm) and 1-ethyl-3-methylimidazolium tosylate (EMImTOS). The orientational dynamics are complex with relaxation involving several power law decays followed by a final exponential decay. A mode coupling theory (MCT) schematic model, the Sj?gren model, was able to reproduce the PMPIm data very successfully over a wide range of times from 1 ps to hundreds of ns for all temperatures studied. Over the temperature range from room temperature down to the critical temperature Tc of 231 K, the OHD-OKE signal of PMPIm is characterized by the intermediate power law t(-1.00+/-0.04) at short times, a von Schweidler power law t(-0.51+/-0.03) at intermediate times, and a highly temperature-dependent exponential (alpha relaxation) at long times. This form of the decay is identical to the form observed previously for a large number of organic van der Waals liquids. MCT analysis indicates that the theory can explain the experimental data very well for a range of temperatures above Tc, but as might be expected, there are some deviations from the theoretical modeling at temperatures close to Tc. For EMImTOS, the orientational dynamics were studied on the ps time scale in the deeply supercooled region near its glass transition temperature. The orientational relaxation of EMImTOS clearly displays the feature associated with the boson peak at approximately 2 ps, which is the first time domain evidence of the boson peak in ionic organic liquids. Overall, all the dynamical features observed earlier for organic van der Waals liquids using the same experimental technique are also observed for organic ionic liquids.     

Cytochrome c552 mutants: structure and dynamics at the active site probed by multidimensional NMR and vibration echo spectroscopy

Spectrally resolved infrared stimulated vibrational echo experiments are used to measure the vibrational dephasing of a CO ligand bound to the heme cofactor in two mutated forms of the cytochrome c552 from Hydrogenobacter thermophilus. The first mutant (Ht-M61A) is characterized by a single mutation of Met61 to an Ala (Ht-M61A), while the second variant is doubly modified to have Gln64 replaced by an Asn in addition to the M61A mutation (Ht-M61A/Q64N). Multidimensional NMR experiments determined that the geometry of residue 64 in the two mutants is consistent with a non-hydrogen-bonding and hydrogen-bonding interaction with the CO ligand for Ht-M61A and Ht-M61A/Q64N, respectively. The vibrational echo experiments reveal that the shortest time scale vibrational dephasing of the CO is faster in the Ht-M61A/Q64N mutant than that in Ht-M61A. Longer time scale dynamics, measured as spectral diffusion, are unchanged by the Q64N modification. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to confirm that the dynamical difference induced by the Q64N mutation is primarily an increase in the fast (hundreds of femtoseconds) frequency fluctuations, while the slower (tens of picoseconds) dynamics are nearly unaffected. We conclude that the faster dynamics in Ht-M61A/Q64N are due to the location of Asn64, which is a hydrogen bond donor, above the heme-bound CO. A similar difference in CO ligand dynamics has been observed in the comparison of the CO derivative of myoglobin (MbCO) and its H64V variant, which is caused by the difference in axial residue interactions with the CO ligand. The results suggest a general trend for rapid ligand vibrational dynamics in the presence of a hydrogen bond donor.