Biomedical subjects

M D Fayer

Publications and source records attributed to M D Fayer.

At least 19 recordsLinked to original sources

PubMed2007

Deprotonation dynamics and stokes shift of pyranine (HPTS).

The short and intermediate time scale dynamics of the photoacid pyranine (1-hydroxy-3,6,8-pyrenetrisulfonic acid, commonly referred to as HPTS) are studied with visible pump-probe spectroscopy in various solvents to elucidate the nature of its proton-transfer kinetics in water. The observed time dependences of HPTS are compared with those of the methoxy derivative, MPTS. A global fitting procedure is employed to model both the spectral shift (Stokes shift) caused by solvent reorganization and deprotonation of pyranine in water. Three distinct time-dependent features can be clearly identified. They are the Stokes shift (1 ps in H(2)O and 1.5 ps in D(2)O), followed by the deprotonation processes, which gives rise to a biexponential decay of the protonated species with time constants (in H(2)O) of 3 and 88 ps. By the use of a model previously discussed in the literature, the biexponential process can be interpreted as an initial deprotonation step followed by the longer time scale process which separates the resulting ion pair. The results presented here are consistent with some of the previous reports but unambiguously identify and quantitatively measure the Stokes shift as a separate and distinct phenomenon from the deprotonation process, in contrast to other reports that have suggested that all short time (a few picoseconds) dynamics are merely a Stokes shift.

Journal Article↗

PubMed2007

Ultrafast 2D IR vibrational echo spectroscopy.

The experimental technique and applications of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy are presented. Using ultrashort infrared pulses and optical heterodyne detection to provide phase information, unique information can be obtained about the dynamics, interactions, and structures of molecular systems. The form and time evolution of the 2D IR spectrum permits examination of processes that cannot be studied with linear infrared absorption experiments. Three examples are given: organic solute-solvent complex chemical exchange, dynamics of the hydrogen-bond network of water, and assigning peaks in an IR spectrum of a mixture of species.

Journal Article↗

PubMed2006

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.

Benzene↗

PubMed2006

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.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

Ultrafast two-dimensional infrared vibrational echo chemical exchange experiments and theory.

Ultrafast two-dimensional (2D) infrared vibrational echo experiments and theory are used to examine chemical exchange between solute-solvent complexes and the free solute for the solute phenol and three solvent complex partners, p-xylene, benzene, and bromobenzene, in mixed solvents of the partner and CCl4. The experiments measure the time evolution of the 2D spectra of the hydroxyl (OD) stretching mode of the phenol. The time-dependent 2D spectra are analyzed using time-dependent diagrammatic perturbation theory with a model that includes the chemical exchange (formation and dissociation of the complexes), spectral diffusion of both the complex and the free phenol, orientational relaxation of the complexes and free phenol, and the vibrational lifetimes. The detailed calculations are able to reproduce the experimental results and demonstrate that a method employed previously that used a kinetic model for the volumes of the peaks is adequate to extract the exchange kinetics. The current analysis also yields the spectral diffusion (time evolution of the dynamic line widths) and shows that the spectral diffusion is significantly different for phenol complexes and free phenol.

Journal Article↗

PubMed2006

Ultrafast carbon-carbon single-bond rotational isomerization in room-temperature solution.

Generally, rotational isomerization about the carbon-carbon single bond in simple ethane derivatives in room-temperature solution under thermal equilibrium conditions has been too fast to measure. We achieved this goal using two-dimensional infrared vibrational echo spectroscopy to observe isomerization between the gauche and trans conformations of an ethane derivative, 1-fluoro-2-isocyanato-ethane (1), in a CCl4 solution at room temperature. The isomerization time constant is 43 picoseconds (ps, 10(-12) s). Based on this value and on density functional theory calculations of the barrier heights of 1, n-butane, and ethane, the time constants for n-butane and ethane internal rotation under the same conditions are approximately 40 and approximately 12 ps, respectively.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

Photoinduced electron transfer and geminate recombination in the group head region of micelles.

A pump-probe spectroscopic study of photoinduced forward electron transfer and geminate recombination between donors and acceptors located in the head group regions of micelles is presented. The hole donor is octadecyl-rhodamine B (ODRB) and the hole acceptor is N,N-dimethyl-aniline (DMA). The experiments are conducted as a function of the DMA concentration in the dodecyltrimethylammonium bromide and tetradecyltrimethylammonium bromide micelles. In spite of the fact that the absorptions of both the ODRB radical and ground state bleach spectrally overlap with the ODRB excited state absorption, a procedure that makes it possible to determine the geminate recombination dynamics is presented. These experiments are the first to measure the dynamics of geminate recombination in micelles, and the experiments have two orders of magnitude better time resolution than previous studies of forward transfer. The experimental data are compared to statistical mechanics theoretical calculations of both the forward transfer and the geminate recombination. The theory includes important aspects of the topology of the micelle and the diffusion of the donor-acceptors in the micelle head group region. A semiquantitative but nonquantitative agreement between theory and experiments is achieved.

Aniline Compounds↗

PubMed2006

Tracking water's response to structural changes in Nafion membranes.

As the water content of Nafion membranes increases, the local environments of water molecules change due to reorganization of the pendant side chains in the hydrophilic domains. Changes in local structure as a function of water content are studied by measuring the IR spectra and the vibrational lifetimes of the hydroxyl stretch of dilute HOD in H(2)O. The main features of the IR spectra are fit well by a weighted sum of the spectra of bulk water and almost dry Nafion, suggesting a two-environment model. An additional small peak on the high frequency side of the main band associated with non-hydrogen-bonded water embedded in the polymer near the interface is analyzed quantitatively as a function of the membrane water content. The spectra of this peak show that a significant reorganization of the interfacial region occurs when the water content of the membrane exceeds the threshold for ion conduction. Vibrational excited state population relaxation times (lifetimes) of the main band lengthen substantially as the water content of the membrane is decreased. The population decays are not single exponentials and indicate that multiple ensembles of water molecules exist, and the characteristics of the individual ensembles change with water content. This is in contrast to the spectra of the main water absorption band, which is only sensitive to two classes of water molecules.

Journal Article↗

PubMed2006

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy.

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.

Journal Article↗

PubMed2006

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.

Journal Article↗

PubMed2006

Photoinduced electron transfer and geminate recombination in liquids on short time scales: Experiments and theory.

The coupled processes of intermolecular photoinduced forward electron transfer and geminate recombination between the (hole) donor (Rhodamine 3B) and (hole) acceptors (N,N-dimethylaniline) are studied in three molecular liquids: acetonitrile, butyronitrile, and benzonitrile. Two color pump-probe experiments on time scales from approximately 100 fs to hundreds of picoseconds give information about the depletion of the donor excited state due to forward electron transfer and the survival kinetics of the radicals produced by forward electron transfer. The data are analyzed with a model presented previously that includes distance dependent forward and back electron transfer rates, donor and acceptor diffusion, solvent structure, and the hydrodynamic effect in a mean-field theory of through solvent electron transfer. The forward electron transfer is in the normal regime, and the Marcus equation for the distance dependence of the transfer rate is used. The forward electron transfer data for several concentrations in the three solvents are fitted to the theory with a single adjustable parameter, the electronic coupling matrix element Jf at contact. Within experimental error all concentrations in all three solvents are fitted with the same value of Jf. The geminate recombination (back transfer) is in the inverted region, and semiclassical treatment developed by Jortner [J. Chem. Phys. 64, 4860 (1976)] is used to describe the distance dependence of the back electron transfer. The data are fitted with the single adjustable parameter Jb. It is found that the value of Jb decreases as the solvent viscosity increases. Possible explanations are discussed.

Journal Article↗

PubMed2006

Three homeotropically aligned nematic liquid crystals: comparison of ultrafast to slow time-scale dynamics.

The dynamics of two nematic liquid crystals, 4-(trans-4(')-n-octylcyclohexyl)isothiocyanatobenzene and 4-(4-pentyl-cyclohexyl)-benzonitrile, are investigated as a function of temperature both in the homeotropically aligned nematic phase and in the isotropic phase using optical heterodyne-detected optical Kerr effect experiments, which measures the time derivative of the polarizability-polarizability-correlation function (orientational relaxation). Data are presented over a time range of 500 fs-70 micros for the nematic phase and 500 fs to a few hundred nanoseconds for the isotropic phase. The nematic dynamics are compared with a previously studied liquid crystal in the nematic phase. All three liquid crystals have very similar dynamics in the nematic phase that are very different from the isotropic phase. On the slowest time scale (20 ns-70 micros), a temperature-independent power law, the final power law, t(-f) with f approximately 0.5, is observed. On short time scales (approximately 3 ps to approximately 1 ns), a temperature-dependent intermediate power law is observed with an exponent that displays a linear dependence on the nematic order parameter. Between the intermediate power law and the final power law, there is a crossover region that has an inflection point. For times that are short compared to the intermediate power law (approximately <2 ps), the data decay much faster, and can be described as a third power law, although this functional form is not definitive. The isotopic phase data have the same features as found in previous studies of nematogens in the isotropic phase, i.e., the temperature-independent intermediate power law and von Schweidler power law at short to intermediate times, and a highly temperature-dependent long time exponential decay that is well described by the Landau-de Gennes theory. The results show that liquid-crystal dynamics in the nematic phase exhibit universal behavior.

Journal Article↗

PubMed2006

A mode coupling theory description of the short- and long-time dynamics of nematogens in the isotropic phase.

Optical heterodyne-detected optical Kerr effect (OHD-OKE) experimental data are pre-sented on nematogens 4-(trans-4-n-octylcyclohexyl)isothiocyanatobenzene (8-CHBT), and 4-(4-pentyl-cyclohexyl)-benzonitrile (5-PCH) in the isotropic phase. The 8-CHBT and 5-PCH data and previously published data on 4-pentyl-4-biphenylcarbonitrile (5-CB) are analyzed using a modification of a schematic mode coupling theory (MCT) that has been successful in describing the dynamics of supercooled liquids. At long time, the OHD-OKE data (orientational relaxation) are well described with the standard Landau-de Gennes (LdG) theory. The data decay as a single exponential. The decay time diverges as the isotropic to nematic phase transition is approached from above. Previously there has been no theory that can describe the complex dynamics that occur at times short compared to the LdG exponential decay. Earlier, it has been noted that the short-time nematogen dynamics, which consist of several power laws, have a functional form identical to that observed for the short time behavior of the orientational relaxation of supercooled liquids. The temperature-dependent orientational dynamics of supercooled liquids have recently been successfully described using a schematic mode coupling theory. The schematic MCT theory that fits the supercooled liquid data does not reproduce the nematogen data within experimental error. The similarities of the nematogen data to the supercooled liquid data are the motivation for applying a modification of the successful MCT theory to nematogen dynamics in the isotropic phase. The results presented below show that the new schematic MCT theory does an excellent job of reproducing the nematogen isotropic phase OHD-OKE data on all time scales and at all temperatures.

Journal Article↗

PubMed2005

Dynamics of nanoscopic water: vibrational echo and infrared pump-probe studies of reverse micelles.

The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H2O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, approximately 1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is approximately 10 times longer than the dynamics in bulk water. The vibrational echo data for the smallest reverse micelle displays a dependence on the detection wavelength, which may indicate that multiple ensembles of water molecules are being observed.

Deuterium↗

PubMed2005

Accidental vibrational degeneracy in vibrational excited states observed with ultrafast two-dimensional IR vibrational echo spectroscopy.

The coupling between the OD stretch v=2 level and benzene-ring modes in 2-methoxyphenol-OD (hydroxyl H replaced by D) is observed with ultrafast two-dimensional (2D) IR vibrational echo spectroscopy. Because of this coupling, the 1-2 transition peak in the 2D spectrum is split into a doublet with peaks of approximately equal amplitudes. Several molecules and solvents were used to study this phenomenon. Near-IR (NIR) spectroscopy measurements and density-functional theory calculations (B3LYP6-31+G(d,p) level) were also applied. Experimental results and calculations show that the OD stretch 1-2 transition is coupled to a combination band related to the benzene-ring motions. A simple quantum-mechanical model indicates that the combination band has a frequency of 5172 and 5176.5 cm(-1) in CCl4 and hexane, respectively. The transition between this combination band and the ground state is too weak to detect by NIR. The transition between this band and the OD stretch first excited state is also so weak that most of the intensity of the doublet comes from the oscillator strength produced by coupling to the OD stretch. The model gives the coupling strengths as 6.5 and 7 cm(-1) in CCl4 and hexane, respectively.

Journal Article↗

PubMed2005

Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations.

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.

Histidine↗