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Robin M Hochstrasser

Publications and source records attributed to Robin M Hochstrasser.

30 records · Page 2Linked to original sources
PubMed2005

Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution.

The linear-infrared and two-dimensional infrared (2D IR) spectra in the amide-I' region of the alanine dipeptide and its (13)C isotopomers in aqueous solution (D(2)O) are reported. The two amide-I' IR transitions have been assigned unambiguously by using (13)C isotopic substitution of the carbonyl group; the amide unit at the acetyl end shows a lower transition frequency in the unlabeled species. The ratio of their transition dipole strengths remains almost unchanged upon (13)C substitution, indicating the absence of intensity transfer between two vibrators. The 2D IR cross peaks directly associated with intramode coupling in this case show a small off-diagonal anharmonicity (0.2 +/- 0.2 cm(-1)), leading to a small coupling constant (1.5 +/- 0.5 cm(-1)). The coupling and the 2D IR spectra in two different polarizations (zzzz and zxxz) are as expected for a polyproline-II (PP(II))-like conformation for dialanine, with the backbone dihedral angles (phi, psi) determined to be in the range of (-70 degrees +/- 25 degrees, +120 degrees +/- 25 degrees). Ab initio DFT calculations and normal mode decoupling analysis in the Ramachandran subspace in the neighborhood of PP(II) conformation confirm the presence of a region where the coupling is vanishingly small and support these experimental findings. The relationship between the coupling and off-diagonal anharmonicity is consolidated by examining the distribution of the latter from an ensemble averaged Hamiltonian incorporating uncorrelated diagonal frequency distributions and a small coupling (<2 cm(-1)); it is found that the most probable value for the off-diagonal anharmonicity falls into the range of experimental observations. Further, incorporating DFT results, the simulated linear-IR and 2D IR can reproduce the essential features of the measurements, including the transition frequency positions and apparent peak intensities. All the experimental results and simulations are consistent with a PP(II)-like conformation for the alanine dipeptide in aqueous solution, in which two amide-I' modes are highly localized and whose frequency distributions are uncorrelated.

Alanine↗
PubMed2005

Dynamics of amide-I modes of the alanine dipeptide in D2O.

The equilibrium dynamics of the acetyl and amino amide-I groups of the alanine dipeptide were examined separately using (13)C isotopic selection and 2D IR. The population relaxation times of the amide transitions were measured to be in the range 500 fs by means of heterodyne transient grating methods. The vibrational frequency correlation functions consisted in all cases of a motionally narrowed part, a component near 800 fs, and a constant part representing a distribution of structures that is static on the few ps time scale. The intermediate time scale is attributed to fluctuations in the stretching and bending of hydrogen bonds between the carbonyl and water.

Alanine↗
PubMed2004

Multidimensional infrared spectroscopy of the N-H bond motions in formamide.

The heterodyned two-dimensional (2D) IR spectra and equilibrium dynamics of the N-H stretching motion of DCONHD in deuterated formamide, DCOND(2), were studied with 80 fs pulses at 3 microm. The time evolution of the heterodyned 2D IR spectra, pump-probe spectra, and photon echo peak shift demonstrate that interstate dynamics is occurring by relaxation of the original N-H excitation. The N-H vibrational frequency correlation function can be expressed as a sum of three exponentials with correlation times 0.24 ps, 0.8 ps, and 11 ps. The intermediate component is attributed to motions of the N-Hcdots, three dots, centeredO unit involving only slight angular variations of the N-H bond. The slow component is attributed to the structure breaking and making. The anisotropy decay confirmed that the significant angular N-H bond motion occurs on the 11 ps time scale. The fast component, which is the least well determined, might correspond to the modulation of the H-bond distance without angular motion. The correlation coefficient between the pumped and relaxed state distributions was +0.51, implying that the excited state phase memory is only slightly diminished by the relaxation of the N-H excitation. The relaxed modes are concluded to be local to the driven N-H mode.

Computer Simulation↗
PubMed2004

Nature of structural inhomogeneities on folding a helix and their influence on spectral measurements.

Extensive conformational sampling and calculations of vibrational coupling provide a quantitative basis for the structurally inhomogeneous spectra of the amide unit in aqueous solutions containing folded and unfolded state distributions of helices. Replica exchange molecular dynamics simulations of the capped helical peptide, AA(AAKAA)(3)AAY, is carried out over a range of temperatures, where the system populates the folded and unfolded states. This sampling defines a set of ensembles that characterizes the conformational variability for configurations identified by their fraction of helical content. The effects of hydrogen bonding, both internal and external (with water), and the coupling between amide-I modes are computed as a function of temperature and helical content. End-to-end distance and coupling distributions are also computed. The solvent H-bonding, which is present at all temperatures, shifts the amide-I band toward lower frequency compared with the unsolvated band. Upon thermal denaturation of the peptide, the amide-I band shifts to higher frequency because the increase in solvent H-bonding fails to compensate for the loss in internal (helical) H-bonds. The loss of uniformity of the mode coupling along the helix at higher temperatures accounts for the well-known thermal broadening of the amide IR spectrum. The calculated inhomogeneities of segments of the peptide predict experimental properties of isotope-edited helices.

Amides↗
PubMed2004

Vibrational coupling, isotopic editing, and beta-sheet structure in a membrane-bound polypeptide.

The N-acetylated hexapeptide WLLLLL (AcWL5) partitions into lipid membranes and is believed to assemble into an antiparallel beta-sheet. As a test of this structural assignment, the peptide bonds of residues 2-6 were labeled with (13)C and allowed to adsorb onto a supported lipid membrane. Peptides bound to the membrane were examined for evidence of coupling between the labeled vibrational modes in adjacent beta-strands with internal reflection infrared spectroscopy. Experimental results indicate that the amide I absorption band in D(2)O (i.e., amide I') attributable to (13)C is selectively enhanced when the label is at any one of several positions along the peptide backbone. Simulations employing an excitonic model with through-bond and through-space interactions were performed on AcWL5 models in parallel and antiparallel beta-sheet configurations. The simulations yield spectra in good agreement with the experimental results, accounting for the enhancement of both (13)C band intensities and band frequencies. They also yield insight into the physical origin and structure selectivity of the distinctive amide I' band shapes that arise in isotopically edited spectra. It is concluded that the beta-sheet formed by membrane-bound AcWL5 is indeed antiparallel, and the enhancement of (13)C bands in the infrared spectra of these peptides is caused by both interstrand and intrastrand coupling to (12)C modes.

Amides↗
PubMed2004

Interrogating conformationally dependent electron-transfer dynamics via ultrafast visible pump/IR probe spectroscopy.

We demonstrate for the first time the utility of time-resolved visible pump/mid-infrared (IR) probe spectroscopy to interrogate directly, and provide unique infomation regarding, conformationally dependent photoinduced ET dynamics and the subsequent structural evolution of the resulting charge-separated (CS) state. Exemplary polarized visible pump/IR probe experiments involving N-[5-(10,20-diphenylporphinato)zinc(II)]-N'(octyl)pyromellitic diimide (PZn-PI) and [5-[4'-(N-(N'-octyl)pyromellitic diimide)phenyl)ethynyl]-10,20-diphenylporphinato]zinc(II) (PZn()PI) show that it is possible to assess the mean PZn-to-PI interplanar torsional angle of electronically excited structural conformers that undergo ET within the sub-ps time domain for both of these donor-spacer-acceptor (D-Sp-A) systems. Further transient specroscopic experiments carried out on PZn()PI determine how this angle evolves with time. Because vibrational transition moments are often known and typically localized, this work underscores that polarized visible pump/IR probe spectroscopy defines a valuable tool to interrogate structrure in both electronically excited and CS states; this fact, coupled with the ultrafast time resolution and high senseitivity offered by this technique, make it ideally suited to probe a range of mechanistic issues relevant to charge-transfer reactions.

Electrons↗
PubMed2003

Direct observation of triplet state emission of single molecules: single molecule phosphorescence quenching of metalloporphyrin and organometallic complexes by molecular oxygen and their quenching rate distributions.

Single molecules are detected through the phosphorescence emission of their triplet states. Emission of the triplet states of single molecules of Pt octabutoxycarbonyl porphyrin (PtOBCP) and ruthenium(II)-tris-4,7-diphenyl-1,10-phenanthroline dichloride (Ru(dpp)(3)Cl(2)) is reported. The single molecule phosphorescence is very sensitive to molecular oxygen. Each molecule has its own characteristic quenching rate by oxygen, and the distribution of these rates is measured for (Ru(dpp)(3)Cl(2)) on a quartz surface. The large variance of this distribution is presumed to be caused by fluctuations in the pseudobimolecular rate coefficient and the local oxygen concentration. The possibility of creating a quantitative single oxygen molecule sensor is suggested.

Luminescent Measurements↗
PubMed2003

Anthracene-BODIPY cassettes: syntheses and energy transfer.

Compounds based on the 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY) framework are excellent fluorescent markers. When BODIPY dyes of this type are conjugated to functionalities that absorb at relatively short wavelengths, those functionalities can, in some molecules, transmit the absorbed energy to the BODIPY which then fluoresces. In such cases the BODIPY fragment acts as an acceptor while the other group serves as a donor. Energy transfer efficiencies in such donor-acceptor cassette systems must vary with the relative orientation of the two components, and with the structure of the linkers that attach them. This study was designed to probe these issues for the special case in which the linkers between the donor and acceptor fragments are conjugated. To do this, the cassettes 3-10 were prepared. Electrochemical studies were performed to provide insight into the degree of donor-acceptor conjugation in these systems. X-ray Crystallographic studies on single crystals of compounds 7 and 9 revealed the favored conformations of the donor and acceptor fragments in the solid state. Absorption, fluorescence, and time-resolved fluorescence spectra of the compounds were recorded, and quantum yields for the cassettes excited at the donor lambda(max) were measured. Fluorescence steady-state anisotropy data were determined for cassettes 3 and 9 to provide information about the mutual direction of the transition dipole moments.

Anthracenes↗
PubMed2003

Dual-frequency 2D-IR spectroscopy heterodyned photon echo of the peptide bond.

The structure fluctuations of the peptide bond interacting with solvent are examined through the coupling and correlations of the frequency distributions of amide I and amide II transitions. The fluctuations of the two modes are anticorrelated as a result of the solvent-induced changes in the mixing of the dominant valence-bond structures of the peptide. Significant anharmonic coupling of the two modes is seen. The results are the application of a new approach to two-dimensional infrared (2D-IR) spectroscopy in which the pulse sequences used to produce the vibrational echoes incorporate two frequencies. This dual-frequency arrangement greatly extends the capabilities of 2D-IR spectroscopy by allowing the coupling between widely separated modes to be characterized in analogy with heteronuclear NMR. The experiment exposes the cross peaks, representing the mode coupling, free of the interference of the strong diagonal peaks that typically dominate 2D-IR spectroscopy. The alignment and dephasing of coupled transitions, in this example the amide I and amide II transition dipoles, is also determined by these experiments.

Amides↗
PubMed2003

Motions of single molecules and proteins in trehalose glass.

The fluorescence intensity-time records of individual metal-free porphyrin cytochrome-c and Zn porphyrin cytochrome-c molecules whose translational motions are restricted by encapsulation in trehalose are examined by single-molecule spectroscopy by means of a two-channel confocal microscope that records transient fluorescence signals in two orthogonal polarization directions. Large angular motions often occur on time scales ranging to many seconds. Measurements of the photobleaching time distributions indicate that the trehalose glass restricts the accessibility of the fluorescent molecules to oxygen.

Cytochrome c Group↗
PubMed2002

Seeing the light: preassembly and ligand-induced changes of the interferon gamma receptor complex in cells.

Our experiments were designed to test the hypothesis that the cell surface interferon gamma receptor chains are preassembled rather than associated by ligand and to assess the molecular changes on ligand binding. To accomplish this, we used fluorescence resonance energy transfer, a powerful spectroscopic technique that has been used to determine molecular interactions and distances between the donor and acceptor. However, current commercial instruments do not provide sufficient sensitivity or the full spectra to provide decisive results of interactions between proteins labeled with blue and green fluorescent proteins in living cells. In our experiments, we used the blue fluorescent protein and green fluorescent protein pair, attached a monochrometer and charge-coupled device camera to a modified confocal microscope, reduced background fluorescence with the use of two-photon excitation, and focused on regions of single cells to provide clear spectra of fluorescence resonance energy transfer. In contrast to the prevailing view, the results demonstrate that the receptor chains are preassociated and that the intracellular domains move apart on binding the ligand interferon gamma. Application of this technology should lead to new rapid methods for high throughput screening and delineation of the interactome of cells.

Animals↗