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Vibrational dephasing of long- and short-lived primary donor excited states in mutant reaction centers of Rhodobacter sphaeroides.

Femtosecond spectroscopy was used to study vibrational dynamics in the first singlet excited state (P*) of the primary donor of bacterial reaction centers (RC)in which primary electron transfer dynamics have been altered by single amino acid modifications. We studied intracytoplasmic RC-only membranes containing Rhodobacter sphaeroides wild-type RCs and RCs bearing mutations in the vicinity of P, where Tyr M210 was modified to His, Leu, and Trp and where Phe L181 was modified to Tyr. These mutations do not change the frequencies of the main low-frequency activated modes, which is consistent with a description in which these modes involve extended regions of the protein. Electron transfer in FL181Y, YM210H, and wild-type RCs at 10 K occurs in approximately 1 ps or less, and damping of the coherences occurs simultaneously with the decay of the P* excited state. These results, and a comparison with YM210L RCs, show that in wild-type RCs the damping is primarily determined by the depletion of P* and not by vibrational dephasing induced by interactions with the bath or nonharmonic coupling. In the YM210L and W mutants, electron transfer occurs on a time scale of hundreds of picoseconds at 10 K. Analysis of the longer-lasting vibrational dynamics in these mutants sets a new lower limit for the intrinsic vibrational dephasing time of 1.2 ps for some modes, but of approximately 2 ps for most activated modes.

Electron Transport↗

Vibrational spectroscopy and analysis of pseudo-tetrahedral complexes with metal imido bonds.

A number of assignments have been previously posited for the metal-nitrogen stretch (nu(M-NR)), the N-R stretch (nu(MN-R)), and possible ligand deformation modes associated with terminally bound imides. Here we examine mononuclear iron(III) and cobalt(III) imido complexes of the monoanionic tridentate ligand [PhBP3] ([PhBP3] = [PhB(CH2PPh2)3]-) to clarify the vibrational features for these trivalent metal imides. We report the structures of [PhBP3]FeNtBu and [PhBP3]CoNtBu. Pseudo-tetrahedral metal imides of these types exhibit short bond lengths (ca. 1.65 A) and nearly linear angles about the M-N-C linkages, indicative of multiple bond character. Furthermore, these compounds give rise to intense, low-energy visible absorptions. Both the position and the intensity of the optical bands in the [PhBP3]MNR complexes depend on whether the substituent is an alkyl or aryl group. Excitation into the low-energy bands of [PhBP3]FeNtBu gives rise to two Raman features at 1104 and 1233 cm(-1), both of which are sensitive to 15N and 2H labeling. The isotope labeling suggests the 1104 cm(-1) mode has the greatest Fe-N stretching character, while the 1233 cm(-1) mode is affected to a lesser extent by (15)N substitution. The spectra of the deuterium-labeled imides further support this assertion. The data demonstrate that the observed peaks are not simple diatomic stretching modes but are extensively coupled to the vibrations of the ancillary organic group. Therefore, describing these complexes as simple diatomic or even triatomic oscillators is an oversimplification. Analogous studies of the corresponding cobalt(III) complex lead to a similar set of isotopically sensitive resonances at 1103 and 1238 cm(-1), corroborating the assignments made in the iron imides. Very minimal changes in the vibrational frequencies are observed upon replacement of cobalt(III) for iron(III), suggesting similar force constants for the two compounds. This is consistent with the previously proposed electronic structure model in which the added electron resides in a relatively nonbonding orbital. Replacement of the tBu group with a phenyl ring leads to a significantly more complicated resonance Raman spectrum, presumably due to coupling with the vibrations of the phenyl ring. Polarization studies demonstrate that the observed modes have A(1) symmetry. In this case, a clearer resonance enhancement of the signals is observed, supporting a charge transfer designation for the electronic transitions. A series of isotope-labeling experiments has been carried out, and the modes with the greatest metal-nitrogen stretching character have been assigned to peaks at approximately 960 and approximately 1300 cm(-1) in both the iron and cobalt [PhBP3]MNPh complexes. These results are consistent with a multiple M-N bond for these metal imides.

Boron Compounds↗

Vibrations of the phenoxyl radical.

Phenoxyl radical (C(6)H(5)O) was prepared photochemically in low-temperature argon matrices. The infrared absorption spectra were obtained for C(6)H(5)O and for the isotopically labeled species C(6)D(5)O and 1-(13)C(12)C(5)H(5)O. All but one IR-active fundamental vibrations were detected, most of them not previously observed. Combination of results from IR linear dichroism measurements on photooriented samples, determination of absolute IR intensities with the help of internal standards, analysis of isotopic shifts, and quantum chemical predictions (B3LYP/cc-pVTZ) led to a detailed assignment of phenoxyl radical vibrations. Significant frequency shifts are observed with respect to previously reported data based on resonance Raman studies in polar solutions. For some vibrations, these shifts reflect environment-induced structural changes, such as increase of the quinoid character of the phenoxyl radical in polar media. In particular, the frequency of the CO stretching vibration, readily observable in both IR and Raman experiments, is extremely sensitive to the environment and can thus be used to probe its polarity.

Free Radicals↗

The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations.

Spectrally resolved infrared stimulated vibrational echo measurements are used to measure the vibrational dephasing of the CO stretching mode of carbonmonoxy-hemoglobin (HbCO), a myoglobin mutant (H64V), and a bacterial cytochrome c(552) mutant (Ht-M61A) in aqueous solution and trehalose glasses. The vibrational dephasing of the heme-bound CO is significantly slower for all three proteins embedded in trehalose glasses compared to that of aqueous protein solutions. All three proteins exhibit persistent but notably slower spectral diffusion when the protein surface is fixed by the glassy solvent. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to reveal that the structural dynamics, as sensed by the CO, of the three proteins in trehalose and aqueous solution are dominated by fast (tens of femtoseconds), motionally narrowed fluctuations. MD simulations of H64V in dynamic and "static" water are presented as models of the aqueous and glassy environments. FFCFs are calculated from the H64V simulations and qualitatively reproduce the important features of the experimentally extracted FFCFs. The suppression of long time scale (picoseconds to tens of picoseconds) frequency fluctuations (spectral diffusion) in the glassy solvent is the result of a damping of atomic displacements throughout the protein structure and is not limited to structural dynamics that occur only at the protein surface. The analysis provides evidence that some dynamics are coupled to the hydration shell of water, supporting the idea that the bioprotection offered by trehalose is due to its ability to immobilize the protein surface through a thin, constrained layer of water.

Computer Simulation↗

Electric field fluctuations drive vibrational dephasing in water.

We present a microscopic description of the vibrational spectroscopy of the OH stretch of HOD in liquid D(2)O. Our model predicts that OH frequency correlations decay with a sharp and rapid ( approximately 35 fs) decrease, followed by a beat at approximately 125 fs from intermolecular oxygen vibrations. On a short time scale ( approximately 200 fs), ultrafast infrared spectroscopy of the OH stretch is sensitive to localized intermolecular motions. For times longer than approximately 200 fs, cooperative molecular rearrangements drive dephasing. The interplay of electric field fluctuations, both local and cooperative, dictate vibrational frequency shifts and destroy vibrational coherence in water.

Computer Simulation↗

OH-stretch vibrational relaxation of HOD in liquid to supercritical D2O.

The population relaxation of the OH-stretching vibration of HOD diluted in D2O is studied by time-resolved infrared (IR) pump-probe spectroscopy for temperatures of up to 700 K in the density range 12 1 OH stretching transition with a 200 fs laser pulse centered at approximately 3500 cm(-1). Above 400 K these spectra show no indication of spectral diffusion after pump-probe delays of 0.3 ps. Over nearly the entire density range and for sufficiently high temperatures (T > 360 K), the vibrational relaxation rate constant, kr, is strictly proportional to the dielectric constant, epsilon, of water. Together with existing molecular dynamics simulations, this result suggests a simple linear dependence of kr on the number of hydrogen-bonded D2O molecules. It is shown that, for a given temperature, an isolated binary collision model is able to adequately describe the density dependence of vibrational energy relaxation even in hydrogen-bonded fluids. However, dynamic hydrogen bond breakage and formation is a source of spectral diffusion and affects the nature of the measured kr. For sufficiently high temperatures when spectral diffusion is much faster than energy transfer, the experimentally observed decays correspond to ensemble averaged population relaxation rates. In contrast, when spectral diffusion and vibrational relaxation occur on similar time scales, as is the case for ambient conditions, deviations from the linear kr(epsilon) relation occur because the long time decay of the v = 1 population is biased to slower relaxing HOD molecules that are only weakly connected to the hydrogen bond network.

Deuterium↗

Visualization and characterization of the infrared active amide I vibrations of proteins.

To facilitate the analysis of frequency-structure correlations in the amide I vibrational spectroscopy of proteins, we investigate visualization methods and spatial correlation functions that describe delocalized vibrations of proteins and protein secondary structures. To study those vibrational modes revealed in infrared spectroscopy, we characterize frequency-dependent bright states obtained from doorway mode analysis. Our visualization methods pictorially color code amplitude and phase of each oscillator within the structure to reveal spatially varying patterns characteristic of excitations within sheets and helices. Spatial correlation functions in the amplitude and phase of amide I oscillators quantitatively address the extent of delocalization and the alpha helical and beta sheet character of these modes. Specifically, we investigate the vibrations of idealized antiparallel beta sheets and alpha helices and perform case studies on three proteins: concanavalin A, myoglobin, and ubiquitin.

Amides↗

Vibrational spectral diffusion of azide in water.

Vibrational spectral diffusion denotes the time-dependent fluctuations of a solute's vibrational frequencies due to local environmental dynamics. Vibrational line shapes are weakly sensitive to spectral diffusion, whereas three-pulse vibrational echoes are much more sensitive. We report here on theoretical studies of spectral diffusion of the asymmetric stretch of the azide anion in heavy water. We run a classical molecular dynamics simulation of rigid azide in rigid water, and at every time step we calculate the azide's anharmonic asymmetric stretch frequency using an optimized quantum mechanics/molecular mechanics method developed earlier. This generates a frequency trajectory, which we use to calculate the absorption line shape and integrated three-pulse echo intensity. Our results for both the line width and the integrated echo intensity are in excellent agreement with experiment. Our calculated frequency time-correlation function is in excellent agreement with experiment for long times (greater than 250 fs) but differs considerably from experiment at short times; our theoretical correlation function has a very pronounced oscillation, presumably due to intermolecular azide-water hydrogen-bond stretching dynamics.

Anions↗

Symmetry properties of vibrational modes in mesoporphyrin IX dimethyl ester investigated by polarization-sensitive resonance Raman and CARS spectroscopy.

The symmetry properties of selected vibrational modes of mesoporphyrin IX dimethyl ester (MP-IX-DME) in solution are investigated under different electronic resonance conditions. The Raman band parameters of the macrocycle modes nu(2), nu(10), nu(11), and nu(19) are determined from a quantitative analysis of polarized spontaneous resonance Raman (RR) and polarization-sensitive (PS) multiplex coherent anti-Stokes Raman scattering (CARS) spectra obtained with pre-resonant B band and resonant Qx band excitation, respectively. Additionally, the molecular geometry and the vibrational modes of MP-IX-DME are calculated by employing density functional theory (DFT) on the B3LYP/6-31G(d) level. Both the DFT-derived structure and the Raman spectroscopic parameters of MP-IX-DME indicate minor deviations from an ideal D2h macrocycle symmetry. To assess the influence of the beta substitution pattern on the in-plane symmetry, calculated normal-mode vectors and several experimentally detected parameters, such as peak positions, depolarization ratios, and coherent phases, are analyzed. The effects of the macrocycle substitution pattern are different for the selected vibrational modes: nu(2) in particular is very sensitive to subtle perturbations of the in-plane symmetry. The considerable activity of totally symmetric vibrations observed in the PS CARS spectra of MP-IX-DME and the correlation of mode symmetries with coherent phases confirm earlier PS CARS results on octaethylporphine (OEP) acquired under the same electronic resonance conditions.

Absorption↗

Surface plasmons and vibrations of self-assembled silver nanocolumns.

Optical and vibrational properties of novel self-assembled silver nanocolumns are studied experimentally and theoretically. The split of the surface plasmon resonance into transverse and longitudinal modes verifies the one-dimensional character of the nanocolumns. In this work, we have identified the acoustic vibration modes of the nanocolumns using Raman scattering, as spheroid-like modes (l = 2, m = +/-2) involving vibrations of the nanocolumns along their minor axes and the existence of surface plasmon-vibration coupling mechanisms.

Computer Simulation↗

Visual stimulation facilitates penile responses to vibration in men with and without erectile disorder.

This study compared reflexogenic and psychogenic penile responses in men with and without erectile disorder. It was hypothesized that men with psychogenic erectile dysfunction respond minimally to vibrotactile stimulation. An enhancement of penile responses was expected when vibration was combined with erotic film. Patients were 50 men with psychogenic erectile dysfunction, 45 men with organic erectile dysfunction, and 50 sexually functional men. The combination of film and vibration resulted in stronger penile responses than the stimuli presented separately. Men with psychogenic erectile dysfunction and sexually functional men did not differ in responses to film and film-and-vibration conditions. As predicted, responses of the 2 groups were different in the vibration condition. Interpretations are provided in terms of attention and appraisal. The findings are relevant to the development of psychophysiological diagnostic procedures.

Adult↗

Electromagnetic vibration process for producing bulk metallic glasses.

It is known that the cooling rate from the liquid state is an important factor in the production of bulk metallic glasses. However, the effects of other factors such as electric and magnetic fields have not been thoroughly investigated. Here, we present a new method for producing bulk metallic glasses by using electromagnetic vibrations with simultaneous imposition of an alternating electric current and a magnetic field. This method was found to be effective in enhancing apparent glass-forming ability in Mg65-Cu25-Y10 (atomic percent) alloys. Indeed, larger bulk metallic glasses could be obtained by the electromagnetic vibration process under the same cooling conditions. We presume that disappearance or decrement of clusters by the electromagnetic vibrations applied to the liquid state cause suppression of crystal nucleation. This electromagnetic vibration process should be effective in other bulk metallic glass systems if the clusters in the liquid state cause the crystal nucleation.

Alloys↗

Does vibration offer any advantage over visual stimulation studies (VSS) in the assessment of erectile capacity?

The purpose of this work was to determine whether vibration stimulation or erotic videotape material can provide an acceptable diagnostic yield for patients with erectile dysfunction (ED) without the patient needing to endure more explicit erotic films, which may be distasteful to some patients, or intracavernous injections, to which there may be a high inhibitory response. Ninety-five subjects were randomly exposed to either vibration or videotape alone and erectile response monitored by the RigiScan. Where no clinical response was recorded by the RigiScan or by self-report by the patient, both stimuli were presented to the subject. Forty-nine subjects received vibration first and 46 received videotape first. Use of clinically based standardised measures revealed neither group achieving above threshold responses to the first stimulation and there were no differences between the two groups. Eight subjects (8%) between both groups exceeded the tip threshold during combination stimulation. Single stimulation with vibration or erotic videotape with provocative RigiScan monitoring is unhelpful in the assessment of ED in any of the diagnostic subgroups of ED. In comparison to previous provocative studies, combination of stimuli sets, whilst increasing penile response (circumferential change and rigidity) did not lead to significant evidence of clinically relevant responses using current RigiScan measures or patient self-report of change. Further studies are necessary to determine the most useful set of stimuli for provocation studies with the RigiScan.

Erectile Dysfunction↗

Vibrational spectroscopy: a 'vanishing' discipline?

The aim of this tutorial review is to convince a broad readership that vibrational spectroscopy, although according to some vibrational spectroscopists seemingly less in focus nowadays than in days past, is far from 'dead'. It may seem to some that infrared and Raman spectroscopy are less in focus than in times past, despite the unique analytical capabilities. Vibrational spectroscopy is particularly powerful for non-destructive characterisation of substances, including living material. But compared to the past, a shift in applications has taken place, bringing new opportunities. This is partly due to the introduction of new features, including imaging and 2D correlation spectroscopy. Another factor is the recognition that vibrational spectroscopy can play a role in new rather than only in the traditional fields of application, e.g. new applications in the life-science field (living cells, cancer research), the characterisation of soil. But also the traditional application in catalysis sees new development within the context of Operando spectroscopy.

Animals↗

The absorption spectra of anisole-h8, anisole-d3 and anisole-d8. The assignment of fundamental vibrations in the S0 and the S1 states.

The REMPI spectra of anisole-h8, anisole-d3 and anisole-d8 have been measured. The assignment of the fundamental vibrations of anisole in the S(1) state is supported by quantum chemical model calculations, the isotopic shifts, the comparison with the frequencies of corresponding vibrations in other monosubstituted benzenes, especially phenol, and the overtones, combinations and progressions observed in the spectrum of anisole-h8. The frequencies of the 42 fundamental vibrations of anisole in the S(1) state are evaluated and compared with the frequencies of the corresponding vibrations in the electronic ground state. Some assignments given earlier in the literature have been revised.

Absorption↗

Comparison of IR and Raman forms of vibrational optical activity.

Natural vibrational optical activity consists of two principal forms. The IR form is known as vibrational circular dichroism (VCD) and is simply the extension of electronic circular dichroism into the IR vibrational region of the spectrum. The Raman form, known as Raman optical activity (ROA), is a new form of optical activity that has no counterpart in the classical forms of optical activity. In this paper, the similarities and differences of the IR and Raman forms of vibrational optical activity will be examined. Although both VCD and ROA were discovered and confirmed in the period from 1973 to 1975, each field has evolved independently with key advances in theoretical description, instrumentation and application coming at different times over the past 20 years. The current relative strengths and weaknesses of VCD and ROA will be discussed, and specific examples of VOA spectra of (-)-alpha-pinene and the amino acid L-alanine, for which overlapping VCD and ROA data are available, will be presented.

Circular Dichroism↗

The effect of vibration on blood flow in skeletal muscle in the rabbit.

1. The blood flow in rabbit gastrocnemius, as measured by photoelectric drop-counter, increased when the muscle was vibrated at frequencies of 22--62 Hz. 2. Blood flow increased rapidly within 1--2 s of the start of vibration, and lasted for the whole time vibration was applied. 3. The increase in blood flow was negatively correlated with the initial blood flow, being greater with lower flows. 4. The magnitude of increase was similar in both innervated and acutely denervated muscles. 5. The arterial blood pressure did not change apart from a very brief fall at the beginning of vibration. Venous pressure rose and, consequently, the perfusion pressure was lower. The increase in blood flow thus indicates a considerable dilatation in the resistance vessels of skeletal muscle.

Animals↗

Effects of preceding movements and contractions on the tonic vibration reflex of human finger extensor muscles.

The vibration sensitivity of feline muscle spindle endings is known to vary as a result of preceding muscle conditioning manoeuvres. If similar after-effects occur in man they should be expected to influence the strength of the tonic vibration reflex (TVR). To study this issue, vibration was applied over the finger extensor tendons of 11 volunteers who actively held their fingers in a semi-extended position. The TVR, measured as electromyographic responses and angular deflections at the metacarpophalangeal joints, was found to be stronger when the extensors prior to the test had been contracted in a shortened position than when they had been contracted in a stretched position. This difference was reduced when the vibration stimulus was preceded by a strong extensor contraction in the test position. The antigravity extensor EMG activity required to keep the fingers in the test position was weaker when the conditioning contraction was performed at a short muscle length than when it was performed at a long muscle length. The variations in magnitude of the TVR can be attributed to 'thixotropic' properties of intrafusal muscle fibres, resulting in a slack following conditioning at a long muscle length. The different EMG levels required for position holding can be explained by similar properties of extrafusal muscle fibres. In conclusion, the results demonstrate the importance of taking the 'history of movement' into account in the design of all TVR studies.

Adult↗