CO vibration as a probe of ligand dissociation and transfer in myoglobin

We report femtosecond visible pump, midinfrared probe, spectrally integrated experiments resolving the dynamics of CO in myoglobin upon photodissociation. Our results show a progressive change in absorption strength of the CO vibrational transition during its transfer from the heme to the docking site, whereas the vibrational frequency change is faster than our time resolution. A phenomenological model gives good qualitative agreement with our data for a time constant of 400 fs for the change in oscillator strength. Density-functional calculations demonstrate that indeed vibrational frequency and absorption strength are not linearly coupled and that the absorption strength varies in a slower manner due to charge transfer from the heme iron to CO.     

Vibrational dynamics of biological molecules: Multi-quantum contributions

High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of ⁵⁷Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.     

Stiffness,resilience, compressibility

The flexibility of a protein is an important component of its functionality. We use nuclear resonance vibrational spectroscopy (NRVS) to quantify the flexibility of the heme iron environment in the electron-carrying protein cytochrome c by measuring the stiffness and the resilience. These quantities are sensitive to structural differences between the active sites of different proteins, as illustrated by a comparative analysis with myoglobin. The elasticity of the entire protein, on the other hand, can be probed quantitatively from NRVS and high energy-resolution inelastic X-ray scattering (IXS) measurements, an approach that we used to extract the bulk modulus of cytochrome c.     

Sub‐picosecond Raman spectrometer for time‐resolved studies of structural dynamics in heme proteins

We describe a pump–probe Raman spectrometer based on a femtosecond Ti:sapphire laser, an optical parametric generator and two optical parametric amplifiers for time‐resolved studies, with emphasis on the structural dynamics in heme proteins. The system provides a 100‐fs pump pulse tunable in the range 500–600 nm and a transform‐limited sub‐picosecond probe pulse tunable in the range 390–450 nm. The spectrometer has spectral (25 cm⁻¹) and temporal (∼0.7 ps) resolutions which constitute an effective compromise for identifying transient heme protein species and for following their structural evolution by spontaneous Raman scattering in the time range 0.5 ps to 2 ns. This apparatus was applied to time‐resolved studies of a broad range of heme proteins, monitoring the primary dynamics of photoinduced heme coordination state and structural changes, its interaction with protein side‐chains and diatomic gaseous ligands, as well as heme vibrational cooling. The treatment of transient Raman spectra is described in detail, and the advantages and shortcomings of spontaneous resonance Raman spectroscopy for ultrafast heme proteins studies are discussed. We demonstrate the efficiency of the constructed spectrometer by measuring Raman spectra in the sub‐picosecond and picosecond time ranges for the oxygen‐storage heme protein myoglobin and for the oxygen‐sensor heme protein FixLH in interaction with the diatomic gaseous ligands CO, NO, and O₂. Copyright © 2010 John Wiley & Sons, Ltd.     

Electron energy loss spectroscopy; history and related matters

This paper begins with some historical remarks regarding the author’s early interest in the use of electron energy loss spectroscopy to probe dynamical phenomena on crystal surfaces. We then discuss the physical nature of the interactions responsible for vibrational and spin waves losses, with attention to their role in related phenomena. PACS 61.14.-x; 68.35.Ja; 68.49.Jk; 68.49.Uv     

Laser probes of intramolecular energy transfer between internal rotation and vibrations in large polyatomics

Laser excited S₁→S₀ fluorescence spectra are obtained from p-fluorotoluene in a supersonic jet in order to probe internal rotational-vibrational coupling. Resolved fluorescence spectra after selective excitation of S₁ levels with high quanta states of the CH₃ internal rotation contain evidence of extensive interactions with isoenergetic vibrational levels. Analogous spectra from states without excitation of the internal rotor show little or no interactions. The results are consistent with a recently developed theory of the intramolecular collisional transfer of rotor energy to the vibrational field.     

Measurement of correlations between low-frequency vibrational modes and particle rearrangements in quasi-two-dimensional colloidal glasses

We investigate correlations between low-frequency vibrational modes and rearrangements in two-dimensional colloidal glasses composed of thermosensitive microgel particles, which readily permit variation of the sample packing fraction. At each packing fraction, the particle displacement covariance matrix is measured and used to extract the vibrational spectrum of the "shadow" colloidal glass (i.e., the particle network with the same geometry and interactions as the sample colloid but absent damping). Rearrangements are induced by successive, small reductions in the packing fraction. The experimental results suggest that low-frequency quasilocalized phonon modes in colloidal glasses, i.e., modes that present low energy barriers for system rearrangements, are spatially correlated with rearrangements in this thermal system.     

Linear concentration dependence of vibrational width and vibrational dephasing paths in aqueous nitrate solutions

A theoretical model of vibrational dephasing of Raman active ions in aqueous electrolyte solutions is presented in which a probe ion is coupled to the bath by direct ion-solvent and ion-ion interactions. Expression for the vibrational width in terms of concentrations and efficiencies of the vibrational frequency modulation by ion-perturber interactions is given in the fast modulation scheme. The observed linear concentration dependence of the vibrational dephasing width of the v ₁(A'₁) mode of NO₃ ^- in aqueous solutions is reasonably well explained from this model, and efficiencies of the dephasing paths through NO₃ ^--water hydrogen bonding interaction and contact NO₃ ^--cation pair formation interaction are estimated. Anions in the solution give only a secondary effect to nitrate vibrational dephasing because of interionic repulsive forces.     

Tunneling spectroscopy as a probe of adsorbate-surface interactions

Tunneling spectroscopy is a sensitive probe of two classes of adsorbate-surface interactions: interactions of the adsorbate with the substrate on which it is adsorbed and adsorbate interactions with the top metal electrode that is evaporated on top of it. The talk by Professor Hipps focuses on the first of these classes. This talk focuses on the second. In general, the interaction of the adsorbed molecules with the top metal electrode produces a down-shift in the vibrational mode position ranging in size from 0.1% to 10% depending on the dipole derivative of the mode and the type of top metal electrode.     

Computational investigation of CO adsorbed on Au<Subscript>x</Subscript>, Ag<Subscript>x</Subscript> and (AuAg)<Subscript>x</Subscript> nanoclusters (x = 1 − 5, 147) and monometallic Au and Ag low-energy surfaces

Density functional theory calculations have been performed to investigate the use of CO as a probe molecule for the determination of the structure and composition of Au, Ag and AuAg nanoparticles. For very small nanoclusters (x = 1 ? 5), the CO vibrational frequencies can be directly correlated to CO adsorption strength, whereas larger 147-atom nanoparticles show a strong energetic preference for CO adsorption at a vertex position but the highest wavenumbers are for the bridge positions. We also studied CO adsorption on Au and Ag (100) and (111) surfaces, for a 1 monolayer coverage, which proves to be energetically favourable on atop only and bridge positions for Au (100) and atop for Ag (100); vibrational frequencies of the CO molecules red-shift to lower wavenumbers as a result of increased metal coordination. We conclude that CO vibrational frequencies cannot be solely relied upon in order to obtain accurate compositional analysis, but we do propose that elemental rearrangement in the core@shell nanoclusters, from Ag@Au (or Au@Ag) to an alloy, would result in a shift in the CO vibrational frequencies that indicate changes in the surface composition.     

P450血红素与CO、NO 和O2结合性质的密度泛涵研究

用两种模型在B3LYP/6-31G(d)水平上研究了双原子分子CO、NO和O2 (通称XO) 与P450血红素的结合性质. 在模型M2中考虑了双原子分子XO附近的丝氨酸残基对其的影响. 结果表明血红素附近的丝氨酸使得XO与血红素的结合更加牢固. 频率分析表明，当XO与血红素结合后X{O伸缩振动频率降低.同时讨论了复合物的HOMO和LUMO轨道的组成.     

Förster Resonance Energy Transfer Study of Cytochrome <Emphasis Type="Italic">c</Emphasis>—Lipid Interactions

Specific interactions between a mitochondrial hemoprotein cytochrome c (cyt c) and cardiolipin, a lipid component of mitochondrial membrane, are crucial to electron shuttling and apoptotic activities of this protein. In the present study the Förster resonance energy transfer (FRET) between anthrylvinyl-labeled phosphatidylcholine as a donor and heme moiety of cyt c as an acceptor was employed to give a quantitative characterization of the protein binding to the model membranes from the mixtures of phosphatidylcholine (PC) with phosphatidylglycerol (PG), phosphatidylserine (PS) or cardiolipin (CL) in different molar ratios. The multiple arrays of the FRET data were globally analyzed in terms of the model of energy transfer in two-dimensional systems combined with the scaled particle adsorption model. The arguments in favor of the specificity of cyt c interactions with CL were obtained, including the higher adsorption potential and the deeper protein insertion in the lipid bilayer.     

Doubly vibrationally enhanced four wave mixing: the optical analog to 2D NMR

We report the development of the four wave mixing vibrational analog to 2D NMR and demonstrate its spectral selectivity, sensitivity to the interactions causing mode coupling, and ability to spectrally resolve isotopic mixtures. The method discriminates against uncoupled vibrational modes and isolates the features that are associated with intra- or intermolecular interactions.     

UV resonance Raman study of TrpZip2 and related peptides: π‐π interactions of tryptophan

Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high‐resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β‐hairpin peptide that is stabilized by edge‐to‐face and face‐to‐face tryptophan π‐π interactions. The vibrational markers of isolated edge‐to‐face π‐π interactions are investigated in the related β‐hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the B_b absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross‐sections of B_b‐coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π‐π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces. Copyright © 2012 John Wiley & Sons, Ltd.     

Role of Intermolecular Interactions in Forming the Vibrational Spectra of Carbohydrate Nitrate Crystals in the Region 1600–1700 cm−1

To elucidate the role of intermolecular interactions in forming the vibrational spectra of the crystals of carbohydrate nitrates in the region 1600–1700 cm^–1, theoretical calculations are performed (in the approximation of an additive model of interatomic interactions with the use of the Green's functions) for the density of vibrational states and the intensity of absorption bands in the IR spectrum of a methyl--D-glucopyranoside tetranitrate molecule in a crystal. It is shown that the splitting of absorption bands in the IR spectral region under consideration relates to the crystal effect.     

Vibrational spectra of AlN/GaN superlattices: Theory and experiment

Computer simulation of the dynamics of layered AlN/GaN superlattices is performed to elucidate the microscopic nature of the vibrational states corresponding to the strongest bands in the Raman spectra. Experimental Raman spectra are shown to consist of two groups of lines, one of which exhibits a two-mode behavior and the other shows a one-mode behavior as the relative layer thicknesses are varied. The results of computer simulation and calculations within the dielectric-continuum approximation suggest that the behavior of the observed vibrational modes is dictated by the degree of their localization and that the interlayer coupling is due to long-range dipole-dipole interactions. It is shown that the delocalized modes, which exhibit one-mode behavior, can be used as a sensitive probe of the structure and composition of superlattices.     

Vibrational quantum interference in Raman-induced Kerr effect: momentum conservation

The pump–probe Raman-induced optical Kerr effect (RIKE) of simple molecular liquids, studied with femtosecond laser pulses, exhibit long lasting beats ascribable to vibrational quantum interference (QI). While energy conservation entails vibrational resonances in RIKE, momentum conservation boils down to wave vector-matching in the pump and probe processes, which calls for the participation of a vibrational excitation wave. The refractive index dispersion around vibrational resonances is intimately related to the focusing angle of the pump (also probe) beam. The larger the focusing angle, the greater the excitation wave number, i.e. the more energetic the vibration in resonance; if the focusing angle is too small, energetic vibrations cannot be observed in vibrational QI, even if energy conservation is fulfilled. If the pump and probe beams are perfectly collimated, then all beams must be collinear in order to conserve momentum.     

Excited-state molecular vibration observed for a probe pulse preceding the pump pulse by real-time optical spectroscopy

It is shown experimentally that the absorbance change observed in the "negative" time range, where probe pulse precedes pump pulse in real-time vibrational spectroscopy is induced only by the excited-state wave-packet motion as theoretically expected. Coherent molecular vibration of a polymer in the excited state was observed in the real-time trace without the effect of wave-packet motion in the ground state, which usually makes it difficult to ascribe the signal either to the ground state or to the excited state.     

Spin fluctuation rates in myoglobin azide: Comparison of Mössbauer and EPR results

We have analyzed the Mössbauer spectra of low-spin ferric myoglobin azide, taken in small applied field from 30 K to 200 K, in terms of a dynamic lineshape model [1]. Our results show fluctuation rates having a temperature dependence which is different from that measured using EPR forT<10 K [2–4] and shed new light on the vibrational modes coupling to the spinS=1/2 of the heme iron.     

Probing solvation dynamics with femtosecond vibrational spectroscopy

We explain why solvent reorganization can induce both red- and blue-shifting of vibrational transitions of a particular probe molecule upon excitation to the S₁ electronic state. We observe with femtosecond vibrational spectroscopy, after hydrogen-bond cleavage dynamics, an additional blue shift of the carbonyl stretch of coumarin 102 of 7 cm^-1 when dissolved in chloroform. Received: 28 June 2000 / Published online: 7 August 2000