2D IR Vibrational Echo Research Articles

Direct observation of dynamic crossover in fragile molecular glass formers with 2D IR vibrational echo spectroscopy.

The dynamics of supercooled liquids of the molecular glass formers benzophenone and ortho-terphenyl were investigated with 2D IR spectroscopy using long-lived vibrational probes. The long lifetimes of the probes enabled structural dynamics of the liquids to be studied from a few hundred femtoseconds to a nanosecond. 2D IR experiments measured spectraldiffusion of a vibrational probe, which reports on structural fluctuations of the liquid. Analysis of the 2D IR data provides the frequency-frequency correlation function (FFCF). Two vibrational probes were examined with equivalent results, demonstrating the observed liquid dynamics are not significantly influenced by the probe molecules. At higher temperatures, the FFCF is a biexponential decay. However, at mild supercooling, the biexponential decay is no longer sufficient, indicating a dynamic crossover. The crossover occurs at a temperature well above the mode-coupling theory critical temperature for the given liquid, indicating dynamic heterogeneity above the critical temperature. Examination of the low temperature data with lifetime density analysis shows that the change is best described as an additional, distinct relaxation that shows behavior consistent with a slow β-process.

Observation and theory of reorientation-induced spectral diffusion in polarization-selective 2D IR spectroscopy

In nearly all applications of ultrafast multidimensional infrared spectroscopy, the spectral degrees of freedom (e.g., transition frequency) and the orientation of the transition dipole are assumed to be decoupled. We present experimental results which confirm that frequency fluctuations can be caused by rotational motion and observed under appropriate conditions. A theory of the frequency-frequency correlation function (FFCF) observable under various polarization conditions is introduced, and model calculations are found to reproduce the qualitative trends in FFCF rates. The FFCF determined with polarization-selective two-dimensional infrared (2D IR) spectroscopy is a direct reporter of the frequency-rotational coupling. For the solute methanol in a room temperature ionic liquid, the FFCF of the hydroxyl (O-D) stretch decays due to spectral diffusion with different rates depending on the polarization of the excitation pulses. The 2D IR vibrational echo pulse sequence consists of three excitation pulses that generate the vibrational echo, a fourth pulse. A faster FFCF decay is observed when the first two excitation pulses are polarized perpendicular to the third pulse and the echo, 〈XXY Y〉, than in the standard all parallel configuration, 〈XXXX〉, in which all four pulses have the same polarization. The 2D IR experiment with polarizations 〈XY XY〉 ("polarization grating" configuration) gives a FFCF that decays even more slowly than in the 〈XXXX〉 configuration. Polarization-selective 2D IR spectra of bulk water do not exhibit polarization-dependent FFCF decays; spectral diffusion is effectively decoupled from reorientation in the water system.

Dynamics of dihydrogen bonding in aqueous solutions of sodium borohydride.

Dihydrogen bonding occurs between protonic and hydridic hydrogens which are bound to the corresponding electron withdrawing or donating groups. This type of interaction can lead to novel reactivity and dynamic behavior. This paper examines the dynamics experienced by both borohydride and its dihydrogen-bound water solvent using 2D-IR vibrational echo and IR pump-probe spectroscopies, as well as FT-IR linear absorption experiments. Experiments are conducted on the triply degenerate B-H stretching mode and the O-D stretch of dilute HOD in the water solvent. While the B-H stretch absorption is well separated from the broad absorption band of the OD of HOD in the bulk of the water solution, the absorption of the ODs hydrogen bonded to BHs overlaps substantially with the absorption of ODs in the bulk H₂O solution. A subtraction technique is used to separate out the anion-associated OD dynamics from that of the bulk solution. It is found that both the water and borohydride undergo similar spectral diffusion dynamics, and these are very similar to those of HOD in bulk water. Because the B-H stretch is triply degenerate, the IR pump-probe anisotropy decays very rapidly, but the decay is not caused by the physical reorientation of the BH₄⁻ anions. Spectral diffusion occurs on a time scale longer than the anisotropy decay, demonstrating that spectral diffusion is not yet complete even when the transition dipole has completely randomized. To prevent chemical decomposition of the BH₄⁻, 1 M NaOH was added to stabilize the system. 2D-IR experiments on the OD stretch of HOD in the NaOH/water liquid (no borohydride) show that the NaOH has a negligible effect on the bulk water dynamics.

New divergent dynamics in the isotropic to nematic phase transition of liquid crystals measured with 2D IR vibrational echo spectroscopy.

The isotropic phase of nematogenic liquid crystals has nanometer length scale domains with pseudonematic ordering. As the isotropic to nematic phase transition temperature (TNI) is approached from above, the orientational correlation length, ξ, of the pseudonematic domains grows as (T - T(*))(-1/2), where T(*) is 0.5-1 K below TNI. The orientational relaxation, which is a collective property of the pseudonematic domains, was measured with optical heterodyne detected-optical Kerr effect (OHD-OKE). The orientational relaxation obeys Landau-de Gennes theory, as has been shown previously. To examine the environmental evolution experienced by molecules in the pseudonematic domains, two-dimensional infrared (2D IR) vibrational echo experiments on the CN stretching mode of the non-perturbative vibrational probes 4-pentyl-4(')-selenocyanobiphenyl (5SeCB) and 4-pentyl-4(')-thiocyanobiphenyl (5SCB) in the nematogen 4-cyano-4(')-pentylbiphenyl (5CB) were performed. The 2D IR experiments measure spectral diffusion, which is caused by structural fluctuations that couple to the CN vibrational frequency. Temperature dependent studies were performed just above TNI, where the correlation length of pseudonematic domains is large and changing rapidly with temperature. These studies were compared to 2D IR experiments on 4-pentylbiphenyl (5B), a non-mesogenic liquid that is very similar in structure to 5CB. The time constants of spectral diffusion in 5CB and 5B are practically identical at temperatures ≥5 K above TNI. As the temperature is lowered, spectral diffusion in 5B slows gradually. However, the time constants for spectral diffusion in 5CB slow dramatically and diverge as T(*) is approached. This divergence has temperature dependence proportional to (T - T(*))(-1/2), precisely the same as seen for the correlation length of pseudonematic domains, but different from the observed orientational relaxation times, which are given by the Landau-de Gennes theory. The data and previous results show that spectral diffusion in 5CB has no contributions from orientational relaxation, and the structural dynamics responsible for the spectral diffusion are likely a result of density fluctuations. The results suggest that the correlation length of the density fluctuations is diverging with the same temperature dependence as the pseudonematic domain correlation length, ξ. The isotropic-nematic phase transition in liquid crystals is described in the context of the slowing of orientational relaxation associated with divergent growth of the orientational correlation length. The results presented here show that there is another divergent dynamical process, likely associated with density fluctuations.

The Influence of Cholesterol on Fast Dynamics Inside of Vesicle and Planar Phospholipid Bilayers Measured with 2D IR Spectroscopy.

Phospholipid bilayers are frequently used as models for cell membranes. Here the influence of cholesterol on the structural dynamics in the interior of 1,2-dilauroyl-sn-glycero-3-phosphocholine (dilauroylphosphatidylcholine, DLPC) vesicles and DLPC planar bilayers are investigated as a function of cholesterol concentration. 2D IR vibrational echo spectroscopy was performed on the antisymmetric CO stretch of the vibrational probe molecule tungsten hexacarbonyl, which is located in the interior alkyl regions of the bilayers. The 2D IR experiments measure spectral diffusion, which is caused by the structural fluctuations of the bilayers. The 2D IR measurements show that the bilayer interior alkyl region dynamics occur on time scales ranging from a few picoseconds to many tens of picoseconds. These are the time scales of the bilayers' structural dynamics, which act as the dynamic solvent bath for chemical processes of membrane biomolecules. The results suggest that at least a significant fraction of the dynamics arise from density fluctuations. Samples are studied in which the cholesterol concentration is varied from 0% to 40% in both the vesicles (72 nm diameter) and fully hydrated planar bilayers in the form of aligned multibilayers. At all cholesterol concentrations, the structural dynamics are faster in the curved vesicle bilayers than in the planar bilayers. As the cholesterol concentration is increased, at a certain concentration there is a sudden change in the dynamics, that is, the dynamics abruptly slow down. However, this change occurs at a lower concentration in the vesicles (between 10% and 15% cholesterol) than in the planar bilayers (between 25% and 30% cholesterol). The sudden change in the dynamics, in addition to other IR observables, indicates a structural transition. However, the results show that the cholesterol concentration at which the transition occurs is influenced by the curvature of the bilayers.

Length Scales and Structural Dynamics in Nematogen Pseudonematic Domains Measured with 2D IR Vibrational Echoes and Optical Kerr Effect Experiments

Nematogen liquids in the isotropic phase are macroscopically homogeneous but on multinanometer length scales have pseudonematic domains with correlation lengths that grow as the isotropic to nematic phase transition temperature (TNI) is approached from above. Orientational relaxation of nematogens in the isotropic phase manifests as two fast power laws and a slow exponential decay when measured by optical heterodyne detected optical Kerr effect (OHD-OKE) experiments. The long time exponential relaxation is associated with complete randomization of pseudonematic domains. We examine the effect of local orientational correlation on spectral diffusion (structural evolution) experienced by a vibrational probe molecule within the pseudonematic domains of 4-cyano-4'-pentylbiphenyl (5CB) using two-dimensional infrared (2D IR) vibrational echo spectroscopy. The addition of low concentration 4-pentyl-4'-thiocyanobiphenyl (5SCB) as a long-lived vibrational probe to 5CB is shown to lower TNI of the sample slightly, but the fast power law dynamics and exponential decays observed by OHD-OKE spectroscopy are unchanged. We compare the complete orientational relaxation and spectral diffusion for samples of 5SCB in 5CB to 5SCB in 4-pentylbiphenyl (5B) at four temperatures above TNI. 5B has a molecular structure similar to 5CB but is not a nematogen. At all but the lowest temperature, the spectral diffusion in 5CB and 5B is described well as a triexponential decay with very similar time constants. The results demonstrate that the presence of local orientational order at temperatures well above TNI does not affect the spectral diffusion (structural evolution) within pseudonematic domains when the correlation lengths are short. However, when the temperature of the sample is held very close to TNI, the spectral diffusion in 5CB slows dramatically while that in 5B does not. It is only as the correlation length becomes very long that its presence impacts the spectral diffusion (structural fluctuations) sensed by the vibrational probes located in pseudonematic domains. The orientational relaxation is modeled with schematic mode coupling theory (MCT). Fitting with MCT provides density and orientational correlation functions. The density correlation decays are similar for 5B and 5CB, but the orientational correlation decays are much slower for 5CB. Additionally, the time dependence of the spectral diffusion in 5CB is strikingly similar to that of the density correlation function decay, while the orientational correlation function decay is far too slow to contribute to the spectral diffusion. Therefore, density fluctuations are likely the source of spectral diffusion at temperatures at least 5 K above TNI.

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

The ultrafast structural dynamics inside the bilayers of dilauroylphosphatidylcholine (DLPC) and dipalmitoylphosphatidylcholine vesicles with 70, 90, and 125 nm diameters were directly measured with 2D IR vibrational echo spectroscopy. The antisymmetric CO stretch of tungsten hexacarbonyl was used as a vibrational probe and provided information on spectral diffusion (structural dynamics) in the alkyl region of the bilayers. Although the CO stretch absorption spectra remain the same, the interior structural dynamics become faster as the size of the vesicles decrease, with the size dependence greater for dipalmitoylphosphatidylcholine than for DLPC. As DLPC vesicles become larger, the interior dynamics approach those of the planar bilayer.

Dynamics of Molecular Monolayers with Different Chain Lengths in Air and Solvents Probed by Ultrafast 2D IR Spectroscopy

The ultrafast dynamics of functionalized alkylsilane monolayers with two different alkyl chain lengths, C11 and C3, are studied by 2D IR vibrational echo spectroscopy. Terminal sites of the monolayers are functionalized with an IR probe, tricarbonyl (1,10-phenanthroline) rhenium chloride (RePhen(CO)3Cl), to report on the structural dynamics of monolayer-air and monolayer-solvent interfaces. Frequency–frequency correlation functions (FFCF) of symmetric CO stretching mode were extracted from 2D IR spectra. The FFCF provides information on the time evolution of surface structures that contribute to the inhomogeneously broadened IR absorption spectrum of the CO stretch by quantifying spectral diffusion. To elucidate the detailed structural dynamics with accurate time constants, FFCF decays were monitored to 60 ps, a major improvement over prior experiments. Without the presence of solvents, C3 monolayers have significantly slower spectral diffusion (66 ps) than C11 monolayer (38 ps). This difference supports the previous postulate that spectral diffusion associated with the molecular monolayer in air involves the structural dynamics of the tethering alkyl chains. With the C11 and C3 monolayers immersed in dimethylformamide (DMF), in which RePhen(CO)3Cl is soluble, the FFCFs of both samples display biexponential decays with the time constants of 5.6 and 43 ps for C11 and 5.9 and 63 ps for C3. The slower time constants are in good agreement with the spectral diffusion time constants observed in the absence of solvent, indicating that these slower components still reflect the monolayers’ dynamics, which are not affected by the presence of the solvent. Because the faster time constants were independent of chain length and similar to that of the RePhen(CO)3Cl headgroup in bulk DMF solution, they are attributed to the dynamics of the interfacial DMF molecules. When monolayers were immersed in hexadecane, in which RePhen(CO)3Cl is not soluble, slower dynamics were again observed for the C3 monolayer than the C11 monolayer. The orientational dynamics of the IR probes were studied using polarization selective heterodyne detected transient grating experiments as well.

Ultrafast Structural Dynamics Inside Planar Phospholipid Multibilayer Model Cell Membranes Measured with 2D IR Spectroscopy

The ultrafast dynamics in the interior of planar aligned multibilayers of 1,2-dilauroyl-sn-glycero-3-phosphocholine (dilauroylphosphatidylcholine, DLPC) are investigated using 2D IR vibrational echo spectroscopy. The nonpolar and water insoluble vibrational dynamics probe, tungsten hexacarbonyl (W(CO)6), is located in the alkane interior of the membranes. The 2D IR experiments conducted on the antisymmetric CO stretching mode measure spectral diffusion caused by the structural dynamics of the membrane from ~200 fs to ~200 ps as a function of the number of water molecules hydrating the head groups and as a function of cholesterol content for a fixed hydration level. FT-IR studies of the lipid bilayers and the model liquids, hexadecane and bis(2-ethylhexyl) succinate, indicate that as the number of hydrating water molecules increases from 2 to 16, there are structural changes in the membrane that partition some of the W(CO)6 into the ester region of DLPC. However, the 2D IR measurements, which are made solely on the W(CO)6 in the alkane regions, show that the level of hydration has no observable impact on the interior membrane dynamics. FT-IR spectra and 2D IR experiments on samples with cholesterol concentrations from 0 to 60% demonstrate that there is a change in the membrane structure and an abrupt change in dynamics at 35% cholesterol. The dynamics are independent of cholesterol content from 10 to 35%. At 35%, the dynamics become slower and remain unchanged from 35 to 60% cholesterol.

Water Dynamics in Divalent and Monovalent Concentrated Salt Solutions

Water hydrogen bond dynamics in concentrated salt solutions are studied using polarization-selective IR pump-probe spectroscopy and 2D IR vibrational echo spectroscopy performed on the OD hydroxyl stretching mode of dilute HOD in H(2)O/salt solutions. The OD stretch is studied to eliminate vibrational excitation transfer, which interferes with the dynamical measurements. Though previous research suggested that only the anion affected dynamics in solution, here it is shown that the cation plays a role as well. From FT-IR spectra of the OD stretch, it is seen that replacing either ion of the salt pair causes a shift in absorption frequency relative to that of the OD stretch absorption in bulk pure water. This shift becomes pronounced with larger, more polarizable anions or smaller, high charge-density cations. The vibrational lifetime of the OD hydroxyl stretch in these solutions is a local property and is primarily dependent on the nature of the anion and whether the OD is hydrogen bonded to the anion or to the oxygen of another water molecule. However, the cation still has a small effect. Time dependent anisotropy measurements show that reorientation dynamics in these concentrated solutions is a highly concerted process. While the lifetime, a local probe, displays an ion-associated and a bulk-like component in concentrated solutions, the orientational relaxation does not have two subensemble dynamics, as demonstrated by the lack of a wavelength dependence. The orientational relaxation of the single ensemble is dependent on the identity of both the cation and anion. The 2D IR vibrational echo experiments measure spectral diffusion that is caused by structural evolution of the system. The vibrational echo measurements yield the frequency-frequency correlation function (FFCF). The results also show that the structural dynamics are dependent on the cation as well as the anion.

Fast Dynamics of HP35 for Folded and Urea-Unfolded Conditions

The changes in fast dynamics of HP35 with a double CN vibrational dynamics label (HP35-P(2)) as a function of the extent of denaturation by urea were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy. Cyanophenylalanine (PheCN) replaces the native phenylalanine at two residues in the hydrophobic core of HP35, providing vibrational probes. NMR data show that HP35-P(2) maintains the native folded structure similar to wild type and that both PheCN residues share essentially the same environment within the peptide. A series of time-dependent 2D IR vibrational echo spectra were obtained for the folded peptide and the increasingly unfolded peptide. Analysis of the time dependence of the 2D spectra yields the system's spectral diffusion, which is caused by the sampling of accessible structures of the peptide under thermal equilibrium conditions. The structural dynamics become faster as the degree of unfolding is increased.

Conformational Dynamics and Stability of HP35 Studied with 2D IR Vibrational Echoes

Two-dimensional infrared (2D IR) vibrational echo spectroscopy was used to measure the fast dynamics of two variants of chicken villin headpiece 35 (HP35). The CN of cyanophenylalanine residues inserted in the hydrophobic core were used as a vibrational probe. Experiments were performed on both singly (HP35-P) and doubly CN-labeled peptide (HP35-P(2)) within the wild-type sequence, as well as on HP-35 containing a singly labeled cyanophenylalanine and two norleucine mutations (HP35-P NleNle). There is a remarkable similarity between the dynamics measured in singly and doubly CN-labeled HP35, demonstrating that the presence of an additional CN vibrational probe does not significantly alter the dynamics of the small peptide. The substitution of two lysine residues by norleucines markedly improves the stability of HP35 by replacing charged with nonpolar residues, stabilizing the hydrophobic core. The results of the 2D IR experiments reveal that the dynamics of HP35-P are significantly faster than those of HP35-P NleNle. These observations suggest that the slower structural fluctuations in the hydrophobic core, indicating a more tightly structured core, may be an important contributing factor to HP35-P NleNle's increased stability.

Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy.

A nitrile-labeled amino acid, p-cyanophenylalanine, is introduced near the active site of the semisynthetic enzyme ribonuclease S to serve as a probe of protein dynamics and fluctuations. Ribonuclease S is the limited proteolysis product of subtilisin acting on ribonuclease A, and consists of a small fragment including amino acids 1-20, the S-peptide, and a larger fragment including residues 21-124, the S-protein. A series of two-dimensional vibrational echo experiments performed on the nitrile-labeled S-peptide and the RNase S are described. The time-dependent changes in the two-dimensional infrared vibrational echo line shapes are analyzed using the center line slope method to obtain the frequency-frequency correlation function (FFCF). The observations show that the nitrile probe in the S-peptide has dynamics that are similar to, but faster than, those of the single amino acid p-cyanophenylalanine in water. In contrast, the dynamics of the nitrile label when the peptide is bound to form ribonuclease S are dominated by homogeneous dephasing (motionally narrowed) contributions with only a small contribution from very fast inhomogeneous structural dynamics. The results provide insights into the nature of the structural dynamics of the ribonuclease S complex. The equilibrium dynamics of the nitrile labeled S-peptide and the ribonuclease S complex are also investigated by molecular dynamics simulations. The experimentally determined FFCFs are compared to the FFCFs obtained from the molecular dynamics simulations, thereby testing the capacity of simulations to determine the amplitudes and time scales of protein structural fluctuations on fast time scales under thermal equilibrium conditions.

Protein Dynamics Studied with Ultrafast Two-Dimensional Infrared Vibrational Echo Spectroscopy

Proteins, enzymes, and other biological molecules undergo structural dynamics as an intrinsic part of their biological functions. While many biological processes occur on the millisecond, second, and even longer time scales, the fundamental structural dynamics that eventually give rise to such processes occur on much faster time scales. Many decades ago, chemical kineticists focused on the inverse of the reaction rate constant as the important time scale for a chemical reaction. However, through transition state theory and a vast amount of experimental evidence, we now know that the key events in a chemical reaction can involve structural fluctuations that take a system of reactants to its transition state, the crossing of a barrier, and the eventual relaxation to product states. Such dynamics occur on very fast time scales. Today researchers would like to investigate the fast structural fluctuations of biological molecules to gain an understanding of how biological processes proceed from simple structural changes in biomolecules to the final, complex biological function. The study of the fast structural dynamics of biological molecules requires experiments that operate on the appropriate time scales, and in this Account, we discuss the application of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy to the study of protein dynamics. The 2D IR vibrational echo experiment is akin to 2D NMR, but it operates on time scales many orders of magnitude faster. In the experiments, a particular vibrational oscillator serves as a vibrational dynamics probe. As the structure of the protein evolves in time, the structural changes are manifested as time-dependent changes in the frequency of the vibrational dynamics probe. The 2D IR vibrational echo experiments can track the vibrational frequency evolution, which we then relate to the time evolution of the protein structure. In particular, we measured protein substate interconversion for mutants of myoglobin using 2D IR chemical exchange spectroscopy and observed well-defined substate interconversion on a sub-100 ps time scale. In another study, we investigated the influence of binding five different substrates to the enzyme cytochrome P450(cam). The various substrates affect the enzyme dynamics differently, and the observed dynamics are correlated with the enzyme's selectivity of hydroxylation of the substrates and with the substrate binding affinity.

Dynamics of Interfaces Studied with Ultrafast 2D IR Vibrational Echo Spectroscopy

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Dynamics at Specific Sites in Proteins Studied by 2D IR Vibrational Echo Spectroscopy

The techniques of two-dimensional infrared (2D IR) spectroscopy enable the study of fluctuations of molecules and their environments on fast timescales. Characterization of specific sites in proteins requires the use of extrinsic vibration probes to alleviate the spectral complexity that hinders the application of IR spectroscopy with protein samples. Heme-bound CO has been a popular vibrational probe of protein active sites and, for example, was employed to characterize the involvement of dynamics in the specificity of cytochrome P450 using 2D IR spectroscopy. In efforts toward extending the 2D IR studies beyond heme proteins, an azidophenylalanine vibrational probe was introduced at a specific site within myoglobin using orthogonal transfer RNA (tRNA)/aminoacyl-tRNA synthetase pairs evolved to insert azidophenylalanine in response to an amber codon. The azidophenylalanine vibrational probe was placed within the heme pocket at Phe43, permitting investigation of one site in myoglobin via two different vibrational probes - the genetically introduced azidophenylalanine and heme bound CO. The use of two probes allowed assessment of the perturbation due to introduction of each and the measurement of the heme pocket dynamics via two perspectives, showing that the reported dynamics were reflective of the protein motions, and not intrinsic to a particular probe. This approach can be used in the future to characterize the dynamics at virtually any site throughout virtually any protein.

Structural Dynamics of a Catalytic Monolayer Probed by Ultrafast 2D IR Vibrational Echoes

Ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy has proven broadly useful for studying molecular dynamics in solutions. Here, we extend the technique to probing the interfacial dynamics and structure of a silica surface-tethered transition metal carbonyl complex--tricarbonyl (1,10-phenanthroline)rhenium chloride--of interest as a photoreduction catalyst. We interpret the data using a theoretical framework devised to separate the roles of structural evolution and excitation transfer in inducing spectral diffusion. The structural dynamics, as reported on by a carbonyl stretch vibration of the surface-bound complex, have a characteristic time of ~150 picoseconds in the absence of solvent, decrease in duration by a factor of three upon addition of chloroform, and decrease another order of magnitude for the bulk solution. Conversely, solvent-complex interactions increase the lifetime of the probed vibration by 160% when solvent is applied to the monolayer.

Time-dependent fifth-order bands in nominally third-order 2D IR vibrational echo spectra.

Progress in the field of 2D IR vibrational spectroscopy has been bolstered by the production of intense mid-IR laser pulses. As higher-energy pulses are employed, a concomitant increase occurs in the likelihood of fifth-order contributions to the 2D IR spectra. We report the appearance of fifth-order signals in 2D IR spectra of CO bound to the active site of the enzyme cytochrome P450(cam) with the substrate norcamphor. Two bands with novel time dependences, one on the diagonal and one off-diagonal, are not accounted for by normal third-order interactions. These bands are associated with a ν = 1-2 vibrational transition frequency. Both bands decay to 0 and then grow back in with opposite sign. The diagonal band is positive at short time, decays to 0, reappears with negative sign, before eventually decaying to 0. The off-diagonal band is negative at short time, decays to 0, reappears positive, and then decays to 0. The appearance and time dependence of these bands are characterized. Understanding these fifth-order bands is useful because they may be misidentified with time-dependent bands that arise from other processes, such as chemical exchange, vibrational coupling, or energy transfer. The presence and unusual time dependences of the fifth-order bands are reproduced with model calculations that account for the fact that vibrational relaxation from the ν = 2 to 1 level is approximately a factor of 2 faster than that from the ν = 1 to 0 level.

Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments.

Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.

Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy.

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.