Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy

Phase stable, shot-to-shot measurement of third- and fifth-order two-quantum correlation spectra using a pulse shaper in the pump-probe geometry

We demonstrate the first phase stable measurement of a third-order 2Q spectrum using a pulse shaper in the pump-probe geometry. This measurement was achieved by permuting the time-ordering of the pump pulses, thus rearranging the signal pathways that are emitted in the probe direction. The third-order 2Q spectrum is self-heterodyned by the probe pulse. Using this method, one can interconvert between a 1Q experiment and a 2Q experiment by simply reprogramming a pulse shaper or delay stage. We also measure a fifth-order absorptive 2Q spectrum in the pump-probe geometry, which contains similar information as a third-order experiment but does not suffer from dispersive line shapes. To do so, we introduce methods to minimize saturation-induced artifacts of the pulse shaper, improving fifth-order signals. These techniques add new capabilities for 2D spectrometers that use pulse shapers in the pump-probe beam geometry.

Molecular Coherent Three-Quantum Two-Dimensional Fluorescence Spectroscopy

We introduce molecular coherent three-quantum (3Q) two-dimensional (2D) fluorescence spectroscopy with phase cycling via shot-to-shot pulse shaping at a 1 kHz repetition rate. This allows us to acquire simultaneously, within a single scan, three fourth-order and six sixth-order signals correlating various one-quantum, two-quantum, and 3Q coherences. We demonstrate the approach on the dye molecule rhodamine 700 and reproduce all nine 2D data sets, including their absolute signal strengths, with simulations using a single, consistent set of model parameters. We observe a linear concentration dependence of all nonlinear signals, evidencing the absence of cascades and many-particle signals of noninteracting molecules. The single-beam, background-free implementation allows direct comparability between various nonlinear signal types and provides information about multiple excited states. Apart from molecules, the method is expected to be applicable to supramolecular systems, polymers, and solid-state materials with the prospect of revealing signatures of bi- and triexcitonic states.

Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids

The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid N-acetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, syn- and anti-. In the syn-conformer the O-H group is oriented at  ~60^∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the -COOH groups adopt an anti-conformation. However, when N-acetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to ~60%.

Coherent two-dimensional Fourier transform spectroscopy using a 25 Tesla resistive magnet

We performed nonlinear optical two-dimensional Fourier transform spectroscopy measurements using an optical resistive high-field magnet on GaAs quantum wells. Magnetic fields up to 25 T can be achieved using the split helix resistive magnet. Two-dimensional spectroscopy measurements based on the coherent four-wave mixing signal require phase stability. Therefore, these measurements are difficult to perform in environments prone to mechanical vibrations. Large resistive magnets use extensive quantities of cooling water, which causes mechanical vibrations, making two-dimensional Fourier transform spectroscopy very challenging. Here, we report on the strategies we used to overcome these challenges and maintain the required phase-stability throughout the measurement. A self-contained portable platform was used to set up the experiments within the time frame provided by a user facility. Furthermore, this platform was floated above the optical table in order to isolate it from vibrations originating from the resistive magnet. Finally, we present two-dimensional Fourier transform spectra obtained from GaAs quantum wells at magnetic fields up to 25 T and demonstrate the utility of this technique in providing important details, which are obscured in one dimensional spectroscopy.

General noise suppression scheme with reference detection in heterodyne nonlinear spectroscopy

We devised a novel two-step reference scheme that can greatly suppress the additive and convolutional noises in heterodyne nonlinear spectroscopy. To optimally remove additive noise, we fully utilized the spectral correlation in multi-channel reference data through a linear combination and regression algorithm. Using our pump-probe 2D IR spectrometer, we demonstrated that our scheme can improve the signal-to-noise ratio by 10-30 times and reach the noise floor of the signal detector. The new algorithm is guaranteed to reduce noise, enables the use of unmatched reference detectors, and does not introduce baseline shift or signal distortion. This scheme is applicable to many heterodyne spectroscopic techniques.

Design of peptide-containing N5-unmodified neutral flavins that catalyze aerobic oxygenations

Simulation of the monooxygenation function of flavoenzyme (Fl-Enz) has been long-studied with N5-modified cationic flavins (FlEt+ ), but never with N5-unmodified neutral flavins (Fl) despite the fact that Fl is genuinely equal to the active center of Fl-Enz. This is because of the greater lability of 4a-hydroperoxy adduct of Fl, FlOOH , compared to those of FlEt+ , FlEtOOH , and Fl-Enz, FlOOH-Enz. In this study, Fl incorporated into a short peptide, flavopeptide (Fl-Pep), was designed by a rational top-down approach using a computational method, which could stabilize the corresponding 4a-hydroperoxy adduct (FlOOH-Pep) through intramolecular hydrogen bonds. We report catalytic chemoselective sulfoxidation as well as Baeyer-Villiger oxidation by means of Fl-Pep under light-shielding and aerobic conditions, which are the first Fl-Enz-mimetic aerobic oxygenation reactions catalyzed by Fl under non-enzymatic conditions.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation

We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.

On the Calculation of Vibrational Frequencies for Molecules in Solution Beyond the Harmonic Approximation

We report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent interactions, the latter being described by means of the polarizable continuum model (PCM). Density functional theory force fields are employed as well as a new implementation of the PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide prototypes show that our approach is able to yield a quantitative agreement with experiments for vacuo-to-solvent harmonic and anharmonic frequency shifts.

Continuously tunable optical multidimensional Fourier-transform spectrometer

A multidimensional optical nonlinear spectrometer (MONSTR) is a robust, ultrastable platform consisting of nested and folded Michelson interferometers that can be actively phase stabilized. The MONSTR provides output pulses for nonlinear excitation of materials and phase-stabilized reference pulses for heterodyne detection of the induced signal. This platform generates a square of identical laser pulses that can be adjusted to have arbitrary time delays between them while maintaining phase stability. This arrangement is ideal for performing coherent optical experiments, such as multidimensional Fourier-transform spectroscopy. The present work reports on overcoming some important limitations on the original design of the MONSTR apparatus. One important advantage of the MONSTR is the fact that it is a closed platform, which provides the high stability. Once the optical alignment is performed, it is desirable to maintain the alignment over long periods of time. The previous design of the MONSTR was limited to a narrow spectral range defined by the optical coating of the beam splitters. In order to achieve tunability over a broad spectral range the internal optics needed to be changed. By using broadband coated and wedged beam splitters and compensator plates, combined with modifications of the beam paths, continuous tunability can be achieved from 520 nm to 1100 nm without changing any optics or performing alignment of the internal components of the MONSTR. Furthermore, in order to achieve continuous tunability in the spectral region between 520 nm and 720 nm, crucially important for studies on numerous biological molecules, a single longitudinal mode laser at 488.5 nm was identified and used as a metrology laser. The shorter wavelength of the metrology laser as compared to the usual HeNe laser has also increased the phase stability of the system. Finally, in order to perform experiments in the reflection geometry, a simple method to achieve active phase stabilization between the signal and the reference beams has been developed.

Two-dimensional double-quantum spectra reveal collective resonances in an atomic vapor

We report the observation of double-quantum coherence signals in a gas of potassium atoms at twice the frequency of the one-quantum coherences. Since a single atom does not have a state at the corresponding energy, this observation must be attributed to a collective resonance involving multiple atoms. These resonances are induced by weak interatomic dipole-dipole interactions, which means that the atoms cannot be treated in isolation, even at a low density of 10(12)  cm(-3).

Spectroscopic studies of protein folding: linear and nonlinear methods

Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics.

Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer

Two-dimensional (2D) vibrational echo spectroscopy has previously been applied to structural determination of small peptides. Here we extend the technique to a more complex, biologically important system: the homodimeric transmembrane dimer from the α chain of the integrin α(IIb)β(3). We prepared micelle suspensions of the pair of 30-residue chains that span the membrane in the native structure, with varying levels of heavy ((13)C=(18)O) isotopes substituted in the backbone of the central 10th through 20th positions. The constraints derived from vibrational coupling of the precisely spaced heavy residues led to determination of an optimized structure from a range of model candidates: Glycine residues at the 12th, 15th, and 16th positions form a tertiary contact in parallel right-handed helix dimers with crossing angles of -58° ± 9° and interhelical distances of 7.7 ± 0.5 angstroms. The frequency correlation established the dynamical model used in the analysis, and it indicated the absence of mobile water associated with labeled residues. Delocalization of vibrational excitations between the helices was also quantitatively established.

Simulation study of chiral two-dimensional ultraviolet spectroscopy of the protein backbone

Amide n-pi* and pi-pi* excitations around 200 nm are prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviolet (UV) circular dichroism for structure characterization. Recently developed ultrafast laser sources may be used to extend these studies to two dimensions. We apply a new algorithm for modeling protein electronic transitions to simulate two-dimensional UV photon echo signals in this regime and to identify signatures of protein backbone secondary (and tertiary) structure. Simulated signals for a set of globular and fibrillar proteins and their specific regions reveal characteristic patterns of helical and sheet secondary structures. We investigate how these patterns vary and converge with the size of the structural motif. Specific chiral polarization configurations of the UV pulses are found to be sensitive to aspects of the protein structure. This information significantly augments that available from linear circular dichroism.

Gas-phase conformation-specific photofragmentation of proline-containing peptide ions

Singly-protonated proline-containing peptides with N-terminal arginine are photodissociated with vacuum ultraviolet (VUV) light in an ESI linear ion trap/orthogonal-TOF (LIT/o-TOF). When proline is the nth residue from the N-terminus, unusual b(n) + 2 and a(n) + 2 ions are observed. Their formation is explained by homolytic cleavage of the C(alpha)-C bond in conjunction with a rearrangement of electrons and an amide hydrogen. The latter is facilitated by a proline-stabilized gas-phase peptide conformation.

Two-quantum many-body coherences in two-dimensional fourier-transform spectra of exciton resonances in semiconductor quantum wells

We present experimental coherent two-dimensional Fourier-transform spectra of Wannier exciton resonances in semiconductor quantum wells generated by a pulse sequence that isolates two-quantum coherences. By measuring the real part of the signals, we determine that the spectra are dominated by two-quantum coherences due to mean-field many-body interactions, rather than bound biexcitons. Simulations performed using dynamics controlled truncation agree with the experiments.

Interactions of tyrosine in Leu-enkephalin at a membrane-water interface: an ultrafast two-dimensional infrared study combined with density functional calculations and molecular dynamics simulations

The interactions of neuropeptides and membranes play an important role in peptide hormone function. Our current understanding of peptide-membrane interactions remains limited due to the paucity of experimental techniques capable of probing such interactions. In this work, we study the nature of opioid peptide-membrane interactions using ultrafast two-dimensional infrared (2D IR) spectroscopy. The high temporal resolution of 2D IR is particularly suited for studying highly flexible opioid peptides. We investigate the location of the tyrosine (Tyr) side chain of leucine-enkephalin (Lenk) in lipid bilayer membranes by measuring spectral diffusion of the phenolic ring vibrational mode in three different systems: Lenk in lipid bilayer membranes (bicelles), Lenk in deuterated water, and p-cresol in deuterated water. Frequency-frequency correlation functions obtained from waiting-time-dependent 2D IR spectra reveal an ultrafast decaying component with an approximately 1 ps time constant that is common for all three systems. On the basis of density functional theory calculations and molecular dynamics simulations, this spectral diffusion component is attributed to hydrogen-bond dynamics of the phenolic hydroxyl group interacting with bulk water. Unlike p-cresol in water, both Lenk systems exhibit static spectral inhomogeneity, which can be attributed to conformational distributions of Lenk that do not interconvert within 4 ps. Our results suggest that the Tyr side chain of Lenk in bicelles is located at the water-abundant region at the membrane-water interface and not embedded into the hydrophobic core.

Toward detecting the formation of a single helical turn by 2D IR cross peaks between the amide-I and -II modes

We have combined two-dimensional infrared (2D IR) spectroscopy and isotope substitutions to reveal the vibrational couplings between a pair of amide-I and -II modes that are several residues away but directly connected through a hydrogen bond in a helical peptide. This strategy is demonstrated on a 3(10)-helical hexapeptide, Z-Aib-L-Leu-(Aib)2-Gly-Aib-OtBu, and its 13C=18O-Leu monolabeled and 13C=18O-Leu/15N-Gly bis-labeled isotopomers in CDCl3. The isotope-dependent amide-I/II cross peaks clearly show that the second and fourth peptide linkages are vibrationally coupled as they are in proximity, forming a 3(10)-helical turn. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model that fully takes into account the amide-I and -II modes. The amide-II local mode frequency is evaluated by a new model based on the effects of hydrogen-bond geometry and sites. Ab initio nearest-neighbor coupling maps of the amide-I/I, -I/II, -II/I and -II/II modes are generated by isotopically isolating the local modes of N-acetyl-glycine N'-methylamide (AcGlyNHMe). Longer range couplings are modeled by transition charge interactions. The effects of the capping groups are incorporated and isotope effects are analyzed based on ab initio calculations of six model compounds. The main features of the 2D IR spectra are reproduced by this modeling. The conformational sensitivity of the isotope-dependent amide-I/II cross peaks is discussed in comparison with the calculated spectra for a semiextended structure. Our experimental and theoretical study demonstrates that the combination of 2D IR and 13C=18O/15N labeling is a useful structural method for detecting helical turn formation with residue-level specificity.

A versatile ultrastable platform for optical multidimensional Fourier-transform spectroscopy

The JILA multidimensional optical nonlinear spectrometer (JILA-MONSTR) is a robust, ultrastable platform consisting of nested and folded Michelson interferometers that can be actively phase stabilized. This platform generates a square of identical laser pulses that can be adjusted to have arbitrary time delay between them while maintaining phase stability. The JILA-MONSTR provides output pulses for nonlinear excitation of materials and phase-stabilized reference pulses for heterodyne detection of the induced signal. This arrangement is ideal for performing coherent optical experiments, such as multidimensional Fourier-transform spectroscopy, which records the phase of the nonlinear signal as a function of the time delay between several of the excitation pulses. The resulting multidimensional spectrum is obtained from a Fourier transform. This spectrum can resolve, separate, and isolate coherent contributions to the light-matter interactions associated with electronic excitation at optical frequencies. To show the versatility of the JILA-MONSTR, several demonstrations of two-dimensional Fourier-transform spectroscopy are presented, including an example of a phase-cycling scheme that reduces noise. Also shown is a spectrum that accesses two-quantum coherences, where all excitation pulses require phase locking for detection of the signal.

Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.

Two-quantum 2D FT electronic spectroscopy of biexcitons in GaAs quantum wells

The motions of electrons in solids may be highly correlated by strong, long-range Coulomb interactions. Correlated electron-hole pairs (excitons) are accessed spectroscopically through their allowed single-quantum transitions, but higher-order correlations that may strongly influence electronic and optical properties have been far more elusive to study. Here we report direct observation of bound exciton pairs (biexcitons) that provide incisive signatures of four-body correlations among electrons and holes in gallium arsenide (GaAs) quantum wells. Four distinct, mutually coherent, ultrashort optical pulses were used to create coherent exciton states, transform these successively into coherent biexciton states and then new radiative exciton states, and finally to read out the radiated signals, yielding biexciton binding energies through a technique closely analogous to multiple-quantum two-dimensional Fourier transform (2D FT) nuclear magnetic resonance spectroscopy. A measured variation of the biexciton dephasing rate indicated still higher-order correlations.

ps-TRIR covers all the bases--recent advances in the use of transient IR for the detection of short-lived species in nucleic acids

Recent developments of the picosecond transient absorption infrared technique and its ability to elucidate the nature and kinetic behaviour of transient species formed upon pulsed laser excitation of nucleic acids are described.

Couplings between peptide linkages across a 3(10)-helical hydrogen bond revealed by two-dimensional infrared spectroscopy

Vibrational couplings between the amide modes are keenly dependent on peptide structure. Site-specific couplings can inform us of molecular conformation in detail. For example, when an amide-I mode couples to an amide-II mode that is three residues away because they are brought into proximity in the presence of an intramolecular C=O...H-N hydrogen bond, the coupling can provide direct evidence for single helical turn formation, a proposed key step in coil-helix transition. In this work, we measure 2D IR spectra of a 3(10)-helical hexapeptide, Z-Aib-l-Leu-(Aib)(2)-Gly-Aib-OtBu, and its (13)C=(18)O-Leu monolabeled and (13)C=(18)O-Leu/(15)N-Gly bis-labeled isotopomers in CDCl(3). The isotope-dependent amide-I/II cross-peaks clearly reveal the existence of vibrational coupling between the second and fourth peptide linkages that are connected through a 3(10)-helical hydrogen bond. Our results demonstrate that the combination of 2D IR and (13)C=(18)O/(15)N labeling is a useful structural method for probing local peptide conformation with residue-level specificity.

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra

We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.

Onset of 3(10)-helical secondary structure in aib oligopeptides probed by coherent 2D IR spectroscopy

We have investigated the onset of the secondary structure and the evolution of two-dimensional infrared (2D IR) spectral patterns as a function of chain length with a study of 3(10)-helical peptides. The results show that 2D IR is highly sensitive to peptide conformation, disorder, and size. An extensive set of 2D IR spectra of C (alpha)-methylated homopeptides, Z-(Aib) n -O tBu ( n = 3, 5, 8, and 10), in CDCl 3 was measured in the amide-I region. The 2D spectral patterns of the tripeptide are quite different from those of the longer peptides. The spectral signatures begin to converge at the pentapeptide and become almost the same for the octa- and decapeptide. Simulations employing a vibrational exciton model were performed, with the local mode frequency shifts estimated from the intramolecular hydrogen bond electrostatic energies. The 2D spectra are well simulated using dihedral angle distributions around the average values (phi, psi) approximately (-57 degrees , -31 degrees) with a width of approximately 21 degrees. The simulated site-dependent amide-I local mode frequencies are in agreement with those from scaled semiempirical AM1 calculations. The tripeptide exhibits a more noticeable discrepancy between the experimental and simulated cross-peak patterns. This behavior suggests the presence of a peptide population outside the single beta-turn conformation. The onset of the 3(10)-helical secondary structure appears to already occur at the pentapeptide level.

Orthogonal sample design scheme for two-dimensional synchronous spectroscopy and its application in probing intermolecular interactions

This paper introduces a new approach to probing intermolecular interactions based on a framework of two-dimensional (2D) synchronous spectroscopy. Mathematical analysis performed on 2D synchronous spectra using variable concentration as an external perturbation shows that the cross-peaks are composed of two parts. The first part reflects intermolecular interactions that manifest in the form of deviation from the Beer-Lambert law. The second part is related simply to the concentration variations of the solutes and is responsible for the generation of interfering cross-peaks not related to the intermolecular interactions in the system. It is the second part that prevents the reliable identification of intermolecular interactions. We propose a way of selecting the concentrations of solutes so that the resultant dynamic concentration vectors of different solutes become orthogonal to one another. Therefore, the contribution of the second part to the cross-peaks can be effectively removed by the dot product of orthogonal vectors. Our new approach has been tested on a simulated chemical system and a real chemical system. The results demonstrate that interfering cross-peaks can be successfully removed from a 2D synchronous spectrum so that the cross-peaks can be used as a reliable tool to characterize or probe intermolecular interactions.

The 2D IR responses of amide and carbonyl modes in water cannot be described by Gaussian frequency fluctuations

The two-dimensional (2D) IR spectral shapes seen for aqueous amide-I' or carbonyls having apparently single bands are not those predicted by Gaussian frequency fluctuations. Their population evolution exposes discrete distributions undergoing picosecond time scale exchange. The energy transfer to other modes provides a clear view of this underlying structure, which is largely attributed to exchanging water configurations. The results suggest new approaches to examine protein-bound water at the residue level.

Infrared Study of the Effect of Hydration on the Amide I Band and Aggregation Properties of Helical Peptides

The amide I' band of a polypeptide is sensitive not only to its secondary structure content but also to its environment. In this study we show how degrees of hydration affect the underlying spectral features of the amide I' band of two alanine-based helical peptides. This is achieved by solubilizing these peptides in the water pool of sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles with different water contents or w0 values. In agreement with several earlier studies, our results show that the amide I' band arising from a group of dehydrated helical amides is centered at approximately 1650 cm-1, whereas hydration shifts this frequency toward lower wavenumbers. More importantly, temperature-dependent infrared studies further show that these helical peptides undergo a thermally induced conformational transition in reverse micelles of low w0 values (e.g., w0=6), resulting in soluble peptide aggregates rich in antiparallel beta-sheets. Interestingly, however, increasing w0 or water content leads to an increase in the onset temperature at which such beta-aggregates begin to form. Therefore, these results provide strong evidence suggesting that dehydration facilitates aggregate formation and that removal of water imposes a free energy barrier to peptide association and aggregation, a feature that has been suggested in recent simulation studies focusing on the mechanism of beta-amyloid formation.

Two-Dimensional Infrared Spectral Signatures of 310- and α-Helical Peptides

Two-dimensional infrared (2D IR) spectra of Calpha-alkylated model octapeptides Z-(Aib)8-OtBu, Z-(Aib)5-L-Leu-(Aib)2-OMe, and Z-[L-(alphaMeVal)]8-OtBu have been measured in the amide I region to acquire 2D spectral signatures characteristic of 3(10)- and alpha-helical conformations. Phase-adjusted 2D absorptive spectra recorded with parallel polarizations are dominated by intense diagonal peaks, whereas 2D rephasing spectra obtained at the double-crossed polarization configuration reveal cross-peak patterns that are essential for structure determination. In CDCl3, all three peptides are of the 3(10)-helix conformation and exhibit a doublet cross-peak pattern. In 1,1,1,3,3,3-hexafluoroisopropanol, Z-[L-(alphaMeVal)]8-OtBu undergoes slow acidolysis and 3(10)-to-alpha-helix transition. In the course of this conformational change, its 2D rephasing spectrum evolves from an elongated doublet, characteristic of a distorted 3(10)-helix, to a multiple-peak pattern, after becoming an alpha-helix. The linear IR and 2D absorptive spectra are much less informative in discerning the structural changes. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model. The through-bond and through-space vibrational couplings are modeled by ab initio coupling maps and transition dipole interactions. The local amide I frequency is evaluated by a new approach that takes into account the effects of hydrogen-bond geometry and sites. The static diagonal and off-diagonal disorders are introduced into the Hamiltonian through statistical models to account for conformational fluctuations and inhomogeneous broadening. The sensitivity of cross-peak patterns to different helical conformations and the chain length dependence of the spectral features for short 3(10)- and alpha-helices are discussed.