Nien-Hui Ge

Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination

The power of two-dimensional (2D) IR spectroscopy as a structural method with unprecedented time resolution is greatly improved by the introduction of IR polarization conditions that completely eliminate diagonal peaks from the spectra and leave only the crosspeaks needed for structure determination. This approach represents a key step forward in the applications of 2D IR to proteins, peptides, and other complex molecules where crosspeaks are often obscured by diagonal peaks. The technique is verified on the model compound 1,3-cyclohexanedione and subsequently used to clarify the distribution of structures that the acetylproline-NH2 dipeptide adopts in chloroform. In both cases, crosspeaks are revealed that were not observed before, which, in the case of the dipeptide, has led to additional information about the structure of the amino group end of the peptide.

Femtosecond studies of electron tunneling at metal-dielectric interfaces

Abstract Femtosecond time-resolved two-photon photoemission spectrocopy (TPPE) has been used to measure the lifetimes of image potential electrons at alkane mono- and bilayers on Ag(111). The n = 1 lifetimes for zero, one, and two layers of n-heptane on Ag(111) are 32 ± 10 fs, 155 ± 20 fs, and 1580 ± 200 fs, respectively. This approximately exponential increase in lifetime is consistent with a tunneling picture in which the adlayer forms a barrier that slows the decay of an image potential electron back into the metal. The existence of the tunneling barrier is consistent with the repulsive electron affinity of the longer chain n-alkanes in the condensed phase. The lifetimes of the higher quantum states indicate that the presence of the monolayer significantly reduces coupling of the image states to the bulk band structure, so that further changes in lifetime are determined by the adlayer barrier and an attempt rate related to the classical oscillation time in the modified image potential well. These results are compared with quantitative predictions of a model by Cole which considers the tunneling barrier presented by the layer and the effect of the layer on the attempt rate. These results are considered in the context of previous TPPE studies of metal-insulator interfaces.

Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra

We have carried out a comparative study of five ab initio electrostatic frequency maps and a semiempirical model for the amide-I and -II modes. Unrestrained molecular dynamics simulation of a 3(10)-helical peptide, Z-Aib-L-Leu-(Aib)(2)-Gly-OtBu, in CDCl(3) is performed using the AMBER ff99SB force field, and the linear and two-dimensional infrared (2D IR) spectra are simulated on the basis of a vibrational exciton Hamiltonian model. A new electrostatic potential-based amide-I and -II frequency map for N-methylacetamide is developed in this study. This map and other maps developed by different research groups are applied to calculate the local mode frequencies of the amide linkages in the hexapeptide. The simulated amide-I line shape from all models agrees well with the previous experimental results on the same system, except for an overall frequency shift. In contrast, the simulated amide-II bands are more sensitive to the frequency maps. Essential features obtained in the electrostatic models are captured by the semiempirical model that takes into account only the intramolecular hydrogen bonding effects and solvent shifts. Detailed comparisons between the models are also drawn through analysis of the local mode frequency shifts. Among all of the maps tested in this study, the new four-site potential map performs quite well in simulating the amide-II bands. It properly predicts the effects of hydrogen bonding on the amide-I and -II frequencies and reasonably simulates the isotope-dependent amide-I/II cross peaks upon (13)C=(18)O/(15)N substitutions.

Stapling of a 310-Helix with Click Chemistry

Short peptides are important as lead compounds and molecular probes in drug discovery and chemical biology, but their well-known drawbacks, such as high conformational flexibility, protease lability, poor bioavailability and short half-lives in vivo, have prevented their potential from being fully realized. Side chain-to-side chain cyclization, e.g., by ring-closing olefin metathesis, known as stapling, is one approach to increase the biological activity of short peptides that has shown promise when applied to 3(10)- and α-helical peptides. However, atomic resolution structural information on the effect of side chain-to-side chain cyclization in 3(10)-helical peptides is scarce, and reported data suggest that there is significant potential for improvement of existing methodologies. Here, we report a novel stapling methodology for 3(10)-helical peptides using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction in a model aminoisobutyric acid (Aib) rich peptide and examine the structural effect of side chain-to-side chain cyclization by NMR, X-ray diffraction, linear IR and femtosecond 2D IR spectroscopy. Our data show that the resulting cyclic peptide represents a more ideal 3(10)-helix than its acyclic precursor and other stapled 3(10)-helical peptides reported to date. Side chain-to-side chain stapling by CuAAC should prove useful when applied to 3(10)-helical peptides and protein segments of interest in biomedicine.

Rapid vibrational imaging with sum frequency generation microscopy

We demonstrate rapid vibrational imaging based on sum frequency generation (SFG) microscopy with a collinear excitation geometry. Using the tunable picosecond pulses from a high-repetition-rate optical parametric oscillator, vibrationally selective imaging of collagen fibers is achieved with submicrometer lateral resolution. We furthermore show simultaneous SFG and second harmonic generation imaging to emphasize the compatibility of the microscope with other nonlinear optical modalities.

Onset of 310-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.

Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains

We have carried out structural determination of capped C(α,α)-diethylglycine (Deg) homopeptides with different chain lengths, Ac-(Deg)(n)-OtBu (n = 2-5), solvated in CDCl(3), and investigated vibrational properties of the amide I and II modes by linear and 2D IR spectroscopy, ONIOM calculations, and molecular dynamics simulations. 2D IR experiments were performed in the amide I region using the rephasing pulse sequence under the double-crossed polarization and the nonrephasing sequence under a new polarization configuration to measure cross-peak patterns in the off-diagonal regions. The 2D IR spectra measured in the amide I and II regions reveal complex couplings between these modes. Model spectral calculations finely reproduced the measured spectral profiles by using vibrational parameters that were very close to the values predicted by the ONIOM method. The agreement led to a conclusion that peptide backbones are fully extended with the dihedral angles (ϕ,ψ) ≈ (±180°,±180°) and that a sequence of intramolecular C(5) hydrogen bonds forms along the entire chain regardless of the chain length. This conclusion was endorsed by analysis of the molecular dynamics trajectories for n = 3 and 5 that showed an exclusive population of the C(5) conformation. The conformationally well-restrained Deg homopeptides serve as an ideal linear exciton chain, which is scarcely obtainable by protein amino acids. We investigated excitonic properties of the linear chain through analytic modeling and compared the measurement and calculation results of the amide I and II modes. The integrated intensity of the amide II band is larger than that of the amide I for the C(5) structure, untypical behavior in contrast with other secondary structures. This comprehensive study characterized the amide I and II spectral signatures of the fully extended conformation, which will facilitate the conformational analysis of artificial oligopeptides that contain such structural motifs.

Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide.

We have investigated the sensitivity of two-dimensional infrared (2D IR) spectroscopy to peptide helicity with an experimental and theoretical study of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3). 2D IR experiments were carried out in the amide-I region under the parallel and the double-crossed polarization configurations. In the latter polarization configuration, the 2D spectra taken with the rephasing and nonrephasing pulse sequences exhibit a doublet feature and a single peak, respectively. These cross-peak patterns are highly sensitive to the underlying peptide structure. Spectral calculations were performed on the basis of a vibrational exciton model, with the local mode frequencies and couplings calculated from snapshots of molecular dynamics (MD) simulation trajectories using six different models for the Hamiltonian. Conformationally variant segments of the MD trajectory, while reproducing the main features of the experimental spectra, are characterized by extraneous features, suggesting that the structural ensembles sampled by the simulation are too broad. By imposing periodic restraints on the peptide dihedral angles with the crystal structure as a reference, much better agreement between the measured and the calculated spectra was achieved. The result indicates that the structure of Z-[l-(alphaMe)Val](8)-OtBu in CDCl(3) is a fully developed 3(10)-helix with only a small fraction of alpha-helical or nonhelical conformations in the middle of the peptide. Of the four different combinations of pulse sequences and polarization configurations, the nonrephasing double-crossed polarization 2D IR spectrum exhibits the highest sensitivity in detecting conformational variation. Of the six local mode frequency models tested, the electrostatic maps of Mukamel and Cho perform the best. Our results show that the high sensitivity of 2D IR spectroscopy can provide a useful basis for developing methods to improve the sampling accuracy of force fields and for characterizing the relative merits of the different protocols for the Hamiltonian calculation.

Mapping molecular orientation with phase sensitive vibrationally resonant sum-frequency generation microscopy

We demonstrate a phase sensitive, vibrationally resonant sum-frequency generation (PSVR-SFG) microscope that combines high resolution, fast image acquisition speed, chemical selectivity, and phase sensitivity. Using the PSVR-SFG microscope, we generate amplitude and phase images of the second-order susceptibility of collagen I fibers in rat tail tendon tissue on resonance with the methylene vibrations of the protein. We find that the phase of the second-order susceptibility shows dependence on the effective polarity of the fibril bundles, revealing fibrous collagen domains of opposite orientations within the tissue. The presence of collagen microdomains in tendon tissue may have implications for the interpretation of the mechanical properties of the tissue.

Femtosecond two-dimensional infrared spectroscopy: IR-COSY and THIRSTY

The femtosecond two-dimensional infrared (2D IR) spectroscopy that was recently developed shows great promise for determining the dynamics of molecular structure at ultrafast time scales that are hard to access by NMR and X-ray diffraction methods. This Perspective focuses on the IR-COSY and THIRSTY methods that are based on heterodyned three pulse photon echoes. The relationships of 2D spectral properties coupling, structure, correlated fluctuations, energy transfer, and orientational motions to experimental results on small peptides and molecules are described. The status of this exciting new field is also discussed.