Yung Sam Kim

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.

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.

2D IR provides evidence for mobile water molecules in β-amyloid fibrils

The motion of water molecules close to amide groups causes their vibrational frequencies to vary rapidly in time. These variations are uniquely sensed by 2-dimensional infrared spectroscopy (2D IR). Here, it is proposed from 2-dimensional experiments on fibrils of amyloid β (Aβ)40 that there are water molecules in the fibrils. The spatial locations of the water (D2O) were inferred from the responses of 18 amide modes of Aβ40 labeled with 13C = 18O. Fast frequency variations were found for residues L17 and V18 and for the apposed residues L34 and V36, suggesting cavities or channels containing mobile water molecules can form between the 2 sheets. Spectroscopic analysis showed that there are 1.2 water molecules per strand in the fibrils. The 13C = 18O substitution of 1 residue per strand creates a linear array of isotopologs along the fibril axis that manifests clearly identifiable vibrational transitions. Here, it is shown from the distributions of amide-I′ vibrational frequencies that the regularity of these chains is strongly residue dependent and in most cases the distorted regions are also those associated with the putative mobile water molecules. It is proposed that Aβ40 fibrils contain structurally significant mobile water molecules within the intersheet region.

Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Aβ40

The 2D IR spectra of the amide-I vibrations of amyloid fibrils from Aβ40 were obtained. The matured fibrils formed from strands having isotopic substitution by 13C18O at Gly-38, Gly-33, Gly-29, or Ala-21 show vibrational exciton spectra having reduced dimensionality. Indeed, linear chain excitons of amide units are seen, for which the interamide vibrational coupling is measured in fibrils grown from 50% and 5% mixtures of labeled and unlabeled strands. The data prove that the 1D excitons are formed from parallel in-register sheets. The coupling constants show that for each of the indicated residues the amide carbonyls in the chains are separated by 0.5 ± 0.05 nm. The isotope replacement of Gly-25 does not reveal linear excitons, consistent with the region of the strand having a different structure distribution. The vibrational frequencies of the amide-I modes, freed from effects of amide vibrational excitation exchange by 5% dilution experiments, point to there being a component of an electric field along the fibril axis that increases through the sequence Gly-38, Gly-33, Gly-29. The field is dominated by side chains of neighboring residues.

Molecular Dynamics and Phase Transition in One-Dimensional Crystal of C60 Encapsulated Inside Single Wall Carbon Nanotubes

One-dimensionalcrystalsof25% 13 C-enrichedC60encapsulatedinsidehighlymagneticallypurified SWNTswereinvestigatedbyfollowingthetemperaturedependenceofthe 13 CNMRlineshapesandtherelaxation ratesfrom300Kdownto5K.High-resolutionMAStechniquesrevealthat32%oftheencapsulatedmolecules,so- called the C60 , are blocked at room temperature and 68%, labeled C60 , are shown to reversly undergo molecular reorientational dynamics. Contrary to previous NMR studies, spinlattice relaxation time reveals a phase transition at 100 K associated with the changes in the nature of the C60 dynamics. Above the transition, the C60 exhibitscontinuousrotationaldiffusion;belowthetransition,C60 executesuniaxialhinderedrotationsmostlikely along the nanotubes axis and freeze out below 25 K. The associated activation energies of these two dynamical regimesaremeasuredtobe6timeslowerthaninfcc-C60,suggestingaquietsmoothorientationaldependenceof the interaction between C60 molecules and the inner surface of the nanotubes.

Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations

The infrared optical response of amyloid fibrils Aβ(1-40) is investigated. Simulations of two models corresponding to different protonation states are compared with experiment. The simulations reveal that vibrational frequency distributions inside the fibrils are dominated by side chain fluctuations. We further confirm earlier suggestions based on 2D-IR measurements that water molecules can be trapped inside the fibrils.

Vibrational dynamics of N–H, C–D, and CO modes in formamide

By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.

Cosolvent Effects on Solute–Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations

Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solutes perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solutes carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

Two-dimensional infrared spectroscopy of dipeptides in trehalose glass

Two-dimensional amide I infrared spectra of three dipeptides in trehalose/D2O glass were collected via heterodyned three-pulse vibrational echo experiments in order to investigate the distribution of peptide structures and the dynamics of structural evolution in this biologically relevant medium. The hydroxylic solvation environment presented to proteins by trehalose/water glasses has been speculated to be similar to water. The 2D IR spectra are spread along the diagonal, revealing the presence of very broad inhomogeneous distributions, and the lack of spectral dependence on waiting-time shows that these distributions are mainly static with only a small spectral diffusion component consistent with the measurements of the frequency–frequency correlation functions. Polarization-dependent measurements show that the average structure of trialanine in trehalose glass is different from that in water (D2O).

Communications: Nanomagnetic shielding: High-resolution NMR in carbon allotropes.

The understanding and control of the magnetic properties of carbon-based materials is of fundamental relevance in applications in nano- and biosciences. Ring currents do play a basic role in those systems. In particular the inner cavities of nanotubes offer an ideal environment to investigate the magnetism of synthetic materials at the nanoscale. Here, by means of (13)C high resolution NMR of encapsulated molecules in peapod hybrid materials, we report the largest diamagnetic shifts (down to -68.3 ppm) ever observed in carbon allotropes, which is connected to the enhancement of the aromaticity of the nanotube envelope upon doping. This diamagnetic shift can be externally controlled by in situ modifications such as doping or electrostatic charging. Moreover, defects such as C-vacancies, pentagons, and chemical functionalization of the outer nanotube quench this diamagnetic effect and restore NMR signatures to slightly paramagnetic shifts compared to nonencapsulated molecules. The magnetic interactions reported here are robust phenomena independent of temperature and proportional to the applied magnetic field. The magnitude, tunability, and stability of the magnetic effects make the peapod nanomaterials potentially valuable for nanomagnetic shielding in nanoelectronics and nanobiomedical engineering.