nanoIR Journal Club

As part of our work in nanoscale infrared (nanoIR) spectroscopy, we regularly come across great research articles. Members of our nanoIR Journal Club receive brief reviews of select papers, collected below. Sign up to automatically receive the monthly Journal Club via email: 

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SINGLE MOLECULE SECONDARY STRUCTURE DETERMINATION OF PROTEINS THROUGH INFRARED ABSORPTION NANOSPECTROSCOPY
Francesco Simone Ruggeri, Benedetta Mannini, Roman Schmid, Michele Vendruscolo and Tuomas P. J. Knowles
Nature Communications 2020, 11, 2945
DOI: 10.1038/s41467-020-16728-1
You can find the full article here: https://doi.org/10.1038/s41467-020-16728-1)

The authors used the photothermal-based AFM-IR technique to achieve the measurements of infrared absorption spectra and chemical maps at the single-molecule level for the first time. The high sensitivity in their measurement enabled the accurate determination of the secondary structure of a single protein molecule that is consistent with the structure of the bulk protein material. The results demonstrated the high sensitivity and high spatial resolution of the AFM-IR technique and paved the way for direct probing of individual biomolecules in a broader context.

To achieve AFM-IR characterization of a single protein molecule, an innovative approach was adopted in the experimental setup. This approach, namely ORS-nanoIR, used an off-resonance, low-power, and short pulse of the infrared beam to excite the single protein molecule. The off-resonance excitation, i.e., laser pulse rate detuned to a frequency 1-2 kHz less than the peak of contact resonance frequency, gave the maximum contrast in laser-induced cantilever deflection signal between the protein sample and the gold substrate. The low power and short pulse operation scheme established a linear response regime of the cantilever to the thermal expansion of the sample induced by infrared absorption. Such conditions also avoided damage of the soft protein sample during the measurement. This innovative experimental approach enabled the acquisition of AFM-IR spectra and maps from a single protein on a time scale of 1 s, with a ~10-20 signal-to-noise ratio. As examples to demonstrate the capabilities of this technique, single molecules of two different protein species, apoferritin and thyroglobulin, were successfully measured, and their secondary structures were accurately determined from the high-quality AFM-IR spectra.


DIRECT OBSERVATION OF BOUND WATER ON COTTON SURFACES BY ATOMIC FORCE MICROSCOPY AND ATOMIC FORCE MICROSCOPY-INFRARED SPECTROSCOPY
Takako Igarashi, Masato Hoshi, Koichi Nakamura, Takeshi Kaharu, and Ken-ichiro Murata
J. Phys. Chem. C 2020, 124, 7, 4196-4201
DOI: 10.1021/acs.jpcc.0c00423
(This article is paywalled, but if you have access to it, you can find it at: https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.0c00423)

In this paper, the very familiar and interesting phenomenon of wet cotton rags becoming stiff after natural drying was studied with AFM and AFM-IR. Results from this work provided evidence of the existence of bound water on the surface of a cotton single fiber under naturally dried conditions. It was proposed that the bound water functions as a cross-linking agent at contact points between single fibers and constructs a 3-D network, and such cross-linking network is responsible for the hardening mechanism of dried cotton fabrics.

In the AFM measurements, the force curves were obtained for cotton single fibers in different humidity environments from RH 0% to 80%, and from the force curves, the adhesion force was calculated. It was observed that the adhesion force increases with the humidity level, which indicates the existence of bound water at the outermost surface of cotton, and the humidity level controls the amount of bound water that contributes to the adhesion force. In the AFM-IR measurements, the AFM-IR spectra were recorded for cotton single fibers under the naturally dried condition and a completely dry condition. The AFM-IR spectrum of naturally dried cellulose fiber showed two strong IR bands at 3300 and 3440 cm-1, which were not observed for the completely dried fiber, and therefore are due to the O-H stretching modes of bound water on the surface of the cotton single fiber. Those two IR bands have very different shapes from those of bulk water and indicate the hydrogen bonding state of bound water is influenced by the interaction with cellulose surfaces. The 3440 and 3300 cm-1 bands were assigned to water at the cotton fiber-water interface and water at the water-air interface, respectively. It was interpreted that the hydrophobic interaction between water and air strengthens the hydrogen bonding among the water molecules and thus shifts the O-H stretching band to a lower wave number.



PROBE-SAMPLE INTERACTION-INDEPENDENT ATOMIC FORCE MICROSCOPY-INFRARED SPECTROSCOPY: TOWARD ROBUST NANOSCALE COMPOSITIONAL MAPPING
Seth Kenkel, Anirudh Mittal, Shachi Mittal, and Rohit Bhargava
ANAL. CHEM, 2018, 90, 8845-8855
DOI: 10.1021/acs.analchem.8b00823
(This article is paywalled, but if you have access to it, you can find it at: https://pubs.acs.org/doi/pdf/10.1021/acs.analchem.8b00823)

Nanoscale topological imaging using atomic force microscopy (AFM) combined with infrared (IR) spectroscopy (AFM-IR) is a rapidly emerging modality to record correlated structural and chemical images. Although the expectation is that the spectral data faithfully represents the underlying chemical composition, the sample mechanical properties affect the recorded data (known as the probe–sample-interaction effect). Although experts in the field are aware of this effect, the contribution is not fully understood. Further, when the sample properties are not well-known or when AFM-IR experiments are conducted by nonexperts, there is a chance that these nonmolecular properties may affect analytical measurements in an uncertain manner. Techniques such as resonance-enhanced imaging and normalization of the IR signal using ratios might improve fidelity of recorded data, but they are not universally effective. Here, we provide a fully analytical model that relates cantilever response to the local sample expansion which opens several avenues. We demonstrate a new method for removing probe–sample-interaction effects in AFM-IR images by measuring the cantilever responsivity using a mechanically induced, out-of-plane sample vibration. This method is then applied to model polymers and mammary epithelial cells to show improvements in sensitivity, accuracy, and repeatability for measuring soft matter when compared to the current state of the art (resonance-enhanced operation). Understanding of the sample-dependent cantilever responsivity is an essential addition to AFM-IR imaging if the identification of chemical features at nanoscale resolutions is to be realized for arbitrary samples.


BOUNDARY-INDUCED AUXILIARY FEATURES IN SCATTERING-TYPE NEAR-FIELD FOURIER TRANSFORM INFRARED SPECTROSCOPY
Jiong Yang, Mohannad Mayyas, Jianbo Tang, Mohammad B. Ghasemian, Honghua Yang, Kenji Watanabe, Takashi Taniguchi, Qingdong Ou, Lu Hua Li, Qiaoliang Bao, Kourosh Kalantar-Zadeh
ACS Nano, 2020, XXXX, XXX, XXX-XXX
DOI: 10.1021/acsnano.9b08895
(view article: https://pubs.acs.org/doi/10.1021/acsnano.9b08895#)

Phonon-polaritons (PhPs) in layered crystals, including hexagonal boron nitride (hBN), have been investigated by combined scattering-type scanning near-field optical microscopy (s-SNOM) and Fourier transform infrared (FTIR) spectroscopy. Nevertheless, many of such s-SNOM-based FTIR spectra features remain unexplored, especially those originated from the impact of boundaries. Here we observe real-space PhP propagations in thin-layer hBN sheets either supported or suspended by s-SNOM imaging. Then with a high-power broadband IR laser source, we identify two major peaks and multiple auxiliary peaks in the near-field amplitude spectra, obtained using scattering-type near-field FTIR spectroscopy, from both supported and suspended hBN. The major PhP propagation interference peak moves toward the major in-plane phonon peak when the IR illumination moves away from the hBN edge. Specific differences between the auxiliary peaks in the near-field amplitude spectra from supported and suspended hBN sheets are investigated regarding different boundary conditions, associated with edges and substrate interfaces. The outcomes may be explored in heterostructures for advanced nanophotonic applications.


DETERMINATION OF POLYPEPTIDE CONFORMATION WITH NANOSCALE RESOLUTION IN WATER
Georg Ramer, Francesco Simone Ruggeri, Aviad Levin, Tuomas P. J. Knowles, Andrea Centrone
ACS Nano, 2018, 12, 7, 6612-6619
DOI: 10.1021/acsnano.8b01425
(view article: https://pubs.acs.org/doi/10.1021/acsnano.8b01425)

The folding and acquisition of proteins native structure is central to all biological processes of life. By contrast, protein misfolding can lead to toxic amyloid aggregates formation, linked to the onset of neurodegenerative disorders. To shed light on the molecular basis of protein function and malfunction, it is crucial to access structural information on single protein assemblies and aggregates under native conditions. Yet, current conformation-sensitive spectroscopic methods lack the spatial resolution and sensitivity necessary for characterizing heterogeneous protein aggregates in solution. To overcome this limitation, here we use photothermal-induced resonance to demonstrate that it is possible to acquire nanoscale infrared spectra in water with high signal-to-noise ratio (SNR). Using this approach, we probe supramolecular aggregates of diphenylalanine, the core recognition module of the Alzheimer’s β-amyloid peptide, and its derivative Boc-diphenylalanine. We achieve nanoscale resolved IR spectra and maps in air and water with comparable SNR and lateral resolution, thus enabling accurate identification of the chemical and structural state of morphologically similar networks at the single aggregate (i.e., fibril) level.