More Like this

1. Theoretical basis for interpreting heterodyne chirality-selective sum frequency generation spectra of water

   https://doi.org/10.1063/5.0181718  

   Konstantinovsky, Daniel; Santiago, Ty; Tremblay, Matthew; Simpson, Garth J.; Hammes-Schiffer, Sharon; Yan, Elsa C. (February 2024, The Journal of Chemical Physics)

   Chirality-selective vibrational sum frequency generation (chiral SFG) spectroscopy has emerged as a powerful technique for the study of biomolecular hydration water due to its sensitivity to the induced chirality of the first hydration shell. Thus far, water O–H vibrational bands in phase-resolved heterodyne chiral SFG spectra have been fit using one Lorentzian function per vibrational band, and the resulting fit has been used to infer the underlying frequency distribution. Here, we show that this approach may not correctly reveal the structure and dynamics of hydration water. Our analysis illustrates that the chiral SFG responses of symmetric and asymmetric O–H stretch modes of water have opposite phase and equal magnitude and are separated in energy by intramolecular vibrational coupling and a heterogeneous environment. The sum of the symmetric and asymmetric responses implies that an O–H stretch in a heterodyne chiral SFG spectrum should appear as two peaks with opposite phase and equal amplitude. Using pairs of Lorentzian functions to fit water O–H stretch vibrational bands, we improve spectral fitting of previously acquired experimental spectra of model β-sheet proteins and reduce the number of free parameters. The fitting allows us to estimate the vibrational frequency distribution and thus reveals the molecular interactions of water in hydration shells of biomolecules directly from chiral SFG spectra. 

   more » « less
2. DFT-based calculation of vibrational sum frequency generation spectral features of crystalline β-sheets in silk: Polarization and azimuth angle dependences

   https://doi.org/10.1063/5.0236676  

   Ryu, Jihyeong; Chen, Sibing; Choi, Juseok; Chen, Xing; Kim, Seong H (December 2024, The Journal of Chemical Physics)

   Sum frequency generation (SFG) necessitates both noncentrosymmetry and coherence over multiple length scales. These requirements make vibrational SFG spectroscopy capable of probing structural information of noncentrosymmetric organic crystals interspersed in polymeric matrices and their three-dimensional spatial distributions within the matrices without spectral interferences from the amorphous components. However, this analysis is not as straightforward as simple vibrational spectroscopy or scattering experiments; it requires knowing the molecular hyperpolarizability of SFG-active vibrational modes and their interplay within the coherence length. This study demonstrates how density function theory (DFT) calculations can be used to construct the molecular hyperpolarizability of a model system and combine it with the SFG theory to predict the polarization and azimuth angle dependences of SFG intensities. A model system with short peptide chains mimicking β-sheet domains in Bombyx mori silk was chosen. SFG signals of the amide-I, II, III, and A bands and one of the CH deformation modes were simulated and compared with the experimental results and the predictions from the group theory. The SFG features of amide-I and A bands of antiparallel β-sheet could be explained with DFT-based theoretical calculations. Although vibrational coupling with neighboring groups breaks the symmetry of the D2 point group, the group theory approach and DFT calculations gave similar results for the amide-I mode. The DFT calculation results for amide-II did not match with experimental data, which suggested vibrational coupling within a larger crystalline domain may dominate the SFG spectral features of these modes. This methodology can be applied to the structural analysis of other biopolymers. 

   more » « less
3. Beyond the “spine of hydration”: Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures

   https://doi.org/10.1063/5.0220479  

   Perets, Ethan A; Konstantinovsky, Daniel; Santiago, Ty; Videla, Pablo E; Tremblay, Matthew; Velarde, Luis; Batista, Victor S; Hammes-Schiffer, Sharon; Yan, Elsa_C Y (September 2024, The Journal of Chemical Physics)

   Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N–H stretch of DNA base pairs and the O–H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove “spine of hydration” is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration. 

   more » « less
4. Early sum frequency generation vibrational spectroscopic studies on peptides and proteins at interfaces

   https://doi.org/10.1116/6.0001859  

   Chen, Zhan (May 2022, Biointerphases)

   This paper summarizes the early research results on studying proteins and peptides at interfaces using sum frequency generation (SFG) vibrational spectroscopy. SFG studies in the C—H stretching frequency region to examine the protein side-chain behavior and in the amide I frequency region to investigate the orientation and conformation of interfacial peptides/proteins are presented. The early chiral SFG research and SFG isotope labeling studies on interfacial peptides/proteins are also discussed. These early SFG studies demonstrate the feasibility of using SFG to elucidate interfacial molecular structures of peptides and proteins in situ, which built a foundation for later SFG investigations on peptides and proteins at interfaces. 

   more » « less
5. Single-conformation spectroscopy of cold, protonated ^D PG-containing peptides: switching β-turn types and formation of a sequential type II/II′ double β-turn

   https://doi.org/10.1039/D1CP04852J  

   Lawler, John T.; Harrilal, Christopher P.; DeBlase, Andrew F.; Sibert, Edwin L.; McLuckey, Scott A.; Zwier, Timothy S. (January 2022, Physical Chemistry Chemical Physics)

   d -Proline ( D Pro, D P) is widely utilized to form β-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a D PG sub-unit that forms a β-turn. To observe whether D PG facilitated this effect in short protonated peptides, conformation specific IR–UV double resonance photofragment spectra of the cold (∼10 K) protonated D P and L P diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800–3700 cm −1 ) and amide I/II (1400–1800 cm −1 ) regions. A model localized Hamiltonian was developed to better describe the 1600–1800 cm −1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N–H bending fundamentals of the NH 3 + group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the D P diastereomer, all the population is funneled into a single conformer which presented as a type II β-turn with A and D P in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II′ β-turn across D PG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II β-turn. In contrast, the L P isomer forms three conformations with very different structures, none of which were type II/II′ β-turns, confirming that L PG is not a β-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAA D PGAAA + H] + to determine whether moving the protonated N-terminus further from D PG would lead to β-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a β-hairpin, but a concatenated type II/type II′ double β-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction. 

   more » « less