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1. Investigating hydration dynamics and protein collective motions by high-precision dielectric spectroscopy

   https://doi.org/10.1117/12.2567857  

   Doan, Luan C ; Nguyen, Vinh Q. ( September 2020 , Proceedings of SPIE)

   null (Ed.)

   Biological processes often take place at surfaces of proteins, where the dynamic and structural properties of aqueous solvents are modified. Information about solvent properties including hydration dynamics and structure, and protein collective motions can be obtained by measuring directly the dielectric response in the megahertz to terahertz frequencies of aqueous protein solutions. Due to the strong absorption of water in this frequency range, the experiment is challenging. Our home built dielectric spectrometer using a vector network analyzer together with frequency extenders allows us to perform the experiment in a wide range of frequency from megahertz to terahertz with a high dynamical range up to 120 dB. A detailed investigation of the dielectric response has revealed the hydration structure including the tightly, loosely bound layers and the number of water molecules in each hydration layer. These water molecules relax with different time constants at different temperatures. As a result, the dynamics of hydrated protein is also probed at different temperatures. Understanding the hydration structure and dynamics of lysozyme in biological conditions can explain the enzymatic activities of biomolecules. 

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2. 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.

    

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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.

    

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4. Assessing the Intrinsic Strengths of Ion–Solvent and Solvent–Solvent Interactions for Hydrated Mg2+ Clusters

   https://doi.org/10.3390/inorganics9050031  

   Delgado, Alexis Antoinette ; Sethio, Daniel ; Kraka, Elfi ( May 2021 , Inorganics)

   Information resulting from a comprehensive investigation into the intrinsic strengths of hydrated divalent magnesium clusters is useful for elucidating the role of aqueous solvents on the Mg2+ ion, which can be related to those in bulk aqueous solution. However, the intrinsic Mg–O and intermolecular hydrogen bond interactions of hydrated magnesium ion clusters have yet to be quantitatively measured. In this work, we investigated a set of 17 hydrated divalent magnesium clusters by means of local vibrational mode force constants calculated at the ωB97X-D/6-311++G(d,p) level of theory, where the nature of the ion–solvent and solvent–solvent interactions were interpreted from topological electron density analysis and natural population analysis. We found the intrinsic strength of inner shell Mg–O interactions for [Mg(H2O)n]2+ (n = 1–6) clusters to relate to the electron density at the bond critical point in Mg–O bonds. From the application of a secondary hydration shell to [Mg(H2O)n]2+ (n = 5–6) clusters, stronger Mg–O interactions were observed to correspond to larger instances of charge transfer between the lp(O) orbitals of the inner hydration shell and the unfilled valence shell of Mg. As the charge transfer between water molecules of the first and second solvent shell increased, so did the strength of their intermolecular hydrogen bonds (HBs). Cumulative local vibrational mode force constants of explicitly solvated Mg2+, having an outer hydration shell, reveal a CN of 5, rather than a CN of 6, to yield slightly more stable configurations in some instances. However, the cumulative local mode stretching force constants of implicitly solvated Mg2+ show the six-coordinated cluster to be the most stable. These results show that such intrinsic bond strength measures for Mg–O and HBs offer an effective way for determining the coordination number of hydrated magnesium ion clusters. 

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5. Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality

   https://doi.org/10.1073/pnas.2015567117  

   Perets, Ethan A. ; Konstantinovsky, Daniel ; Fu, Li ; Chen, Jiantao ; Wang, Hong-Fei ; Hammes-Schiffer, Sharon ; Yan, Elsa C. Y. ( December 2020 , Proceedings of the National Academy of Sciences)

   Biomolecular hydration is fundamental to biological functions. Using phase-resolved chiral sum-frequency generation spectroscopy (SFG), we probe molecular architectures and interactions of water molecules around a self-assembling antiparallel β-sheet protein. We find that the phase of the chiroptical response from the O-H stretching vibrational modes of water flips with the absolute chirality of the (l-) or (d-) antiparallel β-sheet. Therefore, we can conclude that the (d-) antiparallel β-sheet organizes water solvent into a chiral supermolecular structure with opposite handedness relative to that of the (l-) antiparallel β-sheet. We use molecular dynamics to characterize the chiral water superstructure at atomic resolution. The results show that the macroscopic chirality of antiparallel β-sheets breaks the symmetry of assemblies of surrounding water molecules. We also calculate the chiral SFG response of water surrounding (l-) and (d-) LK₇β to confirm the presence of chiral water structures. Our results offer a different perspective as well as introduce experimental and computational methodologies for elucidating hydration of biomacromolecules. The findings imply potentially important but largely unexplored roles of water solvent in chiral selectivity of biomolecular interactions and the molecular origins of homochirality in the biological world.

    

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