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- ItemShort-Range Cooperative Slow-down of Water Solvation Dynamics Around SO42--Mg2+ Ion Pairs(Washington, DC : American Chemical Society, 2022) Kundu, Achintya; Mamatkulov, Shavkat I.; Brünig, Florian N.; Bonthuis, Douwe Jan; Netz, Roland R.; Elsaesser, Thomas; Fingerhut, Benjamin P.The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg2+ and SO42- ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics. Here, we introduce asymmetric SO42- stretching vibrations as new and most specific local probes of solvation dynamics that allow to access ion hydration dynamics at the dilute concentration (0.2 M) of a native electrolyte environment. Highly sensitive heterodyne 2D-IR spectroscopy in the fingerprint region of the SO42- ions around 1100 cm-1 reveals a specific slow-down of solvation dynamics for hydrated MgSO4 and for Na2SO4 in the presence of Mg2+ ions, which manifests as a retardation of spectral diffusion compared to aqueous Na2SO4 solutions in the absence of Mg2+ ions. Extensive molecular dynamics and density functional theory QM/MM simulations provide a microscopic view of the observed ultrafast dephasing and hydration dynamics. They suggest a molecular picture where the slow-down of hydration dynamics arises from the structural peculiarities of solvent-shared SO42--Mg2+ ion pairs.
- ItemThe Bend+Libration Combination Band Is an Intrinsic, Collective, and Strongly Solute-Dependent Reporter on the Hydrogen Bonding Network of Liquid Water(Washington, DC : Americal Chemical Society, 2017) Verma, Pramod Kumar; Kundu, Achintya; Puretz, Matthew S.; Dhoonmoon, Charvanaa; Chegwidden, Oriana S.; Londergan, Casey H.; Cho, MinhaengWater is an extensively self-associated liquid due to its extensive hydrogen bond (H-bond) forming ability. The resulting H-bonded network fluid exhibits nearly continuous absorption of light from the terahertz to the near-IR region. The relatively weak bend+libration water combination band (centered at 2130 cm-1) has been largely overlooked as a reporter of liquid water's structure and dynamics despite its location in a convenient region of the IR for spectroscopic study. The intermolecular nature of the combination band leads to a unique absorption signal that reports collectively on the rigidity of the H-bonding network in the presence of many different solutes. This study reports comprehensively how the combination band acts as an intrinsic and collective probe in various chemically and biologically relevant solutions, including salts of varying character, denaturants, osmolytes, crowders, and surfactants that form reverse micelles and micelles. While we remark on changes in the line width and intensity of this combination band, we mainly focus on the frequency and how the frequency reports on the collective H-bonding network of liquid water. We also comment on the "association band" moniker often applied to this band and how to evaluate discrete features in this spectral region that sometimes appear in the IR spectra of specific kinds of aqueous samples of organic solutes, especially those with very high solute concentrations, with the conclusion that most of these discrete spectral features come exclusively from the solutes and do not report on the water. Contrasts are drawn throughout this work between the collective and delocalized reporting ability of the combination band and the response of more site-specific vibrations like the much-investigated OD stretch of HDO in H2O: the combination band is a unique reporter of H-bonding structure and dynamics and fundamentally different than any local mode probe. Since this band appears as the spectroscopic "background" for many local-mode reporter groups, we note the possibility of observing both local and collective solvent dynamics at the same time in this spectral region.
- ItemPhosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions(Washington, DC : Soc., 2021) Elsaesser, Thomas; Schauss, Jakob; Kundu, Achintya; Fingerhut, Benjamin P.Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)− stretching vibration νAS(PO2)−, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions.
- ItemMagnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations(Washington, DC : Soc., 2021) Schauss, Jakob; Kundu, Achintya; Fingerhut, Benjamin P.; Elsaesser, ThomasIons interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg2+) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA). Employing dialyzed tRNAPhe from yeast and tRNA from Escherichia coli, we follow the population of Mg2+ sites close to phosphate groups of the ribose-phosphodiester backbone step by step, combining linear and nonlinear infrared spectroscopy of phosphate vibrations with molecular dynamics simulations and ab initio vibrational frequency calculations. The formation of up to six Mg2+/phosphate contact pairs per tRNA and local field-induced reorientations of water molecules balance the phosphate-phosphate repulsion in nonhelical parts of tRNA, thus stabilizing the folded structure electrostatically. Such geometries display limited sub-picosecond fluctuations in the arrangement of water molecules and ion residence times longer than 1 µs. At higher Mg2+ excess, the number of contact ion pairs per tRNA saturates around 6 and weakly interacting ions prevail. Our results suggest a predominance of contact ion pairs over long-range coupling of the ion atmosphere and the biomolecule in defining and stabilizing the tertiary structure of tRNA. © 2020 American Chemical Society.