Contact Ion Pairs of Phosphate Groups in Water: Two-Dimensional Infrared Spectroscopy of Dimethyl Phosphate and ab Initio Simulations
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The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated ions, and the molecular coupling mechanisms are far from being understood. In a combined experimental and theoretical approach, we address the properties of contact ion pairs of the prototypical system dimethyl phosphate with Na+, Ca2+, and Mg2+ ions in water. Linear and femtosecond two-dimensional infrared (2D-IR) spectroscopy of the asymmetric (PO2)- stretching vibration separates and characterizes the different species via their blue-shifted vibrational signatures and 2D-IR line shapes. Phosphate-magnesium contact pairs stand out as the most compact geometry while the contact pairs with Ca2+ and Na+ display a wider structural variation. Microscopic density functional theory simulations rationalize the observed frequency shifts and reveal distinct differences between the contact geometries.Keywords:
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Unraveling vibrational coupling is the key to consistently interpret vibrational spectra of complex molecular systems. The vibrational spectrum of the water surface heavily suffers from vibrational coupling, which hinders complete understanding of the molecular structure and dynamics of the water surface. Here we apply heterodyne-detected sum frequency generation spectroscopy to the water surface and accomplish the assignment of a weak vibrational band located at the lower energy side of the free OH stretch. We find that this band is due to a combination mode of the hydrogen-bonded OH stretch and a low-frequency intermolecular vibration, and this combination band appears in the surface vibrational spectrum through anharmonic vibrational coupling that takes place exclusively at the topmost surface.
Rotational–vibrational coupling
Heterodyne (poetry)
Overtone band
Two-dimensional infrared spectroscopy
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In the present work, we give an analytical non-perturbative treatment of mode-mode coupling and anharmonicity occurring in molecular vibrational systems analyzed by 2D-infrared spectroscopy. This analytical description allows a detailed discussion of the intricate structure of the 2D-infrared spectra resulting from the contributions provided by the various possible chronological orderings of the interactions with fields due to overlaps of the pulses. The peculiar role of the vibrational overtones and other combination states on the resonance shapes is elucidated and conditions for a better quantitative analysis are discussed.
Two-dimensional infrared spectroscopy
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Rotational–vibrational coupling
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Molecular spectroscopy
Two-dimensional infrared spectroscopy
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Octadecyltrichlorosilane
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Room-temperature ionic liquids (RTILs) are being increasingly employed as novel solvents in several fields, including chemical engineering, electrochemistry, and synthetic chemistry. To further increase their usage potential, a better understanding of the structure of their surface layer is essential. Bi-layering at the surfaces of RTILs consisting of 1-alkyl-3-methylimidazolium ([Cnmim]+; n = 4, 6, 8, 10, and 12) cations and bis(trifluoromethanesulfonyl)amide ([TFSA]-) anions was demonstrated via infrared-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and molecular dynamics (MD) simulations. It was found that the sum-frequency (SF) signal from the [TFSA]- anions decreases as the alkyl chain length increases, whereas the SF signal from the r+ mode (the terminal CH3 group) of the [Cnmim]+ cations is almost the same regardless of chain length. MD simulations show the formation of a bi-layered structure consisting of the outermost first layer and a submerged second layer in a "head-to-head" molecular arrangement. The decrease in the SF signals of the normal modes of the [TFSA]- anions is caused by destructive and out-of-phase interference of vibrations of corresponding molecular moieties oriented toward each other in the first and second layers. In contrast, the r+ mode of [Cnmim]+ does not experience destructive interference because the peak position of the r+ mode differs marginally at the surface and in the bulk. Our conclusions are not limited to the system presented here. Similar bi-layered structures can be expected for the surfaces of conventional RTILs, which necessitates the consideration of bi-layering in the design and application.
Layering
Amide
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The IR and Raman spectra of two singly layered silicates, silinaite and makatite, have been investigated. The vibrational spectra were assigned based on previous studies of various silicates. The correlation between vibrational modes and the structural properties of silicates under investigation has been made. The IR and Raman spectra of silinaite are in good agreement with the known structure. However, the observed vibrational data of makatite are not completely consistent with those predicted by a factor group analysis based on the published single-crystal data.Key words: layered silicates, silinaite, makatite, vibrational spectroscopy.
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In this paper we report detailed examples of the surface sum frequency generation vibrational spectroscopy (SFG-VS) as a polarization spectroscopic technique for vibrational spectral band assignment and orientational analysis for molecular groups at the interfaces. Surface sum frequency generation vibrational spectroscopy (SFG-VS) has been widely used as an important spectroscopy probe for chemical bonding, structural conformation and molecular interactions of both fundamentally and technologically important interfaces. However, the potential for SFG-VS as a polarization spectroscopic technique is yet to be fully explored. In IR and Raman studies, polarized spectroscopy (PS) can provide information on molecular symmetries, which is necessary for accurate vibrational band assignment in complex chemical environments. We shall show that SFG-vibrational polarization spectroscopy (VPS) is the polarization spectroscopic tool on this purpose for the interface, along with its advantage of submonolayer sensitivity. This ability of SFG-VPS comes from the fact that vibrational bands from different symmetry types do not have strongest peak intensities in the same polarization configuration of the SFG-VPS spectra, because molecular groups are aligned or partially aligned at the interface. We chose to study the SFG-VPS of three diols, namely, ethylene glycol, 1,3-propanediol, and 1,5-pentanediol, at the vapor/liquid interfaces as model systems for the methylene-only molecules. The polarization analysis of the SFG spectra resulted in few explicit polarization selection rules or guidelines for the assignment of the CH stretching modes of the methylene groups. These results could be used to provide clarifications for some of the disagreements and controversies still exist in the literatures. These results can also shed light on the IR and Raman studies on methylene group in the bulk condensed phases.
Methylene
Two-dimensional infrared spectroscopy
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