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A density functional theory study of vibrational coupling between ribose and base rings of nucleic acids with ribosyl guanosine as a model system (2000)

Pelmenschikov, Alexander

College Park, Md. : American Institute of Physics (AIP)

The Journal of Chemical Physics 113 (2000), S. 5986-5990

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ISSN: 1089-7690

Source: AIP Digital Archive

Topics: Physics , Chemistry and Pharmacology

Notes: The vibrational coupling between the ribose and base rings of nucleic acids is modeled by the ribose–guanine vibrational interaction in ribosyl guanosine at the density functional theory (DFT) level. Two coupling patterns are revealed for the in-plane guanine vibrations depending on the strength of the kinematic interaction between ribose and guanine through the glicosidic bond. For relatively weak interactions the coupling can be described in terms of a resonance between two vibrations which are originally close in frequency (the difference in frequency between the vibrations is within ∼20 cm−1). This coupling produces two modes corresponding to the in-phase and out-of-phase combinations of the original ribose and guanine vibrations, analogous to the symmetric and antisymmetric coupled modes of the carbonyl groups in anhydrides, imides, and 1,3-diketo compounds. For strong interactions involving a significant glicosidic bond stretch, the ribose and guanine moieties can no longer be considered as quasi-independent subsystems preserving the forms of their inherent vibrations. An unambiguous identification of the original ribose and guanine vibrations contributing to these combined modes is hardly possible. Taking into account (i) the large number of intrinsic ribose and base vibrations which can potentially participate in the coupling and (ii) the resonant character of many of these interactions, these results suggest that small changes in the ribose ring conformation and glicosidic bond orientation should result in noticeable changes of the related combined modes. This explains the phenomenon of high conformational sensitivity of the corresponding conformational marker bands of nucleic acids in vibrational spectroscopy. © 2000 American Institute of Physics.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1063/1.1290021

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Electronic structure effects from hydrogen bonding in the liquid phase and in chemisorption: an integrated theory and experimental effort (2001)

Pettersson, Lars G. M. ; Nilsson, Anders ; Myneni, Satish ; [et al.]

Chester : International Union of Crystallography (IUCr)

Journal of synchrotron radiation 8 (2001), S. 136-140

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ISSN: 1600-5775

Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001

Topics: Geosciences , Physics

Notes: A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3×2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate–adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed.