Ultrafast Vibrational Dynamics and Infrared Spectroscopy of Biologically Relevant Hydrogen Bonds
Final Report Abstract
The dynamics of multiple intermolecular Hydrogen bonds in the condensed phase often does not proceed independently and correlations might be responsible for properties such as reaction rates. Moreover, the study of correlated dynamics can give insight into the specific bonding situation, its forces and flexibility. Double and triple Hydrogen-bonding is the basic motif responsible for the base pairing in DNA. In order to gain insight into the dynamics of these Hydrogen bonds a “bottomup” approach can be followed, which starts from single base pairs in solution. Here, the N-H stretching vibrations can be used as an infrared active probe of the thermal fluctuation dynamics. For the double Hydrogen bonds, e.g. in adenine-uracil pairs, three possible scenarios could be envisaged: (i) The fluctuations are uncorrelated with respect to the two Hydrogen bonds. (ii) They are positively correlated, i.e. both bonds compress and elongate simultaneously. (iii) They are negatively correlated, i.e. one bond is compressed while the other one is elongated. The type of correlation as well as relevant time scales of the fluctuation dynamics can be unravelled by means of nonlinear infrared spectroscopy, notably two-dimensional photon echo spectroscopy. The simulation of nonlinear spectroscopic signals provides a challenge to theory due to the involvement of a large number of vibrational degrees of freedom. Moreover, standard molecular mechanics force fields provide only a poor description of the spectroscopy of Hydrogen-bonded N- H stretching vibrations, and the forces on the nuclei have to be derived from a quantum mechanical treatment of the electronic structure problem. Thus, QM/MM approaches have to be used, which - in the context of nonlinear spectroscopy - represents a limiting factor in terms of computational efficiency. In this project we have developed efficient strategies for the QM/MM based prediction of nonlinear infrared spectra. Two paths have been followed: (i) Based on a quantization of the fast N-H stretching (and bending) motions a simple mapping approach has been developed, which allows to determine the transition frequency fluctuations along a trajectory at low computational cost. (ii) An all-classical approach to nuclear dynamics, which is based on the quantum-classical correspondence, was implemented employing a new scheme for the calculation of the stability matrix. It requires a minimum number of Hessian calculations such that a QM/MM realization becomes possible. Using the QM/MM mapping approach we have been able to analyze the linear absorption lineshape of the N-H stretching bands of a solvated adenine-uracil pair to find an excellent agreement with experimental data. Further, we simulated the pump-probe signal for this system to complete the model description in terms of vibrational relaxation times. As a major result we have been able to predict the two-dimensional infrared spectrum for this system. Its analysis led us to the conclusion that the fluctuations of the two Hydrogen bonds in the adenine-uracil pair due to thermal motions are not independent and are dominated by a positive correlation.
Publications
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Geometric Correlations and Infrared Spectrum of the Adenine-Uracil Hydrogen Bonds in CDCl3 Solution. Physical Chemistry Chemical Physics 12, 15695-15703 (2010)
Y. Yan, O. Kühn
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IR Spectrum of the O-H...O Hydrogen Bond of Phthalic Acid Monomethylester in Gas Phase and in CCl4 Solution. Journal of Molecular Structure 972, 68-74 (2010)
Y. Yan, M. Petković, G. M. Krishnan, O. Kühn
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Vibrational Dynamics of the Double Hydrogen Bonds in Nucleic Acid Base Pairs. In „Excited-State Hydrogen Bonding and Hydrogen Transfer“ Ke-Li Han and Guang-Jiu Zhao (Eds.) John Wiley & Sons, 2010, p. 1-27
Y. Yan, O. Kühn
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Unraveling the Correlated Dynamics of the Double Hydrogen Bonds of Nucleic Acid Base Pairs in Solution. Journal of Physical Chemistry B 115, 5254-5259 (2011)
Y. Yan, O. Kühn
