title: N-H stretching excitations in adenosine-thymidine base pairs in solution: pair geometries, infrared line shapes, and ultrafast vibrational dynamics.
abstract: We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.
authors.affiliation: Max Born Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max Born Strasse 2A, D-12489 Berlin, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Greve
authors.forename: Nicholas K
authors.initials: NK
authors.lastname: Preketes
authors.forename: Henk
authors.initials: H
authors.lastname: Fidder
authors.forename: Rene
authors.initials: R
authors.lastname: Costard
authors.forename: Benjamin
authors.initials: B
authors.lastname: Koeppe
authors.forename: Ismael A
authors.initials: IA
authors.lastname: Heisler
authors.forename: Shaul
authors.initials: S
authors.lastname: Mukamel
authors.forename: Friedrich
authors.initials: F
authors.lastname: Temps
authors.forename: Erik T J
authors.initials: ET
authors.lastname: Nibbering
authors.forename: Thomas
authors.initials: T
authors.lastname: Elsaesser
mesh_terms: D000241:Adenosine / Q000737:chemistry*; D020029:Base Pairing; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D011789:Quantum Theory; D012996:Solutions; D017550:Spectroscopy, Fourier Transform Infrared; D013936:Thymidine / Q000737:chemistry*; D014732:Vibration
chemical_list: D012996:Solutions; D000241:Adenosine; D013936:Thymidine