Following the energy transfer in and out of a polyproline-peptide.

The intramolecular and intermolecular vibrational energy flow in a polyproline peptide with a total number of nine amino acids in the solvent dimethyl sulfoxide is investigated using time-resolved infrared (IR) spectroscopy. Azobenzene covalently bound to a proline sequence containing nitrophenylalanine as a local sensor for vibrational excess energy serves as a heat source. Information on through-space distances in the polyproline peptides is obtained by independent Förster resonance energy transfer measurements. Photoexcitation of the azobenzene and subsequent internal conversion yield strong vibrational excitation of the molecule acting as a local heat source. The relaxation of excess heat, its transfer along the peptide and to the solvent is monitored by the response of the nitro-group in nitrophenylalanine acting as internal thermometer. After optical excitation, vibrational excess energy is observed via changes in the IR absorption spectra of the peptide. The nitrophenylalanine bands reveal that the vibrational excess energy flows in the peptide over distances of more than 20 Å and arrives delayed by up to 7 ps at the outer positions of the peptide. The vibrational excess energy is transferred to the surrounding solvent on a time scale of 10-20 ps. The experimental observations are analyzed by different heat conduction models. Isotropic heat conduction in three dimensions away from the azobenzene heat source is not able to describe the observations. One-dimensional heat dissipation along the polyproline peptide combined with a slower transversal heat transfer to the solvent surrounding well reproduces the observations.

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization.

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

Mechanism of UV-induced formation of Dewar lesions in DNA.

The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab initio calculations of the exited state. The 4π electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.

The excited-state decay of 1-methyl-2(1H)-pyrimidinone is an activated process.

The photophysics of 1-methyl-2(1H)-pyrimidinone (1MP) dissolved in water is investigated by steady-state and time-resolved fluorescence, UV/Vis absorption, and IR spectroscopy. In the experiments, excitation light is tuned to the lowest-energy absorption band of 1MP peaking at 302 nm. At room temperature (291 K) its fluorescence lifetime amounts to 450 ps. With increasing temperature this lifetime decreases and equals 160 ps at 338 K. Internal conversion (IC) repopulating the ground state and intersystem crossing (ISC) to a triplet state are the dominant decay channels of the excited singlet state. At room temperature both channels contribute equally to the decay, that is, the quantum yields of IC and ISC are both approximately 0.5. The temperature dependence of UV/Vis transient absorption signals shows that the activation energy of the IC process (2140 cm(-1)) is higher than that of the ISC process (640 cm(-1)).

Nitro-phenylalanine: a novel sensor for heat transfer in peptides.

Femtosecond IR-pump-IR-probe experiments with independently tunable pulses are used to monitor the ultrafast response of selected IR absorption bands to vibrational excitation of other modes of Fmoc-nitrophenylalanine. The absorptions of both NO(2)-bands change rapidly within <2 ps upon excitation of other vibrational modes. The results point to considerable coupling between the monitored NO(2) modes and the initially excited modes or low-frequency modes. The latter are populated by a rapid energy redistribution process. The strong IR absorption of the NO(2) stretching bands and the intense coupling to other modes makes the nitro group of nitrophenylalanine a sensitive monitor for vibrational energy arriving at this amino acid.

Thymine dimerization in DNA model systems: cyclobutane photolesion is predominantly formed via the singlet channel.

UV-induced formation of cylcobutane pyrimidine dimers (CPD) in all thymine DNA models have been studied by femtosecond IR spectroscopy. CPDs are shown to form within approximately 1 ps during the decay of the initially excited (1)pi pi * state. The quantum yields phi(D)(ps) determined after the (1)pi pi * decay equal the final yield phi(D)(cw). This gives evidence for a predominance of the singlet channel in CPD formation.

Generation of narrowband subpicosecond mid-infrared pulses via difference frequency mixing of chirped near-infrared pulses.

The widely used setup for the generation of femtosecond infrared (IR) pulses based on parametric amplifiers (OPAs) and difference frequency mixing (DFM) is extended to produce tunable narrowband mid-IR pulses. The insertion of pairs of silicon prisms after the OPA induces adjustable chirp, which leads to the generation of narrowband pulses in the DFM stage. Rapid tunability of the mid-IR wavelength via a computer-controllable actuator can be achieved in a range of approximately 200 cm(-1) at a bandwidth of the IR-pulses between approximately 15 and approximately 50 cm(-1) and pulse energies up to 0.4 microJ. The narrowband mid-IR pulses are well suited for 2D IR spectroscopy.