Łukasz Szyc

Ultrafast Vibrational Dynamics and Local Interactions of Hydrated DNA

Biochemical processes occur mainly in aqueous environments, where interactions with water molecules play a key role for both the structure and function of biomolecules. Deoxyribonucleic acid (DNA), the basic carrier of genetic information, is characterized by an equilibrium double helix structure which is held together by intermolecular hydrogen bonds between base pairs and hydrated by an environment of water molecules with fluctuating hydrogen bonds. Basic vibrational motions of hydrated DNA and the fastest changes in the DNA-water interactions and hydration geometries occur in less than 1 ps. These processes can be accessed by mapping the vibrational dynamics of DNA and water in a time-resolved way by nonlinear ultrafast vibrational spectroscopy. Recent studies provide a detailed understanding of DNA vibrations and their dynamics, and give insight into nonequilibrium properties and structures of hydrated DNA.

The hydrogen-bonded 2-pyridone dimer model system. 1. Combined NMR and FT-IR spectroscopy study.

2-Pyridone (PD), converting to 2-hydroxypyridine (HP) through a lactam-lactim isomerization mechanism, can form three different cyclic dimers by hydrogen bond formation: (PD)(2), (PD-HP), and (HP)(2). We investigate the complexation chemistry of pyridone in dichloromethane-d(2) using a combined NMR and Fourier transform infrared (FT-IR) approach. Temperature-dependent (1)H NMR spectra indicate that at low temperatures (<200 K) pyridone in solution predominantly exists as a cyclic (PD)(2) dimer, in exchange with PD monomers. At higher temperatures a proton exchange mechanism sets in, leading to a collapse of the doublet of (15)N labeled 2-pyridone. Linear FT-IR spectra indicate the existence of several pyridone species, where, however, a straightforward interpretation is hampered by extensive spectral overlap of many vibrational transitions in both the fingerprint and the NH/OH stretching regions. Two-dimensional IR correlation spectroscopy applied on concentration-dependent and temperature-dependent data sets reveals the existence of the (PD)(2) cyclic dimer, of PD-CD(2)Cl(2) solute-solvent complexes, and of PD-PD chainlike dimers. Regarding the difference in effective time scales of the NMR and FT-IR experiments, milliseconds vs (sub)picoseconds, the cyclic dimers (PD-HP) and (HP)(2), and the chainlike conformations HP-PD, may function as intermediates in reaction pathways through which the protons exchange between PD units in cyclic (PD)(2).

Ultrafast Vibrational Dynamics of Adenine-Thymine Base Pairs in DNA Oligomers

N-H stretching excitations of DNA oligomers containing 23 alternating adenine-thymine base pairs are studied in femtosecond two-color pump-probe experiments. For a DNA film in a zero relative humidity atmosphere, transient vibrational spectra and their time evolution up to 10 ps demonstrate negligible spectral diffusion and allow for discerning different N-H stretching bands and the O-H stretching absorption of residual water molecules. Lifetimes on the order of 0.5 ps are found for both N-H and O-H stretching modes. The time-dependent pump-probe anisotropies of the different N-H excitations point to a pronounced coupling among them, whereas the O-H stretching anisotropy remains essentially constant.

Decelerated Water Dynamics and Vibrational Couplings of Hydrated DNA Mapped by Two-Dimensional Infrared Spectroscopy

Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.

Ultrafast energy exchange via water-phosphate interactions in hydrated DNA.

The ionic phosphate groups in the DNA backbone play a key role for DNA hydration. We study ultrafast vibrational dynamics and local interactions of phosphate groups and water by femtosecond two-color pump-probe spectroscopy. The asymmetric (PO(2))(-) stretching vibration nu(AS)(PO(2))(-) of artificial DNA oligomers containing 23 alternating adenine-thymine base pairs displays a lifetime of 340 fs, independent of the hydration level. For DNA at zero relative humidity, excess energy from the decay of the phosphate excitation is transferred within DNA on a 20 ps time scale. For fully hydrated DNA, the water shells around the phosphates serve as a primary heat sink accepting vibrational excess energy from DNA on a femtosecond time scale. OH stretching excitation of water molecules around fully hydrated DNA induces an ultrafast nu(AS)(PO(2))(-) response which includes rearrangements of the hydration shell and a reduction of the average number of phosphate-water hydrogen bonds.

Femtosecond Two-Dimensional Infrared Spectroscopy of Adenine-Thymine Base Pairs in DNA Oligomers

NH and NH(2) stretching excitations of adenine-thymine base pairs in double-stranded DNA oligomers are studied by femtosecond two-dimensional (2D) infrared spectrosopy. The 2D spectra taken for population times of up to T = 1 ps allow for separating the NH stretching mode of thymine from the symmetric and asymmetric NH(2) stretching modes of adenine and to determine their individual line shapes. The spectra demonstrate an essentially homogeneous broadening of the NH stretching band of thymine whereas the NH(2) stretching modes display a pronounced, time-independent inhomogeneous broadening, pointing to disorder in the DNA structure. We observe a (downhill) vibrational energy transfer from the asymmetric NH(2) stretching vibration of adenine at 3350 cm(-1) to the NH stretching mode of thymine at 3200 cm(-1) on a ∼500 fs time scale whereas the inverse (uphill) transfer is negligible.

The hydrogen-bonded 2-pyridone dimer model system. 2. Femtosecond mid-infrared pump-probe study.

2-Pyridone (PD) tautomerises to 2-hydroxypyridine (HP) in liquid solution, the equilibrium of which is solvent dependent. Dimerization of PD and HP leads to the cyclic dimers (PD)(2), (HP)(2), and (PD-HP). A combined NMR and FT-IR study [Szyc, Ł.; et al. J. Phys. Chem. A 2010, 114, 7749-7760] has shown that solutions of 2-pyridone in CD(2)Cl(2) constitute mainly PD-CD(2)Cl(2) solute-solvent complexes and cyclic dimers (PD)(2). Because of a lack of specific marker modes, a contribution of the cyclic dimer (HP)(2) to the NH/OH stretching absorption between 2400 and 3300 cm(-1) could not be fully ruled out. Here, we present the first ultrafast infrared (IR) pump-probe experiments on the NH/OH stretching region of a solution of 2-pyridone in CD(2)Cl(2). The temporally and spectrally resolved data reveal different rate-like relaxation processes with time constants between 150 fs and 20 ps as well as coherent low-frequency oscillations due to hydrogen bond modes. An analysis shows that the transient behavior is dominated by a single hydrogen bonded species. We compare the low-frequency wavepacket motions, observed with 99 and 150 cm(-1) frequencies, with literature values as well as our quantum chemical calculations and conclude that this single molecular species is cyclic (PD)(2).

Note: An environmental cell for transient spectroscopy on solid samples in controlled atmospheres

A sample cell for performing time-resolved spectroscopy on solid samples within an atmosphere of controlled vapor composition was designed and constructed. Control over vapor composition was accomplished using a combination of passive sealing and chemical agents. Performance characteristics especially well-suited to studies using femtosecond mid-infrared spectroscopy were achieved by the use of ultrathin silicon nitride windows and a rapid and reproducible sample cell exchange mechanism.

Aqueous Solvation of Ammonia and Ammonium: Probing Hydrogen Bond Motifs with FT-IR and Soft X-ray Spectroscopy

In a multifaceted investigation combining local soft X-ray and vibrational spectroscopic probes with ab initio molecular dynamics simulations, hydrogen-bonding interactions of two key principal amine compounds in aqueous solution, ammonia (NH3) and ammonium ion (NH4+), are quantitatively assessed in terms of electronic structure, solvation structure, and dynamics. From the X-ray measurements and complementary determination of the IR-active hydrogen stretching and bending modes of NH3 and NH4+ in aqueous solution, the picture emerges of a comparatively strongly hydrogen-bonded NH4+ ion via N-H donating interactions, whereas NH3 has a strongly accepting hydrogen bond with one water molecule at the nitrogen lone pair but only weakly N-H donating hydrogen bonds. In contrast to the case of hydrogen bonding among solvent water molecules, we find that energy mismatch between occupied orbitals of both the solutes NH3 and NH4+ and the surrounding water prevents strong mixing between orbitals upon hydrogen bonding and, thus, inhibits substantial charge transfer between solute and solvent. A close inspection of the calculated unoccupied molecular orbitals, in conjunction with experimentally measured N K-edge absorption spectra, reveals the different nature of the electronic structural effects of these two key principal amine compounds imposed by hydrogen bonding to water, where a pH-dependent excitation energy appears to be an intrinsic property. These results provide a benchmark for hydrogen bonding of other nitrogen-containing acids and bases.

Ultrafast Vibrational Dynamics of Hydrated DNA Studied by Two-Dimensional Infrared Spectroscopy

2-D infrared spectroscopy separates interacting NH stretching modes of DNA from OH stretching excitations of its water shell. DNA-water interactions slow down the structural dynamics of the hydration shell compared to bulk water.