Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Multidimensional infrared spectroscopy of water. I. Vibrational dynamics in two-dimensional IR line shapes

In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.     

Effects of microsolvation on the adenine-uracil base pair and its radical anion: adenine-uracil mono- and dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.     

Double proton transfer in the isolated and DNA-embedded guanine-cytosine base pair

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 A to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of approximately 100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed.     

Vibrational relaxation of azide ions in liquid-to-supercritical water

The dynamics of vibrational energy relaxation (VER) of the aqueous azide anion was studied over a wide temperature (300 K ≤ T ≤ 663 K) and density (0.6 g cm(-3) ≤ ρ ≤ 1.0 g cm(-3)) range thereby covering the liquid and the supercritical phase of the water solvent. Femtosecond mid-infrared spectroscopy on the ν(3) band associated with the asymmetric stretching vibration of the azide anion was used to monitor the relaxation dynamics in a time-resolved fashion. The variation of the vibrational relaxation rate constant with temperature and density was found to be rather small. Surprisingly, the simple isolated binary collision model is able to fully reproduce the experimentally observed temperature and density dependence of the relaxation rate provided a local density correction around the vibrationally excited solute based on classical molecular dynamics simulations is used. The simulations further suggest that head-on collisions of the solvent with the terminal nitrogen atoms rather than side-on collisions with the central nitrogen atom of the azide govern the vibrational energy relaxation of this system. Finally, the importance of hydrogen bonding for the VER dynamics in this system is briefly discussed.     

Fourier transform infrared spectroscopy and theoretical study of dimethylamine dimer in the gas phase

Dimethylamine (DMA) has been studied by gas-phase Fourier transform infrared (FTIR) spectroscopy. We have identified a spectral transition that is assigned to the DMA dimer. The IR spectra of the dimer in the gas phase are obtained by spectral subtraction of spectra recorded at different pressures. The enthalpy of hydrogen bond formation was obtained for the DMA dimer by temperature-dependence measurements. We complement the experimental results with ab initio and anharmonic local mode model calculations of monomer and dimer. Compared to the monomer, our calculations show that in the dimer the N-H bond is elongated, and the NH-stretching fundamental shifts to a lower wavenumber. More importantly, the weak NH-stretching fundamental transition has a pronounced intensity increase upon complexation. However, the first NH-stretching overtone transition is not favored by the same intensity enhancement, and we do not observe the first NH-stretching overtone of the dimer. On the basis of the measured and calculated intensity of the NH-stretching transition of the dimer, the equilibrium constant for dimerization at room temperature was determined.     

Excited‐State Deactivation of Branched Phthalocyanine Compounds

The excited‐state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis‐ and trisphthalocyanines) are studied by using steady‐state and femtosecond transient absorption spectral measurements, where the excited‐state energy‐transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis‐Pc). In trisphthalocyanine (tris‐Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre‐associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady‐state spectra also show a face‐to‐face conformation in bis‐Pc, whereas in tris‐Pc, two of the three phthalocyanine branches form a pre‐associated face‐to‐face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure–property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems.     

Ultrafast Vibrational Dynamics of Membrane‐Bound Peptides at the Lipid Bilayer/Water Interface

Vibrational energy transfer (VET) of proteins at cell membrane plays critical roles in controlling the protein functionalities, but its detection is very challenging. By using a surface‐sensitive femtosecond time‐resolved sum‐frequency generation vibrational spectroscopy with infrared pump, the detection of the ultrafast VET in proteins at cell membrane has finally become possible. The vibrational relaxation time of the N−H groups is determined to be 1.70(±0.05) ps for the α‐helix located in the hydrophobic core of the lipid bilayer and 0.9(±0.05) ps for the membrane‐bound β‐sheet structure. The N−H groups with strong hydrogen bonding gain faster relaxation time. By pumping the amide A band and probing amide I band, the vibrational relaxation from N−H mode to C=O mode through two pathways (direct coupling and through intermediate states) is revealed. The ratio of the pathways depends on the NH⋅⋅⋅O=C hydrogen‐bonding strength. Strong hydrogen bonding favors the coupling through intermediate states.     

H-NMR studies of duplex DNA decamer containing a uracil cyclobutane dimer: implications regarding the high UV mutagenecity of CC photolesions

To determine the origin of the UV-specific CC to TT tandem mutation at the CC site, we made a duplex DNA decamer containing a uracil cis-syn cyclobutane dimer (CBD) as the deaminated model of a cytosine dimer. Two-dimensional 1H-NMR spectroscopy studies were performed on this sequence where two adenines (Ade) were opposite to the uracil dimer. Two imino protons of the uracil dimer were found to retain Watson-Crick hydrogen bonding with the opposite Ade, although the 5'-U(NH) of the dimer site showed unusual upfield shift like that of the 5'-T(NH) of the TT dimer, which seemed to be associated with deshielding by the flanking base rather than with reduced hydrogen bonding. (McAteer et al. 1998, J. Mol. Biol. 282:1013-1032). Hydrogen bondings at the dimer site were also supported by detecting typical strong nuclear Overhauser effects (NOE) between two imino protons and the opposite Ade H2 or NH2. But sequential NOE interactions of base protons with sugar protons were absent at the two flanking nucleotides of the 5' side of the uracil dimer and at the intradimer site, contrasting with its thymine analog where sequential NOE was absent only at the A4-T5 step. In addition, NOE cross peak for U5(NH) <--> A4(H2) was detected, although the NOE interactions of U6(NH) with A7(H2) and A17(H2) were not observed in contrast to the thymine dimer duplex. This different local structural alteration may be affected by the induced right-hand twisted puckering mode of cis-syn cyclobutane ring of the uracil dimer in the B-DNA duplex, even though the isolated uracil dimer had left-hand twisted puckering rigidly. In parallel, these observations may be correlated with observed differences in mutagenic properties between cis-syn UU dimer and cis-syn TT dimer.     

核酸碱基的非谐性振动:正规及错配碱基对的一维和二维红外光谱及其结构基础

用量子化学计算研究了正规Watson-Crick碱基对和四例典型的错配碱基对.对碱基单体和二聚体进行了详细的非谐性频率分析,以揭示其结构方面的一些振动特征.研究发现这些振动特征能在模拟的一维和二维红外光谱中很好地表现出来.利用势能分布研究了所选简正模式的离域化程度,发现从孤立的碱基单体到参与氢键的二聚体,模式的离域化程度变化很大;同时,这些模式的非谐性常数也发生了相应的改变.以人们通常认为的位于红外光谱中6-μm波长区域的羰基伸缩模式为例进行了探讨.     

O-H stretch in phenol and its hydrogen-bonded complexes: band position and relaxation pathways

Anharmonic force fields are a suitable means for identification of vibrational degrees of freedom responsible for the peculiar shape of molecular spectra and the existence of diverse relaxation pathways. In this contribution, we investigated interactions that govern the position of the O-H stretching band in phenol and its dimers with water and ammonia. Dominant couplings are identified, and the nature of relaxation channels is analyzed. The effect of hydrogen bonding on O-H stretching motion and vibrational energy redistribution time through intra- and intermolecular interactions is studied, and possible vibrational predissociation upon O-H stretch excitation is addressed. The results based on computed anharmonic force constants are in accord with the available experimental findings.     

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.     

Study on the vibrational energy relaxation of p-nitroaniline, N,N-dimethyl-p-nitroaniline, and azulene by the transient grating method

The vibrational energy dissipation processes of the electronic ground states of p-nitroaniline and N,N-dimethyl-p-nitroaniline have been studied by transient grating spectroscopy with subpicosecond laser pulses. The rise time of the acoustic signal produced by the energy dissipation process of the hot ground state molecule was monitored. The acoustic signal was analyzed by an equation including the acoustic damping. The solvent temperature rise times in various solvents have been determined. The acoustic signals of azulene in previous papers [Y. Kimura et al., J. Chem. Phys. 123, 054512 (2005); 123, 054513 (2005)] were also reanalyzed using this equation. The temperature rise times in all cases are longer than the vibrational energy relaxation times of the solutes determined by the transient absorption measurements. The difference is discussed in terms of the energy transfer pathways from the solute to the solvent. We concluded that both the hydrogen bonding between the solute and the solvent and the lower frequency modes of the solutes play important roles in determining the energy transfer pathway from the solute to the solvent.     

Ultrafast deactivation processes in aminopyridine clusters: excitation energy dependence and isotope effects

Fast excited-state relaxation in H-bonded aminopyridine clusters occurs via hydrogen transfer in the excited state. We used femtosecond pump-probe spectroscopy to characterize the excited-state reaction coordinate. Considerable isotope effects for partially deuterated clusters indicate that H-transfer is the rate-limiting step and validate ab initio calculations in the literature. A nonmonotonous dependence on the excitation energy, however, disagrees with the picture of a simple barrier along the reaction coordinate. An aminopyridine dimer serves as a model for Watson-Crick base pairs, where similar reactions have been predicted by theory.     

Testing the core/shell model of nanoconfined water in reverse micelles using linear and nonlinear IR spectroscopy

A core/shell model has often been used to describe water confined to the interior of reverse micelles. The validity of this model for water encapsulated in AOT/isooctane reverse micelles ranging in diameter from 1.7 to 28 nm (w0 = 2-60) and bulk water is investigated using four experimental observables: the hydroxyl stretch absorption spectra, vibrational population relaxation times, orientational relaxation rates, and spectral diffusion dynamics. The time dependent observables are measured with ultrafast infrared spectrally resolved pump-probe and vibrational echo spectroscopies. Major progressive changes appear in all observables as the system moves from bulk water to the smallest water nanopool, w0 = 2. The dynamics are readily distinguishable for reverse micelle sizes smaller than 7 nm in diameter (w0 = 20) compared to the response of bulk water. The results also demonstrate that the size dependent absorption spectra and population relaxation times can be quantitatively predicted using a core-shell model in which the properties of the core (interior of the nanopool) are taken to be those of bulk water and the properties of the shell (water associated with the headgroups) are taken to be those of w0 = 2. A weighted sum of the core and shell components reproduces the size dependent spectra and the nonexponential population relaxation dynamics. However, the same model does not reproduce the spectral diffusion and the orientational relaxation experiments. It is proposed that, when hydrogen bond structural rearrangement is involved (orientational relaxation and spectral diffusion), dynamical coupling between the shell and the core cause the water nanopool to display more homogeneous dynamics. Therefore, the absorption spectra and vibrational lifetime decays can discern different hydrogen bonding environments whereas orientational and spectral diffusion correlation functions predict that the dynamics are size dependent but not as strongly spatially dependent within a reverse micelle.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

Direct Vibrational Energy Transfer in Monomeric Water Probed with Ultrafast Two Dimensional Infrared Spectroscopy

Vibrational relaxation dynamics of monomeric water molecule dissolved in d-chloroform solution were revisited using the two dimensional Infrared (2D IR) spectroscopy. The vibrational lifetime of OH bending in monomeric water shows a bi-exponential decay. The fast component (T₁=(1.2±0.1) ps) is caused by the rapid population equilibration between the vibrational modes of the monomeric water molecule. The slow component (T₂=(26.4±0.2) ps) is mainly caused by the vibrational population decay of OH bending mode. The reorientation of the OH bending in monomeric water is determined with a time constant of τ=(1.2±0.1) ps which is much faster than the rotational dynamics of water molecules in the bulk solution. Furthermore, we are able to reveal the direct vibrational energy transfer from OH stretching to OH bending in monomeric water dissolved in d-chloroform for the first time. The vibrational coupling and relative orientation of transition dipole moment between OH bending and stretching that effect their intra-molecular vibrational energy transfer rates are discussed in detail.     

OH-stretch vibrational relaxation of HOD in liquid to supercritical D2O

The population relaxation of the OH-stretching vibration of HOD diluted in D2O is studied by time-resolved infrared (IR) pump-probe spectroscopy for temperatures of up to 700 K in the density range 12 1 OH stretching transition with a 200 fs laser pulse centered at approximately 3500 cm(-1). Above 400 K these spectra show no indication of spectral diffusion after pump-probe delays of 0.3 ps. Over nearly the entire density range and for sufficiently high temperatures (T > 360 K), the vibrational relaxation rate constant, kr, is strictly proportional to the dielectric constant, epsilon, of water. Together with existing molecular dynamics simulations, this result suggests a simple linear dependence of kr on the number of hydrogen-bonded D2O molecules. It is shown that, for a given temperature, an isolated binary collision model is able to adequately describe the density dependence of vibrational energy relaxation even in hydrogen-bonded fluids. However, dynamic hydrogen bond breakage and formation is a source of spectral diffusion and affects the nature of the measured kr. For sufficiently high temperatures when spectral diffusion is much faster than energy transfer, the experimentally observed decays correspond to ensemble averaged population relaxation rates. In contrast, when spectral diffusion and vibrational relaxation occur on similar time scales, as is the case for ambient conditions, deviations from the linear kr(epsilon) relation occur because the long time decay of the v = 1 population is biased to slower relaxing HOD molecules that are only weakly connected to the hydrogen bond network.