Vibrational Transition Moments of Aminopurines: Stretched Film IR Linear Dichroism Measurements and DFT Calculations

New Approaches to Stretched Film Sample Alignment and Data Collection for Vibrational Linear Dichroism

Rapid measurements of vibrational linear dichroism (VLD) infrared spectra are shown to be possible by using stretched polymer films and an extension of existing instrumentation designed for vibrational circular dichroism spectroscopy. Earlier techniques can be extended using additional inexpensive polymer substrates to record good-quality VLD spectra of a significantly wider range of compounds with comparatively short sample-preparation times. The polymer substrates used, polyethylene and polytetrafluoroethylene, are commonly available and inexpensive, and samples are more easily prepared than that for many earlier stretched-film and crystal studies. Data are presented for neutral hydrophobic organic molecules on hydrophobic films including acridine, anthracene, fluorene, and recently synthesized S-(4-((4-cyanophenyl)ethynyl)phenyl)ethanethioate. We extend the approach to polar or ionic species, including 2,2'-bipyridine, 1,10-phenanthroline, and sodium dodecyl sulfate, by oxidizing polyethylene films to change their wetting properties. The combination of new instrumentation and modified sample preparation methods is useful in basic spectroscopy for untangling and assigning complicated infrared spectra. Nevertheless, it is not a panacea as surface-adsorbed molecules are often not monodispersed, and higher analyte concentrations can lead to aggregation and resonance phenomena that have previously been observed for infrared spectra on surfaces. These effects can be assessed by varying the sample concentration. The focus of this paper is experimental, and detailed analysis of most of the spectra lies outside its scope, including some well-studied compounds such as acridine and anthracene that allow comparisons with earlier research.

Biomarkers of cigarette smoking and DNA methylating agents: Raman, SERS and DFT study of 3-methyladenine and 7-methyladenine

3-Methyladenine and 7-methyladenine are biomarkers of DNA damage from exposure to methylating agents. For example, the concentration of 3-methyladenine increases significantly in the urine of cigarette smokers. Surface-enhanced Raman spectroscopy (SERS) has shown much potential for detection of biomolecules, including DNA. Much work has been dedicated to the canonical nucleobases, with comparatively fewer investigations of modified DNA and modified DNA nucleobases. Herein, Raman spectroscopy and SERS are used to examine the adsorption orientations of 3-methyladenine and 7-methyladenine on Ag nanoparticles. Density functional theory (DFT) calculations at the B3LYP level are used to support the conclusions via simulated spectra of the nucleobases and of Ag⁺/nucleobase complexes. The results herein show that 7-methyladenine adsorbs upright via its N3 and N9 atoms side, similarly to adenine. 3-Methyladenine adsorbs in a very tilted or flat orientation on the Ag nanoparticles. These findings will be useful for future SERS or other nanoparticle-based bioanalytical assays for detection of these methyladenines or other modified nucleobases.

Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine

Fluorescent nucleic acid base analogues are important spectroscopic tools for understanding local structure and dynamics of DNA and RNA. We studied the orientations and magnitudes of the electric dipole transition moments (EDTMs) of 6-methyl isoxanthopterin (6-MI), a fluorescent analogue of guanine that has been particularly useful in biological studies. Using a combination of absorption spectroscopy, linear dichroism (LD) and quantum chemical calculations, we identified six electronic transitions that occur within the 25 000–50 000 cm⁻¹ spectral range. Our results indicate that the two experimentally observed lowest-energy transitions, which occur at 29 687 cm⁻¹ (337 nm) and 34 596 cm⁻¹ (289 nm), are each polarized within the plane of the 6-MI base. A third in-plane polarized transition is experimentally observed at 47 547 cm⁻¹ (210 nm). The theoretically predicted orientation of the lowest-energy transition moment agrees well with experiment. Based on these results, we constructed an exciton model to describe the absorption spectra of a 6-MI dinucleotide–substituted double-stranded DNA construct. This model is in good agreement with the experimental data. The orientations and intensities of the low-energy electronic transitions of 6-MI reported here should be useful for studying local conformations of DNA and RNA in biologically important complexes.

ADENINE TAUTOMER ELECTRONIC STRUCTURAL SIGNATURES STUDIED USING DUAL SPACE ANALYSIS

Electronic structural signatures of the adenine-7H tautomer in its ground state ( X 1 A′) have been identified using dual space analysis. The RHF/TZVP and B3LYP/TZVP calculations employed in the present work have shown that proton transfer from N (9) to N (7) makes the purine rings of adenine-7H geometrically closer to purine rather than adenine-9H, at the cost distortion of the amino group local symmetry. The shifts in ring lengths in [Formula: see text] and [Formula: see text], which are proposed in this work as the summation of the bond lengths in the hex- and pentagon-rings, respectively, are [Formula: see text] and [Formula: see text] for adenine-9H and [Formula: see text] and [Formula: see text] for adenine-7H, respectively, from the corresponding rings in purine. We also demonstrate that energetic properties such as the orbital energies are insensitive to tautomerism. However, the N (9) to N (7) proton transfer significantly changes the dipole moments: a large increase from 2.44D (adenine-9H) to 7.49D (adenine-7H) is observed. Finally, four molecular orbitals, 27a′, 25a′, 24a′ and 23a′ are identified in momentum space as bearing the most important structural signatures of the adenine-7H tautomer.

Probing ultrafast dynamics in adenine with mid-UV four-wave mixing spectroscopies

Heterodyne-detected transient grating (TG) and two-dimensional photon echo (2DPE) spectroscopies are extended to the mid-UV spectral range in this investigation of photoinduced relaxation processes of adenine in aqueous solution. These experiments are the first to combine a new method for generating 25 fs laser pulses (at 263 nm) with the passive phase stability afforded by diffractive optics-based interferometry. We establish a set of conditions (e.g., laser power density, solute concentration) appropriate for the study of dynamics involving the neutral solute. Undesired solute photoionization is shown to take hold at higher peak powers of the laser pulses. Signatures of internal conversion and vibrational cooling dynamics are examined using TG measurements with signal-to-noise ratios as high as 350 at short delay times. In addition, 2DPE line shapes reveal correlations between excitation and emission frequencies in adenine, which reflect electronic and nuclear relaxation processes associated with particular tautomers. Overall, this study demonstrates the feasibility of techniques that will hold many advantages for the study of biomolecules whose lowest-energy electronic resonances are found in the mid-UV (e.g., DNA bases, amino acids).

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.

Four Tautomers of Isolated Guanine from Infrared Laser Spectroscopy in Helium Nanodroplets

Infrared laser spectroscopy is used to study the four lowest energy tautomers of guanine, isolated in helium nanodroplets. The large number of vibrational bands observed in the infrared spectrum are assigned by comparing the corresponding experimental vibrational transition moment angles with those obtained from ab initio theory. The result is the conclusive assignment of the spectrum to the N9H-Keto, N7H-Keto, N9Ha-Enol(trans), and N9Hb-Enol(cis) tautomers. The dipole moments of these tautomers are also experimentally determined and compared with ab initio theory.

Dichroic Properties of Bis(benzoxazolyl)stilbene and Bis(benzoxazolyl)thiophene Dispersed into Oriented Polyethylene Films: A Combined Experimental and Density Functional Theory Approach

In this work, a combination of experimental and quantum mechanical investigations is performed for the study of dichroic absorption properties of melt-processed linear low-density polyethylene (LLDPE) oriented films containing < or =0.5 wt % of either 4,4'-bis(2-benzoxazolyl)stilbene (BBS) or 2,5-bis(5-tert-butyl-2-benzoxazolyl)thiophene (BTBBT). The data acquired reveal that the film optical anisotropy and the performances as linear polarizer are strongly dependent on the molecular structure of the chromophore. In particular, the rodlike structure of BBS favors the alignment of the dye along the drawing direction of the PE film, providing dichroic ratios as high as 100 and optical performances as linear polarizer close to the pseudo-affine deformation scheme. On the contrary BTBBT, although characterized by huge anisotropic potentialities, confers the oriented film very poor dichroism and is unsuitable for linear polarizer applications. This behavior is attributed to the more complex banana-shaped structure of BTBBT dye caused by the thiophene 2,5-functionalization that limits the molecule parallel orientation to the drawing direction.

Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution: Implications for the Nonradiative Decay Mechanism

The DNA base adenine and four monomethylated adenines were studied in solution at room temperature by femtosecond pump-probe spectroscopy. Transient absorption at visible probe wavelengths was used to directly observe relaxation of the lowest excited singlet state (S(1) state) populated by a UV pump pulse. In H(2)O, transient absorption signals from adenine decay biexponentially with lifetimes of 0.18 +/- 0.03 ps and 8.8 +/- 1.2 ps. In contrast, signals from monomethylated adenines decay monoexponentially. The S(1) lifetimes of 1-, 3-, and 9-methyladenine are similar to one another and are all below 300 fs, while 7-methyladenine has a significantly longer lifetime (tau = 4.23 +/- 0.13 ps). On this basis, the biexponential signal of adenine is assigned to an equilibrium mixture of the 7H- and 9H-amino tautomers. Excited-state absorption (ESA) by 9-methyladenine is 50% stronger than by 7-methyladenine. Assuming that ESA by the corresponding tautomers of adenine is unchanged, we estimate the population of 7H-adenine in H(2)O at room temperature to be 22 +/- 4% (estimated standard deviation). To understand how the environment affects nonradiative decay, we performed the first solvent-dependent study of nucleobase dynamics on the ultrafast time scale. In acetonitrile, both lowest energy tautomers of adenine are present in roughly similar proportions as in water. The lifetimes of the 9-substituted adenines depend somewhat more sensitively on the solvent than those of the 7-substituted adenines. Transient signals for adenine in H(2)O and D(2)O are identical. These solvent effects strongly suggest that excited-state tautomerization is not an important nonradiative decay pathway. Instead, the data are most consistent with electronic energy relaxation due to state crossings between the optically prepared (1)pipi* state and one or more (1)npi* states and the electronic ground state. The pattern of lifetimes measured for the monomethylated adenines suggests a special role for the (1)npi* state associated with the N7 electron lone pair.

Vibrational transition moment angles in isolated biomolecules: a structural tool

Infrared spectroscopy is used extensively in the study of isolated biomolecules, but it becomes less useful as it is applied to systems of increasing complexity. Even if the individual vibrational bands can be resolved spectroscopically, their assignment becomes problematic when they are more closely spaced than can be determined using ab initio methods. We describe a method that helps to alleviate this difficulty by measuring the direction of the vibrational transition moment for each vibrational band. The molecules of interest (adenine and cytosine) are cooled to 0.37 kelvin in liquid helium nanodroplets and oriented in a large dc electric field. A polarized infrared laser is then used to determine the directions of the infrared transition moments relative to the permanent dipole moment. Comparisons with ab initio calculations provide detailed structural information, including experimental evidence for nonplanarity of adenine and three tautomers of cytosine.