Electronic Structure and Spectroscopy of Nucleic Acid Bases: Ionization Energies, Ionization-Induced Structural Changes, and Photoelectron Spectra

Guanine holes are prominent targets for mutation in cancer and inherited disease

Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease. These alterations occur non-randomly in DNA, being strongly influenced by the local nucleotide sequence context. However, the molecular mechanisms underlying such sequence context-dependent mutagenesis are not fully understood. Using bioinformatics, computational and molecular modeling analyses, we have determined the frequencies of mutation at G • C bp in the context of all 64 5'-NGNN-3' motifs that contain the mutation at the second position. Twenty-four datasets were employed, comprising >530,000 somatic single base substitutions from 21 cancer genomes, >77,000 germline single-base substitutions causing or associated with human inherited disease and 16.7 million benign germline single-nucleotide variants. In several cancer types, the number of mutated motifs correlated both with the free energies of base stacking and the energies required for abstracting an electron from the target guanines (ionization potentials). Similar correlations were also evident for the pathological missense and nonsense germline mutations, but only when the target guanines were located on the non-transcribed DNA strand. Likewise, pathogenic splicing mutations predominantly affected positions in which a purine was located on the non-transcribed DNA strand. Novel candidate driver mutations and tissue-specific mutational patterns were also identified in the cancer datasets. We conclude that electron transfer reactions within the DNA molecule contribute to sequence context-dependent mutagenesis, involving both somatic driver and passenger mutations in cancer, as well as germline alterations causing or associated with inherited disease.

Time-resolved photoelectron imaging of the iodide-thymine and iodide-uracil binary cluster systems

The energetics and dynamics of thymine and uracil transient negative ions were examined using femtosecond time-resolved photoelectron imaging. The vertical detachment energies (VDEs) of these systems were found to be 4.05 eV and 4.11 eV for iodide-thymine (I(-) x T) and iodide-uracil (I(-) x U) clusters, respectively. An ultraviolet pump pulse was used to promote intracluster charge transfer from iodide to the nucleobase. Subsequent electron detachment using an infrared probe pulse monitored the dynamics of the resulting transient negative ion. Photoelectron spectra reveal two primary features: a near-zero electron kinetic energy signal attributed to autodetachment and a transient feature representing photodetachment from the excited anion state. The transient state exhibits biexponential decay in both thymine and uracil complexes with short and long decay time constants ranging from 150-600 fs and 1-50 ps, respectively, depending on the excitation energy. However, both time constants are systematically shorter for I(-) x T. Vibrational autodetachment and iodine loss are identified as the primary decay mechanisms of the transient negative ions of thymine and uracil.

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers

Dipole moments (μ), charge distributions, and static electronic first-order hyperpolarizabilities (β(μ)) of the two lowest-energy keto tautomers of guanine (7H and 9H) were determined in the gas phase using Hartree-Fock, Møller-Plesset perturbation theory (MP2 and MP4), and DFT (PBE1PBE, B97-1, B3LYP, CAM-B3LYP) methods with Dunning's correlation-consistent aug-cc-pVDZ and d-aug-cc-pVDZ basis sets. The most stable isomer 7H exhibits a μ value smaller than that of the 9H form by a factor of ca. 3.5. The β μ value of the 9H tautomer is strongly dependent on the computational method employed, as it dramatically influences the β(μ) (9H)/β(μ) (7H) ratio, which at the highest correlated MP4/aug-cc-pVDZ level is predicted to be ca. 5. The Coulomb-attenuating hybrid exchange-correlation CAM-B3LYP method is superior to the conventional PBE1PBE, B3LYP, and B97-1 functionals in predicting the β(μ) values. Differences between the largest diagonal hyperpolarizability components were clarified through hyperpolarizability density analyses. Dipole moment and first-order hyperpolarizability are molecular properties that are potentially useful for distinguishing the 7H from the 9H tautomer.

Molecular beam mass spectrometry with tunable vacuum ultraviolet (VUV) synchrotron radiation

Tunable soft ionization coupled to mass spectroscopy is a powerful method to investigate isolated molecules, complexes and clusters and their spectroscopy and dynamics(1-4). Fundamental studies of photoionization processes of biomolecules provide information about the electronic structure of these systems. Furthermore determinations of ionization energies and other properties of biomolecules in the gas phase are not trivial, and these experiments provide a platform to generate these data. We have developed a thermal vaporization technique coupled with supersonic molecular beams that provides a gentle way to transport these species into the gas phase. Judicious combination of source gas and temperature allows for formation of dimers and higher clusters of the DNA bases. The focus of this particular work is on the effects of non-covalent interactions, i.e., hydrogen bonding, stacking, and electrostatic interactions, on the ionization energies and proton transfer of individual biomolecules, their complexes and upon micro-hydration by water(1, 5-9). We have performed experimental and theoretical characterization of the photoionization dynamics of gas-phase uracil and 1,3-dimethyluracil dimers using molecular beams coupled with synchrotron radiation at the Chemical Dynamics Beamline(10) located at the Advanced Light Source and the experimental details are visualized here. This allowed us to observe the proton transfer in 1,3-dimethyluracil dimers, a system with pi stacking geometry and with no hydrogen bonds(1). Molecular beams provide a very convenient and efficient way to isolate the sample of interest from environmental perturbations which in return allows accurate comparison with electronic structure calculations(11, 12). By tuning the photon energy from the synchrotron, a photoionization efficiency (PIE) curve can be plotted which informs us about the cationic electronic states. These values can then be compared to theoretical models and calculations and in turn, explain in detail the electronic structure and dynamics of the investigated species (1, 3).

Four Bases Score a Run: Ab Initio Calculations Quantify a Cooperative Effect of H-Bonding and π-Stacking on the Ionization Energy of Adenine in the AATT Tetramer

Benchmark calculations of the lowest ionized state of the (A:T)2 (mixed adenine-thymine) cluster at the geometry taken from the DNA X-ray structure are presented. Vertical ionization energies (IEs) computed by the equation-of-motion coupled-cluster method with single and double substitutions are reported and analyzed. The shift in IE relative to the monomer (A) is -0.7 eV. The performance of the widely used B3LYP, ωB97X-D, and M06-2X functionals with respect to their ability to describe energetics and the character (localization versus delocalization) of the ionized states is also investigated. The shifts in IEs caused by H-bonding and stacking interactions are analyzed in terms of additive versus cooperative effects. It is found that the cooperative effect accounts for more than 20% of the shift in IE relative to the monomer. The cooperative effect and, consequently, the magnitude of the shift are well reproduced by the hybrid quantum mechanics/molecular mechanics scheme in which neutral thymine bases are represented by point charges.

Nonempirically Tuned Range-Separated DFT Accurately Predicts Both Fundamental and Excitation Gaps in DNA and RNA Nucleobases

Using a nonempirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO–LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our calculations demonstrate that a physically motivated, first-principles tuned DFT approach accurately reproduces results from both experimental benchmarks and more computationally intensive techniques such as many-body GW theory. Furthermore, in the same set of nucleobases, we show that the nonempirical range-separated procedure also leads to significantly improved results for excitation energies compared to conventional DFT methods. The present results emphasize the importance of a nonempirically tuned range-separation approach for accurately predicting both fundamental and excitation gaps in DNA and RNA nucleobases.

A VUV Photoionization and Ab Initio Determination of the Ionization Energy of a Gas-Phase Sugar (Deoxyribose)

The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(±0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (±0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate.

Desorption dynamics, internal energies, and imaging of organic molecules from surfaces with laser desorption and vacuum ultraviolet (VUV) photoionization

There is enormous interest in visualizing the chemical composition of organic material that comprises our world. A convenient method to obtain molecular information with high spatial resolution is imaging mass spectrometry. However, the internal energy deposited within molecules upon transfer to the gas phase from a surface can lead to increased fragmentation and to complications in analysis of mass spectra. Here it is shown that in laser desorption with postionization by tunable vacuum ultraviolet (VUV) radiation, the internal energy gained during laser desorption leads to minimal fragmentation of DNA bases. The internal temperature of laser-desorbed triacontane molecules approaches 670 K, whereas the internal temperature of thymine is 800 K. A synchrotron-based VUV postionization technique for determining translational temperatures reveals that biomolecules have translational temperatures in the range of 216-346 K. The observed low translational temperatures as well as their decrease with increased desorption laser power is explained by collisional cooling. An example of imaging mass spectrometry on an organic polymer by using laser-desorption VUV postionization shows 5 μm feature details while using a 30 μm laser spot size and 7 ns pulse duration. Applications of laser-desorption postionization to the analysis of cellulose, lignin, and humic acids are briefly discussed.

Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk

The effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of IE to the bulk value requires the hydration sphere of approximately 13.5 Å radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.