Electronic Structure of the Nucleobases

Importance of Sugar-Phosphate Backbone and Counterions to First-Principles Modeling of Nucleobases

DFT-based first-principles calculations were carried out to understand the electronic structure difference among a backbone-free nucleobase, a backbone-containing Na counterion nucleotide, and a backbone-containing H counterion nucleotide and their difference in the adsorption on graphene and on graphitic-carbon nitride. The study discovered that the inclusion of a sugar-phosphate backbone changes the electron affinity of most nucleobases from electron acceptors to electron donors. The methyl-terminated backbone-free model cannot replicate the steric effect induced by the sugar-phosphate backbone during the adsorption of nucleobases on 2D materials. Overall, we established that the sugar phosphate backbone should be included in the study of DNA nucleobase adsorption on 2D material. We also showed that when it comes to the adsorption on 2D materials, the backbone-containing H counterion model is superior to the Na counterion model because the Na counterion produces a LUMO near the Fermi energy, which may significantly affect the interaction with the 2D material.

Tailored Solution-Based N-heterotriangulene Thin Films: Unravelling the Self-Assembly

The ability of a series of bridged triarylamines, so‐called N‐heterotriangulenes, to form multilayer‐type 2D‐extended films via a solution‐based processing method was examined using complementary microscopic techniques. We found that the long‐range order, crystallinity, and layer thickness decisively depend on the nature of the substituents attached to the polycyclic backbone. Owing to their flat core unit, compounds exhibiting a carbonyl unit at the bridge position provide a superior building block as compared to thioketone‐bridged derivatives. In addition, nature and length of the peripheral substituents affect the orientation of the aromatic core unit within highly crystalline films. Hence, our results stress the significance of a suitable molecular framework and provide deeper understanding of structure formation in 2D‐confined surroundings for such compounds.

Oxygen K-edge X-ray Absorption Spectra

We review oxygen K-edge X-ray absorption spectra of both molecules and solids. We start with an overview of the main experimental aspects of oxygen K-edge X-ray absorption measurements including X-ray sources, monochromators, and detection schemes. Many recent oxygen K-edge studies combine X-ray absorption with time and spatially resolved measurements and/or operando conditions. The main theoretical and conceptual approximations for the simulation of oxygen K-edges are discussed in the Theory section. We subsequently discuss oxygen atoms and ions, binary molecules, water, and larger molecules containing oxygen, including biomolecular systems. The largest part of the review deals with the experimental results for solid oxides, starting from s- and p-electron oxides. Examples of theoretical simulations for these oxides are introduced in order to show how accurate a DFT description can be in the case of s and p electron overlap. We discuss the general analysis of the 3d transition metal oxides including discussions of the crystal field effect and the effects and trends in oxidation state and covalency. In addition to the general concepts, we give a systematic overview of the oxygen K-edges element by element, for the s-, p-, d-, and f-electron systems.

The simulation of X-ray absorption spectra from ground and excited electronic states using core-valence separated DFT/MRCI

We present an extension of the combined density functional theory (DFT) and multireference configuration interaction (MRCI) method (DFT/MRCI) [S. Grimme and M. Waletzke, J. Chem. Phys. 111, 5645 (1999)] for the calculation of core-excited states based on the core-valence separation (CVS) approximation. The resulting method, CVS-DFT/MRCI, is validated via the simulation of the K-edge X-ray absorption spectra of 40 organic chromophores, amino acids, and nucleobases, ranging in size from CO₂ to tryptophan. Overall, the CVS-DFT/MRCI method is found to yield accurate X-ray absorption spectra (XAS), with consistent errors in peak positions of ∼2.5-3.5 eV. Additionally, we show that the CVS-DFT/MRCI method may be employed to simulate XAS from valence excited states and compare the simulated spectra to those computed using the established wave function-based approaches [ADC(2) and ADC(2)x]. In general, each of the methods yields excited state XAS spectra in qualitative and often quantitative agreement. In the instances where the methods differ, the CVS-DFT/MRCI simulations predict intensity for transitions for which the underlying electronic states are characterized by doubly excited configurations relative to the ground state configuration. Here, we aim to demonstrate that the CVS-DFT/MRCI approach occupies a specific niche among numerous other electronic structure methods in this area, offering the ability to treat initial states of arbitrary electronic character while maintaining a low computational cost and comparatively black box usage.

Influence of surface chemistry on optical, chemical and electronic properties of blue luminescent carbon dots

Carbon dots have attracted much attention due to their unique optical, chemical and electronic properties enabling a wide range of applications. The properties of carbon dots can be effectively adjusted through modifying their chemical composition. However, a major challenge remains in understanding the core and surface contributions to optical and electronic transitions. Here, three blue luminescent carbon dots with carboxyl, amino and hydroxyl groups were comprehensively characterized by UV-vis absorption and emission spectroscopy, synchrotron-based X-ray spectroscopy, and infrared spectroscopy. The influence of the surface functionality on their fluorescence was probed by pH-dependent photoluminescence measurements. Moreover, the hydrogen bonding interactions between water and the surface groups of carbon dots were characterized by infrared spectroscopy. Our results show that both core and surface electronic states of blue luminescent carbon dots contribute to electronic acceptor levels while the chemical nature of the surface groups determines the hydrogen bonding behavior of the carbon dots. This comprehensive spectroscopic study demonstrates that the surface chemistry has a profound influence on the electronic configuration and surface-water interaction of carbon dots, thus affecting their photoluminescence properties.

Reversible Stability of Emulsion and Polymer Latex Controlled by Oligochitosan and CO₂

The addition of salt to a colloid solution ensures that emulsions can be easily separated into two phases and that polymer latexes can be coagulated. The switchable stability of emulsions and polymer latexes would improve the properties for their current applications. A switchable process of salt addition can be achieved using CO₂ and switchable water, and it is a novel, benign approach to achieving a switchable ionic strength in an aqueous solution. However, the problem associated with switchable water is that its additives are all synthetic tertiary amines, most of which are harmful to human beings and the environment. Oligochitosan, as a natural product, can also be used as a switchable water additive. In this paper, a new switchable water system using oligochitosan to change the ionic strength was explored for use in several potential industrial applications. The conductivity of the aqueous solution of oligochitosan (0.2 wt.%) was switched from 0.2 to 331 μS/cm through the addition and removal of CO₂. Oligochitosan and CO₂ were successfully utilized to reversibly break a crude oil emulsion. Polystyrene (PS) latexes could also be reversibly destabilized; the zeta potential of the PS latex changed between -5.8 and -45.2 mV in the absence and presence of CO₂ after oligochitosan was dissolved in the PS latex. The use of oligochitosan is a more environmentally friendly means for reversibly separating colloid solutions.

Simulation of X-ray absorption spectra with orthogonality constrained density functional theory

Orthogonality constrained density functional theory (OCDFT) [F. A. Evangelista, P. Shushkov and J. C. Tully, J. Phys. Chem. A, 2013, 117, 7378] is a variational time-independent approach for the computation of electronic excited states. In this work we extend OCDFT to compute core-excited states and generalize the original formalism to determine multiple excited states. Benchmark computations on a set of 13 small molecules and 40 excited states show that unshifted OCDFT/B3LYP excitation energies have a mean absolute error of 1.0 eV. Contrary to time-dependent DFT, OCDFT excitation energies for first- and second-row elements are computed with near-uniform accuracy. OCDFT core excitation energies are insensitive to the choice of the functional and the amount of Hartree-Fock exchange. We show that OCDFT is a powerful tool for the assignment of X-ray absorption spectra of large molecules by simulating the gas-phase near-edge spectrum of adenine and thymine.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.

Observation of cleavage in DNA and nucleotides following oxygen K-shell ionization by measuring X-ray absorption near edge structure

PURPOSE

To investigate which type of bond is more likely to be cleaved in functional groups in DNA including the nucleobases by the K-shell ionization of oxygen of DNA, and to determine whether the production of propenal is specific to the oxygen resonant excitation. To investigate the degradation pattern which depends on the type of nucleobase in the DNA monomer.

MATERIALS AND METHODS

Calf thymus DNA film and four nucleotides (dAMP, TMP, dGMP, and dCMP) films were used as samples. Soft X-rays with energy of 560 eV were used to irradiate the samples, and the changes in the X-ray absorption near edge structure (XANES) spectra during the irradiation were measured. The XANES measurements were performed by using a 0.02 eV scanning photon energy step.

RESULTS

The difference spectra for DNA and nucleotides were similar to those for pyridine deprotonation. The oxygen K-edge regions in the difference spectra were all similar apart from the spectrum obtained at the resonant excitation energy of oxygen in DNA. The spectral change did not depend on the type of nucleotide.

CONCLUSION

(1) Deprotonation of the nucleobase -NH is usually induced by core ionization of carbon, nitrogen, and oxygen; (2) propenal production is specific to the oxygen K-shell resonant excitation; and (3) the pattern of XANES spectral changes does not significantly depend on the type of nucleobase.

Refinement of DNA structures through near-edge X-ray absorption fine structure analysis: applications on guanine and cytosine nucleobases, nucleosides, and nucleotides

In this work we highlight the potential of NEXAFS—near-edge X-ray absorption fine structure—analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (π1*) and amine (π2*) nitrogen absorption bands with a characteristic energy difference (Δ). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around ±0.4−0.5 eV change of Δ, to the spectra due to a switch of single−double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Δ, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing “compressed” and “expanded” models or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2−0.3 Å can result in the reduction of Δ by 0.2−0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create “blocks” in the π-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens more distinguishable with a larger Δ. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.

Electronic structure of genomic DNA: a photoemission and X-ray absorption study

The electronic structure of genomic DNA has been comprehensively characterized by synchrotron-based X-ray absorption and X-ray photoelectron spectroscopy. Both unoccupied and occupied states close to the Fermi level have been unveiled and attributed to particular sites within the DNA structure. A semiconductor-like electronic structure with a band gap of approximately 2.6 eV has been found at which the pi and pi* orbitals of the nucleobase stack make major contributions to the highest occupied and lowest unoccupied molecular orbitals, respectively, in agreement with previous theoretical predictions.

Systematic study of soft X-ray spectra of poly(Dg).poly(Dc) and poly(Da).poly(Dt) DNA duplexes

In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG).poly(dC) and poly(dA).poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges

Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.

The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water

Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementi's double zeta basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO(4)(-), to Na(+), and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zurich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO(4) (-) groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.

Potential energy surfaces of the microhydrated guanine...cytosine base pair and its methylated analogue

A complete scan of the potential and free-energy surfaces of monohydrated and dihydrated guanine...cytosine and 9-methylguanine...1-methylcytosine base pairs was realized by the molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The most stable and populated structures localized were further fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method with a large basis set. A systematic study of microhydration of these systems using a high-level correlated ab initio approach is presented for the first time. The different behavior of guanine...cytosine and adenine...thymine complexes is also discussed. These studies of nucleic acid base pairs are important for finding binding sites of water molecules around bases and for better understanding of the influence of the solvent on the stability of the structure of DNA.

Electronic structure of DNA nucleobases and their dinucleotides explored by soft X-ray spectroscopy

The electronic structures of a series of DNA nucleobases and their dinucleotides were investigated by N 1s X-ray absorption, X-ray photoemission, and resonant X-ray emission spectroscopy. Resonant X-ray emission spectra of the guanine base and its dinucleotide indicate that it has a weak structure at the lowest binding energy; at this energy, it isolates from the main valence band and forms the HOMO state. This indicates that the HOMO state is localized in the guanine base, as claimed by valence and core photoemissions and expected from theoretical predictions. In addition, the XAS and XES profiles of the guanine dinucleotide indicate that disruption of the aromatic character of the six-membered ring results in the localization of the pi state at the imine (-N=) site of the guanine base; this may favor charge transfer among stacked guanine bases and further influence the conductivity of DNA.

Experimental and Theoretical Investigation of the Electronic Structure of 5-Fluorouracil Compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.

Dependence of DNA Electronic Structure on Environmental and Structural Variations

We present experimental and theoretical evidence that varying the local environment and physical structure of dried DNA has a direct impact on its electronic structure. By preparing samples of DNA in various solutions, it was possible to alter the type of ions present during the production of the DNA samples. These variations resulted in differences in the local chemical environment of the dried DNA molecules. X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) were used to probe the variations in the electronic structure of DNA samples. DFT calculations of a stack of 10 adenine (A)-thymine (T) nucleobase pairs show that slight structural variations in stacking height have a direct influence on the electronic structure and result in changes to the HOMO-LUMO gap. The effects of these differences in the local environment on the electronic structure are discussed and are related to the results of conductivity measurements of DNA.

Combined X-ray Absorption Spectroscopy and Density Functional Theory Examination of Ferrocene-Labeled Peptides

A combination of soft X-ray absorption spectroscopy (XAS) measurements and StoBe density functional theory (DFT) calculations has been used to study the electronic structures of the ferrocene-labeled peptides Fc-Pro(n)-OBz (n = 1-4). Excellent agreement between the measured and the simulated data is observed in all cases, and the origin of all major spectral features was assigned. The breaking of the degeneracy of the ferrocene 3e(2u)-like unoccupied molecular orbital under the influence of a substituent attached to a Cp ring was observed experimentally. The influence of the bonding environment on the O 1s and N 1s XAS spectra was examined. A corrected assignment of one of the major features in the Fe 2p XAS spectra of ferrocene is proposed and supported by the DFT simulations, as well as the measured spectra.

Excited State Proton Transfer in Guanine in the Gas Phase and in Water Solution: A Theoretical Study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.