Electron attachment to DNA and RNA nucleobases: An EOMCC investigation

We report a benchmark theoretical investigation of both vertical and adiabatic electron affinities of DNA and RNA nucleobases: adenine, guanine, cytosine, thymine, and uracil using equation of motion coupled cluster method. The vertical electron affinity (VEA) values of the first five states of the DNA and RNA nucleobases are computed. It is observed that the first electron attached state is energetically accessible in gas phase. Furthermore, an analysis of the natural orbitals exhibits that the first electron attached states of uracil and thymine are valence‐bound in nature and undergo significant structural changes on attachment of an extra electron, which reflects in the deviation of the adiabatic electron affinity (AEA) than that of the vertical ones. Conversely, the first electron attached states of cytosine, adenine, and guanine are in the category of dipole‐bound anions. Their structure, by and large, remain unaffected on attachment of an extra electron, which is evident from the observed small difference between the AEA and VEA values. VEA and AEA values of all the DNA and RNA nucleobases are found to be negative, which implies that the first electron attached states are not stable rather quasi bound. The results of all previous theoretical calculations are out of track and shows large deviation with respect to the experimentally measured values, whereas, our results are found to be in good agreement. Therefore, our computed values can be used as a reliable standard to calibrate new theoretical methods. © 2015 Wiley Periodicals, Inc.     

Efficient N-arylation and N-alkenylation of the five DNA/RNA nucleobases

A general approach to N-arylation and N-alkenylation of all five DNA/RNA nucleobases at the nitrogen atom normally attached to the sugar moiety in DNA or RNA has been developed. Various protected or masked nucleobases engaged readily in the copper-mediated Chan-Lam-Evans-modified Ullmann condensation with a range of different boronic acids at room temperature and were subsequently converted to the corresponding deprotected or unmasked adducts. Different N(3)-protecting groups were examined in the case of thymine, where the benzoyl group afforded the highest yields. A 4-alkylthio-substituted pyrimidin-2(1H)-one served as both a cytosine and a uracil precursor and was N-arylated and N-alkenylated in high yields. Adenine was efficiently and selectively N-arylated and N-alkenylated at the N(9) position by employing a bis-Boc-protected adenine derivative, while a bis-Boc-protected 2-amino-6-chloropurine served as guanine precursor and could also be selectively N(9)-arylated and N(9)-alkenylated.     

Ab initio determination of the ionization potentials of DNA and RNA nucleobases

Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra.     

Adsorption of DNA/RNA nucleobases on hexagonal boron nitride sheet: an ab initio study

Our ab initio calculations indicate that the interaction of deoxyribonucleic/ribonucleic acid (DNA/RNA) nucleobases [guanine (G), adenine (A), thymine (T), cytosine (C), and uracil (U)] with the hexagonal boron nitride (h-BN) sheet, a polar but chemically inert surface, is governed by mutual polarization. Unlike the case of graphene, all nucleobases exhibit the same stacking arrangement on the h-BN sheet due to polarization effects: the anions (N and O atoms) of nucleobases prefer to stay on top of cations (B) of the substrate as far as possible, regardless of the biological properties of nucleobases. The adsorption energies, ranging from 0.5 eV to 0.69 eV, increase in the order of U, C, T, A and G, which can be attributed to different side groups or atoms of nucleobases. The fundamental nature of DNA/RNA nucleobases and h-BN sheet remains unchanged upon adsorption, suggesting that the h-BN sheet is a promising template for DNA/RNA-related research, such as self-assembly.     

An improved flow analysis-ion chromatography method for determination of cationic and anionic species at trace levels in Antarctic ice cores

A method was developed for the quantitative determination of cations and anions in Antarctic ice cores at μg L⁻¹ and sub-μg L⁻¹ levels by ion chromatography (IC), after ultra-clean decontamination procedures. Strict manipulation and decontamination procedures were used in sub-sampling, in order to minimise sample contamination. Na⁺, NH₄⁺, K⁺, Mg²⁺ and Ca²⁺ were determined by 12-min isocratic elution (H₂SO₄ eluent). Contemporaneously, in a parallel device, F⁻, MSA (methanesulfonic acid), Cl⁻, NO₃⁻ and SO₄²⁻ were analysed in a single 12-min run with multiple-step elution using Na₂CO₃/NaHCO₃ as eluent. Melted ice samples were pumped from their still-closed containers (polystyrene accuvettes with polyethylene caps), shared between the two ion chromatographic systems, online filtered (0.45 μm Teflon membrane) and pre-concentrated (anions and cations pre-concentration columns) using a flow analysis system, thus avoiding uptake of contaminants from the laboratory atmosphere. Sensitivity, linear range, reproducibility and detection limit were evaluated for each chemical species. Anion or cation detection limits ranged from 0.01 to 0.15 μg L⁻¹ by using a relatively small sample volume (1.5 mL). Such values are significantly lower than those reported in literature for almost all the components. These methods were successfully applied to the analysis of cations and anions at trace levels in the Dome C ice core. The composition of the atmospheric aerosol for the last 850 kyr was reconstructed by high-resolution continuous chemical stratigraphies. Concentration trends in the last nine glacial-interglacial climatic cycles were shown and briefly discussed.     

Coordination of W(CO)5 to DNA and RNA nucleobases: development of a possible heavy-metal labeling complex

Photolysis of W(CO)₆ in acetone solvent in the presence of DNA/RNA nucleobases attached to their ribose sugars has revealed attachment of the W(CO)₅ moiety at N-7, N-1 and N-3 for both guanosine (G) and adenosine (A). Cytidine (C) coordinates only at N-3. Thymidine (T) and uridine (U) do not coordinate via a pyrimidine site, but engage in attack at the C3 ribose position to form a carbene. The isomer distribution of W(CO)₅ to G and A follows a pattern recently discovered for Ru^II of [Ru(hedta)]^– in that the softer metal centers (compared to Pt^II agents) favor binding at N-3 over N-7 in a ratio close to 70:30 for Ru^II on G, matched by a 72:28 ratio for W(CO)₅ with G and 78:22 with A where the ratio represents N-3 plus N-1 coordination : N-7 coordination for the W(CO)₅ series. The results indicate the possibility of developing a water-soluble LW(CO)₄ heavy atom attachment for X-ray structural uses or as a metallo-drug wherein L serves as a solubilizing, trans directing agent in the photolysis of W(CO)₅L.     

Significant pKa perturbation of nucleobases is an intrinsic property of the sequence context in DNA and RNA

The pH titration and NMR studies (pH 6.6-12.5) in the heptameric isosequential ssDNA and ssRNA molecules, [d/r(5'-CAQ1GQ2AC-3', with variable Q1/Q2)], show that the pKa of the central G residue within the heptameric ssDNAs (DeltapKa = 0.67 +/- 0.03) and ssRNAs (DeltapKa = 0.49 +/- 0.02) is sequence-dependent. This variable pKa of the G clearly shows that its pseudoaromatic character, hence, its chemical reactivity, is strongly modulated and tuned by its sequence context. In contradistinction to the ssDNAs, the electrostatic transmission of the pKa of the G moiety to the neighboring A or C residues in the heptameric ssRNAs (as observed by the response of the aromatic marker protons of As or Cs) is found to be uniquely dependent upon the sequence composition. This demonstrates that the neighboring As or Cs in ssRNAs have variable electrostatic efficiency to interact with the central G/G-, which is owing to the variable pseudoaromatic characters (giving variable chemical reactivities) of the flanking As or Cs compared to those of the isosequential ssDNAs. The sequence-dependent variation of pKa of the central G and the modulation of its pKa transmission through the nearest-neighbors by variable electrostatic interaction is owing to the electronically coupled nature of the constituent nucleobases across the single strand, which demonstrates the unique chemical basis of the sequence context specificity of DNA or RNA in dictating the biological interaction, recognition, and function with any specific ligand.     

Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene

In the last years, experimental/theoretical studies have shown that graphene has a strong affinity toward nucleobases, serving as a promising nanomaterial for self‐assembly, sensing, and/or sequencing of DNA/RNA constituents. Then, a complete picture of the properties of the nucleobase–graphene systems is required for its use in technological applications. This work describes a detailed quantum chemical analysis of the aromaticity of adsorbed nucleobases on graphene, comparing between aromaticity indexes based on magnetic, geometry, electron density, and electron delocalization properties of graphene–nucleobase systems. Contrary to the stated by magnetic‐based aromaticity criteria (such as nucleus‐independent chemical shifts), it is proved that the aromatic character of nucleobases is not increased/decreased upon binding on graphene. Therefore, magnetic aromaticity criteria are not recommended to analyze aromaticity in related systems, unless a fragmented scheme be adopted. Finally, these results are expected to expand the knowledge about the understanding of biomolecules‐graphene interactions.     

Characterization of nucleobases in sea buckthorn leaves: An HPTLC approach

The present study aims to establish a high-performance thin layer chromatography (HPTLC)-based comparative analysis, directed toward characterization of nucleobases in aqueous and alcoholic extracts of sea buckthorn leaves from three different varieties: Hippophae salicifolia, Hippophae rhamnoides mongolica, and Hippophae rhamnoides turkestanica. The alcoholic and aqueous leaf extracts from these sea buckthorn varieties were prepared using accelerated solvent extraction technique. A novel HPTLC method for separating and identifying six nucleobases, namely, guanosine, guanine, cytosine, adenine, uracil, and thymine were adopted. HPTLC analysis indicated the presence of one or more of these nucleobases in a total of six leaf extracts evaluated, their quantities varying from 0.23 to 7.76?µg nucleobase per mg of extract. Though a typical trend could not be observed in the values obtained, the extracts were found to be considerably rich with respect to nucleobase contents. The results acquired from HPTLC were subsequently validated by hyphenation with mass spectrometry and also by applying chemometric tools in form of heat maps, hierarchical cluster dendrograms, and principal component analysis. The presence of nucleobases in the leaf extracts was confirmed by HPLC as well but HPTLC proved to be a better approach for characterization of nucleobases in plant extracts, than high performance liquid chromatography (HPLC).     

Bound states of helium atom in dense plasmas

We have obtained the bound 1s^{2 1}S, 1s2s ^1,3S, and 1s2p ^1,3P states energies of helium atom in dense plasma environments in accurate variation calculations. A screened Coulomb potential to represent the Debye model is used for the interaction between the charged particles. A correlated wave function consisting of a generalized exponential expansion has been used to take care of the correlation effect. The 1s^{2 1}S, 1s2s ^1,3S, and 1s2p ^1,3P states energies along with the ionization potential, the energy splitting between the 1s2s ³S, and 1s2s ¹S states, transition energies between the ground state and low‐excited states of He estimated for various Debye lengths, are reported. The results show high degree of accuracy even under strong plasma conditions. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Bound states of oscillators in infinite and finite domains: A semiclassical study

By involving the uncertainty product along with a semiclassical requirement for observables, a simple variational scheme is employed to extract major features of bound states of systems in (?∞,∞) and the same of systems confined in (?L,L). Special attention is paid to perturbative studies on the asymptotic behavior of energies for oscillators in infinite domains and dependence of energy spectra of oscillators in finite domains on various system parameters. A corrected form of the virial theorem is obtained in the latter case. The governing equations for quantum isothermal and adiabatic processes, derived recently, are also shown to be modified for general confined oscillator systems and closed‐form expressions are found. These results are useful in dealing with the quantum Carnot cycles. Advantages of the present route over other semiclassical strategies are stressed. Pilot calculations demonstrate nicely the efficacy of the endeavor under various situations. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Crystal structures of deprotonated nucleobases from an expanded DNA alphabet

Reported here is the crystal structure of a heterocycle that implements a donor–donor–acceptor hydrogen‐bonding pattern, as found in the Z component [6‐amino‐5‐nitropyridin‐2(1H)‐one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine–pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ₆‐2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ido)sodium]–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1)], denoted Z‐Sod, {[Na(C₅H₄N₃O₃)(H₂O)]·C₅H₅N₃O₃·H₂O}_n, and ammonium 2‐amino‐6‐oxo‐3‐nitro‐1,6‐dihydropyridin‐1‐ide–6‐amino‐5‐nitropyridin‐2(1H)‐one–water (1/1/1), denoted Z‐Am, NH₄⁺·C₅H₄N₃O₃⁻·C₅H₅N₃O₃·H₂O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.     

An investigation of the conformational states of the methylamide of N-acetyl-L-histidine

Summary 1. All the conformational states of the methylamide of N-acetyl-L-histidine have been calculated.2. It has been shown that in the case of the tautomer of the imidazole ring with a hydrogen atom on the atom, form R of the main chain is preferred, and in the tautomer with the proton on and also in the protonated state of the side chain B forms are preferred.3. The conformational equilibrium is displaced in the direction of form I.M. M. Shemyakin Institute of Biochemistry, Academy of Sciences of the USSR, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 371–378, May–June, 1976.     

One‐electron redox properties of DNA nucleobases and common tautomers

The redox properties of DNA play an influential role in several important processes such as DNA mutation and the interaction of DNA with drugs. Structural changes in DNA nucleobases from its canonical form to its tautomeric forms can alter these properties and may lead to DNA mutation due to altered base‐pairing properties. Experimental results for the standard value of DNA redox properties vary due to choice of methodology and solvent. Theoretical determination of these properties is helpful in pinpointing standard values but still vary depending on methodology and chosen experimental benchmark. However, it is of importance to identify the overall trend of electron mobility within DNA while providing reliable standard values for redox reactions. In this work, we present the results of theoretical calculations for redox properties. Using the thermodynamic cycle, we can approximate reliable values. We report the electron affinities, ionization potentials, and redox potential for the canonical DNA nucleobases and their rare tautomers. For each of these properties, we evaluate its overall trend to gain a greater understanding of the role that electron attachment and electron mobility have within the DNA strand. All calculations are computed at the M06‐2X/6–31++G(d,p) level of theory. © 2014 Wiley Periodicals, Inc.     

An investigation of the1 B 1 excited states of water

The first seven¹ B ₁ excited states of water are investigated within the framework of the single centre method. Energies, wave-functions and electronic densities are found using one basis set of 25 Slater type orbitals and one of 40 orbitals (both with non-integer principal quantum numbers). All singly excited configurations of¹ B ₁ symmetry are taken into account. For each state the orbital parameters (n's and's) are carefully optimized. The energy differences between neighboring excited states are, when the comparison can be made, in good agreement with experiment as is also the major contributing configuration of each state. Particular emphasis is placed on the electronic rearrangement that occurs during excitation and this is explicitly brought out by the contour maps of the electronic density. These maps show satellite-clouds in the excited states.

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Zusammenfasung Die ersten sieben¹B₁-Zustände von Wasser werden mittels der Einzentrenmethode untersucht. Energien, Wellenfunktionen und Elektronendichten werden auf Grund je eines Basissatzes von 25 bzw. 40 Slater-Funktionen mit nicht-ganzzahligen Exponenten bestimmt. Dabei werden alle einfach angeregten¹ B ₁-Konfigurationen mit einbezogen and für jeden Zustand die Orbitalparameter sorgfältig optimalisiert. Die Energiedifferenzen zwischen benachbarten Zuständen sind in den Fällen, in denen der Vergleich mit dem Experiment möglich ist, richtig. Besondere Bedeutung wird den Elektronenumlagerungen beigemessen, die während der Anregung auftreten; sie werden in den Konturen-Bildern, die die Satellitenwolken in den angeregten Zuständen zeigen, wiedergegeben.

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Resumé Les sept premiers états excités¹ B ₁ de l'eau sont étudiés dans le cadre de la méthode à un seul centre. Les énergies, les fonctions d'onde et les densités électroniques sont trouvés successivement dans des bases de 25 et de 40 orbitales de type Slater (dans les deux cas avec des nombres quantiques prin cipaux non entiers). Toutes les configurations monoexcitées de symétrie¹ B ₁ sont prises en compte. Les paramètres orbitaux (n et sont soigneusement optimisés pour chaque état. Lorsque la comparaison avec l'expérience peut être faite on trouve des différences correctes entre les énergies d'état excités voisins, ainsi qu'une bonne identification des configurations essentielles correspondantes. On insiste particulièrement sur le réarrangement électronique qui se produit au cours de l'excitation et qui est explicitement révélé par les cartes d'isodensité. Ces cartes présentent des nuages satellites dans les états excités.

     

Synthesis of Ionic Liquids Using Non Conventional Activation Methods: An Overview

Summary. The synthesis of ionic liquids under non conventional activation methods is historically reviewed and completed with the recent developments of “one-pot” synthesis and combination of these activation methods.     

Excited states dynamics of DNA and RNA bases: characterization of a stepwise deactivation pathway in the gas phase

Radiationless deactivation pathways of excited gas phase nucleobases were investigated using mass-selected femtosecond resolved pump-probe resonant ionization. By comparison between nucleobases and methylated species, in which tautomerism cannot occur, we can access intrinsic mechanisms at a time resolution never reported so far (80 fs). At this time resolution, and using appropriate substitution, real nuclear motion corresponding to active vibrational modes along deactivation coordinates can actually be probed. We provide evidence for the existence of a two-step decay mechanism, following a 267 nm excitation of the nucleobases. The time resolution achieved together with a careful zero time-delay calibration between lasers allow us to show that the first step does correspond to intrinsic dynamics rather than to a laser cross correlation. For adenine and 9-methyladenine a first decay component of about 100 fs has been measured. This first step is radically increased to 200 fs when the amino group hydrogen atoms of adenine are substituted by methyl groups. Our results could be rationalized according to the effect of the highly localized nature of the excitation combined to the presence of efficient deactivation pathway along both pyrimidine ring and amino group out-of-plane vibrational modes. These nuclear motions play a key role in the vibronic coupling between the initially excited pipi* and the dark npi* states. This seems to be the common mechanism that opens up the earlier phase of the internal conversion pathway which then, in consideration of the rather fast relaxation times observed, would probably proceed via conical intersection between the npi* relay state and high vibrational levels of the ground state.     

Bound states and scattering resonances of OH(A)-He

The OH-He complex has been observed using laser excitation of the A 2sigma+-X 2pi transition. The bands of the complex were close to the monomer rotational lines that terminate on the n = 0, 1, and 2 levels of OH(A). The unresolved band associated with He.OH (A,n=0) was redshifted from the OH parent line by 1.6 cm(-1), providing a direct measurement of D0'-D0". The complex features associated with n = 1 and 2 were identified as scattering resonances. They have been assigned by comparison with resonance structures derived from close-coupling calculations. The ab initio potential energy surface of H.-S. Lee, A.B. McCoy, R.R. Toczylowski, and S.M. Cybulski, [J. Chem. Phys. 113, 5736 (2000)] was used in these calculations. The level of agreement between the observed and predicted resonances indicated that the ab initio surface is reasonably accurate.