Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations

Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, the most important tertiary interaction type in functional RNAs. This study provides an in-depth structure and stability analysis for these two base pair families. Gas-phase-optimized geometries are reported for 12 cis and 7 trans SE/SE base pairs and contrasted to their X-ray counterparts. Interaction energies are computed at the RIMP2 level of theory using the density-functional-theory-optimized geometries. There is a good overall agreement between the optimized and X-ray geometries of the cis SE/SE base pairs. In contrast, only three of the seven trans SE/SE binding patterns could be optimized without a significant distortion of the X-ray geometry. Note, however, that many SE/SE base pairs participate in broader networks of interactions; thus it is not surprising to see some of them to deviate from the X-ray geometry in a complete isolation. Computed interaction energies reveal that all 12 known cis SE/SE binding patterns are very stable. Among the trans SE/SE binding patterns, only the rG/rG, rG/rC, and rA/rG base pairs are sufficiently stable in the crystal geometry. Prediction has been made for some structures not yet detected by crystallography, namely, cis rC/rC, rG/rC, rG/rU, and rU/rU and trans rG/rA base pairs. Interestingly, the new cis SE/SE binding patterns are not necessarily isosteric with the remaining 12 members of this family. The trans rG/rA base pair represents a viable option for base pairing in RNA to be identified by future X-ray studies. In a complete lack of structural information, prediction of other unknown members of the trans SE/SE family was not attempted. Analysis of the interaction energies shows a very large electron correlation component of the interaction energy, pointing at the elevated role of dispersion energy as compared to other types of base pairs. This likely is profitable for stabilization of SE/SE binding patterns in polar environments and could be one of the reasons why the A-minor motif is the leading type of tertiary interactions in RNAs.     

Isotopic effects in H-atom abstraction from matrix molecules by methyl radicals in poly(methyl methacrylate). Determination of the scale of relative reagent motions

The H-abstraction by ?H₃ and ?D₃ radicals from PMMA molecules is investigated at 77 and 120 K. The film samples are prepared from the mixture of normal and deuterated PMMA. The reaction is of the first order with respect to radical concentration. Its rate is retarded in time as compared to the exponential law. An analysis of the molecular product ratio for the reaction allows the primary isotopic effect to be estimated. The initial reaction rate depends nonmonotonously on the proportion of the deuterated polymer in the matrix. Namely, there exists a range of isotopic compositions, with the reaction rate increasing with the portion of a deuteropolymer in the mixture. At 77 K the reaction rate of ?D₃ is lower than that of ?H₃ in PMMA of a mixed isotopic composition. This results from the proximity of ?D₃ with unreactive parental macromolecules, which reduces the local H concentrations around ?D₃ as compared to the mean concentration. At 120 K the radical decay rates do not differ. This fact cannot be explained by unfrozen mobilities of radicals at high temperatures or by their migration from parental macromolecules. The phenomenon is interpreted in terms of thermal fluctuations involving a great area around a radical and ensuring its migration within this area. The electron spin echo method is used to estimate the distance between a radical and its parental macromolecule, a ≥ 9.6 Å. This is the lower limit of the reaction accessibility.     

Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical

In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.     

Model studies of DNA C5' radicals. Selective generation and reactivity of 2'-deoxyadenosin-5'-yl radical

The reaction of hydrated electrons (e(aq)(-)) with 8-bromo-2'-deoxyadenosine has been investigated by radiolytic methods coupled with product studies and addressed computationally by means of DFT-B3LYP calculations. Pulse radiolysis revealed that this reaction was complete in approximately 0.3 mus, and, at this time, no significant absorption was detected. The spectrum of a transient developed in 20 mus has an absorbance in the range 300-500 nm (epsilon(max) congruent with 9600 M(-1) cm(-1) at 360 nm), and it was assigned to aromatic aminyl radical 3. Computed vertical transitions (TD-UB3LYP/6-311+G) are in good agreement with the experimental observations. Radical 3 is obtained by the following reaction sequence: one-electron reductive cleavage of the C-Br bond that gives the C8 radical, a fast radical translocation from the C8 to C5' position, and an intramolecular attack of the C5' radical at the C8,N7 double bond of the adenine moiety. The rate constant for the cyclization is 1.6 x 10(5) s(-1). On the basis of the theoretical findings, the cyclization step is highly stereospecific. The rate constants for the reactions of C5' and aminyl 3 radicals with different oxidants were determined by pulse radiolysis methods. The respective rate constants for the reaction of 2'-deoxyadenosin-5'-yl radical with dioxygen, Fe(CN)(6)(3)(-), and MV(2+) in water at ambient temperature are 1.9 x 10(9), 4.2 x 10(9), and 2.2 x 10(8) M(-1) s(-1). The value for the reaction of aminyl radical 3 with Fe(CN)(6)(3-) is 8.3 x 10(8) M(-1) s(-1), whereas the reaction with dioxygen is reversible. Tailored experiments allowed the reaction mechanism to be defined in some detail. A synthetically useful radical cascade process has also been developed that allows in a one-pot procedure the conversion of 8-bromo-2'-deoxyadenosine to 5',8-cyclo-2'-deoxyadenosine in a diastereoisomeric ratio (5'R):(5'S) = 6:1 and in high yield, by reaction with hydrated electrons in the presence of K(4)Fe(CN)(6).     

Factors controlling the relative stabilities of cis- and trans-[PtX2L2] isomers: Chatt and Wilkins--50 years on

DFT computations reveal that cis-trans preferences in [PtX2(PR3)2] species are due to a combination of electrostatics, pi-backbonding, antisymbiosis, and solvation effects.     

An investigation of the relative stabilities of the isomers of CF2N2: Comparison of ab initio and MNDO calculations

Ab initio SCF calculations at the HF/3-21G level and semi-empirical MNDO calculations have been used to locate the stationary points on the CF₂N₂ energy surface. Perfluorodiazomethane is predicted to be most stable isomer, but perfluorodiazirine is predicted to lie only ca 41 kJ higher in energy at the SCF level. There are significant differences between the ab initio and MNDO results for the ordering of some of the isomers. Frequency calculations give results in good agreement with the limited experimental data on these molecules.     

On the direction and magnitude of radical substituent effects: the role of polar interaction on thermodynamic stabilities of benzylic C-H bonds and related carbon radicals

The C-H bond dissociation enthalpies (BDEs) of polarized benzylic molecules, i.e., para-substituted phenylacetonitriles (PANs), and the spin variations of the radicals of the general type p-GC6H4CH*-Y were investigated using density functional theory (DFT) calculations. In contrast to the commonly observed S-type substituent effect (see text), the present work shows that there should be three (rather than one) primary patterns (i.e., S, O, and counter-O) for remote G to affect spin and radical stability, depending upon the polarity of the alpha-Y group. Correlation analyses reveal that both the direction and magnitude of spin/radical effects are quantitatively related to the intensity of polar interaction in radical system, as registered by either the calculated group charges of the phenyl ring (C(Ph)) or by the polar constant sigma(+)s (Figures 1-4). A unified platform (Scheme 1) to rationalize the apparent differences of radical substituent effect is proposed.     

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.     

Direct dynamics studies on hydrogen abstraction reactions of CH3CHFCH3 and CH3CH2CH2F with OH radicals

The hydrogen abstraction reactions of CH3CHFCH3 and CH3CH2CH2F with the OH radicals have been studied theoretically by a dual-level direct dynamics method. The geometries and frequencies of all the stationary points are optimized by means of the DFT calculation. There are complexes at the reactant side or exit route, indicating these reactions may proceed via indirect mechanisms. To improve the reaction enthalpy and potential barrier of each reaction channel, the single point energy calculation is performed by the MC-QCISD/3 method. The rate constants are evaluated by canonical variational transition state theory (CVT) with the small-curvature tunneling correction method (SCT) over a wide temperature range 200-2000 K. The canculated CVT/SCT rate constants are consistent with available experimental data. The results show that both the variation effect and the SCT contribution play an important role in the calculation of the rate constants. For reactions CH3CHFCH3 and CH3CH2CH2F with OH radicals, the channels of H-abstraction from -CHF- and -CH2- groups are the major reaction channels, respectively, at lower temperature. Furthermore, to further reveal the thermodynamics properties, the enthalpies of formation of reactants CH3CHFCH3, CH3CH2CH2F, and the product radicals CH3CFCH3, CH3CHFCH2, CH3CH2CHF, CH3CHCH2F, and CH2CH2CH2F are studied using isodesmic reactions.     

A theoretical study on the low-lying excited states of 2,2':5',2'-terthiophene and 2,2':5',2':5',2'-quaterthiophene.

The nature and properties of the low-lying singlet and triplet valence excited states of 2,2':5',2'-terthiophene (terthiophene) and 2,2':5',2':5',2'-quaterthiophene (tetrathiophene) are discussed on the basis of high-level ab initio computations. The spectroscopic features determined experimentally for short alpha-oligothiophenes are rationalised on theoretical grounds. Special attention is devoted to the nonradiative decay process through intersystem crossing (ISC) from the singlet to the triplet manifold, which is known to be relatively less efficient in tetrathiophene. Along the geometry relaxation of the S1 state of terthiophene, the S1 and T2 states become degenerate, which leads to a favourable situation for the occurrence of ISC. The parallel process is expected to be less favoured in tetrathiophene because of the less efficient spin-orbit coupling and the increase of the S1-T2 energy gap.     

2-Aminopurine: a probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids

Spectroscopic techniques are employed to probe relationships between structural dynamics and charge transfer (CT) efficiency in DNA duplexes and DNA:RNA hybrids containing photoexcited 2-aminopurine (Ap). To better understand the variety of interactions and reactions, including CT, between Ap and DNA, the fluorescence behavior of Ap is investigated in a full series of redox-inactive as well as redox-active assemblies. Thus, Ap is developed as a dual reporter of structural dynamics and base-base CT reactions in nucleic acid duplexes. CD, NMR, and thermal denaturation profiles are consistent with the family of DNA duplexes adopting a distinct conformation versus the DNA:RNA hybrids. Fluorescence measurements establish that the d(A)-r(U) tract of the DNA:RNA hybrid exhibits enhanced structural flexibility relative to that of the d(A)-d(T) tract of the DNA duplexes. The yield of CT from either G or 7-deazaguanine (Z) to Ap in the assemblies was determined by comparing Ap emission in redox-active G- or Z-containing duplexes to otherwise identical duplexes in which the G or Z is replaced by inosine (I), the redox-inactive nucleoside analogue. Investigations of CT not only demonstrate efficient intrastrand base-base CT in the DNA:RNA hybrids but also reveal a distance dependence of CT yield that is more shallow through the d(A)-r(U) bridge of the A-form DNA:RNA hybrids than through the d(A)-d(T) bridge of the B-form DNA duplexes. The shallow distance dependence of intrastrand CT in DNA:RNA hybrids correlates with the increased conformational flexibility of bases within the hybrid duplexes. Measurements of interstrand base-base CT provide another means to distinguish between the A- and B-form helices. Significantly, in the A-form DNA:RNA hybrids, a similar distance dependence is obtained for inter- and intrastrand reactions, while, in B-DNA, a more shallow distance dependence is evident with interstrand CT reactions. These observations are consistent with evaluations of intra- and interstrand base overlap in A- versus B-form duplexes. Overall, these data underscore the sensitivity of CT chemistry to nucleic acid structure and structural dynamics.     

Chemical and structural implications of 1',2'- versus 2',4'- conformational constraints in the sugar moiety of modified thymine nucleosides

In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1',2'-azetidine- and 1',2'-oxetane-fused thymidines, as well as their 2',4'-fused thymine (T) counterparts such as LNA-T, 2'-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1',2'-fused or a tricyclic 2',4'-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37 degrees +/- 27 degrees , phi(m) = 25 degrees +/- 18 degrees ) of the 1',2'-fused systems, and (ii) pure North type (P = 19 degrees +/- 8 degrees , phi(m) = 48 degrees +/- 4 degrees ) for the 2',4'-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1',2'- or 2',4'-linked modification. The comparison of pK(a)s of the 1-thyminyl aglycon as well as that of endocyclic sugar-nitrogen obtained by theoretical and experimental measurements showed that the nature of the sugar conformational constraints steer the physicochemical property (pK(a)) of the constituent 1-thyminyl moiety, which in turn can play a part in tuning the strength of hydrogen bonding in the basepairing.     

Thermodynamics of vinyl ethers—XI: The effect of the alkoxy group on the relative stabilities of 2-alkoxy-3-methyl-1-butenes and corresponding 2-butenes

The effect of the alkoxy group (RO-; R=Me, Et, MeOCH₂CH₂, ClCH₂CH₂, i-Pr, s-Bu, (Et)₂CH, C₆H₅) on the relative stabilities of 2-alkoxy-3-methyl-1-butenes and corresponding 2-butenes has been studied by chemical equilibration in cyclohexane solution at various temperatures. The relative stability of the latter isomer is favored by (a) increasing size, (b) increasing electron-attracting character, and (c) increasing conjugative power of the R group. The last-mentioned point is especially important; in the case R = phenyl, the value of ΔH° (g, 298·15 K) of the isomerization of the former to the latter is 12–13 kJ mol^?1 more negative than in cases where conjugation between the ether oxygen and the R group is not possible.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Structures and relative stabilities of [C2H6N] ions: A non-empirical and MNDO study

Non-empirical molecular orbital calculations have been performed on the seven possible [C₂H₆N]⁺ isomers at different levels of sophisitcation. The results suggest that the ions possessing a resonance contribution with a filled octet are the most stable ones. Barriers to CH₃ — and NH₃ —rotation have also been computed and are generally quite low ( 5 kJ mol⁻¹).     

Density-functional calculation of CeO2 surfaces and prediction of effects of oxygen partial pressure and temperature on stabilities

We have used density-functional theory to investigate (111), (110), (210), (211), (100), and (310) surfaces of ceria (CeO2). Compared with previous interatomic-potential-based studies, our calculations reported a slightly different relative stability ordering and significantly lower surface energies for the stoichiometric surfaces. Using a defect model, the surface stabilities were evaluated as functions of oxygen partial pressure and temperature. Our investigations were restricted to ideal surface terminations, without considering defect formation on those surfaces. We found that at 300 K, the stoichiometric (111) has the lowest free energy for a wide range of oxygen partial pressures up to 1 atm, and only at ultrahigh vacuum does the Ce-terminated (111) becomes the most stable one. The transition point for the Ce-terminated (111) surfaces moves to higher oxygen partial pressures when temperature increases. To improve the prediction of electron density of states, we used the local-density approximation plus U(J) correction method to correct the on-site Coulomb correlation and exchange interaction due to the strongly localized Ce-4f electrons. The optimal parameter combination of U = 7 eV and J = 0.7 eV was found to improve the O 2p-Ce 4f gap without much degradation of ground-state bulk properties or the O 2p-Ce 5d gap. The bulk and surface electronic structures were then analyzed based on the improved density of states.     

Studies on the Interaction of Cobalt Mixed-Ligand Coordination Compound Containing Tetrapyrido [3,2-a: 2' 3'-c: 3″ 2″ h: 2'″, 3'″-j] phenazine with DNA

A new monometallic complex [Co(phen)2tpphz]3+ (where tpphz is tetrapyrido [3,2-a: 2',3'-c: 3″,2″-h: 2'″,3'″-j] phenazine) was synthesized by the reaction of 5,6-diamino-1,10-phenanthroline with [Co(phen)2(phendione)]3+. It was characterized by elemental analysis, molar conductivity, IR, 1H NMR, ultraviolet and fluorescence spectroscopy. The interaction of the complex with DNA was also investigated. The complex shows the absorption hypochromicity, fluorescence enhancement, the specific viscosity increased when bound to calf thymus DNA. The cyclic voltammetry (CV) measurement showed a change in peak current with the addition of DNA. All the results provide the support for the intercalative binding mode of the mononuclear complex.