Molecular orbital theory of the hydrogen bond : XXXII. The effect of H and Li association on the A---T and G---C pairs

Ab initio molecular orbital calculations have been performed to determine the structures and stabilization energies of the A---T and G---C base pairs and their complexes with H⁺ and Li⁺, H⁺ and Li⁺ association stabilizes the A---T pair except for Li⁺ association at O₄ in thymine. Protonation of thymine stabilizes the A---T pair to a greater extent than protonation of adenine. The association of H⁺ and Li⁺ with guanine stabilizes the G---C pair, but protonation of cytosine destabilizes G---C. Changes in the structures of the hydrogen bonds in the A---T and G---C pairs reflect changes in hydrogen bond strengths.     

DNA碱基(对)及其Zn2+复合物对CO2,N2,H2小分子的吸附

用M062X/6-31+G^*方法探讨了腺嘌呤(A)、 胸腺嘧啶(T)、 鸟嘌呤(G)、 胞嘧啶(C)及其碱基对(AT, GC)以及Zn²⁺复合物(AAA-Zn²⁺, AAT-Zn²⁺和GGC-Zn²⁺)对混合小分子H₂, N₂, CO₂的吸附情况, 系统研究了其相互作用模式及吸附强度, 预测了常见混合气体分子与碱基(对)及复合物的吸附位置. 研究表明, CO₂倾向于以氢键的形式结合到碱基(对)的氨基氢或亚氨基氢上, 而N₂和H₂分子则倾向于结合到这些碱基(对)的平面π电子上, 以堆垛的形式存在. 根据吸附强度大小, 预测了由这些碱基为骨架合成的金属有机骨架(MOF)吸附材料对小分子的选择性吸附顺序为H₂22. 研究表明, 以AT对结合金属Zn²⁺为节点的纯天然碱基对构成的MOF要比实验合成的AA碱基对与Zn²⁺结合的MOF具备更好的吸附和分离性能.     

At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study

The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.     

Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

Analysis of ultrafast relaxation in photoexcited DNA base pairs of adenine and thymine

The photoinduced dynamics in base pairs of adenine and thymine were analyzed by femtosecond pump-probe spectroscopy. On the short-time scale up to a few picoseconds, the characteristic time constants for the dimers are quite similar to the corresponding values of the monomers. This leads to the conclusion that ultrafast intramolecular relaxation proceeds via ππ^* and nπ^* states of one component within the dimer. On the long-time scale, we obtained a novel time constant of roughly 40 ps for the thymine dimer and the adenine–thymine base pair. This time constant was never observed in the monomers and is tentatively assigned to an intermolecular relaxation process, possibly via a hydrogen transfer state.     

Theoretical study of tautomeric and ionizing effects of guanine,cytosine, and their methyl derivatives

The study of pre-translational effects (ionization, tautomerization) and post-translational effects (methylation) of guanine and cytosine has only recently been the focus of some studies. These effects can potentially help regulate gene expression as well as potentially disrupt normal gene function. Because of this wide array of roles, greater insight into these effects in deoxyribonucleic acids (DNA) are paramount. There has been considerable research of each phenomenon (tautomerization, methylation and ionization) individually. In this work, we attempt to shed light upon the pre- and post-translational effects of guanine and cytosine by investigating the electron affinities (EAs) and ionization potentials (IPs) of the major and minor tautomers and their methyl derivatives. We performed all calculations using the density functional theory B3LYP functional accompanied with 6-311G (d,p), 6-311+G (d,p), and 6-311++G (df,pd) basis sets. Our results reveal that the cytosine tautomer has a higher EA and IP than the guanine tautomers. The higher EA suggest that an electron that attaches to the GC base pair would predominately attach to the cytosine instead of guanine. The higher IP would suggest that an electron that is removed from the GC base pair would be predominately removed from the guanine within the base pair. Understanding how tautomerization, ionization, and methylation differences change effects, discourages, or promotes one another is lacking. In this work, we begin the steps of integrating these effects with one another, to gain a greater understanding of molecular changes in DNA bases.     

用反相离子对高效液相色谱法测定DNA中鸟嘌呤加胞嘧啶的百分含量

本文提出了用反相离子对高效液相色谱测定脱氧核糖核酸(DNA)在88%甲酸水解产物中鸟嘌呤加胞嘧啶的摩尔百分含量的方法,用阶式梯度技术分离五种碱基。     

Photoionization cross sections involving an explicitly correlated initial state: Combination of multiconfigurational linear response and the stieltjes—tchebycheff moment theory

We have performed outer valence photoionization cross section calculations for N₂ and O₂. To do this we have combined several linear response techniques, in particular time-dependent Hartree—Fock (TDHF), multiconfigurational time-dependent Hartree—Fock (MC TDHF), and a modification of MC TDHF (MMC TDHF) with Stieltjes—Tchebycheff moment theory (STMT). To our knowledge, these MC TDHF and MMC TDHF calculations are the first which combine explicitly correlated Green function approaches with STMT. Since, in addition, these calculations are fully coupled, we expect the MC TDHF and in particular the MMC TDHF—STMT results to be highly reliable. For both N₂ and O₂ our MC TDHF—STMT and MMC TDHF—STMT results are in overall agreement with previous static exchange STMT results; however, there are a few significant differences and differences in detail in the partial and total photoionization cross sections. In particular, for example, for N₂ we note that the MMC TDHF—STMT does not give a “hump” resonance in the cross section for the (1π_u⁻¹)A²Π_u ionic state. In O₂ we note that the (3σ_g⁻¹) cross section obtained using MMC TDHF—STMT is substantially lower than the static exchange results.     

Oligonucleotide cross-linking with copper ions. Spectral and quantum chemical study

Copper(II) complexes with synthetic oligonucleotides consisting of repeating adenine–thymine and guanine–cytosine complementary base pairs have been studied by UV spectroscopy and simulated by DFT quantum chemical calculations at the B3LYP/6-311G++(d,p) level of theory with inclusion of solvation (hydration) effects. The obtained data suggest selective interaction of copper(II) ions with guanine–cytosine complementary pairs, followed by DNA cross-linking at those sites.     

Kinetics of depletion of Co(b F) and Co(a F) atoms by O2

The kinetics of depletion of the lowest two electronically excited states, Co(b ⁴F_J) and Co(a ²F_J), upon interactions with O₂ and N₂ are studied in a fast-flow reactor at a He pressure of 0.70 Torr. The depletion of Co(b ⁴F) or Co(a ²F) by O₂ was efficient. The depletion rate constants were observed to be different among spin-orbit levels within one electronic state. Because reactive channels are not energetically accessible for these two states, the depletion was mostly attributed to electronic energy transfer to vibration or translation of O₂. Efficient depletion upon interaction with O₂ was interpreted through the occurrence of an intermediate formed by the interaction between singly occupied anti-bonding π^* orbital of O₂ and 3d orbitals of Co.     

Structural and electronic property changes of the nucleic acid bases upon base pair formation

A systematic study of structures and electronic properties has been carried out for the nucleic acid bases adenine, guanine, thymine, and cytosine and for the base pairs adenine–thymine and guanine–cytosine. We focus our attention on these properties, which experience significant changes when single nucleic bases join to form base pairs. Such properties are expected to play an important role during the formation of the DNA molecule in its B conformation. All-electron calculations with inclusion of correlation effects were performed according to the local and nonlocal density functional approaches. We compare our results with previous ab initio and semiempirical values and with available experimental data. Advantages and disadvantages for these density functional-based methods are discussed. We conclude that applications of such models to investigate larger compounds of a similar nature are promising. © 1994 by John Wiley & Sons, Inc.     

Infrared spectroscopic and photochemical study of water-ozone complexes in solid argon

Infrared spectroscopy has been coupled with the matrix isolation technique, firstly for a study of the molecular complexes between ozone and water, secondly to investigate the mechanism of the water photooxidation by ozone at 15 K by UV light. The 1:1, 1:2 and 2:1 complexes are isolated and mainly characterized by a shift in the infrared absorption of the H₂O (D₂O) submolecule. Force field calculations involving anharmonicity corrections allows us to conclude into the non-equivalence of the two OH oscillators within the 1:1 complex. This result suggests the formation of a very weak hydrogen bond of the type HOH...OO₂. By photolysis of the water-ozone mixture in solid argon (λ < 310 nm), formation of H₂O₂ with very small amounts of O₂H and OH is observed. This process occurs through the reaction between the O(¹D) atom generated by photodissociation of O₃ belonging to the one H₂O: O₃ pair and the water molecule of the same pair, without diffusion of the oxygen atom.     

Matrix isolation infrared spectroscopic and theoretical study of noble gas coordinated dipalladium–dioxygen complexes

The reaction products of palladium atoms with molecular oxygen in solid argon have been investigated using matrix isolation infrared absorption spectroscopy and quantum chemical calculations. In addition to the previously reported mononuclear palladium–dioxygen complexes: Pd(η²–O₂) and Pd(η²–O₂)₂, dinuclear palladium–dioxygen complexes: Pd₂(η²–O₂) and Pd₂(η²–O₂)₂ were formed under visible light irradiation and were identified on the basis of isotopic substitution and theoretical calculations. In addition, experiments doped with xenon in argon coupled with theoretical calculations suggest that the Pd(η²–O₂), Pd₂(η²–O₂) and Pd₂(η²–O₂)₂ complexes are coordinated by two argon or xenon atoms in solid argon matrix, and therefore, should be regarded as the Pd(η²–O₂)(Ng)₂, Pd₂(η²–O₂)(Ng)₂ and Pd₂(η²–O₂)₂(Ng)₂ (NgAr or Xe) complexes isolated in solid argon.     

The Protonated Guanine–Cytosine Base Pair

Protonated base pairs were recently implicated in the context of DNA proton transfer and charge migration. The effects of protonating different sites of the guanine–cytosine (GC) base pair are studied here by using the DZP++ B3LYP density functional method. Optimized structures for the protonated GC base pair are compared with those of parent GC and the neutral hydrogenated GC radical (GCH). Proton and hydrogen‐atom additions significantly disturb the structure of the GC base pair. However, the structural perturbations arising from protonation are often less than those arising from hydrogenation of GC. Protonation of the GC base pair causes significant strengthening of the interstrand hydrogen bonds and a concomitant increase in the base dissociation energies. The adiabatic ionization potentials (AIPs), vertical ionization potentials (VIPs), and proton affinities (PAs) for the different protonation sites of the GC base pair are predicted. The N7 site of guanine is the preferred site for protonation of the GC base pair.     

Hydroxide complexes of lanthanides-III Gadolinium(III) in perchlorate medium

From the precipitation borderline in the pM′—pH diagram, determined experimentally under CO₂-free conditions, the stability constants of the mononuclear and polynuclear species of gadolinium hydroxide have been established. The values found are log*β₁ = −7.3, log*β₂ = −14.6, log*β₃ = −21.9, log*β_4,3 = −19.0 and log *K_s0 = 17.0. They refer to fresh precipitates, prepared at room temperature in sodium perchlorate medium with an ionic strength of 1.     

Hydroxide complexes of lanthanides--II: samarium(III) in perchlorate medium

From the precipitation borderline in the pM′—pH diagram, determined experimentally under CO₂-free conditions, the stability constants of the mononuclear and polynuclear species of samarium hydroxide have been established. The values found are log*β₁ = −7.5, log*β₂ = −15.0, log*β₃ = −22.7, logβ_{4, 3} = −19.5 and log*K_s0 = 17.5. They refer to fresh precipitates, prepared at room temperature in sodium perchlorate medium with an ionic strength of 1.     

A spectroscopic study on the reaction-controlled phase transfer catalyst in the epoxidation of cyclohexene

The epoxidation of cyclohexene with hydrogen peroxide in a biphase medium (H₂O/CHCl₃) was carried out with the reaction-controlled phase transfer catalyst composed of quaternary ammonium heteropolyoxotungstates [π-C₅H₅N(CH₂)₁₅CH₃]₃[PW₄O₁₆]. A conversion of about 90% and a selectivity of over 90% were obtained for epoxidation of cyclohexene on the catalyst. The fresh catalyst, the catalyst under reaction conditions and the used catalysts were characterized by FT-IR, Raman and ³¹P NMR spectroscopy. It appears that the insoluble catalyst could degrade into smaller species, [(PO₄){WO(O₂)₂}₄]³⁻, [(PO₄){WO(O₂)₂}₂{WO(O₂)₂(H₂O)}]³⁻, and [(PO₃(OH)){WO(O₂)₂}₂]²⁻ after the reaction with hydrogen peroxide and becomes soluble in the CHCl₃ solvent. The active oxygen in the [W₂O₂(O₂)₄] structure unit of these soluble species reacts with olefins to form the epoxides and consequently the corresponding W---Ob---W (corner-sharing) and W---Oc---W (edge-sharing) bonds are formed. The peroxo group [W₂O₂(O₂)₄] can be regenerated when the W---Ob---W and W---Oc---W bonds react with hydrogen peroxide again. These soluble species lose active oxygen and then polymerize into larger compounds with the W---Ob---W and W---Oc---W bonds and then precipitate from the reaction solution after the hydrogen peroxide is consumed up. Part of the used catalyst seems to form more stable compounds with Keggin structure under the reaction conditions.     

Origin of additional satellites in electron paramagnetic resonance spectra of rare earth ion pairs

Electron Paramagnetic Resonance (EPR) spectrum of pairs of two identical rare earth ions is considered in the case where the two ions feel slightly different crystal fields giving different g factors. When the differences Δg between the g factors give a Zeeman difference term ΔgβB₀ of the order of magnitude of the interaction between the two ions, the pair spectrum is composed of four lines instead of two: the usual doublet structure, and two additional satellites around the main central transitions. It is shown that for rare earth ions, the shape of the EPR pair spectrum is very sensitive to small g factor differences. This situation is illustrated by the case of neodymium pairs in the SrAl₁₂O₁₉ host.     

α-Zirconium phosphonates as new supports for metallocene catalysts

Homoleptic and mixed -zirconium phosphonates (ZrPs) -Zr(O₃PR)₂ (R = Me, Buⁿ, Buⁱ, Hex, Oct and Ph) and -Zr(O₃PR¹)_2−x(O₃PR²)_x were readily prepared in high yields from zirconyl choride and the corresponding phosphonic acids in suitable solvent mixtures under hydrothermal conditions at low fluoride concentrations. They form crystalline aggregates consisting of platelets from ca. 10–20 monolayers thickness, with well-defined surface structures. Impregnation with Cp₂ZrCl₂ by sublimation or slurry methods provided the first examples of ZrP-supported alkene polymerization catalysts. Crystal morphology and interlayer spacing are unaffected by the impregnation process. Solid-state NMR spectroscopy provides evidence for the integrity of the adsorbed metallocene structure. Covalent attachment of Cp^*ZrCl₃ to functionalized ZrPs of the type -Zr(O₃PR¹)_1.8(O₃PC_nH_2nOH)_0.2 is similarly possible. The new catalysts polymerize ethene with good to excellent activities under mild conditions, even at remarkably low methylalumoxane/zirconocene ratios of 10:1. The polymer is obtained as free-flowing particles, which reflect the morphology of the catalyst supports.     

Marked variations of dissociation energy and H-bond character of the guanine-cytosine base pair induced by one-electron oxidation and Li+ cation coupling

The variation of dissociation energy and H-bond character of the G-C cation and the Li-GC cation have been investigated by employing density functional theory (B3LYP) with the 6-31+G* basis set. The one-electron oxidation and the coupling of Li(+) to the guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li(+) with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations is different from that in the neutral GC base pair. The proton-transfer process between N(1) of the guanine and N(3) of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out of plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton-transfer process shows that the GC(+) before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC(+) system, the Li-GC(+) without proton transfer is the dominating species in the gas phase.