Marked influences on the adenine-cytosine base pairs by electron attachment and ionization

The reverse wobble and the reverse Hoogsteen adenine-cytosine mispairs regarding their radical cations and anions are studied with the hybrid three-parameter B3LYP density functional method and 6-31+G(d), 6-311+G(2df,2p) basis sets. Hydrogen bonding mispairs are remarkably influenced by electron attachment and ionization. Only one stronger hydrogen bond N6-H (in adenine)...N3 (in cytosine) exists in the radical pair, while the strengths of two N-H...N hydrogen bonds in the neutral pair are comparable. Geometrical coplanarity is found for the neutral and cationic pairs, in contrast to the anionic pairs in which the cytosine moiety exhibits significant deformation due to electron attachment. Dissociation energies for the neutral and radical pairs are slightly higher than those of the adenine-thymine pairs but much smaller than those of the guanine-cytosine pairs. Valence-bound anions of these two adenine-cytosine pairs are thermodynamically stable by 0.1-0.2 eV with respect to the neutral pairs. On the basis of the comparison between the experimental data of the solvated clusters and the calculated values, these two pairs can be quantitatively equivalent to the clusters in which each base is solvated by five water molecules.     

Proton-coupled hole hopping in nucleosomal and free DNA initiated by site-specific hole injection

Nucleosomes were reconstituted from recombinant histones and a 147-mer DNA sequence containing the damage reporter sequence 5'-…d([2AP]T[GGG](1)TT[GGG](2)TTT[GGG](3)TAT)… with 2-aminopurine (2AP) at position 27 from the dyad axis. Footprinting studies with ˙OH radicals reflect the usual effects of "in" and "out" rotational settings, while, interestingly, the guanine oxidizing one-electron oxidant CO(3)(˙-) radical does not. Site-specific hole injection was achieved by 308 nm excimer laser pulses to produce 2AP(˙+) cations, and superoxide via the trapping of hydrated electrons. Rapid deprotonation (~100 ns) and proton coupled electron transfer generates neutral guanine radicals, G(-H)˙ and hole hopping between the three groups of [GGG] on micro- to millisecond time scales. Hole transfer competes with hole trapping that involves the combination of O(2)(˙-) with G(-H)˙ radicals to yield predominantly 2,5-diamino-4H-imidazolone (Iz) and minor 8-oxo-7,8-dihydroguanine (8-oxoG) end-products in free DNA (Misiaszek et al., J. Biol. Chem. 2004, 279, 32106). Hole migration is less efficient in nucleosomal than in the identical protein-free DNA by a factor of 1.2-1.5. The Fpg/piperidine strand cleavage ratio is ~1.0 in free DNA at all three GGG sequences and at the "in" rotational settings [GGG](1,3) facing the histone core, and ~2.3 at the "out" setting at [GGG](2) facing away from the histone core. These results are interpreted in terms of competitive reaction pathways of O(2)(˙-) with G(-H)˙ radicals at the C5 (yielding Iz) and C8 (yielding 8-oxoG) positions. These differences in product distributions are attributed to variations in the local nucleosomal B-DNA base pair structural parameters that are a function of surrounding sequence context and rotational setting.     

Structures and energetics of the deprotonated adenine-uracil base pair, including proton-transferred systems

The B3LYP/DZP++ level of theory has been employed to investigate the structures and energetics of the deprotonated adenine-uracil base pairs, (AU-H)-. Formation of the lowest-energy structure, [A(N9)-U]- (which corresponds to deprotonation at the N9 atom of adenine), through electron attachment to the corresponding neutral is accompanied by proton transfer from the uracil N3 atom to the adenine N1 atom. The driving force for this proton transfer is a significant stabilization from the base pairing in the proton transferred form. Such proton transfer upon electron attachment is also observed for the [A(N6b)-U]- and [A(C2)-U]- anions. Electron attachment to the A-U(N3) radical causes strong lone pair repulsion between the adenine N1 and the uracil N3 atoms, driving the two bases apart. Similarly, lone pair repulsion in the anion A(N6a)-U causes the loss of coplanarity of the two base units. The computed adiabatic electron attachment energies for nine AU-H radicals range from 1.86 to 3.75 eV, implying that the corresponding (AU-H)- anions are strongly bound. Because of the large AEAs of the (AU-H) radicals, the C-H and N-H bond dissociation in the AU- base pair anions requires less energy than the neutral AU base pair. The computed C-H and N-H bond dissociation energies for the AU- anion (i.e., the AU base pair plus one electron) are in the range 1.0-3.2 eV, while those for neutral AU are 4.08 eV or higher.     

Density functional study toward understanding dehydrogenation of the adenine-thymine base pair and its anion

The dehydrogenated radicals and anions of Watson-Crick adenine-thymine (A-T) base pair have been investigated by the B3LYP/DZP++ approach. Calculations show that the dehydrogenated radicals and anions have relatively high stabilities compared with the single base adenine and thymine. The electron attachment to the A-T base pair and its derivatives significantly modifies the hydrogen bond interactions and results in remarkable structural changes. As for the dehydrogenated A-T radicals, they have relatively high electron affinities and different dehydrogenation properties with respect to their constituent elements. The relatively low-cost hydrogen eliminations correspond to the (N9)-H (adenine) and (N1)-H (thymine) bonds cleavage. Both dehydrogenation processes have Gibbs free energies of reaction DeltaG degrees of 13.4 and 17.2 kcal mol-1, respectively. The solvent water exhibits significant effect on electron attachment and dehydrogenation properties of the A-T base pair and its derivatives. In the dehydrogenating process, the anionic A-T fragment gradually changes its electronic configuration from pi* to sigma* state, like the single bases adenine and thymine.     

Electron attachment to the hydrogenated Watson-Crick guanine cytosine base pair (GC+H): conventional and proton-transferred structures

The anionic species resulting from hydride addition to the Watson-Crick guanine-cytosine (GC) DNA base pair are investigated theoretically. Proton-transferred structures of GC hydride, in which proton H1 of guanine or proton H4 of cytosine migrates to the complementary base-pair side, have been studied also. All optimized geometrical structures are confirmed to be minima via vibrational frequency analyses. The lowest energy structure places the additional hydride on the C6 position of cytosine coupled with proton transfer, resulting in the closed-shell anion designated 1T (G(-)C(C6)). Energetically, the major groove side of the GC pair has a greater propensity toward hydride/hydrogen addition than does the minor grove side. The pairing (dissociation) energy and electron-attracting ability of each anionic structure are predicted and compared with those of the neutral GC and the hydrogenated GC base pairs. Anion 8T (G(O6)C(-)) is a water-extracting complex and has the largest dissociation energy. Anion 2 (GC(C4)(-)) and the corresponding open-shell radical GC(C4) have the largest vertical electron detachment energy and adiabatic electron affinity, respectively. From the difference between the dissociation energy and electron-removal ability of the normal GC anion and the most favorable structure of GC hydride, it is clear that one may dissociate the GC anion and maintain the integrity of the GC hydride.     

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.     

Stepwise vs. concerted pathways in scandium ion-coupled electron transfer from superoxide ion to p-benzoquinone derivatives

Superoxide ion (O2˙-) forms a stable 1 : 1 complex with scandium hexamethylphosphoric triamide complex [Sc(HMPA)(3)(3+)], which can be detected in solution by ESR spectroscopy. Electron transfer from O2˙- -Sc(HMPA)(3)(3+) complex to a series of p-benzoquinone derivatives occurs, accompanied by binding of Sc(HMPA)(3)(3+) to the corresponding semiquinone radical anion complex to produce the semiquinone radical anion-Sc(HMPA)(3)(3+) complexes. The 1 : 1 and 1 : 2 complexes between semiquinone radical anions and Sc(HMPA)(3)(3+) depending on the type of semiquinone radical anions were detected by ESR measurements. This is defined as Sc(HMPA)(3)(3+)-coupled electron transfer. There are two reaction pathways in the Sc(HMPA)(3)(3+)-coupled electron transfer. One is a stepwise pathway in which the binding of Sc(HMPA)(3)(3+) to semiquinone radical anions occurs after the electron transfer, when the rate of electron transfer remains constant with the change in concentration of Sc(HMPA)(3)(3+). The other is a concerted pathway in which electron transfer and the binding of Sc(HMPA)(3)(3+) occurs in a concerted manner, when the rates of electron transfer exhibit first-order and second-order dependence on the concentration of Sc(HMPA)(3)(3+) depending the number of Sc(HMPA)(3)(3+) (one and two) bound to semiquinone radical anions. The contribution of two pathways changes depending on the substituents on p-benzoquinone derivatives. The present study provides the first example to clarify the kinetics and mechanism of metal ion-coupled electron-transfer reactions of the superoxide ion.     

Structure and dynamics of photogenerated triplet radical ion pairs in DNA hairpin conjugates with anthraquinone end caps

A series of DNA hairpins (AqGn) possessing a tethered anthraquinone (Aq) end-capping group were synthesized in which the distance between the Aq and a guanine-cytosine (G-C) base pair was systematically varied by changing the number (n - 1) of adenine-thymine (A-T) base pairs between them. The photophysics and photochemistry of these hairpins were investigated using nanosecond transient absorption and time-resolved electron paramagnetic resonance (TREPR) spectroscopy. Upon photoexcitation, (1*)Aq undergoes rapid intersystem crossing to yield (3*)Aq, which is capable of oxidizing purine nucleobases resulting in the formation of (3)(Aq(-?)Gn(+?)). All (3)(Aq(-?)Gn(+?)) radical ion pairs exhibit asymmetric TREPR spectra with an electron spin polarization phase pattern of absorption and enhanced emission (A/E) due to their different triplet spin sublevel populations, which are derived from the corresponding non-Boltzmann spin sublevel populations of the (3*)Aq precursor. The TREPR spectra of the (3)(Aq(-?)Gn(+?)) radical ion pairs depend strongly on their spin-spin dipolar interaction and weakly on their spin-spin exchange coupling. The anisotropy of (3)(Aq(-?)Gn(+?)) makes it possible to determine that the π systems of Aq(-?) and G(+?) within the radical ion pair are parallel to one another. Charge recombination of the long-lived (3)(Aq(-?)Gn(+?)) radical ion pair displays an unusual bimodal distance dependence that results from a change in the rate-determining step for charge recombination from radical pair intersystem crossing for n < 4 to coherent superexchange for n > 4.     

Reactions of simple and peptidic alpha-carboxylate radical anions with dioxygen in the gas phase

α-Carboxylate radical anions are potential reactive intermediates in the free radical oxidation of biological molecules (e.g., fatty acids, peptides and proteins). We have synthesised well-defined α-carboxylate radical anions in the gas phase by UV laser photolysis of halogenated precursors in an ion-trap mass spectrometer. Reactions of isolated acetate (˙CH(2)CO(2)(-)) and 1-carboxylatobutyl (CH(3)CH(2)CH(2)˙CHCO(2)(-)) radical anions with dioxygen yield carbonate (CO(3)˙(-)) radical anions and this chemistry is shown to be a hallmark of oxidation in simple and alkyl-substituted cross-conjugated species. Previous solution phase studies have shown that C(α)-radicals in peptides, formed from free radical damage, combine with dioxygen to form peroxyl radicals that subsequently decompose into imine and keto acid products. Here, we demonstrate that a novel alternative pathway exists for two α-carboxylate C(α)-radical anions: the acetylglycinate radical anion (CH(3)C(O)NH˙CHCO(2)(-)) and the model peptide radical anion, YGGFG˙(-). Reaction of these radical anions with dioxygen results in concerted loss of carbon dioxide and hydroxyl radical. The reaction of the acetylglycinate radical anion with dioxygen reveals a two-stage process involving a slow, followed by a fast kinetic regime. Computational modelling suggests the reversible formation of the C(α) peroxyl radical facilitates proton transfer from the amide to the carboxylate group, a process reminiscent of, but distinctive from, classical proton-transfer catalysis. Interestingly, inclusion of this isomerization step in the RRKM/ME modelling of a G3SX level potential energy surface enables recapitulation of the experimentally observed two-stage kinetics.     

Structure and properties of ionic fullerene complex Co(+)(dppe)2·(C60˙-)·(C6H4Cl2)2: distortion of the ordered fullerene cage of C60˙- radical anions

New ionic complex {Co(+)(dppe)(2)}·(C(60)˙(-))·(C(6)H(4)Cl(2))(2) (1) was obtained by the reduction of a Co(dppe)Br(2) and C(60) mixture by TDAE in o-dichlorobenzene followed by precipitation of crystals by hexane. Optical and EPR spectra of 1 indicated the formation of C(60)˙(-) radical anions and diamagnetic Co(+)(dppe)(2) cations. The structure of 1 solved at 100(2) K involves chains of C(60)˙(-) arranged along the lattice a-axis with a center-to-center distance of 10.271 ?. The chains are separated by bulky Co(+)(dppe)(2) cations and solvent molecules. All components of 1 are well ordered allowing the distortion of the C(60)˙(-) radical anion to be analyzed. An elongation of the C(60)˙(-) sphere by 0.0254(2) was found. It is essentially smaller than those in the salts (Cp*(2)Ni(+))·(C(60)˙(-))·CS(2) and (PPN(+))(2)·(C(60)(2-)) with greater distortion of the fullerene cage. The calculation of the electronic structure of fullerene by the extended Hückel method showed slight splitting of the C(60) LUMO, due to the distortion, by three levels. Two levels are located 180 and 710 cm(-1) higher than the ground level. The averaged 6-6 and 5-6 bonds in C(60)˙(-) with lengths of 1.397(2) and 1.449(2) ? are close to those determined for the C(60)(2-) dianions in (PPN(+))(2)·(C(60)(2-)), but are slightly longer and shorter, respectively, than the length of these bonds in neutral C(60).     

Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine

The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.     

B型DNA中鸟嘌呤-胞嘧啶碱基对内双质子转移反应

采用ONIOM(M06-2X/6-31G^*:PM3)方法研究了单个鸟嘌呤-胞嘧啶(GC)碱基对和含GC碱基对的四种排序的DNA三聚体(dATGCAT, dGCGCGC, dTAGCTA, dCGGCCG)的双质子转移反应. 通过分析其双质子转移方式、质子转移过程中各结构的能量和氢键变化, 总结出环境因素对GC碱基对双质子转移机理的影响. 气相中, dCGGCCG三聚体中发生分步双质子转移, 其它四种模型中均发生协同双质子转移. 分析发现质子转移方式受上下相邻碱基对的静电相互作用和质子接受位的质子亲和势影响, dATGCAT和dGCGCGC排序有助于质子H4a转移, 而dTAGCTA和dCGGCCG排序有助于质子H1转移, 胞嘧啶的N3位较高的质子亲和势有助于质子H1转移. 水溶剂中, 上下相邻碱基对的静电相互作用被减弱, 水溶剂稳定了分步转移过程中的单质子转移产物, 因此分步转移机理占据优势, 五种模型中均出现分步双质子转移, 在此过程中能量变化趋势相似. 溶剂效应有利于单质子转移, 却增加了双质子转移反应的反应能.     

Photosensitized xanthone-based oxidation of guanine and its repair: a laser flash photolysis study

The photosensitized oxidation of guanine (G) by the triplet state of xanthone (XT) and the repair for photo-damaged G(-H)(·) by ferulic acid (FCA) were investigated using the laser flash photolysis technique. The rate constants of the reaction of triplet state of XT with G and with FCA were determined as 4.5×10(9) and 8.0×10(9) L mol(-1) s(-1), respectively. Laser exposure was performed on the N(2)-saturated acetonitrile/water (v/v, 1:1) solution containing G, XT and FCA. The transient absorption spectra indicated that the triplet state of XT first reacted with G predominantly to form the oxidized radical G(-H)(·). The radical G(-H)(·) was rapidly repaired by FCA, and the rate constant for the repair reaction was determined as 1.1×10(9) L mol(-1) s(-1). These results demonstrated that non-enzymatic repair is a feasible method for repairing photosensitized DNA bases oxidation.     

Electrostatic and electrophilic catalysis in the reductive cleavage of alkyl aryl ethers. The influence of ion pairing on the regioselectivity

Electrophilic and electrostatic catalysis have been identified as distinct contributions that affect the reactivity of radical anions in the reductive cleavage of alkyl aryl ethers. Two modes of mesolytic scission of these radical anions are possible: homolytic (dealkylation, a thermodynamically favored but kinetically forbidden process) and heterolytic (dealkoxylation). From our studies (alkali metal reductions, electrochemical studies, use of substrates with a preformed positive charge in certain positions of their structure) it can be concluded that the heterolytic scission is very much dependent on the electrophilic assistance by the counterion and it is only observed in contact ionic pairs with unsaturated cations (electrophilic catalysis). On the other hand, the homolytic scission is observed in solvent-separated ionic pairs, and it is especially efficient when the pair has a controlled topology with a tetralkylammonium cation (saturated cation) near the oxygen atom. The effect of the cation has, in this case, electrostatic origin (electrostatic catalysis), probably lowering the barrier of the intramolecular pi-sigma electron transfer process and thus reducing the kinetic control of the reaction in such a way that the thermodynamically more favorable process is produced.     

Electron Attachment to Hydrated Oligonucleotide Dimers: Guanylyl‐3′,5′‐Cytidine and Cytidylyl‐3′,5′‐Guanosine

The dinucleoside phosphate deoxycytidylyl‐3′,5′‐deoxyguanosine (dCpdG) and deoxyguanylyl‐3′,5′‐deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5′ end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3′ end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine‐containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The π‐stacking interaction between nucleobases G and C seems unlikely to improve the electron‐capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron‐capturing ability of cytosine should be attributed to the intensified proton accepting–donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O? C σ bond and N‐glycosidic bond breakage, might be expected for the radical anions of the guanosine–cytosine mixed oligonucleotides.     

Formation of μ(2)-hydroxo-bonded (MgPc)2OH- assemblies and (C60(-))2 dimers in ionic fullerene {(MgPc)2OH-}2·(C60(-))2·(cation+)4 complexes

Ionic complexes containing μ(2)-hydroxo-bonded (MgPc)(2)OH(-) phthalocyanine assemblies and C(60)(-) anions: {(MgPc)(2)OH(-)}(2)·(C(60)(-))(2)·(PMDAE(+))(4)·(C(6)H(5)CN)(4) (1); {(MgPc)(2)OH(-)}(2)·(C(60)(-))(2)·(TMP(+))(4)·(C(6)H(5)CN)(3)·(C(6)H(4)Cl(2))(2.5) (2) (where PMDAE(+) is the cation of N,N,N',N',N'-pentamethyldiaminoethane and TMP(+) is the N,N'N'-trimethylpiperazinium cation) have been obtained as single crystals. The ionic ground state of the complexes is justified by the EPR spectra and the spectra in the IR and NIR ranges. The C(60)˙(-) radical anions are dimerized both in 1 and 2 in the 240-220 K range. Dimerization is accompanied by the reversible transition of the complexes from paramagnetic to diamagnetic state. MgPc forms unusual (MgPc)(2)OH(-) assemblies, in which the hydroxo-anion coordinates to two MgPc molecules by a μ(2)-fashion. The length of the Mg-O bonds is 1.936-1.955(2) ?, the Mg-O-Mg angle is 133.37-135.27(4)° and the displacement of the Mg atoms out of the mean 24-atom phthalocyanine plane is 0.77-0.86 ?. The packing of spherical fullerene and planar phthalocyanine molecules is attained in a crystal by the insertion of fullerenes between phenylene groups of phthalocyanines. It has been shown that metal phthalocyanines in ionic complexes with C(60) form M(II)Pc·(L(-)) assemblies, whereas metalloporphyrins form M(II)porphyrin·(C(+)) assemblies.     

Effects of microsolvation on the adenine-uracil base pair and its radical anion: adenine-uracil mono- and dihydrates

Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.     

Unexpected metal-induced isomerisms and phosphoryl migrations in Pt(II) and Pd(II) complexes of the functional phosphine 2-(bis(diphenylphosphino)methyl)-oxazoline

The reaction of the functional diphosphine 1 [1 = 2-(bis(diphenylphosphino)methyl-oxazoline] with [PtCl(2)(NCPh)(2)] or [PdCl(2)(NCPh)(2)], in the presence of excess NEt(3), affords [Pt{(Ph(2)P)(2)C···C(···NCH(2)CH(2)O)}(2)] ([Pt(1(-H)-P,P)(2)], 3a) and [Pd{(Ph(2)P)(2)C···C(···NCH(2)CH(2)O)}(2)] ([Pd(1(-H)-P,P)(2)], 3b), respectively, in which 1(-H) is (oxazoline-2-yl)bis(diphenylphosphino)methanide. The reaction of 3b with 2 equiv of [AuCl(tht)] (tht = tetrahydrothiophene) afforded [Pd(1(-H)-P,N)(2)(AuCl)(2)] (4), as a result of the opening of the four-membered metal chelate since ligand 1(-H), which was P,P-chelating in 3b, behaves as a P,N-chelate toward the Pd(II) center in 4 and coordinates to Au(I) through the other P donor. In the absence of a base, the reaction of ligand 1 with [PtCl(2)(NCPh)(2)] in MeCN or CH(2)Cl(2) afforded the isomers [Pt{(Ph(2)P)(2)C═C(OCH(2)CH(2)NH)}(2)]Cl(2) ([Pt(1'-P,P)(2)]Cl(2) (5), 1' = 2-(bis(diphenylphosphino)methylene)-oxazolidine) and [Pt{(Ph(2)P)(2)C═C(OCH(2)CH(2)NH)}{Ph(2)PCH═C(OCH(2)CH(2)N(PPh(2))}]Cl(2) ([Pt(1'-P,P)(2'-P,P)]Cl(2) (6), 2' = (E)-3-(diphenylphosphino)-2-((diphenylphosphino)methylene)oxazolidine]. The P,P-chelating ligands in 5 result from a tautomeric shift of the C-H proton of 1 to the nitrogen atom, whereas the formation of one of the P,P-chelates in 6 involves a carbon to nitrogen phosphoryl migration. The reaction of 5 and 6 with a base occurred by deprotonation at the nitrogen to afford 3a and [Pt{(Ph(2)P)(2)C···C(···NCH(2)CH(2)O)}{Ph(2)PCH═COCH(2)CH(2)N(PPh(2))}]Cl ([Pt(1(-H)-P,P)(2'-P,P)]Cl (7)], respectively. In CH(2)Cl(2), an isomer of 3a, [Pt{Ph(2)P)(2)C···C(···NCH(2)CH(2)O)}{Ph(2)PC(PPh(2))═COCH(2)CH(2)N}] ([Pt(1(-H)-P,P)(1(-H)-P,N)] (8)), was obtained as a side product which contains ligand 1(-H) in two different coordination modes. Complexes 3b·4CH(2)Cl(2), 4·CHCl(3), 6·2.5CH(2)Cl(2), and 8·CH(2)Cl(2) have been structurally characterized by X-ray diffraction.     

Comparative studies between hydrated hydrogen bonded and stacked DNA base pair

Influence of hydration on the Watson–Crick guanine–cytosine hydrogen bonded (h-bonded) base pair (GC) and stacked pair (G/C) was investigated in their first hydration shell. An electrostatic based approach has been used to identify the potential binding sites for water molecules around GC and G/C pairs. Several geometries of the complexes, GC…(H₂O)_n and G/C…(H₂O)_n (n=1–6) were investigated using HF/6-31G** and HF/6-31G++** methods. Further minimization calculations were performed at both B3P86/6-31G** and MP2/6-31G** levels to assess the role of electron correlation contribution in the hydration process. It can be concluded from the present findings that the stacked base-pair hydrate better than the corresponding h-bonded base pair, and DNA base pairs can accommodate up to 4–5 water molecules whereas stacked pair do accommodate 5–6 water molecules.     

Revisiting the effects of sequence and structure on the hydrogen bonding and π-stacking interactions in nucleic acids

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the π-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the analyses. Focusing solely on Watson-Crick base pairs, from the values of the electron density between interacting nuclei (at the bond critical points), we provide quantitative data on individual weak interactions. For hydrogen bonding, in addition to quantifying the scissoring effect in GC base pairs, the origin of the controversy around the relative stability of AT and AU base pairs is identified and resolved. Thus, it is illustrated how the conclusion as to their relative stability rests on the specific choice of oligonucleotides compared. For π-stacking, sequence effects for tandem AT base pairs are captured, quantified, and explained, and the greater sensitivity of GC, over AT, sequences to the rise parameter is established. The results presented here show that, from experimental geometries and their electron densities, previously determined effects of the sequence and structure of a duplex on the stabilizing interactions can be captured, quantified, and traced back to the geometry of the base pairs.