Selective Formation of Pd-DNA Hybrids Using Tailored Palladium-Mediated Base Pairs: Towards Heteroleptic Pd-DNA Systems.

The formation of highly organized metal-DNA structures has significant implications in bioinorganic chemistry, molecular biology and material science due to their unique properties and potential applications. In this study, we report on the conversion of single-stranded polydeoxycytidine (dC15 ) into a Pd-DNA supramolecular structure using the [Pd(Aqa)] complex (Aqa=8-amino-4-hydroxyquinoline-2-carboxylic acid) through a self-assembly process. The resulting Pd-DNA assembly closely resembles a natural double helix, with continuous [Pd(Aqa)(C)] (C=cytosine) units serving as palladium-mediated base pairs, forming interbase hydrogen bonds and intrastrand stacking interactions. Notably, the design of the [Pd(Aqa)] complex favours the interaction with cytosine, distinguishing it from our previously reported [Pd(Cheld)] complex (Cheld=chelidamic acid). This finding opens possibilities for creating heteroleptic Pd-DNA hybrids where different complexes specifically bind to nucleobases. We confirmed the Pd-DNA supramolecular structural assembly and selective binding of the complexes using NMR spectroscopy, circular dichroism, mass spectrometry, isothermal titration calorimetry, and DFT calculations.

Single-Stranded DNA as Supramolecular Template for One-Dimensional Palladium(II) Arrays.

Atomic-level control over the position and growth of a single and continuous metal chain is an ambitious goal that often requires complex and costly processes. Herein, we demonstrate that 1Pd-DNA molecules, comprising a continuous single chain of PdII ions, can be prepared by a simple self-assembly reaction between the complex [Pd(Cheld)(CH3 CN)] (1Pd_CH3 CN) (Cheld=chelidamic acid) and single-stranded DNA homopolymers (ss-DNA) containing adenine (A) or 7-deazaadenine (X) bases. The single PdII -base pairs [1Pd(N1-A)] and [1Pd(N1-X)] were synthesized and characterized in solution and solid-state (X-ray diffraction) revealing an arrangement similar to that of natural Watson-Crick base pairs. Subsequently, 1Pd-DNA hybrids were prepared, characterized, and their structures studied by small-angle X-ray scattering (SAXS) and ab-initio calculations. The results indicate that the 1Pd-DNA structures resemble that of double-stranded DNA, with one strand being replaced by a supramolecular stack of continuous PdII complexes.

Comparative Structural Study of Metal-Mediated Base Pairs Formed outside and inside DNA Molecules.

The formation of copper(II)-mediated base pairs involving pyridine-2,6-dicarboxylate derivatives and canonical nucleosides has proven to be a smart approach to introduce copper(II) ions at specific locations of DNA duplexes. However, the structural characteristics of these metalized base pairs have not yet been revealed, and their effect on DNA structures is difficult to assess. Herein, for the first time, we report on the different structural details of copper-mediated base pairs formed by themselves and in DNA duplexes. The individual base pairs [Cu(mcheld)(N3-Cyt)(H2O)]·3H2O (1Cu_Cyt), [Cu(mcheld)(N7-Ade)(H2O)2]·2H2O (1Cu_Ade), [Cu(mcheld)(N7-Gua)(H2O)] (1Cu_Gua), and [Cu(mcheld)(N1-7CAde)(H2O)]·H2O (1Cu_7CAde) were obtained from the reaction of the metal complex [Cu(mcheld)(H2O)2] (1Cu) (mcheld = 4-methoxypyridine-2,6-dicarboxylic acid) with model nucleosides (Cyt = N1-methylcytosine, Ade = N9-ethyladenine, Gua = N9-propylguanine, 7CAde = N9-propyl-7-deazaadenine). The crystal structure of the five complexes was determined by means of single-crystal X-ray diffraction. Furthermore, the formation of the 1Cu_Cyt and 1Cu_Gua base pairs in the middle of DNA duplexes, duplex DNA15 (917 atoms) and DNA10 (649 atoms), respectively, was studied using highly demanding ab initio computational calculations. These theoretical studies aimed to validate, from a structural point of view, whether base pairs of the kind 1Cu_nucleosides can be included in a DNA double helix and how this situation affects the double-helical structure. The results indicate that the 1Cu_Cyt and 1Cu_Gua base pairs can be formed in a DNA molecule without significant structural constraints. In addition, the double-helix DNA structure remains virtually unchanged when it contains these Cu(II)-mediated base pairs.

Green and Bio-Based Solvents.

Chemical reactions and many of the procedures of separation and purification employed in industry, research or chemistry teaching utilize solvents massively. In the last decades, with the birth of Green Chemistry, concerns about the employment of solvents and the effects on human health, as well as its environmental impacts and its dependence on non-renewable raw materials for manufacturing most of them, has drawn the attention of the scientific community. In this work, we review the concept of green solvent and the properties and characteristics to be considered green. Additionally, we discuss the different possible routes to prepare many solvents from biomass, as an alternative way to those methods currently applied in the petrochemical industry.

Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

DNA sequences comprising noncanonical 7-deazaguanine (7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-AgI -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of AgI ions, 7C G-C and 7C A-T Watson-Crick base pairs (7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-AgI -C and 7C A-AgI -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern.

Insight into the informational-structure behavior of the Diels-Alder reaction of cyclopentadiene and maleic anhydride.

The course of the Diels-Alder reactions of cyclopentadiene and maleic anhydride were studied. Two reaction paths were modelled: endo- and exo-selective paths. All structures within the transient region were characterized and analyzed by means of geometrical descriptors, physicochemical parameters and information-theoretical measures in order to observe the linkage between chemical behavior and the carriage of information. We have shown that the information-theoretical characterization of the chemical course of the reaction is in complete agreement with its phenomenological behavior in passing from reactants to products. In addition, we were able to detect the main differences between the two reaction mechanisms. This type of informational analysis serves to provide tools to help understand the chemical reactivity of the two simplest Diels-Alder reactions, which permits the establishment of a connection between the quantum changes that molecular systems exert along reaction coordinates and standard physicochemical phenomenology. In the present study, we have shown that every reaction stage has a family of subsequent structures that are characterized not solely by their phenomenological behavior but also by informational properties of their electronic density distribution (localizability, order, uniformity). Moreover, we were able to describe the main differences between endo-adduct and exo-adduct pathways. With the advent of new experimental techniques, it is in principle possible to observe the structural changes in the transient regions of chemical reactions. Indeed, through this work we have provided the theoretical concepts needed to unveil the concurrent processes associated with chemical reactions.

Structural consequences of the N7 and C8 translocation on the metal binding behavior of adenine.

7-Deaza-8-aza-adenine, namely 4-aminopyrazolo[3,4-d]pyrimidine (H4app), is a bioisoster of adenine (Hade) resulting from the translocation of N7 and C8 atoms on the purine moiety. With the aim of studying the influence of this translocation on the metal binding abilities of H4app, we have prepared and structurally characterized two ternary copper(II) complexes having H4app and one N-benzyl-iminodiacetate chelator (MEBIDA or FBIDA, with a methyl or fluoro group in para- of the benzyl aromatic ring): [Cu(2)(MEBIDA)(2)(µ(2)-N1,N8-H4app)(H(2)O)(2)]·4H(2)O (1) and [Cu(4)(FBIDA)(4)(µ(2)-N8,N9-H4app)(2)(H(2)O)]·3.5H(2)O (2). Furthermore, thermal, spectral, and magnetic properties have been also investigated. In 1, H(N9)4app is disordered over two equally pondered positions and the µ(2)-N1,N8 coordination mode is assisted by N6-H···O and N9-H···O intramolecular interactions, respectively. The acyclic nonlinear molecular topology of 2 is strongly influenced by two intramolecular H-bonding interactions (O-H···O-carboxylate) involving the apical aqua ligand of a terminal Cu(II) atom. Thus, both compounds have in common the Cu-N8 bond. In order to better understand our limited structural information, DFT calculations for the individual tautomers of H4app as well as mononuclear Cu(II) model systems have been carried out. According to previous results, we conclude that H(N9)4app is the most stable tautomer followed by H(N8)4app. When N9 and N8 are metalated, then the tautomer H(N1)4app can come into play as observed in compound 2. Likewise, the findings concerning compound 1 suggest that the formation of a Cu-N1 bond in H4app results was favored compared to neutral adenine, for which only one case has been reported with such coordination despite the large variety of related Cu(II)-Hade described in the literature.

From 7-azaindole to adenine: molecular recognition aspects on mixed-ligand Cu(II) complexes with deaza-adenine ligands.

For a better understanding of the versatile behaviour of adenine as a ligand, a series of 10 ternary copper(II) complexes with deaza-adenine ligands [7-azaindole (1,6,7-trideaza-adenine, H7azain), 4-azabenzimidazole (1,6-dideaza-adenine, H4abim), 5-azabenzimidazole (3,6-dideaza-adenine, H5abim), and 7-deaza-adenine (H7deaA)] have been synthesised and characterised by X-ray diffraction. Likewise, all the compounds studied have been analysed by spectral and thermal methods. The proton tautomers and donor capabilities of the above-mentioned deaza-adenine ligands have been calculated by DFT. We conclude that the increasing presence of N-donors in deaza-adenine ligands favours the proton tautomerism and their versatility as co-ligands. Notably, H7azain consistently uses the same tautomer, H4abim uses two different tautomers but is not protonated by the pentadentate H(2)EDTA(2-) ligand, and H(N1)5abim displays the µ(2)-N7,N9 mode, whereas H(N9)7deaA binds Cu(II) by N3 in cooperation with an intra-molecular N9-H···O interaction or using the unprecedented bidentate µ(2)-N1,N3 bridging mode.

Insights on the binding ability of a new adenine analog: 7-amine-1,2,4-triazolo[1,5-a]pyrimidine. Synthesis and magnetic study of the first copper(II) complexes.

Conventional reactions of the new multidentate ligand 7-amine-1,2,4-triazolo[1,5-a]pyrimidine (7atp, 1) with copper(II) salts lead to four novel multidimensional coordination complexes [Cu(7atp)(mal)(H(2)O)(2)]·H(2)O (2), [Cu(2)(µ-7atp)(4)(H(2)O)(2)](ClO(4))(4)·3H(2)O (3), {[Cu(7atp)(2)(µ-ox)]·3H(2)O}(n) (4) and {[Cu(7atp)(2)(µ-suc)]·2H(2)O}(n) (5), where ox(2-), mal(2-) and suc(2-) mean oxalate, malonate and succinate, respectively. In these compounds, the 7atp ligand coordinates monodentately through its atom N3, except for compound 3, which displays N3-N4 coordination mode, giving rise to all to structures with diverse topologies and dimensionality. Compound 2 is a mononuclear entity, 3 consists of dinuclear species, 4 is a zig-zag chain with oxalate as a bridging ligand and 5 is a succinate-bridged mono-dimensional system. All polynuclear metal complexes show antiferromagnetic interactions of with J values ranging from -0.12 to -49.5 cm(-1). The ligand donor capabilities have been estimated by topological analyses of the electron density (QTAIM) and electron localization function (ELF), obtained by DFT calculations. The compounds are the first structurally characterized copper(II) complexes containing the 7atp ligand.

Dinuclear silver(I) complexes for the design of metal-ligand networks based on triazolopyrimidines.

Silver(I) coordination complexes with the versatile and biomimetic ligands 1,2,4-triazolo[1,5-a]pyrimidine (tp), 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine (dmtp) and 7-amine-1,2,4-triazolo[1,5-a]pyrimidine (7atp) all feature dinuclear [Ag(2)(µ-tp)(2)](2+) building units (where tp is a triazolopyrimidine derivative), which are the preferred motif, independently of the counter-anion used. According to AIM (atoms in molecules) and ELF (electron localization function) analyses, this fact is due to the great stability of these dinuclear species. The complexes structures range from the dinuclear entities [Ag(2)(µ-tp)(2)(CH(3)CN)(4)](BF(4))(2) (1), [Ag(2)(µ-tp)(2)(CH(3)CN)(4)](ClO(4))(2) (2), [Ag(2)(µ-7atp)(2)](ClO(4))(2) (3) and [Ag(2)(µ-dmtp)(2)(CH(3)CN)](PF(6))(ClO(4)) (4) over the 1D polymer chain [Ag(2)(µ-CF(3)SO(3))(2)(µ-dmtp)(2)](n) (5) to the 3D net {[Ag(2)(µ(3)-tp)(2)](PF(6))(2)·âˆ¼6H(2)O}(n) (6) with NbO topology.

N, P, and As ylides and aza- and arsa-Wittig reactions from topological analyses of electron density.

The nature of bonding between N, P, and As constituent atoms in ylide systems with the R(3)XYR' formula (X = N, P, As; Y = N, P, As; R = F, H; R' = H, CH(3)) has been characterized by ab initio (MP2/6-311++G**) and density functional theory (B3LYP/6-311++G**) calculations. Its electronic structure has been analyzed through electron density with the quantum theory of atoms in molecules and the electron localization function (ELF). The characteristics of the central bond are inspected with the calculated rotational barriers. The results show that N has a behavior different from that of the remaining pnicogen atoms (P, As), where the bond is much stronger. Fluorine substituents strengthen the X-Y bond, reduce the bond distance, and increase the electron density in the central bond so that the substituent pulls charge from the bond in the pnicogen X atom. For the N-pnicogen ylides, the results showed different bonding characters between F and X atoms; depending on the position of the F atom, the difference of the bond character is sensed by the basin synaptic order, as it is deduced from the analysis of the ELF basins. The energy profiles of the rotational barriers have been calculated at the MP2/6-311++G** level, indicating that the electronegativity of the substituents is a relevant factor that has consequences in the characteristics of the X-Y bond.

Edge effects, electronic arrangement, and aromaticity patterns on finite-length carbon nanotubes.

Previous investigations have revealed that even long carbon nanotubes (CNTs) retain bond patterns that are characterized by the localization of Clar rings. Even for CNTs with 10 nm length, an alternated, oscillating structure of Clar and Kekulé patterning was also found, indicating that these arrangements may possibly persist for even longer nanotubes, given that they are finite. In the present work, we perform a detailed and comprehensive theoretical study of this phenomenon, in order to find the causes that give rise to these patterns. A complete set of CNTs with different chiralities, diameters (up to 2 nm), lengths (up to 10 nm) and endings (capped, uncapped, and tailored endings) was considered for such purposes. The results indicate that the Clar patterning appears not only on armchair CNTs, but also on those with chiral angle values close to 30°, and this results in a stabilization of the structure, when compared with the uniform, zigzag CNTs. This stabilizing effect points to the causes that underlie the three Nakamura CNT types, resulting as the superposition of structures with a maximal number of Clar rings. Although there is a strict dependence on the border shape, the main cause of the bond patterning in long tubes is to be found in the intrinsic wrapping of each CNT, because the type and number of oscillations present in the longest structures do not depend on the particular length. Nevertheless, the three Nakamura types of armchair tubes appear to subsist beyond the appearance of oscillations, because each of these sets evolves in a different manner, and energy properties that link them together. Apart from the geometry, Clar patterning was investigated through NICS (Nucleus Independent Chemical Shifts) measures, which reveal a connection between the Clar rings and a local concentration of aromaticity.

CoNTub v2.0--algorithms for constructing C3-symmetric models of three-nanotube junctions.

Here, a method is described for easily building three-carbon nanotube junctions. It allows the geometry to be found and bond connectivity of C(3) symmetric nanotube junctions to be established. Such junctions may present a variable degree of pyramidalization and are composed of three identical carbon nanotubes with arbitrary chirality. From the indices of the target nanotube, applying the formulas of strip algebra, the possible positions of the six defects (heptagonal rings) needed can be found. Given the multiple possibilities that arise for a specific pair of indices, the relation between the macroscopic geometry (interbranch angles, junction size, and pyramidalization) and each specific solution is found. To automate the construction of these structures, we implemented this algorithm with CoNTub software, version 2.0, which is available at ( http://www.ugr.es/local/gmdm/contub2 ). In addition, a classification of three-nanotube junctions, 3TJ, in seven types based on the location of defects has been proposed, i.e. 3TJ(0:0:6), 3TJ(0:1:5), 3TJ(0:2:4), 3TJ(0:3:3), 3TJ(1:1:4), 3TJ(1:2:3), and 3TJ(2:2:2) types.

NMR assignment in regioisomeric hydroquinones.

A set of regioisomeric pairs of tricyclic hydroquinones, analogues of antitumor 9,10-dihydroxy-4,4-dimethyl-5,8-dihydroanthracen-1(4H)-one (1) and other derivatives, were synthesized and their regiochemistry and NMR spectra assigned by using (1)H-detected one-bond (C-H) HMQC and long-range C-H HMBC, in good agreement with theoretical O3LYP/Alhrichs-pVTZ calculations. The 5-hydroxymethyl derivatives (11, 15, 19) showed a (3)J(H, H) coupling constant of methylene protons evidencing the presence of a seven-membered intramolecular hydrogen bonded ring, not observed for the 8-hydroxymethyl isomers.

Protecting-group-free synthesis of chokols.

As a result of a combined theoretical and experimental study, we describe a two-step protocol for the preparation of an optically pure, multifunctional, cyclopentanic core shared by a number of natural products. This process is based on a hitherto unreported Ti(III)-mediated diastereoselective cyclization in which the hydroxy-directed template effect played by the Ti(III) species was found to be crucial for the stereoselective outcome of the reaction. The viability of this concept was confirmed with the first protecting-group free synthesis of three enantiopure chokols, namely, chokols K, E, and B.

Porous nanotube network: a novel 3-D nanostructured material with enhanced hydrogen storage capacity.

A multiscale theoretical approach (ab initio and Grand Canonical Monte Carlo calculations) was used to investigate hydrogen storage in a novel three-dimensional carbon nanostructure. Our results show that a large-pore PNN can overpass the gravimetric capacity of 20% at 77 K while a Li-doped PNN can reach the value of 8% at room temperature.

Lignin as renewable raw material.

Lignin is by far the most abundant substance based on aromatic moieties in nature, and the largest contributor to soil organic matter. Millions of tonnes of several lignin preparations are produced by the paper industry every year, and a minimal amount of lignin is isolated by direct extraction of lignin from plants. Lignin is used either directly or chemically modified, as a binder, dispersant agent for pesticides, emulsifier, heavy metal sequestrant, or component for composites and copolymers. For value-added applications of lignin to be improved, medium- and long-term conversion technologies must be developed, especially for the preparation of low-molecular-weight compounds as an alternative to the petrochemical industry.

Reversible attachment of platinum alloy nanoparticles to nonfunctionalized carbon nanotubes.

The formation of monodisperse, tunable sized, alloyed nanoparticles of Ni, Co, or Fe with Pt and pure Pt nanoparticles attached to carbon nanotubes has been investigated. Following homogeneous nucleation, nanoparticles attach directly to nonfunctionalized single-walled and multi-walled carbon nanotubes during nanoparticle synthesis as a function of ligand nature and the nanoparticle work function. These ligands not only provide a way to tune the chemical composition, size, and shape of the nanoparticles but also control a strong reversible interaction with carbon nanotubes and permit controlling the nanoparticle coverage. Raman spectroscopy reveals that the sp(2) hybridization of the carbon lattice is not modified by the attachment. In order to better understand the interaction between the directly attached nanoparticles and the nonfunctionalized carbon nanotubes, we employed first-principles calculations on model systems of small Pt clusters and both zigzag and armchair single-walled carbon nanotubes. The detailed comprehension of such systems is of major importance since they find applications in catalysis and energy storage.

Weakening C-O bonds: Ti(III), a new reagent for alcohol deoxygenation and carbonyl coupling olefination.

Investigations detailed herein, including density functional theory (DFT) calculations, demonstrate that the formation of either alkoxy- or hydroxy-Ti(III) complexes considerably decreases the energy of activation for C-O bond homolysis. As a consequence of this observation, we described two new synthetic applications of Nugent's reagent in organic chemistry. The first of these applications is an one-step methodology for deoxygenation-reduction of alcohols, including benzylic and allylic alcohols and 1,2-dihydroxy compounds. Additionally, we have also proved that Ti(III) is capable of mediating carbonyl coupling-olefination. In this sense, and despite the fact that for over 35 years it has been widely accepted that either Ti(II) or Ti(0) was the active species in the reductive process of the McMurry reaction, the mechanistic evidence presented proves the involvement of Ti(III) pinacolates in the deoxygenation step of the herein described Nugent's reagent-mediated McMurry olefination. This observation sheds some light on probably one of the mechanistically more complex transformations in organic chemistry. Finally, we have also proved that both of these processes can be performed catalytically in Cp(2)TiCl(2) by using trimethylsilyl chloride (TMSCl) as the final oxygen trap.

Carbon...carbon weak interactions.

A theoretical study of the complexes formed by systems with electron-deficient and electron-excessive carbon atoms was carried out using DFT and ab initio methods up to the CCSD(T)/aug-cc-pVTZ computational level. Stable complexes with interaction energies between -6.0 and -22.8 kJ mol(-1) were obtained that correspond to weak C...C interactions. The atoms in molecules analysis of the complexes confirmed the presence of these interactions. Natural energy decomposition analysis and electron localization function analysis were performed to gain further insight into the nature of the interaction. Polarization is the most important stabilizing term in these complexes.