Unveiling the solution structure of a DNA duplex with continuous silver-modified Watson-Crick base pairs.

The challenge of transforming organized DNA structures into their metallized counterparts persists in the scientific field. In this context, utilizing DNA molecules modified with 7-deazapurine, provides a transformative solution. In this study, we present the solution structure of a DNA duplex that can be transformed into its metallized equivalent while retaining the natural base pairing arrangement through the creation of silver-modified Watson-Crick base pairs.

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 (dC ) 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.

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 Pd ions, can be prepared by a simple self-assembly reaction between the complex [Pd(Cheld)(CH CN)] (1Pd_CH CN) (Cheld=chelidamic acid) and single-stranded DNA homopolymers (ss-DNA) containing adenine (A) or 7-deazaadenine (X) bases. The single Pd -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.

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.

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.

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.

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).

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.

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.

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)·∼6H(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.

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.

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.

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.

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.

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.

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.

CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation.

Clar-Kekule structuring in armchair carbon nanotubes.

Geometrical patterns on armchair nanotubes and their dependence on length (up to 10 nm) have been studied using first-principles methods. The results indicate that finite nanotubes do not show a uniform bond structure. The previous structural classification of armchair nanotubes in Clar, Kekule, and incomplete-Clar types becomes unified with lengthening, not in a bond-uniform structure, as PBC models report, but into an alternated sequence of Clar and Kekule domains in all cases, with possible mechanical and electronic consequences.

Evidence of an unexpectedly long C-C bond (>2.7 A) in 1,3-metalladiyne complexes [Cp2MCCR]2 (M = Ti, Zr): QTAIM and ELF analyses.

Topological analyses of the electron density using the quantum theory of atoms in molecules (QTAIM) and electron localization function (ELF) have been carried out, at the B3LYP/DGVZVP and MP2/DGVZVP theoretical levels, on different 1,3-metalladiyne cyclic compounds [Cp2M(CCR)]2, (M = Ti, Zr; R = F, CH3, H, SiH3). The QTAIM results indicate the presence of an extraordinarily long C-C bond (in a 2.7-3.

On the nature of metal-carbon bonding: AIM and ELF analyses of MCH(n) (n = 1-3) compounds containing early transition metals.

Ab initio and DFT calculations have been performed on a series of organometallic compounds, according to the formula MCH(n), where M = K, Ca, Sc, Ti, V, Cr, or Mn and n = 1-3. Various theoretical methods are compared, the B3LYP level yielding the same agreement with the experimental geometries available as the correlated MP2 and CISD methods, with the 6-311++G(3df,2p) basis set for C and H and Wachter's (15s11p6d3f1g)/[10s7p4d3f1g] basis set for transition metals. The main geometric and electronic features of the molecules studied are described, analyzing the M-C bonding characteristics in terms of the atoms in molecules theory (AIM) and the electron localization function (ELF).