Computational calculations of pKa values of imidazole in Cu(II) complexes of biological relevance

The imidazole ring is part of the lateral chain of histidine. One of the main features of this amino acid is the ability to coordinate copper, especially Cu(2+), because of the intermediate base nature of its imidazole ring, which has a great biological relevance. Proteins such as cytochrome c oxidase, a crucial enzyme in the respiratory chain, and β-amyloid peptide, implicated in the pathology of Alzheimer's disease, are examples of proteins containing histidines in their coordination sphere. Several studies indicate that the presence of this metal ion produces a decrease in the pK(a) of the imidazole ring of histidine. However, there are no reports of systematic studies of pK(a) variation in these types of metal cation complexes. In this work we use density functional theory to study the dependence of imidazole pK(a) with the number of imidazole rings in Cu(2+) coordination environments. The pK(a) of isolated imidazole (ImH), and the pK(a) of imidazole in Cu(2+)(ImH)(m)(H(2)O)(4-m) (m=1-3) complexes have been studied using two different functionals, B3LYP and MPWB1K, which have different percentage of exact exchange, and the highly-correlated CCSD(T) method. Results show that imidazole pK(a) decreases between 2 and 7 units depending on the method employed and the number of imidazole rings coordinating the metal cation. Taking into account that the pK(a) of imidazole is 14, this decrease could be relevant in biological processes.     

Photosensitive azobispyridine gold(I) and silver(I) complexes

The neutral and cationic dinuclear gold(I) compounds [(μ-N-N)(AuR)(2)] (N-N = 2,2'-azobispyridine (2-abpy), 4,4'-azobispyridine (4-abpy); R = C(6)F(5), C(6)F(4)OC(12)H(25)-p, C(6)F(4)OCH(2)C(6)H(4)OC(12)H(25)-p) and [(μ-N-N){Au(PR(3))}(2)](CF(3)SO(3))(2) (N-N = 2-abpy, 4-abpy, R = Ph, Me) have been obtained by displacement of a weakly coordinated ligand by an azobispyridine ligand. The corresponding silver(I) dinuclear [(μ-2-abpy){Ag(CF(3)SO(3))(PPh(3))}(2)] and polynuclear [{Ag(CF(3)SO(3))(4-abpy)}(n)] compounds have been obtained. The molecular structures of [(μ-2-abpy){Au(PPh(3))}(2)](CF(3)SO(3))(2) and [(μ-4-abpy){Au(PMe(3))}(2)](CF(3)SO(3))(2) have been confirmed by X-ray diffraction studies and feature linear gold(I) centers coordinated by pyridyl groups, and non-coordinated azo groups. In contrast the X-ray structure of [(2-abpy){Ag(CF(3)SO(3))(PPh(3))}(2)] shows tetracoordinated silver(I) centers involving chelating N-N coordination by pyridyl and azo nitrogen atoms. The gold(I) compounds with a long alkoxy chain do not behave as liquid crystals, and decompose before their melting point. The soluble gold(I) derivatives are photosensitive in solution and isomerize to the cis azo isomer under UV irradiation, returning photochemically or thermally to the most stable initial trans isomer. The silver(I) derivative [(2-abpy){Ag(CF(3)SO(3))(PPh(3))}(2)] also photoisomerizes in solution under UV irradiation, showing that its solid state structure, which would block isomerization by azo coordination, is easily broken. These processes have been monitored by UV-vis absorption and (1)H NMR spectroscopy. All these compounds are non-emissive in the solid state, even at 77 K.     

O-O bond activation in H2O2 and (CH3)3C-OOH mediated by [Ni(cyclam)(CH3CN)2](ClO4)2: different mechanisms to form the same Ni(III) product?

Reaction of [Ni(II)(cyclam)(CH(3)CN)(2)](ClO(4))(2) (1) with tert-butylhydroperoxide (TBHP) or H(2)O(2), in acidic media results in a formation of [Ni(III)(cyclam)(CH(3)CN)(2)](3+) species (2), the nature of which is characterized by UV-vis, EPR and XPS. The formation rate of 2 is much higher when H(2)O(2) is used as oxidant. In absence of acid, TBHP reacts with 1 generating the same Ni(III) species but, in contrast, no reaction is observed between H(2)O(2) and 1. Addition of cis-stilbene as an oxidable substrate quenches the formation of Ni(III) for reaction with H(2)O(2) only. Overall, these observations reveal a different reaction mechanism when reacting H(2)O(2) with 1 than when reacting the same metal complex with TBHP, despite the fact that the final product is the same. The proposed pathways arising from these observations consist in a homolytic O-O cleavage for the reaction of 1 with TBHP in CH(3)CN, but a proton assisted heterolysis for the O-O activation in H(2)O(2). Density functional calculations (B3LYP and OPBE) on the thermodynamic feasibility of the two reaction processes support the proposed mechanisms, since the O-O homolysis is strongly disfavored when H(2)O(2) is used as reactant.     

Do H-bond features of silica surfaces affect the H2O and NH3 adsorption? Insights from periodic B3LYP calculations

The adsorption of a single H(2)O and NH(3) molecule on different fully hydroxylated α-quartz, cristobalite, and tridymite surfaces has been studied at the B3LYP level of theory, within a periodic approach using basis sets of polarized triple-ζ quality and accounting for basis set superposition error (BSSE). Fully hydroxylated crystalline silica exhibits SiOH as terminal groups whose distribution and H-bond features depend on both the considered silica polymorph and the crystallographic plane, which gives rise to isolated, H-bond interacting SiOH pairs or infinitely connected H-bond chains. A key point of the present study is to understand how the H-bond features of a dry crystalline silica surface influence its adsorption properties. Results reveal that the silica-adsorbate (H(2)O and NH(3)) interaction energy anticorrelates with the density of SiOH groups at the surface. This counterintuitive observation arises from the fact that pre-existing H-bonds of the dry surface need to be broken to establish new H-bonds between the surface and the adsorbate, which manifests in a sizable energy cost due to surface deformation. A simple method is also proposed to estimate the strength of the pre-existing H-bonds at the dry surfaces, which is shown to anticorrelate with the adsorbate interaction energy, in agreement with the above trends.     

Ripening and Storage Time Effects on the Aromatic Profile of New Table Grape Cultivars in Chile

The aim of this study was to determine the volatile profiles of new seedless table grape cultivars Timco™, Magenta™, Krissy™ and Arra15™ and compare them with the traditional table grape variety Crimson seedless. The volatile profiles were extracted employing solid-phase microextraction and analyzed with gas chromatography coupled with mass spectrometry. Terpenes were present in very different proportions, with the Magenta, Krissy, and Arra15 varieties showing much higher quantities than Crimson and Timco. β-Ionone and octanal, important indicators in the aromatic flavor quality of table grapes, were present in higher levels in Crimson and Arra15, and this might be responsible for driving consumer preference. These compounds significantly increased during ripening, except in Crimson, and gradually decreased from harvest to the end of the storage in all the cultivars. Evolution during ripening was different depending on the variety but the general tendency terpenes was to increase from veraison to harvest. A postharvest study revealed that Crimson could have a better conservation of the volatile components during postharvest storage compared with Timco and Krissy. These results could help in plant breeding programs and to make decisions for new planting according to needs for storing fresh table grapes given distances to consumer markets.     

Pd-H elimination reactions in palladium(II) allylic complexes

The ease of H elimination from the 4- (beta-) position in a series of allylic complexes [Pd(5-C(6)F(5)-1-3-eta(3)-cyclohexenyl)XL](n+) (X, L = Br, N-, P-donor, C(6)Cl(2)F(3); n = -1, 0, +1) was compared by analyzing their decomposition products at 50 degrees C. Pd-H elimination does not occur for cationic complexes, whereas it is the main decomposition pathway for neutral and anionic complexes. In addition to the charge of the complex, the ease of this Pd-H elimination is determined by the trans influence of the ligands (aryl > PMe(3) > Br, N-donor).     

Mixed Adenine/Guanine Quartets with Three trans‐a2PtII (a=NH3 or MeNH2) Cross‐Links: Linkage and Rotational Isomerism,Base Pairing,and Loss of NH3

Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross‐linked by three linear metal moieties such as trans‐a₂Pt^II (with a=NH₃ or MeNH₂) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans‐[{Pt(NH₃)₂(N7‐9‐EtA‐N1)₂}{Pt(MeNH₂)₂(N7‐9‐MeGH)}₂][(ClO₄)₆] ? 3H₂O ( 1 ) (with 9‐EtA=9‐ethyladenine and 9‐MeGH=9‐methylguanine) was crystallized from water and found to adopt a flat Z‐shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9‐MeGH, a meander‐like construct, trans,trans,trans‐[{Pt(NH₃)₂(N7‐9‐EtA‐N1)₂}{Pt(MeNH₂)₂(N7‐9‐MeGH)₂}][(ClO₄)₆] ? [(9‐MeGH)₂] ? 7 H₂O ( 2 ) is formed, in which the two extra 9‐MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1 . Compound 1 , and likewise the analogous complex 1 a (with NH₃ ligands only), undergo loss of an ammonia ligand and formation of NH₄⁺ when dissolved in [D₆]DMSO. From the analogy between the behavior of 1 and 1 a it is concluded that a NH₃ ligand from the central Pt atom is lost. Addition of 1‐methylcytosine (1‐MeC) to such a DMSO solution reveals coordination of 1‐MeC to the central Pt. In an analogous manner, 9‐MeGH can coordinate to the central Pt in [D₆]DMSO. It is proposed that the proton responsible for formation of NH₄⁺ is from one of the exocyclic amino groups of the two adenine bases, and furthermore, that this process is accompanied by a conformational change of the cation from Z‐form to U‐form. DFT calculations confirm the proposed mechanism and shed light on possible pathways of this process. Calculations show that rotational isomerism is not kinetically hindered and that it would preferably occur previous to the displacement of NH₃ by DMSO. This displacement is the most energetically costly step, but it is compensated by the proton transfer to NH₃ and formation of U(?H⁺) species, which exhibits an intramolecular hydrogen bond between the deprotonated N6H^? of one adenine and the N6H₂ group of the other adenine. Finally the question is examined, how metal cross‐linking patterns in closed metallacyclic quartets containing two adenine and two guanine nucleobases influence the overall shape (square, rectangle, trapezoid) and the planarity of a metalated purine quartet.     

A generic small-molecule microarray immobilization strategy

Small-molecule microarrays are often limited by the requirement for each compound undergoing immobilization to contain a common functional group or by the need to prepare glass slides containing photo-reactive groups. Herein, we present a generic strategy that allows any compound library to be immobilized. This was achieved by printing a fluorous-tagged photo-reactive 3-aryl-3-trifluoromethyldiazirine, which undergoes non-selective insertion into compounds following UV-activation, onto fluorous-functionalized glass slides. The arrays could be reused following aqueous stripping and re-assessment of the compounds with the same protein or another target of interest.     

Cationic intermediates in the Pd-catalyzed negishi coupling. kinetic and density functional theory study of alternative transmetalation pathways in the Me-Me coupling of ZnMe2 and trans-[PdMeCl(PMePh2)2

The complexity of the transmetalation step in a Pd-catalyzed Negishi reaction has been investigated by combining experiment and theoretical calculations. The reaction between trans-[PdMeCl(PMePh(2))(2)] and ZnMe(2) in THF as solvent was analyzed. The results reveal some unexpected and relevant mechanistic aspects not observed for ZnMeCl as nucleophile. The operative reaction mechanism is not the same when the reaction is carried out in the presence or in the absence of an excess of phosphine in the medium. In the absence of added phosphine an ionic intermediate with THF as ligand ([PdMe(PMePh(2))(2)(THF)](+)) opens ionic transmetalation pathways. In contrast, an excess of phosphine retards the reaction because of the formation of a very stable cationic complex with three phosphines ([PdMe(PMePh(2))(3)](+)) that sequesters the catalyst. These ionic intermediates had never been observed or proposed in palladium Negishi systems and warn on the possible detrimental effect of an excess of good ligand (as PMePh(2)) for the process. In contrast, the ionic pathways via cationic complexes with one solvent (or a weak ligand) can be noticeably faster and provide a more rapid reaction than the concerted pathways via neutral intermediates. Theoretical calculations on the real molecules reproduce well the experimental rate trends observed for the different mechanistic pathways.     

Cooperative effects at water-crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study

Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.