Adsorption of CO on Cu (110) and (100) surfaces using COSMO-based DFT

Density functional theory (DFT) combined with the conductor-like solvent model (COSMO) can provide valuable atomistic level insights into CO adsorption on Cu surface interactions in liquid paraffin. The objective of this research was to investigate the solvent effect of liquid paraffin. It was found that both structural parameters and relative energies are very sensitive to the COSMO solvent model. Solvent effects can improve the stability of CO adsorption on Cu (110) and (100) surfaces and the extent of CO activation.     

Theoretical studies on doubly and triply linked polymers of Ge9 clusters

Experimental isolation of singly-bonded polymers of Ge₉, Sn₉ clusters and oligomers of doubly linked Ge₉ clusters encouraged us to explore other possibilities of polymerizing Ge₉ units. The electron counts in the reported oligomers are not consistent with simple ideas of localized intercluster bonding; demanding a detailed theoretical analysis. Band structure calculations suggest delocalized bonding with a charge requirement of 2− per Ge₉ unit for all polymeric doubly linked chains. DFT-based geometry optimization of model doubly linked polymers shows that one of the two possible forms is stable and has a band gap of ≈1.0 eV. A detailed bonding analysis of a theoretical model, Rb₄Ge₁₈, shows that the increased inter-polyhedral bond weakens the intra-polyhedral bonding. Ternary fusions are found to be generally unstable - for triple linkages the intrapolyhedral bonding is still further reduced; the polymers appear to be unstable towards dissociation into individual Ge₉ units.     

Synthesis, crystal structure and EPR of a hydrogen bonded two-dimensional network of Cu(II) complex with N-(2-hydroxybenzyl)-2-amino-1-ethanol

Hsalea (N-(2-hydroxybenzyl)-2-amino-1-ethanol) and its Cu(II) complexes, Cu(salea)₂ (1) and CuH₋₁(salea)·1.5H₂O (2), were prepared and characterized. X-ray structural analyses of 1 show that two amino N and two deprotonated phenoxy O atoms of the two ligands coordinate equatorially to Cu(II). Two alcoholic O atoms coordinate weakly at axial positions. Each molecule utilizes two alcoholic H atoms and two phenoxy O atoms to form hydrogen bonds with four surrounding molecules, leading to a two-dimensional network structure. EPR and electronic spectra of 1 are consistent with the elongated octahedral coordination polyhedron.     

Spectroscopic and structural studies of 6-(1-methylbenzimidazol-2-yl)-1H-pyridin-2-one and of an unusual T4(2)7(2)6(2)7(2) water tape stabilized by the copper(II) coordination polymer

The solid-state structures of 6-(1-methylbenzimidazol-2-yl)-1H-pyridin-2-one (HL) and the copper(II) complex [Cu(L⁻)₂(OH₂)]·2H₂O (1) are established by X-ray crystallography and also by means of physicochemical and spectroscopic methods. The molecules of HL form a self-complementary head-to-tail hydrogen-bonded dimer through C-H?N and C-H?O contacts to give an infinite 1D chain. The copper(II) complex (1) is five-coordinate with distorted trigonal-bipyramidal (TBP) geometry of the N₄O donor atoms. The electronic and EPR data are in agreement with the X-ray structure of 1, showing that HL coordinates to copper(II) centre as a mono-anionic ligand through deprotonated pyridone N atom and the tertiary benzimidazole nitrogen atom to form a neutral complex in which the water molecule occupies the fifth position. The 1D water tape, T4(2)7(2)6(2)7(2) is anchored to the host through hydrogen bonds between coordinated water molecule [O(3w)] as acting double H-donor, pyridone carbonyl groups [O(2) and O(1)] as double H-acceptor and the lattice water molecules [O(4w) and O(5w)] as double H-donor and single H-acceptor).     

Complexes of copper(II) formate with 2-(phenylamino)pyridine and 2-(methylamino)pyridine: New copper formato paddle-wheel compounds

The derivatives of Cu(HCOO)₂ · 4H₂O with 2-(phenylamino)pyridine and 2-(methylamino)pyridine, [Cu₂(μ-HCOO)₄(PhNHpy)₂] (1), [Cu₂(μ-HCOO)₄(MeNHpy)₂] (2) and Cu(HCOO)₂(MeNHpy)₂ (3), have been synthesized and characterized. Compounds 1 and 2 show the paddle-wheel structure of [Cu₂(μ-HCOO)₄L₂], with four syn-syn bridging formato groups and two molecules of PhNHpy or MeNHpy coordinated to the axial positions, respectively. Intramolecular hydrogen bonds are formed in both cases: two in each dimer of 1 and four in the dimer of compound 2. The dimer units are oriented in two different directions. Dimers with the same orientation form rows along the “c” and the “a” axis in compounds 1 and 2, respectively, with a π-π stacking of the pyridine rings. In compound 1, an intercalation of the phenyl rings of contiguous rows of dimers gives rise to a succession of phenyl rings at a distance of 4.38 Å and an angle of 30.44° between alternate rings. They are antiferromagnetic. Signals of the triplet state are observed in their EPR spectra and the zero-field splitting parameter has been determined. Compound 3 obeys the Curie-Weiss law and the magnetic results indicate the absence of magnetic interaction between Cu(II) atoms.     

First Principles Modeling of Dissociative Adsorption at Crystal Surfaces: Hydrogen on Pt(111)

Multiscale simulation has the potential of becoming the new modeling paradigm in chemical sciences. An important class of multiscale models involves the mapping of a finer scale model into an approximate surface that is used by a coarser scale model. As a specific example of this class we present the case of the adsorption dynamics of diatomic molecules on single crystal catalyst surfaces. The prototype system studied is the dissociative adsorption of H₂ on Pt(111). The finer scale model consists of density functional theory (DFT) periodic slab calculations that provide a small dataset for training an atomistic scale potential energy surface. The coarser scale model uses a semi-classical molecular dynamics (MD) algorithm to obtain the sticking coefficient as a function of the incident energy. Comparison to experimental data and published simulation work is presented. Finally, major challenges in multiscale modeling of chemical reactivity in coupled DFT/MD simulations are discussed, specifically the need for a systematic method of assessing the accuracy of the coarse graining process.     

Adsorption behaviors of hydrogen sulphide on Au(110) nanoslit array surfaces using molecular dynamics simulations

The adsorption behaviour of gas molecules on detector surfaces has a profound influence on the sensitivity of the detector. For this reason, this study used molecular dynamics simulation to explore the dynamic adsorption behaviour of hydrogen sulphide (H₂S) molecules on various types of Au surfaces, including a planar Au(1?1?0) structure and three types of slit array structures. The influence of system temperature, adsorbate concentration and the slit width of nanoarrays on diffusivity, average adsorption energy and static adsorption amount were systematically examined. Simulation results indicate that the self-diffusivity of the adsorbate molecules increases with temperature but decreases with adsorbate concentration. At low concentrations (~3 mol/L), each type of Au(1?1?0) surface structure shows good capacity to adsorb all H₂S molecules. With increasing concentration at 6.5 mol/L, the high concentration leads to adsorption saturation and many free H₂S molecules in the planar Au(1?1?0) structure. Moreover, desorption also begins to appear on the planar structures at a temperature of 300 K (at 6.5 mol/L). The simulation results indicate that the columnar array structures with a slit width ≥5.76 Å allow molecules to swiftly spread into the slits and provide more stable adsorption sites (i.e. with a higher adsorption energy), which can effectively address the issues of high-temperature desorption and adsorption saturation. Particularly at low temperatures (≤100 K), slit structures presented a level of static adsorption of H₂S that was 30% to 35 higher than that of planar structures.     

Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family

Vibrational circular dichroism spectra (VCD) in the mid‐IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N‐trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines. Chirality 27:907–913, 2015. © 2015 Wiley Periodicals, Inc.     

Construction of simplified models to simulate estrogenic disruptions by esters of 4-hydroxy benzoic acid (parabens)

Four parabens (methyl, n-butyl, benzyl and isobutylparaben) were theoretically studied in order to evaluate their estrogenic activity through simplified models. The experimental structure of the human estrogen receptor ligand-binding domain in complex with 17β-estradiol was used as the starting point to construct the models. The complex between 17β-estradiol and three fragments of the estrogenic receptor (Arg, Glu and His), resulted in a reasonable simplified model of interaction. The replacement of 17-β-estradiol by parabens was evaluated by conformational analyses and interaction energy calculations at BHandHLYP/cc-PVTZ(-f)+ level of theory. According with the calculated interaction energies, methylparaben is the paraben with higher estrogenic activity, which is in agreement with experimental studies of extraction and quantification of parabens in tumors. The antibacterial activity of parabens was also explored considering the formation of potassium salts in the phenolic OH groups. From the obtained relative energy values, methylparaben is the most active preservative.     

Copper(II) and cadmium(II) complexes of 2-pyridinyl-4-pyridinylmethanone: Supramolecular architectures consolidated by hydrogen bonding and π-π interaction

2-Pyridinyl-4-pyridinylmethanone (L) has been shown to behave as a monodentate ligand via its 4-pyridyl ring in three new metal(II) complexes, all of which exhibit supramolecular architectures assembled through weak interactions including hydrogen bonding and π-π stacking. Effects of the inorganic anions on the structure of the Cd(II) complexes of L are also discussed.     

Solution studies of some new oxamides - co-ordination behaviour towards Cu(II) ions

The co-ordination chemistry of some new oxamides towards Cu(II) ions was studied using various techniques: potentiometry, voltammetry, spectroscopy (UV-Vis, CD and EPR) and ESI-MS spectrometry. All tested compounds chelate the copper(II) ions with formation of 1:1 and 1:2 (metal-to-ligand ratio) complexes. The Cu(II) ions are bound by 1N, 2N or 3N nitrogen donor systems. Additionally, an unusual co-ordination to amide N-atoms without additional anchoring site is suggested. The (14)N hyperfine splitting observed for the system ox6-Cu(II) above pH 10 clearly indicates the involvement of at least three N donor atoms in the copper ion binding. Moreover, the surrounding by three amide-N and one carbonyl-O stabilizes the high oxidation state of copper(III), although such complexes are very unstable in solution.     

Mechanism of dopachrome tautomerization into 5,6-dihydroxyindole-2-carboxylic acid catalyzed by Cu(II) based on quantum chemical calculations

Background

Tautomerization of dopachrome to 5,6-dihydroxyindole-2-carboxylic acid (DHICA) is a biologically crucial reaction relevant to melanin synthesis, cellular antioxidation, and cross-talk among epidermal cells. Since dopachrome spontaneously converts into 5,6-dihydroxyindole (DHI) via decarboxylation without any enzymes at physiologically usual pH, the mechanism of how tautomerization to DHICA occurs in physiological system is a subject of intense debate. A previous work has found that Cu(II) is an important factor to catalyze the tautomerization of dopachrome to DHICA. However, the effect of Cu(II) on the tautomerization has not been clarified at the atomic level.

Methods

We propose the reaction mechanism of the tautomerization to DHICA by Cu(II) from density functional theory-based calculation.

Results

We clarified that the activation barriers of α-deprotonation, β-deprotonation, and decarboxylation from dopachrome are significantly reduced by coordination of Cu(II) to quinonoid oxygens (5,6-oxygens) of dopachrome, with the lowest activation barrier of β-deprotonation among them. In contrast to our previous work, in which β-deprotonation and quinonoid protonation (O5/O6-protonation) were shown to be important to form DHI, our results show that the Cu(II) coordination to quinonoid oxygens inhibits the quinonoid protonation, leading to the preference of proton rearrangement from β-carbon to carboxylate group but not to the quinonoid oxygens.

Conclusion

Integrating these results, we conclude that dopachrome tautomerization first proceeds via proton rearrangement from β-carbon to carboxylate group and subsequently undergoes α-deprotonation to form DHICA.

General significance

This study would provide the biochemical basis of DHICA metabolism and the generalized view of dopachrome conversion which is important to understand melanogenesis.     

Regulatory processes and population cyclicity in laboratory populations ofAnagasta kühniella (Zeller) (Lepidoptera: Phycitidae)

AsMatsumoto andHuffaker (1973) concluded that their initial universe size was too small for the proper separation of the effects of host density and dispersion on parasite performance, a larger universe of 38 1/2″ (length) ×38 1/2″ (width) ×3″ (height) was used. When individual parasites were exposed to fixed densities and dispersion patterns of host, they displayed an overall decrease in the parasitization rate when compared to the small universe. In all cases aHolling -type response resulted. When a group of 10 parasites per test was employed a Nicholsonian type of response resulted. In an experimentally confined space, the parasites displayed a mutual behavioral interference resulting in emigration which accelerated as the parasite density increased.     

Hydrogen peroxide can be generated by tau in the presence of Cu(II)

Alzheimer's disease has been closely related with oxidative stress, which might be responsible for the dysfunction or death of neuronal cells that contributes to disease pathogenesis. Impaired copper homeostasis makes contribution to the oxidative stress and consequently to several neurodegenerative conditions. Inappropriate binding of Cu(II) to cellular proteins are currently being explored as sources of pathological oxidative stress in several neurodegenerative disorders. Here we report that a fragment of tau protein possesses copper reduction activity and initiates the copper-mediated generation of hydrogen peroxide. The tau peptide was found to be oxidized to form disulfide bond-linked dimer. The hydrogen peroxide generated was quantified by TCEP/DTNB (tris(2-carboxyethyl) phosphine hydrochloride/5,5'-dithio-bis(2-nitrobenzoic acid). Since the copper reduction capacity and the generation of hydrogen peroxide were believe to be a major toxicological pathway of Abeta peptide, the functional similarity shared by tau and Abeta implies a new perspective of tau pathology.     

Using Lewis acidity differences in chelating ligands to control molecular structure and supramolecular assembly of Cu(II) complexes

The electronic effects of the fluorine atoms in hfacac (hexafluoroacetylacetonato) compared with acac (acetylacetonato) in Cu(II) complexes are used to control the molecular and supramolecular structure of Cu(II) compounds. While bis(acac)Cu(II) (acac = acetylacetonato) is known to be able to have a fifth-position coordination, bis(hfacac)Cu(II), (hfacac = hexafluoroacetylacetonato) may have two extra ligands. This, together with the reliable “supramolecular reagent” isonicotinamide, as the additional ligand, are used to go from a zero-dimension structure, with Cu-acac, to an extended supramolecular two-dimension network, with Cu-hfacac. The molecular and crystal structure of bis(acetylacetonato-O,O′)-(isonicotinamide-N) copper(II), 1, and bis(hexafluoroacetylacetonato-O,O′)-trans-bis(isonicotinamide-N) copper(II), 2, are reported.     

Radical production by hydrogen peroxide/bicarbonate and copper uptake in mammalian cells: modulation by Cu(II) complexes

The presence of the bicarbonate/carbon dioxide pair is known to accelerate the transition metal ion-catalysed oxidation of various biotargets. It has been shown that stable Cu(II) complexes formed with imine ligands that allow redox cycling between Cu(I) and Cu(II) display diverse apoptotic effects on cell cultures. It is also reported that Cu(II)-tetraglycine can form a stable Cu(III) complex. In the present study, radical generation from H₂O₂ and H₂O₂/HCO₃⁻ in the presence of these two different classes of Cu(II) complexes was evaluated by monitoring the oxidation of dihydrorhodamine 123 and NADH and by the quantitative determination of thiobarbituric acid reactive substances (TBARs method). Cu(II)-imine complexes produced low levels of reactive species whereas Cu(II)-Gly-derived complexes, as well as the free Cu(II) ion, produced oxygen-derived radicals in significantly larger amounts. The effects of these two classes of complexes on mammalian tumour cell viability were equally distinct, in that Cu(II)-imine complexes caused apoptosis, entered in cell and remained almost unaffected in high levels whilst, at the same concentrations, Cu(II)-Gly peptide complexes and Cu(II) sulphate stimulated cell proliferation, with the cell managing copper efficiently. Taken together, these results highlight the different biological effects of Cu(II) complexes, some of which have been recently studied as anti-tumour drugs and radical system generators, and also update the effects of reactive oxygen species generation on cell cycle control.     

Crystal structure of bis(N-methylethylenediammonium) hexabromodicuprate(I)

The crystal structure of the title compound (C₃H₁₂N₂)₂Cu₂Br₆, is monoclinic, space group P2₁/n, with lattice constants a=8.222(2), b=11.214(2), c=10.646(2) Å, β=91.97(1)° and V=981.0(3) ų. The structure contains anionic Cu₂Br₆²⁻ dimers and N-methylethylenediammonium (henceforth MEDA²⁺) cations. The centrosymmetric dimer units are composed of two edge-shared CuBr₄ tetrahedra, with bridging Cu-Br distances 0.08 Å longer than the terminal distances. A pair of MEDA²⁺ cations hydrogen bond to each dimer via two of the -NH₃⁺ hydrogen atoms and one of the -NH₂⁺- hydrogen atoms. Additional hydrogen bonding between the cations and anions tie the structure together in a complex supramolecular network.     

Copper-thioarylazoimidazole complexes: Structures, photochromism and redox interconversion between Cu(II) ↔ Cu(I) and correlation with DFT calculation

Reaction of Cu(ClO₄)₂·6H₂O, SRaaiNR′ (1-alkyl-2-[(o-thioalkyl)phenylazo]imidazole) and NH₄SCN (1:1:2 mol ratio) affords distorted square pyramidal, [Cu^II(SRaaiNR′)(SCN)₂] (3) compound while identical reaction with [Cu(MeCN)₄](ClO₄) yields -SCN- bridged coordination polymer, [Cu^I(SRaaiNR′)(SCN)]_n (4). These two redox states [Cu^II and Cu^I] are interconvertible; reduction of [Cu^II(SRaaiNR′)(SCN)₂] by ascorbic acid yields [Cu^I(SRaaiNR′)(SCN)]_n while the oxidation of [Cu^I(SRaaiNR′)(SCN)]_n by H₂O₂ in presence of excess NH₄SCN affords [Cu^II(SRaaiNR′)(SCN)₂]. They are structurally confirmed by single crystal X-ray diffraction study. Cyclic voltammogram of the complexes show Cu(II)/Cu(I) redox couple at ∼0.4 V and azo reductions at negative to SCE. UV light irradiation in MeCN solution of [Cu^I(SRaaiNR′)(SCN)]_n (4) show trans-to-cis isomerisation of coordinated azoimidazole. The reverse transformation, cis-to-trans, is very slow with visible light irradiation while the process is thermally accessible. Quantum yields (?_t→c) of trans-to-cis isomerisation are calculated and free ligands show higher ? than their Cu(I) complexes. The activation energy (E_a) of cis-to-trans isomerisation is calculated by controlled temperature experiment. Copper(II) complexes, 3, do not show photochromism. DFT and TDDFT calculation of representative complexes have been used to determine the composition and energy of molecular levels and results have been used to explain the solution spectra, photochromism and redox properties of the complexes.     

Spectro-electrochemical and DFT studies of a planar Cu(II)-phenolate complex active in the aerobic oxidation of primary alcohols

A square-planar compound [Cu(pyrimol)Cl] (pyrimol = 4-methyl-2-N-(2-pyridylmethylene)aminophenolate) abbreviated as CuL-Cl) is described as a biomimetic model of the enzyme galactose oxidase (GOase). This copper(II) compound is capable of stoichiometric aerobic oxidation of activated primary alcohols in acetonitrile/water to the corresponding aldehydes. It can be obtained either from Hpyrimol (HL) or its reduced/hydrogenated form Hpyramol (4-methyl-2-N-(2-pyridylmethyl)aminophenol; H₂L) readily converting to pyrimol (L⁻) on coordination to the copper(II) ion. Crystalline CuL-Cl and its bromide derivative exhibit a perfect square-planar geometry with Cu-O(phenolate) bond lengths of 1.944(2) and 1.938(2) Å. The cyclic voltammogram of CuL-Cl exhibits an irreversible anodic wave at +0.50 and +0.57 V versus ferrocene/ferrocenium (Fc/Fc⁺) in dry dichloromethane and acetonitrile, respectively, corresponding to oxidation of the phenolate ligand to the corresponding phenoxyl radical. In the strongly donating acetonitrile the oxidation path involves reversible solvent coordination at the Cu(II) centre. The presence of the dominant Cu^II-L chromophore in the electrochemically and chemically oxidised species is evident from a new fairly intense electronic absorption at 400-480 nm ascribed to a several electronic transitions having a mixed π → π^∗(L) intraligand and Cu-Cl → L charge transfer character. The EPR signal of CuL-Cl disappears on oxidation due to strong intramolecular antiferromagnetic exchange coupling between the phenoxyl radical ligand (L) and the copper(II) centre, giving rise to a singlet ground state (S = 0). The key step in the mechanism of the primary alcohol oxidation by CuL-Cl is probably the α-hydrogen abstraction from the equatorially bound alcoholate by the phenoxyl moiety in the oxidised pyrimol ligand, Cu-L, through a five-membered cyclic transition state.     

Regulatory processes and population cyclicity in laboratory populations ofAnagasta kühniella (Zeller) (lepidoptera: Phycitidae) V. Host finding and parasitization in a “small” universe by an entomophagous parasite,Venturia canescens (Gravenhorst) (Hymenoptera: Ichneumonidae)

Summary Host finding by the entomophagous parasite,Venturia canescens (Grav.), parasitizingAnagasta kühniella (Zeller) was studied. Studies utilizing fixed densities and dispersion patterns of the hosts where no choice of density groupings was offered showed that within the experimental conditions used, host density relationships were more important than dispersion. Decreasing the time hosts were exposed to a parasite from 72 hours to 24 hours did not alter the overall parasitization. In both cases progressively less hosts were parasitized as host density increased, which exemplified aHolling-type of response. However, when host densities were varied within the same universe, independent of dispersion patterns, and the parasites were given a “choice” of host densities to attack, an increasing percentage of hosts in the higher host density groups were parasitized; thus a density-dependent behavioral response was exhibited. These studies were conducted as a partial fulfillment in the Ph. D. program of one of us (B. M. Matsumoto) and form a part of a broad investigation into the processes operating in the dynamics of arthropod populations under grants toC. B. Huffaker from the U. S. Public Health Service, National Institutes of Health and the U. S. Department of Agriculture.