Millennium Nucleus
Molecular Engineering for Catalysis and Biosensors

What we learned...


Nature of the Excited State of Triangulo Silver N-Heterocyclic Carbenes. Insights from Relativistic DFT Calculations
Alvaro Muñoz-Castro
J. Phys. Chem. A, 2012, 116 (1), 520-525 [0.000, 0]
DOI:   10.1021/jp2071277
Insights into the ground and excited states involved in the reported luminescent behavior of a complex involving the Ag3 core stabilized by pyridil derivatives of N-heterocyclic carbenes has been achieved by means relativistic DFT calculations including scalar and spin–orbit coupling. The stabilization of the [Ag3]3+ core is enhanced by the population of a highly symmetric bonding Ag3 orbital, composed of 75% from the 5s, 15% from 5p, and 10% from 4d. Thus, stabilization of the Ag3 core involves a slightly bonded d10 metallic core in addition to the pure nonbonding argentophilic interaction picture. It is suggested that the population of this highly bonding [Ag3]3+ orbital is responsible of the short Ag–Ag bond length observed in the studied compounds. The characterized electronic excitations allows to rule that the metal–ligand to ligand charge-transfer transitions account for the luminescent properties. The calculated Stokes shifts are in good agreement with the experimental data.

Regioselective C-H Activation of Cyclometalated Bis-Tridentate Ruthenium Complexes
Stacy S. R. Muise, Holly A. Severin, Bryan D. Koivisto, Kiyoshi C. D. Robson, Eduardo Schott, and Curtis P. Berlinguette
Organometallics, 2011, 30 (24), 6628-6635 [0.000, 0]
DOI:   10.1021/om200784j
A series of bis-tridentate Ru(II) complexes consisting of trimethyl-4,4?,4?-tricarboxylate-2,2?:6?,2?-terpyridine (Me3tctpy) and derivatized 6-phenyl-2,2?-bipyridine (pbpy) ligands are reported. Each complex is attached to a terminal triphenylamine (TPA) substituent at the central ring of pbpy through a thiophene bridge to benefit light absorption, while the anionic ring of pbpy is functionalized with substituents to modulate the metal-based redox potential. The cyclometalation step was found to favor the isomer where the electron-donating groups (EDGs; i.e., ?OEt, ?SEt) are situated ortho to the organometallic bond rather than the sterically favored para position, while the para isomer is formed in exclusivity when electron-withdrawing groups (e.g., ?CF3) are installed on the anionic ring. Moreover, the distribution of the isomeric products is affected by the identity of the chalcogen: ortho:para = 1:0 and 3:1 where EDG = ?OEt and ?SEt, respectively. Because our molecular scaffold rules out certain cyclometalation pathways (e.g., oxidative addition, agostic interactions, ?-bond metathesis), we are able to experimentally establish that the observed regioselectivity is in accordance with an electrophilic metalation where the relative stabilities of the products and carbanionic intermediates govern the ratio of the isomers formed.

Spin-orbit effects on a gold-based superatom: a relativistic Jellium model
Alvaro Muñoz-Castro and Ramiro Arratia-Perez
Phys. Chem. Chem. Phys., 2012, 14, 1408-1411 [0.000, 0]
DOI:   10.1039/C1CP22420D
The inclusion of relativistic effects always brings to the scientific community great and stimulating surprises. To consider the spin–orbit term, which accounts for the interaction between the spatial and spin coordinates, requires the use of double point groups of symmetry in order to solve the Dirac equation or the two component approximation to it, leading to total angular momenta (j) functions, atomic or molecular spinors, instead of pure orbital angular momenta (l), atomic or molecular orbitals. Large and small components, derived from the Dirac treatment, depict wavefunctions corresponding to fermions, electrons, which are described for the first time for a superatom case. In addition, their behavior is revisited in order to clarify the effects of the inclusion of the spin–orbit coupling into the electronic structure calculations, which can be extended to other superatoms, clusters, molecules and atoms.

Theoretical and Experimental Study of Bonding and Optical Properties of Self-Assembly Metallophthalocyanines Complexes on a Gold Surface. A Survey of the Substrate-Surface Interaction.
Ingrid Ponce, J. Francisco Silva, Ruben Oñate, Sebastian Miranda-Rojas, Alvaro Muñoz-Castro, Ramiro Arratia-Pérez, Fernando Mendizabal, and José H. Zagal
J. Phys. Chem. C 2011, 115, 23512-23518 [0.000, 0]
DOI:   10.1021/jp208734f
The formation of self-assembly monolayers (SAMs) based on a gold substrate and a thiolate ligand as -anchor- fragment of metallophtalocyanine has been employed as strategy toward the obtention of modified electrodes. In this Article, the formation of SAM’s involving iron and cobalt phtalocyanines anchored by 4-aminothiophenol (4-ATP) and 4-mercatopyridine (4-MP) to the Au(111) surface is explored by both experimental and theoretical studies for a better understanding of their bonding pattern and optical properties. The self-assembly metallophthalocyanines complexes on gold electrode exhibits an interesting charge donation from the 4-ATP or 4-MP toward both gold substrate and phtalocyanine, denoting an effective gold-MPc interaction mediated by the titled anchor ligands. In addition, the optical properties of the self-assembled complexes supported on the gold electrode exhibit in conjuction with the well-described Q-band an interesting charge transfer from the Pc (?) toward the gold surface, as could be observed in the FePc-4MP-Au26 assembly.

Behavior of [2.2]paracyclophane in magnetic fields: A survey of the magnetic response properties from chemical shift tensor maps
Alvaro Muñoz-Castro
Chem. Phys. Lett 2011, 517 (1-3), 113-115 [0.000, 0]
DOI:   10.1016/j.cplett.2011.10.028
[2.2]Paracyclophane, is a fascinating compound that consist of two π-stacked benzene rings in parallel planes which are held together by two p-ethyl bridges, where the close proximity of the aromatic rings leads to unique properties and distinctive features. The graphical analysis of each component of the chemical shift tensor (δ), reveals the magnetic complexity of such entity dominated by both ring current and anisotropic effects. In addition to the enhance magnetic response due to the additive interaction between the magnetic fields generated by the diatropic ring currents on each aromatic ring (ring current effect). The analysis of the δxx and δyy components, reveals the influence of the anisotropic effect from the p-ethyl bridges leading to deshielding regions at the center of [2.2]paracyclophane, which contribute to the anisotropic behavior observed.

Bonding and Magnetic Response Properties of Several Toroid Structures: Insights of the Role of Ni2S2 as Building Block from Relativistic DFT Calculations
Alvaro Muñoz-Castro
J. Phys. Chem. A 2011, 115, 10789-10794 [0.000, 0]
DOI:   10.1021/jp2028438
Relativistic density functional calculations were carried out on several nickel toroid mercaptides of the general formula [Ni(µ-SR)2]n, with the aim to characterize and analyze their stability and magnetic response properties, in order to gain more insights on their stabilization and size-dependent behavior. The Ni-ligand interaction has been studied by means projected density of states and energy decomposition analysis, which denotes its stabilizing character. The graphical representation of the response to an external magnetic field is applied for very first time taking into account the spin-orbit term. This map allows to characterize clearly the magnetic behavior inside and in the closeness of the toroid structure showing the prescence of paratropic ring currents inside the Nin ring, and in contrast, diatropic currents confined in each Ni2S2 motif denoting an aromatic behavior (in terms of magnetic criteria). The calculated data suggests that the Ni2S2 moiety can be regarded as a stable constructing block, which can afford several toroid structures of different nuclearities in agreement to the reported in the experimental literature. In addition, the effects of the relativistic treatment over the magnetic response properties on these lighter compounds are denoted by comparing nonrelativistic, scalar relativistic and scalar plus spin-orbit relativistic, showing that are acting, although its non-pronunced role.

Probing the aromaticity of the [(HtAc)32-H)6], [(HtTh)32-H)6],+, and [(HtPa)32-H)6] clusters
Rodrigo Ramírez-Tagle, Leonor Alvarado-Soto, Ramiro Arratia-Perez, Radovan Bast, and Luis Alvarez-Thon
J. Chem. Phys. 2011, 135 (10), 104506 [0.000, 0]
DOI:   10.1063/1.3632056
In this study we report about the aromaticity of the prototypical [(HtAc)32-H)6], [(HtTh)32-H)6]+, and [(HtPa)32-H)6] clusters via two magnetic criteria: nucleus-independent chemical shifts (NICS) and the magnetically induced current density. All-electron density functional theory calculations were carried out using the two-component zeroth-order regular approach and the four-component Dirac-Coulomb Hamiltonian, including scalar and spin-orbit relativistic effects. Four-component current density maps and the integration of induced ring-current susceptibilities clearly show that the clusters [(HtAc)32-H)6] and [(HtTh)32-H)6]+ are non-aromatic whereas [(HtPa)32-H)6] is anti-aromatic. However, for the thorium cluster we find a discrepancy between the current density plots and the classification through the NICS index. Our results also demonstrate the increasing influence of f orbitals, on bonding and magnetic properties, with increasing atomic number in these clusters. We think that the enhanced electron mobility in [(HtPa)32-H)6] is due the significant 5f character of its valence shell. Also the participation of f orbitals in bonding is the reason why the protactinium cluster has the shortest bond lengths of the three clusters. This study provides another example showing that the magnetically induced current density approach can give more reliable results than the NICS index.

Enhanced Catalytic activity of Fe phthalocyanines linked to Au(111) via conjugated self-assembled monolayers of aromatic thiols for O2 reduction
Ingrid Ponce, J. Francisco Silva, Ruben Oñate, Marcos Caroli Rezende, Maritza Paez, Jorge Pavez, José H. Zagal
Electrochemistry Communications 2011, 13 (11), 1182-1185 [0.000, 0]
DOI:   10.1016/j.elecom.2011.08.050
We have obtained and characterized self assembled monolayers (SAMs) of 4-aminothiophenol (4-ATP) and 1-(4-mercaptophenyl)-2,6-diphenyl-4-(4-pyridyl)pyridinium tetrafluoroborate (MDPP) functionalized with iron phthalocyanine (FePc) adsorbed on gold (111) electrodes. The catalytic activity of these SAMs/FePc was examined for the reduction of O2 in aqueous media (pH =4) and compared with that of bare gold and of gold coated directly with FePc molecules. Scanning tunneling microscopy (STM) studies confirm the functionalization of the 4-ATP by FePc. The electrocatalytic studies carried out with Au/FePc, Au/4-ATP/FePc and Au/MDPP/FePc electrodes show that the O2 reduction takes place by a 4-electron transfer to give water in contrast to a 2-electron-transfer process observed on the bare gold. The activity of the electrodes increases as follows: Au < Au/FePc < Au/4-ATP/FePc

Theoretical study of the protonation of [Pt3(µ-L)3(L')3] (L=CO, SO2, CNH; L'=PH3, CNH)
Fernando Mendizabal, Daniela Donoso and Darwin Burgos
Chem. Phys. Lett. 2011, 514, 374-378 [0.000, 0]
DOI:   10.1016/j.cplett.2011.08.068
Ab initio calculations suggest that a series of clusters of the [Pt3(?-L)3(L′)3(?3-H]+ type (L = CO, SO2, CNH; L′ = PH3, CNH) are stable. We have studied these clusters at the HF, MP2, B3LYP, PBE and TPSS theory levels. The magnitude of the interaction energies and distances indicates a substantial covalent character of the Pt3–H bond, confirmed by orbital diagrams. In addition, the Fukui index of electrophilic attack and electrophilicity index on the unprotonated clusters were used to explore possible sites where chemical reactivity may play a role.

Theoretical study of the local reactivity of electrophiles of the type MPR3+ (M=Cu, Ag, Au ;R=-H, -Me, -Ph)
Darwin Burgos, Claudio Olea-Azar, and Fernando Mendizabal
J. Mol. Model. 2011 18 (5), 2021-2029 [0.000, 0]
DOI:   10.1007/s00894-011-1213-2
Reactivity prediction in the series of MPR3+ fragments ( M = Au, Ag, Cu; R = -H, -Me, -Ph) has been achieved at the ab initio (HF and MP2) and density functional theory (B3LYP and PBE) levels. We have used global and local descriptors based on conceptual DFT such as hardness, Fukui function and electrophilicity index. For all methods and fragments, we have found an equal trend in reactivity using both the global and local electrophilicity index: QR-AuPR3+ > CuPR3+ ˜ AgPR3+ > NR-AuPR3+. It is also found that the electrophilicity power decreases as the volume of R increases.

Free energy relationships in electrochemistry: a history that started in 1935
Anthony John Appleby, José Heráclito Zagal
J. Solid State Electrochem 2011,15, 1811-1832 [0.000, 0]
DOI:   10.1007/s10008-011-1394-8
This article is a historical overview of free energy relationships in electrochemistry with the purpose of giving the reader an integrated view on how these correlations are interconnected in various aspects starting with free energy correlations for outer-sphere and inner-sphere processes, Tafel correlations, the Butler-Volmer equation, and electron transfer theories. The citation of the literature is far from complete and is aimed to stimulate the reader to further reading.

Relativistic calculations of aminotroponiminate complexes containing group 15 (P, As, Sb, Bi) elements
Lucian-Cristian Pop, Desmond Mac-Leod Carey, Alvaro Muñoz-Castro, Luminita Silaghi-Dumitrescu, Annie Castel, Ramiro Arratia-Pérez
Polyhedron 2011, 30 (5), 841-845 [0.000, 0]
DOI:   10.1016/j.poly.2010.12.023
The relativistic electronic structure calculations of N,N′-chelated pnictogenium cations containing aminotroponiminate units, (E = P(1), As(2), Sb(3), Bi(4)), have been investigated employing density functional (DF) methods, including spin–orbit relativistic corrections, via the two-component zeroth order regular approximation (ZORA) Hamiltonian. The role of replacement of the pnictogen atom when going down into the 15 group was discussed on the basis of geometrical parameters, Hirshfield charge analyses, DF reactivity indexes. The degree of electronic delocalization into the five- and seven membered rings was estimated via the electron localization function (ELF) and the nuclear independent chemical shifts (NICS) indexes.

Our results show an existence of a lack of systems 24 to act as donor ligands for the metal complexation, compared with 1, due to the positive charge over the pnictogen atoms besides the lone-pair orbital of the pnictogen atom which lies at low energies from their corresponding reacting HOMO’s. It is also interesting to note some effects over the aromaticity when going down into the 15 group, i.e., the C5 ring is affected by the change of the pnictogen atom, while the aromaticity on the C7 ring is not affected, as suggested by the analysis of the ELF, NICS and geometrical parameters.

Optimizing the electrocatalytic activity of surface confined Co macrocyclics for the electrooxidation of thiocyanate at pH 4
M. Sancy, J. Pavez, M. A. Gulppi, I. L. de Mattos, R. Arratia-Perez, C. Linares-Flores, M. Paez, T. Nyokong and J. H. Zagal
Electroanalysis 2011, 23 (3), 711-718 [0.000, 0]
DOI:   10.1002/elan.201000599
We have studied the trends in catalytic activity of several Co macrocyclics confined on the surface graphite electrodes for the oxidation of thiocyanate. A plot of log i (at constant E) versus the formal potential of the catalyst gives a volcano correlation, indicating that the Co(II/I) redox potential needs to be tuned, in order to achieve maximum reactivity. Graphite electrodes modified with Co phthalocyanine at pH 4 exhibit linear amperometric response for thiocyanate concentration in the range 10−7 and 10−3 M. Theoretical calculations show that electrocatalytic activity (as log i at constant E) plotted versus the energy of the LUMO of the Co complex also gives a volcano correlation.

A DFT/TDDFT Study of Porphyrazines and Phthalocyanine Oxo-Titanium Derivatives as Potential Dyes in Solar Cells
X. Zárate, E. Schott, D., R. Arratia-Perez
Int. J. of Quantum Chem. 2011, 111 (15), 4186-4196 [0.000, 0]
DOI:   10.1002/qua.22998
Density functional theory and time dependent density functional theory calculations at the level of LDA/BP86/TZ2P were performed systematically on several Ti(IV) complexes of porphyrazines and one phthalocyanine. We performed an analysis of the frontier molecular orbitals of the ground state electronic structures and also discuss in particular the good concordance of our results with the experimental data, which affords to predict the geometrical and optical properties of new complexes (3, 4, and 7). We also emphasize the characterization of the UV–vis absorption spectra and propose transitions that contribute to the Q and B bands. Some useful calculated properties in complexes 2, 3, and 7, like: high light absorption in the visible region of the spectra, transitions involved in these bands with a determined direction, charge separation, bigger highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO-LUMO) gaps than complexes 4 and 5, and the energy of their LUMO orbitals (that are higher than the lowest energy level of the conduction band of the TiO2) indicate that system complexes 2, 3, and 7 could act as light-harvesting sensitizers for dye-sensitized solar cells (DSCs). These proposals were made using a model of the previously experimentally known phthalocyanine, which was used as sensitizer in DSCs devices, comparing its electronic properties with the herein proposed sensitizers.

Preparation and ESR characterization of polyalkyl-s-indacenyl anion-radicals from polyalkyl-1,5-dilithio-s-indacenes
C. Adams, J. Araneda, C. Morales, I. Chavez, J. M. Manriquez, D. Mac-Leod Carey, N. Kair, A. Castel, P. Rivière, M. Rivière-Baudet, M. Dahrouch, N. Gatica
Inorg. Chim. Acta 2011, 366 (1), 44-52 [0.000, 0]
DOI:   10.1016/j.ica.2010.10.002
Polyalkyl-(or chloropolyalkyl)-s-indacenyl anion radicals were obtained from the organodilithium derivatives of the corresponding substituted-1,5-dihydro-s-indacenes by three different methods: (i) UV photolysis, (ii) oxidation by a ferrocenium salt, (iii) single electron transfer reaction from an electron rich olefin. The last reaction (iii) involves transient formation of an unstable polyalkyl-lithio-s-indacenyl imidazolidinium salt. The same salt, obtained by another way by reacting 1,3-dimethylimidazolidinium chloride with the polyalkyl-1,5-dilithio-s-indacene, also leads to the corresponding lithium polyalkyl-s-indacenyl anion radical. All lithium polyalkyl-s-indacenyl anion radicals studied were characterized from their ESR spectra. They present a characteristic symmetrical spin distribution. On the contrary a Rhodium-COD polyalkyl-s-indacene radical presents a non symmetrical spin distribution.

Geometrically Specific Imino Complexes of the [Re63-Se)8]2+ Core-Containing Clusters
Xiaoyan Tu, Huong Truong, Eli Alster, Alvaro Muñoz-Castro, Ramiro Arratia-Pérez, Gary S. Nichol, Zhiping Zheng
Chem. Eur. J. 2011, 17 (2), 580-587 [0.000, 0]
DOI:   10.1002/chem.201001975
The reactions of nitrile complexes of the [Re63-Se)8]2+ core-containing clusters, [Re63-Se)8(PEt3)n(CH3CN)6−n]2+ [n=5 (1); n=4, cis- (2) and trans- (3); n=0 (4)], with organic azides C6H5CH(CH3)N3 and C6H5CH2N3 produced the corresponding cationic imino complexes of the general formula [Re63-Se)8(PEt3)n(L)6−n]2+ [L=PhN=CHCH3: n=5 (5); n=4, cis- (6) and trans- (7); n=0 (8) and L=HN=CHPh: n=5 (9); n=4, cis- (10) and trans- (11)]. These novel complexes were characterized by NMR spectroscopy (1H and 31P) and single-crystal X-ray diffraction. A mechanism involving the migration of one of the groups on the azido α-C atom to the α-N atom of the azido complex, concerted with the photo-expulsion of N2, was invoked to rationalize the formation of the imino complexes. Density functional theory (DFT) calculations indicated that due to the coordination with and activation by the cluster core, the energy of the electronic transition responsible for the photo-decomposition of a cluster-bound azide is much reduced with respect to its pure organic counterpart. The observed geometric specificity was rationalized by using the calculated and optimized preferred ground-state conformation of the cluster-azido intermediates.

Theoretical study of the s2-p interaction between Tl(I) and Olefinic systems on hypothetical [Tl(C2H4)2]+ and [Tl(C2H2)n]+ (n = 2,3) complexes
D. Donoso and F. Mendizabal
J. Chil. Chem. Soc. 2010, 55 (4), 503-505 [0.000, 0]
The atraction between [C2H4]2 and [C2H2]2,3 and Tl(I) in the hypothetical [Tl(C2H4)2]+ and [Tl(C2H2)n]+ (n = 2,3) complexes was studied using ab initio methods. It was found that the changes around the equilibrium C-Tl distance and in the interaction energies are sensitive to the electron correlation potential. We evaluated these effects using sevel levels of theory, including HF, MP2, MP4 and CCSD(T). The equilibrium C-Tl distances in the complexes are in the range of 294 pm to 338 pm. The interaction energy differences obtained at the equilibrium distance range from 55 to 110 kJ/mol at the different levels used. These results indicate that the complexes formed are in the category of van der Waals systems. Also, these results indicated that the interaction between olefinic systems and Tl(I) are a real minimum on the potential energy surfaces.

Theoretical study of the interaction between Pt(0) and MPH3+ fragments in complexes of the [Pt3 (µ-CO)3(PH3)3]–MPH3+ (M = Cu+, Au+, Ag+) type
Daniela Donoso, Fernando Mendizabal
Theor. Chem. Acc. 2011, 129, 381-387 [0.000, 0]
DOI:   10.1007/s00214-010-0856-x
Ab initio calculations suggest that a series of complexes of the [Pt3(μ-CO)3(PH3)3]–MPH3+ type (M = Cu, Au, Ag) are stable. We have studied these complexes at the HF, MP2, B3LYP, and PBE levels of theory. The magnitude of the interaction energies and Pt3–M distances indicate a substantial covalent character of the bond, the latter being confirmed by orbital diagrams. The chemical bond is sensitive to electron correlation effects. In addition, the Fukui index of nucleophilic attack and electrophilicity index on the metal were used to explore possible sites where chemical reactivity may play a role.

Adsorption essays of palladium in modified silica gel with Thiouronium groups: experimental and theoretical studies
Alexander Carreño G., Eduardo Schott V., Ximena Zárate B., Ramiro Arratia-Perez, Juan Carlos Vega De K., Miguel Mardones L., Juan M. Manríquez M., Ivonne Chávez M.
J. Chil. Chem. Soc. 2011, 56 (2) , 692-696 [0.000, 0]
The silylant 3-cloropropyltriethoxysilyl was anchored over silica gel in anhydrous conditions in order to react with thiourea to obtain modified silica gel with thiouronium. The aim to obtain an inorganic support that is able to hijack metals from the VIII group such as palladium. The product was characterized by Sbet and FTIR infrared spectroscopy. For the determination of the structure in the modified silica gel NMR spectra of silicon and carbon were preformed in solid state. The coordination form of the modified silica gel to the metal was studied computationally in the context of the DFT theory, using the ADF code. This was a collaborative work with "Fundación Chile" for the recuperation of precious metals from the mining industry

Theoretical study of the local reactivity of electrophiles of the type MPR3+ (M = Cu, Ag, Au ;R = -H, -Me, -Ph)
Darwin Burgos, Claudio Olea-Azar and Fernando Mendizabal
J. Mol. Model. 2011, published online 30 Aug. [0.000, 0]
DOI:   10.1007/s00894-011-1213-2
Reactivity prediction in the series of MPR3+ fragments ( M = Au, Ag, Cu; R = −H, -Me, -Ph) has been achieved at the ab initio (HF and MP2) and density functional theory (B3LYP and PBE) levels. We have used global and local descriptors based on conceptual DFT such as hardness, Fukui function and electrophilicity index. For all methods and fragments, we have found an equal trend in reactivity using both the global and local electrophilicity index: QR-AuPR3+ > CuPR3+ ≈ AgPR3+ > NR-AuPR3+. It is also found that the electrophilicity power decreases as the volume of R increases.