Millennium Nucleus
Molecular Engineering for Catalysis and Biosensors

What we learned...


Spin-orbit effects on electronic delocalization. Aromaticity in a discrete square tetrapalladium sandwich complex
A. Munoz-Castro, D. Mac-Leod Carey, and R. Arratia-Perez
J. Chem. Phys. 2010, 132, 164308 [2.952, 2014]
DOI:   10.1063/1.3382340
In this article, we report the relativistic electronic structure, including spin-orbit interaction, employing all-electron density functional theory calculations on the multimetallic sandwich compound [(CNT)Pd4(COT)]1+ (1), which can be considered as a [Pd4]2+ fragment flanked by two ring-ligands, namely, cyclononatetraenyl (CNT1?) and cyclooctatetraene (COT), as well as the dimer of 1, hereafter 2. The calculations suggest that the Pd4-ligand interaction is mainly electrostatic, being the main responsible term for the stabilization of the almost fully occupied 4d shell [Pd4]2+ fragment. The ring currents and electronic delocalization estimated via the nuclear independent chemical shifts indices and electron localization function, allow us to describe a significant ?-aromaticity at the center of the Pd4 square in 1, which in conjunction with the aromaticity arising from the ligands induce considerable aromatic character inside of the multimetallic metallocene.

Electronic delocalization, energetics, and optical properties of Tripalladium Ditropylium halides, [Pd3 (C7H7)2X3]1- (X = Cl-, Br-, and I-)
A. Muñoz-Castro, R. Arratia-Perez
J. Phys. Chem. A 2010, 114 (15), 5217-5221 [0.000, 0]
DOI:   10.1021/jp101038u
Here we report relativistic electronic structure calculations employing all-electron density functional theory (DFT) including scalar and spin−orbit interaction, on the multimetallic sandwich compound [Pd3(C7H7)2X3]1− (X = Cl (1), Br (2), and I (3)), which can be considered as a [Pd3X3]3− fragment flanked by two ring-ligands [(C7H7)2]2+. The calculations suggest that the [Pd3X3]3−−ligand interaction is mainly arising from electrostatic contributions, where the formally zerovalent Pd atoms allows backdonation of charge from the halide X1− atoms to the [(C7H7)2]2+ ligands, resulting in a net charge of about +0.4 for each Pd atoms that decreases from 1 to 3. The electronic delocalization estimated via the NICS indexes and the ELF function allows us to describe a significant stabilizing σ-aromaticity at the center of the Pd3 triangle, which decreases from [Pd3Cl3]3− to [Pd3I3]3− (1 to 3) due to the softer character of the iodine counterpart, that donates extra charge to the ligands. The calculated electronic transitions via TD-DFT are in reasonable agreement with the experimental data obtained in CH2Cl2 solution, indicating that the most intense transition involves a core-centered [Pd3X3]3 transition toward the [(C7H7)2]2+ ligands, with mainly X1− character in the former molecular spinor that is responsible for the variation of the observed λmax according to the variation of X1−.

[Cp*Ru(s-indacene)RuCp*] and [Cp*Ru(s-indacene)RuCp*]+: Experimental and theoretical findings concerning the electronic structure of neutral and mixed valence organometallic systems
D. Mac-Leod Carey, C. Morales-Verdejo, A. Munoz-Castro, F. Burgos, D. Abril, C. Adams, E. Molins, O. Cador, I. Chavez, J.M. Manriquez, R. Arratia-Perez, J.Y. Saillard
Polyhedron 2010, 29 (3), 1137-1143 [0.000, 0]
DOI:   10.1016/j.poly.2009.12.002
The reaction of 2,6-diethyl-4,8-dimethyl-s-indacenyl-dilithium (Li2Ic′) with [Cp*RuCl]4 gives the organometallic binuclear bis-pentamethylcyclopentadienyl-ruthenium-s-indacene complex, [{Cp*Ru}2Ic′] (1, Ic′ = 2,4-diethyl-4,8-dimethyl-s-indacene), in high yields. The subsequent oxidation of 1 with a ferricinium salt ([Fc]+[BF4]) gives the mixed valence compound [{Cp*Ru}2Ic′]+[BF4] (1+). Compound 1 was structurally characterized by X-ray crystallography, finding that both {Cp*Ru} fragments are coordinated to opposite sites of the Ic′ ligand. The structural and electronic features of 1 and 1+ have been rationalized by Density Functional Theory (DFT) calculations, which suggest that both metallic centers get closer to the Ic′ and subtle electronic reorganizations occurs when chemical oxidation takes place. Cyclic voltammetry and ESR experiments suggest a high electronic interaction between the metallic centers mediated by the Ic′ bridging ligand. Time dependent DFT (TD-DFT) calculations were carried out to understand and assign the intervalence band present in the mixed-valent specie (1+). The main achievement of this article is to feature the relationship of the experimental data with the computational results obtained with the Amsterdam Density Functional package (ADF). Both experimental and theoretical facts demonstrate that the mixed valence system (1+) is a delocalized one, and it can be classified as a Class III system according to the Robin & Day classification.

Calculated molecular properties of triangular Tribenzo and Perfluoro-Tribenzo Trimercuronin macrocycles
A. Muñoz-Castro, D. Mac-Leod Carey, R. Arratia-Perez
J. Phys. Chem. A 2010, 114 (1), 666-672 [0.000, 0]
DOI:   10.1021/jp90843r
Trimeric perfluoro-ortho-phenylene mercury(II) cluster is a prototypical example of a macrocyclic multidentate Lewis acid. In this study we report the electronic structure, the calculated absorption and vibrational spectra via all-electron scalar and spin?orbit relativistic DFT calculations for [Hg(o-C6H4)]3 (1), [Hg(o-C6F4)]3 (2), and the dimeric form of 2, ([Hg(o-C6F4)]3)2 (3). Due to the inclusion of the spin?orbit interaction, double point groups were used (D3h* and D3d*). The calculations suggest small paratropic ring currents at the center of 1 and being smaller for 2 due to the withdrawn properties of the perfluorated ligand. The luminescent properties of the solid state of 2 are well represented by the postulated model of dimer 3, which mimic the solid state, where the proposed mechanism involves a vibronically coupled emission process. The calculated λabsorptionmax of 3 show an intense peak at 347 nm, which compares well with the reported band at 355 nm; also, the calculated λemission= 431 nm is close to the experimental value of 440 nm. Moreover, the calculated structural changes of the first excited state (3*) are reflected in the large value of the calculated Stoke shifts of 84 nm, which is in quite good agreement with the value of 85 nm extracted from the experimental data.

Inside a Superatom: The M7q (M = Cu, Ag, q = 1+, 0, 1-) Case
A. Muñoz-Castro, D. Mac-Leod Carey, R. Arratia-Perez
Chem. Phys. Chem. 2010, 11(3), 646-650 [4.772, 2014]
DOI:   10.1002/cphc.200900714
All-electron relativistic density functional calculations are performed to obtain the electronic structure and nucleus-independent chemical shifts (NICS) of D5hpentagonal-bipyramidal (PBP) Cu7qand Ag7q(q=1+,0,1−) clusters. Scalar and spin–orbit relativistic effects are taken into account at two levels: the two-component zero-order regular approximation (ZORA) Hamiltonian and fully relativistic four-component calculations via the Dirac equation. These clusters are treated by including the spin–orbit effect in the jellium model, within the double-valued point group (D5h*) establishing the symmetry correlations between the molecular and the atomic spinors given by the full rotation group. These clusters show highly spherical aromaticity, which is suggested to increase the hardness of the superatom. Thus, the calculations suggest that the paramagnetic Cu7 and Ag7 clusters can be regarded as pseudohalogens.

Toward the synthetic control of the HOMO-LUMO gap in binuclear systems: Insights from density functional calculations
A. Muñoz-Castro, D. Mac-Leod Carey, C. Morales-Verdejo, I. Chavez, J. M. Manriquez, R. Arratia-Perez
Inorg. Chem. 2010, 49 (9), 4175-4178 [0.000, 0]
DOI:   10.1021/ic902326y
Computational methods based on density functional theory have been applied to address the design of tailored HOMO−LUMO gap bimetallic complexes. We focus our attention on the [Cp*Fe−(L)−FeCp*] system, where two ferrocenyl units are linked through the dianion of fused ring ligands such as pentalene, s-indacene, dicyclopenta-[b,g]-naphthalene, dicyclopenta-[b,i]-anthracene and dicyclopenta-[b,l]-tetracene. Our DFT calculations on the title organometallic complexes suggest a controlled decrease in the HOMO−LUMO gap, which is desirable for studies on electron-transfer phenomena, as well as the design potential devices for molecular electronic purposes.

Quantum relativistic investigation about the coordination and bonding effects of different ligands on uranyl complexes
D. Paez-Hernandez, R. Ramirez-Tagle, E. Codorniu-Hernandez, L. Montero-Cabrera, R. Arratia-Perez
Polyhedron 2010, 29 (3), 975-984 [0.000, 0]
DOI:   10.1016/j.poly.2009.11.019
The coordination and bonding effects of equatorial ligands such as fluoride (F), chloride (Cl), cyanide (CN), isocyanide (NC), and carbonate (CO3−2) on uranyl dication (UO22+) has been studied using relativistic density functional theory. The ZORA Hamiltonian was applied for the inclusion of relativistic effects taking into account all the electrons for the optimization and the explicit inclusion of spin–orbit coupling effects. Geometry optimizations including the counterions and frequencies analysis were carried out with PW91 and PBE functional. Solvents effects were considered by using the conductor like screening model (COSMO) for water and acetonitrile. The Time-Dependent Density Functional Theory (TDDFT) was used to calculate the excitation energies with GGA SAOP functional and the electronic transitions were analyzed using double group irreducible representations. The theoretical results are in a good agreement with experimental IR, Raman and EXAFS spectra and previous theoretical results. New information about the effect of different (donor and acceptors) ligands on the bonding of uranyl ion and on the electronic transitions involved in these complexes is provided with a possible impact on the understanding of the uranyl coordination chemistry.

DFT-modeling of the tungsten (V) cofactor of hyperthermophilic Pyrococcus furiosus tungsto-bispterin enzyme via the calculated EPR parameters
R. Veloso-Bahamonde, R. Ramirez-Tagle, R. Arratia-Perez
Chem. Phys. Lett. 2010, 491 (4-6), 214-217 [0.000, 0]
DOI:   10.1016/j.cplett.2010.04.013
Here we report a DFT relativistic scalar and spin–orbit study that considers the structural optimization of the complete tungsten (V) cofactor by studying the paramagnetic site of the Pyrococcus furiosus tungsto-bispterin enzyme. The best-fit superimposed X-ray structure shows an important similarity with the aldehyde ferredoxin oxidoreductase (1AOR) structure, and, the W(V) cofactor exhibits a Kramers doublet as the ground state, which agrees with the EPR observations. We conclude that it is quite necessary to include relativistic scalar and spin–orbit effects to describe the whole tungsten (V) cofactor in the P. furiosus tungsto-bispterin enzyme.

Tellurium(0) as a ligand: Synthesis and characterization of 2-Pyridyltellurolates of Platinum(II) and structures of [Pt{2-Te-3-(R)C5H3N}2Te(PR03)] (R = H or Me)
R. S. Chauhan, G. Kedarnath, A. Wadawale, A. Muñoz-Castro, R. Arratia-Perez, V. K. Jain, W. Kaim
Inorg. Chem. 2010, 49, 4179-4185 [0.000, 0]
DOI:   10.1021/ic902347s
Treatment of toluene solutions of the ditellurides [Te2{C5H3N(R)-3}2] (R = H or Me) with [Pt(PPh3)4] yielded two types of complexes, [Pt{2-Te-3-(R)C5H3N}2(PPh3)2] (1ad) as the major products and [Pt{2-Te-3-(R)C5H3N}2Te(PPh3)] (2ad) as minor products. The above complexes can also be obtained by the reaction of [PtCl2(PR′3)2] (PR′3 = PPh3 or PPh2(2-C5H4N)) with 2 equiv of Na(2-Te-C5H3R). The complexes were characterized by elemental analyses and UV−vis, NMR (1H and 31P), and (in part) XPS spectroscopy. The molecular structures of [Pt(2-Te-C5H4N)2Te(PPh3)] (2a) and [Pt{2-Te-C5H3(Me)N}2Te(PPh3)] (2b) were established by single crystal X-ray diffraction. Both complexes exhibit a distorted square-planar configuration at the platinum(II) centers. The two mutually trans positioned 2-pyridinetellurolate ligands [2-Te-C5H3(R)N] coordinate to the central platinum atom in a monodentate fashion through the tellurium atoms. The tellurium(0) atom adopts a “bent T” configuration as it is bridging the 2-Te- C5H3(R)N molecules via N−Te−N bonds (166° angle) and coordinates to PtII in the trans position to PPh3. The novel bis(pyridine)tellurium(0) arrangement resembles the bis(pyridine)iodonium structure. The calculated NICS indices and ELF functions clearly show that the compounds 2a and 2b are aromatic in the region defined by the Te−C−N−Te−Pt five-membered rings.

Relativistic electronic structure of cadmium(II) multidecker phthalocyanine compounds
A. Munoz-Castro, D. Mac-Leod Carey, R. Arratia-Perez
Polyhedron 2010, 29 (1), 451-455 [0.000, 0]
DOI:   10.1016/j.poly.2009.06.038
Cadmium phthalocyanines (Pc) give rise to multilayered compounds, which may have potential application in material science. The Cd(II) single macrocycle (1) (C4v), double decker [CdPc2] (2) (D4), triple decker [Cd2Pc3] (3) (D4h) and quadruple decker [Cd3Pc4] (4) (D4d), are already characterized experimentally. The electronic structures of the multidecker compounds were compared against the single macrocycle (1) which is used as benchmark. Relativistic electronic structure were carried out via DFT calculations using the two components ZORA Hamiltonian including both scalar and spin–orbit effects. Double point groups were used to take into account the inclusion of the spin–orbit coupling, and their group correlation is shown. The calculations show that the quadruple decker is the most reactive and behaves like a one-dimensional molecular metal.

Metallophthalocyanine based molecular materials as catalysts for electrochemical reactions
J. H. Zagal, S. Griveau, J. F. Silva, T. Nyokong, F. Bedioui
Coord. Chem. Rev. 2010, 254, 2755-2791 [0.000, 0]
DOI:   10.1016/j.ccr.2010.05.001
Metallophthalocyanines confined on the surface of electrodes are active catalysts for a large variety of electrochemical reactions and electrode surfaces modified by these complexes can be obtained by simple adsorption on graphite and carbon. However, more stable electrodes can be achieved by coating their surfaces with electropolymerized layers of the complexes, that show similar activity than their monomer counterparts. In all cases, fundamental studies carried out with adsorbed layers of these complexes have shown that the redox potential is a very good reactivity index for predicting the catalytic activity of the complexes. Volcano-shaped correlations have been found between the electrocatalytic activity (as log I at constant E) versus the Co(II)/(I) formal potential (E°′) of Co-macrocyclics for the oxidation of several thiols, hydrazine and glucose. For the electroreduction of O2 only linear correlations between the electrocatalytic activity versus the M(III)/M(II) formal potential have been found using Cr, Mn, Fe and Co phthalocyanines but it is likely that these correlations are “incomplete volcano” correlations. The volcano correlations strongly suggest that E°′, the formal potential of the complex needs to be in a rather narrow potential window for achieving maximum activity, probably corresponding to surface coverages of an M-molecule adduct equal to 0.5 and to standard free energies of adsorption of the reacting molecule on the complex active site equal to zero. These results indicate that the catalytic activity of metallophthalocyanines for the oxidation of several molecules can be “tuned” by manipulating the E°′ formal potential, using proper groups on the macrocyclic ligand. This review emphasizes once more that metallophthalocyanines are extremely versatile materials with many applications in electrocatalysis, electroanalysis, just to mention a few, and they provide very good models for testing their catalytic activity for several reactions. Even though the earlier applications of these complexes were focused on providing active materials for electroreduction of O2, for making active cathodes for fuel cells, the main trend in the literature nowadays is to use these complexes for making active electrodes for electrochemical sensors.

Spin-Orbit and Solvent Effects in the Luminescent[Re6Q8(NCS)6]4-, Q = S, Se, Te Clusters: Molecular Sensors and Molecular Devices
R. Ramírez-Tagle, L. Alvarado-Soto, L. Hernández-Acevedo and R. Arratia-Pérez
J. Chil. Chem. Soc. 2010, 54, 331 [0.000, 0]
DOI:   10.4067/S0717-97072010000100010
Relativistic time-dependent density functional (TDDFT) calculations including spin orbit interactions via the zero order regular approximation (ZORA) and solvent effects using the COSMO model were carried out on the [Re6Q8(NCS)6]4- , (Q = S, Se, Te) clusters. These calculations indicate that the lowest energy allowed electronic transitions are characterized by being of LMCT type. The calculated absorption maximum tends to shift to longer wavelengths as the face-capping chalcogenide ligand becomes heavier. Thus our calculations predict that the [Re6Te8(NCS)6]4- cluster might be also luminescent. Due to the unusual properties exhibited by these and other isoelectronic and isostructural hexarhenium (III) chalcogenide clusters, hexamolybdenum halide clusters and hexatungsten halide clusters, we propose here the design of nanodevices, such as, molecular sensors and molecular nanocells for molecular electronics.

Theoretical study of the interaction between Au(I) and I on the [AuI2]–I2 complexes
F. Mendizabal
J. Mol. Struct. Theochem 2010, 955, 71-74 [0.000, 0]
DOI:   10.1016/j.theochem.2010.05.033
We studied the interaction between [AuI2] and I2 using ab initio methodology. We found that the changes around the equilibrium intermolecular distance Aucdots, three dots, centeredl2 and in the interaction energy differences are sensitive to the electron correlation potential. We evaluated these effects using several levels of theory, including MP2, MP4 and CCSD(T); and size of the basis set on atoms. The equilibrium distances Au–l2 in the complexes are in the range 380–392 pm. The obtained interaction energies differences at the equilibrium distance range from 4.3 to 14.7 kJ/mol at the different levels used. These results indicate that the complexes formed are in the category of van der Waals systems. At long-distances, the behaviour of the [AuI2]cdots, three dots, centeredI2 interaction may be related mainly to charge-induced dipole and dispersion terms. Both terms are important.

Phenyl 3,5-di-tert-butyl-2-hydroxybenzoate
A. Carreño, M. Preite, J. M. Manriquez, A. Vega and I. Chavez
Acta Cryst. 2010, E66, o3290 [0.000, 0]
DOI:   10.1107/S1600536810044028
The title molecule, C21H26O3, has a six-membered planar carbon ring as the central core, substituted at position 1 with phenoxycarbonyl, at position 2 with hydroxy and at positions 3 and 5 with tert-butyl groups. The structure shows two independent but very similar molecules within the asymmetric unit. For both independent molecules, the ester carboxylate group is coplanar with the central core, as reflected by the small C-C-O-C torsion angles [179.95 (17) and 173.70 (17)°]. In contrast, the phenyl substituent is almost perpendicular to the carboxylate -CO2 fragment, as reflected by C-O-C-C torsion angles, ranging from 74 to 80°. The coplanarity between the central aromatic ring and the ester carboxylate -CO2- group allows the formation of an intramolecular hydrogen bond, with O-O distances of 2.563 (2) and 2.604 (2) Å.

DFT study on the electronic structure, energetics and spectral properties of several bis(organohydrazido(2-)) molybdenum complexes containing substituted phosphines and chloro atoms as ancillary ligands
X. Zárate, E. Schott, D. Mac-Leod Carey, C. Bustos, R. Arratia-Perez
J. Mol. Struct. Theochem 2010, 957, 126-132 [0.000, 0]
DOI:   10.1016/j.theochem.2010.07.021
A theoretical study of the geometrical and electronic structure of several structurally related bis(organohydrazido(2-))-molybdenum complexes containing substituted phosphines and chloro atoms as ancillary ligands, of formula [Mo(NNPh2)2Cl2(PPh3)2] (1), [Mo(NNPh2)2Cl2(PMePh2)2] (2), [Mo(NNPh2)2Cl2(PMe2Ph)2] (3), [Mo(NNPh2)2Cl2(PMe3)2] (4) and [Mo(NNPh2)2Cl2(PH3)2] (5), was carried out. In order to analyze the electronic effects when the phosphines are changed, a decomposition energy analysis was performed, finding that the Mo–Cl interactions have long distance and ionic character with poor “p” antibonding contributions. Besides, the metal–phosphine interactions have little covalent character, while the Mo-hydrazido(-2) interaction with significant orbital contribution, indicates a strong covalent character with respect to the rest of the ligands. On the other hand, the calculated electronic transitions using the Time-Dependent Density Functional Theory (TDDFT) are also presented at GGA and B3LYP theoretical levels, and despite of the limitations of the first method, we obtained a good correlation with B3LYP analysis performed. Also, the calculated excitations are in good agreement with the experimental data for (2) and (3), moreover, we were able to predict the electronic transitions that could be observed in the proposed (1), (4) and (5) complexes and these results indicate that these compounds are stable and they should be able to be synthesized.

Iron porphyrin attached to single-walled carbon nanotubes: Electronic and dynamical properties from ab initio calculations
I. Ruiz-Tagle, W. Orellana
Phys. Rev. B 2010, 82, 115406 [0.000, 0]
DOI:   10.1103/PhysRevB.82.115406
Covalent and noncovalent attachment of an iron porphyrin (FeP) on the surface of single-walled carbon nanotubes (CNTs) are addressed by density-functional-theory calculations and molecular-dynamic simulations. We investigate the stability and electronic properties of several CNT-FeP assemblies in order to shed light in the experimentally reported electrocatalytic activity of carbon-supported Fe macrocycles and the role of the linking structure. Two mechanisms for the FeP attachment on metallic and semiconducting CNTs were considered: by physisorption through π-π stacking interaction and by chemisorption through sp2 and sp3 bonding configurations. Our results suggest that FeP covalently linked to metallic CNTs would be the best electrocatalytic systems due to its metallic character at room temperature, suggesting that they may work as an electrode with the ability to transport charge to the macrocycle. Semiconducting CNTs would be unlikely because the FeP-CNT assembly preserves the semiconducting character. Noncovalent attachment of FeP onto both CNTs is also unlikely due to the absence of physical contact and the unsuccessful FeP fixation.

Oxidative Perhydroxylation of [closo-B12H12]2− to the Stable Inorganic Cluster Redox System [B12(OH)12]2−/.−: Experiment and Theory
Nguyen Van, Ioannis Tiritiris, Rainer F. Winter, Biprajit Sarkar, Priti Singh, Carole Duboc, Alvaro Munoz-Castro, Ramiro Arratia-Perez, Wolfgang Kaim, and Thomas Schleid
Chem. Eur. J. 2010, 16, 11242-11245 [0.000, 0]
DOI:   10.1002/chem.201001374
It′s radical: A surprisingly simple reaction converts the normally inert prototypical hydridoborate cluster [closo-B12H12]2− not only to [closo-B12(OH)12]2− but also, at less-elevated temperatures, to the new [hypocloso-B12(OH)12].− radical anion (see figure). Both approximately icosahedral closo and hypocloso cluster ions were structurally characterized as the cesium salts and their properties were assessed experimentally and theoretically.